Evolution: Whatever works

[Paul C. Anagnostopoulos]

In the midst of evolution conversations here, some of us have mentioned that "anything goes" in evolution. If it works, it sticks around. The central dogma of molecular biology (http://www.accessexcellence.org/RC/VL/GG/central.html) is becoming frayed around the edges, and strange biological mechanisms are being discovered every week. One of the first oddities were ribozymes, which are bits of RNA that play enzymatic roles. The major components of the ribosome are RNA structures.

In the 26 May issue of Science, there is an article about a "riboswitch." A riboswitch is an untranslated region of messenger RNA that can adopt one of two conformations depending on the presence of some other substance. One of the conformations allows some controlled process to occur, while the other does not. The article describes a switch that recognizes the presence of TPP. So here we have some DNA being transcribed into mRNA, but the mRNA acting as a switch rather than being translated into a protein.

In the same issue, there is an article about a regulatory single-neucleotide polymorphism (rSNP) involved in alpha-thalassemia. Located between the transcription regulators and a group of alpha-globin genes is a non-gene region that is normally silent. However, a single-neucleotide mutation causes this region to behave like a transcription promoter and interfere with the transcription of the alpha-globin genes. So here we have a new kind of disease-causing transcription regulator in what was formerly "junk" DNA.

Whatever works, folks. If someone wants to claim that this is all designed, don't hire that person to work on a software development project.

~~ Paul

[hammegk]

... If someone wants to claim that this is all designed, don't hire that person to work on a software development project.

~~ Paul
No, unless you want code that actually works.

Also, makes 'ya wonder about our ability to recognize "junk".

[Dr Adequate]

No, hammy --- we're all certain that you can't recognize junk.

[Meffy]

No, unless you want code that actually works.
There's a vast difference between "works" and "can be kept working without divine intervention." I've dealt with projects that happened at one time to have "worked" just fine... but which were not worth the cost of keeping current. IOW, they were complete losses.

[hammegk]

There's a vast difference between "works" and "can be kept working without divine intervention."
LOL. You might want to think about what you actually said there. :D

And poor Dr-Inadequate (except for personal attacks) .... :rub:

[Lamuella]

Also, makes 'ya wonder about our ability to recognize "junk".

That it does. And if we can't recognize "junk" then our ability to recognize "design" other than our own must be equally suspect. Thank you for making this timely and informative comment on Dembski's Explanatory Filter.

[hammegk]

We agree Dembski's ideas are not worth much, if not worth less. ;)

[Paul C. Anagnostopoulos]

Also, makes 'ya wonder about our ability to recognize "junk".
Indeed, the whole junk DNA story acts as an admonishment to scientists not to be too dogmatic in their pronunciamentos. Fortunately, scientists learn a lesson, perhaps reluctantly, while certain other groups probably will not.

~~ Paul

[Meffy]

LOL. You might want to think about what you actually said there. :D
I thought before I "said" it; that was sufficient. And I'm not theorizing, I've been there for real. "LOL." =9_9=

[Wowbagger]

One man's junk is another thing's treasure.

That is the way of nature.

[hammegk]

Or, one thing's junk (rna/dna) is another thing's treasure (rna/dna).:D


I thought before I "said" it; that was sufficient. And I'm not theorizing, I've been there for real. "LOL." =9_9=
Er, yes. The point was would you care to maintain the current rna/dna code? Something manages to. ;)

[Meffy]

Ah, now I see what you're getting at. I was working at the program code side of the metaphor, not the chemical one. But the question has no meaning IMO. I don't believe the current DNA/RNA code is maintained by a "something" at all. It does what it does on its own.

[Paul C. Anagnostopoulos]

Yes, the thing that manages to "maintain" the current code is the same thing that formed it in the first place. In fact, there is no distinction between development and maintenance.

~~ Paul

[hammegk]

I agree both of you could hold a logical worldview -- 100% physicalism -- that supports your assumptions. I only ask if you actually do hold that worldview? If not, what logically defensible worldview do you hold? Or do you choose to have faith it makes no difference?

[Meffy]

I choose to ask that you guess and be happy with your guess, which might be right or wrong. I have zero interest in "defending a worldview" for your entertainment.

[hammegk]

Your "choice" ... ;) Interesting concept, depending on your worldview.

