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Tags evolution , creationists , creationism

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Old 23rd January 2007, 11:42 PM   #1761
The Atheist
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Originally Posted by Dr Richard View Post
In what way do they not exactly decribe a replicator but come close?

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 problem is that you are now shifting the goalposts. But hey, I can do this.....

RNA
DNA

next problem.....
Thanks for the link in the previous post.

Now I'm wondering how it's possible that you can make so much sense in half a dozen lines while all Articulett's done in about 6000 lines is scream "creationist".
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Old 24th January 2007, 12:01 AM   #1762
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Originally Posted by articulett View Post
I have a Masters of Science in Genetic Counseling, and worked in that field for several years before attending law school--during the Dover trial--that case and my first TAM meeting made me feel like I could be doing a lot more good in the world by teaching biology and critical thinking--so, I am.
Thanks. I'd begun to wonder about your critical thinking as it seemed to be more of the harrassment style than seeking answers, but I'll take your word for it.
Originally Posted by articulett View Post
And I'd really love to see a conversation between you, John, and Kleinman so I can see if you understand and agree with each other or are making sense to any one other than yourselves.
Oh, that's an easy one. I wouldn't understand any of it.
Originally Posted by articulett View Post
Yes, I know you hate me because I pointed out that Yahtzi's assessment of your error in logic was correct--but getting all upset and taking it personally doesn't really help you learn anything.
Now you're just being childish, A - I don't hate you. B - I've never claimed to be an expert on this subject, so if I make mistakes I'm happy to own them and C - the only beef I've had with you is what seems to be hounding a bloke because you disagree with him. If John turns out to be a creationist, I'll bring the matches to the burning.
Originally Posted by articulett View Post
Yes, I know very well I can be wrong. That's why I look for evidence. That's why I ask specific questions and pay careful attention to the answers. I know you think you are supporting your claims and that anyone can see it--but I don't. To me, you sound like Dann. You make unsupported claims and then sling ad homs when someone points it out.
Nope, I sling ad homs all the time, nothing to do with whether I'm right or not.
Originally Posted by articulett View Post
You make up little side issues so everyone is distracted from your error in logic and then try to make it look like I'm a sneer worthy person. Like Hammy you take great offense at anyone who points out your errors while claiming to be the victim of attacks that you started. By the way, I don't think you are a creationist despite your unsupported claim that I think everyone who doesn't agree with me is; and I don't think Dann is either. I just think you have poor dialog and communication skills and that you can't fathom that you could possibly be one to make logical errors. You would be a "skeptoid" to me in reference to the thread of the same title.
I have no problem with making the odd logical error, I'm no slave to logic. As I said, I'm no scientist; sometimes gut instinct is as good as any. You can keep the "skeptoid" label for yourself as well, I make no claim to be a "skeptic". Instead of Occam's Razor I use the bulldozer, sometimes squashing the facts along the way. It probably is frustrating for you, but I always get what I want in the end. Live with it. My language and comprehension skills - take me on anyday. I'll just make sure it's a subject I know something about.
Originally Posted by articulett View Post
Hey, I'm guilty too. I thought it was obvious that Hewitt was a creationist--hence my god reference. Apparently others hadn't reached that same conclusion as readily as I had-- I presented evidence when John asked why I believed him to be a creationist, and others seem to have reached the same conclusion. In any case, no one including you seems to know exactly what his theories are. And I still think he is a creationist--he answers questions in the same shifty way that creationists do--it works on people like you; it doesn't work on me.
Were you a Mother Superior in a previous life?
Originally Posted by articulett View Post
So then, what are your fine references now that I've given you mine?
I have a B Com in Finance and an MBA in Human Resources. I don't expect to be able to hold a conversation with you on genetics and evolution any more than I'd expect you to know about outplacement. The fact that you're infinitely more knowledgeable than me on the subject doesn't worry me a bit. We each have our specialties.

One last comment. I just noted Dr Richard's post and link. He's just stepped up and placed relevant information without the crusade. You don't think that maybe your style is letting you down a little? Sometimes, sticking to the basics without the histrionics gets more attention.

Just a thought.
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Old 24th January 2007, 02:44 AM   #1763
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Originally Posted by kjkent1 View Post
Dr Kleinman, Hewitt, Articulate, Cyborg, et. al.

What is the minimum genome size capable of reproduction/division/replication (or whatever other term you may deem relevant)?

I ask this question because it seems to me that unless we can specify a precise lower limit on the genetic composition of a life form, we can't calculate the odds of its developing by pure chance. However, we only need one life form to develop by chance before natural selection can start influencing future biological changes, so the simpler the initial life form can be, the more likely it can develop by chance.

Any suggestions/evidence?
Concerning the nature of a replicator. In some pedantic formal senses, one could argue that even an organism is not a replicator because living things do not copy themselves completely de novo, they do need inputs. So what one needs to do is begin with a definition and concept of replicator that seems relevant. The following point was made by Grand(e) and Dawkins does agree with it. An organism is only a replicator in the sense that it replicates its pattern. It takes in relatively disordered material from the outside world and imposes onto that material a copy of itself, meaning a copy of its own pattern or structure or its data. It is a matter of thermodynamics that a free energy supply is needed in order to perform this data copying and all organism must make use of an exogenous free energy supply.
For purposes of biological and biochemical discussion, a replicator is something that takes in relatively simple, disordered, low energy molecules, and makes use of an energy supply to impose a replica of its own pattern onto the arrangement of those atoms and molecules.

I believe that the smallest known replicators are cells. The smallest known cells are a matter of debate but some candidates include intracellular parasites, such as the PPLOs (pleuropneumonia like organisms) which, I believe, have just a few hundred genes. However, such things live as parasites within other cells and enjoy a very stable environment. I believe the smallest known free living bacteria have of the order of 1200-1300 genes but that is just from memory. There was a post on this forum, not long ago, which identified it but I don't remember its name.
In any event, a thousand genes would be about 600k base pairs or more. Whatever figure you choose, it is very high and that is not surprising. A cell has to be a Von Neumann machine, a machine which contains the data needed to describe itself, the programs needed to drive its own operations and the physical actuators needed to put those programs into effect. Any such machine is going to involve a large amount of data and some complicated equipment.

The problem is, "How could both the data and the equipment come into being together?" There are really only three general ways in which this could happen.
1. It all happened by chance. The problem with this is that, even on the most generous of assumptions, such a complex machine could not have arisen by chance.
2. It was designed. The problem with this is that it is not really an answer. Whether the designer was God, as the bible suggests, or an alien, as Crick suggests, the designer must himself have been a machine of great complexity and we must still wonder about where that designer came from. Design is, really, a transfer of the problem.
3. Evolution but this too has problems. Evolutionary theory, as presently constructed, describes how one organism can change into another, it does not describe how organisms, as Von Neumann machines, can arise de novo. The task, therefore, is to so construct evolutionary theory that one can describe an evolutionary process in a purely chemical environment and show how that process can lead to the kinds of phenomena we now identify as biology. That is one aspect of what I work on.

However, note that I just said is that one must describe an evolutionary process that does not begin with a replicator. That seems to be Articulett's problem with me. She believes in Dawkins and I don't. I do not believe that replicators, otherwise known as Von Neumann machines, can lie at the base of evolution. I think the base of evolution is data and data flows. I think that it is the sun's data supply, as well as its energy supply, that drove evolution within a chemical environment and which led to life.
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Old 24th January 2007, 03:02 AM   #1764
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Originally Posted by The Atheist View Post
Thanks for the link in the previous post.

Now I'm wondering how it's possible that you can make so much sense in half a dozen lines while all Articulett's done in about 6000 lines is scream "creationist".
I am glad Dr. Richard makes sense to you because he doesn't to me. He posted a bare link and did not explain what relevance he attaches to it. He seems to be insinuating an opinion rather than expressing it.

