Tag Archives: Mike Behe

Peer-reviewed paper: Michael Behe’s “First Rule of Adaptive Evolution”

Christianity and the progress of science
Christianity and the progress of science

Let’s take a look at Mike Behe’s first rule of adaptive evolution, which states that most examples of adaptation in evolutionary experiments involve a loss of function, or a modification of an existing function. Not new functionality.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.

Abstract:

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.

Excerpt:

After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(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 this point is empirically supported by the research reviews in the paper. He writes:

As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.

Peer-reviewed paper: Michael Behe’s “First Rule of Adaptive Evolution”

Christianity and the progress of science
Christianity and the progress of science

JoeCoder was writing some JavaScript code last night and he ran into a problem where a 3rd-party open source library was not performing as expected. So he got the non-minified version of the library and commented out two lines to get the behavior he wanted. He said this to me “Michael Behe’s first rule of adaptive evolution has been confirmed once again.” So, let’s take a look at Mike Behe’s first rule of adaptive evolution.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.

Abstract:

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.

Excerpt:

After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(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 this point is empirically supported by the research reviews in the paper. He writes:

As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.

Peer-reviewed paper: Michael Behe’s “First Rule of Adaptive Evolution”

Apologetics and the progress of science
Apologetics and the progress of science

JoeCoder was writing some JavaScript code last night and he ran into a problem where a 3rd-party open source library was not performing as expected. So he got the non-minified version of the library and commented out two lines to get the behavior he wanted. He said this to me “Michael Behe’s first rule of adaptive evolution has been confirmed once again.” So, let’s take a look at Mike Behe’s first rule of adaptive evolution.

The paper was published in the Quarterly Review of Biology. I found it on PubMed.

Abstract:

Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre-existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

By far the most common adaptive changes in the examples we have are due to loss of function or modification of pre-existing function?

Evolution News has a post up about the paper.

Excerpt:

After reviewing the effects of mutations upon Functional Coding ElemenTs (FCTs), Michael Behe’s recent review article in Quarterly Review of Biology, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” offers some conclusions. In particular, as the title suggests, Behe introduces a rule of thumb he calls the “The First Rule of Adaptive Evolution”: “Break or blunt any functional coded element whose loss would yield a net fitness gain.” In essence, what Behe means is that mutations that cause loss-of-FCT are going to be far more likely and thus far more common than those which gain a functional coding element. In fact, he writes: “the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene.” Since organisms will tend to evolve along the most likely pathway, they will tend to break or lose an FCT before gaining a new one. He explains:

It is called the “first” rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure.(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 this point is empirically supported by the research reviews in the paper. He writes:

As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported

After asking “Why is this the case?” Behe states, “One important factor is undoubtedly that the rate of appearance of loss-of-FCT mutations is much greater than the rate of construction of new functional coded elements.” He draws sound and defensible conclusions from the observed data:

Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory–by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. … In general, if a sequence of genomic DNA is initially only one nucleotide removed from coding for an adaptive functional element, then a single simple point mutation could yield a gain-of-FCT. As seen in Table 5, several laboratory studies have achieved thousand to million-fold saturations of their test organisms with point mutations, and most of the studies reviewed here have at least single-fold saturation. Thus, one would expect to have observed simple gain-of-FCT adaptive mutations that had sufficient selective value to outcompete more numerous loss-of- FCT or modification-of-function mutations in most experimental evolutionary studies, if they had indeed been available.

But this stark lack of examples of gain-of-functional coding elements can have important implications:

A tentative conclusion suggested by these results is that the complex genetic systems that are cells will often be able to adapt to selective pressure by effectively removing or diminishing one or more of their many functional coded elements.

Behe doesn’t claim that gain-of-function mutations will never occur, but the clear implication is that neo-Darwinists cannot forever rely on examples of loss or modification-of-FCT mutations to explain molecular evolution. At some point, there must be gain of function.

Now, there was a response to this paper from Jerry Coyne on his blog, and then a rebuttal from Mike Behe in a separate article on Evolution News.

New peer-reviewed article argues for irreducible complexity in birds

From Evolution News.

