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.

Michael Behe compares apples to oranges while waiting for two mutations

Plasmodium malariae

A recent scientific article published in Genetics criticized Michael Behe and “exposed flaws” in his thinking.  The article in question, Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution, provides a mathematical model of the rate for two different mutations to occur in order.  They show that the time for prespecified mutations is within reason and support this by using two real world examples from humans and fruit flies.  Behe doesn’t believe it.

Behe had previously calculated the mutation rate that makes the protozoan P. falciparum (causes malaria) resistant to the antibiotic chloroquine that arose from two prespecified mutations in one protein.  He argued that this would take 1,000,000,000,000,000 years to achieve a similar pair of mutation in humans based on human population numbers and age until reproduction.   He seems to think that this is evidence to support intelligent design.

There are several problems with Behe’s thinking.  The most obvious is that Behe is comparing completely different organisms.  The mutation rate between various organisms can be very different.  In writing this post, I quickly determined from following the links from Wikipedia that the error rate of other protozoan (not specifically P. falciparum) seems to be around 100 fold lower than humans.  Not exactly the best comparison is it?

Other errors in Behe’s thinking include

• Behe calculated the requirement for prespecified mutations; Evolution is not prespecified
• These mutations could have arisen many times without our knowledge.  Unless Behe knows the sequence of every single P. faciparum, he can not really know how often these mutations occurred
• Behe’s calculations seem to make the common statistical error of treating two consecutive events as one event.  For example, the odds of a couple that already have two girls having another girl is still 1 in 2, not 1 in 8 like you would get if you asked what are the odds in the beginning of having 3 girls

The original authors had many other complaints against Behe’s assessment, but they are fairly technical and beyond the scope of this blog.  If your interested, follow the links below.  Even without these criticisms, it is clear that Behe’s mind is being clouded over by the motivation of having an intelligent designer.

One interesting thing to note is that the authors actually call out Michael Behe by name in the abstract. I actually think this is semi-unprofessional. At the same time however, I think it also shows a lot of gumption. They must have known that not only would Behe respond with sharp criticism.

Further reading:

Behe’s blog

Behe’s response to Rick Durrett and Deena Schmidt

Durrett and Schmidt’s response to Behe’s response

Waiting for Two Mutations

Behe’s 2007 paper on the subject

Flock of Dodos: The Intelligent Design – Evolution Circus

After waiting patiently for it to reach the top of my Netflix cue, I recently watched Randy Olsen’s “Flock of Dodos”.  Although I haven’t seen Expelled yet, I believe “Flock of Dodos” is its antithesis.  Randy Olsen, PhD is a trained marine biologist and former tenured professor, while Ben Stein was a political speech writer and professor of law.  Right from the start, you can see that one side is treating the evolution/intelligent design debate coming from the side of science and the other from the side of politics. Presumably, Stein would say that his film comes from an outsiders perspective so he is able to present an unbiased opinion. 

 

Olsen does a good job giving both sides of the debate their fair share of time.  He even interviews Michael Behe, one of the superstars of Intelligent Design, and lets him speak freely.  Of course the pro-evolution proponents are plentiful.  He even brings together a group of evolutionary biologists to play poker and discuss Intelligent Design.  He also covers much of the Kansas school board debacle and the Dover, PA trial. 

 

The movie has a light and cheerful feel, which was obviously intentional yet appreciated. So many documentaries, even highly acclaimed ones, are outright boring. Olsen achieves this feeling by sprinkling in amusing cartoons, colorful anecdotes, and of course lightly mocking people.  He even introduces us to his mother, Muffy Moose, who appears that she needs a movie or two of her own.  The “dodos” Olsen is referring to are not just Intelligent Design proponents.  He makes a point to say that the scientists who do not combat attacks evolutionary theory are as much dodos as anyone.

  

One of the things that I really appreciated about the movie was the way that Olson made fun of the idea of Intelligent Design. In particular, he and his interviewees mockhow badly some things were designed. The worst example of intelligent design (or the best example of unintelligent design) was digestive system of rabbits. Apparently, rabbits have their fermentation organ (where the complex plant material is digested) at the very end of their digestive system. In order for the rabbits to fully digest a meal, it has to eat its own poop. Behold: Intelligent! Design!

  

Olson makes the comment during the movie that when scientists try to share their side of the story, they are talking above the general audience. Not completely their fault as most have been working in their area of expertise most of their lives, and therefore they have a hard time bringing the conversation to a lower level. However, I think the problem is even worse than Olson believes. The target audience of the documentary was you average person, but one of the people who watched the documentary with me was a little lost. After all, she said she stopped learning about biology during “leaf collecting.” This leads me to believe that our educations system may be lacking, but that is a subject of another post.

 

My general feeling after finishing the movie, is that there is a war of ideas, where the two sides are playing by different rules.  The evolutionists are using facts and evidence, while Intelligent Design proponents are using catch phrases and religious appeal.  Intelligent design proponents are not evil or malicious (for the most part). In fact, most in the movie came across as being honest, caring, and kind-hearted. These attributes could be part of the problem because they are a little too nice, a little too naive, and a lot too trusting.

