Annoying creationists [Archive] - Page 7

kleinman

8th January 2007, 03:57 PM

That about sums it up. So why are you evolutionarians so annoyed? Annoyed? Hardly. It's more that it's staggering how arrogant you are with your call to 'evolutionists' to do the maths when you're basically saying that they have! You're the one who has done bugger all.
Isn’t that something, I’m getting it both ways. I can say that the theory of evolution has no mathematical basis and then take an evolutionarian written mathematical model of random point mutations and natural selection and say that it proves that macroevolution is mathematically impossible. It almost sounds inconsistent until you think about for a little while. I don’t think it is arrogant to tell evolutionarian to prove the math for their own theory. You are the ones who claim have science on your side.
So what is the relativistic effect in the theory of evolution that will fix the mathematics that ev reveals for random point mutations and natural selection?Way to go Mr Does-Not-Get-The-Point.

You using ev to disprove evolution is the equivalent of using Quake to disprove Einsteinian physics.

Do you get that Quake is an entirely insufficient representation of real world physics or not?

Do you get that ev is an entirely insufficient representation of real world evolution or not?
I have no idea what Quake is.

If you think other forms of mutations will rescue your theory, your task is simple. Modify ev with these other mutation mechanisms and show us how a gene evolves de novo.
# of generations to accomplish de novo evolution of a gene by random point mutations and natural selection > time availableThat does not answer the question.
Sure it does, that’s the whole point of this accounting problem. Ev reveals how slow random point mutations and natural selection is, much to slow to evolve a gene de novo, even with the artificially idealistic selection mechanism used by Dr Schneider.
Would you be willing to run a set of experiments with your variant of Evj? If so, use these parameters:

population 32 / binding sites 8 / weight width 9 / site width 10 / 1 mutation per 512 bases

Then vary the genome size from 1024 by factors of 2 and record the number of generations to perfect creature. I've run this model up to a genome size of 128K.These are my results so far (genome size, mutations, run 1, run 2, run 3):
1024, 2, 190, 197, 206
2048, 4, 219, 210, 262
4096, 8, 256, 256, 268
8192, 16, 322, 357, 332
16384, 32, 394, 375, 366
32768, 32, 474, 474, 430
65536, 32, (running)
Why don’t you post the full code for your ”sum of the strength of the mistakes” calculation, so we can all participate in this arithmetic. It sure looks like you are ignoring the mistakes in the nonbinding site region of the genome.
What kind of precise selection process that occur in nature would evolve a gene de novo? You must have drunk more than a few beers after celebrating that issue of agreement with hammegk in order to come up with this idea.

Sure ev shows that information can evolve in a genome. It just takes more time than the history of the earth to get a gene de novo.Your argument is subtly "evolving" (or maybe you're just adding a little more argument and subtly moving the goalpost a tad).
Take a look at my initial posts on the Evolutionisdead forum. The only thing that I have added since then is a target measure for macroevolution that can be tested (that is de novo evolution of a gene).
Until very recently you were content to argue that ev was flawed because it could not evolve a gene fast enough. Now you seem to be suggesting that even if the selection mechanism were modify to make ev work fast enough, this wouldn't satisfy you, because your new position is that the gene must evolve without anything more than completely random selection.
I have never argued the ev was flawed because a binding site did not evolve quickly enough. The flaw is in the theory of evolution. The problem for evolution by random point mutation and natural selection is that it is a profoundly slow process for large genomes. The selection mechanism Dr Schneider has used is already very rapid (at least for short genomes).
Please explain why a a genome cannot have a selective advantage to an organism at a relatively simple stage of its evolution, which is substantially different from the selective advantage present at some relatively later and more complex point.
I’m not quite sure what you are asking here. I don’t think natural selection has changed with time. What natural selection does is give organisms with particular characteristics for a given environment a reproductive advantage and those without those characteristics are selected against. This is related to my argument about the de novo evolution of a gene. Until you have sufficient number of bases to code for a protein that is beneficial to the organism, you have no selective benefit. Without the selective benefit, you have only random mutations without selection to explain the evolution of a gene de novo.
As you have already conceded, ev is very fast for short genomes, so there would be no barrier to a quick evolution without selection to some very simple selective advantage, followed by more environmentally channeled selection speeding the evolutionary process toward a more complex advantage.
If you turn off selection in ev, the binding sites that have evolved revert to random sequences.
That modification that Unnamed appears to be changing much more than the threshold.He explained what he did: What I did was, for each mistake, to add the distance between the valuation and threshold, and use the result as the sorting order. This is a finer measure than the raw number of mistakes, but it still goes to zero when mistakes = 0, so it converges to the same place.
What is the “valuation”. What is the distance between the valuation and threshold. Unnamed needs to post all the changes he has made in the code. Let’s all have fun with this calculation.
I just got this result:
65536, 32 mutations/generation (should be 128), 827 generations to perfect creature. Whoa, Nelly! Is that possible?
Why with these rates of information acquisition you can evolve a human genome in about 15 minutes.

Unnamed

8th January 2007, 04:12 PM

Why don’t you post the full code for your ”sum of the strength of the mistakes” calculation, so we can all participate in this arithmetic. It sure looks like you are ignoring the mistakes in the nonbinding site region of the genome.

What is the “valuation”. What is the distance between the valuation and threshold. Unnamed needs to post all the changes he has made in the code. Let’s all have fun with this calculation.

These are all my changes in "Simulator.java". I removed lines marked with "-" and added lines marked with "+".

--- evjava 4/Simulator.java 2006-06-26 14:03:38.000000000 -0400
+++ evjava 3/Simulator.java 2007-01-08 17:55:29.000000000 -0500
@@ -415,7 +415,7 @@
for (int p = 0; p <= bug.length/2 - 1; ++p) {
int c = bug.length - p - 1;

- if (bug[p].mistakes == bug[c].mistakes) {
+ if (bug[p].sortValue == bug[c].sortValue) {
switch (tie) { // Two creatures have tie scores:
case Param.TIE_BOTH: // Both survive.
break;
@@ -548,7 +548,7 @@
// Following are valid only if scored:
private int valuation[]; // Valuation of each position.
private int spuriousHits = 0; // Number of spurious bindings obtained.
- private int sortValue; // Value used to sort creatures.
+ public int sortValue; // Value used to sort creatures.

// This constructor is used to create creatures at the beginning
// of a run. Each creature's chromosome is random.
@@ -710,19 +710,25 @@
gene = param.getInt(Param.spuriousGene),
nongene = param.getInt(Param.spuriousNongene);

- mistakes = spuriousHits = 0;
+ float sv;
+ sv = mistakes = spuriousHits = 0;
for (int p = 0; p <= chromosome.length - width; ++p) {
if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
+ sv += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
} else {
- if (siteInd[p]) mistakes += missed;
+ if (siteInd[p]) {
+ mistakes += missed;
+ sv += Math.abs(valuation[p] - threshold);
+ }
}
}

- sortValue = mistakes; // We will sort on the mistake
+ sortValue = (int)(Math.min(sv, Integer.MAX_VALUE));
+ //sortValue = mistakes; // We will sort on the mistake
// count, unless randomized.
}

Results so far with version 2.37:

1024, 231, 260, 186
2048, 264, 257, 266
4096, 263, 263, 253
8192, 273, 347, 333
16384, 345, (running)

Why with these rates of information acquisition you can evolve a human genome in about 15 minutes.
I know! Ain't that cool :D ?

kleinman

8th January 2007, 04:46 PM

// This constructor is used to create creatures at the beginning
// of a run. Each creature's chromosome is random.
@@ -710,19 +710,25 @@

gene = param.getInt(Param.spuriousGene),
nongene = param.getInt(Param.spuriousNongene);

- mistakes = spuriousHits = 0;
+ float sv;
+ sv = mistakes = spuriousHits = 0;
for (int p = 0; p <= chromosome.length - width; ++p) {
if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
+ sv += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
} else {
- if (siteInd[p]) mistakes += missed;
+ if (siteInd[p]) {
+ mistakes += missed;
+ sv += Math.abs(valuation[p] - threshold);
+ }
}
}

- sortValue = mistakes; // We will sort on the mistake
+ sortValue = (int)(Math.min(sv, Integer.MAX_VALUE));
+ //sortValue = mistakes; // We will sort on the mistake
// count, unless randomized.
}

Unnamed, what you are doing here is ignoring errors in the non-binding site region. Your variable sv appears to be a measure of the accuracy of the match of the weight matrix to a particular position. As soon as you have any improvement in the match in the binding site region, errors are ignored in the non-binding site region.

You are ignoring harmful mutations.

hammegk

8th January 2007, 04:49 PM

Please, if I am at some point too technical, confusing or vague, state which point that is, so that I may elucidate. Barcoding is nothing very difficult, but failure to communicate what I mean may have resulted, as English is not my first language.
Thanks for you comments. You are doing fine with English.

... Tragopogon mirus and Tragopogon miscellus ...
I took a look online, and after following several citations felt like Alice after she went down the rabbit hole.

I can see how proponents of Modern Evolutionary Theory could feel the results bolster their position. Other arguments could be made from opponents, with the literature full of loose ends waiting to be tugged sfaics.

So you are looking for an example of speciation in which the resulting taxa is not only a new species, genus, or tribe but a new family or even new order?
Perhaps we could agree on something more along the lines of a new, clearly different, phenotype substantiating genotype changes?

Couldn't the geologic timespans nature seems to require to provide change be much compressed by conscious human selection and technology?

Again, thanks for your responses.

cyborg

8th January 2007, 05:05 PM

I have no idea what Quake is.

Ah, that just shows how uneducated you are.

Quake is the quintessential example of when the first person perspective game took on a new level of graphical representation. The engine in question has evolved to encompass a wide variety of physical rules in the universes it can create. It is in short a system for creating a universe. It is not important per se, the important thing here is that you understand that it is a computer model of a world much like ev is a computer model of our world, except it models a rather different aspect of it.

The point is that the Quake engine, for all the sophistication it has attained during its revisions since it first appeared ten years ago, falls quite short of providing an accurate physical representation of our universe.

And hence if I were to take the Quake engine, say this represents physics and then use it to show that relativity is nonsensical because it doesn't occur in Quake and then say I have therefore disproved relativity I would be in a considerable degree of error. Would you not concur?

You are doing the same thing with ev. You cannot possibly say that you have disproved evolution with ev when the program is quite clearly as inadequate at modelling the real and complicated aspects of evolution as the Quake engine fails to capture the real and complicated aspects of physics.

You are beating the goddamn living daylights out of a giant strawman.

If you think other forms of mutations will rescue your theory, your task is simple. Modify ev with these other mutation mechanisms and show us how a gene evolves de novo.

No. You do not get it. This is YOUR task. You want to disprove evolution mathematically then YOU should be the one trying to improve the model.

You really are damn lazy though aren't you? Much easier to just run a program, post some numbers and shout loudly about how nobody is going to listen to you because of their bias against your god or love of evolution or some such nonsense.

Sure it does,

No it does not.

that’s the whole point of this accounting problem. Ev reveals how slow random point mutations and natural selection is, much to slow to evolve a gene de novo, even with the artificially idealistic selection mechanism used by Dr Schneider.

Irrelevant. I require that you define what a macroevolutionary event is in ev. You cannot say such events do not occur if you cannot define what that event is. It is entirely inadequate to simply say the process is too slow with realistic values. YOU MUST DEFINE WHAT THE EVENT IS TO SHOW THAT IT CANNOT OCCUR.

Jeez, what part of that can you not comprehend?

Can you or can you not identify a macroevolutionary event - realistic values be damned?

Paul C. Anagnostopoulos

8th January 2007, 05:24 PM

I just received my complimentary copy of:

Martin A. Nowak, 2006, Evolutionary Dynamics: Exploring the Equations of Life, Harvard University Press, Cambridge, MA.

Apropos and highly recommended.

~~ Paul

Unnamed

8th January 2007, 05:26 PM

if ((valuation[p] = siteValuation(p, width)) >= threshold) {
if (!siteInd[p]) {
if (p < availablePos) mistakes += gene; else mistakes += nongene;
sv += Math.abs(valuation[p] - threshold);
++spuriousHits;
}
}
}

Translating...

if the site p is a match,
but the site p is not a binding site, then
add the strength of this error to sv

Unnamed, what you are doing here is ignoring errors in the non-binding site region.
No I'm not, unless I was doing it by mistake.

Your variable sv appears to be a measure of the accuracy of the match of the weight matrix to a particular position. As soon as you have any improvement in the match in the binding site region, errors are ignored in the non-binding site region.
I don't ignore any error that was previously counted as a "mistake".

You are ignoring harmful mutations.
The updated procedure generates a perfect individual, showing that I am indeed penalizing errors. If I didn't, how could I get a perfect individual at the end? I am still using the same criterion (mistakes == 0).

Updated values:
1024, 231, 260, 186
2048, 264, 257, 266
4096, 263, 263, 253
8192, 273, 347, 333
16384, 345, 304, 315
32768, 440, 422, 474
65536, 432, 443
132072, 584

Paul C. Anagnostopoulos

8th January 2007, 05:38 PM

Unnamed, what you are doing here is ignoring errors in the non-binding site region. Your variable sv appears to be a measure of the accuracy of the match of the weight matrix to a particular position. As soon as you have any improvement in the match in the binding site region, errors are ignored in the non-binding site region.

You are ignoring harmful mutations.
No, I don't think so. sv accumulates the absolute difference between every position's valuation and the threshold.

A variation would be to use the absolute difference for binding sites, but a fixed number for non-binding sites. The idea would be that spurious bindings are equally harmful regardless of the strength of the binding.

~~ Paul

Paul C. Anagnostopoulos

8th January 2007, 05:40 PM

Updated values:
1024, 231, 260, 186
2048, 264, 257, 266
4096, 263, 263, 253
8192, 273, 347, 333
16384, 345, 304, 315
32768, 440, 422, 474
65536, 432, 443
132072, 584
This is frightening.

Assuming you have no bugs, this shows us that the particular selection criterion used by Ev is critical to the speed of evolution, and that we certainly cannot draw any sweeping conclusions about the real world.

~~ Paul

joobz

8th January 2007, 05:45 PM

This is frightening.

Assuming you have no bugs, this shows us that the particular selection criterion used by Ev is critical to the speed of evolution, and that we certainly cannot draw any sweeping conclusions about the real world.

~~ Paul
Wow, who would have thought that computer simulations would have inherent assumptions that may not apply to the real world.:rolleyes:

Paul C. Anagnostopoulos

8th January 2007, 05:52 PM

Unnamed, just checking that you are using these parameters:

population 32
binding sites 8
weight width 9
site width 10
1 mutation per 512 bases

~~ Paul

Paul C. Anagnostopoulos

8th January 2007, 05:53 PM

Wow, who would have thought that computer simulations would have inherent assumptions that may not apply to the real world.
I don't know, but those people should be disabused of the notion now, for sure.

~~ Paul

kleinman

8th January 2007, 06:30 PM

I have no idea what Quake is.Ah, that just shows how uneducated you are.
Cyborg, I have never said I was educated in everything. I’m only claiming I know something about ev and what this computation is saying about random point mutations and natural selection.
If you think other forms of mutations will rescue your theory, your task is simple. Modify ev with these other mutation mechanisms and show us how a gene evolves de novo.No. You do not get it. This is YOUR task. You want to disprove evolution mathematically then YOU should be the one trying to improve the model.
I’m content to say that the theory of evolution is without a mathematical basis and that ev shows that random point mutations and natural selection is so profoundly slow that nothing can evolve by this mechanism. You can stomp your foot and say it is my task, but it is your theory to prove. I doubt any evolutionarians who have knowledge of mathematics will try to include other mechanisms of mutations because all these mechanisms will still face the same 4^G effect of the increasing search space as the genome length is increased. That is the mathematical hurdle that the theory of evolution can not overcome. In addition, there is no selection process for a partially completed gene.
Sure it does,No it does not.
Does to, does to.
that’s the whole point of this accounting problem. Ev reveals how slow random point mutations and natural selection is, much to slow to evolve a gene de novo, even with the artificially idealistic selection mechanism used by Dr Schneider.Irrelevant. I require that you define what a macroevolutionary event is in ev. You cannot say such events do not occur if you cannot define what that event is. It is entirely inadequate to simply say the process is too slow with realistic values. YOU MUST DEFINE WHAT THE EVENT IS TO SHOW THAT IT CANNOT OCCUR.

Jeez, what part of that can you not comprehend?

Can you or can you not identify a macroevolutionary event - realistic values be damned?
When an evolutionarian retracts their belief in the theory of evolution. That is a macroevolutionary event. Annoying an evolutionarian, that’s a microevolutionary event.
Unnamed, what you are doing here is ignoring errors in the non-binding site region.No I'm not, unless I was doing it by mistake.
I think if you keep track of the value of valuation[p] in the following equation,
sv += Math.abs(valuation[p] - threshold);
you will see that this number will be much larger in the binding site region due to the good match of the weight matrix. In the non-binding site region this value will remain small. You are effectively giving a higher weight to good mutations in the binding site region than to harmful mutations in the non-binding site region. You can achieve the same effect if you set the value for the variable gene=1 and nongene=0 and still sort on the variable “mistakes”.
Your variable sv appears to be a measure of the accuracy of the match of the weight matrix to a particular position. As soon as you have any improvement in the match in the binding site region, errors are ignored in the non-binding site region.I don't ignore any error that was previously counted as a "mistake".
But you are weighting errors which is effectively ignoring harmful mutations in the non-binding site region.
You are ignoring harmful mutations.The updated procedure generates a perfect individual, showing that I am indeed penalizing errors. If I didn't, how could I get a perfect individual at the end? I am still using the same criterion (mistakes == 0).
You are still selecting for good and harmful mutations in the binding site region. Here is a simple computational experiment you can do. Set the values for gene=1 and nongene=0 and sort on mistakes rather than sv. Then compare the number of generation for convergence for you series that you have run with sv. I believe you will obtain almost the same number of generations for convergence for the two approaches. The gene=0, nongene=1 case should converge a little more quickly because that approach completely ignores mistakes in the non-binding site region. Your approach with sv does not completely ignore errors in the non-binding site region which is why you get a slight increase in generations for convergence as you increase the genome length but effectively, you are ignoring harmful mutations in the non-binding site region.

This is not necessarily an unrealistic approach to the selection process. Months ago I proposed that instead of starting with a random genome, start with a real genome and then define your selection process such that if there is a fatal mutation in the non-binding site region that this creature be selected out no matter what is happening in the binding site region.

Unnamed, what you are doing here is ignoring errors in the non-binding site region. Your variable sv appears to be a measure of the accuracy of the match of the weight matrix to a particular position. As soon as you have any improvement in the match in the binding site region, errors are ignored in the non-binding site region.

You are ignoring harmful mutations.No, I don't think so. sv accumulates the absolute difference between [i]every[/vi] position's valuation and the threshold.

A variation would be to use the absolute difference for binding sites, but a fixed number for non-binding sites. The idea would be that spurious bindings are equally harmful regardless of the strength of the binding.
What is the value for valuation[p] for a match in the binding site region versus a mismatch in the non-binding site region? If valuation[p] in the binding site region is much greater than valuation[p] in the non-binding site region, you have reduced the weight of errors in the non-binding site region. This is equivalent to ignoring harmful mutations in the non-binding site region. And as we all know, most mutations are harmful.

Sorry about that Paul, nice try.

Paul C. Anagnostopoulos

8th January 2007, 07:07 PM

What is the value for valuation[p] for a match in the binding site region versus a mismatch in the non-binding site region? If valuation[p] in the binding site region is much greater than valuation[p] in the non-binding site region, you have reduced the weight of errors in the non-binding site region. This is equivalent to ignoring harmful mutations in the non-binding site region. And as we all know, most mutations are harmful.
What do you mean by "binding site region"? There are binding sites and then there are all the other positions on the chromosome.

What matters is the absolute difference between the valuation and the threshold. Unnamed is doing this:

for binding sites:
bound successfully: nothing
not bound: increase sv by absolute difference

for all other sites:
bound spuriously: increase sv by absolute difference
not bound: nothing

After a few generations, there are no spurious bindings. This is true with the current selection algorithm, too. So what matters is how far away from the threshold the binding site valuations are. The further they are, the worse for the creature.

Now suppose a mutation causes a spurious binding all of a sudden. At the beginning of the simulation, its absolute difference will be smaller than those of the binding sites (the threshold tends to be high), and so the harmful mutation counts against the creature less than an unbound binding site. Later on in the simulation, as the binding site valuations are approaching the threshold, the harmful mutation counts against the creature about the same as an unbound binding site.

We could test this by increasing sv by a fixed amount for spurious bindings. A good value would be, say, threshold/2.

~~ Paul

Paul C. Anagnostopoulos

8th January 2007, 07:07 PM

Unnamed, could you run the 32K case and tell me the number of births and deaths?

~~ Paul

PixyMisa

8th January 2007, 08:07 PM

The previous statements are clear that Dr Schneider believes that ev simulates the real world.

Yes, but it is equally clear that it is a limited model and is not adequate for - nor (thanks Paul) intended to be - a valid simulation of phyletic evolution.

That’s reassuring, because it is completely illogical to believe such a thing. So where do you believe genes came from?

If you are talking strictly about evolution, then all genes come from other genes.

If you are talking about abiogenesis, then I don't know; nobody does. Though there are some interesting hypotheses.

You might find that Dr Schneider doesn’t agree with your view. I am sure that I don’t.

As has now been explained to me - and to the forum in general - you have misrepresented what Dr Schneider's program claims to do. I noted that it could not properly model phyletic evolution; it was pointed out that it is not intended to model phyletic evolution, and Dr Schneider has made no claims that it can.

Unless you believe that genes are eternal, they had to come into being somehow.

Perfectly true. But that is not (directly) the subject of evolution, and certainly not the problem that Dr Schneider was studying.

Do you think genetic code is eternal?

No; I do not believe that anything is eternal.

Since ev is a mathematical model, you should be able to enumerate what you think is wrong about the model. Why don’t you tell us what is wrong with this simulation of random point mutations and natural selection?

I haven't studied it as closely as others here, so my answer is incomplete at best. But the thing that is obvious to me is the modeling of populations doesn't even resemble what happens in the real world. It is adequate for a proof that evolution is possible; it is not adequate for calculating rates of propagation of evolutionary changes or for modeling phyletic evolution.

Nor does Dr Schneider claim this.

What I am trying to explain here is that recombination and natural selection can give rapid phenotypic changes in a species.

Yes, this is true. Also irrelevant.

It is this rapid phenomena that Darwin inappropriately extrapolated to mutation and natural selection when he was interpreting the differences between finch beaks in isolated populations. Gould did the same when he postulated his concept of punctuated equilibrium. This concept is applicable to recombination and natural selection but not to mutation and natural selection.

The question can be settled by genetic study, but in the general case, it is not possible for recombination to account for observed speciation. And I'm not sure what your point is. Recombination does not produce new genes; we do observe new genes in speciation events, and we know how they got there: through mutation.

Don’t forget, I also co-opted the micro/macroevolution concept as well. There is so little else in the theory of evolution that is worth co-opting.

Micro- vs. macro-evolution is not part of the Theory of Evolution. The terms are used by some biologists to refer to arbitrary distinctions in quantifying evolutionary change. There is no qualitative difference between micro- and macro-evolution. They are caused by exactly the same processes.

Consider that phylum are simply a categorization scheme that can be defined any way you want. Since Gould hypothesis of punctuated equilibrium fits more logically with recombination and natural selection, it is less likely to find evidence of gradualism (on the macroevolutionary scale) by the mechanism of recombination and natural selection.

Recombination cannot result in phyletic evolution.

What about macroevolution=de novo evolution of a gene? Of course PixyMisa believes genes are eternal.

No. I merely point out that the expression "de novo evolution" is a contradiction in terms. You mean "de novo creation", or something similar.

Macroevolution=de novo creation of a gene. (edited by me)

This does not happen. Nor is it required.

PixyMisa

8th January 2007, 08:09 PM

To an illiterate dolt such as myself

La la la...

Need I say Mice is Mice?And different species of mice are different species of mice.

PixyMisa

8th January 2007, 08:16 PM

Perhaps we could agree on something more along the lines of a new, clearly different, phenotype substantiating genotype changes?

That's what he said. You are asking for changes not on the species level but on the level of family or order - two or three levels up the taxonomic tree.

Couldn't the geologic timespans nature seems to require to provide change be much compressed by conscious human selection and technology?Not that much, no.

Remember, all dogs are one species, despite the substantial outward variations, and we've been breeding those for at least 10,000 years.

hammegk

8th January 2007, 08:29 PM

And different species of mice are different species of mice.
If y'all find mice and dogs meet your criteria as a demonstration of anything other than the fact that Mendel was basically right, your choice.

Remember, all dogs are one species, despite the substantial outward variations, and we've been breeding those for at least 10,000 years.
Oops. I guess we agree, there. One species; check.

Nah, I think something in the lab a bit more malleable than mammals might be a place to start ... oh, iirc, you evolutionarians have been trying in the labs since the early 50's?

If you are talking strictly about evolution, then all genes come from other genes.
Even the first one? ;)

PS. Don't you have a corrupt database somewhere that needs fixing?

kleinman

8th January 2007, 08:44 PM

What is the value for valuation[p] for a match in the binding site region versus a mismatch in the non-binding site region? If valuation[p] in the binding site region is much greater than valuation[p] in the non-binding site region, you have reduced the weight of errors in the non-binding site region. This is equivalent to ignoring harmful mutations in the non-binding site region. And as we all know, most mutations are harmful.What do you mean by "binding site region"? There are binding sites and then there are all the other positions on the chromosome.
The binding site region is the portion of the genome where a match to the weight matrix is considered to be correct. In Dr Schneider’s original selection scheme, a failure to match in this region causes an error, where as matches in the region not assigned to the binding sites do cause errors. Now Unnamed is using the value summed from the weight matrix minus the threshold to determine the selection. The problem with this is his variable sv is biased to the matches in the binding site region. The value obtained from a good match of the weight matrix to a particular position in the binding site region gives a large value to valuation[p] which will dominate the selection process against poor matches against sites in the non-binding site region of the genome. Once you have a good match to a binding site in the binding site region, the large value for valuation[p] for that binding site will prevent a mutation which causes a match (albeit poor) in the non-binding site from affecting the selection process because valuation[p] will be a smaller in magnitude for that erroneous match. Erroneous matches in the non-binding site region no longer are exerting as much influence on the selection process.

This in effect is ignoring potentially harmful mutations in the non-binding site region of the genome. Once you have several good binding sites in the binding site region of the genome, it is very unlikely that these creatures will ever be selected against because of the high values of valuation[p] for these sites which will nullify whatever happens in their nonbinding site regions.

For a good discussion of how the weight matrix is used to compute a match, see the paper An Evaluation of “Ev” by I.G.D Strachan which is available on the internet. http://www.iscid.org/papers/Strachan_EvEvaluation_062803.pdf

PixyMisa

8th January 2007, 09:01 PM

If y'all find mice and dogs meet your criteria as a demonstration of anything other than the fact that Mendel was basically right, your choice.

Mendel was right about what?

We have observed speciation - albeit not, despite all our efforts, in dogs.

Oops. I guess we agree, there. One species; check.Yes, all dogs belong to a single species. This has been pointed out to you before.

Nah, I think something in the lab a bit more malleable than mammals might be a place to start ... oh, iirc, you evolutionarians have been trying in the labs since the early 50's?Yes, and researchers have succeeded on a number of occasions, as you have seen in the documents you've been directed to.

Even the first one?As I said, that's not evolution. You're talking about abiogenesis, and no-one knows how that happened, because there is no physical evidence left anywhere. There are a number of hypotheses as to how it may have happened, but none have been worked out in sufficient detail or backed by sufficient experimental evidence to be fully convincing.

If you are talking about evolution, though, then genes are never created de novo. New genes are always formed through mutations of existing genes. (And as a side note, recombination never creates new genes.)

PS. Don't you have a corrupt database somewhere that needs fixing?No.

Unnamed

8th January 2007, 09:14 PM

Unnamed, just checking that you are using these parameters:

population 32
binding sites 8
weight width 9
site width 10
1 mutation per 512 bases
Ok, I'm attaching the dialog again.

Current data:
1024, 231, 260, 186
2048, 264, 257, 266
4096, 263, 263, 253
8192, 273, 347, 333
16384, 345, 304, 315
32768, 440, 422, 474, 288
65536, 432, 443
132072, 584, 563
262144, (running 146 generations, 15 mistakes to fix)

Unnamed, could you run the 32K case and tell me the number of births and deaths?
32768, 288 generations, 4624 births, 4592 deaths, 2465 by selection

We could test this by increasing sv by a fixed amount for spurious bindings. A good value would be, say, threshold/2.
I can't get it to work well. First, I had to use threshold/200, because sv was saturating (becoming larger than MAX_INT). Now, it seems that the procedure is selecting for a small absolute value of threshold rather than small number of mistakes. That's curious, but it makes sense: a few mutations can lower threshold, and therefore (spuriousHits*threshold), much faster than correcting each mistake. I can still try a fixed value, but linking it to threshold is not working.

In addition, there is no selection process for a partially completed gene.
I don't think that's true, but if it were, then my change would be meaningless.

I think if you keep track of the value of valuation[p] in the following equation,

sv += Math.abs(valuation[p] - threshold);

you will see that this number will be much larger in the binding site region due to the good match of the weight matrix. In the non-binding site region this value will remain small. You are effectively giving a higher weight to good mutations in the binding site region than to harmful mutations in the non-binding site region.
That makes more sense than your previous post. I won't dispute that, but Paul's suggestion should provide a test for that. But remember that there are many more non-binding sites than binding sites, so one could argue that I am giving more weight to non-binding sites.

You are still selecting for good and harmful mutations in the binding site region. Here is a simple computational experiment you can do. Set the values for gene=1 and nongene=0 and sort on mistakes rather than sv. Then compare the number of generation for convergence for you series that you have run with sv. I believe you will obtain almost the same number of generations for convergence for the two approaches.
When I set nongene=0 I get a "perfect" creature that still has binding mistakes. It converges much slower than my sv code (I gave up waiting after 3x the number of generations, because the number of mistakes stopped decreasing).

This is not necessarily an unrealistic approach to the selection process. Months ago I proposed that instead of starting with a random genome, start with a real genome and then define your selection process such that if there is a fatal mutation in the non-binding site region that this creature be selected out no matter what is happening in the binding site region.
But then it's not de novo evolution of information, defeating the purpose of the experiment.

What is the value for valuation[p] for a match in the binding site region versus a mismatch in the non-binding site region? If valuation[p] in the binding site region is much greater than valuation[p] in the non-binding site region, you have reduced the weight of errors in the non-binding site region. This is equivalent to ignoring harmful mutations in the non-binding site region. And as we all know, most mutations are harmful.
I don't know what the values are, and I don't think you can say that because you don't know either.

This is frightening.

Assuming you have no bugs, this shows us that the particular selection criterion used by Ev is critical to the speed of evolution, and that we certainly cannot draw any sweeping conclusions about the real world.
I'd say the same happens for real-world evolution. Whatever can't be selected efficiently will evolve slowly, while showstoppers like fatal mutations and novel genes will just jump out of the process.

Once you have several good binding sites in the binding site region of the genome, it is very unlikely that these creatures will ever be selected against because of the high values of valuation[p] for these sites which will nullify whatever happens in their nonbinding site regions.
Once the binding site is good, it ceases to contribute to sv. Only errors contribute to sv.

kjkent1

8th January 2007, 09:30 PM

RecoveringYuppy

8th January 2007, 09:41 PM

For instance, you keep talking about evolving hemoglobin de novo. Who says that the gene must begin as a hemoglobin gene? Why can't it start out providing some other selective advantage, then proceed to some other selective advantage, so that at present it happens to be a hemoglobin gene because we're here to observe it (anthropic principle), and sometime 10 million years in the future, it may be some other sort of gene that provides some selective advantage, or, perhaps no gene at all?

I mentioned this before but it got lost in the noise. The point you are making is well illustrated by hemoglobin. In the first place, there is no single hemoglobin gene. Hemoglobin is the product of of multiple reactions catalyzed by several enzymes and precursor proteins. And many of the individual components have other uses or are closely related to other enzymes and proteins. And there are an extremely large number of hemoglobins.

PixyMisa

8th January 2007, 10:25 PM

PS. Don't you have a corrupt database somewhere that needs fixing?

No.

Though come to think of it, I do have a 1.6TB RAID array with a failed disk...

Unnamed

8th January 2007, 10:33 PM

The 256k case converged:
262144, 463 generations

kjkent1

8th January 2007, 10:37 PM

I mentioned this before but it got lost in the noise. The point you are making is well illustrated by hemoglobin. In the first place, there is no single hemoglobin gene. Hemoglobin is the product of of multiple reactions catalyzed by several enzymes and precursor proteins. And many of the individual components have other uses or are closely related to other enzymes and proteins. And there are an extremely large number of hemoglobins.

I love this thread. People actually know what they're talking about (except for me -- I'm barely hanging on by my white knuckles).

Kotatsu

9th January 2007, 01:12 AM

I can see how proponents of Modern Evolutionary Theory could feel the results bolster their position. Other arguments could be made from opponents, with the literature full of loose ends waiting to be tugged sfaics.