[Meffy]

Ah, no -- depending from my worldview. And brachiating about happily.

[rocketdodger]

No, hammy --- we're all certain that you can't recognize junk.

It occured to me, after seeing the scene in "the 40 Year Old Virgin" where the guy responds with nothing but questions, that hammy must get more action than any other human on the planet.

[delphi_ote]

In the midst of evolution conversations here, some of us have mentioned that "anything goes" in evolution. If it works, it sticks around. The central dogma of molecular biology (http://www.accessexcellence.org/RC/VL/GG/central.html) is becoming frayed around the edges, and strange biological mechanisms are being discovered every week. One of the first oddities were ribozymes, which are bits of RNA that play enzymatic roles. The major components of the ribosome are RNA structures.

In the 26 May issue of Science, there is an article about a "riboswitch." A riboswitch is an untranslated region of messenger RNA that can adopt one of two conformations depending on the presence of some other substance. One of the conformations allows some controlled process to occur, while the other does not. The article describes a switch that recognizes the presence of TPP. So here we have some DNA being transcribed into mRNA, but the mRNA acting as a switch rather than being translated into a protein.

In the same issue, there is an article about a regulatory single-neucleotide polymorphism (rSNP) involved in alpha-thalassemia. Located between the transcription regulators and a group of alpha-globin genes is a non-gene region that is normally silent. However, a single-neucleotide mutation causes this region to behave like a transcription promoter and interfere with the transcription of the alpha-globin genes. So here we have a new kind of disease-causing transcription regulator in what was formerly "junk" DNA.

Whatever works, folks. If someone wants to claim that this is all designed, don't hire that person to work on a software development project.

~~ Paul
Fascinating, Paul. I've done a lot of reading about ribozymes, and the riboswitch is very interesting to me. The implications for an RNA World in this research are huge!

But once again we're squabbling with someone who can't appreciate it. *sigh*

[hammegk]

What makes you think I don't appreciate science and its' results? I have some doubts about the usefulness of open-ended thermonukes, perhaps.

(I make a w.a.g. I am the "squabbler" you state wouldn't. If wrong I apologise.)

[T'ai Chi]

Whatever works, folks. If someone wants to claim that this is all designed, don't hire that person to work on a software development project.


..because a software developer's skills are somehow intimately related to their knowledge of biology.

[Paul C. Anagnostopoulos]

..because a software developer's skills are somehow intimately related to their knowledge of biology.
No, because a software developer's opinion of good vs. bad design may be slightly off track if they think that biological mechanisms are designed.

Anyway, it was a joke.

~~ Paul

[Eos of the Eons]

http://www.uwgb.edu/dutchs/PSEUDOSC/Top10MythsEvol.HTMMyth #10. Complexity Cannot Arise Naturally
The Second Law of Thermodynamics is often paraphrased as:

”Things always go from bad to worse”
”Disorder in the Universe is always increasing"
The Second Law of Thermodynamics is about entropy, which is defined as (Heat Absorbed in a process)/Temperature Entropy can decrease locally if it increases elsewhere. Intuitive notions of “disorder” are of no relevance whatsoever. Any discussion of the Second Law that does not specifically define entropy and show how it relates to evolution is worthless.

Chemical reactions are not random. For example, the atoms in a crystal of table salt are arranged as below, with sodium and chlorine atoms in a strictly alternating square array. If we take the simple-minded approach that we have a one-half probability of getting a sodium or chlorine atom in each spot, the chance of getting 100 atoms arranged as below is (1/2)100 or one in 1.26 x 1030. That's roughly one followed by 30 zeros. According to this reasoning, table salt is impossible.

Na Cl Na Cl Na Cl Na Cl Na Cl
Cl Na Cl Na Cl Na Cl Na Cl Na
Na Cl Na Cl Na Cl Na Cl Na Cl
Cl Na Cl Na Cl Na Cl Na Cl Na
Na Cl Na Cl Na Cl Na Cl Na Cl
Cl Na Cl Na Cl Na Cl Na Cl Na
Na Cl Na Cl Na Cl Na Cl Na Cl
Cl Na Cl Na Cl Na Cl Na Cl Na
Na Cl Na Cl Na Cl Na Cl Na Cl
Cl Na Cl Na Cl Na Cl Na Cl Na
But of course the reasoning is ridiculous. The chances of getting that arrangement of atoms is close to 100 per cent.

