December 2010 Quarterly Review of Biology

It’s critical to distinguish between “beneficial” mutations and “constructive” mutations. It can be “beneficial” to an organism in some circumstances to render a gene nonfunctional by degrading it. If that is the case, then any of a very large number of change to its amino acid sequence will do the job, and so the rate of “beneficial” mutations will be very high. I discuss this in The Edge of Evolution. For example, it is beneficial in malaria-ridden territory for humans to degrade the functioning of an enzyme abbreviated G6PD. A very large number of separate mutations to that gene have been isolated, all of which are “helpful” because they all mess up the protein’s activity. In his long term evolution experiment with E. coli Richard Lenski has identified about a half dozen “beneficial” mutations — they *all* appear to be degradative mutations. It seems very likely that the report below is just identifying beneficial-but-degradative mutations. That’s interesting, but degradative mutations tell us nothing about how molecular systems can be constructed.

While the result is interesting, readers of The Edge of Evolution will not be very surprised by it. As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems. The bottom line is that the beneficial mutations reported in the new Science paper most likely are degradatory mutations, and so don’t address the challenges outlined in The Edge of Evolution.

Nevertheless, a broad subset of adaptations cannot be accommodated by the sequential model, most notably those in which multiple mutations must be acquired to confer a benefit. Such traits, here referred to as complex adaptations, include the origin of new protein functions involving multiresidue interactions, the emergence of multimeric enzymes, the assembly of molecular machines, the colonization and refinement of introns, and the establishment of interactions between transcription factors and their binding sites, etc. The routes by which such evolutionary novelties can be procured include sojourns through one or more deleterious intermediate states. Because such intermediate haplotypes are expected to be kept at low frequencies by selection, evolutionary progress would be impeded in large populations were sequential fixation the only path to adaptation. However, in all but very small populations, complex adaptations appear to be achieved by the fortuitous appearance of combinations of mutations within single individuals before fixation of any intermediate steps at the population level (e.g., refs. 17–26).

Lynch`s arguments fall into a pattern I commented on in the previous thread -- it is interesting that there are ways for (near-) simultaneous mutations to happen, but there aren`t a lot of reasons to think that this is a common requirement for e.g. binding sites, acquiring new substrate metabolism ability, multiprotein machines, etc. There is lots of evidence (eg in vitro evolution) that the simpler features (eg) binding sites) are often reachable by accumulation of single mutations, and the more complex things by a circuitous route involving one or more changes of function, but without deleterious intermediates.

Yes, and English is 'degraded' Old Frisian, and French is 'degraded' Latin.

FFS.

Lynch‘s arguments fall into a pattern I commented on in the previous thread – it is interesting that there are ways for (near-) simultaneous mutations to happen, but there aren‘t a lot of reasons to think that this is a common requirement

more complex things by a circuitous route involving one or more changes of function, but without deleterious intermediates.

Taken together, the data on the rates of AU↔GC switches, on the frequencies of segregating GU and AC intermediate alleles and on the clustering of substitutions involved in a Watson–Crick switch demonstrate that evolving mt-tRNAs often cross fitness valleys of a substantial depth of about 10-3 or even about 10-2. This selection against intermediate alleles is due to the impact of altered tRNAs both on the fitness of the organism and on the rate of propagation of a mitochondrion within the germ line25 and characterizes the efficiency of transmission of a mitochondrial genotype between generations. Alleles with such low fitnesses cannot be fixed in a population, and crossing the deep valleys must occur without the assistance of genetic drift2, 3. Instead, compensatory evolution in mt-tRNAs involves a compensatory substitution emerging in the rare genotype carrying a segregating strongly deleterious allele, making their simultaneous fixation possible2, 3. Thus, strongly deleterious alleles can serve as evolutionary stepping stones by providing access to isolated fitness peaks. Whether or not such stepping stones can be used to cross wider fitness valleys remains an open question.

Lynch's paper is here BTW:

http://www.indiana.edu/~lynchlab/PDF/Lynch187.pdf

and another recent one worth reading:

http://www.indiana.edu/~lynchlab/PDF/Lynch182.pdf

So where has Dr. Behe been speaking? I can't imagine a college inviting him.

