Molecular Evolution Proven

Michael Behe is an especially dangerous creationist, because he isn’t the strident, shrill looney that you typically see on that side of the fence. His arguments actually sound plausible to many people, even those who reject other creationist claims as downright absurd.

I’m currently reading Darwin’s Black Box (I’ll eventually post a review). In there, he points out that there is ample evidence for the evolution of large structures, such as legs and ribs. However, he claims there is no evidence for evolution on the molecular scale. He has a point here. Molecules typically don’t leave fossils. He especially wants to know how the more complex structures—such a his favorite “whipping boy”, the bacterial flagellum—evolved.

Behe believes in “irreducible complexity”, which is his claim that some molecular machines are so complex that they could not have evolved. He claims that if you remove one piece, the whole thing breaks. Evolution occurs piece by piece; the necessary intermediate structures would not have evolved, since they would not have provided any function.

From there he jumps to the ridiculous conclusion that God must have done it.

Wrong! You Lose!

Well, now Behe has been proven wrong. We now know how molecular evolution occurred in one case, and it works just fine without God.

Science Daily reports:

Scientists have determined for the first time the atomic structure of an ancient protein, revealing in unprecedented detail how genes evolved their functions.

“Never before have we seen so clearly, so far back in time,” said project leader Joe Thornton, an evolutionary biologist at the University of Oregon. “We were able to see the precise mechanisms by which evolution molded a tiny molecular machine at the atomic level, and to reconstruct the order of events by which history unfolded.” [Emphasis added. Flagellate that, Behe!]

What Thornton and his assistant Jamie Bridgham wanted to do was determine how a particular protein, the glucocorticoid receptor (GR), evolved its ability to interact with cortisol (a stress hormone).

They used computational techniques and a large database of modern receptor sequences to determine the ancient GR’s gene sequence from a time just before and just after its specific relationship with cortisol evolved.

So what they’re doing, if I’m interpreting the article correctly, is determining what this protein looked like right before it evolved one particular behavior. In order to conduct the new behavior, what would have to be added or changed to this protein?

Michael Behe would probably allege (if more than one mutation was necessary) that you can’t get there from here.

Now that Thornton and Bridgham have the DNA sequence, they still needed to get a sample of the protein. Remember that DNA is just the blueprint that tells how a protein is to be made. If you want to study the protein, you need to get some of it.

The ancient genes — which existed more than 400 million years ago — were then synthesized, expressed, and their structures determined using X-ray crystallography, a state-of-the art technique that allows scientists to see the atomic architecture of a molecule. The project represents the first time the technique has been applied to an ancient protein.

What that means is that they synthesized the genes, injected it into the DNA of bacteria (I’m guessing on this point, but that’s the usual method), and then let the bacteria produce the protein.

The important thing to know about this step is that proteins get their functionality from their three-dimensional shape. That’s where the X-ray crystallography came in.

The structures allowed the scientists to identify exactly how the new function evolved. They found that just seven historical mutations, when introduced into the ancestral receptor gene in the lab, recapitulated the evolution of GR’s present-day response to cortisol.

This is the part that Michael Behe would find interesting. Note how this new functionality requires seven mutations. Behe would claim that this is irreducibly complex. You need all seven. Take one away, and you’ve got nothing. Or do you?

They were even able to deduce the order in which these changes occurred, because some mutations caused the protein to lose its function entirely if other “permissive” changes, which otherwise had a negligible effect on the protein, were not in place first.

This is important. They were able to deduce the order in which these changes occurred! That’s watching evolution in action. Even though we don’t have a fossil record of this occurring, we now know how this structure had to evolve.