Notice that these articles are ten years old. I have no idea if any of these ends have been tugged at since, but I know that the results of Song et al. inspired at least one other article (Soltis & Soltis, which I believe I referenced above); possibly either group has continued the work, but I don't really know where I should look for it.

Perhaps we could agree on something more along the lines of a new, clearly different, phenotype substantiating genotype changes?

It's a pity that Song et al. don't elaborate on exactly what the phenotypic differences between AB/BA, AC/CA and the parent plants are, apart from the fertilities. However, they do point out that the differences are there. And as the natural polyploid hybrids are sufficiently different --- phenotypically --- to have warranted separate species status long before the coming of molecular studies, I'd hazard a guess that there are substantial phenotypical differences between, for instance, Brassica rapa (A genome) and B. juncea (AB/BA genime).

However, as I've said I am no botanist, and don't know how much of a difference is needed for someone to describe a new species. And, furthermore, I am not you, why elaboration on your part is needed before "clearly different" can be agreed upon. Supposedly --- and to my knowledge we have only Song's et al. brief sentence to go on --- there is some variation between the F5 plants and the parent plants in terms of leaf shape, leaf colour, branching patterns, and number of side shoots. If these are characters traditionally used to assign species status to other plants within the same genus (or higher taxonomical level), and the devaitaions in the F5 plants from the parent plants are large enough, surely this speaks in favour of this being at least an initial example of the kind of speciation you are after?

Couldn't the geologic timespans nature seems to require to provide change be much compressed by conscious human selection and technology?

Do you mean, "Is experiments on artificially produced plants really comparable to what goes on in nature?"

Soltis & Soltis raises this question as well, but with a different slant (I think). They notice that while the artificially produced F2 plants are homozygous (due to the protocol and methods used by Song et al., I believe), the natural polyploid hybrids are likely heterozygous (due to the processes with which allopolyploidy occurs). Soltis and Soltis draw the conclusion that they are, based on about ten other studies which apparently show this. I haven't looked at any of these studies, though, so for the moment, I'll have to take their word for it until I have downloaded the referenced articles.

However, I do assert that allopolyploidization could be a much quicker speciation process than many others --- polyploidization, whether allo- or auto-, is virtually instantaneous, and if the progeny is deemed sufficiently different to form a new species (which often seems to be the case due to reproductive incompatibility between progeny and parents), then you have a kind of Insta-Species mechanism.

Many of these polyploids are ephemeral, though, unless they in some way can get around the incompatibility and reproduce by some other mode. Many oligochaetes, for instance, couple sexual reproduction to asexual reproduction in a seasonal pattern, which means that a new polyploid individual may produce many polyploid individuals by, for example, paratomy or architomy, with which they can then reproduce when the season for sexual mating arrives.

Anyway: I think the central finding of Song et al. is the possibility of rapid genome change through allopolyploidization. Whether or not this actually occurs in nature is not answered in their article, nor --- satisfactorily --- in Soltis and Soltis'. However, when I have time today, I shall browse through the referenced material and see what I can find. Soltis and Soltis, in particular, has a lot of seemingly useful references, although I am uncertain to what extent my university has access to all the botanical journals, as I rarely have reason to look for them.

Kotatsu

9th January 2007, 04:00 AM

Nah, I think something in the lab a bit more malleable than mammals might be a place to start ... oh, iirc, you evolutionarians have been trying in the labs since the early 50's?

This is where oligochaetes are very handy --- often easy to breed, generally short generation times, and they show more or less every kind of reproductive system known. In the worm I've worked with the most, Lumbriculus variegatus this is especially true, as it is architomic (1), and regenerates very quickly. For the purposes of my studies (I am a systematicist), I have never had occasion to let them grow very much, but they generally regenerate about half a centimetre per 3-4 weeks without any added nutrients, just spring water. I believe this rate is higher when it's fed properly (I have some articles on it, but can't remember the numbers).

To my knowledge, no studies using this or any other suitable oligochaete to study the same kind of processes as reported by Song et al. have been done, but I think there's a group somewhere in central US (Duluth?) that has recently started with something similar, though I base this on a vague recollection from a speech at a conference half a year ago.

The problem is then transferred from lack of malleability to lack of suitable characters on which to detect phenotypic change, as several of the more common worms (especially those which have short generation times and are easy to use) seem to be polyphyletic or show genotypic or phenotypic differences to begin with.

---
(1) That is, it can reproduce by having either end pinched off, whereupun the pinched-off part undergo morphological and physiological changes to produce a new worm, after a given pattern. Not to be confused with paratomy, where the differentiation of the tissues which will form the new worm occurs before the actual split.

Cuddles

9th January 2007, 05:15 AM

Yes, all dogs belong to a single species. This has been pointed out to you before.

I actually disagree with this. As a little gedanken, imagine that almost all dogs were wiped out leaving only great danes and chihuahuas. How many species do we have? Given the general definition of two groups of organism that are incapable of interbreeding, we have two. Now put all the other dogs back. What has changed to suddenly make those two species back into one?

The problem is exactly the same as that with classifying fossils. There are very rarely sudden changed that form new species, it is usually a gradual process in which the transitional forms can be viewed as either belonging to the original species or the new one, depending on how you look at it. This is why the phylogenic tree can only be drawn for one point in time, since transitional forms blur the lines between species and would prevent it being drawn at all.

The problem with dogs is that all (or at least a lot of) the transitional forms are present at the same time, which means that it is not really possible to say either that there is one species or that there are more, since there is no way to draw a line that demarcates species or to group all of them into one interbreeding species. All we can really say is that our definition of species is not perfect and dogs are one area where it simply doesn't work. Of course, this is one of the major problems creationarians seem to have - they simply don't seem able to accept that species, genes and even life are not fixed things, both they and their definitions are fluid and there will always be exceptions no matter what definition we use, the best we can manage is a good working definition that serves in most situations.

Given this, it makes no sense at all to speak of things like "macroevolution". Since we can't rigidly define a species, it is pointless to try to distinguish between changes within a species and changes to a new species since we can't know when a new species is created.

cyborg

9th January 2007, 05:16 AM

Cyborg, I have never said I was educated in everything.

Are you educated in ANYTHING?

You have thus far demonstrated:

1) Inadequate logic
2) Inadequate mathematics
3) Inadequate computer science
4) Inadequate theology

Just what the hell is it you are educated in? I suppose it must be to be annoying then.

I’m only claiming I know something about ev and what this computation is saying about random point mutations and natural selection.

No, you're claiming that Quake should be able to tell us about relativistic physics because despite ev clearly not being anywhere near a comprehensive model of evolution it should be able to show that events you cannot define cannot occur.

I’m content to say that the theory of evolution is without a mathematical basis and that ev shows that random point mutations and natural selection is so profoundly slow that nothing can evolve by this mechanism.

You cannot simultaneously say evolution is without mathematical basis and then say ev is the mathematical basis upon which you have disproved evolution.

Are you profoundly slow or what?

Do you understand why Quake is an insufficient model of physics or not?

Do you understand why ev is an insufficient model of evolution or not?

Maybe I am going too fast...

English? Understand? Understand English???

Does to, does to.

Apparently not.

5) Inadequate English

You can stomp your foot and say it is my task, but it is your theory to prove.

No. You are trying to disprove evolution mathematically. It is therefore your task.

I doubt any evolutionarians who have knowledge of mathematics will try to include other mechanisms of mutations because all these mechanisms will still face the same 4^G effect of the increasing search space as the genome length is increased.

Proof.

Show your working. Algebra please. Assertion is not mathematics.

When an evolutionarian retracts their belief in the theory of evolution. That is a macroevolutionary event.

And when does this occur in ev?

Annoying an evolutionarian, that’s a microevolutionary event.

And when does this occur in ev?

Paul C. Anagnostopoulos

9th January 2007, 05:35 AM

The binding site region is the portion of the genome where a match to the weight matrix is considered to be correct. In Dr Schneider’s original selection scheme, a failure to match in this region causes an error, where as matches in the region not assigned to the binding sites do cause errors.
I think you misspoke here.

Now Unnamed is using the value summed from the weight matrix minus the threshold to determine the selection.
The absolute value thereof.

The value obtained from a good match of the weight matrix to a particular position in the binding site region gives a large value to valuation[p] which will dominate the selection process against poor matches against sites in the non-binding site region of the genome.
Binding sites that are matched do not contribute to the value of sv.

~~ Paul

PixyMisa

9th January 2007, 05:37 AM

I actually disagree with this. As a little gedanken, imagine that almost all dogs were wiped out leaving only great danes and chihuahuas. How many species do we have?

Depends on your definition of species, of course.

Given the general definition of two groups of organism that are incapable of interbreeding, we have two.

I wouldn't count on that. They are genetically compatible, and they'll assuredly try to interbreed. They're dogs. ;)

Now put all the other dogs back. What has changed to suddenly make those two species back into one?

Continuity of the spectrum of genetic variation within the species.

The problem is exactly the same as that with classifying fossils. There are very rarely sudden changed that form new species, it is usually a gradual process in which the transitional forms can be viewed as either belonging to the original species or the new one, depending on how you look at it. This is why the phylogenic tree can only be drawn for one point in time, since transitional forms blur the lines between species and would prevent it being drawn at all.

Absolutely.

The problem with dogs is that all (or at least a lot of) the transitional forms are present at the same time, which means that it is not really possible to say either that there is one species or that there are more, since there is no way to draw a line that demarcates species or to group all of them into one interbreeding species.

Agreed. But given a continuous spectrum and active interbreeding throughout that spectrum, it usually makes more sense to classify it as a single species.

All we can really say is that our definition of species is not perfect and dogs are one area where it simply doesn't work.

I wouldn't say that. What I would say is that the definition of species is somewhat arbitrary - and necessarily so.

Of course, this is one of the major problems creationarians seem to have - they simply don't seem able to accept that species, genes and even life are not fixed things, both they and their definitions are fluid and there will always be exceptions no matter what definition we use, the best we can manage is a good working definition that serves in most situations.

Yep. Hammy's "I know one when I see one" being an example of this.

Given this, it makes no sense at all to speak of things like "macroevolution". Since we can't rigidly define a species, it is pointless to try to distinguish between changes within a species and changes to a new species since we can't know when a new species is created.

Micro- and macro-evolution are relative terms, at best. The creationarians think that they are qualitatively different - which is of course untrue.

Kotatsu

9th January 2007, 08:45 AM

I took a look online, and after following several citations felt like Alice after she went down the rabbit hole.

Regarding Tragopogon sp. and Brassica I have downloaded the article by Soltis et al. and some additional articles by Song's group, but it seems parts of the university server just broke down, so I couldn't get all the articles I wanted (I can't seem to access the university library). Anyway, I shall look through these tonight and see what they say.

Paul C. Anagnostopoulos

9th January 2007, 09:51 AM

Unnamed:

Will you create a variant of your variant and run the same series of experiments? This time, rather than totaling the distances between the valuations and the threshold, just use the maximum one.

~~ Paul

kleinman

9th January 2007, 10:32 AM

In addition, there is no selection process for a partially completed gene.Your comment here seems to suggest that you have some a priori knowledge of what a completed gene will be before it evolves. For instance, you keep talking about evolving hemoglobin de novo. Who says that the gene must begin as a hemoglobin gene? Why can't it start out providing some other selective advantage, then proceed to some other selective advantage, so that at present it happens to be a hemoglobin gene because we're here to observe it (anthropic principle), and sometime 10 million years in the future, it may be some other sort of gene that provides some selective advantage, or, perhaps no gene at all?
This is classic evolutionarian thinking. Speculate all you want, just don’t call this science.
This is equivalent to ignoring harmful mutations in the non-binding site region. And as we all know, most mutations are harmful.If the region is non-binding, then how can the mutation be either harmful or beneficial? According to Schneider's "EV" paper, the mistakes in the non-binding region are simply "wasteful binding of the recognizer." I assume this means "junk DNA." Schneider continues: "For simplicity these mistakes are counted as equivalent, since other schemes should give similar final results."

Apparently, "unnamed" has just demonstrated that while "other schemes" may give similar "final" results, the final results are obtained in several orders of magnitude less generations.
Dr Schneider’s selection process does not have a sound scientific basis but I accept it because it demonstrates something about the mathematics of random point mutations and natural selection. Unnamed’s selection process is counter what is observed. You can not ignore mutations in other portions of a genome and just consider mutations at the location you want to evolve. Unnamed’s selection process is unscientific.
Cyborg, I have never said I was educated in everything.Are you educated in ANYTHING?
I’m educated enough to annoy evolutionarians!
I’m content to say that the theory of evolution is without a mathematical basis and that ev shows that random point mutations and natural selection is so profoundly slow that nothing can evolve by this mechanism.You cannot simultaneously say evolution is without mathematical basis and then say ev is the mathematical basis upon which you have disproved evolution.
I can, I did and its true.
When an evolutionarian retracts their belief in the theory of evolution. That is a macroevolutionary event.And when does this occur in ev?
Remember, macroevolutionary event take some time.
Annoying an evolutionarian, that’s a microevolutionary event.And when does this occur in ev?
That happens all the time.
The binding site region is the portion of the genome where a match to the weight matrix is considered to be correct. In Dr Schneider’s original selection scheme, a failure to match in this region causes an error, where as matches in the region not assigned to the binding sites do cause errors.I think you misspoke here.
You are correct, the match to the weight matrix has to exceed the threshold.
Now Unnamed is using the value summed from the weight matrix minus the threshold to determine the selection.The absolute value thereof.
Do you want to tell us why he has to use the absolute value?
The value obtained from a good match of the weight matrix to a particular position in the binding site region gives a large value to valuation[p] which will dominate the selection process against poor matches against sites in the non-binding site region of the genome.Binding sites that are matched do not contribute to the value of sv.
Which is why Unnamed has to use very small values for threshold in order for his scheme to work, otherwise binding sites in the binding site region no longer contribute to the selection process.

cyborg

9th January 2007, 10:44 AM

I’m educated enough to annoy evolutionarians!

A feat worthy of a five-year-old who has learnt to say, "why?"

Congratulations on this haughty intellectual achievement.

I can, I did and its true.

Either ev is the mathematical representation of evolution and hence evolution is mathematically grounded and you have some sort of justification for saying ev can disprove evolution or evolution doesn't have any mathematical grounding and hence ev cannot possibly have anything to do with evolution being that it is essentially an exercise in mathematics.

You cannot have it both ways. Choose.

Remember, macroevolutionary event take some time.

Again, I would like to be able to know how long this is exactly. I therefore require that you tell me how I can identify a macroevolutionary event. I do not care if your conclusion is that ev shows that in real life macroevolution cannot occur - I want you to show me how to identify macroevolution in ev.

That happens all the time.

Which still fails to answer the question.

6) Inadequate reading comprehension

kleinman

9th January 2007, 11:08 AM

I’m educated enough to annoy evolutionarians!A feat worthy of a five-year-old who has learnt to say, "why?"
I thought it would take at least a seven or eight year old to annoy evolutionarians. So you better teach your theory to infants before they have learned to say “why?”
I can, I did and its true.Either ev is the mathematical representation of evolution and hence evolution is mathematically grounded and you have some sort of justification for saying ev can disprove evolution or evolution doesn't have any mathematical grounding and hence ev cannot possibly have anything to do with evolution being that it is essentially an exercise in mathematics.

You cannot have it both ways. Choose.
Here is where you are missing the distinction. The theory of evolution started without a mathematical basis. So along comes Dr Schneider who writes a mathematical model of random point mutations and natural selection. I look at the model and see this as plausible representation of the phenomena. When you use realistic genome lengths and mutation rates in the model, the rate of information is so profoundly slow that it disproves macroevolution by this mechanism.

So I choose both.
Remember, macroevolutionary event take some time.Again, I would like to be able to know how long this is exactly. I therefore require that you tell me how I can identify a macroevolutionary event. I do not care if your conclusion is that ev shows that in real life macroevolution cannot occur - I want you to show me how to identify macroevolution in ev.
I keep setting up the target of de novo evolution of a gene. It seems that PixyMisa thinks this is abiogenesis. Joobz won’t tell us how ribose can be formed nonenzymatically yet PixyMisa seems to think that entire genes can form in the primordial soup. Where is the science?
That happens all the time.Which still fails to answer the question.
Sure it does, what is the name of this thread? Maybe we are in the equilibrium part of the punctuated equilibrium.

cyborg

9th January 2007, 11:17 AM

hammegk

9th January 2007, 11:22 AM

Maybe we are in the equilibrium part of the punctuated equilibrium.
I'd say we're waiting on a Newton to tie together in some rigorous way the actual bits of science that underlie Modern Ev Theory . I can't decide if the current just-so-story is a steaming pile waiting to collapse under it's own weight, or is just so nebulus the first strong breeze will destroy it.

cyborg

9th January 2007, 11:30 AM

I'd say we're waiting on a Newton to tie together in some rigorous way the actual bits of science that underlie Modern Ev Theory .

No, we need software engineers and biologists, not mathematicians. Mathematicians (I hesitate to say like kleinman since he has demonstrated some quite laughable blunders) simply do not seem to be able to appreciate how different the quality of the problem is. (Hey kleinman, at least you've got a start realising that 4^G is the beginning of recognising the programming space but software is no more about formulating 2^P than genetics is 4^G). I've seen the programming they teach mathematicians at university level - man oh man, it sure does explain a few things.

kleinman

9th January 2007, 12:03 PM

I thought it would take at least a seven or eight year old to annoy evolutionarians. So you better teach your theory to infants before they have learned to say “why?”Hmm, I thought that was the job of your camp. To stomp out questioning and to instil obedience to mysterious gods.
I think it is the responsibility of older people to teach younger people. I have no interest in stomping out questioning. I also know you can not instill obedience to God but you can teach young people the value of being obedient to God and the costs to being disobedient to God.
When you use realistic genome lengths and mutation rates in the model, the rate of information is so profoundly slow that it disproves macroevolution by this mechanism.So again I must ask - WHAT is macroevolution?
I know this answer annoys you so I give it again, the de novo evolution of a gene.
So I choose both.Ah, cognitive dissonance at its finest.
Are you sure that the dissonance is in my cognition and not in your comprehension?
I keep setting up the target of de novo evolution of a gene.7) Inadequate memory

The words 'de novo evolution of a gene' did not pass your lips until fairly recently.
This is my 241st post on this thread. I first used the words “de novo evolution of a gene” on my 4th post on this thread.
Maybe we are in the equilibrium part of the punctuated equilibrium.I'd say we're waiting on a Newton to tie together in some rigorous way the actual bits of science that underlie Modern Ev Theory . I can't decide if the current just-so-story is a steaming pile waiting to collapse under it's own weight, or is just so nebulus the first strong breeze will destroy it.
I believe there is some truth in the modern theory of evolution. I believe that recombination and natural selection is a commonly observed phenomena and that mutations occur that cause severe genetic damage and rarely beneficial affects. Where I think the theory breaks down is when evolutionists extrapolate the very rapid changes to a population that can occur with recombination and natural selection to mutation and natural selection. Gould’s hypothesis of punctuated equilibrium makes sense if you apply the concept to recombination and natural selection but breaks down when applying the concept to mutation and natural selection as shown by ev and the evidence in the fossil record. Darwin did likewise, he confused the rapid changes that recombination and natural selection can accomplish with mutation and natural selection.

As you can see from Cyborg’s postings, he equates any challenge to his theory that I am trying to force him to believe in God. What Cyborg doesn’t understand is that you can believe in God and still be a scientist.

cyborg

9th January 2007, 12:27 PM

I think it is the responsibility of older people to teach younger people. I have no interest in stomping out questioning. I also know you can not instill obedience to God but you can teach young people the value of being obedient to God and the costs to being disobedient to God.

That's instil - I refer you to number 5 on the list of your inadequacies.

Yahweh does not exist. Therefore it is redundant to teach value of obedience or disobedience to beings that do not exist.

Or -

You teach obedience to a false god. You will see in time how costly this mistake is when you are in Hades.

Take your pick.

I know this answer annoys you so I give it again, the de novo evolution of a gene.

Right. Now we are getting somewhere. You never gave me that answer so it can't have ever annoyed me. Could have saved a lot of trouble.

The next question then becomes what you consider to be the change of state in ev that signifies the creation of a gene.

Are you sure that the dissonance is in my cognition and not in your comprehension?

Yes. If ev is mathematically adequate to disprove evolution then it is quite irrelevant if evolution did not start out with the mathematical adequacy of ev - we have, according to you, a mathematically solid theory.

You cannot have it both ways. Is it solid or is it not? If ev is adequate to disprove evolutionary theory then it must surely be a rigorous mathematical model of it.

This is my 241st post on this thread. I first used the words “de novo evolution of a gene” on my 4th post on this thread.

Then I shall retract. Your list recedes. Lucky boy.

I believe there is some truth in the modern theory of evolution. I believe that recombination and natural selection is a commonly observed phenomena and that mutations occur that cause severe genetic damage and rarely beneficial affects.

Ah, so you are basically stating that things can only ever get worse.

Where I think the theory breaks down is when evolutionists extrapolate the very rapid changes to a population that can occur with recombination and natural selection to mutation and natural selection.

Eh? The theory breaks down because recombination is not point mutation?

That. Is. Silly.

Darwin did likewise, he confused the rapid changes that recombination and natural selection can accomplish with mutation and natural selection.

Um, I don't think Darwin knew anything of mutation, such that genetics was unknown in his time.

As you can see from Cyborg’s postings, he equates any challenge to his theory that I am trying to force him to believe in God.

Let us say I am convinced by your arguments.

What am I to conclude now that you have demonstrated that life as we see it cannot have evolved?

Answer that and stay fashionable.

What Cyborg doesn’t understand is that you can believe in God and still be a scientist.[/SIZE][/FONT]

I understand that perfectly.

What YOU don't understand is that not everything a scientist does is automatically scientific. Bringing a god into the equation ends science dead. It is to give up on inquiry.

kjkent1

9th January 2007, 12:46 PM

This is classic evolutionarian thinking. Speculate all you want, just don’t call this science.Grow up, Alan.

My speculation is at least as scientific as are your scientific claims. Example:Dr Schneider’s selection process does not have a sound scientific basis but I accept it because it demonstrates something about the mathematics of random point mutations and natural selection. Here, you tell us that Schneider's modeled selection process does not have a sound scientific basis, and then you tell us that it's good enough to defeat RMNS as a scientific theory. Well, if NS is part of the theory of RMNS, and you believe NS is unsound in Schneider's model, then your claim that Schneider's model of RMNS falsifies real-world random mutation and natural selection is merely "speculation" until you actually test your theory with a "sound" selection process.

You need to work a little harder on your logical and scientific reasoning before you start condescending to others.

Myriad

9th January 2007, 01:21 PM

The 256k case converged:
262144, 463 generations

Given that it takes more information to converge with longer genomes, this appears to be approaching the performance predicted by MacKay's statistical model for asexual reproduction, of one bit per generation (for the whole population) regardless of genome length. MacKay's model assumes a selection function that independently values each base in the genome. Ev applies less specificity to the nonbinding bases, which should reduce the rate of information gain for a given mutation rate, but that apparently also permits an increase in the allowable mutation rate above MacKay's predicted workable maximum of 1 per genome per generation.

The bad news (as Kleinman has been pointing out for months, in fact it's the whole reason he pointed me to MacKay) is that in MacKay's model, increasing the population won't make it evolve any faster. The good news is that it's obviously quite fast enough already.

The other good news is that MacKay predicts considerably higher mutation tolerances and information increase rates for reproduction with recombination.

Respectfully,
Myriad

kleinman

9th January 2007, 01:29 PM

Where I think the theory breaks down is when evolutionists extrapolate the very rapid changes to a population that can occur with recombination and natural selection to mutation and natural selection.Eh? The theory breaks down because recombination is not point mutation?
What you are having a hard time grasping is that you can accomplish microevolutionary changes very rapidly with recombination and natural selection. Darwin inappropriately attributed the variations in finch beaks to mutation and natural selection when what he was observing was the affects of recombination and natural selection. Recombination and natural selection can accomplish rapid morphological changes in a population. Point mutation and natural selection is a profoundly slow process for achieving change, ev shows this.
Darwin did likewise, he confused the rapid changes that recombination and natural selection can accomplish with mutation and natural selection.Um, I don't think Darwin knew anything of mutation, such that genetics was unknown in his time.
He did not have the data we have now. However this same inappropriate extrapolation was made by Stephen Gould when he postulated punctuated equilibrium for mutation and natural selection. Gould knew about DNA and mutations but his hypothesis only makes sense when applied to recombination and natural selection.
As you can see from Cyborg’s postings, he equates any challenge to his theory that I am trying to force him to believe in God.Let us say I am convinced by your arguments.

What am I to conclude now that you have demonstrated that life as we see it cannot have evolved?

Answer that and stay fashionable.
You will have to find another reason not to believe in God.
What Cyborg doesn’t understand is that you can believe in God and still be a scientist.I understand that perfectly.

What YOU don't understand is that not everything a scientist does is automatically scientific. Bringing a god into the equation ends science dead. It is to give up on inquiry.
I try to keep this discussion on a mathematical basis. I occasionally will give my view about God but it has always been because of questioning by other posters. I don’t think you should give up on inquiry, I think you should seek the Truth.
This is classic evolutionarian thinking. Speculate all you want, just don’t call this science.Grow up, Alan.

My speculation is at least as scientific as are your scientific claims. Example:Dr Schneider’s selection process does not have a sound scientific basis but I accept it because it demonstrates something about the mathematics of random point mutations and natural selection.
Do you really think that the partial binding of a protein represents a realistic selection process for the de novo evolution of a gene or even a binding site for that matter? What benefit is there for a binding site without an associated gene? Why would a binding site evolve without a gene? So you speculate about how a hemoglobin gene can evolve and I’ll speculate on the unreality of Dr Schneider’s selection process.
Here, you tell us that Schneider's modeled selection process does not have a sound scientific basis, and then you tell us that it's good enough to defeat RMNS as a scientific theory. Well, if NS is part of the theory of RMNS, and you believe NS is unsound in Schneider's model, then your claim that Schneider's model of RMNS falsifies real-world random mutation and natural selection is merely "speculation" until you actually test your theory with a "sound" selection process.
Even with Dr Schneider’s idealized selection process, you can’t accumulate the information quickly enough to support the theory of evolution. A more realistic selection process (if one exists) only makes the theory of evolution look more ridiculous.
The 256k case converged:
262144, 463 generations The bad news (as Kleinman has been pointing out for months, in fact it's the whole reason he pointed me to MacKay) is that in MacKay's model, increasing the population won't make it evolve any faster. The good news is that it's obviously quite fast enough already.
Now if only there were no such thing as a harmful mutation, you would have something to celebrate.

Paul C. Anagnostopoulos

9th January 2007, 02:17 PM

The bad news (as Kleinman has been pointing out for months, in fact it's the whole reason he pointed me to MacKay) is that in MacKay's model, increasing the population won't make it evolve any faster. The good news is that it's obviously quite fast enough already.
Interesting. What was that reference again?

Unnamed: Run all the experiments again, except with a population of 512.

~~ Paul

Paul C. Anagnostopoulos

9th January 2007, 02:19 PM

... its true.
Uh oh. :D

~~ Paul

kjkent1

9th January 2007, 02:29 PM

Do you really think that the partial binding of a protein represents a realistic selection process for the de novo evolution of a gene or even a binding site for that matter? What benefit is there for a binding site without an associated gene? Why would a binding site evolve without a gene? So you speculate about how a hemoglobin gene can evolve and I’ll speculate on the unreality of Dr Schneider’s selection process.I hereby acknowledge your admission that the allegation that Schneider's ev model shows that evolution is mathematically impossible, is merely your unscientific speculation.

Even with Dr Schneider’s idealized selection process, you can’t accumulate the information quickly enough to support the theory of evolution. A more realistic selection process (if one exists) only makes the theory of evolution look more ridiculous.Per your admission (above), your conclusion here is unscientific speculation.

Paul C. Anagnostopoulos

9th January 2007, 02:29 PM

So you speculate about how a hemoglobin gene can evolve and I’ll speculate on the unreality of Dr Schneider’s selection process.
So then you won't be using Ev to speculate about the real world any more, right?

~~ Paul

Edited to add: Cross-posted with kjkent1.

Paul C. Anagnostopoulos

9th January 2007, 02:43 PM

joobz

9th January 2007, 03:02 PM

So what happens if we divide the generation count by Rfrequency? Do we get a constant?

genome, generations, Rfrequency, generations/Rfrequency

1024, 231, 7.0, 33
2048, 264, 8.0, 33
4096, 263, 9.0, 29.2
8192, 273, 10.0, 27.3
16384, 345, 11.0, 31.4
32768, 440, 12.0, 36.7
65536, 432, 13.0, 33.2
132072, 584, 14.0, 41.7
262144, 463, 15.0, 30.9

Ain't that interesting.

~~ Paul
Can you explain why?

Myriad

9th January 2007, 03:20 PM

Interesting. What was that reference again?

MacKay, David J.C., Information Theory, Inference, and Learning Algorithms, Cambridge University Press, 2003. Chapter 19, pp. 269-280

Here's the chapter in PDF:
http://www.inference.phy.cam.ac.uk/mackay/itprnn/ps/265.280.pdf

Whole book PDF here:
http://www.cs.toronto.edu/~mackay/itprnn/book.pdf

Other format options here:
http://www.inference.phy.cam.ac.uk/mackay/itila/book.html

Cambridge book catalog entry for it here:
http://www.cambridge.org/us/catalogue/catalogue.asp?isbn=9780521642989

Comparison with Harry Potter here:
http://www.inference.phy.cam.ac.uk/mackay/itila/Potter.html

Respectfully,
Myriad

kleinman

9th January 2007, 03:23 PM

Given that it takes more information to converge with longer genomes, this appears to be approaching the performance predicted by MacKay's statistical model for asexual reproduction, of one bit per generation (for the whole population) regardless of genome length.So what happens if we divide the generation count by Rfrequency? Do we get a constant?

genome, generations, Rfrequency, generations/Rfrequency

1024, 231, 7.0, 33
2048, 264, 8.0, 33
4096, 263, 9.0, 29.2
8192, 273, 10.0, 27.3
16384, 345, 11.0, 31.4
32768, 440, 12.0, 36.7
65536, 432, 13.0, 33.2
132072, 584, 14.0, 41.7
262144, 463, 15.0, 30.9

Ain't that interesting.
Hey Paul, what part of the evolutionary landscape is ev now modeling? Are you now going to retract your retraction about ev modeling reality?

Now that you have successfully gotten ev to converge more quickly (by ignoring harmful mutations on the nonbinding site region of the genome) are you going to the lab and prove your results?
So you speculate about how a hemoglobin gene can evolve and I’ll speculate on the unreality of Dr Schneider’s selection process.So then you won't be using Ev to speculate about the real world any more, right?
Do you think an even more unrealistic selection process than the one used by Dr Schneider that produces clearly unrealistic results is the way to prove your point? Remember, the results I obtained from ev was with Dr Schneider’s version of the model which was peer reviewed and published in Nucleic Acids Research. Do you think they would accept the results generated by Unnamed’s selection process?

You are really struggling in this discussion when you have to do this.

You go down this rabbit trail for a while and I’ll check back with you later.

kjkent1

9th January 2007, 03:24 PM

So then you won't be using Ev to speculate about the real world any more, right?

~~ Paul

Edited to add: Cross-posted with kjkent1.

LOL.

In fairness to Kleinman, I'm certain his next response will be that what he means by not "sound" is that the ev natural selection model is not "realistic." Rather it is "idealized," so it should provide better results than any possible realistic selection model.

However, this does not necessarily follow, because Alan has refused to show how no other possible selection model can overcome the problem of numbers of generations to reach convergence.

And, as "unnamed" seems to have demonstrated that his/her selection model can overcome the numbers of generations problem, the issue is now, whether this new selection method is more or less realistic than Dr. Schneider's "idealized" original method?

If we really want to solve this problem, we will need some consensus among a few geneticists who know enough about computer programming to be able to reasonably evaluate any proposed algorithms.

Hey, if this gets published, I want my name on it.

Edit: I see that Kleinman has now posted substantially as I predicted here. Now, he's simultaneously calling Schneider's original selection model "unrealistic" and "unnamed"'s model more unrealistic, while still speculating that ev proves evolution impossible.

If there were any more "speculatin'" go'in on here, we'd need a brass spittoon.

John Hewitt

9th January 2007, 04:04 PM

LOL.

In fairness to Kleinman, I'm certain his next response will be that what he means by not "sound" is that the ev natural selection model is not "realistic." Rather it is "idealized," so it should provide better results than any possible realistic selection model.

Please, I surrender, please would somebody tell me what LOL means?

Robin

9th January 2007, 04:22 PM

Please, I surrender, please would somebody tell me what LOL means?
I would like to know too. I have always assumed it was an emoticon gone wrong.

cyborg

9th January 2007, 04:49 PM

What you are having a hard time grasping is that you can accomplish microevolutionary changes very rapidly with recombination and natural selection. Darwin inappropriately attributed the variations in finch beaks to mutation and natural selection when what he was observing was the affects of recombination and natural selection.

Again, I don't recall mutation ever coming up as far as Darwin is concerned. He had no knowledge of the mechanisms of evolution because genetics was unknown.

