On Time and Space

The long-term evolution experiment (LTEE) began in 1988, and the E. coli populations are approaching 60,000 generations.  That’s a long time for an experiment, and I hope it continues for much, much longer.

But when I give talks about the LTEE, I also try to remind people that 26 years is only a drop in the proverbial bucket of evolutionary time.  If you were to add these experimental populations to the tree of life—or even to a tree showing only other E. coli strains—they would not be visible to the eye because the branches they represent—tiny twigs, really—would be so short (in time) and so close (in genetic distance) to their ancestors.

On Time and the LTEE

Life has existed on Earth for roughly 3.5 to 4 billion years.  That’s about 140 million times longer than the LTEE has existed.  Expressed the other way around, this experiment has been running for about 0.0000007% of the time that life has been evolving on our planet.

As a said, a mere drop in the bucket of time …

That’s a somewhat mixed metaphor, though, with “a drop in the bucket” being a statement about space and relative volumes, not about time.  And that got me wondering about the spatial scale of the LTEE relative to the spatial scale of the biosphere.

If the LTEE is just 0.0000007% as old as life on Earth, what fraction of the space—of the total biovolume—of life on our planet exists in the confines of the LTEE?

On Space and the LTEE

That’s a harder a question to answer.  We know the volume of the LTEE:  there are 12 flasks, one for each of the evolving populations, and each flask contains 10 milliliters (mL) of liquid medium.  (In medicine, by the way, a drop has been defined as 1/20th of a mL, so each flask in the LTEE contains 200 drops.)  If we sum across the populations, then the LTEE occupies 120 mL.

Before you read further:  What’s your quick intuition?  Is the LTEE larger on this spatial scale than on the temporal scale?  Or is the LTEE smaller?

 

Volumes and Numbers

How should we estimate the volume of Earth’s biosphere?  Here are three back-of-the-envelope approaches to get a rough sense of the scale.

1)  Most of the Earth is covered by its oceans, which are full of life.  While life is not equally abundant throughout the oceans, none of that space is entirely devoid of life.  The total volume of Earth’s oceans is about 1.3 billion cubic km.  That’s a lot of mL!  A mL is a cubic centimeter, or cc, and that’s 1/(100^3) = 1 millionth of a cubic meter.  A cubic meter is 1/(1000^3) = 1 billionth of a cubic kilometer, and the oceans contain over a billion of those cubic kilometers.

So the 120 mL in the LTEE correspond to 120 / (1.3 x 10^9 x 10^9 x 10^6), or about 9 x 10^-22 of what  the oceans contain.  That’s just 0.000000000000000000009% of the volume of the oceans.

By this calculation, then, the temporal scale of the LTEE is ~75 trillion times greater than its spatial scale, when both are expressed relative to nature.  If the LTEE is “a drop in the bucket” with respect to time, then that drop has to be diluted by a factor of 75 trillion with respect to the oceans.

2)  Let’s try another quick-and-dirty calculation.  Most life, in the oceans and on land, is near the Earth’s surface.  The surface area of our planet is about 510 million square kilometers.  If we take just the top meter, that’s equivalent to 510/1000  = 0.51 million cubic kilometers.  That’s about 1/2600 of the volume of the ocean.  But even this conservative estimate of the volume of the biosphere makes the relative scaling of the LTEE with respect to time and space differ by a factor of 30 billion.

3)  Here’s one more approach—it’s based not on the volume of the physical environment but, instead, on the number of organisms in the LTEE and in the biosphere.  When grown to stationary-phase density in the LTEE environment (i.e., when the limiting resource, glucose, is depleted), the ancestral bacteria could achieve a maximum density of ~5 x 10^7 cells per mL.  Most populations have evolved so that they now produce slightly fewer, but larger, cells; and one population has evolved the ability to use the citrate that is also in the medium, and it now reaches a density that is several times greater than the other populations.  In any case, given 10 mL of medium for each population, and 12 populations, the total population size across the LTEE is on the order of 10^10 cells.

And how many cells exist in the Earth’s biosphere?  Whitman et al. (1998, PNAS) estimated that there are more than 10^30 prokaryotes—bacteria and archaea combined—in the biosphere, and they make up the great majority of all living things.

So by this approach, using the number of cells as a proxy for the spatial scale, the size of the biosphere is over 10^20 (a hundred-million-trillion) times larger than the LTEE.  We’re back into the trillions in terms of the relative scaling of the temporal and spatial scales of the LTEE.