Ah, but what are those “permissive changes” and how did they happen? The permissive changes were random, benign mutations! This is how evolution works. Mutations happen all the time:

  1. Some mutations are useful and convey an immediate benefit to the organism, which allows it to better fit its environment. This gives it a survival advantage, so it’s more likely to live long enough to reproduce and pass along the beneficial mutation. Bingo! One small step along the evolutionary path.
  2. Some mutations are harmful and either kill the organism outright or reduce its fitfulness in its environment. This mutation is therefore selected against by the environment. This is evolution’s self-correcting mechanism.
  3. Many mutations are benign. They have no effect on an organism’s ability to survive. Therefore, they just sit there in the population. As that organism and its descendents reproduce, that benign mutation spreads throughout a subset of the population. Any population is full of countless benign mutations like this. Now if the environment were to change, some of these mutations would, by chance, convey an advantage in this new environment. That’s another way species evolve. But failing that, the mutation just sits there in some members of the population.

The atomic structure revealed exactly how these mutations allowed the new function to evolve. The most radical one remodeled a whole section of the protein, bringing a group of atoms close to the hormone. A second mutation in this repositioned region then created a tight new interaction with cortisol. Other earlier mutations buttressed particular parts of the protein so they could tolerate this eventual remodeling.

One of the collaborators, Eric Ortlund, said:

“We were able to walk through the evolutionary process from the distant past to the present day. Until now, we’ve always had to look at modern proteins and just guess how they evolved.”

It’s that guessing that gave Michael Behe the hook he needed to claim that God did it. Well now we no longer need to guess. Scientists have shown how one molecular structure evolved. With a lot of hard work, we can probably show how the other structures evolved.

The theory of evolution is yet again triumphant. God, and Michael Behe, need not apply.

18 Responses to “Molecular Evolution Proven”

  1. Ron Britton Says:

    Thanks for the compliment. I’ve seen the article discussed in the blogosphere for the last couple of days. The Discovery Institute and Michael Behe have both posted denials at their blogs.

    The bottom line is that this is exactly the sort of work that Michael Behe said isn’t being done. Now that it’s being done, he has no place to retreat to. So he just claims that it’s not the same thing at all. Ha!

    BTW, I see that you posted your article about this ten days ago! You’re ahead of us all.

  2. h3nry Says:

    Good summary! I have posted on the same topic, but yours is in more detail. It is interesting to note that for some reason, this research result hasn’t got the attention it deserves in the blogosphere or in the media. Personally I think the mutation dependency will correct a lot of misunderstanding about the mathematical improbability that lots of creationists claim.

  3. Edward Kerr Says:

    I read the article and the comments regarding the mutations and the supposed evolving of protein are inaccurate. What is being observed is the designed reactions to environmental changes. The importance of this research should be focused on these designed reactions in order to study towards the more complex issues regarding harmful viruses reacting to defend against antibiotics. Single celled viruses appear to be able communicate within their environment to identify friend or foe; this too is a designed function and is an exciting field of study that could lead to countless benefits for us all.

  4. Genesius Says:

    …the comments regarding the mutations and the supposed evolving of protein are inaccurate. What is being observed is the designed reactions to environmental changes.

    Evidence? Surely you don’t expect us to simply take your word for it?

    …The importance of this research should be focused on these designed reactions in order to study towards the more complex issues regarding harmful viruses reacting to defend against antibiotics.

    Antibiotics aren’t used against viruses. They’re used against bacteria.

    Single celled viruses…

    Viruses are just a protein coat over a strand of DNA (or RNA for retroviruses). There’s no such thing as a “single celled virus”

  5. Chris Street Says:

    I’ve just started blogging (today) on Creationism v Evolution

    I bought Michael Behe ‘Darwins Black Box’ a few years ago – but its still in my ‘to be read’ book section.

    From Science Daily:

    “The work involving the protein is detailed in a paper appearing online Aug. 16 in Science Express (abstract here):
    where the journal Science promotes selected research in advance of regular publication.”

    The University of Oregon have the press release:

    Supporting Online Material for Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis:
    contents: Materials and Methods, Figures, Tables and References

    It would be interesting to read the full Science article – cost $10

    I’ve reposted some of the Science article here:

  6. Senator Craig Says:

    Genesius, your critique is totally uncalled for. In the context of Edward Kerr’s post, single cell viruses are obviously meant to be understood as the opposite of multiple-cell viruses, which are bigger.