Recombination and natural selection can accomplish rapid morphological changes in a population. Point mutation and natural selection is a profoundly slow process for achieving change, ev shows this.

Which leads me to the question I did not ask last time - are you saying that recombination is somehow not a part of evolution? You keep on referring to it as if it is something that is hitherto an unconsidered effect.

]He did not have the data we have now. However this same inappropriate extrapolation was made by Stephen Gould when he postulated punctuated equilibrium for mutation and natural selection. Gould knew about DNA and mutations but his hypothesis only makes sense when applied to recombination and natural selection.

Again the above.

You will have to find another reason not to believe in God.

So are you saying I should conclude that a god (Zeus or Thor perhaps, one of those gods that is likely to exist, not like Yahweh) is responsible for the diversity of life or not?

Hmm, new list.

1) Entirely adequate at not answering simple questions

I try to keep this discussion on a mathematical basis.

Then bring on the damn maths!

I occasionally will give my view about God but it has always been because of questioning by other posters. I don’t think you should give up on inquiry, I think you should seek the Truth.

Which, in your opinion, must lead to me concluding Yahweh is the force which allows life to be what it is - evolution being unable to account for it.

Truth or truthiness?

Myriad

9th January 2007, 06:30 PM

Please, I surrender, please would somebody tell me what LOL means?

I would like to know too. I have always assumed it was an emoticon gone wrong.

I will tell you, but think about this first: If you've been wondering this for a long time, have you ever considered searching for the answer in other ways? For instance, if you Google "Internet Abbreviations" you'll get many links that will take you right to the answer.

(Give a man the meaning of a net acronym, and you've enlightened him for an hour; teach a man to look stuff up with a search engine, and you've confused him for life. Or something like that.)

Now, do you still want me to just tell you?

It means "laughing out loud."

Disappointing, ain't it?

Respectfully,
Myriad

joobz

9th January 2007, 07:21 PM

I will tell you, but think about this first: If you've been wondering this for a long time, have you ever considered searching for the answer in other ways? For instance, if you Google "Internet Abbreviations" you'll get many links that will take you right to the answer.

Or more simply lol
As this question goes, I don't really know if it was a sarcastic question on thier part or not. But I do find it wierd when anyone these days says something like..."I wonder XXXX" and doesn't perform a quick search to get a quick first look.

RecoveringYuppy

9th January 2007, 07:24 PM

Yeah, how does anyone find JREF without coming across LOL first??

John Hewitt

10th January 2007, 01:42 AM

Or more simply lol
As this question goes, I don't really know if it was a sarcastic question on thier part or not. But I do find it wierd when anyone these days says something like..."I wonder XXXX" and doesn't perform a quick search to get a quick first look.
I know the answer to that
As this question goes, I don't really know if it was a sarcastic question on thier part or not. But I do find it wierd when anyone these days says something like..."I wonder XXXX" and doesn't perform a quick search to get a quick first look.
Shall I tell you tha answer?

Shall I?

The answer is

God didn't design my brain with a "Google it first" module.

joobz

10th January 2007, 06:34 AM

God didn't design my brain with a "Google it first" module.
I have only one response to that.

LOL.:D

-well played, sir. well played!:clap:

Paul C. Anagnostopoulos

10th January 2007, 06:41 AM

Hey Paul, what part of the evolutionary landscape is ev now modeling? Are you now going to retract your retraction about ev modeling reality?
It's modeling something like weak and strong binding. See my previous reference.

Now that you have successfully gotten ev to converge more quickly (by ignoring harmful mutations on the nonbinding site region of the genome) are you going to the lab and prove your results?
Can you explain why you think it's ignoring harmful mutations? Your preceding explanations contained errors, so I'm not sure what your explanation is now.

Do you think an even more unrealistic selection process than the one used by Dr Schneider that produces clearly unrealistic results is the way to prove your point?
Please explain why you think Unnamed's selection method is more unrealistic.

~~ Paul

cyborg

10th January 2007, 06:58 AM

Please explain why you think Unnamed's selection method is more unrealistic.

Paul, that one is easy.

It does not agree with his conclusion.

joobz

10th January 2007, 07:12 AM

Paul, that one is easy.

It does not agree with his conclusion.
Oh, and the mathematics. Don't forget to use the word mathematics in bizzarre and not quite appropriate ways.

repeat after me
Simulation runs <> mathematics
Edit: for c fans
simulation runs := mathematics

RecoveringYuppy

10th January 2007, 07:23 AM

You mean !=

joobz

10th January 2007, 11:54 AM

You mean !=
yeah,typo. My bad.:o

kjkent1

10th January 2007, 12:56 PM

OK, I think I've found a link that resolves everything related to this thread:

http://www.youtube.com/watch?v=jmvlZQZzFts

Enjoy!

Unnamed

10th January 2007, 02:01 PM

Will you create a variant of your variant and run the same series of experiments? This time, rather than totaling the distances between the valuations and the threshold, just use the maximum one.
I am not sure I understand. Do you want to multiply the maximum distance by the number of mistakes? Because otherwise a creature with a single strong mistake could score much higher than a creature with multiple weak mistakes. Or maybe that's the point, I don't know.

I'll do that when I finish running the examples with population 512.

Unnamed: Run all the experiments again, except with a population of 512.
These are the first results:

genome, population, run1, run2, run3
1024, 64, 165, 176, 199
1024, 128, 163, 157, 181
1024, 256, 150, 162, 147
1024, 512, 146, 127, 144
2048, 512, 188, 167, 147
4096, 512, 225, 171, 176
8192, 512, 194, 192, 154
16384, 512, 248, 211, 212

I am having trouble with genomes larger than 16k. I set the parameters but the application freezes when I press "OK". I presume it's computing something, but it takes too long. I'll see if I can solve that and run the remaining cases.

The bad news (as Kleinman has been pointing out for months, in fact it's the whole reason he pointed me to MacKay) is that in MacKay's model, increasing the population won't make it evolve any faster. The good news is that it's obviously quite fast enough already.

The other good news is that MacKay predicts considerably higher mutation tolerances and information increase rates for reproduction with recombination.
Myriad, it seems that you understand this much better than I do, so if you have any suggestion I would be glad to implement and test it, like I am doing for Paul.

Unnamed

10th January 2007, 02:03 PM

Unnamed’s selection process is counter what is observed. You can not ignore mutations in other portions of a genome and just consider mutations at the location you want to evolve. Unnamed’s selection process is unscientific.
Kleiman's strawman version of my selection process is indeed unscientific.

I’m educated enough to annoy evolutionarians!
I'm not annoyed, just disappointed.

Which is why Unnamed has to use very small values for threshold in order for his scheme to work, otherwise binding sites in the binding site region no longer contribute to the selection process.
You didn't understand what I said. I had to divide threshold by a constant because the sum of errors was becoming too large to fit in a 32-bit integer. I didn't change the threshold itself. All sites (binding and non-binding) contribute equally, but there are many more non-binding sites than binding. But the proof of my selection process is in the perfect creature: it has no mistakes of any kind. That can't happen if I "ignore" any kind of mistake.

Paul C. Anagnostopoulos

10th January 2007, 02:29 PM

I am having trouble with genomes larger than 16k. I set the parameters but the application freezes when I press "OK". I presume it's computing something, but it takes too long. I'll see if I can solve that and run the remaining cases.
Your Java memory limit is too low. Use the -Xmx option when you run Evj.

~~ Paul

Unnamed

10th January 2007, 03:20 PM

Your Java memory limit is too low. Use the -Xmx option when you run Evj.
Yes, that was it. I'll post when I get new results.

Unnamed

10th January 2007, 09:10 PM

This is it for today:

genome, population, run1, run2, run3
1024, 512, 146, 127, 144
2048, 512, 188, 167, 147
4096, 512, 225, 171, 176
8192, 512, 194, 192, 154
16384, 512, 248, 211, 212
32768, 512, 282, 251, 247
65536, 512, 236, 280, 275

I'll try the other idea later, but the 128k case is taking forever and I need my processor back.

Paul C. Anagnostopoulos

12th January 2007, 06:57 AM

With a population of 32:

genome, population, run1, run2, run3
1024, 231, 260, 186
2048, 264, 257, 266
4096, 263, 263, 253
8192, 273, 347, 333
16384, 345, 304, 315
32768, 440, 422, 474
65536, 432, 443
132072, 584

With a population of 512:

1024, 512, 146, 127, 144
2048, 512, 188, 167, 147
4096, 512, 225, 171, 176
8192, 512, 194, 192, 154
16384, 512, 248, 211, 212
32768, 512, 282, 251, 247
65536, 512, 236, 280, 275

So the population certainly has some effect.

~~ Paul

kleinman

13th January 2007, 01:53 PM

How have you all been doing? I’ve been thinking about Paul’s concept of Rcapacity, Unnamed’s selection process and the threshold used in ev and have decided these are concepts worth co-opting. All of these issues are mathematically interrelated.

Paul’s interpretation that Rcapacity represent the inability of the weight matrix to find binding sites is nonsense. The weight matrix is simply finding more binding sites in the non-binding site region of the genome and that region dominates the selection process so that binding sites are no longer evolving in the binding site region when using Dr Schneider’s selection scheme. Unnamed has overcome this effect by weighting the selection process to the binding sites in the binding site region and neglecting the effect of errors in the non-binding site region. The threshold variable also can be used to do some tuning of this effect.

Another way of viewing the mathematics of ev is that there are two separate selection conditions. One selection condition is the location and evolution of binding sites in the binding site region is optimized and the other selection condition is that binding sites not be located in the non-binding site region is optimized. Selection of a proper threshold value can be used to achieve an optimum for both conditions to some extent until errors in the non-binding site region overwhelm the selection of sites in the binding site region.

These conditions spell big trouble for the concept of a step wise selection process for the de novo evolution of genes. Consider the following example. Instead of evolving binding sites on a portion of a genome and not evolving binding sites on another portion of the genome, evolve two different genes simultaneously on the same genome, for example hemoglobin and insulin. Unless both genes are being evolved with the same selection of creatures, one gene may dominate and prevent the evolution of the other, just as errors in the non-binding site region are preventing the evolution of binding sites in the binding site region.

Not only are Dr Schneider’s and Unnamed graduated selection processes nonexistent, if they did exist, they would conflict mathematically with one another as each tries to evolve their own genes. I do like getting it both ways!

Dr Adequate

13th January 2007, 06:25 PM

I do like getting it both ways! What you do in your free time is entirely up to you.

CapelDodger

13th January 2007, 06:44 PM

What you do in your free time is entirely up to you.
Who said it was free?

Dr Adequate

14th January 2007, 01:48 AM

Then it seems that he mixes his business with his pleasure.

And all this time we thought that his only kink was a taste for public humiliation.

Paul C. Anagnostopoulos

14th January 2007, 08:47 AM

kleinman

14th January 2007, 09:27 AM

Paul’s interpretation that Rcapacity represent the inability of the weight matrix to find binding sites is nonsense.Sorry, but that's your interpretation of what I said. What I said was that the binding sites do not have sufficient information capacity for the weighting process to distinguish them uniquely from all the other positions on the chromosome. No matter how many times I say this, you don't seem to get it. Imagine a megabase genome and a binding site length of 3 bases. Do you think 6 bits is enough to uniquely identify specific sites on that genome?
And your restatement is still nonsense. What is happening with Dr Schneider’s selection process as the genome length is being increased is there are more potential locations in the non-binding site region where binding sites can be potentially be identified and cause mistakes. Once the genome length reaches a certain length, these mistakes in the non-binding site region dominate the selection process. It has nothing to do with the weighting process to distinguish them uniquely from all other positions on the chromosome. Why don’t you test your concept of Rcapacity with Unnamed’s selection process? Since Unnamed’s selection process is designed to almost completely ignore mistakes in the non-binding site region, see whether you can converge genome lengths longer than would be possible based on your concept of Rcapacity.
The weight matrix is simply finding more binding sites in the non-binding site region of the genome and that region dominates the selection process so that binding sites are no longer evolving in the binding site region when using Dr Schneider’s selection scheme.The sites are evolving, along with the rest of the genome. They just can't evolve a unique identification code.
Now you are saying that the entire genome is evolving??????? The only thing you can say is evolving in the non-binding site region of the genome is a lack of binding sites, otherwise the non-binding site region remains random.
Unnamed has overcome this effect by weighting the selection process to the binding sites in the binding site region and neglecting the effect of errors in the non-binding site region.As far as I know, Unnamed has run no experiments where Rcapacity could be a problem. Furthermore, he is not neglecting the effect of spurious bindings. If you think he is, please present your case.
You took Dr Schneider’s model of random point mutations and natural selection as reality before you did any study of the model. You are now taking Unnamed selection process as valid. You must really enjoy retracting your statements.

It is simple enough to test your concept of Rcapacity with Unnamed’s selection process. Simply take Dr Schneider’s original case and start doubling the genome length and see where convergence fails. If you don’t want to run the series, post Unnamed’s version of ev on the net and let us run the series.

Paul C. Anagnostopoulos

14th January 2007, 10:32 AM

kjkent1

14th January 2007, 11:17 AM

I'm probably misunderstanding way too much about the present argument, but allow me to chatter a bit, and then kindly correct my thinking if it's off base.

It seems to me that "unnamed"'s selection method is a more accurate description of actual evolutionary processes, than was Dr. Schneider's original algorithm.

The original version of ev was intended to show how evolution occurs in the binding site region of the genome. However, Schneider's version counted as mistakes, mutations in the non-binding portion, and thereby over-emphasized the deleterious effects of mutations which would actually have no substantive effect on a new creature. The non-binding site portion of the genome is "junk" -- it doesn't contribute anything to the organism.

In the real world, doubtless, at some point, a sufficient number of mutations to a junk portion of a genome may suddenly create a substantive effect on the organism, and I think it would be fair to try to quantify the moment when this occurs and the probability of the occurrence being deleterious vs. beneficial.

Once accomplished, this would give us a better idea of the number of generations required to perfect a creature, because it would undoubtedly slow the evolutionary process somwhat, on the assumption that mutations are empirically known to be more frequently deleterious than beneficial.

However, it also seems to me that this activity occurring in the non-binding site portion of the genome, at some point could be the cause of an entirely new function in the target organism. That is, an aggregation of otherwise irrelevant mutations which occur in the junk portion of a germ cell of an organism over time, could suddenly start providing a selective advantage by pure accident. Perhaps this is a cause of what is so frequently argued about as a being a "macro-evolutionary" event.

kleinman

14th January 2007, 11:52 AM

And your restatement is still nonsense. What is happening with Dr Schneider’s selection process as the genome length is being increased is there are more potential locations in the non-binding site region where binding sites can be potentially be identified and cause mistakes. Once the genome length reaches a certain length, these mistakes in the non-binding site region dominate the selection process. It has nothing to do with the weighting process to distinguish them uniquely from all other positions on the chromosome.Could you explain mathematically what you mean by "dominate the selection process"? Have you watched an Evj run with an Rcapacity problem? For example, if you run this model:

population 32
genome size 4096
binding sites 16
weight width 3
site width 4

You'll have Rcapacity = Rfrequency = 8 bits. You'll never get past 16 mistakes. And yet, miraculously, the mean age at 30,000 generations is about 3,600. In what sense are spurious bindings dominating?
What I mean mathematically by “dominate the selection process” is as follows:

Total mistakes = mistakes in binding site region + mistakes in non-binding site region

With a short genome case, the mistakes in the non-binding site region will be a small number. As you lengthen the genome, the number of possible sites for mistakes increase in the non-binding site region (where the majority of the mutations are occurring) and your selection process is stuck trying to minimize the number of mistakes in the non-binding site region rather than selecting for the occasional good mutation that might occur in the binding site region. If you want to get a quantitative measure of this effect, define a couple of variables –BindingMistakes and NonBindingMistakes for your creatures and track these variables and see which ones are affecting selection more.
Since Unnamed’s selection process is designed to almost completely ignore mistakes in the non-binding site region, see whether you can converge genome lengths longer than would be possible based on your concept of Rcapacity.Ah, now it's "almost completely" ignoring mistakes.

Unnamed: Let's try it. Run your original series of experiments, but use a weight width and binding site width of 4 and 5.
The reason I say “almost completely” or dominates is because valuation[p] does have a small nonzero value in the nonbinding site region and this is reflected by the small increases in generations for convergence as you increase the genome length. If you compare valuation[p] in the binding site region with the non-binding site region, it will have a much larger magnitude in the binding site region because this is where you have the best matches with the weight matrix.

This situation is different than the case where you set your variable gene=1 and nongene=0 and use mistakes to do selection. Here you have completely uncoupled the selection process in the binding site region from mutations in the non-binding site region. In this situation, you are “completely” ignoring mistakes in the non-binding site region of the genome and the generations for convergence is not affected by genome length (for a mutation rate fixed to a number of bases).
Now you are saying that the entire genome is evolving??????? The only thing you can say is evolving in the non-binding site region of the genome is a lack of binding sites, otherwise the non-binding site region remains random.You answered your own quesiton.
Do you understand the answer?
You took Dr Schneider’s model of random point mutations and natural selection as reality before you did any study of the model. You are now taking Unnamed selection process as valid. You must really enjoy retracting your statements.I might agree with your second sentence if I knew what you meant by "valid."
Here are a few synonyms for the word valid, suitable, applicable, legitimate, appropriate. Perhaps if you gave us a physical interpretation of Unnamed’s selection process you might understand why I say this process is invalid. More specifically, explain this conditional statement:
if ((valuation[p] = siteValuation(p, width)) >= threshold)
What will be the value of valuation[p] in the binding site region vs the value in the nonbinding site region?

Paul C. Anagnostopoulos

14th January 2007, 01:00 PM

With a short genome case, the mistakes in the non-binding site region will be a small number. As you lengthen the genome, the number of possible sites for mistakes increase in the non-binding site region (where the majority of the mutations are occurring) and your selection process is stuck trying to minimize the number of mistakes in the non-binding site region rather than selecting for the occasional good mutation that might occur in the binding site region.
Sigh.

population 64
genome size 512
bindings sites 16
weight width 2
site width 3

Rcapacity = 6, Rfrequency = 5. Converges in 9,152 generations.

increase genome size to 1024

Rcapacity = 6, Rfrequency = 6. Never converges. Are you arguing that the increase from 512 to 1024 bases is enough for the spurious bindings to swamp selection?

How about if we fix the genome size and just vary the widths?

population 64
genome size 1536
bindings sites 2

weight width, site width, Rcapacity, Rfrequency, generations

6, 7, 14, 9.58, 8991
5, 6, 12, 9.58, 37198
4, 5, 10, 9.58, 42550
3, 4, 8, 9.58, never converges

The difference in size of the gene + binding sites between the final two cases is 34 bases. You're saying an increase of 34 out of 1536 bases in the junk region is enough to swamp selection?

Do you understand the answer?
Yes.

Perhaps if you gave us a physical interpretation of Unnamed’s selection process you might understand why I say this process is invalid. More specifically, explain this conditional statement:
if ((valuation[p] = siteValuation(p, width)) >= threshold)
What will be the value of valuation[p] in the binding site region vs the value in the nonbinding site region?
When there is no binding, the valuation is less than the threshold. When there is a binding, the valuation is greater than the threshold. Which case are you talking about?

~~ Paul

kleinman

14th January 2007, 07:23 PM

With a short genome case, the mistakes in the non-binding site region will be a small number. As you lengthen the genome, the number of possible sites for mistakes increase in the non-binding site region (where the majority of the mutations are occurring) and your selection process is stuck trying to minimize the number of mistakes in the non-binding site region rather than selecting for the occasional good mutation that might occur in the binding site region. Sigh.

population 64
genome size 512
bindings sites 16
weight width 2
site width 3

Rcapacity = 6, Rfrequency = 5. Converges in 9,152 generations.

increase genome size to 1024

Rcapacity = 6, Rfrequency = 6. Never converges. Are you arguing that the increase from 512 to 1024 bases is enough for the spurious bindings to swamp selection?

How about if we fix the genome size and just vary the widths?

population 64
genome size 1536
bindings sites 2

weight width, site width, Rcapacity, Rfrequency, generations

6, 7, 14, 9.58, 8991
5, 6, 12, 9.58, 37198
4, 5, 10, 9.58, 42550
3, 4, 8, 9.58, never converges

The difference in size of the gene + binding sites between the final two cases is 34 bases. You're saying an increase of 34 out of 1536 bases in the junk region is enough to swamp selection?
In answer to your questions, yes. If you track the errors in the binding site region and non-binding site region, you would see this. Once the errors in the non-binding site region are greater than in the binding site region, these errors control the selection process. The problem here is not that the weight matrix can not find matches, the weight matrix is finding matches on the non-binding site portion of the genome. These non-binding site errors are selecting out creatures no matter how far along the binding sites have evolved in the binding site region.
Perhaps if you gave us a physical interpretation of Unnamed’s selection process you might understand why I say this process is invalid. More specifically, explain this conditional statement:
if ((valuation[p] = siteValuation(p, width)) >= threshold)
What will be the value of valuation[p] in the binding site region vs the value in the nonbinding site region?When there is no binding, the valuation is less than the threshold. When there is a binding, the valuation is greater than the threshold. Which case are you talking about?
Both, valuation[p] will have values much greater than 1 in the binding site region and rarely if ever have a value that large in the non-binding site region.

Paul C. Anagnostopoulos

15th January 2007, 05:41 AM

In answer to your questions, yes. If you track the errors in the binding site region and non-binding site region, you would see this. Once the errors in the non-binding site region are greater than in the binding site region, these errors control the selection process. The problem here is not that the weight matrix can not find matches, the weight matrix is finding matches on the non-binding site portion of the genome. These non-binding site errors are selecting out creatures no matter how far along the binding sites have evolved in the binding site region.
So everything goes along just fine and then suddenly, with an increase of about 2% in the amount of junk DNA, the spurious bindings in the junk DNA swamp selection completely. And this happens right when Rfrequency crosses Rcapacity. All righty then.

And it even happens with a mere 1% increase in the junk DNA, right on cue:

population 64
genome size 4096
bindings sites 2

weight width, site width, Rcapacity, Rfrequency, generations

6, 7, 14, 11, 164160
5, 6, 12, 11, 386780
4, 5, 10, 11, never converges

Both, valuation[p] will have values much greater than 1 in the binding site region and rarely if ever have a value that large in the non-binding site region.
I don't think you understand how the valuations work.

~~ Paul

Paul C. Anagnostopoulos

15th January 2007, 06:51 AM

Ah, but Kleinman does have a point. Perfect creatures can certainly evolve with Rsequence significantly lower than Rfrequency. That means that the Rcapacity problem could be forestalled if the selection process was finer-grained. I bet Unnamed's selection process doesn't run into Rcapacity problems as quickly.

Hey, I can test this, too. I'll run the last case in my previous post with with a missing binding mistake count of 10 instead of 1 (click Advanced on the New dialog). That gives more importance to missing bindings than to spurious bindings. Let's see if it converges ...

Yes! It converges in 59,700 generations.

~~ Paul

kleinman

15th January 2007, 08:22 AM

Intelligent Design has no answers. It can only make itself look palatable by making evolution look less palatable. It lives in a cardboard refrigerator box and throws rocks through the windows of evolution's unfinished mansion. ---Beleth
I’m still waiting for an evolutionarian to explain what the components of the DNA replicase system were doing before this system evolved. I would call this a good example of irreducible complexity. The only reason the theory of evolution had any palatability was that mathematics had been ignored. Don’t blame me that your own evolutionarian written, peer reviewed and published mathematical model of random point mutation and natural selection makes your theory look unpalatable. Your unfinished mansion does not meet code, it needs to be torn down.
In answer to your questions, yes. If you track the errors in the binding site region and non-binding site region, you would see this. Once the errors in the non-binding site region are greater than in the binding site region, these errors control the selection process. The problem here is not that the weight matrix can not find matches, the weight matrix is finding matches on the non-binding site portion of the genome. These non-binding site errors are selecting out creatures no matter how far along the binding sites have evolved in the binding site region.So everything goes along just fine and then suddenly, with an increase of about 2% in the amount of junk DNA, the spurious bindings in the junk DNA swamp selection completely. And this happens right when Rfrequency crosses Rcapacity. All righty then.

And it even happens with a mere 1% increase in the junk DNA, right on cue:

population 64
genome size 4096
bindings sites 2

weight width, site width, Rcapacity, Rfrequency, generations

6, 7, 14, 11, 164160
5, 6, 12, 11, 386780
4, 5, 10, 11, never converges
What you call “goes along just fine” is showing increasing generations for convergence as you decrease the binding site width. You can have more erroneous sites in the non-binding site region with a smaller site width. When you said the following:
What I said was that the binding sites do not have sufficient information capacity for the weighting process to distinguish them uniquely from all the other positions on the chromosome
It this statement is true, once the genome exceeds a given length, then the weight matrix should not be able to uniquely identify erroneous sites in the non-binding site region. So with a mere 1% increase in the junk DNA, you suddenly do not have sufficient information capacity for the weighting process to distinguish them uniquely from all the other positions on the chromosome?
Both, valuation[p] will have values much greater than 1 in the binding site region and rarely if ever have a value that large in the non-binding site region.I don't think you understand how the valuations work.
If valuation[p] is not the value generated based on the match between the weight matrix and a particular locus on the genome then why don’t you explain to use how this value is generated?
Ah, but Kleinman does have a point. Perfect creatures can certainly evolve with Rsequence significantly lower than Rfrequency. That means that the Rcapacity problem could be forestalled if the selection process was finer-grained. I bet Unnamed's selection process doesn't run into Rcapacity problems as quickly.

Hey, I can test this, too. I'll run the last case in my previous post with with a missing binding mistake count of 10 instead of 1 (click Advanced on the New dialog). That gives more importance to missing bindings than to spurious bindings. Let's see if it converges ...

Yes! It converges in 59,700 generations.
Paul, you just made my point. Not only is Unnamed’s selection process finer grained, it markedly reduces the effect of errors in the non-binding site region. If you reduce the effect of harmful mutations in the non-binding site region, you not only get faster convergence, you reduce the effect of increasing genome length. This concept you are using has no basis in reality but don’t let that interfere with your theory.

Paul C. Anagnostopoulos

15th January 2007, 08:55 AM

Paul C. Anagnostopoulos

15th January 2007, 09:03 AM

I just watched a simulation in slow motion to see how the worst creature behaves. Because of selective sweep, the worst creature has the same number of mistakes as the best creature, all due to missing binding sites. Then, all of a sudden, the worst creature's mistake count jumps by a significant amount. I have 2 binding sites and a missed binding site point count of 10, so the baseline mistake count is 20. Here are some mistake counts of the worst creature when it jumps from 20:

279, 81, 365, 75, 215, 89, 2263

So it's not that a spurious site or two shows up. It's clearly a mutation in the gene (weight matrix or threshold) that completely destroys the creature. So why does the finer-grained selection help? This requires some investigation.

~~ Paul

Edited to add: This is an incomplete story. Spurious sites do show up occasionally.

Paul C. Anagnostopoulos

15th January 2007, 09:37 AM

I ran the standard model about 50 times and got an Rsequence range of 3.03 to 4.98. Then I ran the standard model with missed site mistake points of 10 and got an Rsequence range of 1.55 to 4.14.

What's going on? Does the finer-grained selection simply allow it to find the low Rsequence values that would normally occur occasionally, or is it more interesting than that?

And is there a correlation between the number of generations and the Rsequence value?

~~ Paul

Paul C. Anagnostopoulos

15th January 2007, 10:30 AM

Aha! I think it's easier for Ev to evolve away a spurious binding than it is for it to evolve a match at a binding site. So if you favor fewer missing binding sites over fewer spurious binding sites, then things converge faster. That's what setting the missed site mistake points to 10 does. Kleinman is correct, although I'm still not sure about his explanation.

Rcapacity is a separate issue. I think the finer-grained selection allows Ev to find the solutions with lower Rsequence values. But Rcapacity still sets limits. I'll see if I can find them.

Both the missing site mistake points and Rcapacity issues may be nothing more than artifacts of Ev's particular model.

~~ Paul

kleinman

15th January 2007, 10:32 AM

It this statement is true, once the genome exceeds a given length, then the weight matrix should not be able to uniquely identify erroneous sites in the non-binding site region. So with a mere 1% increase in the junk DNA, you suddenly do not have sufficient information capacity for the weighting process to distinguish them uniquely from all the other positions on the chromosome?What does it mean to uniquely identify erroneous sites? If there is insufficient capacity to uniquely identify the binding sites, then not only will the binding sites fail to match, but spurious bindings will occur. The weight matrix will be unable to distinguish them.

I think if you could formalize your claim about what is happening, we would find that we are saying the same thing.
“Uniquely identifying” sites is your terminology. If I understand Dr Schneider’s selection process, if the dot product of the weight matrix with values assigned to bases in a site equals or exceeds the threshold value, a site has been identified. This arithmetic should not be affected by the length of the genome.

I have formalized my claim about what is happening but I will repeat it again. Start with the following equation:

Total mistakes = mistakes in binding site region – mistakes in non-binding site region

The mistakes in the binding site region can be at most equal to the total number of sites, gamma. The mistakes in the non-binding site regions can vary and increases as the length of the genome increase. Dr Schneider has designed a selection process that requires sites be maximized on one portion of the genome and minimize on the other portion. The minimization process becomes more difficult as the genome is lengthened until a genome length is reached where it is very unlikely for minimization be achieved. It has nothing to do with the weight matrix being able to “uniquely” identifying a binding site. The weight matrix is always able to identify a match when it exists. The problem is that errors in the non-binding site region are causing evolved creatures (in the binding site region) to be selected out.

The question that should be asked is whether this selection process has any relationship to reality? I contend that it does to some extent. What this is analogous to is a creature with a completely evolve genome except for a single fatal mutation.
If valuation[p] is not the value generated based on the match between the weight matrix and a particular locus on the genome then why don’t you explain to use how this value is generated?The valuation is simply the value obtained when the weight matrix is applied to a particular position on the chromosome. In order to be considered a match, it must be greater than or equal to the threshold. A missing binding site will be below the threshold. A spurious binding will be above the threshold.
This is the way I understand the meaning of valuation[p]. For a weight matrix five bases wide, you obtain a ten bit number which can have the integer values between -512…+511. For larger weight matrices, valuation[p] can have values much larger than this when a good match is achieved. This is why Unnamed’s selection process using valuation[p] biases selection to the binding site region where large values of valuation[p] are obtained.
Paul, you just made my point. Not only is Unnamed’s selection process finer grained, it markedly reduces the effect of errors in the non-binding site region. If you reduce the effect of harmful mutations in the non-binding site region, you not only get faster convergence, you reduce the effect of increasing genome length. This concept you are using has no basis in reality but don’t let that interfere with your theory.You still haven't explained why you think Unnamed's method reduces the effect of harmful mutations. Let me think about it. A spurious binding will be above the threshold, and its distance from the threshold added to the sort value. A missing binding site will be below the threshold, and its distance from the threshold added. You must be saying that the spurious binding distances will be smaller than the missing site distances. That might be true at the beginning of the simulation, when the missing site valuations are perhaps far from the threshold, but as the simulation progresses the missing site valuations creep toward the threshold. It is the fine-grained creep that gets the job done faster.

It appears that finer-grained selection overcomes the Rcapacity problem to some degree, finding solutions at the low end of the Rsequence range. Let's find out what the Rsequence range is: stay tuned.

I have no idea how this relates to the real world. You'll remember that I guessed that the Rcapacity problem isn't something that matters in real life.
As said above, valuation[p] has much larger value for a good match in the binding site region than a not so good match in the non-binding site region. Using mistakes to do selection gives equal weight to errors in either the binding site or non-binding site regions.
I just watched a simulation in slow motion to see how the worst creature behaves. Because of selective sweep, the worst creature has the same number of mistakes as the best creature, all due to missing binding sites. Then, all of a sudden, the worst creature's mistake count jumps by a significant amount. I have 2 binding sites and a missed binding site point count of 10, so the baseline mistake count is 20. Here are some mistake counts of the worst creature when it jumps from 20:

279, 81, 365, 75, 215, 89, 2263

So it's not that a spurious site or two shows up. It's clearly a mutation in the gene (weight matrix or threshold) that completely destroys the creature. So why does the finer-grained selection help? This requires some investigation.
How does Dr Schneider evolve the weight matrix?

Paul C. Anagnostopoulos

15th January 2007, 10:54 AM

“Uniquely identifying” sites is your terminology. If I understand Dr Schneider’s selection process, if the dot product of the weight matrix with values assigned to bases in a site equals or exceeds the threshold value, a site has been identified. This arithmetic should not be affected by the length of the genome.
Correct.

I have formalized my claim about what is happening but I will repeat it again. Start with the following equation:

Total mistakes = mistakes in binding site region - mistakes in non-binding site region
That's not the correct equation, but let's continue ...

The mistakes in the binding site region can be at most equal to the total number of sites, gamma. The mistakes in the non-binding site regions can vary and increases as the length of the genome increase.
Your second sentence is too simplistic. The potential spurious bindings increases as the genome size increases.

Dr Schneider has designed a selection process that requires sites be maximized on one portion of the genome and minimize on the other portion. The minimization process becomes more difficult as the genome is lengthened until a genome length is reached where it is very unlikely for minimization be achieved.
This is also too simplistic. It certainly becomes more difficult to eliminate the spurious bindings, but this depends on the selection method, mutation rate, population, and so forth.