On Time, Space, and the LTEE

By all three approaches, then, the LTEE is vastly older with respect to the history of life on Earth than it is large with respect to the size of Earth’s biosphere.

The LTEE really is a long-running experiment, as experiments go.

But the LTEE is a “drop in the bucket” with respect to how long life has been evolving on Earth.  And it is a vastly more miniscule “drop in the bucket” when compared to the spatial extent and number of living organisms on our planet.

Maybe I should give the LTEE a new name—the “incredibly tiny but relatively long-term evolution experiment.”

[Photo of a water drop on a leaf taken by tanakawho and shared on Wikipedia (en.wikipedia.org/wiki/File:Water_drop_on_a_leaf.jpg).]

Water drop from Wikipedia

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An Absence of Posts, an Abundance of Talks, and More

Dear Reader:  No, I have not given up on this blog.  But I’ve been busy, busy, busy!

In the last four weeks alone, I have traveled to the University of Arizona, Harvard University, Duquesne University, and Princeton University.  Besides giving talks at each place (two public lectures and two academic seminars, with cumulative audiences of well over a thousand people), I have met with dozens and dozens of amazing scientists, from graduate students and postdocs to faculty both young and old.  It’s been a blast:  an exhausting blast, but a blast all the same!

And next week?  I’m hosting four terrific colleagues from two continents who will work with me to begin making sense of hundreds of newly sequenced genomes from the LTEE.

Oh, and we have some more job searches starting next week.

And did I mention?  We just had a fascinating (if I may so myself) and complex paper come out today in Science (on-line express for now) on the most deeply divergent (i.e., oldest sustained polymorphism) of the 12 LTEE populations.  And no, it’s not about the citrate eaters from population Ara–3.

Plucain, J., T. Hindré, M. Le Gac, O. Tenaillon, S. Cruveiller, C. Médigue, N. Leiby, W. R. Harcombe, C. J. Marx, R. E. Lenski, D. Schneider.  2014.  Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.  Science.

It’s population Ara–2 instead, where two lineages—dubbed the Larges (L) and Smalls (S)—have coexisted for several tens of thousands of generations.  In superb research led by Dr. Jessica Plucain that she did in the lab of my long-time collaborator (and dear friend!) Prof. Dom Schneider (Grenoble, France), Jessica led the work to identify—out of hundreds of mutations—three that are sufficient to allow a “constructed” S ecotype (i.e., the ancestor plus three derived alleles) to invade and stably coexist with the evolved L ecotype.  Ecological context and specific genetic interactions are key to establishing this “half” of the polymorphism … and the other “half” of the story— what makes the L ecotype special—might well turn out to be just as complex, or perhaps even more so.

The S and L types are especially challenging (even painful!) to work with because this population became a mutator very early on—before the two lineages diverged—and so there are many, many mutations to contend with; moreover, they make colonies on agar plates that are quite challenging to score and count.  So congratulations to Jessica, Dom, and other members of Dom’s lab for their perseverance in studying this extremely interesting population.

Also on the list of authors are Prof. Chris Marx and two members of his lab.  They performed metabolic analyses showing how the carbon fluxes through the central metabolism of the S ecotype have diverged from both the ancestor and the L ecotype.  Chris was a postdoc in my lab almost a decade ago, but most of his work (then and since) has been on experimental evolution using Methylobacterium, and so this is the first paper we’ve co-authored.

There was a production error, though, in the on-line version of our paper; the final sentence of the abstract was dropped (except for one word).  The abstract, in total, should read as follows:

“Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed this lineage to invade and stably coexist with the other. These mutations all affected regulatory genes and collectively caused substantial metabolic changes. Moreover, the particular derived alleles were critical for the initial divergence and invasion, indicating that the establishment of this polymorphism depended on specific epistatic interactions.”

