Field of Science

Another epic TC-S quote

‘I think it best to put forward simple, detailed and specific hypotheses, since these have a better chance of stimulating (and being refuted or corroborated by) future research than are vague or unnecessarily complicated ones.’ (Cavalier-Smith 1993a p. 339.) (quoting himself in TC-S 2010 Biol Lett supplementary data PAPER.) [emphasis mine]

I'm gonna have to do a live blogging of a reading from the Book of Tom someday. I think that would be epic entertainment!

For those who are confused, may I refer you to:

Simple! (TC-S, 2006 Biol Direct; open access)

Disclaimer: Again, for those 'out of the loop' (so lucky...), this is not an attack against Cavalier-Smith or anything. If I didn't find his stuff interesting and worthwhile, I wouldn't be reading it in the first place. Just sayin', in case someone randomly scolds me for being mean to Tom. Which in itself is a rather humorous concept...

Speaking of which, lemme crudely summarise what the latest TC-S "Eozoa crisis" is about in a couple trees:

Note the Excavates (Euglenozoa+Percolozoa+Metamonads). Left image based on TC-S 2009 JEM(free access), right image on TC-S 2010 Biol. Lett.; some taxa translated to terms people actually use. And yes, I was having too much fun with phylo software again, this time TreeView...

Basically, Tom apparently now thinks the root of Eukarya is in the bikonts, more specifically: between Euglenozoa (eg. Euglena, Trypanosomes) and the rest of Eukaryotes. He renames Excavata to Eozoa, and all other eukaryotes to Neozoa. Some other shit happens, but basically he thinks Euglenozoans are too special. However, it is their 'derivedness' that kind of worries me there -- more special != outgroup (of course he knows that), and perhaps all other things equal, rare 'weirder' things are less likely to be basal than more 'normal' things.

What bugs me here is that he actually MAKES SENSE. This hypothesis is utterly bizzare, strange and absurd. But on the other hand...reading more about might not be. Grrr. This is the main problem with Tom: he says ridiculous things, but throws out some pretty complicated and substantial evidence that takes considerable effort to reject. Even when he's obviously wrong (and probably knows it too). Thus, unlike the low-grade crazies that put out shitty hypotheses that you can throw out in a second and ignore, Tom's craziness is quality. It takes effort to deal with, and a very worthwhile effort.

Until you do a word count on one of his papers (eg. TC-S 2006 Biol Direct) and find out it to be 40K words. Holy shit.

I'll cover this in more detail once the dust in my head settles a little, and once I can slowly start rebuilding my understanding of early eukaryotic evolution after this massive blow. What a way to start off a new year!

PS: Off topic, but go check out this amazingly well-written newspaper article on dinoflagellates -- I'm impressed with the quality of research the author has done! Seldom seen in popular science writing these days...


  1. "Dinoflagellates often replace thymine with something called hydroxymethyluracil. "

    .. wha?

  2. actually, unusual bases are more common than you'd think -- the tRNA has quite a few odd bases (presumably modified after transcription though?), for example. As for DNA, apparently a small portion even of 'boring' genomes like ours contains unusual modified bases. Apparently, trypanosomes modify their thymines too into something else: Lukes et al 2009 PNAS)

    More info (free access):

    the discovery of hydroxymethyluracil in dinos

    Doesn't seem like the cause is particularly well understood, although I am not a biochemist and am currently too lazy to investigate this further...

    So yeah, she didn't make that up ^^

  3. The word verification for this message was "diney"... whyyy? ;-;

  4. lol! Again, deep cosmic significance.

    Why do you see word verification? Is it required for non-google accounts or what? Just curious... *oblivious to the settings on my own freaking blog...*

  5. Ha! "I think it best to put forward simple, detailed and specific hypotheses ... and to make up five million new friggen names for everything" covers it better. I know what you mean about the crazy-that-seems-to-make-sense though, it was the same when I first read the whole rational for why Gram negatives came first.

    I love that article! Found it via twitter just moments before you posted it :)

    (btw, every post on blogger asks for a word recognition before you comment, it's under the comment box and above the 'choose an identity' thing)

  6. I've just realised why TCS sounds so familiar...It's all over my lab notes and it means "Two component system" XD

  7. Cavalier-Smith was in a long-running spat with my former PhD supervisor. I have no idea if the two of them still glower at each other at conferences, but your post brought back memories... some of the happier memories of my time in that lab.

    More evidence that crazy =!= stupid, and that some people can be simultaneously bonkers and brilliant.


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