It has nothing to do with the weight matrix being able to “uniquely” identifying a binding site. The weight matrix is always able to identify a match when it exists. The problem is that errors in the non-binding site region are causing evolved creatures (in the binding site region) to be selected out.
By definition, if a match exists, the weight matrix can identify it. The problem is that it becomes almost impossible for matches to evolve at the binding sites and not at other sites, when a unique pattern of bases cannot exist at the binding sites. If a sequence logo cannot form, then evolution gets nowhere.

Your final sentence is correct, but what is causing the errors in the junk DNA? Lots of things. One of those things is the Rcapacity problem.

This is the way I understand the meaning of valuation[p]. For a weight matrix five bases wide, you obtain a ten bit number which can have the integer values between -512…+511. For larger weight matrices, valuation[p] can have values much larger than this when a good match is achieved. This is why Unnamed’s selection process using valuation[p] biases selection to the binding site region where large values of valuation[p] are obtained.
That wasn't clear from your discussion, especially when you said "... valuation[p] will have values much greater than 1 in the binding site region ...". Your final sentence here still doesn't make sense. The valuation of a matched binding site does not contribute to the sort value.

As said above, valuation[p] has much larger value for a good match in the binding site region than a not so good match in the non-binding site region.
But the valuation of a matched binding site is irrelevant to the sort value.

How does Dr Schneider evolve the weight matrix?
The weight matrix, threshold, binding sites, and junk all evolve in concert by random point mutation.

~~ Paul

kleinman

15th January 2007, 03:26 PM

I have formalized my claim about what is happening but I will repeat it again. Start with the following equation:

Total mistakes = mistakes in binding site region - mistakes in non-binding site regionThat's not the correct equation, but let's continue ...
Sorry, typo error, should be:
Total mistakes = mistakes in binding site region + mistakes in non-binding site
The mistakes in the binding site region can be at most equal to the total number of sites, gamma. The mistakes in the non-binding site regions can vary and increases as the length of the genome increase.Your second sentence is too simplistic. The potential spurious bindings increases as the genome size increases.
You are splitting hairs using the word “potential”. What do you think the probability is that the number of spurious bindings decrease or stay the same as the genome size increases?
Dr Schneider has designed a selection process that requires sites be maximized on one portion of the genome and minimize on the other portion. The minimization process becomes more difficult as the genome is lengthened until a genome length is reached where it is very unlikely for minimization be achieved. This is also too simplistic. It certainly becomes more difficult to eliminate the spurious bindings, but this depends on the selection method, mutation rate, population, and so forth.
Really? Does your concept of Rcapacity depend on mutation rate and population when using Dr Schneider’s selection method? Any selection method that diminishes the effects of harmful mutations in the non-binding site region will converge more quickly. If you completely ignore harmful mutations in the non-binding region, you uncouple the evolution of the binding sites in the binding site region from the length of the genome. There just isn’t any basis in reality for such a selection method.
It has nothing to do with the weight matrix being able to “uniquely” identifying a binding site. The weight matrix is always able to identify a match when it exists. The problem is that errors in the non-binding site region are causing evolved creatures (in the binding site region) to be selected out.By definition, if a match exists, the weight matrix can identify it. The problem is that it becomes almost impossible for matches to evolve at the binding sites and not at other sites, when a unique pattern of bases cannot exist at the binding sites. If a sequence logo cannot form, then evolution gets nowhere.

Your final sentence is correct, but what is causing the errors in the junk DNA? Lots of things. One of those things is the Rcapacity problem.
You can not get a sequence logo to form when selection is being driven by errors in the non-binding site region.

Why don’t you enumerate the things which cause errors in the non-binding site region?
This is the way I understand the meaning of valuation[p]. For a weight matrix five bases wide, you obtain a ten bit number which can have the integer values between -512…+511. For larger weight matrices, valuation[p] can have values much larger than this when a good match is achieved. This is why Unnamed’s selection process using valuation[p] biases selection to the binding site region where large values of valuation[p] are obtained.That wasn't clear from your discussion, especially when you said "... valuation[p] will have values much greater than 1 in the binding site region ...". Your final sentence here still doesn't make sense. The valuation of a matched binding site does not contribute to the sort value.
The valuation of a match binding site does not contribute to the sort value but a close to threshold but failed match in the binding site region will have a large value of valuation[p]. If gamma=16 and you start with 16 mistakes in the binding site region, you get 16*valuation[p] in the binding site region that outweighs the small number of mistakes in the non-binding site region. Track valuation[p] in the binding site region and non-binding site region and see exactly what you are sorting on.
As said above, valuation[p] has much larger value for a good match in the binding site region than a not so good match in the non-binding site region.But the valuation of a matched binding site is irrelevant to the sort value.
Track valuation[p] in the binding site region and non-binding site region and get the data which tells exactly what you are sorting with.
How does Dr Schneider evolve the weight matrix?The weight matrix, threshold, binding sites, and junk all evolve in concert by random point mutation.
What is the mutation rate assigned to the weight matrix? How does the threshold evolve?

All this discussion on the selection process is simply an academic exercise since there is no selection process as formulated by Unnamed and for that matter Dr Schneider’s selection method that are seen in reality. Natural selection can only determine if a particular mutation is immediately useful or harmful. If the mutation is neutral, there is no selection for or against that mutation and you are left with the probability problem without selection to evolve your genes de novo.

One of the most ardent supporters of your theory said it quite well:
Life isn't like that. Evolution has no long term goal.

Have I co-opted another evolutionarian idea?

Paul C. Anagnostopoulos

15th January 2007, 04:51 PM

You are splitting hairs using the word “potential”. What do you think the probability is that the number of spurious bindings decrease or stay the same as the genome size increases?
I suspect it increases, but in a quite complex manner. We see creatures with ages of 6000 generations.

Really? Does your concept of Rcapacity depend on mutation rate and population when using Dr Schneider’s selection method? Any selection method that diminishes the effects of harmful mutations in the non-binding site region will converge more quickly. If you completely ignore harmful mutations in the non-binding region, you uncouple the evolution of the binding sites in the binding site region from the length of the genome. There just isn’t any basis in reality for such a selection method.
In the real world, a spurious binding in pure junk DNA would be harmless. There appears to be a basis for selection of weak and strong bindings. You can't simply dismiss it, although I agree that we don't know how the various Ev models relate to reality.

The valuation of a match binding site does not contribute to the sort value but a close to threshold but failed match in the binding site region will have a large value of valuation[p].
And a small distance from the threshold, which is what contributes to the sort value.

If gamma=16 and you start with 16 mistakes in the binding site region, you get 16*valuation[p] in the binding site region that outweighs the small number of mistakes in the non-binding site region.
It is not the valuation that is added to the sort value, but the distance between the valuation and the threshold. These distances will start out large and then diminish as the binding site valuations creep toward the threshold. They will certainly swamp a single spurious binding, but so does the current selection method. They will not swamp a swarm of spurious bindings, such as might arise from a mutation in the gene.

But I agree with you that Unnamed's selection method is weighing missing bindings more heavily than spurious bindings, as does my experiments with the missing binding mistake points set to 10. See my post #1594. This speeds up evolution by favoring a creature with, say, 2 missing bindings and 5 spurious bindings over a creature with 3 missing bindings and 0 spurious bindings. Do you think something like that can't occur in nature?

What is the mutation rate assigned to the weight matrix? How does the threshold evolve?
The mutation rate is constant across the entire chromosome. Mutations are randomly applied to the entire chromsome.

All this discussion on the selection process is simply an academic exercise since there is no selection process as formulated by Unnamed and for that matter Dr Schneider’s selection method that are seen in reality.
Then you have lost your mathematical argument against evolution.

~~ Paul

joobz

15th January 2007, 05:03 PM

CapelDodger

15th January 2007, 06:24 PM

Then you have lost your mathematical argument against evolution.

~~ Paul
Bish, bosh, job done. Now for stage two : the frantic row-back. I don't see this guy as a quitter. He has far too high an opinion of himself.

articulett

15th January 2007, 06:54 PM

Bish, bosh, job done. Now for stage two : the frantic row-back. I don't see this guy as a quitter. He has far too high an opinion of himself.

Well, he can run the mathematical figures to show that the earth cannot be spherical and that the universe cannot be expanding....

With cooperation like that from Paul, he can be generating disproofs of everything that goes against whatever it is he chooses to believe. He can make a book: "Kleinman's mathamatical proofs of how everything scientists know is wrong."

with the follow up--

"And therefore my God is True" by John Hewitt.

cyborg

16th January 2007, 05:33 AM

We've already covered this.

He's already explained that ev is both adequate enough to disprove macroevolution and far too inadequate to be the mathematical basis of evolution.

It's simple really when you don't think about it.

John Hewitt

16th January 2007, 08:13 AM

With cooperation like that from Paul, he can be generating disproofs of everything that goes against whatever it is he chooses to believe. He can make a book: "Kleinman's mathamatical proofs of how everything scientists know is wrong."

with the follow up--

"And therefore my God is True" by John Hewitt.

Could you please explain how you introduce the role of "my God" into this comment.

articulett

16th January 2007, 10:02 AM

Could you please explain how you introduce the role of "my God" into this comment.

Well, this thread is entitled "annoying creationists"--annoying creationists tend to have something in common. They're not really like the YEC's who are readily laughed off...They, in fact, seem rather intelligent and grasp some of the basics of science, logic, and math--except when it somehow conflicts with their god belief. If it conflicts with their god belief, their logic stops at the door and they start playing crazy semantic games similar rather the way people squeeze supposed insightful platitudes and "higher truths" from primitive and barbaric texts clearly written by human without a dash of anything divine or even prescient. These people often believe themselve to be compassionate and open minded without having a clue as to how close minded and didactic they sound when it comes to their pet theories. They are weirdly brainwashed because they believe that some invisible guy killed his kid (who was really him) for some sin long ago that no-one is really quite certain about--and they've been told that this happened for them-because someone loved them so much. They've been told that it's arrogant to even question the story. And they are so easy to spot after a while. They just have very rigid standards of "proof" for a very narrow area (and no proof will ever be enough) and absolutely no need for proof when it comes to believing in the divinity of some primitive texts authors and meanings and interpretations.

What can I say--when you've had it inculcated in you from childhood that you get to live happily ever after for believing insane things, you sometimes grow into an annoying creationist. To me, you guys always argue the same pet point over and over--the one that somehow convinced you--or the theory that keeps your personal version of what god is alive.

All your arguments boil down to "my god is real" to me. And, I think you'd understand it if someone was a Scientologist or Muslim extremists and all their posts seemed to be a means of supporting whatever it is they had come to believe--you'd see how futile conversation was--you'd feel sort of bad that a bright person was so brainwashed by their beliefs that they were missing some really cool facts. You'd marvel at how they couldn't seem to see in themselves that which is so transparent to others. You'd roll your eyes at the way they hold themselves up to be objective arbitors of truth that was so clearly confirmation bias for the "truth" they wanted. It's sort of like if you wanted to show an Amish kid all the cool technology and stuff they could do with the computer--but you couldn't...and it all boils down to "because I'm Amish"...Nobody wants to be an evil temptress (temptor) scaring someone into thinking the devil is trying to get them to bite from the tree of knowledge--but that's exactly what biologists have become to certain Christians. If actual non-religious scientists had problems with evolution, it would lend an aura of credibility to your case. But if the only ones having a problem are the ones who believe in a certain kind of god--then it's very clear why you guys are so persistent and unyielding and seemingly unaware of how you come across on the topic no matter how carefully the information is laid out for you. Rather than feeling frustration for more wasted time with those who have a strong motive for not comprehending, sometimes it's just easier to make fun. You guys have impervious egos anyhow...I don't think it's particularly harmful.

To me, you guys all sound sort of like Behe at the trial when no amount of evidence disproving his irreducibile complexity theory would ever be enough to make him let go of it. Faith is just a very tenacious little bugger to get rid of.
And most of us have to show some amount of deference to "it" in our regularly daily lives because rationality and tolerance isn't really a strong point of those who adhere to any particular dogma--moreso, when they believe their eternity is affected by such beliefs.

So, I think we can all stop pretending that the problems you guys have with evolution is about "facts"--it's not. It's about your beliefs. It's about the fact that whatever it is you think god is or does--he surely would have picked something more miraculous then evolution to bring the likes of you about.

Is there a single creationist who isn't a strong theist? Are there any dogmatic and seemingly educated non-theists playing semantic games about Turing Machines or "closet dualism" or "memes don't exist" or "math makes evolution an impossibility" theory? Are there any non-theists who use terms like scientism, evolutionarian, and proudly point out thesis' that only make sense to fellow theists? Are there any non-theists who have such an angry visceral reaction to outspoken atheists like Dawkins that seem unconnected to facts?

See, science and facts and truth are the same for everybody. Tests and facts and info. I learn is the same as being taught to students of all languages all over the world. It's easy to "see". But your theories only make sense to people who have been immersed in a certain belief system. It doesn't matter what the humans mapping genomes believe--the info. is all the same and readily interpreted by others mapping genomes. Physics in China is the same as in India. Biology in America is the same as in Denmark. But none of that is true for anything you say nor Kleinman says. You tell yourselves that we skeptics can't follow because your thinking is beyond ours--so advanced. But why is it that you need to believe in a certain version of creator in order for your info. to be comprehensible? Why are you so blind to very specific facts and types of knowledge? Why don't you see that which is obvious, I'm guessing, to everyone who doesn't share your version of God?

Why is hammy so ready with ad homs rather than facts or answers to questions? Because you guys have a strong need to believe in something that doesn't jive with the facts. What else should we conclude. The only evidence of your brilliant logic and scholarship seems to exist in your own head. But to non-believers that is about as relevant as Tom Cruises claims about Scientology. Every believer believes that fhis ellow believers are smarter, righter and more moral than those who believe differently, don't they?

John Hewitt

16th January 2007, 11:01 AM

Well, this thread is entitled "annoying creationists"--annoying creationists tend to have something in common.
<snip>
Why is hammy so ready with ad homs rather than facts or answers to questions? Because you guys have a strong need to believe in something that doesn't jive with the facts. What else should we conclude. The only evidence of your brilliant logic and scholarship seems to exist in your own head. But to non-believers that is about as relevant as Tom Cruises claims about Scientology. Every believer believes that fhis ellow believers are smarter, righter and more moral than those who believe differently, don't they?
So, do you feel that my work is creationism?
Are you aligning my position with that of Tom Cruise?
If so, why?

The Atheist

16th January 2007, 11:15 AM

Posted to John Hewitt:
To me, you guys all sound sort of like Behe at the trial when no amount of evidence disproving his irreducibile complexity theory would ever be enough to make him let go of it. Faith is just a very tenacious little bugger to get rid of.

Since John already made this comment to you:I think it is true that there are many gaps in our understanding of evolution but I do not recall trying to fill one of them with God. Could you please explain why you keep introducing supernatural entities into discussion concerning me?
That seems to suggest he isn't doing anything of the kind.

Are you saying John's a liar?

Or is anyone who doesn't concur with your thinking automatically a creationist?

I've seen John state on several occasions that he isn't driven by god or creationism. Why do you doubt it? I've found no reference to gods in his websites.

CapelDodger

16th January 2007, 04:22 PM

Could you please explain how you introduce the role of "my God" into this comment.
Do you mind? We were talking about you, not to you :rolleyes: .

See, you've set articulett off, now we'll never get him to settle :mad: .

articulett

17th January 2007, 01:52 AM

Do you mind? We were talking about you, not to you :rolleyes: .

See, you've set articulett off, now we'll never get him to settle :mad: .

I'm not set off. But who is going to settle what? Kleinman?

articulett

17th January 2007, 02:20 AM

So, do you feel that my work is creationism?
Are you aligning my position with that of Tom Cruise?
If so, why?

Yes. Tom Cruise's religion teaches that there is no such thing as "chemical imbalances"--so he has his atennae tuned into anything that supports that bias and can't seem to even comprehend the data that negates it. He seemingly has no study on the subject and yet has concluded that he is an expert. Clearly, it would be difficult to teach him about imbalances involved in manic depressiveness or even diabetes--since that, too, is a chemical imbalance. He's closed himself off from learning the very thing he thinks that he's an expert in.

And yes, I think you are a creationist. The meme thread only makes it more obvious to me.

There are creationists like Francis Collins--and he understands evolution, accepts it as a fact (the more you know, the harder it is to deny it), but his way of keeping his belief in god alive is to believe that god is behind it all--evolution was part of god's plan and god is outside of human understanding. This is pretty cool, because then he can learn and appreciate new info. as it comes in. But to me, creationists have very specific areas where they just don't seem to "hear" or see or be curious about the information that is being discovered. They dismiss it or igore. This information is always about a specific belief that have which is a necessary ingredient for them to keep believing in their god. On the flip side they can be very knowledgeable in other areas and show no problem with comprehension of simple facts--sometimes they will even show curiosity towards new info. But their main focus is always to disprove the part of evolution that they have the biggest problem with--the part that threatens their god belief. It's not like they are really trying to find out the answer--it's more like they are obsessed with showing that the answers others have come up with is wrong.

Annoying creationists tend to attack Dawkins often without reading him or even understanding the basics no matter how carefully explained. You've done that a bit--if not here, then on the meme thread...and I think it's because he doesn't believe in your god. Because the arguments you use just don't make sense--I mean they seem to to you--and maybe they do to other believers--but they just sound similar to kleinman's statments to me--like if you dismiss him and refuse to compute the information then evolution never has to make sense to you and that somehow protects the belief you want to have.

You get dodgy when it comes to religion, but all creationists do. It's why the term "intelligent design" was invented--to pretend it's all about a sincere discovery for truth...when it's really about a sincere attempt at disproving evolution so that you can insert god (or whatever it is you believe in regards to creation...that it must have been pre-planned or whatever.) Wowbagger gave a pretty good analysis of your website--but you just skimmed over the really important points.

Maybe I'm wrong. But let me ask you about Behe. As I'm sure you know, at the Dover trial he kept using his irreducible complexity model--clearly to him, this is the key to disproving evolution--just like Kleinman's math model is. And no matter how many papers he was presented with that showed exactly how the flagellum or blood clotting cascade or whatever could have and probably did evolve--it wasn't enough--nothing will ever be enough... but even before we knew that flagellum could evolve the information in those papers was true. Even if we could not prove that the flagellum was not irreducibly complex--that never ever means that it was, indeed, irreducibly complex. It only means that we didn't understand it's complexity yet. Right?
Perhaps, it is a smidgen of evidence in favor of a designer--but it's not anything that negates evolution. But to Behe it is--it has to be--because he thinks his salvation depends on believing in his god and he needs a reason to believe and his reason is irreducible complexity.

You have lots of problems with evolution--the very same kinds of problems that Behe has. You have no real alternative explanation or data yet you are highly critical of those who have data in favor of evolution--particularly if those people don't believe in your god. I don't know of anyone who has this trait who doesn't believe in some sort of god that "requires a certain belief to have salvation". Maybe I'm completely mistaken. Maybe lots of non-religious people have problems with evolution or for whom the data is not convincing. But I know a plethora of non-religious people. It's only those with certain beliefs who have this rabid obsession with pointing out the gaps in evolutionary theory. Often times it seems to be the only threads they participate in. And I just presume it's for the same reasons that Tom Cruise confidently states "there is no such thing as a chemical imbalance".

Biologists are generally excited about new discoveries and finding out more clues--but the creationists never even seem interested in them. They're so focused on proving that evolution cannot be true, that they make it impossible to learn of the great discoveries which only strengthen the notion that it is.

Anyhow--if you want me to cut and paste I'd be glad to show you all the statements that convince me you are a creationist and that your beliefs about god are what motivates your posts, understanding, and lack thereof. And I'd be glad to learn that I am wrong. Would a creationist ever say the same? Would you want to know if you were wrong or do you just think you cannot be?

articulett

17th January 2007, 02:52 AM

Could you please explain how you introduce the role of "my God" into this comment.

Maybe I'm wrong... So let me ask you some questions. You, Hammy, Kleinman, and Von Neumann all believe that the current evolutionary model is incorrect--that is, that there is a big flaw in the theory and that scientists are unaware of this flaw or hiding it or something--right? Is this true for you? Do you believe that evolution is a flawed explanation regarding life on earth and the subsequent speciation of animals and plants? You say as much in many of your writings.

All of the above mentioned people and Behe have differing problems with Evoution via natural selection, right?--the main points of contention are a bit different. For you it's about genes versus oscillations and what the replicating unit is. For Kleinman it's the mathematics involved, etc. Do you understand the arguments of the others mentioned--that is, do you think you could successfully sum up the flaws they perceive in evolutionary theory? Have other people, creationist or not, been able to successfully describe the main problems with evolutionary theory as you see it?

Are there any non-religous people who can sum up your argument in a simple way that most biologists could understand?

How does your particular differ from evolutionary theory?

Would you say that you are a proponent of "intelligent design" or that Darwins theories should be taught in high school with disclaimers...and if so, what would you have those disclaimers say?

What do you think of Behe?

I think those questions will give everyone a good idea of where you are coming from.

Forgive me, if I've inadverdantly labeled you a creationist when you are not. Creationists are often particularly bothered by that term because they think it lessens their scientific credibility. Moreover, they are very adept at semantic games as anyone who reads the dover transcripts can readily see. They avoid definitions and play semantic games and my guess is that it's an effort to sound confusing so that no one can pin you down on anything you say and you can weasel out and claim you said otherwise.

But lets be very clear here. You are adamantly opposed to genes being considered replicators. You view the cell itself as the key to replication in life forms and not DNA. This is stated again and again and again on the meme thread. Many people have gone into detailed information as to why that's sort of a semantic dodge, but you don't seem to hear it--you just keep saying that scientists are incorrectlyl referring to genes as replicators.

To me--that says "semantic dodge to discredit evolution". But I could, of course, be wrong.

Also, in your articles you keep making claims about how scientists nevr explain something or other--but to me, no matter how much some things are explained to creationists, they just can't "hear" it...just like Behe and his irreducible complexity argument...

articulett

17th January 2007, 03:28 AM

Posted to John Hewitt:

Since John already made this comment to you:
That seems to suggest he isn't doing anything of the kind.

Are you saying John's a liar?

I don't know...is Behe a liar? Tom Cruise? Kleinman? Kurious Kathy? I don't think of them as liars. I just think their confidence in a belief has robbed them of the ability to understand where they might be mistaken. They have such huge defenses and levels of proof required to unseat their beliefs while being utterly blind to the flimsiest proof for that belief. When people don't answer their questions or that can't comprehend something, they use that as proof that they know more than everyone else or that their thinking is beyond that of "evolutionarians" and that awful Dawkins guy. The more you debate these guys, the more you just start to sense it. If you get frustrated with them, they use it as proof that they've stymied skeptics or scientists.

[/QUOTE]Or is anyone who doesn't concur with your thinking automatically a creationist?[/QUOTE]

Not at all. I just start suspecting it when people flat out ignore religious questions...and have problems with evolution that I've never heard from a non-religious person. Do you understand and support Hewitts claims that genes aren't replicators and his oscillation theory of abiogenesis etc.? I presume you aren't religious. So manybe you could sum it up. When talking with creationists it just starts to feel lke a twilight zone--the more you think you grasp where they are coming from, the more they slip away and pretend they're saying something else. Are you familar with Behe and his arguments? How do you think Hewitt is different. What about Von Neumann.

[/QUOTE]I've seen John state on several occasions that he isn't driven by god or creationism. Why do you doubt it? I've found no reference to gods in his websites.[/QUOTE]

Well, blame the Discovery Institute for that. It's part of their wedge strategy. They want to poke holes in Darwinism using scientific terminology so no on can accuse them of having religious biases. But maybe Hewitt has real honest to goodness problems with evolution that someone can explain to me better--and maybe someone else can explain to him what wowbagger and many others have tried to point out, clarify, etc.

http://forums.randi.org/showthread.php?t=70215&page=3

So why do you think he posted on the annoying creationist thread? And why do you think he's so adamant about genes not being considered replicators? And why do you think I think all people who don't agree with me are creationists. I thought I was pretty careful and detailed in laying out my case, and I'm more than willing to consider I'm wrong. But, it's true--I plead guilty--I have stopped trying to make sense of his posts because I just presumed he is a creationist, and I already know that's a futile battle. So please tell me why you think I've made a hasty and incorrect conclusion. We might all learn something. Are you familiar with Von Neumann?--he's really smart and he pretends he's not a creationist...he will deny it--but, well, from my perspective and others--he definitely is. You can't pin him down on the word creationist--but the clues are manifest all over the place--I'd be glad to cut and paste and be more specific if anyone was actually interested and glad to learn that I am incorrect as well.

Cuddles

17th January 2007, 05:08 AM

Not at all. I just start suspecting it when people flat out ignore religious questions...and have problems with evolution that I've never heard from a non-religious person. Do you understand and support Hewitts claims that genes aren't replicators and his oscillation theory of abiogenesis etc.? I presume you aren't religious. So manybe you could sum it up. When talking with creationists it just starts to feel lke a twilight zone--the more you think you grasp where they are coming from, the more they slip away and pretend they're saying something else. Are you familar with Behe and his arguments? How do you think Hewitt is different. What about Von Neumann.

I would just like to add that it might be interesting for you to read John's original thread about "The wave model for particle motion and capping in cells", or something similar. He believes that scientists ignore new ideas and are actively involved in fraud to prevent any theories that challenge their own, especially his, being recognised. I think it is possible that he is not actually a creationist but is forced to come up with very similar arguments against established science due to paranoid beliefs rather than religious ones. Although for the record I also believe he is actually just a creationist.

cyborg

17th January 2007, 06:01 AM

He believes that scientists ignore new ideas and are actively involved in fraud to prevent any theories that challenge their own, especially his, being recognised.

The war cry of woos everywhere.

Bitch about everybody else rather than making your own case so earth-shatteringly watertight that it's impact is much like that of a depleted Uranium tank busting shell.

(Oh, kleinman that means that at some point you might actually want to use some mathematics. Hell I've even tried to help you define the event you want to show is impossible so that I can work on the analysis of the evj algorithm. Running simulations is not mathematics).

John Hewitt

17th January 2007, 06:09 AM

Maybe I'm wrong... So let me ask you some questions. You, Hammy, Kleinman, and Von Neumann all believe that the current evolutionary model is incorrect--that is, that there is a big flaw in the theory and that scientists are unaware of this flaw or hiding it or something--right? Is this true for you? Do you believe that evolution is a flawed explanation regarding life on earth and the subsequent speciation of animals and plants? You say as much in many of your writings.
Right, I think that there are flaws in evolutionary theory as it is normally presented and that, for the most part, the scientific community are unaware of those flaws.

All of the above mentioned people and Behe have differing problems with Evoution via natural selection, right?--the main points of contention are a bit different. For you it's about genes versus oscillations and what the replicating unit is. For Kleinman it's the mathematics involved, etc. Do you understand the arguments of the others mentioned--that is, do you think you could successfully sum up the flaws they perceive in evolutionary theory? Have other people, creationist or not, been able to successfully describe the main problems with evolutionary theory as you see it? It is not for me to represent other people's position, only my own.

Are there any non-religous people who can sum up your argument in a simple way that most biologists could understand? I don't know. I am quite happy for people to present their own understanding of anybody's work.

How does your particular differ from evolutionary theory? To the best of my understanding, my work is entirely evolutionary. I have repeatedly asked you to explain why you think it is not

.... or what Tom Cruise or unicorns or whatever have to do with me.

articulett

17th January 2007, 09:32 AM

Right, I think that there are flaws in evolutionary theory as it is normally presented and that, for the most part, the scientific community are unaware of those flaws.

It is not for me to represent other people's position, only my own.

I don't know. I am quite happy for people to present their own understanding of anybody's work.

To the best of my understanding, my work is entirely evolutionary. I have repeatedly asked you to explain why you think it is not

.... or what Tom Cruise or unicorns or whatever have to do with me.

I think your statement about there be no such things as memes is similar to Tom Cruise's statement that there is no such thing as chemical imbalances. I promise to explain more later, but judging from cuddles and cyborgs responses--as well as Schneibsters and Wowbaggers, I think others have a similar conclusion. I have to collate at Tam, but I will be back later if you really want to hear more. I will even cut and paste, but it's kind of a time waster unless we are on the same page as to what I will be illustrating (quotes of yours that are very similar to creationists). Let me ask you this, what would be sufficienct if anything for you to find the theory of evolution valid--what sort of evidence. How can we tell that you are not a Behe where every example showing how something isn't irreducibly complex only makes him run to find yet another example that he thinks is...or to refuse to comprehend the conclusion...or to say it's not enough.? And, while we're at it, just for the record--do you believe that life was designed by a more complex designer? Yes or no? What is your biggest problem with Darwinism and memes and Dawkins. It's the way you dance around these questions and the Behe like way you dodge conclusions that put your pet theory into question while never really proffering up decent evidence for an alternate theory that makes me think so. Evolution is pretty basic. Your failure to grasp some simple parts about it is as maddening as kleinmans desire to make a math problem that shows that "x" number of genomic mutations couldn't have happened give "x" number of eons. It's a wierd approach--like saying that we need the math formula to prove that we could have whatever of number of grains of sand we have on this universe. Your approach seems similarly wierd--Von Neumanns too. And you all seem to be pretty smart and literate--moreso than Hammy and his episomological monistic whatever closet dualist whatchamatheory. But you all seem to have a stick up your butt about Darwin and Dawkins. But no matter how carefully people follow along your reasoning and try to pin down your basic problem and address it--you do a quick limbo, a couple of pedantic turns of the phrase, a re-defining of a term, and a semantic redefinition or complete avoidance of key questions--all while talkin about how evolutarians and scientists are being dogmatic yet never really illustrating anything that makes non religious people see the dogmatism (from what I can tell).

Maybe Atheist is an atheist who can translate and show us how it has nothing to do with religion and everything to do with scientific bias and the underlying strenght and evidence behind your claim--

Plus, creationist are known to be dishonest and claim not to be a creationist. So saying your not a creationist doesn't really do anything to make me think you aren't. Anyone involved with creationists for any length of time probably feel similarly. It's kind of amusing how people learn to dodge and weave to keep their god alive (dishonesty for christ)--I suspect it has to do with teaching oneself to find "higher truths" in barbaric bronze age texts. But I would be glad to be mistaken. The smallest of evidence will do. But not just your word. Maybe you are the person who truly does have an amazing theory that will revolutionize our thinking about the evolution of life and make Darwin a dead end. Maybe scientists really are the ones' fooling themselves and you are the only one who isn't. Maybe others understand what you are saying who don't believe in any god. But in my experience...such claims are common--but the evidence never is. And those making the claims tend to use outdated info. to support their theories and show an amazing lack of curiosity about new data.

I rest my case until later. I hope, I'm absolutely wrong and trust the evidence will be forthcoming if that's the case and that your answers will clarify things for me--atheists answers might also.

kjkent1

17th January 2007, 10:03 AM

John Hewitt

17th January 2007, 11:08 AM

articulett

17th January 2007, 04:36 PM

Personally, and after reading Dr. Hewitt's online works, I don't see anything which suggests that he is mixing science with theology. But, maybe I'm missing something.

More to the point, why are we dancing around the issue? If someone thinks that John is a design advocate or creationist, they should ask John directly. Here, I'll do it:

John, are you an intelligent design advocate and/or a creationist?

Thanks in advance.

It takes a while to spot--but look at the specific questions he's not answering. He really won't say whether he's a believer or not. This is only something I see creationists trying to sound like they are purely being scientific do. Do you know any atheists who will argue science and make implications about their beliefs without saying them. Why do you think he won't say whether he believes in an intelligent designer. Why do you think he thinks Evolution, Darwin, and Dawkins are flawed thinkers and he uses and misuses language and old studies and quotes out of context to imply conclusions--but he never says anything really that he can be pinned down on. He's said he thinks some creationists have better arguments than some evolutionist (or all evolutionists...apparenty...his website is about scientific lies. You've read his work and his web page--Do you understand his problem with evolution? Do you understand why he'd repeatedly say that genes are replicators--rather it's the cell? Do you understand his oscillation theory that scientists are trying to suppress? Can you tell me what he finds to be a better argument in Behe's case. Do you believe that there could ever be an amount of evidence presented to him where he'd say--"gee...now that I look at it--evolution is a pretty strong theory...have you heard the latest...?"

No creationist used the term "god" because people will rightly conclude that the reason they really have a problem with evolution is "god". But they avoid all terminology that sounds religious, but you get a feel for them by the people they dislike and disparage, the failure to grasp or even hear certain basic concepts or questions (note all the questions he's ignored.) Maybe he really believes that evolution is a bad explanation and that his theory is better--so can you make sense of his theory? Can you explain why he avoids all questions relating to religion (he also avoids questions in regard to carbon dating, speciation, and the like...and he seems very certain about old information...but completely uninterested in more information.

