Behe's new paper

[QuestionMark]

Outhouse,
I wasn't aware that's what I was doing. I'll take that into consideration.
Thank you,
QM

 

[fantome profane]

It's probably a good idea to remember that his ideas are less ambiguous when given more space and time to explain them such in his book the Edge of Evolution (which at the time was considered pseudoscientific quackery, the major premise of which is now being published in QRB).

Do you think you could tell us, in your own words, what exactly do you think the major premise of that book was?



I have also read that book, and it will surprise some people that I quite enjoyed it. It was well written, intelligent and informative. But what struck me most about that book is what Behe did not do. And it is something he did not do in his first book either. And although I have not read it I understand from the comments in this thread that it is something he has also not done in this recent paper. And that thing that he did not do was make a case for intelligent design. Remember that making a case against evolution (or a case for the limits of evolution) does not equal making a case for intelligent design.

 

[painted wolf]

PW,
I follow Behe's career closely. He's doing more work than anyone gives him credit for. The establishment does not like his idea, and so he rarely gets published. When he does publish they ask him to take out any references to intelligent design.

No, that isn't how it works. If he wanted to publish a paper on intelligent design he would have to have a worked out hypothesis, an experiment to demonstrate that hypothesis and the results of that experiment and the consequent data. Behe has admitted that he has no idea how to test or even if he can test his hypothesis... which is why it is unscientific at the moment.
He can publish scientific work whenever he wants. He spends a lot of time on the lecture circuit and little in the lab, which reduces his scientific work output.

The only thing that keeps him from publishing more is himself.

As for his testimony in the Dover trial, I think that he was honest and forthright but as a witness you don't really have much power. It's not like he was an attorney making closing remarks. Courts aren't usually dramatic and don't usually present the best each side has to offer. I think that we would agree that if Behe were not limited to answering someone's inquisition then he'd give a much better presentation on why ID is scientifically relevant.

He said that astrology was as much science as Intelligent Design and would have to be taught in school if ID was.

He was very honest and forthright... and I never bothered to read the closing remarks.

As for whether or not his work is skilled, I think wisdom will defer to the test of time.

One can not teach in a major university without some skill.

But as for whether it supported ID I think it's pretty clear, if Darwinian processes cannot create functional coded elements in the simplest life forms with the highest mutation and reproduction rates then one would hardly be led to believe that more complex life forms with longer reproduction cycles would experience greater Darwinian effect. This works on the inference to the best explanation.

There is no irreducibly complex system that has been identified. So far nothing has been shown to be "unevolveable". As for Functional Coded Elements... it is p
efined, poorly exampled and in Behe's paper he admits that it is possible if the lab experiements had longer run times.

Were you expecting a mathematical style proof?

nope... I was expecting some experimental evidence... but math is a nice bonus. There is actually a lot of math in evolution such as they Hardy-Weinburg Equilibrium formula.

Remember that Darwinism itself is a 'long argument' an inference to the best explanation.

Perhaps 150 years ago, but evolution (Darwinism hasn't been around for a long time) has a lot of experimental evidence both in the lab and in the field.
Evolution is a change in allele frequencies in populations over time... even Behe doesn't argue that.

You can't prove Darwinism in the way that people are expecting Behe to prove ID.

I don't know about "Darwinism" but evolution is tested every day in labs around the world. The results of those experiments are published by the hundreds to thousands every year.
There has yet to be a single experiment demonstrating ID. Not one.

A nice summary of the long argument is given in Meyer's new book though, if you're interested.

What book is that?
Though unfortunately science isn't determined by pop-sci books... it's determined by lab work.

[Looking forward,
QM

wa:do

 

[Nepenthe]

Nepenthe,
Consensus is the lowest level of evidence. Lots of people disagreed with Darwin. Lots of people disagreed with Gould. Lots of people disagree with Behe!

