Tag Archives: history of science

Happy birthday, Charles and Abe

Charles Darwin was born into wealth and privilege in England 210 years ago, while across the ocean on the same day Abraham Lincoln was born to a poor family in Kentucky.

Besides the coincidence of their birthdays, there are other interesting connections. Lincoln is known, of course, for preserving the Union and freeing slaves through the Emancipation Proclamation. But Lincoln also signed the law that established the National Academy of Sciences, which provides pro bono scientific advice to the federal government. And while Darwin is known for his work on evolution, he was also a prominent overseas voice in the abolitionist movement. During the voyage of HMS Beagle, Darwin had a heated argument with the captain, Robert FitzRoy, who defended the institution of slavery.

Darwin was onboard the ship as a gentleman naturalist, but the voyage was far from easy. Planned as a 2-year expedition, it was almost 5 years before 27-year-old Darwin returned to England in 1836. He was frequently seasick and, back home, often ill. Nevertheless, his observations, specimens, and notes laid the groundwork for his thinking that culminated with On the Origin of Species in 1859. That book presented Darwin’s evidence for descent with modification (what we now call evolution), and it put forward a mechanism—natural selection—that explains how species acquire traits that fit them to their environments.

Many of us first encounter the idea of evolution as children, when we see pictures or fossils of dinosaurs and other long-ago creatures. But evolution isn’t confined to the past; it continues to occur all around us. Some ongoing evolution causes problems for our health and wellbeing, such as pathogenic microbes evolving resistance to antibiotics. In many cases, though, evolution is used to solve problems in agriculture, biotechnology, and engineering. For example, Frances Arnold won a 2018 Nobel Prize in Chemistry for her work using evolution to generate valuable enzymes with improved and even new functions.

In my lab, we study evolution in action using bacteria, taking advantage of their rapid generations. We can freeze and later revive living cells, allowing us to compare organisms from different generations—in essence, time travel! In an ongoing experiment I started in 1988, we’ve watched 12 populations of E. coli evolve for over 70,000 generations. We can quantify the Darwinian process of adaptation by natural selection, and we’ve sequenced the bacteria’s genomes to understand the coupling between adaptation and genotypic evolution. We’ve even seen the emergence of a new metabolic function that transcends the usual definition of E. coli as a species.

It’s amazing just how much evolution has taken place during a few decades in these small flasks. It leaves me with awe at what evolution has achieved over the last four billion years on our planet … and with wonder about what more will unfold in the fullness of time.

LTEE flasks repeating

This post was written for the National Academy of Sciences Facebook page, where it also appears.

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Fun in Philadelphia

Madeleine and I just spent a few magical days in Philadelphia, where I was inducted into the American Philosophical Society. While I had heard of the APS, and knew it had a long history, I didn’t know very much about it until a few years ago, when I heard about some colleagues being elected.

The APS was founded in 1743 by Benjamin Franklin, making it the oldest learned society in the United States, and making this the 275th anniversary year. George Washington was a member. Thomas Jefferson was a member. In fact, Jefferson was President of the APS while he was also serving as Vice President and President of the United States. Barrack Obama is another member. In other words, there’s a bit of history associated with the APS.

Our hotel was almost next door to the APS, including the Benjamin Franklin Hall (with the auditorium where the meeting was held) as well as the museum and library. (More on those later.) Here’s the view from our hotel room the evening we arrived. Yes, that’s Independence Hall, where the Declaration of Independence was approved on July 4, 1776.

Independence Hall at night

The highlights of the meeting for me are almost beyond description, but here’s an attempt.

The people: From colleagues across all fields to the staff and officers of the APS, everyone was exceptionally welcoming to Madeleine and me. (Partners and spouses are as much a part of the meeting as the members.) I got to see some longtime friends from the field of evolutionary biology including David and Marvalee Wake; I got to chat with people from other fields who I’ve met before, but rarely get to see, including population biologist Joel Cohen and geneticist Michael Young; I got to meet people for the first time including APS President Linda Greenhouse, an expert on the Supreme Court, and her husband Eugene Fidell, who works in military law. And many other warm, welcoming, and interesting people.