I think it's because he found an area that he thinks disproves evolution and he wants to make everyone aware of it...whether it's for his god or his own pet theory or a bit of both--I can't tell, and he won't tell...and he may be lying to himself about it anyhow. I would just like someone to show me how he's different than Behe or Kleinman. We can probably presume that both are creationists and that their beliefs influence what they do and don't understand in regards to science and their belief that scientists are out to suppress "the truth" for some unfathomable reason. Hewitt and Von Neumann have very similar "blind spots" and they have obsessions with a key argument which no one but themselves seem to understand as far as I can tell--and so I conclude they are creationists trying to pretend their objections are purely scientific and rational and so they couch their language in tsk tsk semantics.

Since John won't tell us of his beliefs and creationists are dishonest as Judge Jones noted in the Behe case and they never reveal what would convince them that evolution is a sound understanding--what else should I conclude. I used to presume honest intent upon everone at a skeptics forum--but I've had a slew of conversations with similar people and eventually, like Pavlov's dogs--I see certain ways of using language and avoiding being pinned down--and I just start to feel like I've been trying to engage in a dialogue with someone who will only accept or hear words that support a belief he's already reached on his own.

So, yes, I think he's a creationist. The way he answered and avoids questions only confirms it to me. I think Kleinman is a creationist as is Hammy as is Von Neummann. I think they are creationists of the same kind Behe is. I think no amount of evidence would ever be enough for them to conclude that Evolution is a fact. I think they avoid all new information because they are afraid it might threaten the belief they prefer to think of as fact. I'm sure if I'm wrong, the truth will out--and maybe even some scientist will take note of one of these guys' theories and tell all the other lying scientists that they've been wrong all along--that evolution can't be true...and then they will explain why in a way everyone can understand and then they willl proffer the better explanation that fits the ever amassing data that these guys show no interest in.

I think John Hewitt is Behe and Kleinmann and Von Neumann with a different approach--they all believe themselves to be the one who will overturn evolutionary paradigm and bring upon the new age of scientific understanding.
I would like to think he's a very sincere guy with a really keen interest in understanding how life evolved--but I believe he's a guy who think he already knows how life came to be, and it wasn't through Darwinian evolution.

And I'd love it if someone could boil down his theory to me because I'm either too stupid to understand it--too defrauded by those lying scientists he refers to without naming and/or because nobody understands it but him. I understand Kleinman--He believes he has a mathematial proof that disproves evolution, but Von Neumann and Hewitt have theories that no one seems to be able to sum up very well. And they both have problems with evolution that are really hard to nail down. And all 3 of them think that scientists are refusing to give their theories adequate consideration though I think they are purposely avoiding understanding some pretty simple concepts. And all the creationists are vague about their beliefs and play semantic games.

So am I missing something? Have I nailed it? Is John Hewitt an enigma? Is his theory any good? Can anyone pin down his big bugaboo with evolution?
Can anyone clue me into something that makes me see he's not a creationist now that I've jumped to this conclusion. Can anyone who is not religious decode his intent in saying there are no such thing as memes? It's weird phraseology...and I've heard very similar phraseology from creationists. Please clue me in to something other than the fact that he doesn't mention god--because no creationist does. That is why the term "intelligent design" was invented. God gets you kicked out of court. But an alternative explanation other than evolution coupled with a disclaimer on evolution is the newest way to insert god into fact based teaching and throw "god threatening discoveries" into doubt.

articulett

18th January 2007, 12:08 AM

Does anybody know a non-creationist who wouldn't readily admit it so if asked "are you a creationist?". If someone were to ask me if I was a creationist, I'd say "no." I'm assuming other non-creationists would say the same--so if you are a non-creationist can you think of a reason for not answering that question. Because if I could hear a confirmed non-creationist give me a good reason, then I might think I was wrong about John Hewitt being a creationist (or intelligent design "scientist" or someone who is letting his god get in the way of his scientific understanding and communication thereof). Anyone?

John Hewitt

18th January 2007, 02:10 AM

It takes a while to spot--but look at the specific questions he (John Hewitt) is not answering. He really won't say whether he's a believer or not.
I have told you my beliefs about evolutionary theory - they are given at some length on my web site, "Sex and Philosophy."
Why do you think he thinks Evolution, Darwin, and Dawkins are flawed thinkers and he uses and misuses language and old studies and quotes out of context to imply conclusions--but he never says anything really that he can be pinned down on. I do not think Darwin was a flawed thinker but I do have serious reservations about Dawkins.

He's said he thinks some creationists have better arguments than some evolutionist <snip> Do you understand his problem with evolution? Do you understand why he'd repeatedly say that genes are (not) replicators -- rather it's the cell? <snip> Can you tell me what he finds to be a better argument in Behe's case. Do you believe that there could ever be an amount of evidence presented to him where he'd say--"gee...now that I look at it--evolution is a pretty strong theory...have you heard the latest...?" Behe correctly pointed out that many aspects of life are not explained by evolutionary theory. Genes, for example, are not replicators and the mechanism of their origin is, as Behe puts it, one of Darwin's "black boxes."

Note all the questions he's ignored. <snip> Hewitt and Von Neumann have very similar "blind spots" and they have obsessions with a key argument which no one but themselves seem to understandI have not ignored your questions, you have ignored mine. For example, why do you keep introducing supernatural entities and attaching them to my name? I do not know Von Neumann's argument, I hope he will refer to it.

Since John won't tell us of his beliefs <snip> yes, I think he's a creationist. The way he answered and avoids questions only confirms it to me. I think Kleinman is a creationist as is Hammy as is Von Neummann. I think they are creationists of the same kind Behe is. I think no amount of evidence would ever be enough for them to conclude that Evolution is a fact. As I have repeatedly said, my beliefs are as described in my work which work is evolutionary.

So am I missing something? Have I nailed it? Is John Hewitt an enigma? Is his theory any good? Can anyone pin down his big bugaboo with evolution?
Can anyone clue me into something that makes me see he's not a creationist now that I've jumped to this conclusion. Can anyone who is not religious decode his intent in saying there are no such thing as memes? It's weird phraseology...and I've heard very similar phraseology from creationists. Please clue me in to something other than the fact that he doesn't mention god--because no creationist does. That is why the term "intelligent design" was invented. God gets you kicked out of court. But an alternative explanation other than evolution coupled with a disclaimer on evolution is the newest way to insert god into fact based teaching and throw "god threatening discoveries" into doubt.I have no idea what facts or arguments might cause you to think rationally.
Please note that my web site, "A Habit of Lies: How Scientists Cheat," does describe scientific lying and does name the cell biologists involved. By contrast, "Sex and Philosophy" does not direct any such charge.

The Atheist

18th January 2007, 02:56 AM

Maybe Atheist is an atheist who can translate and show us how it has nothing to do with religion and everything to do with scientific bias and the underlying strenght and evidence behind your claim
I see kjkent1 has the same trouble as me - can't see any god writing John's poems for him.

I accept what you say about dishonesty, but I've found John to be pretty open and honest about everything so far. He has a radical, new approach to evolution, and as far as can tell, it makes sense. Whether his points are similar to creationists is irrelevant. I often quote Jesus and I'm an atheist.

In the meantime, until someone is actually able to debunk John's work, and I don't see that being easy to achieve, I'm giving him more than the benefit of the doubt. He's been an intelligent, thoughful and sincere bloke from day 1. He was immediately attacked - in about his 2nd post - as an ID campaigner, all because someone had seen him dismissive of currently "accepted" evolutionary theories. Automatically, he becomes an ID guy. I don't believe your critique of his work anounts to much more than "I don't like it". You say he's difficult to understand, I thought what he's said is a model of clarity, and I'm no evolution expert. I can understand the data input basis. And since you mention abiogenesis, until that one's worked out, all bets are off.

Given that our knowledge of evolution is so limited, the smart plan would be to have a critical look at all evidence and work on the subject. Why do ID guys find it so easy to attack evolutionary theories? Because of their incompleteness and the subjectivity of the developers. John may have something of value, or he may be one of the greatest BS artists the world ever seen.

Time will tell.

Cuddles

18th January 2007, 09:55 AM

Cuddles

18th January 2007, 10:12 AM

He was immediately attacked - in about his 2nd post - as an ID campaigner, all because someone had seen him dismissive of currently "accepted" evolutionary theories. Automatically, he becomes an ID guy.

This thread (http://forums.randi.org/showthread.php?t=66330) was the first he posted in, and this thread (http://forums.randi.org/showthread.php?postid=2020171#post2020171) was, I think, the second. He was not immediately attacked, either for being a creationist or for any other reason. His ideas were patiently discussed, along with their apparent flaws and lack of either evidence or support from anyone else in his field. On the other hand, he constantly attacked scientists, especially biologists, and even more especially evolutionary biologists, as frauds and idiots who either failed to understand his theory or actively tried to supress it. His views in expressed in the thread about his theory and the homeopathy thread did not serve to make any friends and gave rise to many people's suspicions about his true beliefs. It is not all that surprising that when he now posts in a thread about creationists, with views apparently sympathetic to at least some creationist ideas, that many people give voice to their suspicions.

Yahzi

18th January 2007, 10:58 AM

Please note that my web site, "A Habit of Lies: How Scientists Cheat,"
Is "obfuscation" one of those ways of cheating?

You were asked a direct question. A simple one. And your answer has been paragraphs of obfuscation.

You keep saying evolution is inadequate to explain life. Perhaps you would like to answer a more direct question: Is materialism adequate to explain life? Can life on Earth be solely the product of material elements, forces, and physical laws?

If you aren't a metaphysical naturalist, you're a creationiod. That's how it goes. Either material nature created life, or something else did.

Yahzi

18th January 2007, 10:59 AM

The fact that there are many people here who have independently come to the same conclusion tends to support this.
I figured out he was a creationiod when I realized I couldn't tell the difference between his posts and Klienman's.

:D

Yahzi

18th January 2007, 11:02 AM

John may have something of value, or he may be one of the greatest BS artists the world ever seen.
A false dichotomy.

Another option is that he's just another run-of-the-mill garden variety creationist who has enough scientific training to know he can't admit it.

Dr. Francis Collins is a much better bs-artist, because he managed to fool one a demonstrably smart, well-educated, productive scientist. Namely... Dr. Francis Collins.

joobz

18th January 2007, 11:39 AM

I figured out he was a creationiod when I realized I couldn't tell the difference between his posts and Klienman's.

:D

Truthfully, I never saw John as a creationist. But then I don't consider Hammegk a creationist either. They both are dismissive and negative toward evolution, true. But I don't think that means they are creationist either.

I also don't know if i'd consider John's argument for the notion of multiple orders of evolution as novel either. It seems that i've seen that idea expressed in multiple versions before. Especially when talking about prions, civilization, cellular ordering and Paul's ev model.

I've enjoyed most of their arguments and haven't seen them be intentially deceitful in anything they've posted. I can't say the same for Kleinman. He intentially ignores facts and conclusions that has been clearly presented to him. His obvious background knowledge in engineering (heat transfer was his work) leads me to believe he's intentionally being duplicitous.

I would never insult John Hewitt or Hammegk by drawing comparisons between them and Kleinman.

The Atheist

18th January 2007, 12:08 PM

It is not all that surprising that when he now posts in a thread about creationists, with views apparently sympathetic to at least some creationist ideas, that many people give voice to their suspicions.
You have more patience than me!

I know he was participating in a thread very early on and someone was hammering him about being ID, which he denied then as he denies now. I can never bother looking that stuff up, but I recall it completely as that's what drove me to check out John's websites.

I don't read the homeopathic threads, so I'd missed him in there, but with the link (thanks), I see what you mean. Yes, he made comments which didn't endear himself to people, but he also stated that homeopathy was worthless. Again, I find myself agreeing with his comments, and I find myself completely unsurprised at the vitriol attacking his stance. I'm pissed off that I wasn't reading that thread, I'd have been in on his side like a shot. He could have had the moral high ground while I kicked everyone in the nuts.

Maybe it's because I'll usually side with the underdog, maybe it's because I like his style - answer question obliquely then ignore it - and maybe I quite like people who aren't scared to put the boot in to the majority. Maybe I just like people who have "sex" in their theory name. Hell, apart from being 10^8 x smarter than me, he's a lot like me. Of course I like him!

On the other hand, if he is lying about being ID, I'll join in at the front of the queue braying for his blood. I've seen plenty of cons in my time and this one just doesn't give off that aroma.

John Hewitt

18th January 2007, 12:09 PM

Originally posted by kjkent1
Personally, and after reading Dr. Hewitt's online works, I don't see anything which suggests that he is mixing science with theology. But, maybe I'm missing something.

More to the point, why are we dancing around the issue? If someone thinks that John is a design advocate or creationist, they should ask John directly. Here, I'll do it:

John, are you an intelligent design advocate and/or a creationist?

Thanks in advance.
And here I don't think you are mssing anything at all but I prefer to avoid personalised phrasing. What I, personally, advocate is what I describe in my own work and my own web site. In that work I do not intentionally include any element of a creator or of preexisting design - neither do I include unicorns or Tom Cruise.

It is true that I have read many of the writings of ID proponents and I find them to be much better criticisms of evolutionary theory than some, whom I shall forbear from naming, are willing to acknowledge.

I am reminded rather of the differences of opinion between Wallace and Darwin on the origin of the human mind. Both those gentlemen, you will recall, agreed that the human mind could not have arisen by natural selection. Wallace's solution was to suggest divine intervention to guide the descent of human's into a facsimile of God; Darwin's, on the other hand, was to suggest sexual selection as an improvement to natural selection. Behe seems to be in the mould of Wallace but I feel that Darwin's approach was the correct one. Namely that, when theory fails, the solution is to improve the theory, not to rant at the critics, as do some in this forum, or to deny the facts.
is a perfect example of why many of us think he is. When asked a very direct yes/no question he chooses to answer with three long paragraphs which skate around the subject without ever quite answering it. I have never met a non-creationist who would not simply say that they are not creationists, but there are many creationists who refuse to admit they are such, either dressing it up as ID or simply refusing to give a straight answer. Given that John falls squarely into the last camp it is the obviuos assuption to make that he is in fact creationist, IDist, or whatever he chooses to call it. The fact that there are many people here who have independently come to the same conclusion tends to support this.

I have no idea how you conclude from the above quote that I am skating around the subject, that I am being evasive or that I am a creationist. What I said seems to me perfectly clear.
We are, or at least I am, talking about science - I am not talking about faith. I prefer to talk about thought not faith, about my ideas and about evidence, considered opinion and rational thought. I do not choose to talk in terms of what I believe.

That being so, I will leave the empty declarations of faith to you. I offer you no faith beyond saying that what I have written in my web site is the best interpretation of evolutionary theory I have yet been able to develop. It nonetheless remains a provisonal document subject to revisions that are consequent upon evidence or sensible arguments - if I ever hear one.

However, any such revisions will reflect my views not someone else's. I am under no duty to accept an opinion merely because the person who expresses it claims to be an evolutionist. Neither do I see any reason to reject every one of Behe's arguments, or those of any other IDer, merely because you dissent from the conclusions they have arrived at. I do, in fact, accept some of Behe's arguments, specifically his opinion that much of the machinery of the cell is a "black box" whose origin we do not currently understand and which cannot be understood in terms of conventional genetics.

In the meantime, my work is clearly evolutionary and contains no input of divine intervention. I therefore ask, yet again, why do you, Articulett, and others, keep associating me with supernatural ideas?

John Hewitt

18th January 2007, 12:23 PM

Truthfully, I never saw John as a creationist. But then I don't consider Hammegk a creationist either. They both are dismissive and negative toward evolution, true. But I don't think that means they are creationist either.

I also don't know if i'd consider John's argument for the notion of multiple orders of evolution as novel either. It seems that i've seen that idea expressed in multiple versions before. Especially when talking about prions, civilization, cellular ordering and Paul's ev model.

Yes, I always find Hammegk's comments wry but more or less accurate. The multilevel selection is not original to me. It can be construed as having roots in Popper but the main current advocate of multilevel selection is Sloan Wilson. So far as I know, my interpretation of levels in terms of differing data inputs and loci of selection is original to me - but it will probably turn out that some other chap did it in 1970.

articulett

18th January 2007, 12:30 PM

I figured out he was a creationiod when I realized I couldn't tell the difference between his posts and Klienman's.

:D

I know--you just start getting a feel for these things. The smarter ones can fool you for a bit--

But, that aside, can anyone sum up Johns alternative theory to me, because I can't get it to make sense. Is there a way to test it or disprove it or prove it? Can you, Atheist?

Is Kleinman going to come back and say, "gee, you've disproved my mathematical linchpin that shows the problem with evolution, I was mistaken." Do creationists ever conclude they might be wrong. I just think that as long as everything isn't explained in pat and easy to understand answers, they will use the gaps to insert doubt--even though I think there are much huger gaps in far more accepted scientific theories such as atomic theory or radiometric dating. We don't know everything--but it increasingly looks like we are on the right path in all the above. And, as I suspected, it looks like we are on the right path in concluding that John Hewitt is a creationist. The nice thing about good theories is that the evidence just keeps accumulating; whereas in bad theories--the evidence leads nowhere and doesn't further understanding of anything.

The Atheist

18th January 2007, 12:30 PM

A false dichotomy.What have you been drinking?
Another option is that he's just another run-of-the-mill garden variety creationist who has enough scientific training to know he can't admit it.Have you read his work? Not an option.
Dr. Francis Collins is a much better bs-artist, because he managed to fool one a demonstrably smart, well-educated, productive scientist. Namely... Dr. Francis Collins.There's your false dichotomy.

John Hewitt

18th January 2007, 12:37 PM

I don't read the homeopathic threads, so I'd missed him in there, but with the link (thanks), I see what you mean. Yes, he made comments which didn't endear himself to people, but he also stated that homeopathy was worthless. Again, I find myself agreeing with his comments, and I find myself completely unsurprised at the vitriol attacking his stance. I'm pissed off that I wasn't reading that thread, I'd have been in on his side like a shot. He could have had the moral high ground while I kicked everyone in the nuts.
Works for me

Maybe it's because I'll usually side with the underdog, maybe it's because I like his style - answer question obliquely then ignore it - and maybe I quite like people who aren't scared to put the boot in to the majority. Maybe I just like people who have "sex" in their theory name. Hell, apart from being 10^8 x smarter than me, he's a lot like me. Of course I like him!

On the other hand, if he is lying about being ID, I'll join in at the front of the queue braying for his blood. I've seen plenty of cons in my time and this one just doesn't give off that aroma.
The "sex and philosophy" domain name comes about because sexuality was the only application of bioepistemic evolution I had come up with when I chose it. Since epistemology is a branch of philosophy, the name comes about fairly naturally.

The deciding factor was my aged mother - I told her I was thinking of calling my web site "sex and philosophy" and she collapsed laughing. Then I thought, "OK, at least it will be remembered."

articulett

18th January 2007, 12:37 PM

A false dichotomy.

Another option is that he's just another run-of-the-mill garden variety creationist who has enough scientific training to know he can't admit it.

Dr. Francis Collins is a much better bs-artist, because he managed to fool one a demonstrably smart, well-educated, productive scientist. Namely... Dr. Francis Collins.

Francis Collins has no problems with Darwinian evolution--he knows his genetics and it's just too obvious the more you study genomes. His beliefs about God are in a separate sphere. He believes that god is outside knowing and in this way he keeps it away from his science--which is a good thing--because his reasons for believing in god (especially the Christian version) are on much shakier ground than his acceptance of evolution and evidence therein.

Most scientists wish he'd keep his religious bs between himself and other believers, but those Christians feel the ever present need to spread the "good news". Others think he's a gem, because he shows that even Christians can accept evolution. Evolution doesn't lead to atheism. I think it calls the whole original sin thing into question which is why god supposedly killed his kid (who was him), but that doesn't seem to bother him, and as long as kids can at least have the opportunity to learn a bit about evolution, I don't care at all about his beliefs. I wonder if Collins would understand Hewitt's theory...?

articulett

18th January 2007, 12:54 PM

What have you been drinking?
Have you read his work? Not an option.
There's your false dichotomy.

Actually, you posted the false dichotomy--(he's either X or Y). You've said that he says he's not a creationist--where does he say that? Why do you think he didn't answer the question directly? How would you have answered the question? If someone was a creationist, why do you think it might be advantageous to skirt the issue? And the statement about Francis Collins is not a dichotomy at all (he's either X or Y). And what's your take on John's theory? Where is it better than Ev by natural selection? What is his main problem with Ev by natural selection? Or is it more of a fine tuning of Ev. And what do you think of his claim that genes aren't replicators--it's the cells that are the replicators?

I don't think Hewitt is really saying anything and using the science he does know to sound like he's saying something. His whole theory would require a definition as to what life is and whether a cell can be alive without a nucleus, I think.

--He's using a lot of words to say nothing at all, and that is a common woo technique--obfuscate. It's what the best defense attorneys are good at. I could be wrong. Can anyone answer the above questions to me in a way that doesn't sound like a further obfuscation or semantic dodge?

John Hewitt

18th January 2007, 01:04 PM

Francis Collins has no problems with Darwinian evolution--he knows his genetics and it's just too obvious the more you study genomes. His beliefs about God are in a separate sphere. He believes that god is outside knowing and in this way he keeps it away from his science--which is a good thing--because his reasons for believing in god (especially the Christian version) are on much shakier ground than his acceptance of evolution and evidence therein.
But you see, genetics is not Darwinian evolution - he knew nothing about genes. It was Fisher who connected genetics with natural selection in the 1930s. However, as soon as you have multilevel selection, that connection breaks apart and genetics becomes just one example of evolution. Moreover, from the point of view of data, genetics cannot be conceived as a prototype of evolution in general - genes have a very specialized data format.
Thus, multilevel selection recreates Fisher's problem, the need to give a general mechanistic explanation of evolution as a process.
I wonder if Collins would understand Hewitt's theory...?
You could think it through for yourself.

articulett

18th January 2007, 01:39 PM

I would never insult John Hewitt or Hammegk by drawing comparisons between them and Kleinman.

I hate to burst your bubble, but Hammegk has affirmed his belief in "intelligent design". That being said, I agree there are different rankings in reguard to intelligence and deception amongst those I've pegged as creationists. And I do think John is the most polite by far, and very intelligent as well.

The Atheist

18th January 2007, 02:00 PM

I know--you just start getting a feel for these things. The smarter ones can fool you for a bit--So your sig says.

I am, however, beginning to wonder whether that concept has taken on proportions of "anyone who disagrees with me is incompetent.
But, that aside, can anyone sum up Johns alternative theory to me, because I can't get it to make sense. Is there a way to test it or disprove it or prove it? Can you, Atheist?
Well, John seems to sum it up pretty thoroughly - and briefly - here (http://www.sexandphilosophy.co.uk/conclusions.htm). Far better to read's his summation than mine as I'd only be copying.

Can it be proved/disproved? That's a very good point as I think John's come up with something quite scary for scientists - a theory which can probably never be prven, but is certainly open to disproof. Maybe that's another attraction, someone willing to stake a reputation and career on something which is 100% capable of being shot down in flames, yet cannot be adequately proven. That's backing oneself.
Is Kleinman ...I have no interest in Kleinman.
I just think that as long as everything isn't explained in pat and easy to understand answers, they will use the gaps to insert doubt ...
Does that mean that all you have are the easy, off-pat answers? Are you applying those "critical thinking" skills to yourself and your position?
And, as I suspected, it looks like we are on the right path in concluding that John Hewitt is a creationist. The nice thing about good theories is that the evidence just keeps accumulating; whereas in bad theories--the evidence leads nowhere and doesn't further understanding of anything.Nice assertion on which path you're sure John's on.

To date, all of the "evidence" you've found to back up that assertion amounts to "I don't like John's science" and "he uses arguments I've seen from IDists".

I see you're a Dawkins flag-waver. No doubt you caught him at TAM. I like the bit in the video of it where he talks to Randi about "paranormality" and "perinormality" [sp?]. There are still things we don't know enough about. God isn't one of them, evolution is.

Until you can flaw John's work - in serious terms - or until he places a foot in the "goddidit" camp, then I suggest you're walking a line where a step the wrong side of it may result in you being covered in "woo".

Hell, if you can refute John's theories, be my guest. I'm sure John himself would actually thank you as well. Everything I've seen from him to date smacks of honesty; give it a go.

joobz

18th January 2007, 02:27 PM

I hate to burst your bubble, but Hammegk has affirmed his belief in "intelligent design". That being said, I agree there are different rankings in reguard to intelligence and deception amongst those I've pegged as creationists. And I do think John is the most polite by far, and very intelligent as well.
No problem. I have no bubble to burst here. I'm always open to hearing new evidence and adjusting my views/beliefs accordingly.

perhaps that makes me a Namby Pamby scientist.;)

The Atheist

18th January 2007, 03:10 PM

Actually, you posted the false dichotomy--(he's either X or Y). You've said that he says he's not a creationist--where does he say that? Have a look at his posts, woman!
Why do you think he didn't answer the question directly?Yeah, I admire that. People ask me a stupid question and I tell 'em to #### off. People ask John a stupid question and he gives you an oblique answer because he's already stated his position, several times.
How would you have answered the question?See the bit above about #### off.
If someone was a creationist, why do you think it might be advantageous to skirt the issue? Well, if I'd seen John doing that, I'd probably try to answer. I think you're doing exactly what the anti-homeopathy brigade did. Someone didn't agree with their agenda, even though he was technically "on their side", so gets rubbished for putting up a sound, valid and quite irrefutable argument.Irrefutable, becaue it was based upon reality, rather than some neo-fascist "Skeptic World" where TruthTM is the only answer, EVER!

Fortunately, we still live in the former.
And what's your take on John's theory?Sharp. Very sharp. Controversial, clever, well-thought out, finely scripted into layman English. Highly convincing.
Where is it better than Ev by natural selection?Abiogenesis.
What is his main problem with Ev by natural selection? You should direct that to John.
Or is it more of a fine tuning of Ev. And what do you think of his claim that genes aren't replicators--it's the cells that are the replicators?Replication isn't the point. The point is which replication works and which doesn't. Without a means of harnessing the replication, nothing happens. John has posited a potential answer to this question. It might be wrong, but it also might be right.

I'm not flag-waving for John; A - he doesn't need it & B - I have no particular loyalty to him, but I like to see ideas explored when they seem to offer merit. More so when it challenges established thought - which then responds in typical, derisory fashion. What does that sort of behaviour suggest to you?
I don't think Hewitt is really saying anything and using the science he does know to sound like he's saying something. His whole theory would require a definition as to what life is and whether a cell can be alive without a nucleus, I think.

--He's using a lot of words to say nothing at all, and that is a common woo technique--obfuscate. It's what the best defense attorneys are good at. I could be wrong. Can anyone answer the above questions to me in a way that doesn't sound like a further obfuscation or semantic dodge?Long on empty rhetoric and short on answers.

fishbob

18th January 2007, 03:17 PM

Maybe it's because I'll usually side with the underdog, maybe it's because I like his style - answer question obliquely then ignore it - and maybe I quite like people who aren't scared to put the boot in to the majority.

You can't answer questions obliquely then ignore the subject and at the same time put the boot to anybody. I'm wondering about you, now.

John Hewitt

18th January 2007, 05:14 PM

And what's your take on John's theory? Where is it better than Ev by natural selection? What is his main problem with Ev by natural selection? Or is it more of a fine tuning of Ev. And what do you think of his claim that genes aren't replicators--it's the cells that are the replicators?

I do not have any problem with natural seelction per se, I think it works fine in its proper place. The problem is that there are some things that cannot be interpreted by natural selection. Darwin identified one when he discussed the origin of the brain in the "Descent of Man." There, he replaced natural selection with sexual selection.
From a bioepistemic point of view, sexual selection is different from natural selection in that it involves another form of data besides DNA sequence, it involves sensory data. The act of sexual selection involves a choice of sexual partner from among various candidates. That choice requires sensory organs with which to examine the possible choices along with a memory and a brain with which to make the comparisons. Thus, sexual selection drives the development of sense organs and brains, as well as peacocks' tails.
Other forms of selection can apply in other ranks and orders of evolution and I think a proper appreciation of evolution requires a proper analysis of those evolutionary processes.

As for your question "And what do you think of his claim that genes aren't replicators--it's the cells that are the replicators?" Really! How many times does the same thing need to be said?

A replicator is an entity that can replicate itself. Given the necessary chemical and energy inputs, cells and other organisms can replicate themselves; they are replicators. No matter what chemicals or energy is provided to a gene, it cannot replicate itself. Genes are copied by the cell during the cell's own replication. This is not a claim on my part, it is standard pre-university biology. Even Dawkins, in The Selfish Gene, accepts the description I have given but he then goes on to claim that genes were once some kind of primordial replicators that have subsequently lost their ability to replicate. There is no evidence whatever to support that claim and the actual observation remains what I have described.

John Hewitt

18th January 2007, 05:37 PM

You can't answer questions obliquely then ignore the subject and at the same time put the boot to anybody. I'm wondering about you, now.
The question at issue is "Are you an IDer or creationist." My answer is
1. That we are discussing scientific ideas not personal attributes.
2. That scientific debate should not be personalised.
3. That my scientific ideas express my opinions.
4. My scientific work is subject to change in response to evidence.
5. My work does not represent a faith. I do not demand declarations of faith from anybody.
6. You are not entitled to demand that I swear an oath of allegiance to your opinions or faith in some prescribed evolutionary text.
7. My scientific work does not involve ID or creationism or God or fairies or unicorns or little green men or pixies or leprochauns or the world of Narnia or .....

I have no idea how those answers could be considered unclear.

The Atheist

18th January 2007, 05:46 PM

You can't answer questions obliquely then ignore the subject and at the same time put the boot to anybody. I'm wondering about you, now.
Want to offer some odds on that? I see it happening, right now. Maybe you need to re-read John's posts, maybe you need to get a pommy to translate them into American, but he's doing just that.

Wonder about me is right, I sometimes wonder about me as well.

kjkent1

18th January 2007, 07:01 PM

The question at issue is "Are you an IDer or creationist." My answer is
1. That we are discussing scientific ideas not personal attributes.
2. That scientific debate should not be personalised.
3. That my scientific ideas express my opinions.
4. My scientific work is subject to change in response to evidence.
5. My work does not represent a faith. I do not demand declarations of faith from anybody.
6. You are not entitled to demand that I swear an oath of allegiance to your opinions or faith in some prescribed evolutionary text.
7. My scientific work does not involve ID or creationism or God or fairies or unicorns or little green men or pixies or leprochauns or the world of Narnia or .....

I have no idea how those answers could be considered unclear.

I didn't realize I would stir up a malestrom. Maybe I should rephrase the question:

Do you accept the results of the scientific method, regardless of how a scientifically derived conclusion might interfere with your personal philosophical/theological beliefs?

Note: I'm agnostic, but I have no argument with theists or atheists, except where they insist that a certain conclusion must follow from a hypothesis, regardless of any intervening verifiable experimental results.

PixyMisa

18th January 2007, 07:03 PM

Well, John seems to sum it up pretty thoroughly - and briefly - here (http://www.sexandphilosophy.co.uk/conclusions.htm). Far better to read's his summation than mine as I'd only be copying.

Wow, that's really awful writing.

As far as I can make out, he's proposing the abandonment of more than a century of painstakingly collected evidence for... Well, exactly what is unclear. Hand-waving, to judge from that page.

Can it be proved/disproved? That's a very good point as I think John's come up with something quite scary for scientists - a theory which can probably never be prven, but is certainly open to disproof.

Baloney.

For one thing, I see nothing that even suggests a coherent hypothesis. For the other, more important, thing, falsifiable theories are science's bread-and-butter. If you think such things are "quite scary for scientists", then you clearly know nothing of science.

PixyMisa

18th January 2007, 07:05 PM

Yes, I always find Hammegk's comments wry but more or less accurate.

In this thread? In which he has repeatedly demonstrated his profound lack of relevant knowledge?

Cynical, yes. Wry, not so much. Accurate, not at all.

PixyMisa

18th January 2007, 07:09 PM

From a bioepistemic point of view, sexual selection is different from natural selection in that it involves another form of data besides DNA sequence, it involves sensory data.

Yes, it involves sensory data. In precisely the same way that any other form of natural selection does.

That choice requires sensory organs with which to examine the possible choices along with a memory and a brain with which to make the comparisons.

All of which applies equally well to any other form of natural selection.

The Atheist

18th January 2007, 07:45 PM

I didn't realize I would stir up a malestrom. Maybe I should rephrase the question:

Do you accept the results of the scientific method, regardless of how a scientifically derived conclusion might interfere with your personal philosophical/theological beliefs?Isn't that already answered here:

1. That we are discussing scientific ideas not personal attributes.
2. That scientific debate should not be personalised.
4. My scientific work is subject to change in response to evidence.

fishbob

18th January 2007, 07:48 PM

The question at issue is "Are you an IDer or creationist." My answer is
1. That we are discussing scientific ideas not personal attributes.
2. That scientific debate should not be personalised.
3. That my scientific ideas express my opinions.
4. My scientific work is subject to change in response to evidence.
5. My work does not represent a faith. I do not demand declarations of faith from anybody.
6. You are not entitled to demand that I swear an oath of allegiance to your opinions or faith in some prescribed evolutionary text.
7. My scientific work does not involve ID or creationism or God or fairies or unicorns or little green men or pixies or leprochauns or the world of Narnia or .....

I have no idea how those answers could be considered unclear.

I did not ask that question.
And my comment was not directed at you.