[Edited on 07-Mar-2014:  The on-line PDF at Science Express now has the complete abstract.]

~~~

The picture below shows Dom Schneider and Richard Lenski in Paris in 2013.  They are holding a petri dish that Jessica Plucain made to celebrate the 25th birthday of the LTEE.

Dom and Rich, Paris, 2013

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Resources for People Interested in Learning about Evolution

Over on Twitter, a poster was interested in learning more about evolution and how it works.

I suggested the poster begin with Evolution 101, a website produced by the University of California Museum of Paleontology.

I then recommended four superb books (including one suggested by another poster).  These are all written with wonderful style and terrific content by world-class authors.

I’d begin with Carl Zimmer’s Evolution: The Triumph of an Idea.  This beautifully illustrated book was written as a companion to the PBS series on Evolution that aired in 2001.

The next three books are a bit more advanced, but still very accessible, and they could be read in any order.

The Greatest Show on Earth: The Evidence for Evolution by Richard Dawkins

Why Evolution is True by Jerry Coyne

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin

I could make many, many more suggestions.  But that’s a start, and now I’ll let others weigh in with suggestions in the Comments below. 

Please label your selections as for the Beginner, Intermediate, or Advanced student (and by student, I mean anyone, regardless of age or prior studies, who wants to learn about the science of evolution).

Please include only one link per post; otherwise, the spam filter may delete your post.  Also, I will delete any inappropriate suggestions.

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Zachary Blount on “Ham on Nye” Debate, Follow-up #3

I’m very pleased to present this guest post written by Dr. Zachary Blount, aka Dr. Citrate, as an in-depth follow-up to the “Ham on Nye” science versus creation debate.  Zack did his undergraduate studies at Georgia Tech, and then obtained a masters degree from the University of Cincinnati.  After that, he came to MSU, where he completed his Ph.D. in 2011.  With his doctoral work generating so many interesting results and new questions, Zack stayed on here as a postdoctoral researcher.  His current research is funded by a grant from the John Templeton Foundation Program on Foundational Questions in Evolutionary Biology.

Zack has devoted years to studying the evolution of the ability to grow on citrate that occurred in one of the 12 populations from the long-term evolution experiment (LTEE) with E. coli.  We still don’t fully understand all of the steps involved.  But a simple “on/off” switch it is not!

However, even if it had been a single, simple mutation that allowed the cells to grow on citrate, that still would have been evolution … it still would have been a beneficial mutation in the context of the experiment … and it would still have demonstrated the acquisition of new information encoded in the genomes of the bacteria that fits them to their environment.  Of course, if it were so easy as a single, simple mutation, then we would have seen that capability evolve in many or all of the populations. But after almost 60,000 generations to date, only one population has evolved that ability.

You can read about the technical details of our findings in two papers here and here, as well as in a recent paper from a team at the University of Texas, Austin.

In what follows, the nomenclature Cit+ refers to the bacteria that evolved the ability to grow on citrate in the presence of oxygen, while Cit refers to the bacteria – their ancestors and other E. coli – that lack that ability.

 – Richard Lenski

* * * * *

My work on the evolution of aerobic growth on citrate in one of the LTEE populations has received a fair amount of attention over the years.  (Sometimes there is a bit of a dream-like quality to it all.  I still have a hard time conceiving that people unknown to me know about what this here kid from north Georgia has done.)  The attention is rather gratifying because I’ve spent many years and a great deal of effort in school and in the lab to become an evolutionary biologist. But why did I do all that in the first place? Because I find evolution to be endlessly fascinating, beautiful, and even inspiring.

It means a lot to know that the work I spent several thousands of hours toiling away on has made a contribution to science.  Even more satisfying is that my work has come to be viewed as a go-to example of evolution in action that may, perhaps, inspire in others some of the same feelings that have motived me.

Of course, this attention has also been a bit troubling because it has led to repeated disparagement, dismissal, distortion, and misrepresentation of my work by both professional and amateur creationists.  These creationists often get entirely wrong the work my colleagues and I toiled long and hard to do, likely because they haven’t bothered to read our papers, learn the details and methods, or think much about the results.  (I suspect some duplicity is in there, too.)  Reflexive, unthinking dismissal bothers me – maybe because my parents and devoutly Southern Baptist Granny told me when I was a child that this is something that civilized folk simply should not do.

This brings me to the recent debate between the legendary science educator Bill Nye and the legendary obfuscator and anti-science showman Ken Ham.  It was the standard sort of set-up, with Nye defending evolution and science against creationism, and Ken Ham, well, doing what Ken Ham does.

