Tag Archives: mutation

Evolution goes viral! (And how real science works)

This is the fourth in a series of posts about a new book by Michael Behe, Darwin Devolves. Behe is a leading proponent of intelligent-design creationism (IDC), which asserts that known processes cannot adequately account for evolution and, therefore, some intelligent agent must be involved in the process. Behe is a professor of biochemistry, which gives him knowledge and credentials that most IDC advocates do not have. However, my posts explain why I think his logic is unsound and his evidence weak and biased.

In brief, Behe argues that random mutation and natural selection are almost entirely degradative forces that break or blunt the various functions encoded by genes, producing short-term advantages that are so pervasive that they prevent constructive adaptations, which he claims are very unlikely to emerge in the way that evolutionary biologists have proposed. Unlike young-Earth creationists, Behe accepts the descent of living species from common ancestors over billions of years. To reconcile these seemingly conflicting views, Behe invokes that an intelligent agent (presumably God, though IDC proponents avoid that word so that their ideas might appear to be scientific) has purposefully guided evolution over its long history by somehow inserting new genetic information into chosen lineages along the way. To make his strange argument, Behe works very, very hard to convince readers that standard evolutionary processes are (i) really, really good at degrading functions, and (ii) really, really bad at producing anything new.

In my first post, I explained that Behe’s arguments confuse and conflate what is easy and commonplace over the short run (i.e., mutations that break or blunt functional genes) with the lasting impacts of less frequent but constructive adaptations (i.e., new functions and subsequent diversification) over the long haul of evolution. My second post examined a case involving polar bears, which Behe highlighted as a compelling example of degradative evolution, but where a careful review of the science suggests that gene function improved. Behe also highlighted results from my lab’s long-term evolution experiment with bacteria, but in my third post I explained that he overstates his case by downplaying or dismissing evidence that runs counter to his argument.

In this post, I’ll discuss an experiment that Behe ignores in Darwin Devolves. (Behe clearly knows the work, because he wrote about it on the Discovery Institute’s anti-evolution blog. But as usual, he spun the story to obscure the problems for his arguments, all the while accusing the scientists who collect data to test hypotheses of spinning the story.) In fact, as I’ll explain, the results also undermine the claims in Behe’s two previous books, Darwin’s Black Box and The Edge of Evolution, about the supposed shortcomings of evolution.

(Before presenting this experiment, I want to mention briefly two other papers that readers interested in what else Behe missed or downplayed might want to read. First, Rees Kassen posted a preprint of a paper on “Experimental evolution of innovation and novelty.” He reviews empirical evidence and discusses conceptual issues bearing on the origin of new functional abilities observed in many experiments with bacteria and other microbes. Second, Chris Adami, Charles Ofria, Rob Pennock, and I published a paper over 15 years ago that demonstrated the logical fallacy of Behe’s assertions about irreducible complexity. Behe mentions that paper derisively, without addressing its substance in Darwin Devolves, as follows: “A computer simulation of computer program development that ignores biology entirely.” A more accurate statement would have been: “Computer programs can evolve by random mutation and natural selection the ability to perform complex functions that show the concept of irreducible complexity is total nonsense.” The rest of this post is longer than I planned, because I want to provide background for readers who aren’t microbiologists, and because—like so much of science—it’s an interesting story with unexpected twists and turns along the way.)

IV. Phage lambda evolves a new capability without breaking anything

There are a lot of viruses in the world. Fortunately, most of them don’t infect humans. Many of them infect bacteria, as it so happens. In fact, before antibiotics were used as therapeutic agents, there was hope that bacteriophages (“bacteria eaters”), or phages for short, would be useful in treating diseases. And now, with the evolution of pathogenic bacteria that are resistant to many or all available drugs, researchers are reconsidering the possibility of using phages to treat some infections.

My lab is best known for the long-term evolution experiment (LTEE) with E. coli bacteria. But over the years, my students have also performed other experiments with a variety of microbes, including some viruses that infect E. coli. One of those viruses is called lambda. For decades, lambda was probably the most intensively studied virus on the planet—just as E. coli was a model for understanding bacterial genetics and physiology, lambda became a model for understanding viral genetics and infection.

One reason lambda became a hit was because it has an interesting life cycle. After lambda enters a bacterial cell (and assuming the cell lacks some internal defenses), the virus can do one of two things. It can commandeer the host, hijacking the cellular machinery to produce a hundred or so progeny before bursting the host cell and releasing its “babies” to find new cells to infect. Alternatively, the virus’s DNA may be integrated into the host’s chromosome, hiding out and being replicated alongside the host’s genes—though the virus may later exit the chromosome and reactivate its lethal program. (Pretty neat, and a bit scary, right?)

Well, as cool as that is, it’s not what my student Justin Meyer (now on the faculty at UCSD) was studying. He was using a strain of lambda that can’t integrate into the bacterial cell’s chromosome—a successful infection takes only the first route, killing the cell in the course of making more viruses. Justin was studying this simpler virus because we were interested in whether the evolution of the bacterial hosts in response to the presence of lambda virus might depend on what food we gave the bacteria.

Let’s back up and explain why that might matter. Viruses like lambda don’t just glom onto any part of a bacterial cell; instead, they adsorb to specific receptors on the cell’s surface, with a successful attachment triggering the injection of their DNA into the cell. Lambda recognizes a particular cell-surface protein called LamB. (Despite decades of study of the interaction between lambda and E. coli, including experiments that specifically sought to see whether mutants could exploit other receptors, no one had ever seen lambda use any other receptor.) Of course, E. coli doesn’t make LamB for the sake of the virus. The LamB protein is one of several “porin” proteins that E. coli produces, and which serve as channels to allow molecules, like sugars, to cross the outer cell envelope. (Other proteins transport sugars across the inner cell membrane.) LamB, in particular, is a fairly large channel that allows the sugars maltose and maltotriose to enter the cell. Maltose and maltotriose are made of two and three linked glucose molecules, respectively. Glucose, being smaller, can readily enter a cell via smaller channels. When growing on glucose, E. coli cells don’t bother to produce much LamB protein. However, when cells sense that maltose or maltotriose, but not glucose, is present they activate the gene that encodes LamB. In doing so, however, the cells become more vulnerable to lambda, because that protein serves not only to transport these larger sugars but also as the receptor for the virus.