And clearer responses might be something like:
'yes' or 'no' or 'irrelevant' or 'none of your damn business'.

5 words at most.

fishbob

18th January 2007, 07:52 PM

Want to offer some odds on that? I see it happening, right now. Maybe you need to re-read John's posts, maybe you need to get a pommy to translate them into American, but he's doing just that.

Wonder about me is right, I sometimes wonder about me as well.

No pommy handy, does 'putting the boot' to someone mean something like annoying the crap out of them until they get disgusted and leave?

The Atheist

18th January 2007, 07:56 PM

Wow, that's really awful writing.You're right, it is. The whole post is a mess - haste makes waste.
As far as I can make out, he's proposing the abandonment of more than a century of painstakingly collected evidence for... Well, exactly what is unclear. Hand-waving, to judge from that page.Really? Again, I get a completely different picture. I see someone who thinks the gaps can be filled with a process which known evolutionary components. My writing might vary occasionally, but my comprehension skills are 1st class.

Have you read through the whole thing? Might be worth your while.
Baloney.

For one thing, I see nothing that even suggests a coherent hypothesis.see above.

For the other, more important, thing, falsifiable theories are science's bread-and-butter. If you think such things are "quite scary for scientists", then you clearly know nothing of science.
You've missed the point here. Of course it's falsifiable.

The scary part comes in it being falsifiable by someone else's positive result. Note the negativity about John's claims! You're dying for him to fall over, even before you understand what he's saying. Falsify his theory then. I guess the simple way to do that is to get a gene to replicate outside the cell. That's all it takes to blow him right out of the water.

Anyone tried to do that yet?

fishbob

18th January 2007, 08:00 PM

Isn't that already answered here:

Obliquely at best. Not in any sense clear or definitive.

kjkent1

18th January 2007, 09:24 PM

Isn't that already answered here:1. That we are discussing scientific ideas not personal attributes.
2. That scientific debate should not be personalised.
4. My scientific work is subject to change in response to evidence.I suppose so, but I figured since I started the argument, that I would try to clarify it.

Anyway, I don't find John Hewitt disingenuous. He is at least educated in the subject matter, and he posts under his real name. This is worthy of some respect.

articulett

19th January 2007, 12:13 AM

What does that sort of behaviour suggest to you?
Long on empty rhetoric and short on answers.

Exactly. That's exactly what John's behavior suggests to me. I have read his posts. I think you didn't sum up his theory or his arguments, because you can't. I have read his posts. They are hard to read...But let me give you some links to the very post you mentioned, and I know you won't believe it, but to anyone who has spent anytime debating creationists or teaching their children, they can see the signs. But, as always, everyone is free to believe as they choose. From your link

Accordingly, the original problem became an attempt to merge scientific philosophy and scientific results - that is to say, merge general statements about scientific method and ethics, with evolutionary theory. An interesting, if abstract, academic question but one to which a solution appeared problematic, since evolutionary theory and scientific ethics seemed entirely incompatible. How could an idea system like scientific ethics and philosophy, involving strict rules of behavior and thought, arise from evolutionary theory, an apparently anarchic system that demands victory by any means?

He's basically saying evolution can't explain things like morality--it's the basis of Francis Collins' God--and most believers who also accept evolution. God must exist, because where would morality come from is the argument. These type of creationist cannot here or will not here all the explanations of animals exhibiting extradinorily similar behavior in the morality department and we actually understand a lot about how it evolves. Creationism 101--try and show something about Human Life that evolution can't account for--then insert your god. Humans rescue humans that are not related is one argument--but the fact is, all humans are related and so is all life--the closer the life form is to you--the more genes you share...and many animals form social groups and many mammals will care for and rescue those who aren't their own. There's great video where a hippo tries to save a baby antelope from an alligator attack... http://youtube.com/watch?v=yxSvFYph0u8 The idea that morality couldn't evolve is at the basis of his argument...as well as other characteristics. At least that's what I think he's saying--no one else seems to be summing him up.

Even so, it is notable how the smaller problem of scientific cheating offers itself as a microcosm of the larger one. Scientific cheating contains evolutionary theory because that theory is the central pillar of biological thinking. Power enters the problem because evolutionary theory merges with political science through the need for individuals to possess the power to survive and reproduce, hence the ideas of Machiavellian intelligence that have become popular in evolutionary psychology. Knowledge appears in the problem of scientific cheating, because science is all about generating "reliable knowledge" in the phrase scientific philosopher John Ziman (1978) chose as his title. At the same time, the very concept of cheating implies the existence of ethical codes to be broken.

Scientists are cheating...(e.g. they're not letting his theory in), and cheating implies "ethics" (which according to his theory couldn't have evolved). My dog tricks my other dog all the time...and looks guilty when I catch her. She also has some other damn fine ethics and no one put them there. Humans prefer some traits in animals and select for them--they do the same in eachother.

Evolutionary theory, as Darwin well recognized, was not just a new biological theory, it was a new philosophy. This work would argue that it was an epistemology, where an epistemology is a process that generates knowledge when applied to an information set. In this, its most basic form, evolutionary theory should not be seen as a scientific theory as it is doubtful whether it could ever be practically tested. The concept of an evolved creature, possessed of no knowledge except that from evolution, objectively testing a theory of evolution, contains elements of self-reference that might lead to an infinite regress.

He says evolution can't be tested. Flat out lie. We have found hormones responsible for pair bonding and genes associated with various personality traits and they apply to animals other than ourselfs...we even see mirror neurons which are responsible for empathy in other animals and the core of morality. We can say, "if evolution is true, than there should be an overall advantage to reciprocity and social cooperation in groups"--and that is what we see. Bats have a communal blood sharing policy--the winners of the evenings hunts, share with the losers--but someone who takes a lot and doesn't give is punished. Even apes show very similar behavior. We can say "if evoluton is true, then other social groups will show strong parallels to humans"--particularly the more closely related they are. And that is exactly what we see.

Evolution has bestowed on mankind knowledge on which to base decisions, hands with which to implement them and ambition for the power that makes choice possible. With the passage of time, we have come to possess so much more knowledge than animals, so many more choices, that humans, alone among the animals may be said to possess free will.

Free will. Code word for religion. Free Will isn't really even a scientific term. It really isn't well defined as far as I can tell, though it is the basis of religion. Life is a test of this "free will". Let's see--are priests who molest children exercising free will? Certainly no-one chooses to be attracted to children. So whatever will he is or isn't exercising--it's very different from the one I'd be exercising, because I have no attraction to children.

To me, it's obvious. Clearly others have picked it up as well. Scientists aren't cheating--his theory is unnecessary and hard to follow. It boils down to--humans must have something "extra" to account for free will, ethics, cheating, etc.--and that something extra is an intelligent designer. That's why John avoids using genes as the replicator. Genes code for all the traits we see in animals, and they encode for all the traits we see in ourselves as well. We evolved to learn from our environment...we've evolved language...from that, we have taken some great strides in thinking--but we don't have "something extra"--(a soul)-- or if we do--there is no measurable evidence for it and inserting it because there must be something to account for that which we do not understand is a violation of Occams razor. John knows this. His obfuscation is to keep people like you from knowing this.

Or maybe I've interpreted the words incorrectly. But no-one seems to be clarifying--and John is very difficult to read--he muddys the language in certain areas though he shows clarity in others. The muddyness is "god". If you couldn't define his argument or his problem with evolution--it's because he wasn't clear about either. He was throwing out semantic games whether he is aware of it or not...and he's very good--so it takes some time to pin down what he's saying--and, frankly, I really haven't got that kind of time to waste anymore. Creationists never change their views and they are deceptive and talk on and on without saying anything and then blame everyone else for nobody understanding them.

I'm tired of trusting the wrong people. It's why I'm a skeptic. When asked point blank--people who are not creationists say so.

John Hewitt

19th January 2007, 12:54 AM

Maybe I should rephrase the question:

Do you accept the results of the scientific method, regardless of how a scientifically derived conclusion might interfere with your personal philosophical/theological beliefs?

I would reply to that by saying that, in formulating my personal opinions, which I express in my scientific work, I accept the results of properly applied scientific method.

John Hewitt

19th January 2007, 01:00 AM

Yes, it involves sensory data. In precisely the same way that any other form of natural selection does.

All of which applies equally well to any other form of natural selection.

I think this claim is incorrect. Natural selection is merely about survival and reproduction. The concept of natural selection can be applied to organisms that are devoid of sense organs and, I would imagine, that was the situation in early evolution.

Sexual selection is different and can only apply to organisms that examine prospective mating partners. In other words, make use of data derived from sense organs.

The Atheist

19th January 2007, 01:05 AM

Well, I certainly won't argue your passion!

It seems to me that you've cherry-picked a couple of examples and ignored the majority. Bats behave one way, lions, hyenas and wolves don't. If one proves human evolution, do the others disprove it?

I'll take your points on board, but to me, when a bloke answers a straight question with a straight answer, I'll believe him until he's been shown to be lying. You haven't come close to that, other by your own assertion.

Given that John has books published and has been working on this for may years, don't you think he might have slipped god in if that's where he was headed? Bit of a waste for a creationist to spend all those years, having all those theories published, putting up hundreds of web pages, and all not to advance the creationist agenda?

kjkent1

19th January 2007, 01:12 AM

I would reply to that by saying that, in formulating my personal opinions, which I express in my scientific work, I accept the results of properly applied scientific method.

Seems reasonable to me.

Another question: do you believe that certain higher level functions exhibited by humans, such as ethics, morals, altruism, etc., could not possibly have evolved?

John Hewitt

19th January 2007, 01:32 AM

I have read his posts. They are hard to read...But let me give you some links to the very post you mentioned, and I know you won't believe it, but to anyone who has spent anytime debating creationists or teaching their children, they can see the signs.
woo woo

But, as always, everyone is free to believe as they choose. From your link
Accordingly, the original problem became an attempt to merge scientific philosophy and scientific results - that is to say, merge general statements about scientific method and ethics, with evolutionary theory. An interesting, if abstract, academic question but one to which a solution appeared problematic, since evolutionary theory and scientific ethics seemed entirely incompatible. How could an idea system like scientific ethics and philosophy, involving strict rules of behavior and thought, arise from evolutionary theory, an apparently anarchic system that demands victory by any means?

He's basically saying evolution can't explain things like morality--it's the basis of Francis Collins' God--and most believers who also accept evolution. God must exist, because where would morality come from is the argument. <snip> At least that's what I think he's saying--no one else seems to be summing him up.

No, it was a question I was asking, and I was more concerned with scientists than hippos.
Even so, it is notable how the smaller problem of scientific cheating offers itself as a microcosm of the larger one. Scientific cheating contains evolutionary theory because that theory is the central pillar of biological thinking. Power enters the problem because evolutionary theory merges with political science through the need for individuals to possess the power to survive and reproduce, hence the ideas of Machiavellian intelligence that have become popular in evolutionary psychology. Knowledge appears in the problem of scientific cheating, because science is all about generating "reliable knowledge" in the phrase scientific philosopher John Ziman (1978) chose as his title. At the same time, the very concept of cheating implies the existence of ethical codes to be broken.

Scientists are cheating...(e.g. they're not letting his theory in), and cheating implies "ethics" (which according to his theory couldn't have evolved).

No, again you miss the context. This evolutionary study derives from "A Habit of Lies: How Scientists Cheat." I was not suggesting that evolutionary theorists were cheating, (though as an irrelevant aside there are some instances) I was noting the fraud in science that I had previously described.

Evolutionary theory, as Darwin well recognized, was not just a new biological theory, it was a new philosophy. This work would argue that it was an epistemology, where an epistemology is a process that generates knowledge when applied to an information set. In this, its most basic form, evolutionary theory should not be seen as a scientific theory as it is doubtful whether it could ever be practically tested. The concept of an evolved creature, possessed of no knowledge except that from evolution, objectively testing a theory of evolution, contains elements of self-reference that might lead to an infinite regress.

He says evolution can't be tested. Flat out lie.
No, I am noting that evolution is BOTH a philosophy and a scientific theory. To the extent that it is a philosophy, I do find it to be untestable. Evolution is testable only when articulated into a concrete context.

To me, it's obvious. Clearly others have picked it up as well. Scientists aren't cheating--his theory is unnecessary and hard to follow.

There are numerous, documented instances of scientists cheating.

It boils down to--humans must have something "extra" to account for free will, ethics, cheating, etc.--and that something extra is an intelligent designer. That's why John avoids using genes as the replicator. Genes code for all the traits we see in animals, and they encode for all the traits we see in ourselves as well. We evolved to learn from our environment...we've evolved language...from that, we have taken some great strides in thinking--but we don't have "something extra"--(a soul)-- or if we do--there is no measurable evidence for it and inserting it because there must be something to account for that which we do not understand is a violation of Occams razor. John knows this. His obfuscation is to keep people like you from knowing this.

How do you get from not using genes as replicators to souls? I am not trying to obfuscate anything, I am just trying to get people to understand that genetics is an incomplete description of evolution.

John Hewitt

19th January 2007, 01:40 AM

Another question: do you believe that certain higher level functions exhibited by humans, such as ethics, morals, altruism, etc., could not possibly have evolved?
The evolutionary question is not whether such things evolved it is how they evolved. Bioepistemic evolution argues that the best way of understanding the origin of such traits is to to see humans as actors (subsystems, if you will) within the evolving system of culture, rather than simply as evolving systems in their own right. Actors within a system cooperate rather than compete.

kjkent1

19th January 2007, 02:05 AM

John Hewitt

19th January 2007, 03:02 AM

Question is: what happens when a culture collapses? What is encoded and what is learned?

On a different tack, I've never seen cooperation, and I'm not a kid. What I see is negotiation, i.e., competition which requires that individuals bargain for their respective and mutual survival, usually leading to one of the sides getting the best deal and obtaining superior circumstances as a consequence. All of which seems to fit quite nicely with the idea of natural selection.
You have often seen cooperation - consider which side of the road you drive on. I think that humans have acquired traits that lead them to form groups and will do so even if, intially, they do not know one another or if their culture has previously collapsed. The group they form is a hierarchy and competition is usually for place in that hierarchy.

I am not sure what you mean by "fit(s) quite nicely with the idea of natural selection." Social groups lead, so it seems to me, to social selection and one must consider the types of selection occuring within the information flows of a social hierarchy. The issue here is partly the unit of selection and partly whether it is even appropriate to talk about units of selection.
The fact of human cooperation does not fit very well with natural selection based on genes or even individuals as the units of selection but we have gene-culture coevolution and, if social evolution dominates, which I think it does in humans, then human genetic evolution will adapt to serve the needs of social knowledge. That will lead to humans adapting to function not just as competitors but to becoming actors within social evolution and, as such, they can be expected to exhibit cooperative and altruistic traits toward other members of their social group.

Cuddles

19th January 2007, 05:32 AM

I think this claim is incorrect. Natural selection is merely about survival and reproduction. The concept of natural selection can be applied to organisms that are devoid of sense organs and, I would imagine, that was the situation in early evolution.

Sexual selection is different and can only apply to organisms that examine prospective mating partners. In other words, make use of data derived from sense organs.

This is one of the funniest things I've read in a long time. Which part of sexual selection isn't natural? In what way is selecting for various traits in a partner not selecting for the genes that produce these traits?

cyborg

19th January 2007, 05:55 AM

Sexual selection is different and can only apply to organisms that examine prospective mating partners. In other words, make use of data derived from sense organs.

John, in what way is my genetics not in some way responsible for the sexual selections females may decide to make with regards to me?

The physical manifestation of my genetics - i.e. my body - and all its various facets are a reflection of the quality of my genetics are they not?

John Hewitt

19th January 2007, 06:55 AM

This is one of the funniest things I've read in a long time. Which part of sexual selection isn't natural? In what way is selecting for various traits in a partner not selecting for the genes that produce these traits?
Sexual selection cannot possibly select for genotype, it can only select for observable phenotype. The observation requires data derived from sense organs.

John Hewitt

19th January 2007, 06:58 AM

John, in what way is my genetics not in some way responsible for the sexual selections females may decide to make with regards to me?

The physical manifestation of my genetics - i.e. my body - and all its various facets are a reflection of the quality of my genetics are they not?
Only in some respects. Some girls may not like the colour of your tie. (This is a serious comment - many manifestations of observable phenotype are plainly and obviously nothing to do with genotype.)

Cuddles

19th January 2007, 07:27 AM

Sexual selection cannot possibly select for genotype, it can only select for observable phenotype. The observation requires data derived from sense organs.

Only in some respects. Some girls may not like the colour of your tie. (This is a serious comment - many manifestations of observable phenotype are plainly and obviously nothing to do with genotype.)

And the phenotype is caused by...? Would you like to provide some example of things that are "plainly and obviously nothing to do with genotype"?

cyborg

19th January 2007, 07:44 AM

Only in some respects. Some girls may not like the colour of your tie. (This is a serious comment - many manifestations of observable phenotype are plainly and obviously nothing to do with genotype.)

The ability to select aesthetically correct plumage seems somewhat tied to my genetics rather than simply a learned skill. There are clearly people who seem to have an 'eye' for what is correct and others who appear to have a total inability to understand why their website with huge text and green on magenta text is fugly.

A tie is not merely a tie, it is a test; like the plumage of a peacock. The woman is testing my genetics by observing what I have done with them - at a very superficial level. There are many tests of course - I just have to show her that I have other qualities that she is interested in.

Remember, sexual reproduction is about the recombination of genetics from two parties. The basic goal of the gene has not changed - if you will forgive the anthropomorphism: move towards the best genetic code for a given environment. The sexual issue leads to issues of genetic compatibility. At the most basic level of things like plants this has given rise to sexual selection mechanisms in the most basic sense - to avoid self pollination. Human sexuality is no different in this regard - we have mechanisms to help us avoid being attracted to our own family members.

I don't really get the thrust of your argument. Sexual selection is not somehow entirely divorced from genetics.

bigred

19th January 2007, 09:01 AM

Sometimes these annoying creationists just piss me off:

http://www.evolutionisdead.com/forum/viewtopic.php?p=11670&sid=3406e76df02b7fb9f60af262a63c3a63#11670

~~ Paul
I guess you should only debate people who won't annoy you (or disagree with you) then. :rolleyes: sheesh Paul - remember, you sought THEM out.

In fact from what I can gather skimming the link, the whole talk is more "scientific" than I would've expected, esp from a site called "evolution is dead." Looks highly in-depth, in fact. Hope you felt like you got/are getting some interesting discussions there.

John Hewitt

19th January 2007, 09:10 AM

I don't really get the thrust of your argument. Sexual selection is not somehow entirely divorced from genetics.
I did not say that sexual selection is entirely divorced from genotype, I said that selection operates on observable phenotype not on genotype. I also said that the act of observation requires sense organs to acquire the observational data and a brain with which to interpret it. Do you have a problem with that?

kjkent1

19th January 2007, 11:04 AM

You have often seen cooperation - consider which side of the road you drive on. I think that humans have acquired traits that lead them to form groups and will do so even if, intially, they do not know one another or if their culture has previously collapsed. The group they form is a hierarchy and competition is usually for place in that hierarchy.

I am not sure what you mean by "fit(s) quite nicely with the idea of natural selection." Social groups lead, so it seems to me, to social selection and one must consider the types of selection occuring within the information flows of a social hierarchy. The issue here is partly the unit of selection and partly whether it is even appropriate to talk about units of selection.
The fact of human cooperation does not fit very well with natural selection based on genes or even individuals as the units of selection but we have gene-culture coevolution and, if social evolution dominates, which I think it does in humans, then human genetic evolution will adapt to serve the needs of social knowledge. That will lead to humans adapting to function not just as competitors but to becoming actors within social evolution and, as such, they can be expected to exhibit cooperative and altruistic traits toward other members of their social group.

I disagree that agreement as to which side of the road to drive on is an example of cooperation. It is the result of a negotiation between opposing drivers who, but for their agreement, would run head on into each other. Each side gets something: the ability to proceed in the direction the desire, and each side gives up something: one half of the road surface.

Maybe it's all semantics, but I don't find that cooperation exists. I find it an illusion. Even soldiers in the same troop/unit negotiate for their respective survival by mutually agreeing to protect each other.

However, I agree that if a particular cultural behavior remains the status quo for a long enough period of time, then as with any other relatively stable environmental stress, the cultural behavior may help shape the genetic future of the organisms who exist within the culture.

This is what humans are currently doing. For example, we culturally believe that a certain class of person makes a better lawyer. So, we screen for that class of person by giving a standardized test that effectively permits only the target class to become lawyers. Then we pay those people, in large part, to run our government/society.

Consequently, we create legislation which represents the sort of thinking which is screened for in those tests, and we can observe the result in the way our laws are enforced and how this effects society.

250 years ago in the USA, our legislators and jurists were much more free thinking. The result was more novel legislation and enforcement, and more freedom for the individual. Today, those legislators and jurists are overwhelmingly cut from nearly identical cloth, and the result is that we can't tell one political party from the other, and further, we are increasingly more narrow minded in our legislating solutions to societal problems -- and ultimately, less free, as individuals.

Self-directed evolution in action, in my view.

cyborg

19th January 2007, 11:07 AM

I did not say that sexual selection is entirely divorced from genotype, I said that selection operates on observable phenotype not on genotype. I also said that the act of observation requires sense organs to acquire the observational data and a brain with which to interpret it. Do you have a problem with that?

Yes.

You are taking a top-down approach. You are starting with ostensibly the most complicated manifestations of sexual selection and declaring the mechanisms behind it fundamental.

Phenotype is an expression of genotype. No, it is not a 100% reliable mapping - it is however the best thing going without actually going to the trouble of producing an offspring. Clearly the expense of that operation makes that method of determining genetic compatibility prohibitive - would you not agree?

Starting with the brain as the requirement of sexual selection is far too high level - as I proposed with the basic selection that plants engage in.

desertyeti

19th January 2007, 01:25 PM

Sexual selection cannot possibly select for genotype, it can only select for observable phenotype. The observation requires data derived from sense organs.

Not true.
Sponges which mate by releasing eggs and sperm at the same time have no brain or sensory organs at all. Yet sexual selection woks based on the volume of reproductive cells being released by the individual. It's unconcious sexual selection, but it's still sexual selection.

John Hewitt

19th January 2007, 05:05 PM

Maybe it's all semantics, but I don't find that cooperation exists. I find it an illusion. Even soldiers in the same troop/unit negotiate for their respective survival by mutually agreeing to protect each other.

Maybe it is all semantics but studies on evolution invest a great deal of time explaining the origins of cooperation and altruism.
People end up cooperating with other members of their group. It is true that we interpret the origin of this cooperation as being founded in competition but still the cooperation does come about. Humans and their direct forebears have been cooperating long enough to have a good proportion of natural cooperaters among their number.

John Hewitt

19th January 2007, 05:20 PM

Yes.

You are taking a top-down approach. You are starting with ostensibly the most complicated manifestations of sexual selection and declaring the mechanisms behind it fundamental.

Phenotype is an expression of genotype. No, it is not a 100% reliable mapping - it is however the best thing going without actually going to the trouble of producing an offspring. Clearly the expense of that operation makes that method of determining genetic compatibility prohibitive - would you not agree?

Starting with the brain as the requirement of sexual selection is far too high level - as I proposed with the basic selection that plants engage in.
The term "top-down" is a programming term that might be contrasted with bottom-up but I think I see what you mean. It is true that the data based approach is not reductionist in the same way that genetic analysis is.
The mechanism of sexual selection I describe is pretty much the standard one and clearly does involve brains and sense organs. Since my approach to evolution centres around data, and these are data processing organs, I am interested in sexual selection and sexuality. The other important mechanism of sexual selection is that which arises from male-male competition, winner takes the female. This also has implications for sense organs and brain and, in social animals, I should think it centres around hierarchy and links to female choice.
As an interesting point, in nature humans seem to form long term sexual pairs or mildly polygamous groups and are not *very* promiscuous. This implies that, in humans, sexual seelction will be two way and that male choice of females would have an impact on female biological traits.

I do not know about sexual selection in plants or sponges so I shall refrain from comment on those topics.

cyborg

19th January 2007, 05:34 PM

I do not know about sexual selection in plants or sponges so I shall refrain from comment on those topics.

Right, that's not the problem. The problem is the implicit generalisations about sex BEYOND humans. We're not the only sexual organism you know.

If you only meant to talk about human sexuality then you should have clarified that.

John Hewitt

20th January 2007, 04:12 AM

Right, that's not the problem. The problem is the implicit generalisations about sex BEYOND humans. We're not the only sexual organism you know.

If you only meant to talk about human sexuality then you should have clarified that.
Well, I do think the evolution of species related to humans is more interesting than that of more distant types. Nonetheless, I would be interested to know about the implications of work from other organisms.

hammegk

21st January 2007, 09:39 AM

In this thread? In which he has repeatedly demonstrated his profound lack of relevant knowledge?

Cynical, yes. Wry, not so much. Accurate, not at all.
Damn, your comments sound like .... "Extremely cruel or hateful content directed toward another user".

Talk is cheap, and if my relevant knowledge can be shown to be contrary to facts, I will adjust my position to include those facts -- unlike most here.

Please cite one or more examples to demonstrate your unsustainable slur.

Yahzi

21st January 2007, 02:09 PM

Well
You didn't answer my question.

Do you find materialism (metaphysical naturalism) adequate to explain the totality of human existance and experience?

It's a yes or no answer. If you say yes, you're a scientist. If you say no, you're a woo. And since you're wooing on about evolution, that makes you a creationist woo.

Just come out and say it - "It's all materialism, all the way down!"

John Hewitt

21st January 2007, 03:15 PM

Apathia

21st January 2007, 03:22 PM

You didn't answer my question.

Do you find materialism (metaphysical naturalism) adequate to explain the totality of human existance and experience?

It's a yes or no answer. If you say yes, you're a scientist. If you say no, you're a woo. And since you're wooing on about evolution, that makes you a creationist woo.

Just come out and say it - "It's all materialism, all the way down!"

Help me!
Some questions:

1. Is Science the metaphysical position of Materialism & Reductionism?
2. Is a "woo" someone who doesn't hold that philosophical position?
3. Is any woo a creationist?
4. Is a creationist someone who believes in evolution but has a somewhat altermate theory on the process?

I'm a naturalist myself. I don't subscribe to any supernatural agencies. But since I'm open to the possibility that Darwin's Theory of Natural Selection may need some tweaking and perhaps some additional natural process could be involved, does this make me a woo and a creationist?
Philosophically speaking, Materialism has a number of different flavors. If mine doesn't accord with yours, would that make me a creationist?

cyborg

21st January 2007, 03:28 PM

I think the invocation of any 'spooky' forces such as 'will design intent' (sorry Hammy) pretty much seals the deal. There's no good reason to assume these concepts can operate at the level of DNA.

Apathia

21st January 2007, 03:32 PM

I think the invocation of any 'spooky' forces such as 'will design intent' (sorry Hammy) pretty much seals the deal. There's no good reason to assume these concepts can operate at the level of DNA.

Well, I have no spooky forces. So I hope I'm clear of the witch hunt.
But I will examine my list of ingredients for anything that not "All Natural."

John Hewitt

21st January 2007, 03:56 PM

Help me!
Some questions:

1. Is Science the metaphysical position of Materialism & Reductionism?
2. Is a "woo" someone who doesn't hold that philosophical position?
3. Is any woo a creationist?
4. Is a creationist someone who believes in evolution but has a somewhat altermate theory on the process?

I'm a naturalist myself. I don't subscribe to any supernatural agencies. But since I'm open to the possibility that Darwin's Theory of Natural Selection may need some tweaking and perhaps some additional natural process could be involved, does this make me a woo and a creationist?
Philosophically speaking, Materialism has a number of different flavors. If mine doesn't accord with yours, would that make me a creationist?

I agree with the content and tone of your comments but I feel you are taking Yahzi's question more seriously than it deserves.

His program could have been rephrased thus :-

Begin
Question "Do you agree with me?"
Get answer
If Answer = yes, print "you are a fine scientist"
If Answer = no, print "you are a creationist - harbinger of beelzebub, henchman of the dark one who rides the twilight hours and impales maidens in their beds."
End

Apathia

21st January 2007, 04:26 PM

Yes, my apologies to Yahzi for my reacting to the frame of his argument. Sometimes I forget my promise to myself that I would participate on this forum as long as I could refrain myself from escalating stuff.

kjkent1

21st January 2007, 04:36 PM

I agree with the content and tone of your comments but I feel you are taking Yahzi's question more seriously than it deserves.

His program could have been rephrased thus :-

Begin
Question "Do you agree with me?"
Get answer
If Answer = yes, print "you are a fine scientist"
If Answer = no, print "you are a creationist - harbinger of beelzebub, henchman of the dark one who rides the twilight hours and impales maidens in their beds."
End

Um...this "impales maidens in their beds" thing is worthy of some consideration. I'm thinkin' that I'd like to be a henchman of the dark one -- where do I sign up?

articulett

21st January 2007, 09:54 PM

I'll take your points on board, but to me, when a bloke answers a straight question with a straight answer, I'll believe him until he's been shown to be lying.

Can you please cut and paste his straight answer to the straight question.

articulett

21st January 2007, 10:14 PM

This is one of the funniest things I've read in a long time. Which part of sexual selection isn't natural? In what way is selecting for various traits in a partner not selecting for the genes that produce these traits?

Yep--he uses lots of words to say nothing at all.

And those who think he's not a creationist--just ask yourself this.

Why are his answers oblique. Has he answered any question simply--or are the one's designed to ferret out his biases worded oddly and not the way "normal people" would say it. He's trying to sound scientific, but it is woo. If you're impressed--congratulations--you are a recipient of the wedge strategy. But can you tell what his theory is or what his actual problems with evolution are? He's saying that human traits (free will, ethics, cheating, group selection, etc.--could not have come about only via genes--)he's proposing a secondary mechanism--can anyone determine what that mechanism is? I am impressed by how many people he has fooled. But the term free will (without any definition) is just not used in science--it's a religious term...and he does that creationist thing, where he confuses random mutation with natural selection which is the opposite of random. It is what allows the ratcheting over eons.

Plus he support Behe who is a man whose theory of irreducible complexity has been disproven repeatedly--and there are even computer programs that show how very easily his "irreducibly complex" features can evolve. Do you think John is aware of this--because he sure doesn't seem to find it significant.

I can't believe that people think he's talking "straight". I'd like one example where he answered the question in a way that made you think he wasn't obfuscating...he was just clear--a simple question with a simple answer. If scientists are rejecting his theory, it's because he's not saying anything. Or if he is--no one has been able to sum it up --it's really fuzzy for a theory as is objection to Dawkins, genes as replicators, memes, Darwin, and evolution. He is finds a lot of things "faulty", and he has accused scientists of being liars and cheaters. But I want to know if anyone other than him knows why? Or is it just one of his obfuscations.

Remember, even smart people like skeptics can be fooled--I just got back from TAM where we could see it again and again as we, ourselves, were fooled. If you think he's not a creationist, just tell us (or me or yourself) what his theory is...in a simple way--similar to the way "random events coupled with natural selection" sum up evolution.

articulett

21st January 2007, 10:23 PM

Sexual selection cannot possibly select for genotype, it can only select for observable phenotype. The observation requires data derived from sense organs.

Wrong and blatantly so. Moreover, it's obfuscating: The hormones we make and respond to in our bodies is genetically encoded--our bodies and brains are built from genes--the insides and the observable outsides. Our brain is affected by multiple chemicals--proteins--encoded for in genes. Without genes--there is no body...no brain...no mental traits and no physical phenotype that can be observed. If you don't think nature can select for mental traits then your understanding of science such as the way we selected dogs from wolves is extremely inadequate--and blindingly so. Long before there were observable data--genes were coding for things going on inside the body and brain--and those things are NOT phenotypic. Shame on you for trying to pass this crap off

And we know quite well, that sexual selection produces phenotypic byproducts. But these phenotypic byproducts evolved because they happened to be associated with the healthier (or more reproductively fit) of each species. It is theorized that men developed language because the better communicators got laid more. What goes on in a brain is not "phenotypic"--the resulting behavior change may be.

articulett

21st January 2007, 10:31 PM

In this thread? In which he has repeatedly demonstrated his profound lack of relevant knowledge?

Cynical, yes. Wry, not so much. Accurate, not at all.

Agreed. I'd like to see one "cut and paste" of hammy being accurate. And just one where John is asked a simple question and answers simply. Just one. Because I think these guys are dishonest creationists pretending that they are smarter than all those "Darwinists" who practice "scientism" and their "evolutarian" theories.

Or show me one non creationist who answers the question "are you a creationist" obliquely. My standards for evidence are really low. Just one cut and paste for any of the above.

articulett

21st January 2007, 10:35 PM

Seems reasonable to me.

Another question: do you believe that certain higher level functions exhibited by humans, such as ethics, morals, altruism, etc., could not possibly have evolved?

Can you sum up what you asked and what he said? He answered the question oddly. Why? And you think he said that he doesn't let his beliefs factor in his science--but that is not what he said. He is bs-ing you. Why? Why are is answers so unclear? You seem fine with answers that aren't answers at all.

articulett

21st January 2007, 11:03 PM

The evolutionary question is not whether such things evolved it is how they evolved. Bioepistemic evolution argues that the best way of understanding the origin of such traits is to to see humans as actors (subsystems, if you will) within the evolving system of culture, rather than simply as evolving systems in their own right. Actors within a system cooperate rather than compete.