His link does not describe DNA acting as a replicator but undergoing an autocatalytic reaction. Autocatalysis is a well-known phenomenon that can be demonstrated in school classrooms. It is also a component part of some theories of abiogenesis, including my own.
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Old 24th January 2007, 03:08 AM   #1765
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Originally Posted by Dr Richard View Post
In what way do they not exactly decribe a replicator but come close?

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 problem is that you are now shifting the goalposts. But hey, I can do this.....

RNA
DNA

next problem.....
As a further reply to the above, the link that Dr. Richard provided was of a large polynucleotide fragment autocatalyzing a single rather small change in its structure. This nucleotide fragment already contains all its own data and energy. What can one say? A single autocatalytic event does not amount to a fragment copying itself or making use of an exogenous energy supply from simple molecules. It is a fragment that merely undergoes a minor change in its data and energy content and, as the authors say, this is an example of autocatalysis. Unfortunately it does not come close to being a replicator as described above and I don't think autocatalysis is a big deal. It is a well know phenomenon, even in simple chemistry.
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Old 24th January 2007, 04:36 AM   #1766
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Originally Posted by kleinman View Post
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?

Do you stamp your foot when you say this?

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?

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?

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.

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.

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.
I will repeat my two words, genetic science.

Whatever you think you are on to here is silly. But I'll play along for a while. Until I get bored.

Your underlying premise is totally flawed. We already know evolution is the correct theory because one can follow the genetic trail, manipulate genes, and observe evolution occurring. Am I correct in interpreting your position is that what is observed is not true?

Am I correct that you are stating evolution couldn't be correct merely because you are unaware of how the processes work?

I know how the processes work. It isn't hard to learn. So what is it you think is impossible? New genes? How silly. There are 4 different mechanisms new genes occur in organisms we observe today.

gene transfer mechanisms

Horizontal gene transfer

molecular genetics

genomes in flux

Gene transfer to plants by diverse species of bacteria

There are a multitude of factors you just haven't bothered to learn about here. Unless I have misinterpreted your position. There is a large amount of variation for example in the human genome. When a new selection pressure occurs such as a new epidemic, the genetic diversity assures the genes which may protect some members of the population are already in the population.

The CCR5 deletion is one such example. Persons with 2 copies are highly resistant to HIV yet the mutation arose long before HIV infected humans and being a neutral mutation, there are different percentages in populations based on ancestry alone.

And here you are discussing some nonsense about point mutations being unable to result in new genes? I haven't even begun to discuss the vast amount of knowledge that has been accumulated in genetic science.

Of course, your arguments have been thoroughly discussed both at the Panda's Thumb and Talk Origins, but I suppose in 44 pages those citations have already been posted.
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Old 24th January 2007, 04:49 AM   #1767
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Argument from incredulity
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It is inconceivable that (fill in the blank) could have originated naturally. Therefore, it must have been created.

This argument, also known as the argument from ignorance or "god of the gaps," is implicit in a very many different creationist arguments. In particular, it is behind all arguments against abiogenesis and any and all claims of intelligent design.

1. Really, the claim is "I can't conceive that (fill in the blank)." Others might be able to find a natural explanation; in many cases, they already have. Nobody knows everything, so it is unreasonable to conclude that something is impossible just because you do not know it. Even a noted antievolutionist acknowledges this point: "The peril of negative arguments is that they may rest on our lack of knowledge, rather than on positive results" (Behe 2003).

2. The argument from incredulity creates a god of the gaps. Gods were responsible for lightning until we determined natural causes for lightning, for infectious diseases until we found bacteria and viruses, for mental illness until we found biochemical causes for them. God is confined only to those parts of the universe we do not know about, and that keeps shrinking.
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Old 24th January 2007, 04:53 AM   #1768
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Mutations and new features
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1. Variation of traits is production of novelty, especially where there was no variation before. The accumulation of slight modifications is a basis of evolution.

2. Documentation of mutations producing new features includes the following:
* the ability of a bacterium to digest nylon (Negoro et al. 1994; Thomas n.d.; Thwaites 1985);
* adaptation in yeast to a low-phosphate environment (Francis and Hansche 1972; 1973; Hansche 1975);
* the ability of E. coli to hydrolyze galactosylarabinose (Hall 1981; Hall and Zuzel 1980);
* evolution of multicellularity in a unicellular green alga (Boraas 1983; Boraas et al. 1998);
* modification of E. coli's fucose pathway to metabolize propanediol (Lin and Wu 1984);
* evolution in Klebsiella bacteria of a new metabolic pathway for metabolizing 5-carbon sugars (Hartley 1984);

There is evidence for mutations producing other novel proteins:
* Proteins in the histidine biosynthesis pathway consist of beta/alpha barrels with a twofold repeat pattern. These apparently evolved from the duplication and fusion of genes from a half-barrel ancestor (Lang et al. 2000).

Laboratory experiments with directed evolution indicate that the evolution of a new function often begins with mutations that have little effect on a gene's original function but a large effect on a second function. Gene duplication and divergence can then allow the new function to be refined. (Aharoni et al. 2004)

3. For evolution to operate, the source of variation does not matter; all that matters is that heritable variation occurs. Such variation is shown by the fact that selective breeding has produced novel features in many species, including cats, dogs, pigeons, goldfish, cabbage, and geraniums. Some of the features may have been preexisting in the population originally, but not all of them were, especially considering the creationists' view that the animals originated from a single pair.
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Old 24th January 2007, 05:12 AM   #1769
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Genome Primer
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What We’ve Learned Thus Far The first panoramic views of the human genetic landscape have revealed a wealth of information and some early surprises. Much remains to be deciphered in this vast trove of information; as the consortium of HGP scientists concluded in their seminal paper, “. . .the more we learn about the human genome, the more there is to explore.” A few highlights from the first publications analyzing the sequence follow.
• The human genome contains 3 billion chemical nucleotide bases (A, C, T, and G).
• The average gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases.
• The functions are unknown for more than 50% of discovered genes.
• The human genome sequence is almost (99.9%) exactly the same in all people.
• About 2% of the genome encodes instructions for the synthesis of proteins.
• Repeat sequences that do not code for proteins make up at least 50% of the human genome.
• Repeat sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. Over time, these repeats reshape the genome by rearranging it, thereby creating entirely new genes or modifying and reshuffling existing genes.
• The human genome has a much greater portion (50%) of repeat sequences than the mustard weed (11%), the worm (7%), and the fly (3%).
• Over 40% of the predicted human proteins share similarity with fruitfly or worm proteins.
• Genes appear to be concentrated in random areas along the genome, with vast expanses of noncoding DNA between.
• Chromosome 1 (the largest human chromosome) has the most genes (2968), and the Y chromosome has the fewest (231).
• Genes have been pinpointed and particular sequences in those genes associated with numerous diseases and disorders including breast cancer, muscle disease, deafness, and blindness.
• Scientists have identified about 3 million locations where single-base DNA differences (see p. 9) occur in humans. This information promises to revolutionize the processes of finding DNA sequences associated with such common diseases as cardiovascular disease, diabetes, arthritis, and cancers.

Building a “Systems Level” View of Life

The DNA sequences generated in hundreds of genome projects now provide scientists with the “parts lists” containing instructions for how an organism builds, operates, maintains, and reproduces itself while responding to various environmental conditions. But we still have very little knowledge of how cells use this information to “come alive.” The functions of most genes remain unknown. Nor do we understand how genes and the proteins they encode interact with each other and with the environment. If we are to realize the potential of the genome projects, with far-ranging applications to such diverse fields as medicine, energy, and the environment, we must obtain this new level of knowledge.

One of the greatest impacts of having wholegenome sequences and powerful new genomic technologies may be an entirely new approach to conducting biological research. In the past, researchers studied one or a few genes or proteins at a time. Because life doesn’t operate in such isolation, this inherently provided incomplete—and often inaccurate—views. Researchers now can approach questions systematically and on a much grander scale. They can study all the genes expressed in a particular environment or all the gene products in a specific tissue, organ, or tumor. Other analyses will focus on how tens of thousands of genes and proteins work together in interconnected networks to orchestrate the chemistry of life—a new field called “systems biology” (see “Genomes to Life,” p. 10).