And we know DNA can arise from simpler chemicals because it does so every time your cells divide. Every haircut you get is proof of it. The missing half of the DNA strand is assembled from molecules in the cell fluids.

"But when cells divide, there's a pattern already available" say some anti-evolutionists. Try this: go to the lumber yard and buy the materials for a tool shed. Then put a set of plans on top of the pile, and let me know when the materials spontaneously assemble. I can pour gasoline onto a garbage pile and the molecules in the garbage won't suddenly get the urge to develop into gasoline, even though there's enough carbon and hydrogen to do it. The pattern means nothing. DNA replicates because it can spontaneously self-assemble.



If I wasn't so tired I'd be able to comprehend this cool link better, will go back and read it again tomorrow.

[RandFan]

http://www.uwgb.edu/dutchs/PSEUDOSC/Top10MythsEvol.HTM

If I wasn't so tired I'd be able to comprehend this cool link better, will go back and read it again tomorrow.That is so cool. Thanks.

[Bronze Dog]

Funny how hammy brings up our "worldview (http://rockstarramblings.blogspot.com/2006/05/doggerel-5-worldview.html)," as if that somehow changes the experimental data.

[Meffy]

Good essay, even if I was disappointed by the lack of bad verse. Doggerel indeed. Grumble.

[hammegk]

Funny how hammy brings up our "worldview (http://rockstarramblings.blogspot.com/2006/05/doggerel-5-worldview.html)," as if that somehow changes the experimental data.
When human actions are involved, I'm as skeptical as anyone and more skeptical than most of any claim. Science based on one-of-a-kind unrepeatable past human actions, some dating back more than a century, and used as absolute justification do not count as "hard, factual, science" reapeatable anywhere and anytime.

The foolishness the Amazing One etal debunks speaks solely of scams and cons involving human behaviors.


And re the Eos link .... so what?

[Bronze Dog]

When human actions are involved, I'm as skeptical as anyone and more skeptical than most of any claim. Science based on one-of-a-kind unrepeatable past human actions, some dating back more than a century, and used as absolute justification do not count as "hard, factual, science" reapeatable anywhere and anytime.

The foolishness the Amazing One etal debunks speaks solely of scams and cons involving human behaviors.
One wonders if hammy has a point.

Of course, this doesn't relate to evolution, since the measurements of fossil ages are repeatable, as are the DNA analyses.

[hammegk]

One wonders if hammy has a point.

Of course, this doesn't relate to evolution, since the measurements of fossil ages are repeatable, as are the DNA analyses.
Indeed. Fossils wrenched from the rock are all one-of-a-kinds. Age is often a minor point for discussion.

As to the dna, yup, "life" mutates. No doubt about it. :)

[Bronze Dog]

Indeed. Fossils wrenched from the rock are all one-of-a-kinds. Age is often a minor point for discussion.
But the measurements aren't one-of-a-kind. And, of course, age is important. That's why they've got all those isotope dating, strata, and probably plenty of other dating methods to verify one another.

As to the dna, yup, "life" mutates. No doubt about it. :)
True. Also, lots of organisms share sequences all over the place. For instance, all cats have the same "error" in their genes for tasting sweet stuff, last time I checked.

[hammegk]

Yeah, nothing like a good common ancestor/parallel development debate. :)

[Hellbound]

Yeah, nothing like a good common ancestor/parallel development debate. :)

Unfortunately, one of the debaters is you, which precludes "good".

[blutoski]

Indeed. Fossils wrenched from the rock are all one-of-a-kinds.

Mm. This doesn't mean it isn't hard science. Science is mucho inductive.

When I put a thermometer in a flask, and take the temperature, it's only measuring the average kinetic energy of the molecules that touched it, not 'the liquid' as a whole. The induction is acceptable via common-sense.

All medical studies are done on samples somewhat smaller than 'the entire human population,' and are treated as representative if selected properly.

It is the inductive nature of these findings and the subsequent model's predictive power that arguably makes it science. The testability is not to repeat the 'find' but to predict other finds, not yet discovered. eg: MtDNA relationships correlating to strata dating.