I didn’t mean to quote the University’s official stance on Behe’s support of ID to demonstrate consensus, I mentioned it to show that Behe has a prominent position at an admired university and they disagree with his controversial views while he remains dutifully employed. It shows that there is absolutely nothing preventing Behe from actually pursuing intelligent design scientifically- the very university he works at supports him while disagreeing with his views, but he has yet to publish anything in the scientific literature demonstrating ID. He may be a legitimate scientist but his work on ID is not legitimate science. So the University’s opinion that ID “has no basis in science, has not been tested experimentally, and should not be regarded as scientific”, is the case whether there's a consensus or not.

Plus, I think you're not giving Behe a fair shake when you say he doesn't state what is a case of something not designed. He does this at every conference, and goes to some length in the Edge of Evolution. Single point mutations are clearly not the work of a creator. Did you happen to read that book?

Looking forward to your reply,
QM

I have read it. It didn’t elaborate much beyond what Darwin’s Black Box offered yet makes it clear that Behe accepts evolution and natural selection for the most part. He degenerates into his usual skepticism regarding “simultaneous random mutations” leading to speciation which he replaces by a scientifically unsupported undefined non-random guide. I’ll say he does explain malaria and sickle hemoglobin pretty well.

Levin’s critique of The Edge of Evolution is excellent.
http://ncse.com/rncse/27/1-2/review-edge-evolution

 

[Mr Spinkles]

Hey QM,

As for whether or not his work is skilled, I think wisdom will defer to the test of time. But as for whether it supported ID I think it's pretty clear, if Darwinian processes cannot create functional coded elements in the simplest life forms with the highest mutation and reproduction rates then one would hardly be led to believe that more complex life forms with longer reproduction cycles would experience greater Darwinian effect. This works on the inference to the best explanation.

But then, Behe's paper does not demonstrate, or even attempt to demonstrate, that "Darwinian processes cannot create functional coded elements in the simplest life forms ..." He acknowledges the modification of an FCT over time can lead to gain of FCT. He says one microbial experiment did indeed demonstrate an evolutionary "gain" of FCT by his definitions (see his Table 1). He also repeatedly acknowledges that "adaptive evolution can cause a species to gain, lose, or modify a function".

Secondly, his definitions and his examples are very confused and unclear. In my opinion the confusion serves his purpose, which is to suggest that organisms to not "gain" stuff by Darwinian evolution. Right off the bat he mentions that snakes lost their legs, but it's equally valid to say they gained muscles equipped for undulation and sidewinding. Things only get worse once he defines his terms.

He defines an FCT as a structure in the genome that "specifically" codes for something, like a binding site on a protein. He defines "loss" and "gain" of FCT in terms of the loss or gain of such genetic structures. He explicitly says gain or loss of FTC are not defined by the apparent gain or loss of a phenotype.

But after stating his definitions, he abandons them. For example, he says a single point mutation in the case of sickle-cell does not modify a pre-existing FCT, this is actually a "gain" of FCT because a new phenotype is gained (the hemoglobin proteins, modified by a single amino acid, will now form fibers). According to his definition this should not be a gain, but a modification of a pre-existing FCT, since no "specific, new, functional coded element" was produced in the genome. (Or, you could say a new FTC which makes hemoglobin fibers was produced; but a FTC for normal hemoglobin was also lost, so the net change is the modification of a FTC by a point mutation.) In this case a simple modification of a FTC gave rise to a remarkable "gain" in function (the formation of fibers and malaria resistance). It seems Behe's confusion here serves to avoid the fact that a "modification" of FCT can lead to a remarkable "gain" in function.

Then he says whenever the precise molecular mechanism by which a mutation confers malaria resistance (or some other phenotype) is unknown, this counts as a "modification". (The organism, of course, certainly "gained" something, e.g. malaria resistance). This serves Behe's purpose because the precise molecular mechanism of the adaptation is unknown in many of the studies he cites, which allows him to call the results "modifications", even though one could just as easily say the organism gained something (i.e. the ability to grow in certain chemicals). Why does the change of structure of hemoglobin protein, due to a single amino acid change, count as a "gain", while the ability to grow on lactulose, which perhaps involves unknown changes or many complicated changes in function, only counts as a "modification"?

Behe continues, saying any kind of mutation which decreases catalytic activity is a "loss". So a mutation which increases catalytic activity must count as a "gain" then, right? Not so, says Behe: a decrease is a loss, but an increase is not a gain, it's just a modification. This is a game of "heads I win, tails you lose".