How do genetic variations (SNP patterns) differ across populations?

Charting Human Variation

Slight variations in our DNA sequences can have a major impact on whether or not we develop a disease and on our responses to such environmental factors as infectious microbes, toxins, and drugs. One of the most common types of sequence variation is the single nucleotide polymorphism (SNP). SNPs are sites in the human genome where individuals differ in their DNA sequence, often by a single base. For example, one person might have the DNA base A where another might have C, and so on. Scientists believe the human genome has at least 10 million SNPs, and they are generating different types of maps of these sites, which can occur both in genes and noncoding regions.

Sets of SNPs on the same chromosome are inherited in blocks (haplotypes). In 2002 a consortium of researchers from six countries established a 3-year effort to construct a map of the patterns of SNPs that occur across populations in Africa, Asia, and the United States. Researchers hope that dramatically decreasing the number of individual SNPs to be scanned will provide a shortcut for tracking down the DNA regions associated with common complex diseases such as cancer, heart disease, diabetes, and some forms of mental illness. The new map also may be useful in understanding how genetic variation contributes to responses to environmental factors. (For more information, see the NIH URL, p. 12.)
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Old 24th January 2007, 05:29 AM   #1770
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The reason I put this material here, when you are discussing "large polynucleotide fragment autocatalyzing a single rather small change in its structure", is because the underlying premise that whatever "gaps" one finds in any particular piece of evolutionary theory is not evidence the theory is in any doubt. It is simply time to move on.

On the other hand, if you are merely arguing for one mechanism over another or that this or that gap needs filling or testing, then fine. But to think the "gap" is so wide as to actually put the theory of evolution in doubt is absurd in light of what current genetic scientists have been able to accomplish.
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Old 24th January 2007, 05:39 AM   #1771
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Dr Gerald Joyce, Scripps Institute has been working on abiogenesis for example.
Quote:
We have been able, for example, to evolve variants of the Tetrahymena group I ribozyme that cleave single-stranded DNA with high efficiency and specificity under physiologic conditions. The starting molecule has barely detectable DNA cleavage activity. But after 27 "generations" of in vitro evolution, individuals isolated from the population had accumulated, on average, 17 mutations relative to the wild type and had improved their ability to cleave DNA by 1O5-fold. These designer ribozymes were expressed in Escherichia coil and used to "immunize" the host cell against infection by M13 single-stranded DNA bacteriophage.

In another study, we carried out directed evolution to change the metal dependence of a group I ribozyme, teaching it to operate in the presence of Ca2+ rather than Mg2+ or Mn2+ as is required by the wild type. We were able to correlate specific genetic changes that arose over evolutionary time with their effect on the catalytic properties of the evolving molecules. Our goal at present is to evolve novel ribozymes that carry out a broader range of chemical reactions, including reactions involving substrates other than nucleic acids.
Nano-origami isn't part of the abiogenesis work but it still advances the science.
Quote:
Scientists at Scripps research create single, clonable strand of DNA that folds into an octahedron A group of scientists at The Scripps Research Institute has designed, constructed, and imaged a single strand of DNA that spontaneously folds into a highly rigid, nanoscale octahedron that is several million times smaller than the length of a standard ruler and about the size of several other common biological structures, such as a small virus or a cellular ribosome.

Making the octahedron from a single strand was a breakthrough. Because of this, the structure can be amplified with the standard tools of molecular biology and can easily be cloned, replicated, amplified, evolved, and adapted for various applications. This process also has the potential to be scaled up so that large amounts of uniform DNA nanomaterials can be produced. These octahedra are potential building blocks for future projects, from new tools for basic biomedical science to the tiny computers of tomorrow.

...Shih and Joyce note that because all twelve edges of the octahedral structures have unique sequences, they are versatile molecular building blocks that could potentially be used to self-assemble complex higher-order structures.



As the evidence for evolution is clearly overwhelming, I see the evolution deniers are switching to the new "gap" of life's beginnings. Trying to find Joyce's work I found all sorts of sites proclaiming in essence, "Oh yeah? Well prove this then."

No worry, mate. Since the evidence is overwhelming it happened, scientific research will eventually provide the evidence of how exactly it occurred.
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Old 24th January 2007, 05:46 AM   #1772
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RNA-Catalyzed RNA Ligation on an External RNA Template; Kathleen E. McGinness and Gerald F. Joyce; Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 USA
Quote:
Summary

Variants of the hc ligase ribozyme, which catalyzes ligation of the 3′ end of an RNA substrate to the 5′ end of the ribozyme, were utilized to evolve a ribozyme that catalyzes ligation reactions on an external RNA template. The evolved ribozyme catalyzes the joining of an oligonucleotide 3′-hydroxyl to the 5′-triphosphate of an RNA hairpin molecule. The ribozyme can also utilize various substrate sequences, demonstrating a largely sequence-independent mechanism for substrate recognition. The ribozyme also carries out the ligation of two oligonucleotides that are bound at adjacent positions on a complementary template. Finally, it catalyzes addition of mononucleoside 5′-triphosphates onto the 3′ end of an oligonucleotide primer in a template-dependent manner. The development of ribozymes that catalyze polymerase-type reactions contributes to the notion that an RNA world could have existed during the early history of life on Earth.
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Old 24th January 2007, 05:51 AM   #1773
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Originally Posted by kleinman View Post
What do you think?
Jesus is a hippy.

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Only shocking to an evolutionarian.
Are so you are known as quite the dumbass amongst creationists.

Quote:
Only if you want to be annoyed again.
Bring it.

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Not quite. What Iím banging on about is that natural selection for evolving a gene de novo is nonexistent.
So? I don't give a crap about natural selection. I am interested in divine selection. I want to know how Jesus makes genes.

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The sequence of events that leads to a new gene must be ofselective benefit to the creatures in which it is evolving in.
Rubbish. Jesus did it.

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Perhaps you would be willing to explain how a partially completed gene would be a selective benefit to these creatures?
Absolutely not. I am with you. Clearly Jesus is responsible.

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In particular would you explain to us how the partially completed genes which code for the DNA replicase proteins would be of benefit to the creatures in which these genes would be evolving?
No. Again you seem to fail to grasp the point here.

Then again dementia is an inevitable consequence of ageing. I guess it's really just not possible for you to understand any more. It is nice that the nursing home gives you Internet access though.

That's the only thing that could possibly explain why you are dancing around such a simple question.

I guess you can't tell the difference between a partially completed gene and a 'new' gene then? Is that the problem? You have to resort to flimsy qualitative arguments? Oh, how very persuasive of you. Maybe you'd like to me explain how rubbing the computer is of benefit to the evolving creatures as well?

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The part you are having trouble grasping is that we are biologic machines and you are having difficulty in seeing design in these machines.
Speak for yourself. I'm a cyborg you moron.

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You donít seem to have difficulty in grasping the concept of an archeologist digging up a site and finding artifacts which show signs of intelligence in their construction or the SETI experiment looking for radio signals that do not appear to have a natural origin
When the hell did I say I don't have a problem with this? I hate Indiana Jones and Contact was a stupid movie.

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but for living things, you have rejected the concept of design even when you are confronted with the mathematical impossibility of your own theory.
Mathematicians don't have the first clue what design looks like. That's all I can conclude from their programming abilities.

You haven't shown the mathematical impossibility of the theory. Namely you haven't got a mathematical definition for the de novo event so you cannot hope to show that it is impossible by any selection method - whatever one it is you want to show it is impossible for. (Free choice! Nothing to do with me! You get to choose the selection!) Merely running simulations is not enough. It is not hard proof and frankly you are not much of a mathematician if you think it is.

