Ignoring for a moment the empty rhetoric of Luskin, let's explore how Ayala may answer the question. Oh wait... Ayala already answered the questionLeading evolutionary biologist Francisco Ayala recently wrote in Proceedings for the National Academy of Sciences (PNAS) that "Chance is an integral part of the evolutionary process." Ayala then explained why he thinks Darwinian evolution is right and ID is wrong: "Biological evolution differs from a painting or an artifact in that it is not the outcome of preconceived design. The design of organisms is not intelligent but imperfect and, at times, outright dysfunctional." ("Darwin's greatest discovery: Design without designer," PNAS, 104:8567--8573 (May 15, 2007), emphasis added.) This questionable standard and conclusion is Ayala's punchline against ID.
Of course, the answer is also found in the paper which outlines the dual coding genes.Chance is an integral part of the evolutionary process. The mutations that yield the hereditary variations available to natural selection arise at random, independently of whether they are beneficial or harmful to their carriers. But this random process (as well as others that come to play in the great theatre of life) is counteracted by natural selection, which preserves what is useful and eliminates the harmful. Without mutation, evolution could not happen because there would be no variations that could be differentially conveyed from one to another generation. But without natural selection, the mutation process would yield disorganization and extinction because most mutations are disadvantageous.
Seems that there may indeed be advantages to dual coding, in other words, random variation AND selection, which are exactly the mechanisms of Darwinian evolution. Now that Ayala has answered Luskin's question, perhaps Luskin can enlighten us how ID explains dual coding? Oops, I forgot, ID does not deal with such 'pathetic' questions, to paraphrase ID defender Dembski. And people wonder why ID remains scientifically irrelevant? It is doomed to remain so by its own foundation in ignorance. Now I understand why Luskin failed to link to the article in PNAS, Ayala explains it all.Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions.
47 Comments
PvM · 19 June 2007
ERV · 19 June 2007
Wait, what? Overlapping genes are 'magic' to IDers? What? Am I reading this right? Topic covered on page... 40-ish of the Intro Genetics book Im looking at right now? What?
PvM · 19 June 2007
Link to Luskin's 'arguments'
Andrea Bottaro · 19 June 2007
I read that PLoS Comput Biol article when it came out, but I am not sure I understand their methods (too mathematical for me). If I interpret their conclusions correctly, they say that by chance one would expect an ARF of >500 bp to overlap an existing ORF in 0.1-0.3% of cases (depending on assumptions). Based on a 21,000-gene genome, that would mean 20-60 alternative reading frames by chance alone. Or am I missing something?
If that's the case, the occurrence of each ARF is indeed rare, but several should pop up regularly as genomes evolve, and those with selectable functions of course will be maintained.
Andrea Bottaro · 19 June 2007
By the way, here is Chung's paper, for anyone interested (free access).
ERV · 19 June 2007
*blink*
Sooo...HIV is evidence for ID Creationists god once again.
Id like to thank their god personally for my career. Without Him, Id be forced to spend the day playing with my dog and eating ice cream. Does anyone know His phone number?
Or is it just dual coding in humans thats magic? Like how drug resistance in HIV is normal to Behe, but drug resistant malaria is magic?
LPalmer · 19 June 2007
I think the authors make a mistake with the 'virtually impossible' comment. 0.3% is not virtually impossible. It only gives fuel for the IDers. Also the 'virtually impossible' only refers to generating the sequence by randomization. It has nothing to do with evolutionary processes (ie an ARF can start out smaller, than grow larger in size if it offers evolutionary advantage)
Raging Bee · 19 June 2007
Sorry to go off-topic, but something very strange seems to have happened to the "Biblical Inerrancy vs. Physical Evidence" post: a copy of the entire thread seems to have been embedded within one of the comments, and the screen-refresh rate seems to have slowed drastically. At least that's how it looks from my PC. Y'all may want to look into that.
Or it could just be me. I'll check back later...