    

So for those of you interested in the Evolution / Intelligent Design debate, I recommend that you see this movie.

 

The evolutionary numbers game

In my last post, I brought up how Michael Behe used the fact that 40,000 generations of E. coli were necessary for Richard Lenski’s experiment to find an E.coli who could utilize citrate. In this post, I am going to run through some numbers to show how 40,000 generations is nothing to evolutionary time.  Of course my numbers are going to be rough estimates, but I think it will get the job done.

For the sake of argument, lets say the earth is 10,000 years old (yes, people do believe the earth is this young). If Behe’s math is correct, then E. coli have 2,000 generations a year or 20,000,000 generations over the time of the young earth. More realistically, the earth is 4.5 billion years old, or nearly 10 trillion generations of E. coli. Of course E. coli hasn’t been around the whole time the earth has, but it does put that 40,000 number into perspective.

Let’s say that a beneficial mutation, such as the ability to use citrate, occurs once every 100,000 generations. Given the 10 trillion number above, that would give 100,000 beneficial mutations. Keeping in mind that E. coli only has ~5000 genes, each gene could have changed 20 times.

The last set of numbers we will be addressing is the nearly unfathomable number of bacteria on the planet.  For reference, our bodies alone are estimated to have 1,000 trillion or 10^15 of bacteria (not all E. coli of course) of bacteria (Yes, I know, it is kind of gross). There are over 6 billion people on earth bringing the total of bacteria inside humans to 6 X 10^24.

Now that is a lot of bacteria, just inside people, but how about all over the planet?  Bacteria are everywhere: inside us, on practically every surface, throughout the ocean, and throughout the earth.  It has been estimated that there are 5 X 10^30 bacteria on earth.

10^12 generations of bacteria and 10^30 bacteria.  Those are mind-boggling numbers!  I know the numbers don’t really mean too much by themselves, but just keep them in mind when an IDer tries to convince you that something like 40,000 generations is a big deal.

Behe Doesn’t Believe in Evolution in a Tube

Michael Behe writes on June 6th a post entitled: Multiple Mutations Needed for E. Coli. This post came from his amazon blog, where he is trying to push his book. Behe is writing of course about Richard Lenski’s (et al.) recent publication in PNAS (Proceedings of the National Academy of Sciences). In the article, the authors describe an experiment that has been going on since 1988. Now that is persistence! Richard Lenski is the principal author and has kept the same 12 cultures of E. coli reproducing for the last 20 years. These cultures are grown in two food sources: glucose, which E. coli readily uses and citrate, which E. coli cannot use. After nearly 32,000 generations, one of the E. coli cultures developed, or evolved, the ability to use citrate.

This experiment provides an example of a living organism evolving a new trait in the tightly controlled setting. This type of result had not really been seen before (largely due to the long times necessary) and was something of a missing piece of evidence for evolution. Evolutionary type changes have been observed outside of the lab (isolated lizards, nylon eating bacteria), but not in a true experimental setup.

The changes in the isolated cultures of E. coli were not limited to the ability to utilize citrate. They also exhibited changes from the original cultures that include:

higher maximum growth rates on glucose, shorter lag phases upon transfer into fresh medium, reduced peak population densities, and larger average cell sizes relative to their ancestor.

10 of the 12 E. coli cultures also “evolved increased DNA supercoiling.” When challenged with other carbon sources, such as maltose or lactose, their growth rates differed. These changes are indeed important to keep in mind as more evidence of evolutionary change, but the clear advantage of the gain-of-function change illustrated by the new ability to utilize citrate is monumental.

Predictably, Behe does not seem to be too impressed by the experiment. He makes the point that E. coli divides rapidly and 20 years equates to 40,000 (even though the paper clearly states 31,500) generations and therefore is not that remarkable. This may seem like a lot of generations, but 20 years is not even a blink of the eye in evolutionary timescales. I will give an in depth analysis of the numbers in a later post. Besides, this experiment provides proof of concept that random mutations can lead to a gain-of-function change, one of evolution denier’s talking points, as Casey Luskin as said: “ID is far more interested in explaining the GAIN of biological function rather than loss of function.”

Lenski wanted to further explore how the E. coli were able to gain the ability to use citrate. Was it a single mutation event or was it a series of mutations? In order to determine which was true, he repeated the experiment with cultures that had gone through various numbers of generations, 12 in all. He found that when he took cultures after 20,000 generations, they more quickly were cit+. This led Lenski to conclude that there were multiple mutational events leading to cit+, one of which occurred before the 20,000 generation. An important finding, and one that shows that there can be silent, but beneficial, mutations. Behe disagrees:

If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation.

I am not sure how someone so educated and respected could say something so completely vacuous. In evolution, everything is carried over, whether it has an immediate benefit or not. Maybe one of the mutations that occurred allowed the mutant cell to grow slightly faster than the others. Maybe the mutation was silent and did not help or harm anything. Does Behe really believe that every mutation has to have a large phenotypic effect to be in accord with evolutionary theory?