The talks: There were several talks each day, across a wide range of fields, and they were uniformly lively and interesting. You can see the full program here, and I’ll just mention some of them that especially caught my fancy. Two talks on the history of the US census (Margo Anderson) and on political fights over its implementation (Kenneth Prewitt). Three talks on new technologies used to give voice to the voiceless (Rupal Patel), on interpreting interactions between police and motorists (Dan Jurafsky), and on future cameras that can reveal with extraordinary resolution a fingerprint on an object in a still life photo or capture the image reflected in a subject’s gaze (Shreer Nayar). Toni Morrison received the 2018 Thomas Jefferson Medal for Distinguished Achievement in the Arts, Humanities, and Social Sciences; while she could not attend, a moving letter of acceptance was read on her behalf. Bryan Stevenson received the 2018 Benjamin Franklin Medal for Distinguished Public Service and he gave an inspiring, hard-hitting, beautiful, and moving talk about his childhood and his life’s work for social justice, emphasizing the importance of proximity, memory, empathy, and persistence. You can—and really should—hear his talk on memory and justice. (The award starts at ~35 minutes, followed by a short acceptance speech, and then his hour-long talk at ~42 minutes. Set aside the time; you won’t be disappointed.)

The Treasures: Wow. The APS library includes over 13 million manuscripts, many of extraordinary historical and scientific importance. The amazing staff of the APS, including Library Director Patrick Spero and Museum Director Merrill Mason, pulled out some of the original treasures for us to see. Among them: Thomas Jefferson’s final draft of the Declaration of Independence, with his marginal comments showing the changes that were made (to Jefferson’s consternation) in order to secure approval from Congress. The only document signed by the first four US Presidents: Washington, Adams, Jefferson, and Madison. All four were members of the APS, and they signed pledges to contribute financially to a cross-continental scientific survey of the flora by André Michaux, a French botanist. Although this expedition was eventually stymied by politics, it was a precursor to Lewis and Clark. Speaking of which, another treasure we got to see was one of the journals of the Lewis and Clark expedition, with a beautiful, tiny, hand-drawn map of Cape Disappointment. On the science side, we saw Charles Darwin’s draft of the title page of The Origin of Species, which he had originally titled “An abstract of an Essay on the Origin of Species and Varieties Through Natural Selection.” We also got to see a notebook of the physicist John Wheeler, with his illustration of gravitational collapse producing a “black hole”—this was especially exciting because Wheeler was a mentor of Madeleine’s stepfather, also a theoretical physicist. As I said, wow! The APS has some of these items on display at their Museum, and you can see some of these treasures online as well.

Another treasure: Another great pleasure was spending time with my wonderful friend and MSU colleague Jack Liu. Jack holds the Rachel Carson Chair in Sustainability, and his work focuses on the complex interactions between people and the environment—from protecting pandas and their special habitat in China, to the effects of divorce on energy consumption in American households. As we rode together to and from airports, I learned Jack’s own inspirational story: from a tiny village in China to becoming the first member of his family to attend college; his experience learning English almost from scratch while a doctoral student at the University of Georgia; and becoming the first person from MSU ever elected to the American Philosophical Society.

Jack and me at APS Nov 2018

[Here’s a picture of Jack Liu and me standing below portraits of Franklin and Washington in the APS Auditorium.]

Signing the book at APS

[Here’s a picture that Jack took of me “signing the book” during my induction into the APS.]

Greeting from Linda Greenhouse

[This one, which Jack also took, shows me being officially welcomed by Linda Greenhouse, the APS President, after Robert Hauser (at left), the Executive Officer, has read a statement about my work.]

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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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Erdös with a non-kosher side of Bacon

Erdös number

Paul Erdös was a prolific and important mathematician. He also had hundreds of collaborators from around the world who coauthored papers with him.

Years ago, Casper Goffman explained an idea, called the Erdös number, that describes the “collaborative distance” between Erdös and someone else, where that distance is defined by the smallest number of steps based on coauthored papers. Erdös himself has an Erdös number of 0, while the 511 mathematicians who wrote papers with Erdös have an Erdös number of 1. One of these people is Persi Diaconis, a professional magician and Stanford mathematician specializing in probability theory.