W. Kevin Vicklund · 19 June 2007
Hawks · 19 June 2007
Popper's ghost · 19 June 2007
These IDiots just can't get it through their thick skulls that "nearly impossible" = "possible" = "likely for sufficiently large numbers of events". And when determining how many events are sufficient, you have to get the math right, as they never do, because they treat all the events as independent, when the key insight of Darwin is that they are dependent, due to selection. When, over and over again, the question is about the climb up Mt. Improbable, you would hope that even someone as dense as Luskin could grasp the concept of "asked and answered".
Popper's ghost · 19 June 2007
PvM · 19 June 2007
Popper's ghost · 19 June 2007
Popper's ghost · 19 June 2007
Popper's ghost · 19 June 2007
Torbjörn Larsson, OM · 19 June 2007
Popper's ghost · 19 June 2007
Ok, you did give the link to Luskin's 'arguments' in the comments, and Luskin was addressing the Chung paper. So LPalmer is right in using the word "virtually" (but not right in his quote mining that omitted the crucial "by chance"), I'm wrong that no one said it, and "ironic" is a rather polite term for my major screwup. My sincere apologies for being such a dufus.
But on the substance -- "virtually impossible" is false, but "virtually impossible by chance" is true. .3% is not the chance in question -- the chance in question is that of there being 40 -- very conservatively -- conserved ARF's. Rather than providing fuel to IDists, the paper is presenting a statistical argument that they are a result of selection. When they said "virtually impossible by chance", that's really what they meant -- and whether they are right or wrong, it doesn't give a whit of support to ID arguments.
Popper's ghost · 19 June 2007
Torbjörn Larsson, OM · 19 June 2007
Torbjörn Larsson, OM · 19 June 2007
Popper's ghost · 19 June 2007
Heleen · 20 June 2007
Luskin would have an even harder time with the article by Michael Lynch in the same PNAS supplement.
Frank J · 20 June 2007
Frank J · 20 June 2007
If you click the link in Comment 183867, make sure to scroll to the first of 3 posts. The part about how IDers know (privately at least) that it must be evolution (if not their "Darwinism" caricature), and how they must agree (privately at least) that any "discontinuities" do not disrupt the "biological continuity" of common descent is more compelling than ever in light of their approval of Michael Behe's new book.
Andrea Bottaro · 20 June 2007
OK, I guess in all the bickering my point on the paper got lost. Does anyone understand from their methods section whether the algorithm does/should correct for the number of genes?
From my understanding, they take an ORF, check if it has any ARF longer than some arbitrary value, than change codons around on the ORF in simulated alignments and see whether the ARF is still there. If it's there in only a rare combination of codons on the ORF that allows for the ARF, they consider it a statistically significant ("real") ARF.
What I am not sure of, does this process need to correct for the fact that there are tens of thousands of ORFs in the genome, and the frequency by which these can potentially encode ARFs? Or should it only consider ORFs on an individual basis? I think this is the key to understand the "virtually impossible" statement.
LPalmer · 20 June 2007
LPalmer · 20 June 2007
My use of the 14159 number of genes is not going to be correct. Really one should determine the number of ORFs > 500.
Still it would be nice to know the statistical probability of observing 149 genes, or the statistical probablity of observing none.
Flint · 20 June 2007
Gary Hurd · 20 June 2007
LPalmer · 20 June 2007
Randy · 20 June 2007
one would think that at least a couple of IDers would have seen Princess Bride (given their propensity for Vinzini like logic). Just as Miracle Max knows the difference between mostly dead and dead, just as the there is difference between nearly impossible and impossible.
Miracle Max:Hoo hoo hoo! Look who knows so much, heh? Well, it just so happens that your friend here is only mostly dead. There's a big difference between mostly dead and all dead. Please, open his mouth. Now, mostly dead is slightly alive. Now, all dead...well, with all dead, there's usually only one thing you can do.
Henry J · 20 June 2007
If I'm understanding correctly what "dual coding" means, it sounds like something that a competent bioengineer would avoid, unless it there was some function that couldn't be produced without it.