Also: most fossils are not literally "one of a kind." Sometimes the first of its kind becomes famous, but then we dig up millions more and it's not news. The challenge then becomes storing them all. A friend of mine was surpirsed to learn that we have hundreds of Neandertal skeletons; he thought maybe there were just a few fragments here and there.

I have a fossil I found near cache creek that I viewed under a microscope. There must be literally billions of these little gribblies in a rock the size of my fist.

[hammegk]

Unfortunately, one of the debaters is you, which precludes "good".
Especially for those of you who don't appear to understand your worldview or what it actually entails .... :)


In the midst of evolution conversations here, some of us have mentioned that "anything goes" in evolution. If it works, it sticks around. ...
And the question becomes, given physics and chemistry, could anything that could possibly have replaced it also have "worked"?

[aggle-rithm]

No, because a software developer's opinion of good vs. bad design may be slightly off track if they think that biological mechanisms are designed.

Anyway, it was a joke.

~~ Paul

Also -- and I've brought this up in a previous thread -- organisms more closely resemble poorly-designed and maintained software projects than those that are carefully engineered. Such projects contain layers upon layers of incomprehensible spagetti code, each put into place as a fix for some unintended side effect of a previous layer. You can't really say it's designed, as the coders just blindly react to a specific problem without looking at the big picture. It may work, eventually, but if anything goes wrong it takes a major effort to diagnose and fix the problem.

A lot like life, actually.

[Hellbound]

Especially for those of you who don't appear to understand your worldview or what it actually entails .... :)

Have you applied for the million yet? Since you can read people's thoughts and know what they think better than they know themselves?

Are are you just talking out your rear orifice again, and contributing nothing as usual, while implying some sort of sooper sekrit pro found gnawlege?

Figured it was that one.

[hammegk]

Is hidden in that bit of otherwise meaningless crap the implication that you, at least, understand your worldview and what it entails?

Just guessing -- no attempt at the million -- I'd say, I'd say .............



































NO!



Am I right? :)

[Eos of the Eons]

I don't understand the confusion about my link.


Paul Said:

If someone wants to claim that this is all designed, don't hire that person to work on a software development project.



And my link also addresses the ID claims.

Thing is, dna acts quite predicatably when you look at chemistry, and so does evolution. It's whatever works, and sometimes something good comes out of it.

For some reason that is not enough for some people. Instead we have this idea of a crazy designer, a mad hatter that finds crazy way to design things. If I had control over the situation one would hope I could design it better. Are we going to hear about dna free-will next?

[hammegk]

Thing is, dna acts quite predicatably when you look at chemistry, The choices on folding it makes follow precise order not mandated by chemistry.


and so does evolution.
Change occurs.


It's whatever works, and sometimes something good comes out of it.
Again, the real question is could anything else have possibly worked?


For some reason that is not enough for some people. Instead we have this idea of a crazy designer, a mad hatter that finds crazy way to design things.

Who are those you refer to?


If I had control over the situation one would hope I could design it better.
LOL. Go for it.


Are we going to hear about dna free-will next?
Does the chart of elements involve free-will? Do quark, boson, or lepton interactions?

Cramer's Transactional Interpretation??? :) :p :D

[hgc]

...
Does the chart of elements involve free-will? Do quark, boson, or lepton interactions?...hammy's boson: the energizer bunny of non sequiturs.

[Cecil]

Also -- and I've brought this up in a previous thread -- organisms more closely resemble poorly-designed and maintained software projects than those that are carefully engineered. Such projects contain layers upon layers of incomprehensible spagetti code, each put into place as a fix for some unintended side effect of a previous layer. You can't really say it's designed, as the coders just blindly react to a specific problem without looking at the big picture. It may work, eventually, but if anything goes wrong it takes a major effort to diagnose and fix the problem.

A lot like life, actually. Usually if something goes really wrong, you end up scrapping it altogether, or at least rolling back to a previous version.

Also a lot like life. :)

[hammegk]

hgc's life: an unending sequence of non sequiturs.

[delphi_ote]

hgc's life: an unending sequence of non sequiturs.
Is there such thing as an "I know you are but what am I?" fallacy?

[Meffy]

Is there such thing as an "I know you are but what am I?" fallacy?
Isn't that a special case of the "neener neener neener" dodge?

[hammegk]

That depends on ones' ability to understand, doesn't it? :)