Twice during the debate, Ham discussed my work with the LTEE population that evolved the capacity to grow aerobically on citrate.  The first time was at about 44 minutes, and included a video clip of Dr. Andrew Fabich, a “Biblical creationist” microbiologist at Liberty University.  [You can read the transcript here.]

The evolution of the new Cit+ function is, and has been discussed as, an instance of evolutionary innovation that arose in a controlled experiment in which we can drill down and figure out how it evolved. Ham and Fabich, however, dismissed Cit+ as an innovation or even an instance of evolution using two arguments suggesting that neither knows the work well at all and likely have not read our papers.  (In Ham’s case, this wouldn’t be surprising, as he has been called “willfully ignorant” even by other creationists, which is a bit like being called unkempt by Pig-Pen or in need of a haircut by Cousin Itt.  In Fabich’s case, however, it would betray a lack of professional courtesy, at best.)

First, Ham repeatedly said that some of the bacteria in the LTEE “seemed” to have developed the ability to grow on citrate.  This wording suggests either stupidity or duplicity on our part, as though we either didn’t check or just lied, but the fact of the matter is that there is no “seem” about it.  The Cit+ bacteria do grow on citrate, and they do so under conditions that E. coli normally does not.  This ability is something that is easy to demonstrate, and which I and my colleagues – not only in the Lenski lab but also other labs that are now working with these bacteria – have documented.  And it’s not as though we don’t have the evidence – as Rich has pointed out to another anti-evolution critic, we have many, many, many vials full of them in our freezers.

The second argument was more direct.  Both Ham and Fabich asserted that the Cit+ function did not evolve because using citrate did not involve “any kind of new information … it’s just a switch that gets turned on and off.”  (Fabich went on to state that this “switch” is what we reported.  That is emphatically not true.  It beggars belief that anyone, much less a trained microbiologist, could actually read our 2012 paper, where we reported the genetic basis of Cit+, and come away thinking this.) Variations on that wording are often used by creationists who discuss the citrate work because it implies that Cit+ arose because of a pre-existing regulatory switch and involved no evolution at all.  But that simply is not the case – that wording, dare I say it, is a lie.

If you take E. coli from a medium in which it is growing on glucose, and move it into a medium where the only thing to eat is something else, like lactose, it turns off the expression of some genes specific to growth on glucose, and it turns on other genes necessary to grow on lactose.  That is what is called gene regulation, and that is what biologists mean when they talk about switching functions on and off – existing genetic circuitry that allows an organism to respond to changes in the external and internal environment.  If you transfer normal, Cit E. coli from a glucose medium to a medium with only citrate to eat, they don’t grow.  They just sit there and starve.  Regular E. coli cells have no existing genetic regulatory circuitry that “flips a switch” to allow them to start growing on citrate in the presence of oxygen.  On the other hand, if you do the same thing with the Cit+ cells that evolved in the long-term experiment, the Cit+ cells will start growing happily on citrate.  This difference is not a matter of gene regulation, but an evolved difference between the ancestral strain and the Cit+ lineage that allows Cit+ cells to grow on citrate.

No, the ability to grow on citrate is not a matter of simply flipping a pre-existing regulatory switch.  Continuing the electrical metaphor, the evolved Cit+ function is instead about rewiring.  My dear little Cit+ cells gained their ability to partake of the previously forbidden citrate by a genetic duplication involving a gene, called citT, which encodes a transporter protein that is used during anaerobic growth on citrate.

This duplication did something very special.  You see, one of the major aspects of gene regulation is that genes have associated regulatory DNA sequences, including what are called promoters that control when genes are expressed.  The citT gene is normally controlled by a promoter that tells the cell to turn it on only when there is no oxygen present.  As shown in the Figure below, the gene duplication put one copy of citT next to, and under the control of, a promoter that normally controls another gene called rnk.  The rnk gene is normally turned on when oxygen is present.  The new association between citT and the rnk promoter – what we call the rnk-citT regulatory module – turns citT on when oxygen is present, and allows Cit+ cells to use citrate under the conditions of the LTEE.  (To really feast on the citrate involved additional evolutionary changes, both before and after this rewiring, but I’ll leave that point aside for this post.)

There is a very interesting consequence of how the rnk-citT module originated. While Ham did not make this argument, other creationists have asserted that Cit+ arose simply by a loss of gene regulation, because they have the notion that evolution can only break things.  However, the duplication that gave rise to the rnk-citT module caused no such thing.  There is still a copy of citT that is linked to the same adjacent DNA sequence as before, and there is still a copy of rnk that is under the control of its own promoter.  In other words, the cell got something new without losing anything old.

