Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 1

The so-called ‘Major Transitions’ framework is an attempt to explain the hierarchical structure of life on Earth: genes within chromosomes, chromosomes within cells, cells within cells (eukaryotic cells), individuals within sexual partnerships, cells within multicellular organisms, and organisms within societies. The best-known attempt to unify the origins of these relationships is a book by John Maynard Smith* and Eörs Szathmáry, The Major Transitions in Evolution.

MajorTransitionsCover

First published in 1995, the book focused on the origins of these hierarchical levels, connecting them with the unifying theme that

…entities that were capable of independent replication before the transition can replicate only as part of a larger whole after it.

For example, after a transition from unicellular to multicellular organisms (there were several), cellular reproduction either contributes to the growth of the organism or to production of new multicellular organisms.

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So much wrong

Say what you want about the Discovery Institute; they are prolific! Evolution News & Views alone publishes several articles a day. I’m lucky if I can crank out three a week, and I try to limit the proportion that are about cdesign proponentsists being wrong. It’s a continual temptation, because those posts are easier to write than, say, digging into a peer-reviewed article. PZ promises me that blogging on FtB will eventually earn me enough to buy a cup of coffee, but I have a job. All of this means that I have to let a lot of big, juicy targets sail by. So, quickly:

DentonLeaves

Thank you, Michael Denton; no evolutionary biologist ever considered the possibility that not everything is adaptive. To answer your question, some aspects of leaf shape are adaptive, some are not. Next.

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Intelligent design’s relationship with common descent? It’s complicated.

Noah's Ark by Edward Hicks, 1845. Public domain image from Wikimedia Commons.

Noah’s Ark by Edward Hicks, 1845. Public domain image from Wikimedia Commons.

Cdesign proponentsists frequently claim that intelligent design is not creationism. For example, David Klinghoffer says:

…intelligent design is not the same thing as creationism.

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Pleodorina starrii

32- and 64-celled colonies of Pleodorina starrii.

32- and 64-celled colonies of Pleodorina starrii. Not to scale. Creative Commons License
Pleodorina starrii by Matthew Herron is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

I spent a year in graduate school trying to cross male and female strains of the volvocine green alga Pleodorina californica. A year. I did some other stuff in that time, but I spent an awful lot of it trying to convince these algae to get busy. I threw everything I could think of at them: four different mating media, different temperatures, different lighting conditions…nothing worked. I never recovered a single viable zygote. I needed to cross them to generate some genetic variation for an ambitious artificial selection study, my ‘official’ dissertation project. Eventually, my advisor suggested I ask Hisayoshi Nozaki for advice.

There is little doubt that Dr. Nozaki is the world’s leading expert on volvocine biodiversity, having described about half of the known species (see for example New Volvox Species, Volvox ovalis, and African Volvox in Montana). He responded that the strains of Pleodorina californica I had been failing to breed had been collected many years ago and had probably lost the ability to reproduce sexually (a problem I mentioned in Why don’t we revise volvocine taxonomy?). I had been spinning my wheels, never realizing that I had no hope of success. I should have contacted Dr. Nozaki about eleven months earlier.

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Michael Behe’s “secret obsessions”

In his latest post at Evolution News and Views, Michael Behe calls the authors of posts at New Scientist and Genetic Engineering & Biotechnology News ‘crazy’ and ‘clueless’ for associating arguments about the bacterial flagellum with intelligent design (“New Paper on Flagellum Reveals Secret Obsessions“):

Suppose in the course of a pleasant conversation with a colleague you mentioned your vacation last year in Las Vegas. All of a sudden he starts ranting about Area 51 — Vegas is only a few hours away, right? Did you see any lights in the sky? Any military vehicles heading north? You should stay at the Little A’Le’Inn motel like he has six times. You’ll see some funny stuff there.

You’d probably back away slowly, smiling, wishing him a nice day…

[much later] …One crazy person is a coincidence. Two are a trend…What’s more, if you go by what they write, these folks are utterly clueless about what modern ID proponents actually argue. [my emphasis]

The evidence that these authors are crazy and clueless? The New Scientist‘s assertion that the bacterial flagellum is

Loved by creationists, who falsely think they are examples of “intelligent design”

and that of Genetic Engineering & Biotechnology News that

[T]he bacterial flagellum has been at the center of the thinly veiled creationism movement called intelligent design. Subscribers to this belief system have erroneously postulated that the flagellar motor system is “irreducibly complex” and could not have come about through Darwinian evolutionary mechanisms….It is doubtful these findings will sway the opinion of its detractors, yet they do make it extremely more difficult for them to make their case.

Seriously, that is the sum total of the evidence that these authors are ‘crazy’ and ‘clueless’ on the order of UFO true believers. A bit hyperbolic, I think. But where did these clueless authors get their crazy idea to associate the bacterial flagellum with intelligent design?

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Origins of the sexes: Takashi Hamaji on mating type determination

The evolution of sex is one of the big outstanding problems in evolutionary biology. The origin of sex is one of Maynard Smith and Szathmáry’s “Major Transitions,” on which I’m currently teaching a course here at the University of Montana. Our discussion of sex luckily coincided with the visit of the grad-invited Distinguished Speaker, Sally Otto, an important theorist on this topic (among others). Dr. Otto generously agreed to join us for the discussion, which turned out to be one of the best we’ve had.

