Lenski's Evolving E. coli & A Rebuttal to Answers

In 2009, Richard Lenski produced some of the most detailed documented evidence of the production of new novel traits through natural selection.  In this case, E. coli bacteria developed the ability to transport citrate through their cell wall in oxygenated conditions before metabolizing it.  The mutation chain that occurred was documented in detail and the experiment is notable in giving biologists a much better understanding of the role of potentiating mutations.

These mutations don't produce benefit alone, but are necessary intermediates in the production of new traits.  It is of importance to note that when bacteria containing the potentiating mutation that led to the citrate transport trait were frozen, they retained the ability to re-evolve it.  That demonstrated that the potentiating mutation is a necessary intermediate, providing further verification for the causal chain of mutations.

In addition to the potentiating mutation, subsequent mutations occurred that provided increasing benefit.  The initial ones allowed the bacteria to metabolize a small amount of citrate.  Eventually though, the mutations  greatly improved the function, allowing those bacteria to consume the food source, outcompeting their neighbors.

This experiment isn't about a single chance mutation leading to some benefit.  It is the complete evolution of a new trait through a series subsequent mutations.  The addition of a new feature.  Again the premise of evolution is very simple.  Given a set of organisms, and a set of environmental conditions and states, a certain number of organisms will survive.  The ones that survive will continue to produce offspring and pass on their genes, the others perish and do not.  Random mutation provides some variety to the mix.  Change over time driven by the selection of a given set of organisms over another set that are better able to survive in an environment.

In the following I present Answer's In Genesis's (AIG) response to the results of the experiment, and my rebuttal to their response.

Many evolutionists state that the bacteria are experiencing “adaptive evolution.” However, this is not evolution but rather adaptation. Molecules-to-man evolution requires an increase in information and functional systems. Instead, these bacteria are likely experiencing a loss of information and functional systems as has been observed in other mutant bacteria in Lenski’s lab. While these changes are beneficial in the lab environment, they do not lead to a net gain that moves bacteria in an upward evolutionary direction.

The bacteria in question didn't lose anything.  The E. coli actually gained the ability to transport citrate through its cell wall.  That is not a loss of any kind.  They go on to quote a study on how E. coli can transport and metabolize citrate in low oxygen conditions

Previous research has shown that wild-type E. coli can utilize citrate when oxygen levels are low.⁶ Under these conditions, citrate is taken into the cell and used in a fermentation pathway. The gene (citT) in E. coli is believed to encode a citrate transporter (a protein which transports citrate into the cell).⁶ When oxygen levels are high, it is thought that the citrate transporter does not function or is not produced (even though they still possess the enzymes necessary to utilize citrate).

Lenski's paper itself, also points this out.

The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions.

The evolved trait is not the ability to utilize citrate, but to transport it through its cell wall.  This involves several mutations, and each of them in the chain was documented by Lenski's experiment.  In fact, by freezing different strains at various points in the evolutionary chain, Lenski was able to restart the process at different points repeatedly, and demonstrate the causal chain conclusively.  He reconfirmed the link between the mutation and trait.  The AIG response is simply speculating about what might have happened, which they need not do since reading Lenski's paper, the precise mutation chain is laid out.

Lenski’s lab has not yet identified the genetic alterations of the Cit+ E. coli line, but he believes that there are multiple mutations involved. Studies of the “fossil record” of this line indicate that one or more mutations occurred around generation 20,000 which he terms “potentiating” mutations that were necessary before additional mutations around generation 31,500 led to Cit+ cells. Lenski thinks that the mutations may have activated a “cryptic” transporter

Lenski's lab has found the genetic alterations.  AIG's response is old, so I grant them the benefit of the doubt here.  There have been further publications from Lenski on the subject further confirming the results.

While the fitness of the bacteria has increased (as compared to the starting bacteria), it has come at a cost. For example, all the lines have lost the ability to catabolize ribose (a sugar).³ Some lines have lost the ability to repair DNA.⁴ These bacteria may indeed be more fit in a lab setting, but if put in competition with their wild-type (normal) counterparts in a natural setting, they would not stand a chance.

Let's quote Lenski's paper for context.

