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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16 Comments

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

  1. No need to post this comment but just wanted to point out that in the beginning of Zach’s paragraph #5 there is a replication of “has been, has been” (hmm, maybe that was on purpose – a genetic duplication?). Then near the end is this duplication: ” While Ham did not make this argument, other creationists have asserted that Cit+ arose simply by a loss of gene regulation. 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. “

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  5. “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. ”

    I beg to differ. Their lies, etc., do matter, because they affect people. Same for debates. What people believe is very important for society, and ignoring it or dismissing it is a disservice to scientific progress. It affects science education, which is evidently lagging behind in the US compared to many first-world countries. Having people like Bill Nye reach the coming generations of students to refute the lies, and let them know that the majority of scientists regard creationism with disdain, does matter a great deal.

    • Hi Bjorn – I think if you re-read Zack’s paragraph in full, he’s only saying that nature does not care about these debates and human ignorance. He’s not saying that we shouldn’t care about science education and human understanding of nature. Zack clearly does care, as do you and I.

  6. gil

    new abilties doesnt mean new systems. lets say that we want to add a gps system to a car. we will need at least 2-3 new parts. or in a living thing- 2-3 new proteins. its mean that there is no step wise to get a news system with new parts. its not like to move an abs in the car from the pront of the car to the back(new function). so the evolution cant explain this kind of change. think about self replicat car with dna that need to evolve a gps.

    • Muddled thinking, and sloppy writing.

    • In this case, the citrate-eating bacteria, we have a new system with old (duplicated) parts. That’s amazing enough to be worthy of note, and is certainly an example of positive evolution.

      That doesn’t mean that evolution CANNOT lead to a new system with new parts – it simply isn’t what happened THIS time. To dismiss this discovery as not being evidence of evolution is simply moving the goalposts.

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  8. Warren Johnson

    Hi Zachery,

    Can you direct me to an exposition on gene duplication for the slightly educated, say a bright undergrad in another science? I am a physicist who is not able to really understand the professional biology literature, like your Nature paper, without a lot (hours?) of explanation from an expert, or a much more lengthy attempt at self-education. (No surprise here to an old scientist; most biologists would find papers in Physical Review pretty opaque.)

    For example, I envisioned “gene duplication” as the *addition* of a copy of a preexisting gene, so that the length of the DNA molecule is increased by the the number of base pairs in that gene.

    In contrast, as best as I can tell from your remarks above, what you observed was that two copies of a particular gene had been present from the beginning of the experiment, and that the crucial mutation was the movement of one copy from it’s old location to a new one. The change in location caused a change in function. (And the number of base pairs in the DNA is unchanged.)

    Or maybe it’s more complicated?

    • If you email me (Richard Lenski: address easily found) I will send you a reprint of the PNAS (2008) and Nature (2012) papers that describe this work.

      The duplication event is not as you describe it. There was originally only one copy, not two copies. The second, new copy occurred in tandem and adjacent to the first copy. As a consequence, a region that had been downstream of — and inconsequential for — the original copy was now upstream of the second, new copy.

      That region included regulatory elements that, when combined with the citT structural gene, rewired the cell, in effect generating a new module that had not previously existed. This type of event is sometimes called a “promoter capture” because coding DNA has “captured” — by virtue of a complex mutation — a regulatory region that serves to promote the expression of an otherwise silent gene.

      And this mutation is only part of the story. As our paper in Nature shows, additional mutations — both before and after this rewiring event — were also essential for the cells to make effective use of the citrate in the medium.

  9. Hi Warren,

    Hmmm… That’s a good question. I don’t know of many general treatments of gene duplication. One good place to start would be to look at good introductory texts to evolution that cover molecular topics. The phenomenal science writer Carl Zimmer has one for non-majors called “The Tangled Bank” that covers the basics, and there is more detail in a book for majors that he wrote with Doug Emlen called “Evolution: Making Sense of Life”. Both of these are available from Amazon.

    http://tinyurl.com/lyxguhn
    and
    http://tinyurl.com/km9mflv

    A somewhat more technical review is here:
    http://content.csbs.utah.edu/~rogers/bio5410/Readings/Zhang-TRE-18-292.pdf

    (Please contact me if you are unable to access this article. My address is in the contact information on my website.)

    I would also note that Jacob’s paper on evolutionary tinkering that I reference and link to in my post above gives a good overview of basic related principles.

    I don’t think I am just being humble to say that I think you do far better with biological literature than I do with physics literature!

    You are correct that a duplication involves the addition of the number of base pairs to the genome equivalent to the size of the genetic segment duplicated. So if a segment of 3000 bp is duplicated, then the genome ends up being 3000 bp larger. It is as simple as that. The machinery that maintains the integrity of the genome and performs DNA replication is a bit glitchy, with one of the occasional errors being duplications. Duplications actually happen a great deal, and in fact occur at much higher rates than the base pair changes we tend to think of as “typical” mutations.

    As to what occurred with Cit+, the underlying mutation that caused the immediate switch from Cit- to Cit+ was in fact a duplication. This duplication involved a 2933 bp genetic segment that included the entire citT gene that encodes the citrate transporter that is normally silent when oxygen is present. So the genome actually got 2933 bp larger when that happened because there are now two copies of the duplicated segment. The important thing to realize in this case is that a duplication ends up creating a copy of the duplicated segment that has different adjacent DNA. In this case, the duplication was tandem, meaning that the DNA now has the original segment immediately followed by the copy of that segment. Because the copied segment has the promoter that normally controls the rnk gene at one end, the new copy of the segment now has a copy of the citT gene that is next to the rnk promoter. This then allows the citT gene’s expression to be regulated by the rnk promoter. To summarize: There was only one copy of the citT gene originally. There was a duplication that increased the amount of DNA in the genome by 2933 bp that contained the citT gene and the rnk promoter. The duplication was tandem. The tandem duplication placed the rnk promoter next to the copied citT gene. This new relationship allows citT to be expressed when oxygen is present, causing the capacity to consume citrate aerobically.

    Does that make sense? Please feel free to ask follow up questions!

    Zack

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