You know, algebra and that. Get some formulae together, jiggle them about, see what happens? It is clearly entirely possibly to model the simulation in this way.

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I long ago acknowledged my error on this issue. Yet you bring it up again.
Yes. Why not? You refuse to do maths so there's not much left to do than to conclude you are a blow hard who can't. I'm simply presenting the evidence.

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You will not win this discussion with these tactics.
I beg to differ.

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What makes you so sure?
I'm a cyborg you retard. DUH.
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Old 24th January 2007, 05:52 AM   #1774
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RNA STRUCTURE: Ribozyme Evolution at the Crossroads; Gerald F. Joyce

Review: In Search of an RNA Replicase Ribozyme; Kathleen E. McGinness1 and Gerald M. Joyce
Quote:
The theory that an RNA world played a pivotal role in life's evolutionary past has prompted investigations into the scope of RNA catalysis. These efforts have attempted to demonstrate the plausibility of an RNA-based genetic system, which would require RNA molecules that catalyze their own replication. The mechanistic features of modern protein polymerases have been used to guide the laboratory evolution of catalytic RNAs (ribozymes) that exhibit polymerase-like activity. Ribozymes have been developed that recognize a primer-template complex in a general way and catalyze the template-directed polymerization of mononucleotides. These experiments demonstrate that RNA replicase behavior is likely within the catalytic repertoire of RNA, although many obstacles remain to be overcome in order to demonstrate that RNA can catalyze its own replication in a manner that could have sustained a genetic system on the early Earth.
I have discussed this work before and the argument was mainly that it hasn't been established yet how the RNA molecules initially occurred. I am not aware if that was a legitimate issue or not since I thought Joyce made a reasonable argument for the occurrence of the molecules. However, it's just one more "gap" and here is an example of it beginning to be filled in.
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Old 24th January 2007, 06:23 AM   #1775
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Originally Posted by skeptigirl View Post
Since the evidence is overwhelming it happened, scientific research will eventually provide the evidence of how exactly it occurred.
"It happened"? "exactly"?

Do your unproven and unprovable premises include "I, skeptigirl, am 100% certain god does not exist."? If not, why not? Don't you prefer a logically defensible worldview?
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Old 24th January 2007, 06:38 AM   #1776
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Originally Posted by skeptigirl View Post
RNA STRUCTURE: Ribozyme Evolution at the Crossroads; Gerald F. Joyce

Review: In Search of an RNA Replicase Ribozyme; Kathleen E. McGinness1 and Gerald M. JoyceI have discussed this work before and the argument was mainly that it hasn't been established yet how the RNA molecules initially occurred. I am not aware if that was a legitimate issue or not since I thought Joyce made a reasonable argument for the occurrence of the molecules. However, it's just one more "gap" and here is an example of it beginning to be filled in.
I am not sure to whom you are addressing this post but I find it unfortunate that you refer to links without explaining what you find relevant about them. I have explained before the severity of the problems in the RNA world theory.
My work circumvents those problems and I favour the theory that life began in a random primordial soup, not in a pH and temperature controlled test tube full of purified biochemicals purchased from Sigma. I also prefer my assumption that the sun comes up in the morning and goes down at night, over your faith that there is just a tiny, little gap in your theory.

It really is not sensible to believe that an RNA replicator could have emerged, by chance, within the primordial oceans even though nobody can make such a thing in the controlled conditions of a laboratory.
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Old 24th January 2007, 06:52 AM   #1777
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Originally Posted by John Hewitt View Post
The task, therefore, is to so construct evolutionary theory that one can describe an evolutionary process in a purely chemical environment and show how that process can lead to the kinds of phenomena we now identify as biology. That is one aspect of what I work on.
Sounds reasonable. What do you think of this hypothetical:

http://www.cogsci.indiana.edu/farg/h...htm#fp_organic
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Old 24th January 2007, 07:08 AM   #1778
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Originally Posted by hammegk View Post
"It happened"? "exactly"?

Do your unproven and unprovable premises include "I, skeptigirl, am 100% certain god does not exist."? If not, why not? Don't you prefer a logically defensible worldview?
I am 100% sure gods do not exist. I have presented my case in other threads. The basic premise is the only gods that could exist would need to either not interact with the Universe or hide their tracks. No religion describes such gods. Gods which interact with the Universe would be, by definition, detectable.

There have been no gods detected.

In addition, there is a more plausible explanation for belief in gods. That explanation is gods are a man-made construct.

You don't have to agree. You can also argue semantics or the philosophy of science not testing for gods. I prefer a more pragmatic view. Are you 100% certain there are no invisible pink unicorns in your closet? The semantics argument is with the words 'proof' and 100%. The philosophic argument is with proving a null hypothesis. It's fine to argue those concepts when one is discussing what preceded the Big Bang. But for all intents and purposes, it's useless to leave gods and invisible pink unicorns in one's optional beliefs.

As for evolution, yes it happened. When are you going to accept the overwhelming evidence if you haven't already? The theory of evolution is only being held to some absurd standard of evidence because the Bible believers cannot shift their paradigm. They did the same thing when it was discovered Earth wasn't exactly like the Bible described either.

It's hard to believe in a flat Earth since we can observe directly it's a sphere. I observe evolution in my field every time a drug resistant pathogen emerges.
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Old 24th January 2007, 07:12 AM   #1779
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Originally Posted by John Hewitt View Post
I am not sure to whom you are addressing this post but I find it unfortunate that you refer to links without explaining what you find relevant about them. I have explained before the severity of the problems in the RNA world theory.
My work circumvents those problems and I favour the theory that life began in a random primordial soup, not in a pH and temperature controlled test tube full of purified biochemicals purchased from Sigma. I also prefer my assumption that the sun comes up in the morning and goes down at night, over your faith that there is just a tiny, little gap in your theory.

It really is not sensible to believe that an RNA replicator could have emerged, by chance, within the primordial oceans even though nobody can make such a thing in the controlled conditions of a laboratory.
I posted the discussion over about 5 posts. The edit feature was not working well so on some posts I edited and some I just added things in the following post. They were all together with one exception.

And the posts were mostly in response to kleinman.
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Old 24th January 2007, 08:39 AM   #1780
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Originally Posted by skeptigirl View Post
I am 100% sure gods do not exist.
Nice evasion. I'm 100% certain gods don't exist. The question concerned god.

Quote:
No religion describes such gods. Gods which interact with the Universe would be, by definition, detectable.
Agreed. My discussion concerns the ontology one associates with the Universe (or Multiverse, perhaps). Are you 100% certain that what we have named matter/energy exists? I'm 100% certain thought exists.

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There have been no gods detected.
Unknown. I haven't seen any such detection under the current rubric of science.

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In addition, there is a more plausible explanation for belief in gods. That explanation is gods are a man-made construct.
Yup.

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Are you 100% certain there are no invisible pink unicorns in your closet?
Why yes, I am, knowing the definition of both invisible and pink.

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But for all intents and purposes, it's useless to leave gods and invisible pink unicorns in one's optional beliefs.
My question concerned god.

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As for evolution, yes it happened. When are you going to accept the overwhelming evidence if you haven't already?
What part of available scientific evidence do you have faith I reject?

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The theory of evolution is only being held to some absurd standard of evidence because the Bible believers cannot shift their paradigm. They did the same thing when it was discovered Earth wasn't exactly like the Bible described either.
I have no more faith in the Bible than you do.

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It's hard to believe in a flat Earth since we can observe directly it's a sphere.
You're getting sillier as you go along.

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I observe evolution in my field every time a drug resistant pathogen emerges.
Do you think I dispute those observed facts? I don't.
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Old 24th January 2007, 08:42 AM   #1781
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I'm 100% certain thought exists.
I'm 100% sure that's a meaningless statement.
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Old 24th January 2007, 09:11 AM   #1782
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Annoying Creationists

Originally Posted by kjkent1
What is the minimum genome size capable of reproduction/division/replication (or whatever other term you may deem relevant)?

