Retrogenes in Volvox and Chlamy

The evolution of multicellularity in the volvocine algae appears to have happened primarily through co-option of existing genes for new functions. For example, the initial transition from a unicellular life cycle to a simple multicellular one involved the retinoblastoma gene, as Hanschen and colleagues elegantly demonstrated (see “The evolution of undifferentiated multicellularity: the Gonium genome“). A Volvox gene involved in cellular differentiation, regA, was likely co-opted from an ancestral role in environmental sensing, and a similar origin appears to explain the use of cyclic AMP for the signaling that causes multicellular aggregation in cellular slime molds (see “Volvox 2015: evolution“). 

Some of the changes leading to complex multicellularity, though, clearly did involve new genes. Two gene families involved in building the extracellular matrix that makes up most of a Volvox colony, the pherophorins and metalloproteinases, have undergone multiple duplication events leading to greatly expanded gene families (see “Heads I win; tails you lose: Evolution News & Views on Gonium, part 2“). One mechanism by which genes are duplicated is retroposition, in which a messenger RNA is reverse transcribed into DNA and inserted into the genome:

Fig S1A from Jakalski et al. 2016. Basic mechanism of retroposition. DNA is transcribed into a pre-mRNA by RNA polymerase, introns are spliced out, and a poly(A) tail is added to the 3′ end, resulting in a mature messenger RNA. The mRNA is then reverse-transcribed to DNA and inserted into a new genomic location.

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Teach lies to schoolchildren, because it used to be easy to cross the border

Photo by John Minchillo.

Photo by John Minchillo, downloaded from New Scientist.

Someone over at Uncommon Descent is unhappy with a New Scientist article criticizing Ken Ham’s Ark Park, an explicitly creationist-themed attraction dedicated to Biblical literalism. In the New Scientist article (“School field trips to creationist Ark? Sink that idea right now“), Josh Rosenau argues that teaching school children that the Earth is 6,000 years old, and that a vengeful creator committed genocide by drowning against his creation, is a bad idea.

Uncommon Descent objects, in a post that reveals more about its (unnamed) author than it presents any coherent argument (“New Scientist stomps on Noah’s Ark“) [PG-13 below the fold]:

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New position at Georgia Tech

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Part of the reason posts at Fierce Roller have been so sparse lately is that I’ve been busy moving across the country. I’m now a Senior Research Scientist in the School of Biology at Georgia Tech. I’ll be running a small lab, with two (soon three) postdocs and a very talented grad student.

I spent exactly one day on campus before I left for the ASM Experimental Microbial Evolution meeting, on which I managed to meet with the grad student and one postdoc and to get hooked up to the campus wifi. I have not yet attended new employee orientation or been assigned an employee ID number, so the degree to which I’m actually employed at this moment is a bit murky. Hopefully I’ll get this all sorted next week.

The long-term evolution experiment

I’m attending the 2nd ASM Conference on Experimental Microbial Evolution (#ASMEME) in Washington, DC. The meeting opened last night with a keynote address by Rich Lenski on the long-term evolution experiment (LTEE). If you’re not familiar with it, the LTEE involves twelve populations of E. coli bacteria that have been transferred every damn day for the last 28 years. That’s right, twelve transfers every day since Ronald Reagan was President.

Since E. coli undergoes about 6.6 doublings per day under the experimental conditions, that means that the bacteria in this experiment have been evolving for over 65,000 generations. In that time, it has produced a wealth of information about evolutionary processes and spun out countless related experiments. The LTEE is so iconic that you usually don’t have to explain, at least to evolutionary biologists, which long-term evolution experiment you’re talking about. It has also played a role in some controversies, not least the “Lenski affair.”

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Graduate student position in the Nedelcu lab

If you’re a fan of Volvox and the volvocine algae and have recently received an undergraduate degree in biology or a related field, now’s your chance to get serious about studying them. Aurora Nedelcu is looking for a graduate student to join her lab at the University of New Brunswick. Professor Nedelcu is a major player in the Volvox community, having published foundational papers on diverse aspects of volvocine biology and organized the first two international Volvox meetings. This is a great opportunity to join a vibrant and growing research community:

A graduate student position is available in the laboratory of Aurora Nedelcu, in the Department of Biology at the University of New Brunswick, Fredericton, CANADA. Research in our laboratory is directed towards understanding general, fundamental issues in evolution – such as the evolution of multicellularity, development, cell differentiation, sex, programmed cell death, altruism.  Our research is rooted in the framework of transitions in individuality and evolution of complexity (at a conceptual level), and of cellular responses to stress (at a more mechanistic level).  The experimental model-system we are currently using is the green algal group, Volvocales (see our Volvocales Information Project; http://www.unbf.ca/vip). Highly motivated students with interests in either theoretical/genomics or experimental/molecular approaches, and previous research experience are encouraged to apply. Interested applicants should e-mail a CV, summary of research experience and interests, unofficial transcripts, and contact information for three referees to anedelcu@unb.ca.