The most far-reaching conclusion I can discern is that in very short-term (less than 100 years!) microbial evolution experiments to date, adaptation proceeds primarily but not exclusively by modification, and also by the loss of FCTs in the genome. Many scientists have already pointed out that Nature is not a well-mixed test tube consisting of a single nutrient and a single line of evolving bacteria. If any conditions on Earth are similar to such an experiment, it would be an isolated cave or an extreme environment where very few species live and little environmental change occurs over time. And indeed, these are the environments where simplicity and loss of complex function are generally favored.

More recent research on microbial evolution in rugged fitness landscapes with horizontal gene transfer, and randomly changing environmental conditions, shows that organisms will be constructed in a modular way. Evolution will preserve the construction of many useless or redundant structures, which may happen to be useful when the environment changes, or which may become "new" FCTs by a progression of modification, as Behe acknowledges. A toolbox of genes are eventually built up which can be turned on and off by only one or a few mutations.

At any rate, wherever this interesting research leads I see no evidence it's leading in the direction of ID, which can be described as a magical influence, which occasionally interrupts the laws of conservation of energy, mass, charge, etc. by supernaturally inserting molecules into the genome. It's worth stepping outside microbial test tube experiments for a moment, and considering the new functions that have evolved outside the lab: the domesticated plants and animals compared to their wild ancestors, nylon-eating bacteria, modern aquatic mammals vs. their prehistoric ancestors, and so on.

 

[Autodidact]

Auto,
I get the sense that we're not going to agree and with your closing remark I can't help but think the time spent on exchanges might be better spent reading. My opinions on capitalism are being changed as I write. I find this very interesting: Darwin and Darwinism: The (Alleged) Social Implications of The Origin of Species -- Orr 183 (3): 767 -- Genetics

Looking forward,
QM

Are you trying to tell me what to read? No thanks. If you have a point to make, make it. Otherwise I'll choose my own reading list, thank you. And if you find our conversation not to be a profitable use of your time, you're free to desist whenever you like.

 

[painted wolf]

Are you trying to tell me what to read? No thanks. If you have a point to make, make it. Otherwise I'll choose my own reading list, thank you. And if you find our conversation not to be a profitable use of your time, you're free to desist whenever you like.

Would it hurt to look it over?

I like the part about Darwin's theory of evolution and religion.... especially the part that says that evolution is not anti-theistic.

wa:do

ps. We all suggest reading material to one another... I do so quite often whenever I link to current research.

 

[Mr Spinkles]

You can't prove Darwinism in the way that people are expecting Behe to prove ID.

One of many things the theory of evolution predicted is that we should find marsupial fossils in Antarctica, of all places. Some professors went looking, and found them. Which fossil finds were anticipated by ID?

 

[Mr Spinkles]

No response to post #45? I apologize it is so lengthy ... I hope no one has responded because I gave fair and comprehensive criticism of Behe's paper, and not because I was so verbose ....

 

[David M]

No response to post #45? I apologize it is so lengthy ... I hope no one has responded because I gave fair and comprehensive criticism of Behe's paper, and not because I was so verbose ....

Well its sums up that paper quite well. Behe has published another review paper that doesn't mention ID and whose methodology is rather shabby.

So even when he tries to publish evidence-based science he just demonstrates that hes a poor biologist.

 

[ellenjanuary]

Do you think you could tell us, in your own words, what exactly do you think the major premise of that book was?



I have also read that book, and it will surprise some people that I quite enjoyed it. It was well written, intelligent and informative. But what struck me most about that book is what Behe did not do. And it is something he did not do in his first book either. And although I have not read it I understand from the comments in this thread that it is something he has also not done in this recent paper. And that thing that he did not do was make a case for intelligent design. Remember that making a case against evolution (or a case for the limits of evolution) does not equal making a case for intelligent design.

Gee, thanks. Now i might have to read that book...

I'm gonna go read that paper, too. I've been willfully ignorant. Behe is guilty by association with dumbski; and I've read his work. I mean, biology is kinda boring, but mathematics? That's the stuff, right there!

