Heads I win; tails you lose: Evolution News & Views on Gonium, part 1

Figure 6 from Hanschen et al. 2016. Multicellularity hinges on the evolution of cell cycle regulation in a multicellular context with subsequent evolution of cellular differentiation (here, cell size-based) and increased body size.

Figure 6 from Hanschen et al. 2016. Multicellularity hinges on the evolution of cell cycle regulation in a multicellular context with subsequent evolution of cellular differentiation (here, cell size-based) and increased body size.

Remember how I said they’re prolific? Before I’ve even had a chance to write up my thoughts on the Gonium genome paper, Evolution News & Views has already published theirs. The story has also been picked up by the Washington Post, New Historian, GenNews, and ScienceDaily (that last one looks like just a reprint of the press release from University of the Witwatersrand). By the way, the genome paper is open access, so you don’t need a subscription to see it for yourself.

We already know that cdesign proponentsists are not fans of research into the evolution of multicellularity, and that they have trouble understanding it. In an unsigned article on the Gonium genome at ENV, they admit that

After reading this paper, we’re none the wiser.

That’s too bad. I’m here to help.

[Read more…]

One of the problems with a big tent

…is that the people in your tent only share some of your views. And one of the problems with having a blog is that it’s searchable, so that when you say ‘no one in my tent ever said x,’ it’s easy to show that it’s a lie.

Within the intelligent design tent, there are people like Michael Behe, who believe that species change over time and that they evolved from a common ancestor, differing from evolutionary biologists only in their insistence that some aspects of biology must have been designed:

I am not a creationist and have no reason to doubt common descent.

There are also people in the tent like Casey Luskin, Stephen C. Meyer, and Jonathon Wells who doubt, and spend a lot of their time attacking, common descent (see “Intelligent design’s relationship with common descent? It’s complicated.“).

[Read more…]

Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 2

One of the cool things about studying the so-called major transitions is that they are as interesting to philosophers of science as to biologists. So you really can’t help being exposed to the philosophy of science literature, and many (maybe most) biologists in the field cross the lines at least occasionally. I’ve been to both, and I’m here to tell you that philosophy conferences are more fun than biology conferences.

Last time, I briefly summarized the various forms of the major transitions framework and addressed one of O’Malley and Powell‘s criticisms, that the framework is progressivist. Now I’d like to look at their other two problems: lack of unity and missing events. By and large, I agree with these points, although there are some caveats I’d like to point out. Next time, I’ll consider their proposed solution, which I’m afraid I don’t find helpful.

Disunity is actually O’Malley and Powell’s first criticism, but it will be a bit more complicated than progressivism to address, and I was short on time on part 1. Essentially, they are arguing that the major transitions are not a natural kind, philosophese for groupings that belong together because of some fundamental commonality, as opposed to more arbitrary groupings whose members are only superficially similar. So what are the transitions? Here’s the list from the book:

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

Table 1.2 from Maynard Smith J, Szathmáry E (1995) The Major Transitions in Evolution. Oxford University Press, Oxford.

[Read more…]

Gonium genome published

Figure 1 from Hanschen et al. 2016. (a) Evolution of cell cycle control (C), expanded ECM (E) and somatic cells (S) are denoted. (b) Micrographs of Chlamydomonas (green; scale bar, 10 μm), Gonium (blue; scale bar, 10 μm) and Volvox (black; scale bar, 25 μm) show morphological differences.

Figure 1 from Hanschen et al. 2016. (a) Evolution of cell cycle control (C), expanded ECM (E) and somatic cells (S) are denoted. (b) Micrographs of Chlamydomonas (green; scale bar, 10 μm), Gonium (blue; scale bar, 10 μm) and Volvox (black; scale bar, 25 μm) show morphological differences.

I haven’t read it yet and won’t have time today, but the Gonium pectorale genome paper just came out in Nature Communications! Erik Hanschen is the lead author, and the article is open access. I previously reported on Erik’s talk at Volvox 2015:

[Read more…]

Wired was more eloquent…

Macaca_nigra_self-portrait

Self-portrait of a female Celebes crested macaque (Macaca nigra) in North Sulawesi, Indonesia. Public domain image from Wikimedia Commons.

…but I think I was more succinct. Ryan Merkley, CEO of Creative Commons, has a new article about Sci-Hub on Wired:

If it wasn’t so well-established, the traditional model of academic publishing would be considered scandalous. Every year, hundreds of billions in research and data are funded, in whole or in part, with public dollars. We do this because we believe that knowledge is for the public good, but the public gets very little access to the fruits of its investment. In the US, the combined value of government, non-profit, and university-funded research in 2013 was over $158 billion—about a third of all the R&D in the US that year. Publishers acquire this research free of charge, and retain the copyrights, even though the public funded the work. Researchers aren’t paid by publishers for their research as it’s sold piece-by-piece or by subscription through academic journals. The reviewers who evaluate the research aren’t paid either. So we pay for it, and then we have to pay again if we want to read it.

My slightly abridged version of this sentiment [PG-13 below the fold]:

[Read more…]

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.

[Read more…]

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.

[Read more…]

Dual first authors

Thunderdome

A forthcoming paper in Philosophy of Science has dual first authors, Kate E. Lynch and Pierrick Bourrat (I’ve written about Dr. Bourrat’s work previously, which is part of the reason this is on my radar):

Author order has been decided randomly, therefore both authors are first authors. KEL and PB contributed equally to the manuscript. KEL’s distinct contribution was the ideas developed in Section 3. PB’s distinct contribution was the ideas developed in sections 4 and 5 and the equations in Section 3. Other sections received equal contributions from both authors.

[Read more…]

Intelligent design’s double standard

Double Tourbillon 30° mechanism by Greubel Forsey. Creative Commons image from Wikimedia.

Double Tourbillon 30° mechanism by Greubel Forsey. Creative Commons image from Wikimedia.

Despite protests to the contrary, intelligent design is a god of the gaps argument. Take a look at Discovery Institute blogs, and a large portion of the posts are essentially arguing that some aspect of biology or biochemistry is really, really complicated (for example, Howard Glicksman’s posts at Evolution News & Views). As if there are bunches of evolutionary biologists running around saying life is simple. So most intelligent design arguments boil down to “there’s no plausible evolutionary explanation for this aspect of biology, therefore it must have been designed.” And cdesign proponentsists insist on a high standard of evidence to consider an evolutionary explanation plausible. For example, here’s Michael Behe’s standard for believing that “…complex biochemical systems could arise by a random mutation and natural selection…”:

[Read more…]