Applicants should meet the minimum requirements for acceptance in the Biology Department Graduate Program (see http://www2.unb.ca/biology/Degree_Info/Graduate.html).

Chance favors the minute animalcule: John Tyler Bonner on randomness

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A colleague recently (well, not that recently; sorry, Art) lent me a copy of John Tyler Bonner’s latest book, Randomness in Evolution. Dr. Bonner is emeritus faculty at Princeton University, where he has been since 1947, shortly after World War II interrupted his Ph.D. studies. Among many other contributions, Bonner was a pioneer in the development of the social amoeba (or cellular slime mold) Dictyostelium discoideum as a model system for multicellular development and cell-cell signaling. A member of the National Academy of Sciences and a fellow of the American Association for the Advancement of Science, he has published over twenty books and mountains of peer-reviewed papers.

As much as David Kirk’s Volvox, Bonner’s books The Evolution of Complexity and First Signals: The Evolution of Multicellular Development influenced my decision to study Volvox in grad school. I had the pleasure of meeting Dr. Bonner in 2009 when, as a graduate student, I invited him to give a departmental seminar at the University of Arizona. It really was a pleasure; this is someone who thinks deeply about big questions and has made important contributions to understanding many of the answers.

The central argument of the new book is that randomness plays a larger role, relative to natural selection, in the morphology of small organisms than that of large ones. Typically of Bonner’s work, the book is coherent, readable, and full of fascinating examples. Although the cellular slime molds are his primary study organism, Bonner has long had an interest in, and interesting things to say about, Volvox, so I was excited to read his most recent thoughts.

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Pointing out a lie makes me a “fascist apologist”

Over at Discover Institute blog Uncommon Descent, I pointed out that the central claim of Barry Arrington’s post “Further to ‘When You Scratch a Progressive, You Will Find a Fascist Underneath’” is a lie. In response, Arrington calls me and several other commenters “fascist apologists.”

In the original article, Arrington takes issue with the proposals advanced by the Democratic Platform Drafting Committee:

The Democrats’ platform committee says they have a “Final Draft To Advance Progressive Democratic Values.”

Among those progressive values, criminalizing scientific dissent. A plank calling for criminal prosecution of anyone who dissent’s from “the scientific reality of climate change” was adopted with unanimous consent. Progressives do not tolerate dissent even from calling for the persecution of dissenters. [emphasis in the original]

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Why I’ve been so quiet

Teaching my mom a roll cast, Lower Cold Lake, Montana. Photo by Aeravi.

Teaching my mom a roll cast when I should be blogging. Lower Cold Lake, Montana. Photo by Aeravi.

I’m falling way behind on my goal to post three times a week. It’s not because there isn’t cool science to talk about, and it’s not because the Discovery Institute isn’t still wrong. I’m preparing to move the lab to Atlanta near the end of July, and I have family in town, so most of my free time is filled up. There are weddings, floats, fishing, hiking, backpacking, and lots of eating out (don’t cry for me).

I will be going to several meetings this Fall, and the pace of posts will likely pick back up then:

August 4-7: 2nd ASM Conference on Experimental Microbial Evolution in Washington, DC.

August 21-25: CAN-7 team meeting in Missoula, MT.

September 12-15: NASA Executive Council Meeting in Missoula, MT.

September 29-30: Phycomorph in Limassol, Cyprus.

I’m going to Cyprus!

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I’m heading to Limassol, Cyprus at the end of September to talk about Volvox morphology and evolution. Phycomorph is a European group studying seaweed development and reproduction, with a large focus on cultivation. I have an extra day after the meeting, so hopefully I’ll get to explore a bit.

The organizers were initially worried about the high cost of transportation from Missoula, but I had good news for them: I won’t be flying from Missoula but from Atlanta, which is (seriously) half as expensive. The timing of the flights is a bit unfortunate, though, so I’ll have a couple of very long layovers in Heathrow (17 and 20 hours).

 

The preliminary list of confirmed speakers is:

Phycomorph speakers