Hiatus until March

Due to the extended reading break resulting from the abomination and massive waste of taxpayers' dollars that is the fucking Olympics (I guess that's where Genome Canada's funding went instead? Great allocation of resources we've got there!), I will be mostly internetless at my parents' house for the next two weeks, until 01 Mar.

I didn't have any time to schedule posts or anything (INSANE week), so for now just enjoy the blogroll on your right, lurk around the tree, google random protists or whatever. Gonna try to resume half-decent posting after the break. This term just hasn't been very kind to blogging time thus far...

And the next Tree of Eukaryotes release should happen after the first week of March too. There's a few spelling errors in need of attention, and some taxa.

Anyway, have a good two weeks!

Words that need to disappear forever: "Oncogene"

Srsly, what the fuck is an 'oncogene'? Genes involved in cancer DO NOT FORM ANY SORT OF NATURAL CLASS. You can name a gene family based on phylogeny (best), or function (still ok), but involvement in this massive variety of often-unrelated cell-cycle and growth related defects we lump together as 'cancer'? FUCK NO. And "oncoprotein" makes me hurl even farther.

Furthermore, what the flying fuck is a "proto-oncogene"!? A gene that is just poised to cause/inhibit cancer but evolution hasn't allowed it yet?

'Oncogene', 'oncoprotein' and all derivations thereof must be BANNED. There is no value whatsoever to lumping genes into such categories, especially for cancer research. First of all, we have "cancer-related", which has the vague air about it that is justly deserved ('oncogene' sounds so concrete...); second of all, you'd think that something being vaguely involved in cancer somehow must be about the most useless information ever for cancer researchers. Aren't they more interested in how this gene is involved, not that it can somehow participate in this absurdly complicated process ultimately involving the entire fucking cell?

Anyway, my two cents before I run off to a cell physiol exam... aren't you glad you don't have to teach me? =P

Mystery Micrograph #15

Originally posted at 3.23am 07.02.10
You guys are redeeming yourselves after the horrible Auranticordis performance! =P

Next one!

(To be referenced later)

Rest of the plate to come later, if needed.
10.02.2010 update: Part II of plate (should be easy now)

(To be referenced later)

Assorted links: Protaxites, ciliate sex and publication tweets

Still procrastinating with Sunday Protist, which means I'm actually procrastinating with all the real work I should be doing right now...but here's some random stuff my internet wanderings have taken me to!

Giant columnar fungi(Protaxites) may have actually just been rolled mats of liverworts -- Catalogue of Organisms. Intriguing indeed!

Really nice article on ciliate sex by Olivia Judson. When I first read her dino article earlier, I was like "holy crap a science writer actually got the facts straight! o_O" And then I noticed she's a practicing biologist -- never mind the 'writer gets facts straight' headline. On the other hand, 'scientist can actually write' is in itself quite an impressive headline, so it's no less amazing!

#sci140: A paper in 140 characters (new publishing model). A bunch of geeks decide it's about time to put Twitter to good use -- can you summarise a classic paper (or your own) in 133 characters or less? (7 letters go to the hashtag)

Some of my favourites:

• SelectAgent #sci140 Salt of DNA structure= double helix. Strands anti-parallel; has implications. (PS Rosie didn't help)
• michaelgrr We did some messing about with wire and stuff, found double helix fits the Xray patterns of DNA. Rest is obvious. Suck that, Linus! #sci140
• IanMulvany #sci140 dog + bell + food = saliva. Repeat. Eventually dog + bell = saliva, where's my nobel prize?
• labgrrl Oops, Who would've thought that absolute power corrupts absolutely? (Zimbardo,1971) #sci140
• sciencebase: Dropped heavy and light ball at Pisa; saw landed at same time. Peer review problems now, especially after telescope incident. #sci140
• pssalgado cat in box + decay triggered poison. box closed: cat alive & dead. when box opened: cat live or dead #Schrodinger #sci140
• michiexile #sci140 Complete. Concise. Consistent. Pick two. - Gödel 1931
• aeporreca It’s impossible to determine whether a guy with an infinite piece of paper will ever stop doing maths. http://bit.ly/9qKV5E #sci140
• bparsia All your theorems are belong to us (Euclid, 300BC) #sci140
• axiomsofchoice p,q∈ℕ;p²=2q²⊧p∈2ℤ;gcd(p,q)=1⊧q∈2ℤ+1;∵4∣a²,a∈2ℤ⊧q∈2ℤ⊧⊥;∴√2∉ℚ;QED #sci140 http://ff.im/fFJeG
  

Btw, it's a competition. Get crackin'! (I don't have Twitter so I'll just watch...)