A related problem to the origin of sex is the origin of males and females. Sexual reproduction doesn’t always involve males and females: lots of species that don’t even have males and females have sex. There are lots of traits that we associate with males and females — fancy plumage, differences in body size and type of genitalia, presence and absence of exaggerated weapons — but what actually defines males and females is differences in gamete size. Animals, plants, and other organisms with males and females are oogamous: males have small, swimming sperm, and females have large, immotile eggs. But lots of single-celled eukaryotes have only one size of gamete. We call these isogamous (‘equal gametes’).

Some volvocine algae are isogamous (such as Chlamydomonas), some are oogamous (such as Volvox), and some (such as Pleodorina) are anisogamous (‘unequal gametes’), meaning that the gametes come in two sizes but both can swim. In spite of not having sexes per se, Chlamydomonas, like a lot of isogamous organisms, comes in two ‘mating types’, which are arbitrarily called ‘plus’ and ‘minus.’ The mating types are self-incompatible, in other words plus can only mate with minus and vice versa.

All this variation in mating systems makes the volvocine algae a great model system for understanding the evolution of sex and the sexes (see ‘Volvox 2015: all about sex‘). We know from previous work that males evolved from the minus mating type and females from the plus in this lineage. But males and females have evolved from isogamous ancestors many times, and to my knowledge we don’t know which came from which for any other group.

Takashi Hamaji and colleagues have just published an analysis of the genomic region that determines mating type in Gonium pectorale, an isogamous alga more closely related to Volvox than to Chlamydomonas.

Figure 1 from Hamaji et al 2016. A schematic diagram for phylogenetic relationships of selected volvocine species based on Nozaki et al. (2000); Herron and Michod (2008). The top row illustrates gamete type and structure. Tubular mating structures in isogamous gametes are indicated with red bars at the flagellar base. The possession of a MID gene is shown next to the minus mating type or male gametes. The lower row of cartoons depicts vegetative morphology (not to scale) for the indicated species.

Figure 1 from Hamaji et al 2016. A schematic diagram for phylogenetic relationships of selected volvocine species based on Nozaki et al. (2000); Herron and Michod (2008). The top row illustrates gamete type and structure. Tubular mating structures in isogamous gametes are indicated with red bars at the flagellar base. The possession of a MID gene is shown next to the minus mating type or male gametes. The lower row of cartoons depicts vegetative morphology (not to scale) for the indicated species.

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Changing into my old genes: Betül Kaçar’s molecular paleontology

Tape of life logo

Betül Kaçar has posted another preprint to bioRxiv describing her work combining molecular paleontology with experimental evolution. I’ve written about Dr. Kaçar’s research, and the Discovery Institute’s bizarre interpretations, before, and I won’t be surprised if the cdesign proponentsists feel compelled to respond again.

The new preprint describes experimental evolution in E. coli bacteria genetically engineered to express an ancient protein in place of its modern counterpart. The gene encoding the protein, Elongation Factor Tu (EF-Tu), exists in two copies in the wild-type E. coli genome. Dr. Kaçar’s team deleted one copy and replaced the other with a gene sequence inferred to be similar to that in E. coli‘s ancestor from 700 million years ago.

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Levels of selection in biofilms: Ellen Clarke on individuality

Pseudomonas biofilm. From Spiers et al. 2013.

Pseudomonas biofilm. From Spiers et al. 2013.

The question of what constitutes a biological individual is intimately entangled with questions about levels of selection. Many authors implicitly or explicitly treat individuals as units of evolution or some variation on this theme. A recent appreciation for the complexity of bacterial biofilms has led to comparisons with multicellular organisms. A recent paper by Ellen Clarke bucks this trend by claiming that multispecies biofilms are not evolutionary individuals.

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The flip side of the Galileo Gambit: Denyse O’Leary on multicellularity

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. Pink sticks show GMP; green ribbon shows Pins backbone, with the side chains of all Pins residues that contact the GK protein shown as sticks. The phosphate group on GMP and on Pins residue 436 are shown as orange and red sticks. Black dotted lines, protein-ligand hydrogen bonds. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. The binding modes of extant gk enzymes and GKPIDs are similar and support the same conclusions (see Figure 7—figure supplement 1). (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Figure 7 from Anderson et al. 2016. Evolution of GKPID’s new function by unveiling a latent protein-binding site. (A) The binding surface for Pins in GKPIDs is derived from the GMP-binding surface of gk enzymes. Homology models of Anc-gkdup (left) and Anc-GK1PID (right) are shown as white surface, with all side chains that contact either GMP or Pins as yellow sticks. In the AncGK1PID structure , substitutions at sites in the binding interface are shaded red, including key substitution s36P. (B) The structure of the hinge and GMP/Pins-binding lobes is conserved between the Pins-bound GKPID (blue, rat Dlg, 3UAT), the apo-gk enzyme (brown, S. cerevisiae guanylate kinase 1EX6), and the apo-gk-s36P mutant (gray, 4F4J), all in the open conformation.

Cdesign proponentsists really don’t seem to like research on the evolution of multicellularity. Pretty much any time real scientists learn something new about the origins of multicellularity, writers on intelligent design blogs Evolution News & Views and Uncommon Descent feel compelled to tell us why it’s wrong (for example, here, here, here, here, here, here, here, here, here, here, here, here, and here).

So I shouldn’t be surprised that Denyse O’Leary has weighed in on the latest work out of Ken Prehoda’s lab, in which Prehoda and colleagues identified a mutation crucial for forming and maintaining tissues in animals. Worse, from O’Leary’s point of view, the article describes the evolution of a new protein function, which is anathema to intelligent design thinkers. To say this post is badly argued is overly generous; it’s absolutely devoid of any substantive argument.

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