If you would take the time to study this thread and the related thread on the Evolutionisdead forum you would get these answers and links with more information.

For eukaryotes, the smallest known which Paul posted is Pelagibacter ubique with a genome length of around 1.3 million base pairs. For prokaryotes, Mycoplasma sp. is around 900,000 base pairs. There are symbionts with shorter genome lengths but are not free living organisms and are dependent upon a host.
Originally Posted by articullet
So then, what are your fine references now that I've given you mine?
Originally Posted by The Atheist
I have a B Com in Finance and an MBA in Human Resources. I don't expect to be able to hold a conversation with you on genetics and evolution any more than I'd expect you to know about outplacement. The fact that you're infinitely more knowledgeable than me on the subject doesn't worry me a bit. We each have our specialties.

Atheist, you should be able to understand the bookkeeping problem that the theory of evolution has. You canít balance the evolutionarian checkbook.
Originally Posted by John Hewitt
Concerning the nature of a replicator. In some pedantic formal senses, one could argue that even an organism is not a replicator because living things do not copy themselves completely de novo, they do need inputs. So what one needs to do is begin with a definition and concept of replicator that seems relevant. The following point was made by Grand(e) and Dawkins does agree with it. An organism is only a replicator in the sense that it replicates its pattern. It takes in relatively disordered material from the outside world and imposes onto that material a copy of itself, meaning a copy of its own pattern or structure or its data. It is a matter of thermodynamics that a free energy supply is needed in order to perform this data copying and all organism must make use of an exogenous free energy supply.
For purposes of biological and biochemical discussion, a replicator is something that takes in relatively simple, disordered, low energy molecules, and makes use of an energy supply to impose a replica of its own pattern onto the arrangement of those atoms and molecules.

I believe that the smallest known replicators are cells. The smallest known cells are a matter of debate but some candidates include intracellular parasites, such as the PPLOs (pleuropneumonia like organisms) which, I believe, have just a few hundred genes. However, such things live as parasites within other cells and enjoy a very stable environment. I believe the smallest known free living bacteria have of the order of 1200-1300 genes but that is just from memory. There was a post on this forum, not long ago, which identified it but I don't remember its name.

I think what kjkent1 is looking for is the minimum size genome for a free living organism which I have posted above. The reason this is important is that the genome length is the dominant parameter in Dr Schneiderís model. Until one obtains a free living organism, one is confined to the concept of abiogenesis which is a weaker theory than the theory of evolution. Evolutionarians can not conceive of a selection process that would evolve a gene de novo in a living organism. What kind of selection process would there be in the primordial soup that would evolve a gene?
Originally Posted by John Hewitt
The problem is, "How could both the data and the equipment come into being together?" There are really only three general ways in which this could happen.
1. It all happened by chance. The problem with this is that, even on the most generous of assumptions, such a complex machine could not have arisen by chance.
2. It was designed. The problem with this is that it is not really an answer. Whether the designer was God, as the bible suggests, or an alien, as Crick suggests, the designer must himself have been a machine of great complexity and we must still wonder about where that designer came from. Design is, really, a transfer of the problem.
3. Evolution but this too has problems. Evolutionary theory, as presently constructed, describes how one organism can change into another, it does not describe how organisms, as Von Neumann machines, can arise de novo. The task, therefore, is to so construct evolutionary theory that one can describe an evolutionary process in a purely chemical environment and show how that process can lead to the kinds of phenomena we now identify as biology. That is one aspect of what I work on.

Case 1. is easily proved impossible. Case 3. which ultimately becomes a modified version of Case 1. contradicts mathematical and scientific laws as is being shown in this thread. Case 2. fits observation far better than either Case 1. or Case 3. The problem with Crickís hypothesis of panspermia is that life still had to originate somehow with the aliens who brought it here.
Originally Posted by John Hewitt
However, note that I just said is that one must describe an evolutionary process that does not begin with a replicator. That seems to be Articulett's problem with me. She believes in Dawkins and I don't. I do not believe that replicators, otherwise known as Von Neumann machines, can lie at the base of evolution. I think the base of evolution is data and data flows. I think that it is the sun's data supply, as well as its energy supply, that drove evolution within a chemical environment and which led to life.

John, I agree that photons flow from the sun but where is the data?
Originally Posted by Kleinman
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 Schneiderís model?
Originally Posted by Kleinman


Do you stamp your foot when you say this?

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?

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 donít you give us a realistic selection process which corrects the deficiency in the model? Why donít you describe to us a selection process that would evolve a gene de novo?

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.

Why donít you educate us on a selection process that would rescue your theory from the mathematical vortex that it is being sucked into.

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.
Originally Posted by skeptigirl
I will repeat my two words, genetic science.

I have one word which trumps your two words, mathematics.
Originally Posted by skeptigirl
Whatever you think you are on to here is silly. But I'll play along for a while. Until I get bored.

God forbid that I bore an evolutionarian with facts.
Originally Posted by skeptigirl
Your underlying premise is totally flawed. We already know evolution is the correct theory because one can follow the genetic trail, manipulate genes, and observe evolution occurring. Am I correct in interpreting your position is that what is observed is not true?

What you are observing are microevolutionary processes and extrapolating these processes to macroevolution. Darwin misinterpreted the variations of bird beaks as mutation and selection when what he was observing was recombination and selection. Gould made the same error when he proposed his concept of punctuated equilibrium which is applicable to recombination and natural selection but not to mutation and selection. Evolutionarians have extrapolated the rapid changes that are possible with recombination and natural selection to mutation and natural selection. Dr Schneiderís computer model reveals the problems with this extrapolation.
Originally Posted by skeptigirl
Am I correct that you are stating evolution couldn't be correct merely because you are unaware of how the processes work?

No.
Originally Posted by skeptigirl
I know how the processes work. It isn't hard to learn. So what is it you think is impossible? New genes? How silly. There are 4 different mechanisms new genes occur in organisms we observe today.

gene transfer mechanisms

Horizontal gene transfer

molecular genetics

genomes in flux

Gene transfer to plants by diverse species of bacteria

So letís see you apply some mathematics to your genetic science and do the bookkeeping required to account for your theory. Dr Schneider tried this with random point mutations and natural selection and this mechanism does not balance the books.
Originally Posted by skeptigirl
There are a multitude of factors you just haven't bothered to learn about here. Unless I have misinterpreted your position. There is a large amount of variation for example in the human genome. When a new selection pressure occurs such as a new epidemic, the genetic diversity assures the genes which may protect some members of the population are already in the population.

So choose your mechanism, formulate the mathematics and balance your books. In case you havenít noticed, there is no selection mechanism that would evolve a gene de novo.
Originally Posted by skeptigirl
The CCR5 deletion is one such example. Persons with 2 copies are highly resistant to HIV yet the mutation arose long before HIV infected humans and being a neutral mutation, there are different percentages in populations based on ancestry alone.

Why donít you describe the selection process that would give rise to the HIV virus de novo?
Originally Posted by skeptigirl
And here you are discussing some nonsense about point mutations being unable to result in new genes? I haven't even begun to discuss the vast amount of knowledge that has been accumulated in genetic science.

Why donít you give us the benefit of your vast knowledge and describe the selection process that would give rise to a gene de novo?
Originally Posted by skeptigirl
Of course, your arguments have been thoroughly discussed both at the Panda's Thumb and Talk Origins, but I suppose in 44 pages those citations have already been posted.

Anybody on these links describe the selection process that evolves a gene de novo?
Originally Posted by skeptigirl
The reason I put this material here, when you are discussing "large polynucleotide fragment autocatalyzing a single rather small change in its structure", is because the underlying premise that whatever "gaps" one finds in any particular piece of evolutionary theory is not evidence the theory is in any doubt. It is simply time to move on.

