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A Blind Man Carrying a Legless Man Can Safely Cross the Street: Experimentally Confirming the Limits to Darwinian Evolution

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I never thought it would happen but, in my estimation, Richard Lenski has acquired a challenger for the title of "Best Experimental Evolutionary Scientist." Lenski, of course, is the well-known fellow who has been growing E. coli in his lab at Michigan State for 50,000 generations in order to follow its evolutionary progress. His rival is Joseph Thornton of the University of Oregon who, by inferring the sequences of ancient proteins and then constructing (he calls it "resurrecting") their genes in his lab, is able to characterize the properties of the ancestral proteins and discern how they may have evolved into more modern versions with different properties.

I have written appreciatively about both Lenski and Thornton before, whose work indicates clear limits to Darwinian evolution (although they themselves operate within a Darwinian framework). Thornton's latest work is beginning to show a convergence with Lenski's that greatly boosts our confidence that they both are on the right track. In a recent review (Behe, 2010) I pointed out that all characterized advantageous mutations that Richard Lenski has observed in his twenty-year experiment have turned out to be degradative ones -- in which a gene or genetic control structure was either destroyed or rendered less effective. Random mutation is superb at degrading genetic material, which sometimes is helpful to an organism. In his latest work Thornton, too, shows evolution of a system by degradation, although he speculates that the changes were neutral rather than advantageous.

In Finnegan et al. (2012), "Evolution of increased complexity in a molecular machine," Thornton and colleagues study a ring of six proteins in a molecular machine (that also has many other parts) called a V-ATPase, which can pump protons (acid) across a membrane. The machine exists in all eukaryotes. In most eukaryotic species, however, the hexameric ring consists of five copies of one protein (let's call it protein 1) and one copy of another, related protein (call it protein 2). In fungi, however, the ring consists of four copies of protein 1, one copy of protein 2, and one copy of protein 3. Protein 3 is very similar in sequence to protein 1, so Finnegan et al. (2012) propose that proteins 1 & 3 are related by duplication of an ancestral gene and subsequent modification of the two, originally identical duplicated genes.

How did protein 3 insinuate itself into the ring? The original protein 1, present in five copies in most organisms, already had the ability to bind to itself, plus an ability to bind to one side of protein 2, plus a separate ability to bind to the opposite side of protein 2 (see Finnegan et al.'s Figure 3). Thornton's results are consistent with the idea that, by happenstance, the gene for protein 1 duplicated and spread in the population. These events apparently were neutral, the authors think, not affecting the organism's fitness.

Eventually one of the duplicates acquired a degradative mutation, losing the ability to bind one side of protein 2. This was not a problem because the second copy of the protein 1 gene was intact, and could bind both sides of protein 2, so a complete ring could still be formed. This also spread by neutral processes. As luck might have it, the second gene copy subsequently acquired its own degradative mutation, so that it could no longer bind the other side of protein 2. Again it's no problem, however, because the first mutant copy of protein 1 could bind to the first side of protein 2, bind a few more copies of itself, then bind a copy of protein 3, which still had the ability to bind the other side of protein 2. So a closed, six-member ring could still be formed. This apparently also spread by neutral processes until it took over the entire kingdom of fungi.

The work of Finnegan et al. (2012) strikes me as quite thorough and elegant. I have no reason to doubt that events could have unfolded that way. However, the implications of the work for unguided evolution appear very different to me than they've been spun in media reports. The most glaringly obvious point is that, like the results of Lenski's work, this is evolution by degradation. All of the functional parts of the system were already in place before random mutation began to degrade them. Thus it is of no help to Darwinists, who require a mechanism that will construct new, functional systems. What's more, unlike Lenski's results, the mutated system of Thornton and colleagues is not even advantageous; it is neutral, according to the authors. Perhaps sensing the disappointment for Darwinism in the results, the title of the paper and news reports emphasize that the "complexity" of the system has increased. But increased complexity by itself is no help to life -- rather, life requires functional complexity. One can say, if one wishes, that a congenitally blind man teaming up with a congenitally legless man to safely move around the environment is an increase in "complexity" over a sighted, ambulatory person. But it certainly is no improvement, nor does it give the slightest clue how vision and locomotion arose.