Over 9,000 people have Erdös numbers of 2, meaning they wrote a paper with one or more of Erdös’s coauthors but never wrote a paper with Erdös himself.  Two of these people are Berkeley professors Bernd Sturmfels, in the field of algebraic geometry, and Lior Pachter, a computational biologist.  (Sturmfels coauthored three papers with Diaconis, and he wrote other papers with two more people with Erdös numbers of 1.  Pachter wrote several papers with mathematician Daniel Kleitman, an Erdös coauthor.)

In 2007, I coauthored a paper with Pachter and Sturmfels in which we analyzed epistatic interactions to describe the geometric structure of a fitness landscape:

Beerenwinkel, N., L. Pachter, B. Sturmfels, S. F. Elena, and R. E. Lenski. 2007. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evolutionary Biology 7:60.

So that paper gives me an Erdös number of 3.

Bacon number

A group of students later came up with the idea of a Bacon number, a Hollywood version of the Erdös number that equals the smallest number of film links separating any other actor from Kevin Bacon. (Bacon had been previously described as the “center of the Hollywood universe” after a 1994 interview in which he said he worked with everybody in Hollywood or someone who’s worked with them, according to Wikipedia.)

So Kevin Bacon has a Bacon number of 0, while actors who have appeared in a film with him have Bacon numbers of 1. An actor who appeared in a film with any actors who appeared with Bacon, but not in a film with Bacon himself, have a Bacon number of 2.

Morgan Freeman has a Bacon number of 1 based on a 2013 documentary film called “Eastwood Directs: The Untold Story.” (You missed that one? Me, too.) Well, a couple of weeks ago, I appeared in an episode of the show “Through the Wormhole with Morgan Freeman.”

Erdös-Bacon number

Now there’s a really special number called the Erdös-Bacon number, which is the sum of a person’s Erdös and Bacon numbers. Not many people have an Erdös number, and not many have a Bacon number. And very few people have an Erdös-Bacon number because you have to have written a math or science paper and appeared in a film, and of course with known connections to Erdös and Bacon along both paths.

Cornell mathematics professor Steven Strogatz has an Erdös-Bacon number of just 4, having appeared in a TV documentary film with Kevin Bacon called “Connected: The Power of Six Degrees.” Of course, that film is about the very sort of mathematical links we’re talking about here!

So someone just suggested to me that I now have an Erdös-Bacon number of 5. If so, that would put me ahead of such luminaries as Carl Sagan and Richard Feynman! Awesome!!

The fine print

As I was looking into this exciting possibility, I discovered a website called “The Oracle of Bacon.” It seems to be the semi-official arbiter of Bacon numbers, and it says: “We do not consider links through television shows, made-for-tv movies, writers, producers, directors, etc.”

That documentary about Clint Eastwood, with both Morgan Freeman and Kevin Bacon in it, apparently doesn’t qualify.  So Morgan Freeman’s Bacon number rises to 2 (via many different paths through his many major films).

Even worse, though, my Bacon number evaporates entirely, since my link to Kevin Bacon goes through my appearance on a television show with Morgan Freeman.

So there you have it. I have an officially non-kosher Erdös-Bacon number of 5.

I guess I can live with that.