Coming back to Justin Meyer’s research, we wanted to see how different sugars affected the bacteria’s evolutionary response to lambda. (Justin and I have a paper in press comparing outcomes across the glucose, maltose, and maltotriose environments.) We reasoned that, if the bacteria were fed glucose, they could damage or delete the lamB gene that encodes the LamB protein. If the bacteria mutated the LamB protein, then the virus might counter with a mutation that restored their affinity for the mutated protein; but if the bacteria deleted or otherwise destroyed the LamB protein, we reasoned the virus would go extinct.

However, the first experiment using only the glucose treatment played out differently than what we expected—that’s science, and that’s why you do experiments—and it set Justin’s research off in a new direction. Instead of mutating the lamB gene, the bacteria evolved resistance to the virus by mutating another gene, called malT, that encodes a protein that activates the production of LamB. The viruses didn’t go extinct, however, because there was some residual, low-level expression of the LamB protein. That was enough to keep the viruses going, which also meant they could keep evolving.

To make a long story short, after just 8 days, one of six lambda populations evolved the ability to infect malT-mutated cells by attaching to a different surface protein, one called OmpF (short for outer membrane protein F). This evolved lambda virus could now infect E. coli cells through the original receptor, LamB, or this new one, OmpF. It had gained a new functional capability.

To understand this change, Justin sequenced the genome of this virus. He found a total of 5 mutations compared to the lambda virus with which he had begun. All 5 mutations were in the same gene, one that encodes the J protein in the “tail” of the virus that interacts with the cell surface. He also sequenced the J gene for some other viruses isolated from the same population. He found one virus that had 4 of these 5 mutations, but which could not infect cells via the OmpF receptor. Did that mean that only one of the 5 mutations was necessary to evolve this new function?

As it turns out, the answer is no. To better understand what had happened, Justin scaled up his experiments and ran an additional 96 replicates with lambda, E. coli, and glucose. In 24 cases, the viruses evolved the new mode of infection within three weeks. Justin sequenced the J gene from the viruses able to target OmpF in those 24 cases, and in 24 other cases where the virus could still use only the LamB receptor. He found that all 24 with the new capability had at least 4 mutations; these included 2 changes that were identical in all 24 lines, a third that further mutated one of the same codons (sets of 3 DNA bases that specify a particular amino acid to be incorporated into a protein), and another mutation that was always within a span of 11 codons. All of these mutations cause amino-acid substitutions near the end of the J protein, which is known to interact with the LamB receptor. The J protein is over 1100 amino acids in length, and so this concentration and parallelism (repeatability across lineages) is striking and strongly implies that natural selection favored these mutations.

Remember, too, that nothing is broken. These viruses can now use both the original LamB receptor and the alternative OmpF receptor. (This fact was demonstrated by showing that the viruses can grow on two different constructed hosts genotypes, one completing lacking LamB and the other completely lacking OmpF.)

None of the 24 viruses that had not evolved the ability to use the OmpF receptor had all 4 of these mutations. However, three of them shared 3 of the 4 mutations with viruses that had acquired that new ability. And yet, none of those had any capacity to grow on cells that lacked the LamB receptor. In other words, the set of all 4 of these mutations was needed to produce this new ability—no subset could do the job. (We initially lacked one of the four possible viral genotypes having each subset of 3 mutations. Later work confirmed that all four mutations are required.)

At first glance, it seems like none of the viral lineages should have been able to acquire all 4 mutations, at least if you accept the flawed reasoning from Behe’s previous book on The Edge of Evolution. If you need all 4 mutations for the new function, so the thinking goes, and if none of them provide any degree of that function, then you would need all 4 mutations to occur in one lineage by chance, which is extremely unlikely. (How unlikely is difficult to calculate precisely. To get some inkling, none of the 48 sequenced J genes—including both those that did and did not evolve the new capability—had even one synonymous mutation. Synonymous mutations don’t change the amino-acid sequence of an encoded protein, and so they provide a benchmark for the accumulation of selectively neutral mutations.)

And yet, 24 of the 96 lineages did just that—they evolved the new ability, and in just a few weeks time. If you’re into intelligent design, then I guess you’d have to conclude that some purposeful agent was pretty darn interested in helping the viruses vanquish the bacteria. If you’re a scientist, though, you’re trained to think more carefully and look for natural explanations—ones that you can actually test.

So how could 4 mutations arise so quickly in the same lineage? Natural selection. But wait, didn’t Justin find that all 4 of those mutations were required for the virus to exploit the new OmpF receptor? Yes, he did.

Our hypothesis was that the mutations that set the stage for the virus to evolve the ability to target OmpF were beneficial because they improved lambda’s ability to use its original LamB receptor. But wait, that’s the receptor they’ve always used. Shouldn’t they already be perfectly adapted to using that receptor? How can there be room for improvement?

If you’ve read my posts on polar bears and bacteria, you’ve probably got the idea. When the environment changes, all bets are off as to whether a function is optimally tuned to the new conditions. Lambda did not evolve in the same medium where Justin ran his experiments; and while lambda certainly encountered E. coli and the LamB receptor in its history, the cell surfaces the virus had to navigate in nature were more heterogeneous than what they encountered in the lab. In other words, there might well be scope for the viral J protein to become better at targeting the LamB receptor under the new conditions.