Finnegan et al.'s (2012) work intersects with several other concepts. First, their work is a perfect example of Michael Lynch's idea of "subfunctionalization," where a gene with several functions duplicates, and each duplicate loses a separate function of the original. (Force et al., 1999) Again, however, the question of how the multiple functions arose in the first place is begged. Second, it intersects somewhat with the recent paper by Austin Hughes (2011) in which he proposes a non-selective mechanism of evolution abbreviated "PRM" (plasticity-relaxation-mutation), where a "plastic" organism able to survive in many environments settles down in one and loses by degradative mutation and drift the primordial plasticity. But again, where did those primordial functions come from? It seems like some notable workers are converging on the idea that the information for life was all present at the beginning, and life diversifies by losing pieces of that information. That concept is quite compatible with intelligent design. Not so much with Darwinism.

Finally, Thornton and colleagues latest work points to strong limits on the sort of neutral evolution that their own work envisions. The steps needed for the scenario proposed by Finnegan et al. (2012) are few and simple: 1) a gene duplication; 2) a point mutation; 3) a second point mutation. No event is deleterious. Each event spreads in the population by neutral drift. Notice that the two point mutations do not have to happen together. They are independent, and can happen in either order. Nonetheless, this scenario is apparently exceedingly rare. It seems to have happened a total of one (that is, 1) time in the billion years since the divergence of fungi from other eukaryotes. It happened only once in the fungi, and a total of zero times in the other eukaryotic branches of life. If the scenario were in fact as easy to achieve in nature as it is to describe in writing, we should expect it to have happened many times independently in fungi and also to have happened in all other branches of eukaryotes.

It didn't. Thus it seems a good conclusion that such neutral scenarios are much rarer than some workers have proposed (Gray et al., 2010; Lukes et al., 2011), and that more complex neutral scenarios are unlikely to happen in the history of life.

Literature Cited

Behe, M. J., 2010 Experimental Evolution, Loss-of-function Mutations, and "The First Rule of Adaptive Evolution." Quarterly Review of Biology 85: 1-27.?

Finnigan, G. C., V. Hanson-Smith, T. H. Stevens, and J. W. Thornton, 2012 Evolution of increased complexity in a molecular machine. Nature doi: 10.1038/nature10724.?

Force, A., M. Lynch, F. B. Pickett, A. Amores, Y. L. Yan et al. 1999 Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.?

Gray, M. W., J. Lukes, J. M. Archibald, P. J. Keeling, and W. F. Doolittle, 2010 Irremediable complexity? Science 330: 920-921.

Hughes, A. L., 2011 Evolution of adaptive phenotypic traits without positive Darwinian selection. Heredity (Edinb.) doi: 10.1038/hdy.2011.97.?

Lukes, J., J. M. Archibald, P. J. Keeling, W. F. Doolittle, and M. W. Gray, 2011 How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63: 528-537.


This is the kind of hard science that we need when it comes to evolution. Just claiming things emerged and coming up with a just-so story that may or more than likely may not be true, is not science. Lenski's 50,000 generations of bacteria have come up empty so far.

Thornton et al also have done some good work and still the evidence they were hoping for is lacking.

Seems like a fair analysis by Dr. Behe. Thanks so much!

It's very well known that natural processes tend to be destructive not constructive over time. Does this tie into the concept of entropy/the 2nd law of thermodynamics, or is that specifically related to heat transfer?
I remember when those who used to make the argument that the 2nd law of thermodynamics prevents evolution were ridiculed by saying "how silly of them, don't they know the earth is an open system?". Well, they need to think that through a bit more -- yes, the Earth gets energy from the sun, but it's raw, undirected energy. If it could be harnessed through some sort of solar-powered, life-generating machine, that is a different story. Millions of years of UV exposure is not going to produce increasingly complex life forms, rather it will damage their DNA. Interestingly, autotrophs could not have evolved gradually over time, because how would the intermediates have obtained their food?
I too am a software engineer, and I can appreciate the parallels drawn to it. Information always originates from a mind...randomly typing into a section of code will cause it to break or at most remain neutral. It takes a designer or planner to understand the scheme of things and design something that works. This makes sense but it is not a rigorous argument, so maybe over time we will see ID arguments become stronger.