When they actually bother to explain all of that, creationists still dismiss Cit+ as being an instance of evolutionary innovation because it involved the rearrangement of existing components.  True, the duplication responsible for Cit+ did rearrange components that were already there, but that rearrangement generated a new association between components that did not previously exist, and it produced a new function that also did not previously exist.  To argue that rearrangements cannot produce innovation is akin to arguing that a novelist has done nothing creative in writing her novels because she only used words that already existed.

Ham also made a demand that is common among creationists that betrays a fundamental misunderstanding of evolutionary theory. In the later debate segment [starting at ~2:30], Ham says, “What Bill Nye needs to do for me is to show me example of something…uh, some new function that arose that was not previously possible from the genetic information that was there. And I would claim and challenge you that there is no such example that you can give… you’d have to show an example of brand new function that never previously was possible.  There is no such example, uh, that you can give anywhere in the world.”

According to Ham, evolution cannot be true if this burden can’t be met.  Consider that wording for a moment, though: “… show an example that never previously was possible.”  Not possible?  That’s kind of a high bar given that impossible things don’t happen by definition.  Moreover, it is clear from Ham’s words that he won’t regard any capacity that arises from modification of an existing genome to be an innovation, which means that he must think that evolutionary theory holds that new genes just pop into existence fully formed, without precursor states, like Athena from the head of Zeus.

This goes to the larger problem with how Ham, Ray Comfort, Michael Behe, Georgia Purdom, and others of their ilk approach evolution – they just don’t know much about it, and so what they end up arguing against isn’t the science, but a caricature of the science that exists only in their minds.  Evolutionary novelty does not arise from genes just popping into existence.  That is a silly idea, and one that no evolutionary biologist holds!

Instead, evolution innovates and creates through descent with modification of what already exists, a process that Nobel laureate François Jacob called “evolutionary tinkering”.  This modification arises by random mutations: base changes, deletions, duplications, insertions, and so on – and, depending on the organisms, horizontal genetic exchange and sexual recombination.  Natural selection then preserves and accumulates the useful changes – those that enhance survival and reproduction of the organism in its environment – across the generations.  Often, such innovations are based on just what we see with the Cit+ bacteria – novel rearrangements of old components.  Indeed, Jacob wrote that, “(Evolutionary) novelties come from previously unseen association of old material.  To create is to recombine.”

So Ham and other creationists dismiss how evolutionary theory says evolution works as not being evolution, and then they demand the impossible.  That strikes me as neither fair nor honest.  But in the end, their lies, distortions, misrepresentations, and ignorance don’t matter, just as debates, entertaining though they may be, don’t matter, because nature doesn’t care.  To paraphrase a bumper sticker I once saw, they may not believe in evolution, but nature does!

While they go on cycling through their old and ossified rhetoric according to their fixed and incorrect notions, evolution proceeds, MacGyvering the new from the old. Natural selection can’t do the impossible, but it is pretty darn spiffy at doing the improbable with the rare.

If you are interested in learning more, please visit my website, where you will find my papers available for download.  You can also watch my Ph.D. defense presentation, in which I go into much more detail about the evolution of the Cit+ E. coli.

– Zachary Blount

* * * * *

The figure below shows schematically the tandem duplication in the population that evolved the new ability to grow on citrate.  This duplication produced the new rnk-citT regulatory module by placing the second copy of the citT gene adjacent to the rnk promoter region.  The figure comes from Blount et al., 2012, Nature; it is shown here under the doctrine of fair use.

tandem duplication

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“Ham on Nye” Debate, Follow-up #2

Ken Ham spoke about the research in my lab at two points during the “Ham on Nye” science versus creation debate. The first segment also includes a video clip in which Dr. Andrew Fabich, a “biblical creationist” and microbiologist at Liberty University, talks about our work.

Dr. Zachary Blount is a postdoctoral researcher in my lab who performed most of the work that was discussed.  Zack produced these transcripts of Ham’s and Fabich’s presentations while preparing his response to their distortions and misrepresentations of our work.

First segment, beginning at ~44 minutes:

Ken Ham:

“Let me introduce you to another scientist, Richard Lenski of Michigan State University.  He’s a great scientist.  He’s known for culturing E. coli in the lab, and he found there were some E. coli that actually seemed to develop the ability to grow on substrate, um, on citrate substrate.  But, Richard Lenski is here mentioned in this book [Microbiology: An Evolving Science] and it’s called ‘Evolution in the Lab’.  So, the ability to grow on citrate is said to be evolution, and there are those who say, ‘Hey! This is, this is against the creationists.’  For instance, Jerry Coyne from the University of Chicago says, ‘Lenski’s experiment is also yet another poke in the eye for anti-evolutionists.’  He says, ‘The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events.’  But is it a poke in the eye for anti-evolutionist?  Is it really seeing complex traits evolving?  What does it mean that some of these, uh, bacteria are able to grow on citrate?