To an evolutionary biologist, this hypothesis is so obvious, and the data on the evolution of the J protein sequence so compelling, that it scarcely needs testing. Nonetheless, it’s always good to check one’s reasoning by collecting new data, and another talented student joined the project who did just that. Alita Burmeister (now a postdoc at Yale) competed lambda strains with some (but not all) of the mutations needed to use OmpF against a lambda strain that had none of those mutations. She studied six “intermediate” viruses, each of them isolated from an independent population that later evolved the ability to use OmpF.

Alita ran two sets of competitions between the evolved and ancestral viruses. In one set, the viruses fought over the ancestral bacterial strain; in the other set, they competed for a bacterial strain that had previously coevolved with lambda and become more resistant to infection. Four of the six evolved intermediate viruses outcompeted their ancestor for the naïve bacteria, and all six prevailed when competing for the tough-to-infect coevolved host cells. Alita ran additional experiments showing that the intermediates were better than the ancestral virus at adsorbing to bacterial cells—the precise molecular function that the J protein serves. These results clearly support the hypothesis that the first few mutations in the evolving virus populations improved their ability to infect cells via the LamB receptor.

Natural selection did its thing, in other words, discovering mutations that provided an advantage to the viruses. Some of the resulting viruses—those with certain combinations of three mutations—just happened to be poised in the space of possible genotypes such that a fourth mutation gave them the new capacity to use OmpF.

Now let’s step back and think about what this case says about the validity of the arguments that Behe has made in his three books.

Anybody remember Behe’s first book, Darwin’s Black Box, published in 1996? There, Behe claimed evolution doesn’t work because biological systems exhibit so-called “irreducible complexity,” which he defined as “… a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.” Evolution can’t explain these functions, according to Behe, because you need everything in place for the system to work. Strike one! Lambda’s J protein required several well-matched, interacting amino acids to enable infection via the host’s OmpF receptor. Removing any one of them leaves the virus unable to perform that function. (Alas, Behe’s argument wasn’t merely mistaken, it also wasn’t new—since Darwin, and as explained in increasing detail by later biologists, we’ve known that new functions evolve by coopting and modifying genes, proteins, and other structures that previously served one function to perform a new function.)

The Edge of Evolution, Behe’s second book, claimed that evolution has a hard time making multiple constructive changes, implying the odds are heavily stacked against this occurring. Strike two!! Lambda required four constructive changes to gain the ability to use OmpF, yet dozens of populations in tiny flasks managed to do this in just a few weeks. That’s because the intermediate steps were strongly beneficial to the virus, so that each step along the way proceeded far faster than by random mutation alone.

Darwin Devolves says that adaptive evolution can occur, but that it does so overwhelmingly by breaking things. Strike three!!! The viruses that can enter the bacterial cells via the OmpF receptor are not broken. They are still able to infect via the LamB receptor and, in fact, they’re better at doing so then their ancestors in the new environment. (In his blog post after our paper was published in Science, Behe used the same sleight of hand he used to downplay the evolution of the new ability to use citrate in one LTEE population. That is, Behe called lambda’s new ability to infect via the OmpF receptor a modification of function, instead of a gain of function, based on his peculiar definition, whereby a gain of function is claimed to occur only if an entirely new gene “poofs” into existence. However, that’s not the definition of gain-of-function that biologists use, which (as the term implies) means that a new function has arisen. That standard definition aligns with how evolution coopts existing genes, proteins, and other structures to perform new functions. Behe’s peculiar definition is a blatant example of “moving the goalposts” to claim victory.)

As Nathan Lents, Joshua Swamidass, and I wrote in our book review, “Ultimately, Darwin Devolves fails to challenge modern evolutionary science because, once again, Behe does not fully engage with it. He misrepresents theory and avoids evidence that challenges him.”

If you’ve followed the logic and evidence in the three systems I’ve written about—polar bears adapting to a new diet, bacteria fine-tuning and even evolving new functions as they adapt to laboratory conditions, and viruses evolving a new port of entry into their hosts—you’ll understand why Behe’s arguments against evolution aren’t taken seriously by the vast majority of biologists. As for Behe’s arguments for intelligent design, they rest on his incredulity about what evolution is able to achieve, and they make no testable predictions about how the designer intervenes in the evolutionary process.

[The images below show infection assays for 4 lambda genotypes on 2 E. coli strains. The dark circles are “plaques”—areas in a dense lawn of bacteria where the cells have been killed by the virus. The viruses (labeled at bottom) include the ancestral lambda virus and 3 evolved genotypes. One bacterial strain expresses the LamB receptor (top row), while the other lacks the gene that encodes LamB (bottom row). All 4 viruses can infect the cells that produce LamB, but only the “EvoC” virus is able to infect the cells without that receptor. Images from Meyer et al., 2012, Science paper.]

Lambda plaque assays

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Is the LTEE breaking bad?

Michael Behe has written a third book, Darwin Devolves, that continues his quixotic effort to overturn evolutionary biology. Nathan Lents, Joshua Swamidass, and I wrote a book review for Science. (You can find an open-access copy here.) As our short review states, there are indeed many examples of evolution in which genes and their functions have been degraded, sometimes conferring an advantage to the organism. However, Behe’s book largely ignores the ways by which evolution generates new functions. That’s a severe problem because Behe uses the evidence for the ease of gene degradation to support his claim that our current understanding of the mechanisms of evolution is inadequate.

This is my third in a series of posts delving into various issues where I think Behe’s logic and evidence are weak. These weaknesses undermine his position that the known mechanisms of evolution are inadequate to explain life as we see it in the fossil record and in the diversity of living species. Let me be clear: there is still much to learn about the intricacies of how evolution works, both in terms of a better understanding of the general mechanisms and unraveling all the fascinating particulars of what happened along various lineages. However, I don’t see much chance of future research upending the central role of natural selection—operating over vast time along with mutation, drift, and recombination (including various forms of horizontal gene transfer)—in creating new functions that spark the diversification of life. By contrast, Behe accepts that natural selection occurs, but he treats it almost entirely as a degradative process that weakens and destroys functions. To explain all the new functions that have arisen during evolution (and he accepts the fact that evolution has occurred for billions of years), Behe appeals to an “intelligent agent” who somehow, mysteriously has added new genetic information into evolving lineages.