 

[ellenjanuary]

Oh noes! Eye glaze! I'm gonna hafta appeal to authority:

Finally, this paper gives ID advocates no reason to crow that a peer-reviewed paper supporting intelligent design has finally appeared in the scientific literature. The paper says absolutely nothing—zilch—that supports any contention of ID “theory.”

~from Behe’s new paper « Why Evolution Is True
Yeah, but it's a biologist discussing biology. This mathematician needs a nap.

 

[QuestionMark]

Mr. Sprinkles,
You've made a lot of great points in this thread and I've just gotten to turning my forum brain back on the past few days after a nice break playing video games. I really enjoyed reading your post and I will really enjoy replying to it, if God permits, within a week.

Looking forward,
QM

 

[QuestionMark]

Mr Spinkles,
It's impossible to demonstrate what Darwinian processes 'cannot' do, so it's not surprising that Behe doesn't demonstrate what Darwinian processes 'cannot' do.
Darwinian processes don't merely have to be capable of producing the FCTs, they have to be capable of producing them within the specified amounts of time. If they are extremely rare, then the inference that they do produce them in sufficient time is weakened.
I agree that there is quite a bit to interpret. You gave the case of a snake losing its legs, but was gaining the muscles to undulate (as you say) a gain in FCT? If I start crawling instead of walking my accessory muscles would in some cases become primary, but that wouldn't be a new FCT.

As for definitions, I think that the sickle cell is considered a gain because it's the best category it fits into. I think that he's trying to be charitable to Darwinian processes by saying that even in the case of losing an FCT a modest gain is still a gain. He sees the best argument for Darwinism to be lots of FCT gains, so he calls this one a gain in order to be conservative (he could also call it a loss, but that would seem biased). Remember that neutral modifications are often deleterious, so in explaining the theory of evolution one must consider that in order to be promoted a gene should provide a net gain in a reasonable quick manner. (So, consider that Behe is arguing that even though Sickle Cell could be a loss, a gain, or a modification, it may be best to call it a gain because in the short term it is a gain).

Unknown sources of resistance count as modifications because that's the best category (you wouldn't call them a gain or a loss, because you don't know if a capability was actually gained or lost).

Change in catalytic activity is a loss if the mechanism was changed (rather than simply decreased) so that the catalytic function is no longer possible. That's clearly a loss of FCT, because the organism is no longer capable of carrying out the function.

Do you think it's a bad idea to attempt to qualify changes in the genome? Isn't it essential to see if evolution actually works like we think it does?

At any rate, wherever this interesting research leads I see no evidence it's leading in the direction of ID, which can be described as a magical influence, which occasionally interrupts the laws of conservation of energy, mass, charge, etc. by supernaturally inserting molecules into the genome.

Isn't life itself also quite magical according to this ideology? But, I contest that it's not the insertion of molecules but the insertion (or availability) of information that is added. Sort of like a brain doesn't magically acquire new energy when it learns something, but something which was already there is realized and expressed.

Looking forward,
QM

 

[Mr Spinkles]

Mr Spinkles,
It's impossible to demonstrate what Darwinian processes 'cannot' do, so it's not surprising that Behe doesn't demonstrate what Darwinian processes 'cannot' do.

I disagree, it is possible to show there are certain things Darwinian processes cannot do. But I'm surprised that you would believe this is impossible to demonstrate, since you said:

"As for whether or not [Behe's] work is skilled, I think wisdom will defer to the test of time. But as for whether it supported ID I think it's pretty clear, if Darwinian processes cannot create functional coded elements in the simplest life forms with the highest mutation and reproduction ratesthen one would hardly be led to believe that more complex life forms with longer reproduction cycles would experience greater Darwinian effect." [emphasis added]
​

If, as you say, "it's impossible to demonstrate what Darwinian processes 'cannot' do", then it follows that Behe's paper did not demonstrate "Darwinian processes cannot create functional coded elements ..." Apparently, by the above reasoning, this also means Behe's paper is not skilled and did not provide support for ID.