You are missing the point to this discussion. The argument I am raising here is that Dr Schneiderís ev model of random point mutations and natural selection shows that this mechanism is profoundly slow at accumulating genetic information when realistic genome lengths and mutation rates are used in the model. The rate of information acquisition is far to slow to explain macroevolution by this mechanism. Dr Schneider is the head of computational molecular biology at the National Cancer Institute. His model has been peer reviewed and published in Nucleic Acids Research. If you believe that gene transfer mechanisms, horizontal gene transfer, molecular genetics, genomes in flux or gene transfers to plants by diverse species of bacteria will correct the mathematical deficiency that Dr Schneiderís model reveals in your theory, formulate the mathematics and correct your theory. Otherwise, your theory started without a mathematical basis and remains that way.
Originally Posted by skeptigirl
On the other hand, if you are merely arguing for one mechanism over another or that this or that gap needs filling or testing, then fine. But to think the "gap" is so wide as to actually put the theory of evolution in doubt is absurd in light of what current genetic scientists have been able to accomplish.

What I argue is that random point mutations and natural selection is the cornerstone to your theory. Without this mechanism, all the other mechanisms you describe will not be able to fill the gap left when this mechanism is removed from your theory. Not only does Dr Schneiderís computer model remove random point mutations and natural selection as a viable explanation for macroevolution, it reveals another fatal flaw in your theory, that is a lack of a plausible selection mechanism for the evolution of a gene de novo.
Originally Posted by skeptigirl
As the evidence for evolution is clearly overwhelming, I see the evolution deniers are switching to the new "gap" of life's beginnings. Trying to find Joyce's work I found all sorts of sites proclaiming in essence, "Oh yeah? Well prove this then."

This is evidence for microevolution or genetic modifications by intelligent scientists. Since evolutionarians like to say that macroevolution is simply a series of microevolutionary steps, I have challenged this view that macroevolution is the de novo evolution of a gene. There is no selection process that would do such a thing.
Originally Posted by skeptigirl
I have discussed this work before and the argument was mainly that it hasn't been established yet how the RNA molecules initially occurred. I am not aware if that was a legitimate issue or not since I thought Joyce made a reasonable argument for the occurrence of the molecules. However, it's just one more "gap" and here is an example of it beginning to be filled in.

Since joobz wonít tell us how ribose formed in the primordial soup, perhaps you would tell us?
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Old 24th January 2007, 09:20 AM   #1783
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Originally Posted by John Hewitt View Post
I have the impression that you are asking me to recite and conform to your personal dogma.
What I asked for was a straight answer.

That you chose not to give one is itself sufficient answer for me. However, several other people in this thread are unaware of what your non-answer means, so I feel somewhat compelled to explain it.

Quote:
Does it? Is it? If Hyparxis was unaware of this, he is not alone.
In other words, you agree with Hyparxis that metaphysical naturalism is not adequate to explain life.

Quote:
How about "dunno?" Would that be a middle ground?
In other words, you are uncertain as to whether metaphysical naturalism is adequate to explain life.

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Am I? Which exception is that?
The exception you are championing is an exception to evolution.

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If you feel that my work entails or implies supernatural intervention, then please point out how it does so.
You could, of course, simply state that it does not. But you are too happy to ally yourself with creationists because they are the enemy of your enemy. This, in itself, should be sufficient evidence that you are not metaphysical naturalist.

Before we continue, perhaps we should explain why being a metaphysical naturalist matters. The reason it matters is because if one does not restrict oneself to metaphysical naturalism, then at the end of a very long, tedious conversation one discovers a completely idiotic answer. An answer that makes no sense and contradicts the rest of what we know about the world.

Having read through all of your posts, I see I can provide the perfect example:

Originally Posted by John Hewitt View Post
I think that it is the sun's data supply, as well as its energy supply, that drove evolution within a chemical environment and which led to life.
The sun's "data supply?" What in seven hells are you talking about? The sun produces no "data." It emits a limited amount of information in several spectrums. However, the only information contained in this data flow are the changing temperature patterns of the sun's radiant surface. Compared to the complexity of self-replicating systems, that is an unbelievable paucity of data.

I predict that your "data supply" will be either a poor restatement of current information and energy theory, or a supernatural concept. In other words, it will be either irrelevant or absurd.

But please; expand; explain to all and sundry what clever insights and sterling wisdom the sun dispenses on us daily.
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Old 24th January 2007, 09:21 AM   #1784
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Originally Posted by cyborg View Post
I'm 100% sure that's a meaningless statement.
The quote is from Descartes; "I doubt, therefore I doubt." It is often taken as the one iron-clad assurance of reality. Even if we are brains in vats, if we think we are doubting, we must actually be doubting.

Whether or not it applies to your discussion, I can't say. I have enough trouble tracking Hewitt and his sun-god.
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Old 24th January 2007, 09:29 AM   #1785
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Originally Posted by The Atheist View Post
I have said that currently nothing is a plausible explanation of abiogenesis...

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.
If you are asserting that a non-natural explanation of abiogenesis is possible... then you are pushing the same barrow as the Creationists.

Quote:
To date, John's been honest in the face of concerted attack on him personally.
You call his many evasions "honest?"

Given that we are discussing evolution with a creationist, it is perfectly fair to ask someone bashing evolution whether or not they are a creationist. To take umbrage at such a request, instead of simply saying, "no," is generally considered "the lady doth protest too much."

All he had to do was say that yes, he restricts his work to the arena of science. But as you can see, he does not think science is itself limited to the material, observable world. Or maybe not - yet another question he finds too personally offensive to answer.

Why you want to defend someone who refuses to simply answer questions with a single word is beyond me. Apparently you feel Hewitt has a right to question all of evolution, including casting aspersions on the integrity of evolutionary science, and recieve careful and complete answers; but we may not ask a question of his motivation and expect to recieve a single word.
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Old 24th January 2007, 09:35 AM   #1786
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Originally Posted by The Atheist View Post
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.
As I understand it, John's peers have examined his theories and rejected them.

Yet he has not given up his theories.

In which of the above premises am I mistaken?
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Old 24th January 2007, 10:14 AM   #1787
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Originally Posted by Yahzi View Post
As I understand it, John's peers have examined his theories and rejected them.

Yet he has not given up his theories.

In which of the above premises am I mistaken?
Yahzi, look I am going to be completely clear in my reply to you here. I do not have the faintest idea what "metaphysical naturalism" is. What is more, and I say this as somebody who has read quite a few philosophy books, the branch of philosophy that interests me is epistemology, particularly scientific philosophy. I have little interest in the verbiage that comes labelled as metaphysics or ontology. So when I say "dunno" I really do mean "dunno" and you can add the implied "don't care" as well.

My work on prebiotic evolution is a physico-chemically consistent description of evolution operating in a purely chemical environment. It is the only such system anybody has come up with yet. I don't know whether "my peers" have examined it or not and, in those circumstances, I can hardly know whether or not they have rejected it.

I may add to that, that I am interested in the opinions of only those peers who choose to attach a coherent argument to their opinions. With the exception of Wowbagger, on another thread, I have yet hear such a considered opinion.

Finally, and this is a reply to Kleinman's "John, I agree that photons flow from the sun but where is the data?"

I presume that you own a computer which has at least one data cable attached. That cable is, in fact, a power cable that delivers its energy flux in a form that is modulated to deliver data also. The data cable delivers a low power signal that is amplified by an "intelligently designed" amplifier in your computer that depends on the actual power supply in your computer.

The sun is a data supply because its energy flux turns on and off once a day. The sun delivers a 0,1 data signal once per day. The sun's data signal is very powerful and
can be its own energy supply. As a result, it does not need an amplifier, and its data signal can lead to evolution among the chemical responses. For the details, consider opening
http://www.sexandphilosophy.co.uk
and follow the prebiotic evolution link.
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Old 24th January 2007, 10:22 AM   #1788
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Thank you, kleinman, for moving this thread back on topic.
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Old 24th January 2007, 10:22 AM   #1789
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Originally Posted by Yahzi View Post
As I understand it, John's peers have examined his theories and rejected them.