In my first post, I explained why Behe’s “first rule of adaptive evolution” doesn’t imply what he says it does about evolution writ large. In particular, his overarching thesis confuses frequency over the short run with lasting impact over the long haul of evolution. In my second post, and building on the work of others, I examined a specific case involving polar bears, which Behe argued showed adaptations resulting from degradative evolution. He apparently regarded the case as so compelling that he used it as the lead example in his book, but a careful review of the science suggests an alternative explanation, in which gene function actually improved.

In this post, I examine Behe’s interpretation of findings from a long-term evolution experiment (LTEE) with E. coli bacteria that has been running in my lab for over 30 years. In short, the LTEE represents an ideal system in which to observe degradative evolution, and indeed we’ve seen examples of such changes. However, Behe overstates his case by downplaying or dismissing evidence that runs counter to his thesis.

III. Evolution of functionality in the LTEE

Recall what Behe calls “the first rule of adaptive evolution: break or blunt any functional gene whose loss would increase the number of a species’ offspring.” In support of that rule, Darwin Devolves pays considerable attention to the LTEE. Behe skillfully uses it to build his case that unguided evolution produces adaptations (almost) exclusively by breaking or blunting functional genes. The implication is that constructive adaptations—those that do not involve breaking or blunting genes—require an “intelligent agent” who has introduced new genetic information, by some mysterious process, into certain lineages over the course of life’s history.

Am I surprised that Behe uses the LTEE as one of the centerpieces of Darwin Devolves? No, not at all. Does the LTEE provide strong support for his argument? No, it does not. The LTEE fits the bill for Behe because it’s just about the best case possible to showcase his rule. But just as loss of sight in cave-dwelling organisms is a special case that won’t tell us how eyes evolved, one must be careful when extrapolating from this experiment to evolution writ large. (I say this even though the LTEE is my scientific “baby” and has been a useful model system for studying some aspects of evolution.)

The LTEE was designed (intelligently, in my opinion!) to be extremely simple in order to address some basic questions about the dynamics and repeatability of evolution, while minimizing complications. It was not intended to mimic the complexities of nature, nor was it meant to be a test-bed for the evolution of new functions. The environment in which the bacteria grow is extremely simple. The temperature is kept constant at 37C, the same as our colons where many E. coli live. The LTEE “host” is an Erlenmeyer flask, not an animal with an immune system and other defenses. There are no antibiotics present, no competing species, and no viruses that plague bacteria in nature. And the culture medium contains a single source of energy that the ancestral bacteria can use, namely the sugar glucose. In contrast, E. coli lineages have endured and adapted over millions of years to countless combinations of resources, competitors, predators, toxins, and temperatures in nature.

Indeed, the LTEE environment is so extremely simple that one might reasonably expect the bacteria would evolve by breaking many existing functions. That is because the cells could, without consequence, lose their abilities to exploit resources not present in the flasks, lose their defenses against absent predators and competitors, and lose their capacities to withstand no-longer-relevant extreme temperatures, bile salts, antibiotics, and more. The bacteria might even gain some advantage by losing these functions, if doing so saved time, energy, or materials that the cells could better use to exploit the limited glucose supply.

And just as one would expect, the bacteria have diminished or lost various abilities during the LTEE. For example, all 12 populations lost the ability to use another sugar, called ribose, and they gained a small but measurable competitive advantage as a result. Similarly, half of the lines evolved defects in one or another of their DNA repair systems, which led to hypermutability. While hypermutability resulted from a loss of function at the molecular level, it produced a slight gain in terms of the rate at which those lineages adapted to their new laboratory environment. There are undoubtedly many functional losses that have occurred during the LTEE, some that have been described and others not.

If that was all there were to the story, I might say that Behe’s portrayal was correct, but that he had missed the point—namely, that of course evolution often involves the loss of functions that are no longer useful to the organism. Biologists have known and understood this since Darwin.

But there is more to evolution than that, not only in nature but, as it turns out, even in the simple world of the LTEE. We’ve discovered cases where beneficial mutations evolved in genes that encode proteins that are essential, not dispensable, including ones involved in synthesis of the cell envelope and in structuring DNA so that it can be copied, transcribed, and packed into the tiny space of a cell. We’ve also found genes in which mutations occur repeatedly near key interfaces of the encoded proteins, in ways that imply the fine-tuning of protein functions to the LTEE environment, rather than degradation or loss of those functions.

In Darwin Devolves, Behe asserts (p. 344) that “it’s very likely that all of the identified beneficial mutations worked by degrading or outright breaking the respective ancestor genes.” He includes a footnote that acknowledges our work that suggests the fine-tuning of some protein functions, but there he writes (p. 609): “More recent investigation by Lenski’s lab suggests that mutations in a small minority (10 of 57) of selected E. coli genes may not completely break them but rather, as they put it, ‘fine-tune’ them (probably by degrading their functions).” Why does Behe assert that fine-tuning of genes occurred “probably by degrading their functions”?

Perhaps it’s because this assertion supports his claim, but more charitably I suspect the underlying reason is similar to the problematic inferences that got Behe into trouble in the case of the polar bear’s genes. That is, if one assumes the ancestral state of a gene is perfect, then there’s no room for improvement in its function, and the only possible functional changes are degradative. In my post on the polar bear case, I explained why the assumption that a gene is perfect (or nearly so) makes sense in certain situations. However, that assumption breaks down when an organism encounters a new environment, where the optimal state of a protein might differ from what it was before. Perhaps, for example, a mutation that would have slightly reduced an essential protein’s activity in the ancestral environment slightly improves its activity in the new environment. As I explained earlier, the LTEE environment differs from the conditions that E. coli experienced before being brought into the lab. It would be surprising if some proteins couldn’t be fine-tuned such that their activities were improved under the particular pH, temperature, osmolarity, and other conditions of the LTEE. It is unreasonable to simply assume that fine-tuning mutations “probably” degrade functions when evolving populations—whether of bacteria or bears—encounter new conditions.