But if Kevin Bacon, Morgan Freeman, or any of their Hollywood friends invites me to appear in a real film, I’ll probably accept!

~~~

Note:  It looks like Steven Strogatz’s Erdös-Bacon number of 4 is also compromised because his Bacon number is through a TV movie.  You need to use non-default settings for it to show up on The Oracle of Bacon website.  But maybe it’s less non-kosher, since it was a TV movie, not just a TV show.

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Tiny Things that Live in Little Bottles

As I mentioned in my previous post, it can be a fun challenge to explain your scientific research to people who aren’t scientists.

A week or so ago I came across a website that challenges you to explain something complicated using only the thousand most commonly used words.

So here’s my effort about our long-term evolution experiment with E. coli:

My team works with really tiny things that live in little bottles. We watch the tiny things change over time – over a really long time. The tiny things that do the best have learned to eat their food faster and faster, before the other guys can eat their lunch, so to say.  Well, the tiny things don’t really learn, but it’s kind of like learning – and even better, the best ones pass along what they learned to their kids.  A really cool guy came up with the idea of how this works more than a hundred years ago. My team’s work shows he got it pretty much right. But there’s a lot of stuff he didn’t know, and we’re figuring that out, too.

Several other biologists followed up including Nicole King, Graham Coop, and Josie Chandler (the links are to the simple-words-only descriptions of their own research).

Give it a try, and add your contributions in the comments below!

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Thirty Years

No, the LTEE did not suddenly jump forward by almost 3 years. That milestone will be reached on February 24, 2018.

Next Friday is the end of the semester at MSU and, for me, it will mark 30 years that I’ve been on the faculty: six at UC-Irvine, and 24 here at MSU. (I also taught for one semester at Dartmouth as a sabbatical replacement, while I was doing a postdoc at UMass.)

Holy cow: 30 years. Where did all that time go?

Well, a lot of it was spent advising, supervising, and mentoring graduate students. And those have been some of the most interesting, enjoyable, and rewarding professional experiences that I can imagine.

In fact, this afternoon Caroline Turner defended her dissertation – congratulations Dr. Turner! Her dissertation is titled “Experimental evolution and ecological consequences: new niches and changing stoichiometry.” It contains four fascinating and meaty chapters, two on the interplay between evolutionary and ecological processes in the LTEE population that evolved the ability to grow on citrate, and two on evolved changes in the elemental stoichiometry of bacterial cells over experimental time scales.

Caroline is the 20th student to complete her Ph.D. with me serving as the advisor or co-advisor. Here they all are, with links to their professional pages or related sites.

  1. Felisa Smith, Ph.D. in 1991 from UC-Irvine.
  2. John Mittler, Ph.D. in 1992 from UC-Irvine.
  3. Mike Travisano, Ph.D. in 1993 from MSU.
  4. Paul Turner, Ph.D. in 1995 from MSU.
  5. Greg Velicer, Ph.D. in 1997 from MSU.
  6. Brendan Bohannan, Ph.D. in 1997 from MSU.
  7. Phil Gerrish, Ph.D. in 1998 from MSU.
  8. Farida Vasi, Ph.D. in 2000 from MSU.
  9. Vaughn Cooper, Ph.D. in 2000 from MSU.
  10. Danny Rozen, Ph.D. in 2000 from MSU.
  11. Kristina Hillesland, Ph.D. in 2004 from MSU.
  12. Elizabeth Ostrowski, Ph.D. in 2005 from MSU.
  13. Bob Woods, Ph.D. in 2005 from MSU.
  14. Dule Misevic, Ph.D. in 2006 from MSU.
  15. Gabe Yedid, Ph.D. in 2007 from MSU.
  16. Sean Sleight, Ph.D. in 2007 from MSU.
  17. Zack Blount, Ph.D. in 2011 from MSU.
  18. Justin Meyer, Ph.D. in 2012 from MSU.
  19. Luis Zaman, Ph.D. in 2014 from MSU. (Charles Ofria was the primary advisor.)
  20. Caroline Turner, Ph.D. in 2015 from MSU.

There are also 8 doctoral students at various stages currently in my group at MSU including Brian Wade (Ph.D. candidate), Mike Wiser (Ph.D. candidate), Rohan Maddamsetti (Ph.D. candidate), Alita Burmeister (Ph.D. candidate), Elizabeth Baird, Jay Bundy, Nkrumah Grant, and Kyle Card.

My own advisor – the late, great Nelson Hairston, Sr. – said that he expected his graduate students to shed sweat and maybe even occasional tears, but not blood. I would imagine the same has been true for my students.

Thirty years, holy cow. Time flies when you’re working hard and having fun!

Added November 4, 2015:  And now #21 in my 31st year, as  Mike Wiser successfully defended his dissertation today!

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Window Dressing

The window to the lab has been updated, courtesy of Zack Blount.

62K window dressing

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