Test post: featured images working properly (?)

The last couple of posts have shown up in my feed reader the way I always thought they should: with the image I chose in WordPress as the “Featured Image.” In the past, they have included the first image, no image, or the FreeThought blogs logo.

HelloWorld

I don’t see what the point of identifying an image as “Featured” is if it doesn’t show up in the rss feed. I hope this means I can count on this to happen in the future. Let’s see…I’ve included one image in this post and identified a different image (of the rss icon) as the Featured Image. [Read more…]

Buy your Ph.D.

100 pages ought to do it, I think. If you’re worried that that won’t pass the weight test, just add on a great big appendix; nobody’s going to read it. Think of the time and money you can save! Think of the poor slobs pipetting their youth away while you’re partying. Don’t think about how your committee is going to react to a data-free dissertation at your defense. What can they say? They have to pass you; it’s 200 pages!

StudyBay

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Thoughts on a year of blogging

Facebook reminded me the other day that it’s been a year since I started the original Fierce Roller blog. I didn’t know back then if I’d stick to it this long, and I still don’t know if I’ll keep it up another year. One step at a time.

HelloWorld

My very first blog post.

What is Fierce Roller, exactly? I guess it’s a few different things. One of the ideas from the start was to be a service to the Volvox community, reporting new papers, meetings, and news relating to volvocine algae. But that has only been one aspect. It is also a place for me to talk about my research interests, both scientific and philosophical. Scientific usually means that it has to do with the so-called ‘major transitions’ or related evolutionary themes. I wish I could cover this topic more thoroughly, but it has become a big subfield within evolutionary biology, and I can’t possibly keep up with the relative flood of papers. Philosophical usually means that it has to do with the one discussion in the philosophy of science that I’ve contributed to, about the meaning of biological individuality. There is also, of course, a thread of skepticism, occasionally about ‘alternative’ medicine, but usually responding to creationist arguments.

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Heads I win; tails you lose redux

Image from www.twoheadedquarter.net.

Image from www.twoheadedquarter.net. Only $6.95!

I have previously complained that, for cdesign proponentsists,

…if multicellularity is really complicated, that’s evidence for intelligent design. But if multicellularity is really simple, that’s evidence for intelligent design.

Now here’s another example of this logic. Fellows of the Discovery Institute have been arguing for some time that the human and chimpanzee genomes differ by more than is usually reported, and that this (of course) supports intelligent design. [Read more…]

Please stop calling them pond scum

Gonium pectorale. Credit: Kansas State University.

Gonium pectorale. Credit: Kansas State University.

Yes, they live in ponds; no they don’t form any kind of scum. The press release from Kansas State on the Gonium genome paper, which is reprinted here, here, and here, is titled “Pond scum and the gene pool: One critical gene in green algae responsible for multicellular evolution, understanding of cancer origin.” Gonium forms planktonic colonies of (usually) 8, 16, or 32 cells that swim under their own power and exhibit phototaxis (they’ll swim toward a light source). They are not pond scum. ‘Algae’ and ‘pond scum’ are not synonyms, dig? Leaving aside the distinction between algae and cyanobacteria, calling Gonium pond scum is like saying pineapples are lemons (because both are fruits).

Also…cancer origin, really? You went there? The word ‘cancer’ does not appear in the paper except in the funding acknowledgements (Bradley Olson is partly funded by the KSU Johnson Cancer Center).

Heads I win; tails you lose: Evolution News & Views on Gonium, part 2: Model systems and gene duplication

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Figure 2 from Hanschen et al. 2016. (a) Predicted number of genes in each phylostratum (PS1–PS9) for Chlamydomonas, Gonium and Volvox. (b) Heatmap of transcription factor abundance for all green algae. Significant over- (+) and under-representation (−) in colonial/multicellular lineages (Gonium and Volvox) is denoted (G test of independence, α=0.05). Rows are clustered (left), an accepted phylogeny is depicted (top). (c) Phylogenetic analysis of gene family evolution. Bars to the left and right of the vertical axis denote the lost and gained gene families respectively, relative to its parental node. (d) Venn diagram of the species distribution of Pfam A domains unique to the volvocine algae.

Erik Hanschen, the lead author on the Gonium genome paper, is also an old friend of mine from when we were both in Michael Doebeli’s lab at the University of British Columbia. He kindly agreed to write a guest post responding to Evolution News and Views‘ misunderstandings of his paper. Everything below the fold was written by Erik:

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Time for a revision? Maureen O’Malley and Russell Powell on Major Transitions, part 3

Maureen O’Malley and Russell Powell say that the major transitions framework is in need of repair. They have a point, or rather several good points. I have looked at their criticisms of three different versions (the original framework as laid out in the book by John Maynard Smith and Eörs Szathmáry, Rick Michod’s ‘evolutionary transitions in individuality‘ framework, and Szathmáry’s revised ‘Major Transitions 2.0‘). But what is their proposed fix, and will it have the intended effect?

Figure 4 from O'Malley and Powell 2016. Two major aeons of evolution (modified from Falkowski 2006). ‘Gya’ stands for ‘billion years ago’; the date for the origin of photosynthesis may need to be pushed back (see Crowe et al. 2013).

Figure 4 from O’Malley and Powell 2016. Two major aeons of evolution (modified from Falkowski 2006). ‘Gya’ stands for ‘billion years ago’; the date for the origin of photosynthesis may need to be pushed back (see Crowe et al. 2013).

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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 paperEvolution News & Views has already published theirs. The story has also been picked up by the Washington PostNew HistorianGenNews, 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.

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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.“).

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