The adaptation in the LTEE that has garnered the most public attention, though, is far less subtle. (The attention grew enormously after I had an email exchange with Andrew Schlafly, who runs the “Conservapedia” website.) After more than 30,000 generations, one of the 12 lines evolved the ability to consume citrate in an oxygen-rich environment—something that E. coli normally cannot do. Citrate, it turns out, has been a potential source of carbon and energy in the culture medium ever since the LTEE started. (The citrate is there, despite the inability of E. coli to import it from the medium, because it chelates iron and, in so doing, makes that micronutrient available to the cells.)

Sequencing the genomes of the citrate-using lineage revealed an unusual mutation—a physical rearrangement that brought together regulatory and protein-coding sequences in a new way—and genetic experiments demonstrated that mutation was responsible for this gain of function. In the line that gained the ability to consume citrate, the rearrangement involved duplicating a particular DNA segment; additional experiments showed that other types of rearrangements could also generate this ability. Even now, after more than 70,000 generations, none of the other LTEE populations has managed to evolve this new ability, despite its great benefit to the bacteria. This difficulty reflects several factors: (i) the low rate of occurrence of the necessary rearrangement mutations; (ii) the fact that efficient use of citrate requires certain additional mutations; and (iii) the absence of other, more highly beneficial mutations that could out-compete early, weakly beneficial citrate-using mutants.

To his credit, Behe does write about the lineage that evolved the ability to consume the citrate. However, he dismisses it as a “sideshow” (p. 365), because he refuses to call this new capability a gain of function. Instead, Behe writes (p. 362) that under his self-fulfilling scheme “the mutation would be counted as modification-of-function—because no new functional coded element was gained or lost, just copied.” In other words, Behe won’t count any newly evolved function as a gain of function unless some entirely new gene or control region “poofs” into existence.

But that’s not how evolution works—unless you believe, as Behe apparently does, that God or some other “intelligent agent” intervened to insert new genetic information into various lineages during the course of history. (Suffice it to say that I don’t regard this as a scientifically useful hypothesis, because I don’t think it can be tested.) Evolutionary biology doesn’t require that new genes poof into existence. Instead, old genes and their products are coopted, modified, and used in new ways—a process called exaptation. For example, crystallin proteins in the lenses of our eyes derive from proteins that performed other functions. At a larger physical scale, the wings of birds and bats derive from the forelimbs of their four-legged ancestors, which in turn derive from fins of fishes.

In short, Darwin Devolves presents a biased picture of the LTEE’s findings. Behe is overly confident in asserting that the vast majority of beneficial mutations have degraded functions, when the functional effects of most of these mutations have not been measured under relevant conditions. In any case, the experiment was designed to address issues other than molecular functionality, with the environment deliberated constructed to be as simple as possible. And yet, having closed the door on nearly all opportunities for new functions to evolve, a striking example arose in a tiny flask after a mere decade or two.

[This image shows some of the LTEE populations in their flasks. The one in the center is more turbid because the bacteria have reached a higher density after they evolved the ability to consume citrate in the culture medium.  Photo credit: Brian Baer and Neerja Hajela.]

LTEE lines centered on citrate #11

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Does Behe’s “First Rule” Really Show that Evolutionary Biology Has a Big Problem?

Michael Behe has a new book coming out this month called Darwin Devolves. Nathan Lents, Joshua Swamidass, and I wrote a review of that book for the journal Science. (You can also find an open-access copy of our review here.) It provides an overview of the problems we see with his thesis and interpretations. As our review states, Behe points to many examples of evolution in which genes and their functions have been degraded, but he largely ignores the ways that evolution generates new functions and thereby produces complexity. That’s a severe problem because Behe uses the evidence for the ease of gene degradation to support his overarching implication that the current scientific understanding of the mechanisms of evolution is inadequate and, consequently, the field of evolutionary biology has a “big problem.”

I won’t attempt to summarize Behe’s entire book nor our short review, as people can read those for themselves if they want. Instead, I hope to accomplish three things in this post and two more that will follow. In this first post, I explain why Behe’s so-called “first rule of adaptive evolution” does not imply what he says it does about evolution writ large. In the second post, I’ll discuss whether my long-term evolution experiment (the LTEE for short) does or doesn’t provide strong support for Behe’s position in that regard. In my third post, I’ll explain why I think that Behe’s positions, taken as a whole, are scientifically untenable.

I. Behe’s “First Rule of Adaptive Evolution” Confounds Frequency and Importance

Behe’s latest book is centered around what he calls “The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring.” As he wrote in an immediate, dismissive response to our review: “The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population.”

Let’s work through these two sentences, because they concisely express the thrust of Behe’s book. The first sentence regarding “the tendency of random mutation” is not too bad, though it is overly strong. I would tone it down as follows: “The tendency of random mutation is to degrade genes, and that is sometimes helpful.” My reasons for these subtle changes are that: (i) many mutations are selectively neutral or so weakly deleterious as to be effectively invisible to natural selection; (ii) while loss-of-function mutations are sometimes helpful to the organism, I wouldn’t say that’s “very often” the case (though it may be in some systems, as I’ll discuss in part II); and (iii) even those degradative mutations that are not helpful on their own sometimes persist and occasionally serve as “stepping stones” on the path toward new functionality. This last scenario is unlikely in any particular instance, but given the prevalence of degrading mutations it may nonetheless be important in evolution. (This scenario does not fit neatly within the old-fashioned caricature of Darwinian evolution as only proceeding by strictly adaptive mutations, but it is certainly part of modern evolutionary theory.)