You also believe that humans have something that couldn't evolve via genes, correct? (just say yes or no). Your theory calls this thing "free will" correct?
And this free will is something animals don't have, correct? (simple questions, John). So define free will: (a nice simple scientific explanation, please). And you think your theory is better because it explains social competition; whereas "memes aren't useful for explaining social systems--is this correct?

Here is a simple yes or no question: Do you believe that social living, altruistic type behavior (such as that observed in the hippo), reciprocity, in group amity/ outgroup enmity, etc. can evolve from traits selected on the genetic level-- whether it's a behive or a marauding band of baboons or some other animal?

Are you saying that genes can account for what we observe in animals but not in people? (yes or no) Or is your theory that there must be something other than genes or natural selection can account for what we observe?

Now folks--watch how he ducks and weaves or avoids the question completely. Or he's say some other tangential thing so distract. You'll think he said something--but it will be less valuable than a simple yes or no (which is all I'm asking for. Pay attention to his answers...or his failure to address them. Ask yourself why. I need to teach my skeptic friends to do this--because I have a slew of students who are depending on me to do this for them. Tell me the evidence you need to prove it to yourself, and I will find it. John Hewitt is a creationist. If the evidence I have presented doesn't convince you--ask yourself--what will? And tell me. And tell me what the hell is theory is if you think he's making sense. And what his objection to evolution is.

Don't let him fool you just because he's smart and he's nice. He's still deceiving you...and, probably, himself as well. His beliefs keep him from understanding evolution and finding fault with strawmen and "lying scientists".

Ask yourself--if I was being paid a lot of money by the discovery institute to make people doubt evolution and to get them to think there was a viable alternative theory involving an "intelligent designer"--what would be the way to do so? I suggest to you it's to have men like John sow seeds of doubt. I wish you all could have been at TAM--so you could see again and again how you can see how obfuscations and omissions are used to muck up understanding rather than clarify. It's all the creationists have going for them--this tactic is one that has evolved directly from creationists learning from mistakes on the battlefield...it's creationist crap wrapped all pretty in wrapping paper made from the periodic table so that it looks like science.

I will be glad to back up any of my claims with evidence--just be specific about what you ask for. And if anyone has problems with me or my technique or if they think I'm "like a homeopath" or (insert epithet)--it would be illuminating for all of us if they could cut and paste the direct quotes I make to go with your allegations. Because, Atheist, you have made multiple claims that you have not provided support for. It makes me think you have biases turning what I say into messages I did not intend--messages only "heard" by you. How would you expect someone to react if they had much experience with a certain kind of dishonesty, but people demonized them every time they tried to keep others from being duped?

articulett

21st January 2007, 11:08 PM

Right, that's not the problem. The problem is the implicit generalisations about sex BEYOND humans. We're not the only sexual organism you know.

If you only meant to talk about human sexuality then you should have clarified that.

I'm so glad you dropped by this thread! You'll see, he's like Von Neumann--only he has a whole different obfuscation... He's smart--but says nothing-- You may be the only person on this forum that can see the maddening similarities...If you know enough science, math, etc.--you can jerk people around for a long time without saying anything at all--because creationists really have no actual evidence in their favor. They take pot shots at evolution and pretend to have a theory but no evidence for it--ever. But they always drag you along pretending it's forthcoming and presume it's a Darwinist conspiracy when you point out they are just plain wrong. We can't whip up reality according to what they've come to believe about humanity's "intelligent designer"...

articulett

21st January 2007, 11:21 PM

Damn, your comments sound like .... "Extremely cruel or hateful content directed toward another user".

Talk is cheap, and if my relevant knowledge can be shown to be contrary to facts, I will adjust my position to include those facts -- unlike most here.

Please cite one or more examples to demonstrate your unsustainable slur.

I don't think anyone needs to cite any example for "slurring" you--almost all your posts are either devoid of content or ad homs--you always start it--it's all you do for the most part. I don't think anyone is going to be getting in any trouble for returning the volley. As you may have observed--you do not have a lot of people who see things in the epistomologictheontologicyally way you do. People don't even know what you think...or if you think...and some wonder if you can pass the Turing test-

However, if you are a machine trying to evolve turing passing traits via forum posting and feedback--your natural selection feedback mechanism is broken, because no evolution in higher function or logic has occurred. It's hard for the first replicators to get a toehold--but once systems get started--information tends to multiply exponentially. You barely have a toehold-

articulett

21st January 2007, 11:35 PM

Anyone tried to do that yet?

You have got to be kidding! Do you know what PCR is?

And how would John prove his theory? Having a cell copy itself with it's DNA extracted? Oh that's right...his theory hasn't been actually stated...no one but you seems to know what it is--and you aren't a very good translator--moreover, your ignorance doesn't bode well for John. So, you think it's perfectly fine to mention "free will" in scientific papers (without even a definition mind you)--and that he's not letting god get in the way of his thinking. Free will is the basis of religious teaching (life is a test, original sin, god kills kid who is really him to atone for sin, yada, yada, yada). So what is this free will thing you and he seem so sure of. Do gay people choose to be homosexuals? Do heterosexuals choose who and what they are attracted to? Certainly will is highly tied into brain function, hormones, preferences, genetic leanings, opportunities, temptations, experience, culture, learning, impulse, etc. etc. How can you see the phrase "free will" on a supposedly scientific paper and not understand the obvious? Have you ever seen the term applied like that on any scientific paper? (and believe me, you can bet John will find a different word to obfuscate the same idea very soon.) He assumes humans have something that can't be explained by genetics--he assumes that it's obvious that this is so--this special thing is "free will"--he also mentions ethics and group cooperation and the like--why? He thinks all the science in this area is semantic--because he hasn't read it. We have some stellar examples of how genes can lead to cooperation, seemingly altruistic behavior, and group selection. It's the basis of game theory...heard of it? He can't see it just like he can't "compute" memes because it interferes with his beliefs.

articulett

21st January 2007, 11:59 PM

Well, I have no spooky forces. So I hope I'm clear of the witch hunt.
But I will examine my list of ingredients for anything that not "All Natural."

Woos usually have a belief they are trying to protect they do this by having a complete lack of understanding or curiosity--no matter how carefully something is explained or how much evidence there is. Then they obfuscate and change terms and avoid questions and attack those who attack their ideas....because they are personally invested in those ideas. They preach here, I think, to solidify their faith--but they get cantankerous should anyone suggest they might be deceiving themselves or when asked for evidence.

But creationist woo is particularly deceptive--they pretend to be all sciency--they pretend to have valid arguments about evolution...but they are hard to pin down--and when you pin them down and address their arguments (see Behe and the Dover trial)--no amount of evidence ever is good enough. They pretend to want the facts--but they will only accept facts that fit with their view. Unlike science, they don't actually offer testable theories--testing involves measurement...how would one measure something like free will? They have no facts--but they pretend the gaps in evolution or the problems they see (but aren't there) somehow discredit the theory which is as accepted in biology as everything about atomic theory (atoms, periodic chart, etc.) is in Chemistry. We don't know everything--but we know enough to know that evolution is a fact. John avoids everything having to do with religious claims--even radiometric dating and speciation--he is very non specific about why he as such enmity towards certain people or ideas--but they just so happen to be the very same people creationists seem to hate without ever even reading. They find problems with evolution that no biologist or other scientist seems to see-- but they have no problems with their own hugely flaw and much less supported alternative theory.

It's really sick. They've been slapped for being deceptive and religious--so they are trying to sound sciency--because a lot of people don't have a good understanding of what science is. People read their crap and presume that there is an actual question as to whether evolution explains life as we know it on this earth. There isn't. It just so happens that evolution makes god a little bit irrelevant. And god is a powerful meme. It's hard not to believe the invisible overlord is watching over you if you've seeped yourself in it for too long. So their new strategy is this wedge technique. It involves making Americans stupider than the rest of the developed world by making them think scientists are at odds with evolution--and that scientists are unscrupulous cheaters and liars. And then, they use that doubt to insert some unprovable assumption and that assumption just so happens to involve an intelligent designer that humans are too stupid to understand--in fact, it just so happens, that it would be "arrogant" to question this invisible, untestable, immeasurable, unimaginably complex designer. Besides, one would have to ask such an entity why he could have such powers and make us wait eons to find out the very basics of science such as germ theory. Any intelligent designer worth his salt should be distinguishable from voices in one's head. This one isn't. So obfuscation with truthiness and sciency terminology is the next best thing. Even loveable, smart, trustworthy seeming people can be lying to themselves and lying to others.

If you think free will is a simplistic term that one shouldn't or wouldn't use in science (especially without a definition), then you probably are fairly woo free. But we can all be fooled by woos in areas where we lack expertise. Creationists are particularly vile woo to me--because people trust them...they think these people speak for god...they lie about wanting scientific understanding. They want to muddy science and insert their vapid claims. Kleinman was more obvious...as was Behe. Buffoonishly so. The smarter ones can string you along a lot longer. I've just fallen for this so much that it feels like yet another spoon bender that everyone else assures Randi is "for real". Same crap different wrapping.

Creationist waste the time of intelligent well-intentioned people who actually think they are trying to understand something--they spend detailed time explaining, but creationists can't "hear" and will never change and will only use their discussion with scientists to pretend to themselves or others that scientists take them seriously. I won't be wasting my time on John Hewitt, and I want to warn others of what he is. After that--everyone can play the game with him as long as they want.

Dr Adequate

22nd January 2007, 12:03 AM

Agreed. I'd like to see one "cut and paste" of hammy being accurate.
Then want must be your master.

This is the same guy who said that the evolution of land animals to whales was "microevolution".

:dl:

John Hewitt is kind of interesting, and if kleinman has finished making a fool of himself, I might post more regularly on this thread.

The Atheist

22nd January 2007, 01:20 AM

You have got to be kidding! Do you know what PCR is? Tiny little fragments are not replicating molecules.

And how would John prove his theory? Having a cell copy itself with it's DNA extracted? Oh that's right...his theory hasn't been actually stated...no one but you seems to know what it is--and you aren't a very good translator--moreover, your ignorance doesn't bode well for John.

This is funny!

Whatever I do has no bearing on John whatsoever. Your thinking it might do is just showing up your pre-decided prejudice. That is a truly ridiculous thing to say. I get the impression from your posts of a crusader against ignorance, slaying creationists right and left, then wiping your bloody sword on your kilt.

Your fervour is religious.

So, you think it's perfectly fine to mention "free will" in scientific papers (without even a definition mind you)--and that he's not letting god get in the way of his thinking. Free will is the basis of religious teaching (life is a test, original sin, god kills kid who is really him to atone for sin, yada, yada, yada). So what is this free will thing you and he seem so sure of. See, again you're giving yourself away.

Why am I so sure of it? All I've done so far is state that I think you (and others) are obnoxiously demanding that he answer questions which he's already answered. I also allowed that I found his work interesting. Why are you all of a sudden deciding that I'm so sure about it? Are you psychic?
Do gay people choose to be homosexuals? Nature or nurture, you tell me. Or have you just discovered he gay gene?
Do heterosexuals choose who and what they are attracted to? As far as I can tell, they do indeed. I think homosexuals do, too. They might not choose the gender, but they definitely choose their partners. You keep calling John as a creationist. Your zeal as a determinist is as notable.

Interesting sideline - why haven't you found the gay gene yet?
We have some stellar examples of how genes can lead to cooperation, seemingly altruistic behavior, and group selection. It's the basis of game theory...heard of it? He can't see it just like he can't "compute" memes because it interferes with his beliefs.And just like the hippo and the gazelle, you're cherry-picking to suit your agenda.

You may well be right, but at the moment, your righteousness level is obscuring your own message.

And memes as an example? Dorkinsian rubbish. He should be out selling Amway on the back of it. An invention to back a philosophy; ideas grow and evolve. Genius.

John Hewitt

22nd January 2007, 02:50 AM

Wrong and blatantly so. Moreover, it's obfuscating: The hormones we make and respond to in our bodies is genetically encoded--our bodies and brains are built from genes--the insides and the observable outsides. Our brain is affected by multiple chemicals--proteins--encoded for in genes. Without genes--there is no body...no brain...no mental traits and no physical phenotype that can be observed. If you don't think nature can select for mental traits then your understanding of science such as the way we selected dogs from wolves is extremely inadequate--and blindingly so. Long before there were observable data--genes were coding for things going on inside the body and brain--and those things are NOT phenotypic. Shame on you for trying to pass this crap off

And we know quite well, that sexual selection produces phenotypic byproducts. But these phenotypic byproducts evolved because they happened to be associated with the healthier (or more reproductively fit) of each species. It is theorized that men developed language because the better communicators got laid more. What goes on in a brain is not "phenotypic"--the resulting behavior change may be.

Articulett, thank you for posting in response to me but I do find it difficult to reply to you. You have ten postings here and, to some extent or other, I would disagree with most of them, so I shall just concentrate on sexual selection.

The description I give of sexual selection is, in essence that given by Darwin in the Descent of Man, which included "selection by means of sex" (or some such) in the subtitle. If you are unsure of the difference between natural selection and sexual selection, you might consider looking at "The Origin of Species" and "The Descent of Man" and comparing the selective mechanisms that Darwin was proposing. Sexual selection was further mentioned by Fisher and has been extensively analysed by many people since.

In sexual selection, the selection of a sexual partner cannot possibly be made on the basis of genotype because genotype is not an observable, except to scientists. Only aspects of phenotype are observable and, for many species, that phenotype being observed may seem quite arbitrary, such as the length of the peacock's tail. Nonetheless, peahen's do use tail length as one of their decision criteria to determine mating.

Sexual selection seems to offer a faster mechanism of evolutionary change than does natural selection but it is also thought capable of causing runaway evolutionary processes. Hence one has the sight of peacock's carrying around a tail that certainly does not enhance that individual's immediate life chance – it is the mere chance of female sexual preference that has led to the male's tail. Hence, it seems likely that sexual selection can lead to rapid extinction as well as to rapid evolutionary adaptation.

Now, as you know, I am interested in describing evolution in terms of data, rather than in terms of genes. You are free to think that a silly thing to do, but I am free to disagree with you. I think it is a sensible thing to do and the point I am making about sexual selection is that this form of selection involves data that originate in sensory data not just in DNA. Therefore, that this sensory data must be subject to data processes that will gather, interpret and make selections based on sensory data. Thus sexual selection on a peacock does not drive merely the length of the peacock's tail, it also drives the peahen's ability to gather this sensory data, to interpret that data into information about tail lengths and the identity of prospective suitors, to store that information so as to enable comparison and to make a selection between the observed individual suitors. In other words, sexual selection, as a mechanism, will drive the development of sense organs and brains. This is why Darwin thought sexual selection to be relevant to the evolution of the brain. I think he was right, though his mechanism applies to a great many species, not just to humans. With humans, I think one has to add other factors, particularly social factors.

Nonetheless, sexual selection seems an important factor in human evolution – it is not woo, and it does involve data that is not on DNA.

cyborg

22nd January 2007, 09:13 AM

You may be the only person on this forum that can see the maddening similarities...

In the end it's always about a big non-sequitur.

I don't have any anthrocentric tendencies. You can't persuade me by appeals to humanity.

PixyMisa

22nd January 2007, 09:31 AM

You're right, it is. The whole post is a mess - haste makes waste.

Oh no, I'm not referring to your posts, which are always clear. I'm referring to John Hewitt's writing style. Dreadful. Simultaneously tediously didactic and pointlessly oblique.

Have you read through the whole thing? Might be worth your while.
see above.

I skimmed through it. I can't see anything worthwhile; perhaps you can point out something?

You've missed the point here. Of course it's falsifiable.

The scary part comes in it being falsifiable by someone else's positive result. Note the negativity about John's claims! You're dying for him to fall over, even before you understand what he's saying. Falsify his theory then. I guess the simple way to do that is to get a gene to replicate outside the cell. That's all it takes to blow him right out of the water.

Anyone tried to do that yet?

Huh? This is a standard lab technique that is used all over the world every day. I don't see how that falsifies John's claims, because I don't see a coherent hypothesis, but if you believe that is sufficient, then his claims are false.

PixyMisa

22nd January 2007, 09:35 AM

Tiny little fragments are not replicating molecules.

You asked about genes being replicated outside the cell. This is done all the time.

If you have a different question, ask your question.

kleinman

22nd January 2007, 09:45 AM

Sorry I haven’t been able to give any attention to the thread for the past week but I’ll try to pick up where I left off. This post start with comments made on page 40.
You are splitting hairs using the word “potential”. What do you think the probability is that the number of spurious bindings decrease or stay the same as the genome size increases?I suspect it increases, but in a quite complex manner. We see creatures with ages of 6000 generations.
Since your theory of evolution is dependent on a selection process, it is important to unravel the complexity of this issue. I don’t believe either Dr Schneider’s or Unnamed’s selection process represents any real selection process. However, Dr Schneider’s selection process gives greater weight to mistakes in the non-binding site region than does Unnamed’s selection process causing the generations for convergence to increase with increasing genome lengths.
Really? Does your concept of Rcapacity depend on mutation rate and population when using Dr Schneider’s selection method? Any selection method that diminishes the effects of harmful mutations in the non-binding site region will converge more quickly. If you completely ignore harmful mutations in the non-binding region, you uncouple the evolution of the binding sites in the binding site region from the length of the genome. There just isn’t any basis in reality for such a selection method.In the real world, a spurious binding in pure junk DNA would be harmless. There appears to be a basis for selection of weak and strong bindings. You can't simply dismiss it, although I agree that we don't know how the various Ev models relate to reality.
I hear the terminology “pure junk DNA” and am not prepared to accept this description of the portion of the genome that is not obviously coding polypeptides as being junk. The problem you need to address mathematically is formulating a realistic selection process. I don’t believe you can do this for evolving a gene de novo.
The valuation of a match binding site does not contribute to the sort value but a close to threshold but failed match in the binding site region will have a large value of valuation[p].And a small distance from the threshold, which is what contributes to the sort value.
Too bad this doesn’t represent reality.
If gamma=16 and you start with 16 mistakes in the binding site region, you get 16*valuation[p] in the binding site region that outweighs the small number of mistakes in the non-binding site region.It is not the valuation that is added to the sort value, but the distance between the valuation and the threshold. These distances will start out large and then diminish as the binding site valuations creep toward the threshold. They will certainly swamp a single spurious binding, but so does the current selection method. They will not swamp a swarm of spurious bindings, such as might arise from a mutation in the gene.

But I agree with you that Unnamed's selection method is weighing missing bindings more heavily than spurious bindings, as does my experiments with the missing binding mistake points set to 10. See my post #1594. This speeds up evolution by favoring a creature with, say, 2 missing bindings and 5 spurious bindings over a creature with 3 missing bindings and 0 spurious bindings. Do you think something like that can't occur in nature?
I believe that natural selection will select out a creature with an almost perfect genome if it has a single fatal mutation. Both Dr Schneider and Unnamed’s selection process ignore this real observable phenomena. On the other hand, it is rare that a single mutation will give a real survival benefit. I think antibiotic resistance in bacteria and the sickle cell mutation of hemoglobin are examples of this but neither represent macroevolutionary events.
What is the mutation rate assigned to the weight matrix? How does the threshold evolve?The mutation rate is constant across the entire chromosome. Mutations are randomly applied to the entire chromsome.
Now it make sense that when a mutation occurs to the binding protein sequence (weight matrix) that there would be a large jump in the number of mistakes.

This scheme does allow you to argue that you are not pre-specifying your evolutionary process but how would could you apply this concept to the de novo evolution of a gene?
All this discussion on the selection process is simply an academic exercise since there is no selection process as formulated by Unnamed and for that matter Dr Schneider’s selection method that are seen in reality.Then you have lost your mathematical argument against evolution.
You wish! You are already aware that you need a selection process of some type to explain the theory of evolution (and abiogenesis as well). Without a selection process, the probability of the formation of the complex molecules of life becomes infinitesimally small. Dr Schneider’s selection process (as unrealistic as it is) is worth considering if only to show how slow the process of point mutation and selection is. This discussion we are going through is more accurately defining the fatal flaw in your theory, that is a lack of a selection process that would evolve a gene de novo.
Then you have lost your mathematical argument against evolution.Bish, bosh, job done. Now for stage two : the frantic row-back. I don't see this guy as a quitter. He has far too high an opinion of himself.
The mistake you kids are making in this discussion is that you think a clever response wins the day. I hope you are preparing yourselves for a reality check. There is no selection process that evolves a gene de novo. You evolutionarians have extrapolated mutation and natural selection far beyond what this process is capable of doing. This mathematical exercise with ev has shown how unrealistic your thinking has become. If anyone is doing a frantic row-back, it is you evolutionarians who are looking for a selection process that somehow can rescue your theory.

Yahzi

22nd January 2007, 09:57 AM

Dunno! Do you think it has been so far?
Remember the discussion we had about how not answering direct questions is evidence of evasion?

How much more evasive can you get?

After this, why is there even a shred of doubt?

PixyMisa

22nd January 2007, 10:06 AM

Damn, your comments sound like .... "Extremely cruel or hateful content directed toward another user".

Oh, no, not at all. If I ever write something "extremely cruel or hateful", you'll know.

Talk is cheap, and if my relevant knowledge can be shown to be contrary to factsWhat relevant knowledge?

I will adjust my position to include those factsWhy start now?

Please cite one or more examples to demonstrate your unsustainable slur.I have made no "unsustainable slur", but nonetheless:

Nah, I think something in the lab a bit more malleable than mammals might be a place to start ... oh, iirc, you evolutionarians have been trying in the labs since the early 50's?

Demonstrating your ignorance of or unwillingness to admit the fact that speciation has been observed on a number of occasions.

What you have done is move the goalposts on wheels to define "speciation" and then pretend you've demonstrated how speciation occurs -- there are cats & dogs, species, and we all know basically what I mean by species.

Demonstrating your complete incomprehension of taxonomy.

A speciation event has not been demonstarted in labs, models, or nature.

A simple falsehood.

And please spare us a re-gurgitation of the pap that demonstrates -- in the lab and in nature -- the bacteria that remain bacteria, birds that remain birds, plants that remain the same plant, ring species that remain the same species.

Again demonstrating your total lack of understanding of taxonomy.

Remain, that is, until the appropriate and needed re-definition of species has been provided to cover each specific case.

Now that, Hammy, is what an unsustainable slur looks like.

Yahzi

22nd January 2007, 10:12 AM

Help me!
I shall endeavor too.

At the outset let me explain that experience is the best teacher. My karate instructor can place his right hand on your shoulder, and you cannot hit him with your right hand. Because he can tell, just by the motion in your left shoulder, where your right hand is going. He can tell this because he has years of experience. The rest of us have to wait until the facts become more evident. But that's our limitation, not his.

1. Is Science the metaphysical position of Materialism & Reductionism?
Yes. Science posits that only the material, observable world is necessary or sufficient for explaining the material, observable world. Science is defined by reductionism, insomuch as the process of understanding is virtually defined as reducing phenomona is reduced to its parts.

Were you actually unaware of this?

2. Is a "woo" someone who doesn't hold that philosophical position?
Yes. A woo is someone who believes in the supernatural; i.e., does not believe that the material, observable world can be explained by the material and the observable.

What else would a "woo" be? Do you think there is a third position between "naturalism" and "non-naturalism?"

3. Is any woo a creationist?
As I made it quite clear in my posts, which I can see you did not bother to actually read, a woo who goes on about how evolutionary scientists are liars is almost certainly a creationist.

Woos are defined by the exceptions they champion. Hewitt is championing an exception evolution. Ergo...

4. Is a creationist someone who believes in evolution but has a somewhat altermate theory on the process?
If his alternate theory requires supernatural intervention, then yes.

My question was designed to determine whether Hewitt's theories require supernatural intervention. As you can see, he chose to answer the question with evasion.

I'm a naturalist myself. I don't subscribe to any supernatural agencies. But since I'm open to the possibility that Darwin's Theory of Natural Selection may need some tweaking and perhaps some additional natural process could be involved, does this make me a woo and a creationist?
How is the above paragraph incompatible with a "Yes" answer to my question? Indeed, you go out of your way to repeat the caveat of "natural process." Which was the only thing my question was trying to establish: Are natural processes sufficient?

Philosophically speaking, Materialism has a number of different flavors. If mine doesn't accord with yours, would that make me a creationist?
Do you consider the wholesale rejection of materialism as just a different "flavor?" If not, perhaps you could point to any text I wrote that would justify the above comment.

Are you unable to read the comments I actually type, or are you just addicted to strawmen arguments?

hammegk

22nd January 2007, 10:17 AM

Oh, no, not at all. If I ever write something "extremely cruel or hateful", you'll know.
The only question is "Will D'Ratpack understand it?".

On your diatribe: Do we need another go-around on the moving goalposts evolutionarians require as they wave their arms touting their pseudo-science?

John Hewitt

22nd January 2007, 10:17 AM

You asked about genes being replicated outside the cell. This is done all the time.

If you have a different question, ask your question.

I think perhaps you should trying to distinguish between "replicating molecules," in the sense of molecules that replicate themselves, and "molecules being replicated" in the sense of experimenters replicating pieces of RNA or DNA during recombinant DNA studies. The latter molecules are not replicators in the evolutionary sense. The former are unknown - unless you could cite an example. The Atheist has this point quite clear.

PixyMisa

22nd January 2007, 10:19 AM

Yahzi

22nd January 2007, 10:19 AM

I agree with the content and tone of your comments but I feel you are taking Yahzi's question more seriously than it deserves.
The creation of strawmen is necesary for people who have no logical position to advance.

Question "Do you agree with me?"
Me? Am I the only metaphysical naturalist in the world? Am I the only person who thinks that metaphysical naturalism is necessary to the conduct of science?

Why did you find it necessary to so badly mischaracterize my argument? Oh, that's right... because otherwise you cannot respond to it.

But kudos to you - not only have you avoided answering a simple question, you managed to fool a few other people. In pure honesty, however, I must admit that I suspect that victory to be product of their own carelessness and argumentativeness, not your cleverness.

Now, perhaps, you would like to answer the question as your erstwhile supporter paraphrased it:

Are natural processes sufficient?

Yahzi

22nd January 2007, 10:23 AM

so something that looks and acts like materialism is just as good as the real thing.
I have a firm principle: if a thing is indistinguishable from another thing, in all ways, shapes, and manners, save only for a few philosophical blatherings that are themselves indistinguishable from fiction, then I say those two things are the same.

Or, to put it another way, "If it looks like a duck, and it swims like a duck, and it quacks like a duck, and it's indistinguishable from a duck on the molecular level... it is a duck."

However, your point of procedure is well-placed: given the context of this discussion, I should have made my contentious and controversial prejudices clear.

:D

PixyMisa

22nd January 2007, 10:26 AM

On your diatribe: Do we need another go-around on the moving goalposts evolutionarians require as they wave their arms touting their pseudo-science?

Your assertions on the supposed "moving goalposts" regarding speciation are entirely false, and are based on your lack of knowledge of biology.

Once again: There are several definitions of species that are accepted as scientifically valid and useful. For each and every one of those definitions, we have directly observed speciation.

This is the opposite of moving the goalposts. Whichever of the definitions you choose to examine, speciation has been observed.

kjkent1

22nd January 2007, 10:29 AM

PixyMisa

22nd January 2007, 10:29 AM

I have a firm principle: if a thing is indistinguishable from another thing, in all ways, shapes, and manners, save only for a few philosophical blatherings that are themselves indistinguishable from fiction, then I say those two things are the same.

Or, to put it another way, "If it looks like a duck, and it swims like a duck, and it quacks like a duck, and it's indistinguishable from a duck on the molecular level... it is a duck."

And very tasty. ;)

However, your point of procedure is well-placed: given the context of this discussion, I should have made my contentious and controversial prejudices clear.

:DNo worries. :) When we wander into metaphysics, materialism and naturalism are distinct, and we need to be clear on that, but for science, for the real world, for anything useful, it doesn't make a damn bit of difference.

I think that may have been part of Hyparxis' point, since he clearly says he's a naturalist, which is why I butted in.

RecoveringYuppy

22nd January 2007, 10:32 AM

I think perhaps you should trying to distinguish between "replicating molecules," in the sense of molecules that replicate themselves, and "molecules being replicated" in the sense of experimenters replicating pieces of RNA or DNA during recombinant DNA studies. The latter molecules are not replicators in the evolutionary sense. The former are unknown - unless you could cite an example. The Atheist has this point quite clear.
My firewall at work seems to be blocking every link I don't already have bookmarked today, but are you familiar with Julius Rebek? He's credited with finding replicating molecules. I'll post some links later if you need them.

John Hewitt

22nd January 2007, 10:37 AM

Yes. Science posits that only the material, observable world is necessary or sufficient for explaining the material, observable world. Science is defined by reductionism, insomuch as the process of understanding is virtually defined as reducing phenomona is reduced to its parts.

Were you actually unaware of this?

Does it? Is it? If Hyparxis was unaware of this, he is not alone.

Yes. A woo is someone who believes in the supernatural; i.e., does not believe that the material, observable world can be explained by the material and the observable.

What else would a "woo" be? Do you think there is a third position between "naturalism" and "non-naturalism?"How about "dunno?" Would that be a middle ground?

As I made it quite clear in my posts, which I can see you did not bother to actually read, a woo who goes on about how evolutionary scientists are liars is almost certainly a creationist.

Woos are defined by the exceptions they champion. Hewitt is championing an exception evolution. Ergo...Am I? Which exception is that?

If his alternate theory requires supernatural intervention, then yes.

My question was designed to determine whether Hewitt's theories require supernatural intervention. As you can see, he chose to answer the question with evasion.

How is the above paragraph incompatible with a "Yes" answer to my question? Indeed, you go out of your way to repeat the caveat of "natural process." Which was the only thing my question was trying to establish: Are natural processes sufficient?
I have the impression that you are asking me to recite and conform to your personal dogma. If you feel that my work entails or implies supernatural intervention, then please point out how it does so.

hammegk

22nd January 2007, 10:40 AM

Your assertions on the supposed "moving goalposts" regarding speciation are entirely false, and are based on your lack of knowledge of biology.
Your opinion is noted, and filed appropriately.

Once again: There are several definitions of species that are accepted as scientifically valid and useful. For each and every one of those definitions, we have directly observed speciation.
Yeah, that's my point. The definitions are post-hoc and subject to infinite revision to keep the just-so-story on the tracks.

This is the opposite of moving the goalposts. Whichever of the definitions you choose to examine, speciation has been observed.
Your opinion is noted, and filed appropriately.

Are you ready to jump on the bandwagon real evolutionarians are pushing? It's easy, just type, and mean: "I, PixyMisa am 100% certain that god does not exist.". And no, you don't need my definition. Use any you prefer.

I'm 100% certain Thought Exists. :)

RecoveringYuppy

22nd January 2007, 10:47 AM

So what definition of species do you accept? (Why do I expect I'm not the first to ask you this?)

The Atheist

22nd January 2007, 11:02 AM

You asked about genes being replicated outside the cell. This is done all the time.

If you have a different question, ask your question.
Sorry, again, haste making waste - I meant DNA.

You've also mistaken what I said about John's falsifiability. He's picked a task where if current theory is right, he is going to be shown to be wrong and badly so. IDists have the escape clause of "god made it so". John hasn't given himself that out.

The Atheist

22nd January 2007, 11:42 AM

I'm 100% certain Thought Exists. :)
I think you're right.

articulett

22nd January 2007, 10:15 PM

Remember the discussion we had about how not answering direct questions is evidence of evasion?

How much more evasive can you get?

After this, why is there even a shred of doubt?

There's none here. :)

But I'm putting "Atheist" on my "does not compute" list. It's nice to know which people to put on ignore.

articulett

22nd January 2007, 10:36 PM

Then want must be your master.

This is the same guy who said that the evolution of land animals to whales was "microevolution".

:dl:

John Hewitt is kind of interesting, and if kleinman has finished making a fool of himself, I might post more regularly on this thread.

Please do! Even if Kleinman is not done (those creationists are never done with making fools of themselves are they?)

I wished I could you could have been at TAM! And I'd love to watch you parry with Hewitt--

articulett

22nd January 2007, 10:40 PM

In the end it's always about a big non-sequitur.

I don't have any anthrocentric tendencies. You can't persuade me by appeals to humanity.

Yep--the more they say, the less you understand. Questions are never answered, claims are never supported, and you end up in endless tangential conversational non-sequitars...

articulett

22nd January 2007, 11:21 PM

All I've done so far is state that I think you (and others) are obnoxiously demanding that he answer questions which he's already answered. I

Great--you've stated this several times now. So you'll be cutting and pasting at least one instance where I and/or others obnoxiously demanded an answer from John Hewitt--along with John's previously supplied answer? Then we can all see see what only you seem to see so far. If you don't or can't do so, and don't apologize, then we can conclude you are just a loud mouthed Bozo, right?

Plus you've asserted that he said he wasn't a creationist a couple of times too. Can you cut and paste where he said this? Or are you going to post more non-sequitars about how obnoxious the people who ask questions are.

Are you noticing that no-one other than you seems to be following you?
Back up your claims with easily cut and pasted evidence, please. Or enjoy being on ignore. I suspect you are coming across as a lot more offensive than I am, and I'd be glad to cut and paste should anyone be interested in the evidence.