Henry
dhogaza · 21 June 2007
Stephen · 21 June 2007
Stephen · 21 June 2007
"skipper was thrown overboard"
"kipper was thrown overboard"
Tyrannosaurus · 21 June 2007
It is obvious that Francisco Ayala answered what ever Luskin was questioning/implying anyway. That the answer was already in the essay and Luskin was not able to understand it is not a surprise either. Luskin cannot write coherently how he pretend to argue logically with the likes of Ayala who is light years ahead of him? Oh, I forgot Luskin must have received his knowledge through divine revelation and thus he knows everything.... NOT.
Torbjörn Larsson, OM · 21 June 2007
"This is an interesting game."
"His is an interesting game."
"Not going to use acronyms?"
"OT going to use acronyms?"
Exiled from GROGGS · 25 June 2007
Cool! So the question was "How would dual coded sections of DNA evolve?" boils down to "By random mutation and natural selection."
Fantastic. Ten out of ten for accuracy, and minus several million for usefulness. Do you work for Microsoft?
But seriously, folks .... the point Luskin was making was that the chances of random mutations generating something that dual codes is very small. And the reason he made this point was because each random evolutionary step along the way has to convey an advantage for natural selection to work with. It's easy to see that a dual-coding section of DNA conveys a significant advantage. What isn't easy to see is how you get there from a non-dual-coding piece of DNA.
You have a choice. You can either continue to pat yourselves on the back over another mythical (not even pyrrhic) victory over the forces of darkness, or you can say, "Actually, to be honest, we haven't a clue, and we don't have a handle on the numbers involved." Or you could suggest something a bit more scientific in terms of process and calculation.
Incidentally, PvM, a fully specified sequence of 500 BP has an improbability of about 1 in 10^300. It may not be the same as 1 in 10^150 - but it does acknowledge a limit.
Exiled from GROGGS · 25 June 2007
... and another thing.
"I saw a peacock with a fiery tail.
I saw a blazing comet drop down hail.
I saw a cloud with ivy circles round.
I saw a sturdy oak creep on the ground.
I saw a pismire swallow up a whale.
I saw a raging sea brim full of ale.
I saw a Venice glass sixteen foot deep.
I saw a well full of men's tears that weep.
I saw their eyes all in a flame of fire.
I saw a house as big as the moon and higher.
I saw the sun even in the midst of night.
I saw the man that saw this wondrous sight.
- Anon."
There's an example of of a dual-coding text - and the two codes are properly displaced, not overlapping. That's what's clever about it. Is that the product of an unintelligent process, I wonder?
But that's not a dual-coding stretch of text, yet. Can anyone think of a string of text - over, let's say, 20 characters, that conveys two different, unrelated meanings depending upon where you start? I daresay somebody can. But it would take careful thought and planning.
Henry J · 25 June 2007
David Stanton · 25 June 2007
Exiled from GROGGS wrote:
"And the reason he made this point was because each random evolutionary step along the way has to convey an advantage for natural selection to work with. It's easy to see that a dual-coding section of DNA conveys a significant advantage. What isn't easy to see is how you get there from a non-dual-coding piece of DNA."
As Henry J pointed out, dual coding is probably not an advantage, unless extreme economy is selected for, which it definately is not in eukaryotes.
Also, it does not have to convey an advantage at every step along the way, it just has to be neutral or only slightly deleterious at every step. The function of the first reading frame would maintain the sequence, while the second reading frame would be constrained by the requirements of the first but could still change considerably over time. If this type of thing were truly adaptive then the genetic code would probably not be read in a non-overlapping fashion.
Exiled from GROGGS · 26 June 2007
What I mean is that it's easy to see that a dual-coded piece of DNA conveys an advantage compared to a single-coded piece if the second function that it encodes would otherwise have been absent. From a redundancy POV, you are right - it would make more sense for the two functions to be separate.
David Stanton · 26 June 2007
Exiled from GROGGS,
Agreed. So once again, there is not theoretical reason why such a system could not arise through random mutation and natural selection and no real reason for an intelligent agent to design the system this way from scratch. Makes perfect sense from an evolutionary perspective but not from an ID perspective.
Popper's Ghost · 27 June 2007
Popper's Ghost · 27 June 2007
Popper's Ghost · 27 June 2007