Lenski’s new results; Behe’s red herring

Richard Lenski is an evolutionary biologist who studies evolution by analyzing changes in bacterial populations.  Perhaps he is most famous for his long-term experiment where his group identified a population that evolved to use a nutrient (citrate) that E. coli normally can’t use.  This was a very important finding as it provided proof-of-concept that random mutations alone are sufficient to induce new functions.

In a recently published paper in Nature, Lenski takes the above experiment and analyzes the frequency of mutation throughout these populations.  The goal of this paper was not to show which specific mutations led to the ability of the bacteria to use the new nutrient source.  The goal was to look at the level of overall mutation rate during the experiment.  In the authors own words:

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest.

Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

Of course the Discovery Institute and ID proponents are not going to keep quiet about any work coming from Lenski’s lab as their work provided such an important part of the evolutionary puzzle.  Michael Behe took up the challenge this time and wrote an entry at Evolution News and Views.  Lets address some of Behe’s points.

Behe’s first compliant is that

[Lenski’s group] identified a couple score of mutations which they say are likely beneficial ones. That is almost certainly true, but what they don’t emphasize is that many of the beneficial mutations are degradative — that is, they eliminate a gene or its protein’s function.

First, Behe is attacking the paper for something that is really irrelevant to the point of the paper.  It also doesn’t disprove the original result of that spontaneous mutations that led to a novel attribute.  It is a red herring designed to poke holes in Lenski’s work instead of directly arguing against it.  So why all the degradative mutations?  Well, these experiments were done in a lab under strict conditions (single temperature, no other organisms, defined nutrients) to eliminate other variables. Without these other stimuli, is it any wonder that most changes are degradative?

Behe also criticizes the rise in what is called a mutator line in these experiments.  A mutator strain is one in which mutations arise more frequently than in a normal strain.  Again this doesn’t really address the ideas of the new paper or in the proof-of-concept of Lenski’s original data.

Anyway, who cares that these strains became mutator strains. A mutator just increases the frequency by which mutations arise. Maybe it would have taken 3 times as long for the beneficial mutation to arise if the mutator strain hadn’t evolved. It doesn’t change the fact that the cells evolved into a state where they could use a nutrient that they couldn’t before.   Besides, it is a moot point as one of the original mutation had arose before the 20,000 generation, a time before the mutation that led to mutator strain had occurred.

Finally, Behe closes with the expected tactics that we have grown to love from ID proponents.  The first tactic as illustrated above is to wrongfully criticize valid experiments in favor of evolution.  The second tactic is then to say how this data really proves intelligent design:

Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection.

First, an ID proponent would not expect the E. coli to ever use the new nutrient.  The “power of random mutation and natural selection” led the bacteria to a whole new attribute.  Don’t forget, this experiment lasted only decades, or 1/100,000,000 the time bacteria are believed to inhabit the earth.  Finally, like I stated above, these were very unnatural conditions that would never be experienced during normal life on earth.

The flagellum’s clutch means less design

 
Bacterial Flagellum

Daniel Kearns and colleagues have found that bacterial flagellum(pictured here courtesy of Access Research Network) has the equivalent of a clutch. The Discovery Institute wasted no time in proclaiming that this is more evidence for intelligent design.  In a June 30, 2008 post entitled More Similarities Between Flagellum and Human-designed Machines, Casey Luskin states:

It [flagellum] functions like a human-designed rotary engine that propels a bacterium through a liquid medium in the same way a propeller powers submarine through the ocean…. The flagellum is basically a rotary engine, with a motor, a rotor, a stator, a bearing, a u-joint, and a propeller. Now it turns out that the flagellum has a clutch.

Scientists have known for awhile that the flagellum stops moving in certain situations (i.e. the formation of a biofilm).  This gives us two choices:a brake or a clutch.  Either way, ID proponents would say that the new structure, either a brake or clutch, shows design as human-designed motors have both.  So this discovery does not bolster their argument.

The protein that acts like the clutch, EpsE, has some interesting properties that make it clear that it was not designed for this purpose; it evolved from a protein with another purpose.  For one, it looks like a protein that adds sugars to other proteins or lipids, but removing this ability from the protein does not effect its ability to act like a clutch.  It is part of a group of genes that are needed to make biofilms, not with flagellum genes.  Not exactly the way someone would design the system.

Bacteria swimming vs. motorboat

Bacterial Swimming

I also want to add a little about how the bacterial flagellum is used by bacteria to move in a particular direction.  Logically, if you were going to build a motor (like for a boat), wouldn’t you make it be able to run as long as you needed and in the direction you wanted?  This is not what you find with bacteria.  They go through two different phases, tumbling and straight swimming.  The bacteria swim for awhile in one direction and then turn off the motor and tumble. If they are swimming the direction they want, then they swim longer.  This is repeated unti they get where they are trying to go.  In the image below, I have drawn an example of bacteria (green path) compared to a motorboat(red path) trying to swim towards the red gradient.  If you ask me, this is a terribly inefficent (and unintelligent) way to move, but it does work.