It seems the creationists can't even follow each others' arguments; why don't you engage John and illustrate how one should go about discussing these things, so that we can all learn from your expertise.

kjkent1

23rd January 2007, 12:41 AM

Can you sum up what you asked and what he said? He answered the question oddly. Why? And you think he said that he doesn't let his beliefs factor in his science--but that is not what he said. He is bs-ing you. Why? Why are is answers so unclear? You seem fine with answers that aren't answers at all.

This is not a court of law. I cannot force a witness to answer a direct question via a contempt motion. So, I must accept the answers I am given and then ask more questions until, hopefully, only one answer remains, i.e., the one which I originally sought by direct interrogation.

There is nothing to be gained, in my view, by creating an atmosphere which drives out all dissent. John Hewitt may be a fundamentalist Bible thumper, but what of it? I'm still interested in his views.

Unless a poster uses ad hominem as a means of avoiding answers, I'm not going to get annoyed.

The Atheist

23rd January 2007, 02:21 AM

Great--you've stated this several times now. So you'll be cutting and pasting at least one instance where I and/or others obnoxiously demanded an answer from John Hewitt--
Just to give you an idea of the magnitude of thing I'm talking about, this is culled from just three of your posts on the subject. The two long ones are nothing but a rhetorical attack on the strawman of John's god.

You read these and tell me who has the problem:

"And therefore my God is True" by John Hewitt.

Well, this thread is entitled "annoying creationists"--annoying creationists tend to have something in common. They're not really like the YEC's who are readily laughed off...They, in fact, seem rather intelligent and grasp some of the basics of science, logic, and math--except when it somehow conflicts with their god belief. If it conflicts with their god belief, their logic stops at the door and they start playing crazy semantic games similar rather the way people squeeze supposed insightful platitudes and "higher truths" from primitive and barbaric texts clearly written by human without a dash of anything divine or even prescient. These people often believe themselve to be compassionate and open minded without having a clue as to how close minded and didactic they sound when it comes to their pet theories. They are weirdly brainwashed because they believe that some invisible guy killed his kid (who was really him) for some sin long ago that no-one is really quite certain about--and they've been told that this happened for them-because someone loved them so much. They've been told that it's arrogant to even question the story. And they are so easy to spot after a while. They just have very rigid standards of "proof" for a very narrow area (and no proof will ever be enough) and absolutely no need for proof when it comes to believing in the divinity of some primitive texts authors and meanings and interpretations.

What can I say--when you've had it inculcated in you from childhood that you get to live happily ever after for believing insane things, you sometimes grow into an annoying creationist. To me, you guys always argue the same pet point over and over--the one that somehow convinced you--or the theory that keeps your personal version of what god is alive.

All your arguments boil down to "my god is real" to me. And, I think you'd understand it if someone was a Scientologist or Muslim extremists and all their posts seemed to be a means of supporting whatever it is they had come to believe--you'd see how futile conversation was--you'd feel sort of bad that a bright person was so brainwashed by their beliefs that they were missing some really cool facts. You'd marvel at how they couldn't seem to see in themselves that which is so transparent to others. You'd roll your eyes at the way they hold themselves up to be objective arbitors of truth that was so clearly confirmation bias for the "truth" they wanted. It's sort of like if you wanted to show an Amish kid all the cool technology and stuff they could do with the computer--but you couldn't...and it all boils down to "because I'm Amish"...Nobody wants to be an evil temptress (temptor) scaring someone into thinking the devil is trying to get them to bite from the tree of knowledge--but that's exactly what biologists have become to certain Christians. If actual non-religious scientists had problems with evolution, it would lend an aura of credibility to your case. But if the only ones having a problem are the ones who believe in a certain kind of god--then it's very clear why you guys are so persistent and unyielding and seemingly unaware of how you come across on the topic no matter how carefully the information is laid out for you. Rather than feeling frustration for more wasted time with those who have a strong motive for not comprehending, sometimes it's just easier to make fun. You guys have impervious egos anyhow...I don't think it's particularly harmful.

To me, you guys all sound sort of like Behe at the trial when no amount of evidence disproving his irreducibile complexity theory would ever be enough to make him let go of it. Faith is just a very tenacious little bugger to get rid of.
And most of us have to show some amount of deference to "it" in our regularly daily lives because rationality and tolerance isn't really a strong point of those who adhere to any particular dogma--moreso, when they believe their eternity is affected by such beliefs.

So, I think we can all stop pretending that the problems you guys have with evolution is about "facts"--it's not. It's about your beliefs. It's about the fact that whatever it is you think god is or does--he surely would have picked something more miraculous then evolution to bring the likes of you about.

Is there a single creationist who isn't a strong theist? Are there any dogmatic and seemingly educated non-theists playing semantic games about Turing Machines or "closet dualism" or "memes don't exist" or "math makes evolution an impossibility" theory? Are there any non-theists who use terms like scientism, evolutionarian, and proudly point out thesis' that only make sense to fellow theists? Are there any non-theists who have such an angry visceral reaction to outspoken atheists like Dawkins that seem unconnected to facts?

See, science and facts and truth are the same for everybody. Tests and facts and info. I learn is the same as being taught to students of all languages all over the world. It's easy to "see". But your theories only make sense to people who have been immersed in a certain belief system. It doesn't matter what the humans mapping genomes believe--the info. is all the same and readily interpreted by others mapping genomes. Physics in China is the same as in India. Biology in America is the same as in Denmark. But none of that is true for anything you say nor Kleinman says. You tell yourselves that we skeptics can't follow because your thinking is beyond ours--so advanced. But why is it that you need to believe in a certain version of creator in order for your info. to be comprehensible? Why are you so blind to very specific facts and types of knowledge? Why don't you see that which is obvious, I'm guessing, to everyone who doesn't share your version of God?

Why is hammy so ready with ad homs rather than facts or answers to questions? Because you guys have a strong need to believe in something that doesn't jive with the facts. What else should we conclude. The only evidence of your brilliant logic and scholarship seems to exist in your own head. But to non-believers that is about as relevant as Tom Cruises claims about Scientology. Every believer believes that fhis ellow believers are smarter, righter and more moral than those who believe differently, don't they?

Yes. Tom Cruise's religion teaches that there is no such thing as "chemical imbalances"--so he has his atennae tuned into anything that supports that bias and can't seem to even comprehend the data that negates it. He seemingly has no study on the subject and yet has concluded that he is an expert. Clearly, it would be difficult to teach him about imbalances involved in manic depressiveness or even diabetes--since that, too, is a chemical imbalance. He's closed himself off from learning the very thing he thinks that he's an expert in.

And yes, I think you are a creationist. The meme thread only makes it more obvious to me.

There are creationists like Francis Collins--and he understands evolution, accepts it as a fact (the more you know, the harder it is to deny it), but his way of keeping his belief in god alive is to believe that god is behind it all--evolution was part of god's plan and god is outside of human understanding. This is pretty cool, because then he can learn and appreciate new info. as it comes in. But to me, creationists have very specific areas where they just don't seem to "hear" or see or be curious about the information that is being discovered. They dismiss it or igore. This information is always about a specific belief that have which is a necessary ingredient for them to keep believing in their god. On the flip side they can be very knowledgeable in other areas and show no problem with comprehension of simple facts--sometimes they will even show curiosity towards new info. But their main focus is always to disprove the part of evolution that they have the biggest problem with--the part that threatens their god belief. It's not like they are really trying to find out the answer--it's more like they are obsessed with showing that the answers others have come up with is wrong.

Annoying creationists tend to attack Dawkins often without reading him or even understanding the basics no matter how carefully explained. You've done that a bit--if not here, then on the meme thread...and I think it's because he doesn't believe in your god. Because the arguments you use just don't make sense--I mean they seem to to you--and maybe they do to other believers--but they just sound similar to kleinman's statments to me--like if you dismiss him and refuse to compute the information then evolution never has to make sense to you and that somehow protects the belief you want to have.

You get dodgy when it comes to religion, but all creationists do. It's why the term "intelligent design" was invented--to pretend it's all about a sincere discovery for truth...when it's really about a sincere attempt at disproving evolution so that you can insert god (or whatever it is you believe in regards to creation...that it must have been pre-planned or whatever.) Wowbagger gave a pretty good analysis of your website--but you just skimmed over the really important points.

Maybe I'm wrong. But let me ask you about Behe. As I'm sure you know, at the Dover trial he kept using his irreducible complexity model--clearly to him, this is the key to disproving evolution--just like Kleinman's math model is. And no matter how many papers he was presented with that showed exactly how the flagellum or blood clotting cascade or whatever could have and probably did evolve--it wasn't enough--nothing will ever be enough... but even before we knew that flagellum could evolve the information in those papers was true. Even if we could not prove that the flagellum was not irreducibly complex--that never ever means that it was, indeed, irreducibly complex. It only means that we didn't understand it's complexity yet. Right?
Perhaps, it is a smidgen of evidence in favor of a designer--but it's not anything that negates evolution. But to Behe it is--it has to be--because he thinks his salvation depends on believing in his god and he needs a reason to believe and his reason is irreducible complexity.

You have lots of problems with evolution--the very same kinds of problems that Behe has. You have no real alternative explanation or data yet you are highly critical of those who have data in favor of evolution--particularly if those people don't believe in your god. I don't know of anyone who has this trait who doesn't believe in some sort of god that "requires a certain belief to have salvation". Maybe I'm completely mistaken. Maybe lots of non-religious people have problems with evolution or for whom the data is not convincing. But I know a plethora of non-religious people. It's only those with certain beliefs who have this rabid obsession with pointing out the gaps in evolutionary theory. Often times it seems to be the only threads they participate in. And I just presume it's for the same reasons that Tom Cruise confidently states "there is no such thing as a chemical imbalance".

Biologists are generally excited about new discoveries and finding out more clues--but the creationists never even seem interested in them. They're so focused on proving that evolution cannot be true, that they make it impossible to learn of the great discoveries which only strengthen the notion that it is.

Anyhow--if you want me to cut and paste I'd be glad to show you all the statements that convince me you are a creationist and that your beliefs about god are what motivates your posts, understanding, and lack thereof. And I'd be glad to learn that I am wrong. Would a creationist ever say the same? Would you want to know if you were wrong or do you just think you cannot be?

And that's just three of a very large number of very large posts. If you don't think that's an obnoxious way to carry on with someone who has repeatedly stated that he has no god in his plans, I suggest you look up "obsession" and "obnoxious" in the nearest dictionary.

Then you carry on...

--along with John's previously supplied answer? Then we can all see see what only you seem to see so far. If you don't or can't do so, and don't apologize, then we can conclude you are just a loud mouthed Bozo, right? 'No apology forthcoming here. I would class this as unequivocal

The question at issue is "Are you an IDer or creationist." My answer is ...
7. My scientific work does not involve ID or creationism or God or fairies or unicorns or little green men or pixies or leprochauns or the world of Narnia or .....

I have no idea how those answers could be considered unclear.

Me neither, John.

See that, Articulett? "NO GOD", "NO CREATIONISM", "NO ID". Could that be any clearer?

Plus you've asserted that he said he wasn't a creationist a couple of times too. Can you cut and paste where he said this? Or are you going to post more non-sequitars about how obnoxious the people who ask questions are. See above. In all seriousness, how can you be attacking someone, and at the same time be blind to answers as linked?

Cut and paste is easier than reading, maybe?

Are you noticing that no-one other than you seems to be following you? Oh goody, an appeal to authority and the masses! The fact that I'm swimming against the stream worries me not at all. This is nothing I have a vested interest in and I've said that I'll go with the flow, once the flow is established.
Back up your claims with easily cut and pasted evidence, please. How many times is that you've asked in one post?

I've done it already!
Or enjoy being on ignore.LOL! That's like that "not collecting stamps is a hobby" idea is it? If I'm on ignore, I wouldn't know, or care.
I suspect you are coming across as a lot more offensive than I am, and I'd be glad to cut and paste should anyone be interested in the evidence.AAAAAARRRRGGGHHH!~ I am dead-set going to have nightmares about cutting and pasting. You're not Dorothy Hare are you?
It seems the creationists can't even follow each others' arguments; why don't you engage John and illustrate how one should go about discussing these things, so that we can all learn from your expertise.I've had a couple of discussions with John and found him to be a good bloke so far. He has time to spend on ignoramuses like me and is clearly not a christian. Hell, what do I have to lose having a look?

To me, the essence of all evolution is abiogenesis. It's the question which needs to be answered as it's the last bastion of ID/creationism. I see no evidence of a god in John's theory, just a different way of looking at things. It may all boil down to Lamarckism - there are hints of it in his work, I think - but it also might not be. He has stated many times that his findings fit in with evolution through genes. Can't be all that harmful can it? You're clearly a dedicated materialist (thanks hammegk!) and have great trouble with any thinking which is outside that.

Anything else at this stage? (Please, no more cut-and-paste!)

articulett

23rd January 2007, 03:45 AM

This is not a court of law. I cannot force a witness to answer a direct question via a contempt motion. So, I must accept the answers I am given and then ask more questions until, hopefully, only one answer remains, i.e., the one which I originally sought by direct interrogation.

There is nothing to be gained, in my view, by creating an atmosphere which drives out all dissent. John Hewitt may be a fundamentalist Bible thumper, but what of it? I'm still interested in his views.

Unless a poster uses ad hominem as a means of avoiding answers, I'm not going to get annoyed.

I agree. He's not a fundamentalist bible thumper. I just thought you interpreted his answer as though it answered the question. But I see you are accumulating data. Carry on. I am enjoying your posts, I might add.

Kotatsu

23rd January 2007, 03:50 AM

On your diatribe: Do we need another go-around on the moving goalposts evolutionarians require as they wave their arms touting their pseudo-science?

I haven't been able to read all the posts in this thread recently, but as I recall, you made no response to my last post on the Brassica experiments of Song et al., in which --- as you may recall --- extensive genetic differences, differences in reproductive success, and differences in at least five morphological characters were observed between the three parent plants and four kinds of fifth generation allopolyploid progeny plants. Is this, too, moving goalposts, arm-waiving, and pseudo-science, and if so: How do you reach that conclusion. In what way does this experiment fail? Understand that I am curious only because, if the problems with the paper are described to me, I remain certain that I could find another paper in which these problems are addressed more appropriately (though I am open to the possibility that finding such paper is impossible).

I hardly think the fact that Song et al. didn't call the process speciation should disqualify it from being a --- to me --- adequate example of said process.

John Hewitt

23rd January 2007, 04:16 AM

My firewall at work seems to be blocking every link I don't already have bookmarked today, but are you familiar with Julius Rebek? He's credited with finding replicating molecules. I'll post some links later if you need them.
I have never heard of him but I shall look for his work. If your firewall starts behaving, please post a link.

articulett

23rd January 2007, 04:18 AM

Atheist--you posted my answers to John's questions. I asked you to post evidence in support of your claims that I (and possibly others) asked obnoxious questions that John had already answered. I think my answers were very clear in response to John's very simplistic questions. And John did not say he was not a creationist in that post where you think he does. Is English your second language by chance? Actually, don't answer...pretend I never even tried to communicate with you--we are clearly not on the same page.

I'm just one of those lying cheating scientists who won't let John Hewitt's brilliant and astonishing insights be heard...I have a secret agenda to call people creationists because they don't agree with me (as you carefully ferreted out earlier in this thread--of course, by this theory of yours, I should be calling you a creationist, right?).

Since you understand John so brilliantly, and seem to think DNA cannot be replicated outside of a cell....

http://oregonstate.edu/instruction/bb492/lectures/DNAI.html

--it will be scintillating reading the exciting evidence of why a cell is the true replicator and how Johns' oscillating theory trumps all other abiogenesis theories. I will gratefully sit back as you reveal that which I am too biased to possible understand and hopefully someone will explain (if possible) what exactly his sex paper is saying and including what is meant by "free will". I am able to understand various other theories of abiogenesis, but not Johns.

Surely your character assessment of him being a "good bloke" and me being someone with an agenda will become apparent to all. Then, of course, I will apologize, (though we know that creationists never will--and I suspect you never do either.) Just because I think you have poor argument skills, doesn't mean I'm your enemy, so there is no need to take this personally. And just because I am convinced of John's creationist leanings, doesn't mean I'm not open to evidence proving otherwise. But you have only provided that for yourself. And, as Richard Feynman noted, oneself is the easiest person to fool.

articulett

23rd January 2007, 04:26 AM

I haven't been able to read all the posts in this thread recently, but as I recall, you made no response to my last post on the Brassica experiments of Song et al., in which --- as you may recall --- extensive genetic differences, differences in reproductive success, and differences in at least five morphological characters were observed between the three parent plants and four kinds of fifth generation allopolyploid progeny plants. Is this, too, moving goalposts, arm-waiving, and pseudo-science, and if so: How do you reach that conclusion. In what way does this experiment fail? Understand that I am curious only because, if the problems with the paper are described to me, I remain certain that I could find another paper in which these problems are addressed more appropriately (though I am open to the possibility that finding such paper is impossible).

I hardly think the fact that Song et al. didn't call the process speciation should disqualify it from being a --- to me --- adequate example of said process.

I suspect that nothing will be an adequate example of speciation to John Hewitt, in the same way that nothing is a good example of how "irreducible complexity" evolves for Behe. What he avoids acknowledging says more than the many words he uses to state his case. (Of course Atheist has determined that I like to call all people creationists when they don't agree with me, so look askance at any tidbits I might offer.)

John Hewitt

23rd January 2007, 04:39 AM

I'm just one of those lying cheating scientists who won't let John Hewitt's brilliant and astonishing insights be heard...I have a secret agenda to call people creationists because they don't agree with me (as you carefully ferreted out earlier in this thread--of course, by this theory of yours, I should be calling you a creationist, right?).

Since you understand John so brilliantly, and seem to think DNA cannot be replicated outside of a cell....

http://oregonstate.edu/instruction/bb492/lectures/DNAI.html

--it will be scintillating reading the exciting evidence of why a cell is the true replicator and how Johns' oscillating theory trumps all other abiogenesis theories. I will gratefully sit back as you reveal that which I am too biased to possible understand and hopefully someone will explain (if possible) what exactly his sex paper is saying and including what is meant by "free will". I am able to understand various other theories of abiogenesis, but not Johns.

Thank you for the link to a page on nucleic acid polymerases. I am reasonably familiar with such things.

If an enzyme copies a piece of DNA, then the enzyme may be said to have replicated that DNA only in the sense that the enzyme has copied the DNA. Replicate means something similar to copy but replicate is a much more reflexive verb than copy, so that replicate might be said to mean copy oneself. Replicate has connotations of an object copying itself. Perhaps it is for this reason that these enzymes are not, usually, called replicases but polymerases.

In any event, the link to which you have directed our attention does not describe DNA replicating but being copied by exogenously provided enzymes. I believe that point has been made to you on a number of occasions already so could you please try to understand it. If in doubt, try replacing the word relpicate with the phrase "copy itself" and see if the situation still works. I know of know no example of a nucleic acid replicating itself, that is copying itself.

John Hewitt

23rd January 2007, 10:09 AM

From Articulett about me -
Can you sum up what you asked and what he said? He answered the question oddly. Why? And you think he said that he doesn't let his beliefs factor in his science--but that is not what he said. He is bs-ing you. Why? Why are is answers so unclear? You seem fine with answers that aren't answers at all.
It seems to me that I have made my position perfectly clear on the question of God. I have stated that, to the best of my belief and understanding, my work does not make any reference to God or to any other supernatural being.
I do not feel that I have any duty to declare a commitment to your personal faith, whether that faith is in your own personal God or in some commitment to the writings of Richard Dawkins.

This is not a court of law. I cannot force a witness to answer a direct question via a contempt motion. So, I must accept the answers I am given and then ask more questions until, hopefully, only one answer remains, i.e., the one which I originally sought by direct interrogation.

There is nothing to be gained, in my view, by creating an atmosphere which drives out all dissent. John Hewitt may be a fundamentalist Bible thumper, but what of it? I'm still interested in his views.

Unless a poster uses ad hominem as a means of avoiding answers, I'm not going to get annoyed.

I do not recall banging any bibles. What I bang on about is the structure of evolutionary theory which, in my opinion, is incorrectly expressed at the present time. Scientific theories should be expressed in their most general available form and, in my opinion, evolutionary theory is not being so expressed. Evolutionary theory should, in my opinion, be expressed from a basis in data rather than genes. That, I suggest leads to a different structure for evolutionary theory and a number of new interpretations of human nature. I feel it would be more interesting to discuss those new interpretations than Articulett's personal struggles with God.

kleinman

23rd January 2007, 10:30 AM

I believe that natural selection will select out a creature with an almost perfect genome if it has a single fatal mutation. Both Dr Schneider and Unnamed’s selection process ignore this real observable phenomena. On the other hand, it is rare that a single mutation will give a real survival benefit. I think antibiotic resistance in bacteria and the sickle cell mutation of hemoglobin are examples of this but neither represent macroevolutionary events.Actually, a reasonably objective review of this thread, shows that as soon as unnamed exposed a selection mechanism which defeated your main argument of the unreasonable slowness of RMNS, you have changed your argument to include liberal use of the word "believe," as a means of justifying that argument, rather than using math -- which was your original strong suit.
Kjkent1, it is not sufficient to formulate a mathematical selection mechanism that has no basis in reality in order to try to prove your theory. Evolutionarians have no realistic selection mechanism to evolve a gene de novo and are forced to go to the lengths that Unnamed has done to try and rescue your theory. It reveals the lack of a scientific and mathematical basis of your theory.
In short, your mathematical hypothesis has been falsified. Period.
Ev is not my mathematical hypothesis. This is an example of evolutionarian mathematics which reveals the fatal flaws in your theory.
Now, you can say you believe that one mutation is overwhelmingly more detrimental than beneficial, but your opponent can respond that he/she believes that one beneficial mutation is overwhelmingly more beneficial than all of the detrimental mutations.
That’s not quite what I am saying. The point I am trying to make here is that a single mutation to an otherwise healthy genome can be fatal while your theory requires the accumulation of large numbers of non-fatal mutations in order to evolve a new gene. Not only do I contend that there is no real selection process that would allow for the evolution of such a gene, you are forced to define an unrealistic selection process as done by Unnamed to ignore the possibility of fatal mutations so that the evolutionary process can occur with sufficient rapidity.
In the end, the argument devolves into philosophy, rather than science.
So let’s stick to the arithmetic.
If you want to soundly defeat ev, which was your original purpose, then you will need to make a reasonable attempt to model the actual evolutionary selection mechanism -- something which you have steadfastly claimed is not your responsibility.
I think Dr Schneider’s model of random point mutation and natural selection is a plausible representation of this process. It is not my desire to defeat ev. I believe ev appropriately demonstrates the mathematics of this process. It is Unnamed’s selection process which needs to be demonstrated as having no basis in reality. There are at least two problems with Unnamed’s selection process. The first is that his process almost completely ignores mutations in the non-binding site region and the second is the step wise selection of binding sites has no basis in reality.

I have already suggest a more realistic selection process (which I don’t think will work) but it is the responsibility of evolutionarians to prove their own theory.
And, for a while, you had a valid argument, because you were able to impeach your opponent's proof with a credible reason why ev doesn't work the way it should. However, ev has been rehabilitated by an alternative selection mechanism. And, so now it falls back to you to prove mathematically why this selection method is invalid, or alternatively, to affirmatively prove some other selection method which is "more" valid.
There is no step wise selection process that would evolve a gene de novo. Without a selection process you are stuck with infinitesimally small probabilities for forming genes by random additions of bases.
Until this occurs, everything which follows is just speculation -- and admittedly, some speculation exists on both sides. But the burden is now back on you to improve your argument to the point where it presents credible impeachment evidence.
I am not speculating when I say there is no selection mechanism that would evolve a gene de novo.

cyborg

23rd January 2007, 10:36 AM

kleinman

23rd January 2007, 10:46 AM

There is no step wise selection process that would evolve a gene de novo.Again Kleinman I offer: define the states that are before the new gene and after the new gene. Define this and the simulation can be run to simply find this situation - or rather not if your hypothesis is correct. Use some goddamn mathematics for once.

It is simple. You say there is no step wise process for the evolution of a gene de novo. I am telling you how you can go about showing this quite conclusively. Do you want to do this or not?
Sure cyborg, let’s go down this rabbit trail. Tell us how a gene can evolve de novo. Use whatever definitions you want for the states before and after the formation of the new gene, but don’t speculate, kjkent1 doesn’t like that (unless it supports your hopeless theory).

Paul C. Anagnostopoulos

23rd January 2007, 10:55 AM

The Atheist

23rd January 2007, 11:46 AM

Atheist--you posted my answers to John's questions. I asked you to post evidence in support of your claims that I (and possibly others) asked obnoxious questions that John had already answered.Hate to rain on your parade, but I did just that. If I could be bothered, I can find plenty more.
I think my answers were very clear in response to John's very simplistic questions. And John did not say he was not a creationist in that post where you think he does. Is English your second language by chance? Actually, don't answer...pretend I never even tried to communicate with you--we are clearly not on the same page.Oh boy, that is precious. You want to discuss English; let's get it on! Your posts are poorly written, repetitive drivel. Incoherent thought piling on top of utter baloney, wrapped up in aspersions and assertions.
I'm just one of those lying cheating scientists who won't let John Hewitt's brilliant and astonishing insights be heard...I have a secret agenda to call people creationists because they don't agree with me (as you carefully ferreted out earlier in this thread--of course, by this theory of yours, I should be calling you a creationist, right?).Well, you've already tried to, so that'd be nothing new.
Since you understand John so brilliantly, and seem to think DNA cannot be replicated outside of a cell....

http://oregonstate.edu/instruction/bb492/lectures/DNAI.html See John's post.
--it will be scintillating reading the exciting evidence of why a cell is the true replicator and how Johns' oscillating theory trumps all other abiogenesis theories.You can add to my English critique that you have a propensity for hyperbole. When have iI ever stated that John's theory trumps all other theories?

I have said that currently nothing is a plausible explanation of abiogenesis. To me, it seems very much of theories which dove-tail nicely into other theories, but without solid basis. John's may well be the same, but in the meantime, the jury is out. Unless you're going to claim that you alone know the secret of abiogenesis.
And, as Richard Feynman noted, oneself is the easiest person to fool.I do hope you realise that can refer to anyone...

I have said many times, and I'll repeat it again, that I'm pushing no barrow, other than the one which demands a fair hearing.

To date, John's been honest in the face of concerted attack on him personally. We all know what his credentials are - fill me in on yours.

So far we have "scientist" as your description of yourself, while your profile says "Biology Teacher". Please enlighten us, with the same honesty that John has shown regarding his experience, qualifications and studies....

Thanks.

sphenisc

23rd January 2007, 11:52 AM

Oh boy, that is precious. You want to discuss English; let's get it on! Your posts are poorly written, repetitive drivel. Incoherent thought piling on top of utter baloney, wrapped up in aspertions and assertions.

"aspersions"

The Atheist

23rd January 2007, 11:59 AM

"aspersions"CRAP!
That is one of Murphy's Laws, I'm sure. Make a post about about English and make a typo. I'm sure that's happened every time.

I should have kept to "nasturtiums".

Cheers.

Dr Richard

23rd January 2007, 12:31 PM

Thank you for the link to a page on nucleic acid polymerases. I am reasonably familiar with such things.

If an enzyme copies a piece of DNA, then the enzyme may be said to have replicated that DNA only in the sense that the enzyme has copied the DNA. Replicate means something similar to copy but replicate is a much more reflexive verb than copy, so that replicate might be said to mean copy oneself. Replicate has connotations of an object copying itself. Perhaps it is for this reason that these enzymes are not, usually, called replicases but polymerases.

In any event, the link to which you have directed our attention does not describe DNA replicating but being copied by exogenously provided enzymes. I believe that point has been made to you on a number of occasions already so could you please try to understand it. If in doubt, try replacing the word relpicate with the phrase "copy itself" and see if the situation still works. I know of know no example of a nucleic acid replicating itself, that is copying itself.

Exponential growth by cross-catalytic cleavage of deoxyribozymogens (http://www.pnas.org/cgi/content/full/100/11/6416)

John Hewitt

23rd January 2007, 12:56 PM

Exponential growth by cross-catalytic cleavage of deoxyribozymogens (http://www.pnas.org/cgi/content/full/100/11/6416)

Not exactly a verbose posting - but interesting. They don't actually describe a replicator but in some ways it comes close.

Of course, its not how life evolved you know. The real difficulty it presents is in the first three words of the abstract -
"We have designed"

The problem is to identify replicators we didn't design.

kleinman

23rd January 2007, 01:15 PM

All this discussion on the selection process is simply an academic exercise since there is no selection process as formulated by Unnamed and for that matter Dr Schneider’s selection method that are seen in reality.and
I think Dr Schneider’s model of random point mutation and natural selection is a plausible representation of this process.All righty then.
Paul, if I’ve shown you nothing else, at least I’ve shown you how to use quotes. Are you trying to be an annoying evolutionarian?

So let’s see whether you have caught me contradicting myself. In the first quote above, I contend that neither Dr Schneider’s nor Unnamed’s selection process exist in reality. Do you think this is true or not?

In the second quote, I am referring to the mathematical behavior of random point mutations and natural selection. I have long said that Dr Schneider’s selection process does not represent a realistic selection process but for the sake of discussion, I have not challenged the unreality of this selection process until recently since this issue is being discussed in more detail.

Evolutionarians have to fabricate a selection process to model mathematically since there is no observed selection process that serves as the pattern. Even with Dr Schneider’s fabricated selection process, the rate of information acquisition is so profoundly slow that the theory of evolution is not possible.

All righty then?

Dr Richard

23rd January 2007, 02:01 PM

Not exactly a verbose posting - but interesting. They don't actually describe a replicator but in some ways it comes close.

In what way do they not exactly decribe a replicator but come close?

Of course, its not how life evolved you know.

Thank you for correcting the false impression I was under i.e. that two researchers in 2003 did not create life on earth billions of years ago.

The real difficulty it presents is in the first three words of the abstract -
"We have designed"

The problem is to identify replicators we didn't design.

The problem is that you are now shifting the goalposts. But hey, I can do this.....

RNA
DNA

next problem.....

Skeptic Ginger

23rd January 2007, 02:06 PM

kleinman

23rd January 2007, 02:50 PM

From someone who heard this thread mentioned at TAM and was going to join in, it seems in 44 pages to have gone from issue to issue. So, I'll ignore all that and go with the current exchange on selection PRESSURES as they are more accurately referred to. There are multiple PROCESSES that result in genetic code variation which varying selection pressures then act upon.
At least Dr Schneider put some mathematics to his argument about random point mutations and natural selection. So which PROCESS is going to rescue your theory from the mathematical deficiency that is revealed by Dr Schneider’s model?
I have two words, genetic science. Anyone arguing against evolution for whatever contrived reason, you lose.
Do you stamp your foot when you say this?
Genetic science has ruled out irreducible complexity and all the other nonsense proclaiming evolution theory fails for this reason or that reason. And those who believe they have the, "gotcha", xyz disproves (as if) evolution, are ignorant of at least the last decade of genetic science research. It's likely they are ignorant of the last 3 decades actually.
So you are the evolutionarian who is going to explain what the components of the DNA replicase system were doing before this system evolved? In particular, what were helicase and gyrase doing before DNA could be replicated?
Even if any of the contrived faults in evolutionary theory were valid, the theory is established by such overwhelming scientific evidence, the 'fault' would only imply some tiny detail in the theory rather than the theory itself was questioned. And even then, it could just as easily be the evidence which wasn't yet clear that was the problem, rather than the theory.
These issues raised here are not contrived faults. Data from an evolutionarian written, peer reviewed and published mathematical model of random point mutations and natural selection shows that this process is profoundly slow when using realistic parameters in the model. Why don’t you give us a realistic selection process which corrects the deficiency in the model? Why don’t you describe to us a selection process that would evolve a gene de novo?
For example, if the claims that random mutations didn't have time to see the extent of evolution occurring, it would likely be the mechanisms of random mutation that needed further research, rather than the principles of evolutionary theory. This is one point that seems over the head of those who think xyz makes evolutionary theory false.
Skeptigirl, what you are having trouble understanding is that without random point mutations, how do you transform duplicated genes to new genes? How do you evolve a gene de novo? Random point mutations are the cornerstone for your theory. Unless you can describe a realistic selection process that allows for rapid evolution of new genes by random point mutations, your theory is a flop.
Give up and educate yourself in the current scientific evidence for evolution.
Why don’t you educate us on a selection process that would rescue your theory from the mathematical vortex that it is being sucked into.
But since many are clearly not prepared to give up, go ahead, make your case. I arrogantly state right now, whatever case one might have against evolution will be as absurd as still trying to argue the Earth is flat. We can OBSERVE and MANIPULATE the mechanisms of evolution just as one can circle the Earth and observe its shape.
Skeptigirl, this discussion is being reduced down to an accounting problem. Dr Schneider thought he had solved this problem but failed to use realistic parameters in his model. You have no way to account for the differences between the genomes of different kinds of creatures based on random point mutations and natural selection. If you think other processes will solve this mathematical deficiency, educate us. Otherwise, your interpretations of your observations will only satisfy devout evolutionarians.