Previous analyses of this experiment have shown numerous examples of parallel phenotypic and genetic evolution.All twelve populations underwent rapid improvement in fitness that decelerated over time (2, 3, 22, 23). All evolved 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 (22–26). Ten populations evolved increased DNA supercoiling (27), and those populations examined to date show parallel changes in global gene-expression profiles (4, 28, 29). At least three genes have substitutions in all 12 populations (30, 31), and several others have substitutions in many populations (27–30), even though most loci harbor no substitutions in any of them (32). At the same time, there has also been some divergence between populations. Four have evolved defects in DNA repair, causing mutator phenotypes (3, 33). There is subtle, but significant, between population variation in mean fitness in the glucose-limited medium in which they evolved (2, 23). In media containing other carbon sources, such as maltose or lactose, the variation in performance is much greater (34). And while the same genes often harbor substitutions, the precise location and details of the mutations almost always differ between the populations (27–31).

I don't see where Lenski states they lost the ability to catabolize ribose, but citation 31 is a reference to documented instances where the ability was lost in E. coli. (Cooper VS, Schneider S, Blot M, Lenski RE (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of E. coli B. J Bacteriol 183:2834–2841.)  I have bold-faced the part where he documents defects in DNA in four of the populations.  Not all the resulting Lenski populations had DNA defects.  More from AIG

Lenski states (based on calculated mutation rates in E. coli), “It is clearly very difficult for E. coli to evolve this function. In fact, the mutation rate of the ancestral strain from Cit- to Cit+ is immeasurably low . . . .”¹ If developing the ability to utilize citrate under certain conditions using random mutations of a pre-existing citrate utilization system is so rare, then how even more improbable is it to believe that these same random mutations can lead to completely new information and functional systems

Yes, but as Lenski points out in an exasperated response to Andrew Layton Schlafly

Did you know that your own bowels harbor something like a billion (1,000,000,000) E. coli at this very moment? So remember to wash your hands after going to the toilet, as I hope your mother taught you. Simple calculations imply that there are something like 10²⁰ = 100,000,000,000,000,000,000 E. coli alive on our planet at any moment. Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so. That’s a lot of opportunity for evolution.

Indeed there continue to be publications and journal articles written that continue to confirm and reconfirm the results of Lenski's work.  Along with providing specific genomic evidences for the mutations involved the results demonstrate the specific chain of mutations.  Studies of Lenski's E. coli strains continue to provide insight into evolution of new traits.

Always Allow Your Views to be Challenged

After losing touch for a great while, a good childhood friend challenged my views on evolution.  After much reflection and research a few astounding conclusions were reached.  Firstly, I realized how little I actually knew about the science behind evolution.  This is probably the result of not being particularly interested in the subject of biology in general throughout my school and college years.  From what I recall, I only took about three courses throughout my entire life on the subject.  Thinking back to life science class in middle school, I vaguely recalled the enzymes used to break down starches.  I have a fuzzy memory of learning something about inheritance and the phylogenetic tree in my high school biology class.  Needing to take a biology course as part of my core curriculum in college, I took human biology, and again have no specific recollection of anything.  The information that was presented, forced me to question my confidence in the subject.  So being one to seek truth on my own, I set out on a quest to find answers.  One of the initial things I realized, as a testament to my initial ignorance, is that I didn't even know what a scientific theory truly was.

This leads to my second astonishment.  Upon actually researching the subject, I indeed did find overwhelming evidence for Evolution and common descent.  Before taking the time to read on the subject, I wasn't aware of the progress that had been made.  I began my journey with the assumption of it being unproven.  Remarkably fast though, by reading the resources available, I was convinced at the sheer volume and quality of evidences from multiple independent sources.

Childhood Memories

I was a remarkably curious child and was always asking questions.  While I don't recall the exact question that was asked in this instance, I remember my father taking out the World Book Year Book and flipping to an article on the work of a Dr. Leakey.  His work featured in that years year book detailed extensive fossil findings in Africa.  It was truly astonishing to learn and actually see that human beings are part of the tree of life, classified as Homo sapiens.  Sapiens is Latin for wise or rational, and homo means man (in Greek homo means same.)  Furthermore, it turns out we are decedents of upright walking primates.  In addition, certain modern primates are extremely closely related and all primates are at least cousins, though quite a few times removed.

Being lucky enough to have a relative in the biological sciences growing up, I was showered with books like The Pandas Thumb.  Honestly I wasn't too keen on the details, but I read and took these ideas for granted.  After all, it seemed so obvious to me.  It never crossed my mind that anyone would doubt what I saw to be sound reasoning and good reading material.  Of course, at that age I didn't have the appreciation for strong evidence that is irrefutable.  Things were read, and assimilated.

Other than these few books, and a couple of biology classes in my lifetime is all my biology education consisted of.  I took these ideas for granted, just like other scientific fields on understanding, like physics or chemistry.  The thought never crossed my mind that there would be anything controversial about them.