Behe’s next sentence then asserts the power of the “de-evolutionary” process of gene degradation. This is an unjustifiable extrapolation, yet it is central to Behe’s latest book. (It’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.) Yes, natural selection sometimes increases the frequency of broken and degraded genes in populations. But when it comes to the power of natural selection, what is most frequent versus most important can be very different things. What is most important in evolution, and in many other contexts, depends on timescales and the cumulative magnitude of effects. As a familiar example, some rhinoviruses are the most frequent source of viral infections in our lives (hence the expression “common cold”), but infections by HIV or Ebola, while less common, are far more consequential.

Or consider an investor who bought stocks in 100 different companies 25 years ago, of which 80 have been losers. Ouch? Maybe not! A stock can’t lose more than the price that was paid for it, and so 20 winners can overcome 80 losers. Imagine if that investor had picked Apple, for example. That single stock has increased in value by well over 100-fold in that time, more than offsetting even 80 total wipeouts all by itself. (In fact, research on the stock market has shown the vast majority of long-term gains result from a small minority of companies that, like Apple, eventually become big winners.)

In the same vein, even if many more mutations destroy functions than produce new functions, the latter category has been far more consequential in the history of life. That is because a new function may enable a lineage to colonize a new habitat or realm, setting off what evolutionary biologists call an “adaptive radiation” that massively increases not only the numbers of organisms but, over time, the diversity of species and even higher taxa. As one example, consider Tiktaalik or some relative thereof, in any case a transitional kind of fish whose descendants colonized land and eventually gave rise to all of the terrestrial vertebrates—amphibian, reptiles, birds, and mammals. That lineage left far more eventual descendants (including ourselves), and was far more consequential for the history of life on Earth, than 100 other lineages that might have gained a transient advantage by degrading some gene and its function before eventually petering out.

Asteroid impacts aren’t common either, but the dinosaurs (among other groups) sure felt the impact of one at the end of the Cretaceous. (There remains some debate about the cause of that mass extinction event, but whatever the cause its consequences were huge.) Luckily for us, though, some early mammals survived. Evolution often leads to dead ends, sometimes as a consequence of exogenous events like asteroids, and other times because adaptations that are useful under a narrow set of conditions (such as those caused by mutations that break or degrade genes) prove vulnerable over time to even subtle changes in the environment. It has been estimated that more than 99% of all species that have ever existed are now extinct. Yet here we are, on a planet that is home to millions of diverse species whose genomes record the history of life.

Summing up, Behe is right that mutations that break or blunt a gene can be adaptive. And he’s right that, when such mutations are adaptive, they are easy to come by. But Behe is wrong when he implies these facts present a problem for evolutionary biology, because his thesis confuses frequencies over the short run with lasting impacts over the long haul of evolution.

[The picture below shows the Tiktaalik fossil discovered by Neil Shubin and colleagues.  It was posted on Wikipedia by Eduard Solà, and it is shown here under the indicated Creative Commons license.]

Tiktaalik

 

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Asking for a Skeptic Friend

I sometimes get email from people asking, in one way or another, whether our long-term evolution experiment (LTEE) with E. coli provides evidence of evolution writ large – new species, new information, or something of that sort. I try to answer these questions by providing some examples of what we’ve seen change, and by putting the LTEE into context. Here’s one such email:

Hi Professor Lenski,

I have a quick question. I’m asking because I am having a discussion with someone who is skeptical of evolution. The question is: Over the 50,000 generations of e-coli has any of the e-coli evolved into something else or is it still e-coli?

I am a non-religious person who likes to think of myself as an adherent to science but I am not sure how to respond to my skeptic-friend.

Thank you!

And here’s my reply:

Hello —-,

50,000 generations, for these bacteria, took place in a matter of ~25 years. They have changed in many (mostly small) ways, and remained the same in many other respects, just as one expects from evolutionary theory. Although these are somewhat technical articles, I have attached 3 PDFs that describe some of the changes that we have seen.

Wiser et al. (2013) document the process of adaptation by natural selection, which has led to the improved competitive fitness of the bacteria relative to their ancestors.

Blount et al. (2012) describe the genetic changes that led one population (out of the 12 in the experiment) to evolve a new capacity to grow on an alternative source of carbon and energy.

Tenaillon et al. (2016) describe changes that have occurred across all 12 populations in their genomes (DNA sequences), which have caused all of them to become more and more dissimilar to their ancestor as time marches on.

Best wishes,

     Richard

Although these articles were written for other scientists, they make three big points that I hope almost anyone with an open mind can understand.

  • We see organisms adapting to their environment, as evidenced by increased competitiveness relative to their ancestors.
  • Against this backdrop of more or less gradual improvement, we occasionally see much bigger changes.
  • And at the level of their genomes, we see the bacteria becoming more and more different from their ancestors.

In these fundamental respects, evolution in these flasks works in much the same way that evolution works in nature. Of course, the scales of time and space are vastly greater in nature than they are in the lab, and natural environments are far more complex and variable than is the simple one in the LTEE. But the core processes of mutation, drift, and natural selection give rise to evolution in the LTEE, just as they do (along with sex and other forms of gene exchange) in nature.

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On the Evolution of Citrate Use

Those who follow the long-term evolution experiment (LTEE) with E. coli know that the most dramatic change we have observed to date is the origin of the new ability to grow on citrate. It’s dramatic for several reasons including the fact (external to the LTEE) that E. coli has been historically defined as a species based in part on its inability to grow on citrate in oxic environments and the fact (internal to the LTEE) that it was so difficult for the bacteria to evolve this ability that only one of the populations did so, and that it took over 30,000 generations even though an abundance of citrate has been present in the medium throughout the LTEE. Even after 64,000 generations, only the Ara–3 population has evolved that new ability.