Let me introduce you to another biblical creationist who is a scientist.”

[via video] Andrew Fabich:

“Hi, my name is Dr. Andrew Fabich.  I got my Ph.D. from the University of Oklahoma in Microbiology.  I teach at Liberty University, and I do research on E. coli in the intestine.  I’ve published in secular journals from the American Society for Microbiology, including Infection and Immunity, uh, and Applied and Environmental Microbiology, as well as several others.  My work has been cited even in the past year in the journals Nature, Science Translational Medicine, Public Library of Science, Public Library of Science Genetics.  I, um, it’s cited regularly in those journals, and while I was taught nothing but evolution, I don’t accept that position, and I do my research from a creation perspective.  When I look at the evidence people cite of the E. coli supposedly evolving over 30 years or over 30,000 generations in the lab, and people say that it is now able to grow on citrate.  I don’t deny that it grows on citrate, but it’s not any kind of new information. It’s …  The information’s already there, and it’s just a switch that gets turned on and off, and that’s what they reported in there.  There’s nothing new.”

Ken Ham: 

“See, students need to be told what’s really going on here.  Certainly there’s change, but it’s not change necessary for molecules to man.”

Second segment, beginning at ~2 hours, 30 minutes:

Ken Ham: 

“What Bill Nye needs to do for me is to show me example of something …uh, some new function that arose that was not previously possible from the genetic information that was there.  And I would claim and challenge you that there is no such example that you can give.  That’s why I brought up the example in, uh, my presentation of Lenski’s, uh, experiments in regard to E. coli.  And there were some that seemed to develop the ability to exist on citrate, but as Dr. Fabich said from looking at his research, he’s found that that information was already there.  It’s just a gene that’s switched on and off.  And so, uh, there is no example because, you know, information that’s there in, in the genetic information of different animals, plants, and so on.  There’s no new function that can be added.  Certainly great variation within a kind, and that’s what we look at, but you’d have to show an example of brand new function that never previously was possible.  There is no such example, uh, that you can give anywhere in the world.”

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“Ham on Nye” Debate, Follow-up #1

Many of you saw the “debate” last night on evolution versus creation between Bill Nye, aka The Science Guy, and Ken Ham, from Answers in Genesis.

I was shocked to see our long-term evolution experiment with E. coli cited as support for the young-Earth creationist side.  But maybe I shouldn’t have been shocked, given Ham’s proclivity to change definitions, distort evidence, and ignore reality.

In fact, the results of our experiment fully support and strengthen evolutionary theory.  Of course, all the other existing evidence for evolution – from fossils to DNA, and everything in between – is already so overwhelmingly strong that our work serves mostly to illuminate some details of the evolutionary process that are often hard to see.

During the debate, my image and some text appeared in a slide that Ham showed in his presentation.  The good people at W. W. Norton & Company have given me permission to post below the full document associated with that slide.  It’s from an interview in which Prof. Joan L. Slonczewski (Kenyon College) asked me some questions about my career and research.  The interview appears in the 3rd edition of the textbook, Microbiology: An Evolving Science, authored by Prof. Slonczewski and Prof. John W. Foster (University of South Alabama).

Interview with Richard Lenski in Microbiology: An Evolving Science

[Added Feb. 8, 2014:  And see Dr. Zachary Blount's in-depth reply here.]

 

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Recap: What We’ve Learned about Evolution from the LTEE: Numbers 1-5

This post provides a brief recap, at the halfway point, of the main findings and discoveries from the long-term evolution experiment (LTEE) with E. coli.  My goal is to summarize in a series of ~10 posts the most important findings and discoveries, as I see them, in broad, conceptual terms.  The first five entries are listed here, with links to those posts.

Number 1.  The LTEE offers a simple, compelling demonstration of adaptation by natural selection.

Number 2.  Although the rate of improvement decelerates, it appears that fitness can increase indefinitely even in a constant environment.

Number 3.  The LTEE has produced many striking examples of both parallel and divergent evolution across the replicate populations.

Number 4.  The LTEE provides fascinating cases of the origin and evolution of a novel function and complex ecological interactions.

Number 5.  Some of the LTEE populations have undergone large changes in their mutation rate, which reflect a tradeoff between short-term fitness and long-term evolvability.

The picture below shows a few of the petri dishes used in the LTEE.  It was taken by Brian Baer, MSU.

plate_pile

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