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.


Rejecting Evolution, a path back to the dark ages

Journalist Denyse O’Leary wrote an op-ed in the Calgary Herald defending “Albertans right to reject Darwinian evolution.” It really should have been called “Albertans right to be ignorant of modern biology and medicine and a small step back towards the Dark Ages.” She is attacking a column by Rob Breakenridge where he is disturbed by the lack of belief in evolution in Alberta, Canada.  She says that he should not have written “about big topics without basic research.” O’Leary should take her own advice.

She starts by giving us her take on the 2005 Kitzmiller trial. This is the trial where it was ruled that Intelligent Design was essentially creationism and therefore violated the Establishment Clause of the US Constitution.

The 2005 Judge Jones decision in Pennsylvania, to which Breakenridge devotes much of his column, has not crimped the worldwide growth of interest in intelligent design. That is no surprise. A judge is not a scientist, and Jones cannot plug gaping holes in Darwin’s theory of evolution.

O’Leary is using one of ID proponents newest arguments to deflate the impact of the Kitzmiller trial. They are fond of pointing out that Jones isn’t a scientist. Well guess who else isn’t a scientist? That is right, Denyse O’Leary.  Instead, she is a “Toronto-based journalist; grandmother; Roman Catholic Christian.”  Don’t you just love the hypocrisy?

O’Leary then makes some audacious comments:

Evolution is—contrary to its (largely) publicly funded zealots— in deep trouble, for a number of reasons….Textbook examples of evolution often evaporate when researchers actually study them

And who do you think brought us these results that contradict earlier findings? Yes, scientists. Scientists who supposedly are stuck in the dogma of Darwinian evolution. Challenges to what we thought we knew is what makes Science the best way we have of looking at the world. But lets look at a few of the examples that O’Leary gives that supposedly “evaporate.”

One example that O’leary points to is the disappearance of eyes in the blind cave fish. As PZ Myers pointed out, this adaptation to living in a lightless environment is actually due to an increase in the expression of a particular developmental gene, sonic hedgehog.  This change leads to a stronger jaw with better sensory structures.  Both these changes are quite advantagous for searching for food in dark caves where eyes are useless.

O’Leary even has the gall to make a reference to Michael Behe’s Edge of Evolution (2007) where he

notes that for decades scientists have observed many thousands of generations of bacteria in the lab. And how did they evolve?  Well, they didn’t.

Apparently, O’Leary doesn’t mind lying here saying that no evolution has been observed. As many of you will recall, evolution was observed in one such experiment by Richard Lenski’s group. They observed the gain of the ability of E. coli to utilize a food source (citric acid) that it could not use before. This story was all over the evolution and intelligent design circles. We can forgive Behe here because his book was published before Lenski’s paper, but O’Leary is just being dishonest.

O’Leary goes on to quote polls that show that only 37% of Albertans accept evolution. She even says “Well, good, let’s drive the numbers lower still.” Not only does O’Leary ignore evidence contrary to her position, misconstrue scientific findings related to evolution, and outright lie about recent findings, but she wants people to be scientifically illiterate.

Casey Luskin is blind to blind cave salamanders

Casey Luskin (in Christopher Hitchens and His Cave Myths post) discusses some of Christopher Hitchens views. One of Luskin’s points really made me laugh:

In his debate against Jay Wesley Richards, Hitchens reportedly argued against God by alleging that God would not create certain features we observe, to which Richards aptly replied, “A sneer is not an argument.”

Are you kidding me? Did Jay Wesley Richards really just claim that you cannot use as an argument what God would have or have not done? This is laughable in light of the whole ID movement being based on what we would predict God would do. Hitchens’ comments were indeed a sneer, but more importantly they use the exact same reasoning that intelligent design proponents use. However, IDers conveniently ignore the myriad examples of unintelligent design.

Luskin counters that:

ID proponents regularly point out that evolution is quite good at effecting loss-of-function. While random mutations usually fail miserably at creating new complex biological functions, they are in fact quite good at messing up complex biological functions.

No matter how any ID proponent spins these facts, these “loss-of-function” changes are a prediction of evolutionary theory. They are just moving the goal posts to say that some things do happen by evolution, but other things were done by a designer, whenever convenient for their argument.  Of course, we have seen that evolution has occurred in a lab with the E. coli experiments done by Dr. Lenski’s group.  Here, the bacteria clearly gained the ability to use citric acid as a food source.  This highly controlled experiments shows that gain of function does happen, contrary to Luskin’s belief.

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.

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?