A Tree of Eukaryotes v1.1

(This is an updated version of A Tree of Eukarytes v1.0, with modifications discussed below)

A problem with doing this kind of thing while hanging out in this corner of the world is that as soon as you put up a tree, everyone stops you in the hallway and rants about how cruely their pet clade has been mistreated. Ok, I'm exagerrating a bit, well, a lot, but it was still quite amusing. Someone didn't like the reds, someone else didn't like the apis, multiple people pointed out that my microsporidia were screwed up, etc. In other words, instant peer review!

So here's version 1.1, definitely subject to further changes, and in need of more rigorous peer review. Does something bother you? Please let me know!

A Tree of Eukaryotes, v1.1 (Please keep the references box) Feel free to contact me for a higher res image, Blogger seems to shrink large images when uploading...

Changes include:
- redoing the apicomplexan clade (it's even more of a mess than I thought...)
- adding Komokiacea (they're too cute!) and Synurophytes (someone insisted on it...)
- removed the random floating 'Gonyaulacoids' outside the tree
- rebranched kinetoplastids et al. as (diplonemids,(bodonids(p),trypanosomatids)) (must've been asleep when I grouped diplonemids with bodonids...what the hell?)
- reorganised the chlorophytes to make a little more sense visually
- Opalinid clade goes (blastocystis,(opalinea, proteromonas)), not (protero,(blasto,opalinea))
- Collapsed oxymonad clade to please Opisthokont.
- After having been nagged by about 5 different people about it, unbranched Microsporidia from Rozella (again, what was I thinking? Although some papers do put it there...but I consciously disagree with that!) and polytomised with Zygomycetes, as suggested by some local microsporidia geeks + source [26].
- indicated paraphyly for chytrids, bangiophytes and bodonids; removed paraphyly tag from dinophyceae.

Changes I haven't made yet:
- expanding forams (space constraints, see "expansion pack" though)
- adding pteridiophytes to the land plants (everyone seems to be obsessed with them!) -- again, no space!
- adding Collodaria -- space...
- completely change the amoebozoa based on some new unpublished data off a poster, which pretty much changes everything there. Grrrr. I'll get on that after the break...
- adding images -- no time yet! Again, after the break...

Enjoy!

ToE Expansion pack: Foraminifera!

After getting over my little moment of rage there, I decided to go ahead and redo the forams while I could still vaguely remember the phylogeny, sort of. So here comes the Tree of Eukaryotes Expansion Pack: Forams!

Edit 04.04.10: Note that the majority of forams are actually the paraphyletic allogromiids, which, I am told, are to forams as protists are to eukaryotes.

I hope somebody is happy now, after nagging me about the freaking forams for the past two weeks! I know they deserve more space, and I did them an awful injustice by shrinking the entire group to just 'Forams'. Since I still haven't figured out the space problem (should I just shrink everything to 8pt font and add another 100 taxa or so?), I decided to make a special little expansion pack by crudely offending the Radiolaria and Cercozoa. I'd add more images, but it's almost 3am so...later. Also, this tree is liable to be very wrong, so perhaps I don't really need to polish it up just yet. Some groups seemed a bit confusing...

Apparently it's unknown whether Komokians are forams or not, as no living specimen have been recovered (damn suckers insist on living at the very bottom of the ocean), and it's uncertain whether they even have reticulopodia, although presumably they should. Komokians are so awesome...!

No time to finish the Sunday Protist to'night', but I totally just spoiled the surprise. Yes, it'll be a foram. And yes, it will be weird.


Flakowski, J. (2005). ACTIN PHYLOGENY OF FORAMINIFERA The Journal of Foraminiferal Research, 35 (2), 93-102 DOI: 10.2113/35.2.93

HABURA, A., GOLDSTEIN, S., PARFREY, L., & BOWSER, S. (2006). Phylogeny and Ultrastructure of Miliammina fusca: Evidence for Secondary Loss of Calcification in a Miliolid Foraminifer The Journal of Eukaryotic Microbiology, 53 (3), 204-210 DOI: 10.1111/j.1550-7408.2006.00096.x

LONGET, D., & PAWLOWSKI, J. (2007). Higher-level phylogeny of Foraminifera inferred from the RNA polymerase II (RPB1) gene European Journal of Protistology, 43 (3), 171-177 DOI: 10.1016/j.ejop.2007.01.003

Pawlowski, J. (2003). The evolution of early Foraminifera Proceedings of the National Academy of Sciences, 100 (20), 11494-11498 DOI: 10.1073/pnas.2035132100

"Save" is supposed to SAVE, not CRASH!