Zachary Blount, formerly a graduate student and now a postdoc in my lab, has spent the last decade studying the evolution of this population and its new ability. His two first-authored papers in PNAS (2008) and Nature (2012) demonstrated, respectively, that (i) the origin of the ability to grow on citrate in the LTEE was contingent on one or more “potentiating” mutations that happened before the “actualizing” mutation that conferred the new function first appeared, and (ii) the actualizing mutation was a physical rearrangement of the DNA that brought together a structural gene, citT, that encodes a transporter and a previously unconnected regulatory region to generate a new module that caused the phenotypic transition to Cit+. These papers presented and discussed much more than these two points, of course, but they are the key findings. More recently, Zack was a coauthor on a paper in eLife (2015) by Erik Quandt, Jeff Barrick, and others that identified two mutations in the gene for citrate synthase—one that potentiated the evolution of citrate utilization, and another that subsequently refined that new function.

So we were keenly interested when we saw a new paper titled “Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA” by Dustin Van Hofwegen, Carolyn Hovde, and Scott Minnich. The paper is posted online as an accepted manuscript by the Journal of Bacteriology. What follows here are some overall impressions of their paper that Zack and I put together. We may follow these impressions later with some further analysis and comments.

* * * * *

Let’s begin by saying that it’s great to see other groups working on interesting systems and problems like the evolution of citrate utilization in E. coli.

Moreover, the actual science that was done and reported looks fine and interesting, though we have a few quibbles with some details that we will overlook for now. By and large, the work confirms many of the findings that were reported in our papers cited above:

(i) the ability to grow on citrate in the presence of oxygen can and does evolve in E. coli (Blount et al., 2008);

(ii) when aerobic growth on citrate evolves, it does not do so quickly and easily (Blount et al., 2008) but instead takes weeks or longer—more on that below;

(iii) all strains that have evolved this new ability have physical rearrangements that involve the citT gene and appear also to involve a so-called “promoter capture” whereby a copy of this transporter-encoding gene acquires a new upstream regulatory region (Blount et al., 2012); and

(iv) genetic context matters—the strain one uses affects the likelihood of evolving the Cit+ function (Blount et al., 2008) and the resulting ability to grow on citrate (Blount et al., 2012; Quandt et al., 2015).

The problem, then, is not with the experiments and data. Rather, the problem is that the results are wrapped in interpretations that are, in our view, flawed and fallacious.

“No new genetic information”

The authors assert repeatedly (last sentence of their Importance statement, and first and last paragraphs of their Discussion) that “no new genetic information evolved.” However, that statement flatly contradicts the fact that in their experiments, and ours, E. coli gained the new ability to grow on citrate in the presence of oxygen. We would further add (which we have not emphasized before) that these Cit+ strains can grow on citrate as a sole carbon source—when E. coli grows anaerobically on citrate, it requires a second substrate for growth in order to use the citrate (a phenomenon called “co-metabolism”).

The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science. In this regard, it seems relevant to point out that the corresponding author, Scott Minnich, is a fellow of the Discovery Institute and was an expert witness for the losing side that wanted to allow the teaching of “intelligent design” as an alternative to evolution in public schools in the landmark Kitzmiller v. Dover case.

“Rapid evolution of citrate utilization”

In the title of their paper and throughout, Van Hofwegen et al. emphasize that, in their experiments, E. coli evolved the ability to grow aerobically on citrate much faster than the 30,000 generations and ~15 years that it took in the LTEE. That’s true, but it also obscures three points. First, we already demonstrated in replay experiments that, in the right genetic background and by plating on minimal-citrate agar, Cit+ mutants sometimes arose in a matter of weeks (Blount et al. 2008). Second, rapid evolution of citrate utilization—or any evolution of that function—was not a goal of the LTEE. So while it is interesting that Van Hofwegen et al. have identified genetic contexts and ecological conditions that accelerate the emergence of citrate utilization (as did Blount et al., 2008), that in no way undermines the slowness and rarity of the evolution of this function in the context of the LTEE (or, for that matter, the rarity of Cit+ E. coli in nature and in the lab prior to our work). Third, the fastest time that Van Hofwegen et al. saw for the Cit+ function to emerge was 19 days (from their Table 1), and in most cases it took a month or two. While that’s a lot faster than 15 years, it’s still much longer than typical “direct selections” used by microbiologists where a readily accessible mutation might confer, for example, resistance to an antibiotic after a day or two.

So while we commend the authors’ patience, we do not think the fact that their experiments produced Cit+ bacteria faster than did the LTEE is particularly important, especially since that was not a goal of the LTEE (and since we also produced them much faster in replay experiments). However, in a manner that again suggests an ulterior nonscientific motive, they try to undermine the LTEE as an exemplar of evolution. The final sentence of their paper reads: “A more accurate, albeit controversial, interpretation of the LTEE is that E. coli’s capacity to evolve is more limited than currently assumed.” Alas, their conclusion makes no logical sense. If under the right circumstances the evolution of citrate utilization is more rapid than it is in the LTEE, then that means that E. coli’s capacity to evolve is more powerful—not more limited—than assumed.

“Speciation Event”

To us, one of the most interesting facets of the evolution of the citrate-using E. coli in the LTEE is its implications for our understanding of the evolutionary processes by which new species arise. Part of the reason for this interest—and the one that’s most easily stated in a popular context—is that the inability to grow on citrate is part of the historical definition for E. coli as a species, going back almost a century. But the deeper interest to us lies not in labeling a new species or debating where to draw the line between species—various criteria are used by different scientists, and inevitably there are many cases that lie in grey areas. Rather, as evolutionary biologists, we are most interested in the process of speciation—the ecological and genetic dynamics that lead to changing biological forms that, over time, are more and more like a new species until, eventually, perhaps far in the future, there is no doubt that a new species has evolved.