"ex nihilo nihil fit" is a belief that comes from the idea that something cannot arise from nothing; that would involve a contradiction and is the only real "law" of programming code. In my experience of 40 years of programming and working with data transfer in communications, Shannon entropy has taught me that "information" will always have mutations (line noise) leading to a destructive nature and never do these mutations create an order of a higher magnitude that is beneficial to the original coded message (such code in communications is meant to be sent and received exactly, 'as is' and any mutation never improves upon the meaning of the message being sent). Breaking this law, such in life creating itself (as is the concept of natural origins) would be contradictory in concept.

Such an 'unforeseen' force to compensate for an increase in order, in evolution, has not been shown in PoP (Proof of Principal) in the Theory of Evolution and would rewrite Shannon entropy if such a thing was documented as the Theory 'claims'...

Thank you so much for Behe's thorough and fair treatment of this research. I am thankful of his response which is empty of rhetorical slams, towards those who hold the opposing evolutionary view and manipulation of those who haven't the background to do the evaluation themselves. Keep up the good work and good science!

I love how Behe's cold hard empiricism completely destroys the Darwinian hypothesis', which are reported as fact before they're even tested.

Keep up the good work!

It 'seems' to me, that this shows that all life was perfectly 'placed' here on Earth and that the real "meaning" of the term Evolution is a degrading process that will eventually lead all of life into it's simplest forms. In other words, it seems that Evolution is a process in which things change, but in the opposite direction that is regularly taught and after millions of years, all life on Earth may, but not likely, be reduced to a mere muck of slime through the evolutionary process. Kind of like all machinery eventually breaks down but never has the capacity to rebuilt itself into something better unless an intelligence is working behind the scenes to improve, upgrade or replace the machine. Evolution does not show the intelligent 'factor' that can upgrade or improve the machine but does show the machines ability to mutate into a worse condition that falters eventually. So in the thinking process of someone that believes in ID, the process of Evolution is the natural ageing process over time that degrades but never �magically� improves upon itself by haphazardly means. I look at Shannon entropy in the process of electrically sending and receiving information and never is there an increase of �order� of information being transmitted but a decrease and degradation of information ever present. This is the Evolutionary process of electronic information and nothing exists �naturally� that can account for an increase of information in such a system unless an outside, intelligent force acts upon it.

I am currently reading Darwin Black Box. Impressive! Nice piece you wrote here too.

Dr. Behe, first and foremost I would like to say I greatly appreciate your clarity in making complicated issues easy for the general public to understand, and also want to thank you for sticking to the evidence, no matter what, even when it has led to some pretty nasty smear attacks against you by your critics. You Sir are a true scientist! Also thanks for consistently setting a fine Christian example by maintaining the high road in not responding in kind to your more vicious critics.,,, As well, a question came up from a blogger at UD that I think is a fair question that I was hoping you would briefly address, since I have wondered about the question myself in the past:

Here is the question:

I�d like to ask Dr. Behe how he figures common descent happened if mutations don�t add new molecular machines (which he admitted to in his book) and/or new anatomical features�(or even parts of them.) (per vh at UD)

The most glaringly obvious point is that, like the results of Lenski's work, this is evolution by degradation. All of the functional parts of the system were already in place before random mutation began to degrade them.

Hmm, so natural selection is like every other natural cause in the universe after all; it tends to create disorder out of order, and not vice versa. :-)

Great article! Should be blatantly obvious by now that ID is a much better explanation for the diversity of life on earth than Darwinian evolution.