  7. EricSan Says:

    The Wikipedia article is a good read. I find it absolutely amazing that Behe is allowed to spew his utter nonsense. Then again, he unwittingly marks a point AGAINST evolution in a sense, because he’s able to sell a 200 year old debunked argument (the “watchmaker”) to unsuspecting Americans, so obviously, we haven’t evolved as much as we wish we had. Sadly.

  8. Jr. Says:


    This is on another topic entirely, but it’s sort of worth noting, if you need a quick fundie outrage minute. They changed the Texas Pledge from “I pledge allegiance to thee, Texas, one and indivisible” to “I pledge allegiance to thee, Texas, one state under God, one and indivisible.”

    No word yet on why, but it certainly lost its ring.

  9. Genesius Says:

    Genesius, your critique is totally uncalled for. In the context of Edward Kerr’s post, single cell viruses are obviously meant to be understood as the opposite of multiple-cell viruses, which are bigger.


    Must be tough to type with your tongue that deep in your cheek. . .

  10. Senator Craig Says:

    Laugh all you want, but no matter what you do, watch out for the multi-celled viruses 😉

  11. Jeff Hebert Says:

    Clearly he meant single-celled viruses to mean UNMARRIED viruses. That’s why they’re so dangerous, they’re constantly cruising the immune system looking to get laid.

  12. Ron Britton Says:

    But we must still pass laws to prevent them from getting married!

  13. Jeff Wright Says:

    When will people learn that just because they don’t understand something doesn’t make it complex. Similar to how one isn’t an artist just because they are misunderstood.

  14. Kent J Says:

    I think it is reasonable to say that the understanding we have of the complexities of life on this planet leave room for people to say ” it is REASONABLE to suggest DNA was designed”

    Get my point? The clock maker argument has become 100 times, if not a 1000 times more reasonable since it was first asked.

    I have never met an atheist/evolutionist who was at least reasonable enough to agree that they are asking an aweful lot from me to simply nod my head that EVERYTHING just happened. You may hate behe.. but please… the systems in the human body, if described thoroughly, out loud, to a group of people forced to listen to it.. would leave them dying of old age but i would think ENRAPTURED in the HUGE COMPLEXITY OF THE SYSTEMS WALKING THIS PLANET. And any scientist worth anything better admit that they two are occasionally found SLACK jawed when the enormity of it hits them.

    It is like a tornado blowing through the universe and creating fREAKING EVERYTHING…. you are out of your minds… my goodness.. you evolutoinsists are wack jobs.. and you manage to pull of making us…. doubters (i am a doubter in evolution.. not a BELIEVER in something sound crazy.

    yeah.. i am crazy.. but i am right.

    screw you evolutionists unreasonable fcks.

  15. Brian Says:

    I think I’ll rely on professional scientists to inform me about the validity of evolution rather than an uninformed dolt who obviously could not obtain a passing grade in high school English. Thanks just the same, Kent.

  16. Parrotlover77 Says:

    I’m not exactly sure how Kent J thinks that “Magic Man Did It Using His Magic Hands” is more reasonable or less complex of an undertaking than “gradual change over a very, very long period of time did it.”

  17. Travis Webster Says:

    You are one of the FIRST evolutionists to give Behe any credibility. Nobody who believes in evolution that has half a brain even considers Behe’s argument as good.

  18. Ron Britton Says:


    It’s counterproductive to just wave your hands and say “He’s a creationist, so he must be wrong.” A lot of people out there don’t know enough about either side to have an informed opinion. For their benefit, it is worthwhile taking creationist claims at face value and examining them to see that they have no validity.

    The thing about Behe, is he isn’t a crank like Ken Ham (who thinks T. rex ate coconuts before Adam and Eve got kicked out of the Garden of Eden) or Ray Comfort (who thinks that crocoducks must exist for evolution to be true).

    Behe believes evolution accounts for much of natural history. He just thinks God sticks his magic finger in us every now and then. That’s a comforting fiction for a lot of people. It gives them a story they can tell themselves to quiet the cognitive dissonance they get from knowing that evolution is true but wanting God to be true as well. That’s why it’s worth the time to rationally deconstruct his claims.