In short, speciation is not an event. As Ptacek and Hankison (2009, in Evolution: The First Four Billion Years) put it, “[S]peciation is a series of processes, with a beginning stage of initial divergence, a middle stage wherein species-specific characteristics are refined by various forces of evolution, and an end point at which a new species becomes a completely separate evolutionary lineage on its own trajectory of evolutionary change with the potential for extinction or further diversification into new lineages.” We realize that scientists (ourselves included) often use shorthand and jargon instead of writing more carefully and precisely. We have no doubt that one can find solid scientific papers that talk about speciation events; but except for cases that involve hybridization leading to polyploids that are reproductively isolated in a single generation (as sometimes occurs in plants), this is simply an imprecise shorthand.

In our first paper on the citrate-using E. coli that arose in the LTEE, we clearly emphasized that becoming Cit+ was only a first step on the road to possible speciation (Blount et al., 2008). One criterion that many biologists would apply to investigate speciation is whether a later form merely replaced an earlier form (evolution without speciation) or, alternatively, one lineage split into two lineages that then coexisted (incipient speciation). In fact, we showed that, after the new function evolved, the Cit+ and Cit lineages coexisted (and their coexistence was confirmed using genomic data in Blount et al., 2012). We concluded the 2008 paper by asking explicitly: “Will the Cit+ and Cit– lineages eventually become distinct species?” (emphasis added) and discussing how we might assess their ongoing divergence.

By contrast, Van Hofwegen et al. dismiss the idea of speciation out of hand, not only by calling it an event but by treating the issue as though it hinges, literally, on the individual mutations that produced a Cit+ cell. For example, they write: “[B]ecause this adaptation did not generate any new genetic information … generation of E. coli Cit+ phenotypes in our estimation do not warrant consideration as a speciation event.” And in the penultimate sentence of their paper, they say: “[W]e argue that this is not speciation any more than any other regulatory mutant of E. coli.” (We also note that this is a rather bizarre generalization, as though the gain of function that gave access to a new resource is equal in regards to its speciation potential to, say, the loss of regulation of a function that is no longer used by a lineage in its current environment. Both might well be adaptations, but one seems much more likely to begin the process of speciation.)

In conclusion, Van Hofwegen, Hovde, and Minnich have done some interesting experiments that shed further light on the nature of the mutations and ecological conditions that allow E. coli cells to evolve the ability to grow aerobically on citrate, a function that this species cannot ordinarily perform. However, they misunderstand and/or misrepresent the relevance of this system for evolutionary biology in several important respects. 

And the meaning of historical contingency

The paper by Hofwegen et al. is accompanied by a commentary by John Roth and Sophie Maisnier-Patin. Their abstract begins: “Van Hofwegen et al. demonstrate that E. coli rapidly evolves ability to use citrate when long selective periods are provided. This contrasts with the extreme delay (15 years of daily transfers) seen in the long-term evolution experiments of Lenski and coworkers. Their idea of ‘historical contingency’ may require reinterpretation.”

Historical contingency is a complicated notion, but it essentially means that history matters. In Blount et al. (2008), we made it clear what we mean by historical contingency in the context of the evolution of the Cit+ lineage in one of the LTEE populations. Was this an extremely rare event that could have happened at any time? Or did it instead depend on the occurrence of a sequence of events, a particular history, whereby an altered genetic context evolved—a potentiated background—in which this new function could now evolve?

Roth and Maisnier-Patin’s suggestion that our idea of “historical contingency” may require reinterpretation reflects a false dichotomy between historical contingency, on the one hand, and the effects of different selection schemes, on the other. The fact that evolution might be fast and not contingent on genetic background (though the evidence of Van Hofwegen et al. is, at best, ambiguous in this regard) in one set of circumstances has no bearing on whether it is contingent in another set of circumstances. The historical contingency of Cit+ evolution is not mere conjecture. We showed that the evolution of this new function in the LTEE was contingent. In replay experiments, Blount et al. (2008) showed that that the Cit+ trait arises more often in later-generation genetic backgrounds than in the ancestor or early-generation backgrounds. Moreover, Blount et al. (2012) performed genetic manipulations and showed that a high-copy-number plasmid carrying the evolved module that confers the Cit+ function had very different phenotypic effects when put in a Cit clone from the lineage within which Cit+ evolved than when placed in the ancestor or even other late-generation lineages not on the line of descent leading to the emergence of the Cit+ bacteria. In the clone on the line of descent, this module conferred strong, immediate, and consistent growth on citrate. In the other genetic backgrounds, growth on citrate was weak, delayed, and/or inconsistent.

The hypothesis of historical contingency is not mutually exclusive with respect to causal factors of an ecological or genetic nature—it simply says that factors that changed over time were important for the eventual emergence of Cit+. Moreover, historical contingency was invoked and demonstrated in a specific context, namely that of the emergence of Cit+ in the LTEE—it does not mean that the emergence of Cit+ is historically contingent in other experimental contexts, nor for that matter that other changes in the LTEE are historically contingent—in fact, some other evolved changes in the LTEE have been highly predictable and not (or at least not obviously) contingent on prior mutations in the populations (e.g., Woods et al., PNAS, 2006). [For more on historical contingency and the LTEE, you can download a preprint of Zack’s latest paper from his website: Blount, Z. D. A Case Study in Evolutionary Contingency. Studies in the History and Philosophy of Biology and Biomedical Sciences.]

Erik Quandt offers this analogy to illustrate our point that contingency depends on context: “It’s kind of like the difference between being an average person attempting to dunk a basketball when all by yourself, with unlimited time, and maybe even with a trampoline versus having to get to the rim in a game with LeBron James and the Cavs playing defense. Just because you can do it by yourself under optimal conditions, does this negate the difficulty of doing it in an NBA game or say anything about the kind of history (training and/or genetics) that you would need for that situation?”

* * * * *

LTEE lines centered on citrate #11

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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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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

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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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