Karen S. said: So where has Dr. Behe been speaking? I can't imagine a college inviting him.

There's a list of where he's been speaking here:

http://www.darwinordesign.org.uk/index.php?option=com_content&view=article&id=175&Itemid=28

SteveF said: There's a list of where he's been speaking here: http://www.darwinordesign.org.uk/index.php?option=com_content&view=article&id=175&Itemid=28

There’s a list of where he’s been speaking here: http://www.darwinordesign.org.uk/in[…]mp;Itemid=28

Prof Michael Behe combines the skill of careful research scientist with that of popular communicator. His lectures are informative, entertaining, lavishly-illustrated and entirely accessible to the layman. He is also at ease with questions from his audience.

Karen S. said:

There’s a list of where he’s been speaking here: http://www.darwinordesign.org.uk/in[…]mp;Itemid=28

Thanks for the link. It says,

Prof Michael Behe combines the skill of careful research scientist with that of popular communicator. His lectures are informative, entertaining, lavishly-illustrated and entirely accessible to the layman. He is also at ease with questions from his audience.

I'd agree with the part about being entertaining.

Such traits, here referred to as complex adaptations, include the origin of new protein functions involving multiresidue interactions, the emergence of multimeric enzymes, the assembly of molecular machines, the colonization and refinement of introns, and the establishment of interactions between transcription factors and their binding sites, etc

Would be more so if heeded Ken Miller’s advice to write a textbook on Klingon biochemisty

In 1974, Henry Morris, founder of the Institute for Creation Research and father of the Creation-Science movement, argued in his influential book Scientific Creationism that “The problem is simply whether a complex system, in which many components function unitedly together, and in which each component is uniquely necessary to the efficient functioning of the whole, could ever arise by random processes” (Morris 1974, p. 59). In 1980, young-earth creationist Ariel Roth argued that “Creation and various other views can be supported by the scientific data that reveal that the spontaneous origin of the complex integrated biochemical systems of even the simplest organisms is, at best, a most improbable event” (Roth 1980, p. 83). Behe has simply adapted these creationist notions to his own ends. Consider his definition of IC in Darwin’s Black Box:

I see I misspelled Maarten Boudry’s name. My apologies.

Oh, forgot to mention: I think pan-functional fragility would just be a generalization of the situation Pete Dunkelberg describes in the third section of his talkdesign article.

2) the phrases “effectively ceases functioning” and “non-functional” include any function that the impaired system or one of its components may perform in other contexts… In fact, only an IC system in the second, strong sense would be an obstacle to evolutionary theory, because it would rule out evolutionary precursor systems and function shifts of the system’s components.

A report on Behe's talk:

http://robertsaunders.org.uk/wordpress/2010/11/25/behes-uk-tour-reports-on-the-glasgow-gig/#GARGkNQorZ39

Karen S. said:

... Prof Michael Behe[']s lectures are ... lavishly-illustrated ...

Anybody want to give me odds on whether Harun Yahya sues Behe for “sharing” pictures from his (Yahya’s) “textbook”?

Karen S. said:

Anybody want to give me odds on whether Harun Yahya sues Behe for “sharing” pictures from his (Yahya’s) “textbook”?

He shouldn't, since Yaha copied at least one picture from a fly-fishing catalog.

Karen S. said:

Anybody want to give me odds on whether Harun Yahya sues Behe for “sharing” pictures from his (Yahya’s) “textbook”?

He shouldn't, since Yaha copied at least one picture from a fly-fishing catalog.

Nick - Behe is not touring "England". His tour includes Northern Ireland and Scotland and is on behalf of a Scottish outfit, the Centre for Intelligent Design.

The full sordid details of this tour can be found on our web site; access "Michael Behe in Britain" through our home page at www.bcseweb.org.uk

It's entertaining s well as disturbing.

Intelligent Design is definitely NOT Creationism Dismissing Intelligent Design as 'Creationism' is the easy way of avoiding having to deal with the empirical evidence for design.

Dismissing Intelligent Design as ‘Creationism’ is the easy way of explaining why there is no empirical evidence for design.

There, all fixed.