Excerpt:

In a peer-reviewed paper titled “Evidence of Design in Bird Feathers and Avian Respiration,” in International Journal of Design & Nature and Ecodynamics, Leeds University professor Andy McIntosh argues that two systems vital to bird flight–feathers and the avian respiratory system–exhibit “irreducible complexity.” The paper describes these systems using the exact sort of definitions that Michael Behe uses to describe irreducible complexity:

[F]unctional systems, in order to operate as working machines, must have all the required parts in place in order to be effective. If one part is missing, then the whole system is useless. The inference of design is the most natural step when presented with evidence such as in this paper, that is evidence concerning avian feathers and respiration.

He further notes that many evolutionary authors “look for evidence that true feathers developed first in small non-flying dinosaurs before the advent of flight, possibly as a means of increasing insulation for the warm-blooded species that were emerging.” However, he finds that when it comes to fossil evidence for the evolution of feathers, “[n]one of the fossil evidence shows any evidence of such transitions.”

Regarding the avian respiratory system, McIntosh contends that a functional transition from a purported reptilian respiratory system to the avian design would lead to non-functional intermediate stages. He quotes John Ruben stating, “The earliest stages in the derivation of the avian abdominal air sac system from a diaphragm-ventilating ancestor would have necessitated selection for a diaphragmatic hernia in taxa transitional between theropods and birds. Such a debilitating condition would have immedi¬ately compromised the entire pulmonary ventilatory apparatus and seems unlikely to have been of any selective advantage.” With such unique constraints in mind, McIntosh argues that the “even if one does take the fossil evidence as the record of development, the evidence is in fact much more consistent with an ab initio design position – that the breathing mechanism of birds is in fact the product of intelligent design.”

Let’s take a step back and ask what counts as evidence for (macro) evolution for people who actually care about evidence.

Here’s what counts as evidence:

  1. A smooth sequence of fossils showing the gradual emergence of different body body features across a wide spectrum of body plans. Not just horses and whales, not just micro-evolution. Major changes in body structure, which properly dated fossils, from a wide range of body plans.
  2. A lab experiment that derives a new organ type or body plan from an unmodified organism, like the Lenski experiments tried to do on a smaller scale.
  3. A computer simulation that shows a string of mutations that occur on one organism that would give it a new feature or organ within a reasonable amount of time (less than 4 billion years). The mutations must be probable, and the organism must have improved functionality at each stage of its development. And a calculation would have to be done to show that each beneficial mutation would spread to the rest of the population and survive in the next generation, which is a separate question.

Do we have that evidence in the case of bird evolution (feathers and lungs)? Of course not.

Do we have that evidence in the case of evolution as a whole? Of course not.

People who embrace evolution embrace it on the basis of non-rational, non-evidential factors.

BloggingHeadsTV restores censored video interview of Michael Behe

You can watch the video here, where Michael Behe is interviewed on a variety of topics by an atheist, who is nevertheless impressed by Behe’s book.

Topics:

  • Michael’s book, “The Edge of Evolution” (04:29)
  • Malaria and evolution (06:56)
  • Do proteins point to teleology? (05:59)
  • Have we really hit a wall of understanding? (04:08)
  • Challenges to Michael’s theory of irreducible complexity (05:28)
  • John: The boredom objection to intelligent design (09:13)

Here is Robert Wright’s comment about the restoration of the interview:

This diavlog has now been re-posted. The decision to remove it from the site was made by BhTV staff while I was away and unavailable for consultation…. It’s impossible to say for sure whether, in the heat of the moment, I would have made a decision different from the staff’s decision. But on reflection I’ve decided that removing this particular diavlog from the site is hard to justify by any general principle that should govern our future conduct. In other words, it’s not a precedent I’d want to live with.

Kick off the audio, (or download the MP3), and then read the comments of the Darwinists.

Comments from open-minded, tolerant Darwinists

Many of the commenters don’t mention the interview at all – they didn’t watch it.

Here’s one comment:

I’ve listened to a few seconds of this diavlog, enough to hear John McWhorter call Behe’s nonsense “a very important book.” I can’t remember the last time I lost so much respect for someone so quickly.

And another:

Grab the popcorn: this is bound to be a good thread. (Doubtful I’ll actually watch the diavlog.)

And one last one:

If this creationism thing keeps up no one will want to be on bhtv anymore. A spinoff site is better than no site for us regular viewers. Who’s with me?

Who can have any confidence in a theory when the adherents cannot even be bothered to listen to a tenured biochemist explain his own research which contradicts that theory?