Yet he has not given up his theories.

In which of the above premises am I mistaken?
Can you provide links or further detail on John's theory being debunked?

Not people who just don't like them, actual refutation of his theories?
Originally Posted by Yahzi View Post
If you are asserting that a non-natural explanation of abiogenesis is possible... then you are pushing the same barrow as the Creationists.
I'll ask again, did you notice my name?

Since - as far as I'm aware - nobody has even come up with a plausible theory yet to describe abiogenesis, I'll just sit on the sidelines. Maybe you could fill me in on how abiogenesis works, please.
Originally Posted by Yahzi View Post
You call his many evasions "honest?"

Given that we are discussing evolution with a creationist, it is perfectly fair to ask someone bashing evolution whether or not they are a creationist. To take umbrage at such a request, instead of simply saying, "no," is generally considered "the lady doth protest too much."
I got the impression that John took umbrage at being hounded over a question he'd already answered. He's shown a lot more patience than I would have been capable of. On that basis, I don't blame him a bit for leading you up the garden path.
Originally Posted by Yahzi View Post
All he had to do was say that yes, he restricts his work to the arena of science. But as you can see, he does not think science is itself limited to the material, observable world. Or maybe not - yet another question he finds too personally offensive to answer.
Did you see what you've written there? Do you know of any christians who would be offended by admission of christianity? All the christian scientists I've seen are proud to state their christian beliefs, especially because they're in a minority.
Originally Posted by Yahzi View Post
Why you want to defend someone who refuses to simply answer questions with a single word is beyond me. Apparently you feel Hewitt has a right to question all of evolution, including casting aspersions on the integrity of evolutionary science, and recieve careful and complete answers; but we may not ask a question of his motivation and expect to recieve a single word.
How many words John's used to answer questions has little relevance. The answers are what matters and he's either lying or not. I choose not. Doesn't make his theories right, though.
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Old 24th January 2007, 10:47 AM   #1790
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Originally Posted by kleinman View Post
If you would take the time to study this thread and the related thread on the Evolutionisdead forum you would get these answers and links with more information.

For eukaryotes, the smallest known which Paul posted is Pelagibacter ubique with a genome length of around 1.3 million base pairs. For prokaryotes, Mycoplasma sp. is around 900,000 base pairs. There are symbionts with shorter genome lengths but are not free living organisms and are dependent upon a host.

...

I think what kjkent1 is looking for is the minimum size genome for a free living organism which I have posted above. The reason this is important is that the genome length is the dominant parameter in Dr Schneiderís model. Until one obtains a free living organism, one is confined to the concept of abiogenesis which is a weaker theory than the theory of evolution. Evolutionarians can not conceive of a selection process that would evolve a gene de novo in a living organism. What kind of selection process would there be in the primordial soup that would evolve a gene?
Alan, what I'm looking for is not the "known" minimum size genome, but rather the minimum size genome required for a creature to be capable of gaining information via RMNS. This is, admittedly, very difficult theoretical model, but my point is, that without some certain knowledge of the minimum size possible, there's no way to calculate the probability of that creature being produced by random chance, and thereafter evolving into something more complex.

Also, I asked John for his opinion re the following model, that I found on the web. I'll ask you, too. It appears pretty interesting to me. Perhaps you can point out the pros and cons.

http://www.cogsci.indiana.edu/farg/h...htm#fp_organic
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Old 24th January 2007, 11:35 AM   #1791
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I'm totally enjoying Cyborg's smackdown of Kleinman. And Yahtzi's smackdown of Hewitt.

Atheist, is just peeved because Yahtzee pointed out he made a false dichotomy when he stated: "John may have something of value, or he may be one of the greatest BS artists the world ever seen." Certainly, the answer is neither. And when I pointed out that Yatzi's assessment was correct, he want on to illustrate further how unclear he was on the concept of "false dichotomy" by claiming Yatzi's Francis Collins statement was an example of just that. (It wasn't). Then he felt personally attacked and started in with the ad homs and backed himself into a corner with Hewitt whom he is certain is an "honest bloke" just as he's certain Yatzi "must be drinking" and I call all people creationists when they don't agree with me (blah, blah, further insults, have an agenda, hammypseak, etc.)

I think Hewitt's statement "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." reveals his leanings rather obviously.
At least to one tuned into "Intelligent Designer-ese"

He's aware of flaws that the scientific community is unaware of. He thinks scientists are liars and cheats. Amazingly enough, no one actually seems to understand what exactly his problems with evolution are since he plays semantic games--nor why scientists are "unaware of these flaws"...moreover, no one can really even seem to sum up what Hewitt is saying or what his theory is nor how it is better than the flawed theory that scientists lie about.

And skepticgirl, heads up, don't even get drawn into conversations with Hammegk. He's got a bad case of "intelligent designer-itis" and almost everything he says is irrelevant and/or a personal attack. He's been on this forum for some time and made tons of posts, but no one seems to even know what the hell he thinks--just that he's a bitter creationist curmudgeon who will not ever change his views, --he hangs out at skeptic forums to tell skeptics how arrogant they are for being materialists or closet dualists or some other philosophical claptrap.

Creationists consume a lot of energy, have a disproportionate sense of their own importance, are very difficult to nail down, never accept any evidence that suggests their alternative "theory" (as if it could be called that) was on shaky ground (see Behe/Kleinman), and just get better at dishonesty and obfuscation as they go along. I agree with Joobz--I have a hard time telling Kleinman and Hewitt apart. And Von Neumann too. They seem smart...they do know a lot in key areas, but their own theories obfuscate rather than clarify and they have imaginary problems with evolution or even the word "memes". They are very good at moving the goal posts and turning the conversation into tangential topics so that you can avoid pinning them down on anything. And even when they are proven wrong, like Kleinman and Behe, they just keep resurrecting like zombies as if the ever accumulating evidence for evolution didn't exist and a smattering of evidence for their claims did.

--Some people seem convinced that they must be saying something important, but they never really seem to be able to say what it is. Their statements just seem so oddly worded...like Kleinman's math claim--as if his forumula was the forumula that we rely on to substantiate evolution... I suspect no scientists have disproven Hewitt's claims because they can't make sense of it. Who uses terms like "free will" in their scientific theory??? To disprove something you have to figure out what the person is claiming. John makes many scientifically accurate statements, a few oddly worded statements (akin to "there's no such thing as memes") and then suggests that he has some alternate better theory that scientists are keeping him from sharing--but he never really says what that theory is--whether it's his "oscillation-genes aren't replicators theory" (for which he Credits Behe for inspiring)--or his sexual selection and the rise of "free will" theory.

I notice that no one seems very clear on exactly what he's saying--why? Because he's not actually saying anything. Scientists can't disprove something they can't decode. There are endless creationists just like him with their own theories and they don't even understand each other (which is obvious on this thread and amongst their few if any interchanges). John has the burden of proof to, not only show the flaws in evolution (he hasn't), but show how his theory is better (he hasn't). Creationists are a waste of time. No amount of evidence in favor of evolution will ever convince them. Ask them. Ask them what they would accept as proof. Then show it to them, and see if they accept it. Scientists are pretty clear as to what constitutes proof--clarity of an idea with a test model is a good starting point. Creationists never even get close to that.

Anyhow, carry on. One day I promise to try and be brief and brutal like Yahtzi and cyborg--but cyberballs are new to me, Atheist. Men seem to enjoy sparring, but women take some time to develop the thick skin required for the game. We're more used to smoothing things out and delineating areas of agreement to key in on issues. My skin is getting thicker. I know you don't believe it, but you made more than 10 personal attacks upon my character when I merely pointed out that Yatzi was correct in saying you were presenting a false dichotomy. I attacked your argument; you attacked me and pretended I was the defamer.
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Old 24th January 2007, 11:53 AM   #1792
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Originally Posted by The Atheist View Post
Thanks for the link in the previous post.

