A second highly selected gene, LYST, is associated with pigmentation, and changes in it are probably responsible for the blanching of the ancestors’ brown fur. Computer analysis for the multiple mutations of the gene showed that they too were almost certainly damaging to its function.
In fact, of all the mutations in the seventeen genes that were most highly selected, about half were predicted to damage the function of the respective coded proteins. Furthermore, since most altered genes bore several mutations, only three to six (depending on the method of estimation) out of seventeen genes were free of degrading changes [fn 2]. Put differently, 65 to 83 percent of helpful, positively selected genes are estimated to have suffered at least one damaging mutation.
- Darwin Devolves p. 21
fn 2 is Table S7 of Liu et al.
Can we work through this one item at a time to see what people agree with or disagree with?
And this is basically what Behe is saying. It is beneficial to polar bears that their hair lacks melanin. If a gene is mutated so that it prevents the appearance of melanin in the hair by whatever means then it is advantageous. And it is much easier for mutations to prevent processes from happening than it is to build new structures. It is much easier to alter the function of a TV set by flicking a switch that cuts its power supply than it is to alter it by inserting a novel component into its circuit.
Do we have any examples of exaptation where we have a clear idea of the genetic changes involved?
CharlieM,
I like the example wikipedia (biased skeptic website) uses for exaptation-bird feathers. They speculate that once they were for warmth, and then later got used for flight.
But I much prefer the neutral theory idea. First the feathers were for nothing, then they just so happened to be good for flight.
Hahahahaha….Go Swamidass!
Thanks, this is actually relevant information, because this implies LYST is actually likely to be a “modification of FCT” in the polar bear, as opposed to a “loss of FCT”, going by Behe’s 2010 paper parlance.
And he actually does appear to use these terms in his new book, if you look on Amazon page, some parts of the book are visible, and he uses the term on page 294 there:
It is likely Behe introduces and defines these terms earlier in his book.
Another funny little gem on that visible page:
That is Behe’s attempt to infer modes and patterns of evolution from phylogenetics. Notice the inherent irony in that statement. How does Behe know that the genes in polar bear are “strongly selected” and “damaging”, and therefore is inferred by him to support his first rule of adaptive evolution? BY SEQUENCE COMPARISONS. Inferences made on the basis of the existence of gene sequences with differences in them between different species and different individuals. That’s how it is inferred that they evolved under selection. The very concept Behe now rejects when put to analysis of flagellum proteins.
Hypocritical, selective, double standard.
I see you’ve failed to understand the distinction between the neutral theory of molecular evolution, and phenotypic evolution. In essence, you don’t get the genotype vs phenotype distinction.
Nobody claims the macroscopic physiological attributes of organisms, such as feathers, are neutral or just evolved for no reason at all.
Yes, the cit+ function in Richard Lenski’s LTEE is an example of exaptation. Exaptation between distinct genomic entities have been observed to happen, to create functional associations between previously disparate genetic elements.
A genomic locus (the citrate transporter protein) was duplicated into another part of the genome, and it just so happened to end up under control of a promoter that was active under aerobic conditions, and the translocated gene just so happened to be a citrate transporter that could take up citrate, which just so happened to be present in the growth medium.
So in this instance, it is actaully the promoter, normally involved in regulating a different set of genes, that is exapted to regulate the citrate transporter to create the novel function of aerobic citrate transport.
Really, nobody?
Maybe you better read some more evolutionists websites. Care to bet?
Isn’t that the mistake that Swamidass makes? You’re free to say so here. 🙂
🙂
No response, Mung? Do you realise how big of a paradigm change it would be to have a new mechanism for evolutionary innovation? Why would the ID camp not boast about this awesome scientific milestone?
I know why, there’s nothing there in chapter IV worth shit. Otherwise that would be the main point of the book instead of the ubiquitous, IDiotic, negative argument
Its pretty funny, if we were only talking about molecular evolution, and not changes to the phenotype, HOW could you have anything but neutral mutations? How is a phenotype that isn’t changed any going to be selected over another phenotype that is the same?
Does Rumraket know what selection means do you think?
dazz,
Its in a book. I think its by Futamamamia. Go read it, you will find the answers.
You can probably find some crackpot random internet nobody who says it. You can also find people who think a snake can talk, and that a man once resurrected himself after being dead for three whole days. Go figure.
I haven’t seen him make this mistake. Point it out to me.
Is there anyone here who can make sense of this latest gibberish of phoodoo’s?
Do you understand written english, at all?
You can bet your sweet life that not a single cent of mine will ever go to the scumbags of the DiscoTute. Your refusal to tell us about this supposedly huge discovery speaks volumes anyway
Is that not the same one that Behe discusses in his new book?
Just noticed the most recent podcast by Behe about the criticisms of the book here
I’m sure he’s got some sort of spin about it. In his view it probably only counts as a modification of function.
That’s correct. I’m trying to stay on topic. Feel free to get the book and read Part IV and start your own OP on it.
Oh, bummer. I guess we’ll never know about it. Almost as if it didn’t exist. Very godlike BTW
Sure. What’s the bet precisely? State the entire bet.
I bet that if there is a lottery that is guaranteed to have a winner that there will be a winner no matter how improbable it is. Therefore IDists don’t understand probability.
And you would still be wrong. Can you see why?
Still reading the book. Should I shortcut and just do a search for selection, mutation or gene? Perhaps.
ETA: I didn’t “run away” from anything.
I’ll go with genes.
And as we have seen, it is likely the LYST example discussed in this thread is actually just a case of “modification of FCT” by Behe’s own definition, rather than “loss”. So that’s one potential misrepresentation by Behe about LYST.