[Feel free to disregard completely if rants are not your thing. You've been warned ^^]

You know when you've spent like an hour putting together this really epic diagram based on multiple phylogenies of some obscure organisms, and are just about finished, and suddenly remember to save, and you do, AND IT CRASHES WHILE SAVING, THEREBY SENDING YOUR TREE OFF INTO PHYLOHEAVEN/HELL FOR ALL ETERNITY, leaving you with nothing but a row of tabs in your browser where the once-cited papers lie?

Dear PowerPoint,

I understand you were never meant to be used for drawing trees, nor were your authors likely ever aware that such a thing exists as 'phylogeny', BUT FOR FUCK'S SAKE, IS IT REALLY TOO MUCH TO ASK FOR THAT YOU ACTUALLY SAVE WHEN THE SAVE BUTTON IS HIT, AND NOT DO THE EXACT POLAR OPPOSITE???

PS: FUCK YOU.

Ok, now I'm too angry to finish the already-late Sunday Protist. I'm gonna go punch something and/or swear incessantly, and then sleep. In terms of workload, this week is awful, and then I'm going away until early March (fleeing the fucking Olympics*. I really hope it randomly hits +20 for the next few weeks, to totally and definitively screw them over. Apparently we're having an abnormally warm winter, and the snow has melted off the slopes. Actually, that made me feel a little better! =D [/schadenfreude])

Fodor fails EVOL 101 (in other news, water found to be wet...)

This little article from New Scientist has been circulating about the blogosphere lately:

Survival of the fittest theory: Darwinism's limits by Fodor & Piattelli-Palmarini
(via Jerry Coyne's blog)

Yet another case of New Scientist realising that controversy sells, and so does crappy science journalism. I wouldn't call it anti-science, just horrible misinformed and poorly thought out. But that is not about to stop me from unleashing the mother of all rants. Just because I can. I have a midterm tomorrow, a horribly busy week ahead, and am sort of stressed and grumpy, so what better time is there to rip someone's article to shreds?

Now, I must say, as someone who's rather annoyed by the hyper-adaptationist tones both within and outside biological evolution, I must partly sympathise with some of their argument. But they take it too far, and seriously miss the freaking point. Also, there's a fine line between provocative revolutionaries and drama queens, and they crossed it ages ago.

Let's go!

Much of the vast neo-Darwinian literature is distressingly uncritical. The possibility that anything is seriously amiss with Darwin's account of evolution is hardly considered.

Because we have better things to do than worry about what some guy got wrong 150 years ago?

The methodological scepticism that characterises most areas of scientific discourse seems strikingly absent when Darwinism is the topic.

'Darwinism' is a topic? For the love of FSM, can somebody PLEASE enlighten me on what the fuck IS 'Darwinism'? In all my admittedly still short biological training, I have not once come across such a field. I've scoured evolutionary biology far and wide in search of 'Darwinism', and failed to find it. I know of molecular evolutionary biol, I know of population genetics, I know of cell evolution and genomic evolution and ecological evolution, evolutionary psych, evolutionary linguistics, evolutionary you-name-it... but not once have I c0me across this obscure discipline called Darwinism. Seriously, what am I doing wrong? How can I miss something so well-known by the general public and various outsiders?

OH FOR FUCK'S SAKE EVOLUTION DOES NOT EQUAL DARWINISM!!! I'm not even gonna rebutt that paragraph... *headdesk*

But we don't think it is true. A variety of different considerations suggesting that it is not are mounting up.

Ok, I'm ready. This better be good!

Given a certain amount of conceptual and mathematical tinkering, it follows that, all else again being equal, the fitness of the species's phenotype will generally increase over time, and that the phenotypes of each generation will resemble the phenotype of its recent ancestors more than they resemble the phenotypes of its remote ancestors.

Huh? "Species's phenotype"? I'm definitely no population geneticist (and suck at it), but something seems off about that phrase. Phenotype is something an individual has, not a species! Ok, let's assume they meant the species' average phenotype -- still sounds shaky but meh -- they're trying to say the overall fitness with regards to that trait would gradually increase over time? Well, sure, maybe. That's not really the crux of whatever they call 'Darwinism', since survival is much more important than improvement. 'Improvement' isn't actually necessary, but rather a byproduct of survival. "Survival of the good enough".

And as for the last part, phenotypes resembling those of recent ancestors more so than remote ones...isn't that like, basic inheritance, not selection? What the hell does that have to do with anything?

Skinner's theory, though once fashionable, is now widely agreed to be unsustainable, largely because Skinner very much overestimated the contribution that the structure of a creature's environment plays in determining what it learns, and correspondingly very much underestimated the contribution of the internal or "endogenous" variables - including, in particular, innate cognitive structure.