Intelligent Design is definitely NOT Creationism Dismissing Intelligent Design as 'Creationism' is the easy way of avoiding having to deal with the empirical evidence for design.

http://www.c4id.org.uk/index.php?option=com_content&view=article&id=209:how-the-scientific-consensus-can-hinder-science&catid=42:rnr-articles This article seeks to discuss "Scientific concensus" as it is understood today and how, in the past, scientific consensus has had to undergo seismic shifts. Intelligent Design is repeatedly dismissed by its critics as being unscientific. Many who make this assertion are not suggesting that it has no empirical data to support its claims but rather that it is completely outside the realm of science. This is because of a narrow definition of science that has been developed. What is scientific, according to this definition, is a matter of ongoing debate. Google “problem of demarcation” and you will get some idea of the extent of this discussion and the difficulty of determining where the parameters should be set.

Galileo and scientific consensus Scientific consensus sometimes get so entrenched that it becomes a hindrance rather than a help to the advancement of science. Galileo Galilei had a bit of a run in with the consensus and concluded, “In questions of science the authority of a thousand is not worth the humble reasoning of a single individual”. His scepticism of consensus is understandable when you consider the way in which he was treated.

Was Behe invited to write this "major article" by QRB? What possessed them? I'm pretty sure that Behe had an entire decade in which he had published something like three original research papers. Has this article surfaced yet? Will it be peer-reviewed?

Presumably it's a literature review on the origin of adaptations. I have yet to see Behe do a really thorough review of the literature on any topic (where thorough = I couldn't find important stuff that he missed). It is somewhat conceivable that Behe could do a really thorough job reviewing all major cases of adaptation to antibiotics etc., and he will conclude that these are usually "degrading" mutations and not "constructive" or something. I would think that a competent review would have to mention the many cases where

(a) antiobiotic resistance is gained without "breaking" anything -- e.g. transporting the antibiotic molecules out of the cell, breaking down the molecules, etc.; and the role of duplication in allowing the maintenance of the original function of the genes ancestral to the new adaptation.

(b) compensatory mutations can often pretty thoroughly and rapidly "fix" whatever was "broken" in cases where there was a fitness cost to the intitial adaptation

(c) the dubiousness of extrapolation from adaptation to a very simple environment (e.g. Lenski's cultures), where many things might be lost, to adaptation in a complex environment, where breaking things will much less often be beneficial.

Actually, though, it's pretty inconceivable to me that Behe has the capacity to exhibit this kind of sophistication ahead of time, so likely we'll just see a review of something narrow, like Lenski's work, and then grand conclusions (selection can't do anything!) hidden behind mild phrases so as to get by the reviewers.

Dismissing Intelligent Design as ‘Creationism’ is the easy way of avoiding having to deal with the empirical evidence for design.

harold said:

Dismissing Intelligent Design as ‘Creationism’ is the easy way of avoiding having to deal with the empirical evidence for design.

Okay, what is the empirical evidence FOR intelligent design? Let's start with some objective, testable answers to these question... Who is the designer? What did the designer design? When? How? What is an example of something that might not have been intelligently designed?

Many who make this assertion are not suggesting that it has no empirical data to support its claims but rather that it is completely outside the realm of science.

Nick (Matzke) said: Roger -- my bad! Heh, just looked at the Centre for ID's website:

Intelligent Design is definitely NOT Creationism Dismissing Intelligent Design as 'Creationism' is the easy way of avoiding having to deal with the empirical evidence for design.

Bwa ha ha!

Hey Nick, Thanks, but you know the old saying "I don't care what you say about me as long as you spell my name right." :)