Should we proceed to the next gene?
Only if it is the “most highly selected”, Rumraket.
Mung has clarified that this
refers to the most highly selected genes, not mutations. [‘Mutations’ really made no sense…]
So let’s take that into account, and ask: “Are the genes under the strongest selection more likely to have a majority of non-‘benign’ mutations?
Here goes:
Liu et al used three criteria to identify genes under strong selection in the polar bear since divergence.
1) The homogeneity test statistic (HTS) (which looks for a low polymorphism and high divergence)
2) The HKA test to detect selection that was specific to the polar bear branch, and not the brown bear branch of the tree.
3) The estimated fixation index, Fst (think of it as how little variation there is within a population, as compared with the variation between populations…)
Which metrics might Behe use to zero in on the genes under strongest selection?
Wanna use the HTS? Okay, TTN is the winner and 60 – 80% of mutations in TTN are ‘benign’.
Wanna use the HKA? Well, OR5D13 is the winner and 100% of mutations are ‘benign’.
Wanna use Fst? Oh, TTN is still the winner. Let’s not always see the same hands shall we? The runner-up is AIM1 and 67 – 100% of mutations are ‘benign’.
Even if you accept Behe’s interpretation and use of Liu’s data (and you should not), then Behe’s thesis is not holding up.
You’re cherry picking and you know it. Stop it.
That’s a bold claim! (Might be a bald assertion too, especially the “and you know it” bit). Are you saying DNA-Jock selected examples from data, some of which does not agree with the question “Are the genes under the strongest selection more likely to have a majority of non-‘benign’ mutations?” Can you point to the cherry-missed data?
It is true; I cannot tell a lie. I picked a cherry. Allow me to explain.
Mung pointed out that we must ‘take into account’ that Behe is explicit that he is talking about the genes under the strongest selection.
Liu used three criteria. I listed all three. By each criterion, there was one gene that was the most selected. I listed those genes. Furthermore, I listed the % benign mutations under BOTH predictive algorithms.
Zero cherry picking so far.
However, when I saw that TTN was the winner in two categories, I decided to offer the tiara to the second place finisher in the Fst category, and not to the second place finisher in the HTS category, because it was funnier that way. (Second place in HTS was APOB, which had already been discussed somewhat…)
I was guilty of cherry-picking there. I am sorry.
Now, about the statement
or
or
The first Behe quote here is cherry-picking. The others are good old-fashioned false.
But that’s just hunky dory, and begs for a charitable reading? As you wish.
Given that it was a past event the probability was 1. But really, I just flipped a
coin. Either he was cherry picking or he wasn’t. Either he knew it or he didn’t. The odds were really quite good!
On the scale of cherry picking, how do you rate Behe and DNA-Jock?
“Darwin does devolve. Sometimes. So what?”
“…A minority of the changes correspond to loss of function, including most obviously loss of pigmentation, yet by extreme cherry picking Behe presents the loss of function as dominant…”
Really?
Darwinian science is sh**ty. Most of the times. So what?
Nothing, no evidence, will change someone’s mind if he doesn’t want to change it. Always. So why continue to bother to try???
At least some of us try, perhaps sometimes not as hard as we could, to see and comprehend an alternative point of view. You, however, seem to avoid clarifying or supporting your apparent disdain for evolutionary biology. It’s not a hugely effective technique.
Good article, thanks for the link.
Behe:
Is there any disagreement about which genes belong in the list of 17 “most highly selected polar bear genes”?
I have to disagree… I think this article is bad, for Darwinists, of course…
If I were a Darwinist, I would seriously reconsider my support for this ideology…
No matter what mechanism Darwinists would like to include in their ideology, it really looks bad when the main mechanism of the theory is exposed as the devourer, rather than builder, of new genes and functions and the author dismisses it with: “So what?”
It proves my many points that Darwinism is not about evidence but rather about philosophy and ideology…
What do you think?
Yes, yes there is.
By the way, what did Behe have to say about Farese et al. 1995 in “Darwin Devolves”?
[that’s PNAS 92(5):1774-8]
Thanks.
I’m sure Jock will find something he doesn’t like…
What’s that? Are you suggesting there is a third-way-view?
My favorite part of Behe’s response is this:
“Professor Lenski is perhaps the most qualified scientist in the world to analyze the arguments of the book.”
and
“…Echoing blogged arguments by his lesser-known co-authors of the appalling review of my book in Science, Professor Lenski points out …”
He doesn’t even mention Lents and Swamidass by their names…
I think it is because both of them embarrassed themselves so much, especially recently, that he doesn’t want the critic of his book to lose credibility…That’s why he calls Lenski “…the most qualified scientist in the world to analyze the arguments of the book…” lol
J-Mac,
The embarrassment is not only these guys but also L Moran and K Miller in the past. They publicly used straw man arguments to try and neutralize Behe. A straw man that would minimize their burden of proof.
J-Mac,
What’s a Darwinist?
This is just the beginning…
Wait until embryo development becomes mainstream, including spatial anisotropies…an such… 😉
Ah you think that do you? That’s cute.
After 10 seconds of searching OMIM
emphasis mine.
Sorry to burst your bubble, but I would advise some caution. Chances are that it is Behe that is going to be embarassed. Pulling a single favorable publication from the hundreds of papers on hypercholesterolemia and APOB function does not look all that impressive to me.
Moreover, why is Joshua Swamidass so upset about being called a Darwinist?
Who knows. I’m a Darwinist, in the sense that I think natural selection is important and is a significant part in the explanation for the diversity of life and it’s ability to adapt to environmental challenges.