Now I'm wondering how it's possible that you can make so much sense in half a dozen lines while all Articulett's done in about 6000 lines is scream "creationist".
Backpedaling are you? I wasn't screaming creationist, you just couldn't hear anything I wrote once I pointed out your logical "false dichotomy" error. It's you who was hurling insults left and right and anyone who agreed with those whom you feel attacked you (Yahtzi and I for stating the obvious). I believe your comment to him was that he must be drunk. But you saved your real flames for me--unwittingly making yourself into a cheerleader for a creationist while casting aspersions (aspertions--ha) on my character. And, you had actually started with the ad homs long before your silly logic error. You need to examine how your biases are affecting you rather than presuming everyone elses.
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Old 24th January 2007, 11:57 AM   #1793
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Originally Posted by kjkent1 View Post
Sounds reasonable. What do you think of this hypothetical:

http://www.cogsci.indiana.edu/farg/h...htm#fp_organic
I have looked at it. He seems to postulate some kind of analogue quantity, a degree of "rep" one may say that varies at random. At some point or other this rep exceeds a critical value and the molecule becomes a true replicator.

My critique would be that I cannot imagine what physico-chemical quantity rep would correspond to. Can you?

In addition, I think that any actual replicator, with the properties described by Von Neumann, would be much more complex than a single molecule. There is a fairly recent paper here

http://ees.lanl.gov/staff/steen/pape..._published.pdf

that tries to pin down the minimum characteristics of a biological replicator.

In essence, they have a lipid bilayer, which is a boundary to keep everything together, a metabolism to build and power the system and genetic apparatus to transmit and copy the data and the programs that make the whole thing run.
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Old 24th January 2007, 12:02 PM   #1794
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A summary of the work of Julius Rebek, who I mentioned earlier. A good starting point to find out about replicating systems.

http://en.wikipedia.org/wiki/Julius_Rebek
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Old 24th January 2007, 12:14 PM   #1795
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Originally Posted by RecoveringYuppy View Post
A summary of the work of Julius Rebek, who I mentioned earlier. A good starting point to find out about replicating systems.

http://en.wikipedia.org/wiki/Julius_Rebek
I did look up some of his work earlier and it is nice chemistry, inspired by nucelotide chemistry. I think you should make it clear that this sort of thing is not a viable theory for the origin of life.
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Old 24th January 2007, 12:15 PM   #1796
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Originally Posted by The Atheist View Post
Can you provide links or further detail on John's theory being debunked?

Not people who just don't like them, actual refutation of his theories?
I'll ask again, did you notice my name?

Since - as far as I'm aware - nobody has even come up with a plausible theory yet to describe abiogenesis, I'll just sit on the sidelines. Maybe you could fill me in on how abiogenesis works, please.
I got the impression that John took umbrage at being hounded over a question he'd already answered. He's shown a lot more patience than I would have been capable of. On that basis, I don't blame him a bit for leading you up the garden path.
Did you see what you've written there? Do you know of any christians who would be offended by admission of christianity? All the christian scientists I've seen are proud to state their christian beliefs, especially because they're in a minority.
How many words John's used to answer questions has little relevance. The answers are what matters and he's either lying or not. I choose not. Doesn't make his theories right, though.
See, that's another false dichotomy--there are many things that don't specifically fall into "lying or not". And no one can falsify Johns theories if they don't understand it. How many words John uses doesn't matter?!, --but I use too many!? Wow, are you blind to your hypocrisy. And I contend that you don't even understand Johns theory--I'm not sure anyone does. It's becoming fun to watch you sucked in by a creationist.

Abiogenesis is not something one can readily explain to someone who doesn't understand the term "false dichotomy" or the way science operates (hint: it doesn't go about disproving all wacko claims especially when there is far stronger evidence along the path we're on...)

Your Christian claims are nonsense; the wedge strategy is all about making religion sound like science by never using religious words and obfuscating. Apparently it works on the egotistical.

And according to Hewitt's own theory--Scientists are outside the realm of judging the work of other scientists:

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.

This is a common creationist tactic--god is the ultimate infinite regress (who made god?)--if you can't make faith sound like science; make science sound like faith. Who does he think should test the theory of evolution, philosophers? God?

Put your ego and predetermined conclusions aside for a minute, and quit thinking I'm on a witch hunt for creationists or that you are the fabulous defender of underdogs. I'm using words, not weapons. I don't know if creationists are lying on purpose or if they've convinced themselves and others that they are taking the moral high ground or what. But I do know that it's a waste of time to engage them unless you are doing it for your own mental exercises or amusement. Accordingly, I give a warning and a thumbs up to my fellow skeptics. Sometimes it's nice to know a little bit about the crazy path you are about to embark upon and to keep one's expectations low and to have fun.

If you want to engage a creationist, you need to nail down what their saying first.

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Old 24th January 2007, 12:18 PM   #1797
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Originally Posted by articulett View Post
If you want to engage a creationist, you need to nail down what their saying first.
This is a person who questioned my English skills?
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Old 24th January 2007, 12:36 PM   #1798
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http://www.talkorigins.org/faqs/abioprob/abioprob.html

This first replicator and mathematical probability tactics are well documented attempts to throw a monkey wrench into evolution. I think it's pretty clear where you would need to nail someone down before forumulating aspects of proof or disproof. But ask them what they would accept as proof or disproof first. Otherwise, they'll be vague and move the goal posts while using language that makes them sound pedantic and "on the moral highground". Creationists always get vague and obfuscating as you try to understand; they will act as if YOU are too uneducated to understand their profoundly complex conclusions; wheras, scientists tend to bend over backwards to explain and simpliy (often to a hostile crowd whose religion ensures they will not comprehend.)
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Old 24th January 2007, 12:40 PM   #1799
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Originally Posted by articulett View Post
Abiogenesis is not something one can readily explain to someone who doesn't understand the term "false dichotomy" or the way science operates (hint: it doesn't go about disproving all wacko claims especially when there is far stronger evidence along the path we're on...)
<snip>
And according to Hewitt's own theory--Scientists are outside the realm of judging the work of other scientists:
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.

This is a common creationist tactic--god is the ultimate infinite regress (who made god?)--if you can't make faith sound like science; make science sound like faith. Who does he think should test the theory of evolution, philosophers? God?
I don't think you understand my comments about infinite regress. They come out of studies into the foundations of logical systems, arithmetic at first, and are due to Frege, Russell, Wittgenstein and, ultimately, Godel. It is sufficient that I say again, what I have said before - as a philosophy, I don't think evolution is testable any more than I think arithmetic is testable.

As a matter of fact, arithmetic does become testable when articulated within a concrete context and, in my opinion, the same is true of evolution.

Nobody, certainly not you, understands abiogenesis. There is no evidence for any mechanism. However, the mechanism I propose is derived from bioepistemic evolution and physico-chemically consistent. It is also far more parsimonious than any published alternative, which is what makes it an attractive theory.
The mechanism I have proposed is perfectly clear and there are many concrete developments that could test it. However, even if those tests failed, and my mechanism of prebiotic evolution proved to be wrong, still that would not constitute a test of evolution per se.
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Old 24th January 2007, 12:41 PM   #1800
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Originally Posted by The Atheist View Post
This is a person who questioned my English skills?
Yeah---typo--"they're"...I was going to say "their theory" but changed it to what "they're saying" instead. And I didn't question your English skills--I asked if English was your first language because you didn't seem to understand the concept of a "false dichotomy" while presuming you did. Dann is Danish and made a similarly flawed argument by confusing correlation with causation. If English isn't one's first language than maybe the order of the wording is responsible for their lack of understanding and not just their egotistical certainty that they already know all possible errors in logic that humans can make coupled with their equally flawed conclusions that all those who point out their errors have hidden agendas, must be drunk, etc.
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