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.

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Lenski vs conservapedia

No self-respecting evolution blog can go without mentioning the interactions of Dr. Lenski (of evolution in a tube note) with Mr. Schlafly of Conservapedia. Conservapedia is the religious right’s answer to Wikipedia, because they believe that Wikipedia is biased toward liberal ideas.

Mr. Schlafly (a non-scientist) sent a letter to Dr. Lenski to

request for your data underlying your recent paper….Your work was taxpayer-funded, and PNAS represents that its authors will make underlying data available. I’d like to review the data myself and ensure availability for others, including experts and my students. Others have expressed interest in access to the data in addition to myself, and your website seems well-suited for public release of these data.

For those of you unfamiliar with the process of modern science, peer-reviewed published articles are written in such a way that anyone with the knowledge and the equipment should be able to repeat the presented experiments. The articles also include enough information to prove the point that the authors are trying to make (of course interpretation is sometimes up for debate).

What Mr. Schlafly requested is completely unheard of, unless someone is being investigated for forgery (see Hwang Woo-Suk). What makes it worse is that he is nothing near a scientist. If this sort of practice was allowed to go on regularly, science would come to a grinding halt due to scientists having to constantly dig up old lab books and dust off their old 5 1/4 floppies. This is why no scientific competitor or lay person has the right to ask for this kind of data even though scientists are usually funded by public money.

Now for the good part. Dr. Lenski, after initially replying kindly, sent a scathing letter to Mr. Schlafly.  Rather than selecting specific quotes from the letter, I suggest you go read it yourself.  I promise at least one laugh.

Recently, it has come to my attention that some of the authors at Conservapedia have been using underhanded tactics and censoring people.  I guess I shouldn’t have been too surprised.

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?