Signed Pete Dunkelberg

Nick (Matzke) said: Presumably it's a literature review on the origin of adaptations. I have yet to see Behe do a really thorough review of the literature on any topic (where thorough = I couldn't find important stuff that he missed). It is somewhat conceivable that Behe could do a really thorough job reviewing all major cases of adaptation to antibiotics etc., and he will conclude that these are usually "degrading" mutations and not "constructive" or something. I would think that a competent review would have to mention the many cases where (a) antiobiotic resistance is gained without "breaking" anything -- e.g. transporting the antibiotic molecules out of the cell, breaking down the molecules, etc.; and the role of duplication in allowing the maintenance of the original function of the genes ancestral to the new adaptation. (b) compensatory mutations can often pretty thoroughly and rapidly "fix" whatever was "broken" in cases where there was a fitness cost to the intitial adaptation (c) the dubiousness of extrapolation from adaptation to a very simple environment (e.g. Lenski's cultures), where many things might be lost, to adaptation in a complex environment, where breaking things will much less often be beneficial. Actually, though, it's pretty inconceivable to me that Behe has the capacity to exhibit this kind of sophistication ahead of time, so likely we'll just see a review of something narrow, like Lenski's work, and then grand conclusions (selection can't do anything!) hidden behind mild phrases so as to get by the reviewers.

an FCT is defined as "a discrete but not necessarily contiguous region of a gene that, by means of its nucleotide sequence, influences the production, processing, or biological activity of a particular nucleic acid or protein, or its specific binding to another molecule." FCTs are an extremely broad category of DNA and they include: # promoters; # enhancers; # insulators; # Shine-Dalgarno sequences; # tRNA genes; # miRNA genes; # protein coding sequences; # organellar targeting- or localizationsignals; # intron/extron splice sites; # codons specifying the binding site of a protein for another molecule (such as its substrate, another protein, or a small allosteric regulator); # codons specifying a processing site of a protein (such as a cleavage, myristoylation, or phosphorylation site); # polyadenylation signals; and # transcription and translation termination signals (Michael J. Behe, "Experimental Evolution, Loss-of-Function Mutations and 'The First Rule of Adaptive Evolution'," Quarterly Review of Biology, Vol. 85(4) (December, 2010).) Behe argues that we do not generally observe the evolution of new adaptive FCTs in the laboratory. Rather, when we observe adaptive evolutionary changes in the laboratory, they typically involve loss of function or modification of FCTs. This leads to the question, How do new adaptive FCTs arise? In two subsequent posts, I will discuss Behe's review of FCT evolution in bacteria and viruses, as well as the implications he draws from that data.

Thanks sparc. Sounds like I got my prediction of the paper in the first comment basically right :-)

Kudos to Dr. Behe for his latest peer-reviewed publication. Between it, his tour of the U.K. and his recent scintillating article in The Guardian, he's been on quite the role as of late.

Perhaps those here who wish to criticize this modern-day Galileo's work will up your critiques by taking them beyond this pseudoscientific blog and stepping into the realm of the peer-reviewed world.

Jared Jammer said: Perhaps those here who wish to criticize this modern-day Galileo's work will up your critiques by taking them beyond this pseudoscientific blog and stepping into the realm of the peer-reviewed world.

Jared Jammer said: Kudos to Dr. Behe for his latest peer-reviewed publication. Between it, his tour of the U.K. and his recent scintillating article in The Guardian, he's been on quite the role as of late. Perhaps those here who wish to criticize this modern-day Galileo's work will up your critiques by taking them beyond this pseudoscientific blog and stepping into the realm of the peer-reviewed world.

I admit I enjoyed the article in the Guardian. Behe basically says "I know a priori that stuff was intelligently designed, thus when I look at it, I see exactly what I knew was there before I looked, therefore it's design all along." Yep, scintillating.

As others have noted, the Designer must be as busy Designing unique snowflakes in the winter as Santa Claus is on Christmas Eve. No question every snowflake is designed, and you just gotta be impressed with the endless creativity produced in such enormous volume.

Flint said: I admit I enjoyed the article in the Guardian. Behe basically says "I know a priori that stuff was intelligently designed, thus when I look at it, I see exactly what I knew was there before I looked, therefore it's design all along." Yep, scintillating.

thanks you süper blog

Behe has claimed that all of the beneficial mutations observed in Richard Lenski's E Coli experiment were "degradative". What does he mean by that? Does he mean that the mutations were not beneficial overall? If so, is it true?

When Lenski labels mutation "beneficial", does he take into account the "degradative" factor that Behe refers to? Do the beneficial mutations have the highest fitness?

Jared Jammer said: Kudos to Dr. Behe .. (and) .. his recent scintillating article in The Guardian,