Darwinian processes don't merely have to be capable of producing the FCTs, they have to be capable of producing them within the specified amounts of time. If they are extremely rare, then the inference that they do produce them in sufficient time is weakened.

I completely agree.

I agree that there is quite a bit to interpret. You gave the case of a snake losing its legs, but was gaining the muscles to undulate (as you say) a gain in FCT? If I start crawling instead of walking my accessory muscles would in some cases become primary, but that wouldn't be a new FCT.

I wasn't referring to FCT's, I was just noticing Behe's choice of language and emphasis. Tangentially, I'm not an expert on the subject, but my guess is that the difference in musculature between a snake and a lizard is more significant than, say, the difference between one human who crawls a lot vs. another who walks.

As for definitions, I think that the sickle cell is considered a gain because it's the best category it fits into. I think that he's trying to be charitable to Darwinian processes by saying that even in the case of losing an FCT a modest gain is still a gain. He sees the best argument for Darwinism to be lots of FCT gains, so he calls this one a gain in order to be conservative (he could also call it a loss, but that would seem biased). Remember that neutral modifications are often deleterious, so in explaining the theory of evolution one must consider that in order to be promoted a gene should provide a net gain in a reasonable quick manner. (So, consider that Behe is arguing that even though Sickle Cell could be a loss, a gain, or a modification, it may be best to call it a gain because in the short term it is a gain).

I'm confused. "Neutral modifications are often deleterious"? I honestly think Behe's paper is hopelessly vague and confused. He defines FCT as a gene but then mixes and matches gain/loss in terms of proteins, not genes. He says the two categories of adaptation are phenotypic and "the molecular aspect", but what he should have said is phenotypic and genotypic. Why a change in the binding of a protein does not count as "phenotypic" is unclear to me. I don't think "the best argument for Darwinism [is] lots of FCT gains" because by Behe's confused terminology that would mean a bacterium whose proteins all have many binding sites which bind strongly to every other protein -- in other words, a complete mess.

Maybe instead of worrying about the details of what is an FCT we should focus on what support, if any, we find for ID in his paper, even if we accept (for the sake of argument) all his definitions and assertions. Perhaps then we can avoid a messy argument about definitions and go straight to the meat of the matter.

Accepting, for the sake of argument, all of Behe's definitions and arguments, I find no evidence for ID. He says there are single point mutations, in the human genome, which are gain-of-FCT. He also says a single point mutation in bacterial evolution experiments and several in virus experiments demonstrated gain-of-FCT. He concedes a number of problems and objections to extrapolating this short-term laboratory work to how cells evolved in Nature.

Do you think it's a bad idea to attempt to qualify changes in the genome?

Not at all. But, I do think Behe's attempt is not a very good one.

Isn't it essential to see if evolution actually works like we think it does?

Absolutely.

Isn't life itself also quite magical according to this ideology? But, I contest that it's not the insertion of molecules but the insertion (or availability) of information that is added. Sort of like a brain doesn't magically acquire new energy when it learns something, but something which was already there is realized and expressed.

Granted, but when a brain or computer learn something, something about it changes physically (different neural connections, different strengths, or whatever). Even if the information you refer to becomes available by supernaturally rearranging atoms in DNA, instead of inserting new atoms, this still requires the violation of all the basic physical laws.

 

[Autodidact]

Mr Spinkles,
It's impossible to demonstrate what Darwinian processes 'cannot' do, so it's not surprising that Behe doesn't demonstrate what Darwinian processes 'cannot' do.

Exactly. And that is why the entire premise of Intelligent Design is doomed. In Biology, ID is the premise that there are certain biological features that could not have come about as a result of evolution, and therefore must have been designed by an intelligence. This is impossible. Please tell the Dsicovery Institute people, so they can put their money to better use.

Darwinian processes don't merely have to be capable of producing the FCTs, they have to be capable of producing them within the specified amounts of time. If they are extremely rare, then the inference that they do produce them in sufficient time is weakened.

This is true. It takes math. Please provide.

Do you think it's a bad idea to attempt to qualify changes in the genome? Isn't it essential to see if evolution actually works like we think it does?

Definitely. This is what Biology has been doing for the last 100 years. And we found out that it does.