My Ideas Challenged

Fast forwarding into my twenties after losing and regaining touch with a good friend of mine.  My friend had recently converted to faith, and we drifted onto the topic of evolution.  Turns out we had some points of disagreement, but I had come to this discussion completely uninformed and unprepared.  Honestly, I had never heard any of the objections he presented, and he pointed me to a web site to refer to.

When I got home and checked the site, the author of the materials seemed to present some very interesting arguments.  Because of my relative lack of background, I didn't have the necessary resources to assess the truth of this individuals claims.  This is when I set out to find answers.  Within a few moments I stumbled upon Talk Origins.  Turns out they had a huge collection of claims made by critics of evolution, where they presented evidence, provided sound reasoning and debunked them.  Not only were the claims of the author that was referred to me listed on the site, but also hundreds of other ones too.  This gave me an opportunity to look at the devil's advocate angle.  I've always believed that being forthright about the claims of your opponents and providing well reasoned, evidence based, plain language responses to debunk them demonstrates intellectual integrity.

Learning came fast and hard, when I realized that I didn't even know what a scientific theory was.  Most people are under the impression that a theory is an unproven idea.  But in a scientific context, I means a description.  Take gravity for example.  The is the phenomenon, or force, of gravity; then there is the Theory of Gravitation that mathematically describes how the force acts on things.  Gravity is a force, and it factually exists.  You might not believe in gravity, but when you jump off a building, it believes in you--hitting the ground at terminal velocity.  The same is true for electromagnetism; there is the force itself--a fact--and the description or theory that describes how the force works.

I realized at this point that the author of the website making these claims was criticizing Evolution based on the fact that it was "just a theory."  The author seems to imply that theories like Evolution aren't legitimate. Gravity is "just a theory" as well by that definition.  Of course it is quite an observable fact.  We can also observe that organisms change over time, and that is a fact (specifically the fact of Evolution.)  The description of how and why they change is the Theory of Evolution.

Reading the evidences for  Evolution on the site, complete with references, images, examples, and sound reasoning convinced me that Evolution is a better description of what we know than I ever thought before.  I learned how there is even powerful molecular evidence now, which is about as strong a proof as you get because it allows gene similarity to be numerically quantified.  One of the problems with Evolution is classifying organisms  phylogenetically.  Based solely on morphology, elements of subjectivity are introduced into the classification.  Thanks to these modern methods using molecular, genomic and protienomic evidence, there is now an objective normalizer to the subjective qualities of morphology.

Cytochrome c and Evolution

One of the most powerful evidences for evolution is some of the details of the protein cytochrome c on Talk Origins.  This is their baby, it's original research.  This protein is present in all living things.  An interesting property common to all amino acids, is that mutations have little effect on function.  Indeed, even within species, most amino acid mutations do nothing.  This is called protein functional redundancy (PFR) and is present in all known proteins and genes.  What that means when we are talking about protein cytochrome c, is that no matter what the specific configurations or mutations are present they all work the same, with minor differences in electron transport ability.

Cytochrome c doesn't just work in a wide variety of configurations, it also is essential for life.  Remarkably, experiments have shown that if you knock out the cytochrome c gene of a yeast, and replace it with human cytochrome c it works the same.  If that wasn't stunning enough, yeast cytochrome c differs from human cytochrome c over 40% of the protein.  This is an incredible testament to its redundancy; a consequence being there is no particular reason for any given configuration to have any advantages over another.  If evolution is false, we would not expect to see any correlation between species and cytochrome c, or all species would have the same cytochrome c.  Furthermore, we observe that only about 30 of the 100 amino acids are even required for the protein to function.  If that wasn't enough, any number of the amino acids can be replaced by many other functionally equivalent ones.

So evolution is very vulnerable here.  It would be remarkably easy to fail this delicate test.  There are a total of 2.3×10⁹³ possible functional cytochrome c sequences.  There are more functional cytochrome c sequences than there are atoms in the universe.  Yet chimpanzees and humans have the same cytochrome c sequences.  The chance of this happening outside of a hereditary process is 10^-93 probability (that's 1 one over a number starting with one that has 93 zero's behind it--tiny number.)  It doesn't stop there; when we compare protein sequences with other species, we find that the cytochrome c sequences match the phylogenetic tree arranged by morphological and physiological characteristics.  This provides an independent confirmation of the validity of the phylogenetic and hereditary tree of life.  A back of the napkin calculation (multiplying the probability 10^-93 by some geometrically shrinking number times the number of species, accounting for broader genetic drift across more distantly related species) of the probability of this occurrence by random chance, absent a ancestral relationship, I find is no better than 10^-100.