Oh. So that's where we're going! Skinner's behaviourism became unfashionable in cognitive science and psychology (rightly so, but only because it was extreme -- elements of it may still be quite valid!), and since natural selection is an environmental explanation, it ignores inner developmental constraints and self-organising features. Apparently, Fodor and Piattelli-Palmarini think they're being revolutionary.

Stuart Kauffman beat them to it AGES ago. Thing is, he's a real biologist, and has plenty of modeling and real evidence backing his claims. He's does seem a bit loud about his argument, but considering academia is basically a cage of howler monkeys to begin with, that shouldn't translate to OMG DARWIN IS SO DEAD!!1! (no shit?)

I happen to have Kauffman's The Origins of Order: Self organisation and selection in evolution sitting on my desk, for no good reason. (had to prepare a small talk on neutral evolution a while ago, but didn't quite swallow enough of Kauffman's rather terrifying math for it to be of any use at the time...)

First of all, what Kauffman attacks is what he calls the Neo-Darwinian Synthesis (Kauffman 1993 p10), which is the 'marriage' of what was at that time a Darwinian view of evolution, and Mendelian genetics into a new form of evolutionary biology. This was happening around the 60's, when it actually became feasible to talk about the stuff of biological inheritance -- DNA, genes, etc. Prior to that, evolutionary biology was mostly environment-oriented, mainly because that's all they had to work with. Perhaps that's what Fodor and Piattelli-Palmarini call 'Darwinism'?

A while later was Kimura's Neutral Theory, which while being quite accepted today apparently caused an uproar back in the day (1970's). This theory showed how some evolutionary change can happen independently of selection, by being selectively neutral. Later on we get Ohta's Nearly Neutral Theory (reviewed in Zuckerdandl 1996 J Mol Evol), where even slightly deleterious mutations can be tolerated, since selection would act much more strongly on greatly deleterious mutations rather than the slightly bad ones.

A common fallacy is to assume selection acts immediately and absolutely -- that any slightly bad change will automatically be removed. First off, selection takes time, and sure, if you randomly mutate a population and leave it static indefinitely, selection will eventually weed out all deleterious traits, even the very nearly neutral ones. But environments are messy and too turbulent to justify modelling selection as acting indefinitely. Secondly, selection follows a bit of a probability curve -- the strongly deleterious traits are much more likely to be erradicated within a certain unit of time, but that does NOT mean they necessarily will be! In summary, selection is not black-and-white, and plenty of neutral processes lurk in the background.

Even most selectionists would agree that selection is not a black-and-white thing, and that it works in conjunction with other processes. Our disagreement is how much emphasis to place on natural selection, not whether or not it exists!

Back to Kauffman. He states four issues he has with modern (as of 1993) Neo-Darwinian Synthesis (p10):
- Selection as the sole source of order in organisms. I agree there is a little too much emphasis on selection being the source of order -- self-organisation doesn't suddenly stop once selection comes into play! But most biologists recognise that, I think.

- The concept of a linear "genetic program". (the genome as a computer) He argues for a 'parallel distributed regulatory network', which is generally how developmental biologists view development today. In fact, networks are quite the hype these days...

- The tendency to see organisms as "ad hoc contraptions cobbled together by evolution." In other words, organisms being viewed as pure historical accidents. He argues that various changes have different probabilities, and that a likelihood model is more suitable than 'pure randomness'.

- The concept of developmental constraints in evolution. What Kauffman alludes to is this notion that if selective pressures would favour a certain trait, the organism would eventually develop it. Nowadays, with the rise of evo-devo and a slightly better understanding for how development actually works, everyone recognises developmental constraints!

Note that nowhere in there does Kauffman claim that natural selection is 'dead' or 'useless' -- instead, he argues that other processes are not to be ignored. Fodor and Piattelli-Palmarini, on the other hand, are little more than ignorant drama queens.

Speaking of drama queens, back to their article.

Over the aeons of evolutionary time, the interaction of these multiple constraints has produced many viable phenotypes, all compatible with survival and reproduction. Crucially, however, the evolutionary process in such cases is not driven by a struggle for survival and/or for reproduction. Pigs don't have wings, but that's not because winged pigs once lost out to wingless ones. And it's not because the pigs that lacked wings were more fertile than the pigs that had them. There never were any winged pigs because there's no place on pigs for the wings to go. This isn't environmental filtering, it's just physiological and developmental mechanics.

And...? You've just shocked the entire evolutionary biology community! Fuck!

And then there is this in March 2009 from molecular biologist Eugene Koonin, writing in Nucleic Acids Research (vol 37, p 1011): "Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected." There's quite a lot of this sort of thing around these days, and we confidently predict a lot more in the near future.

More SHOCK! OH NOES, NATURAL SELECTION IS DEAD!!! Perhaps instead of criticising us, your should instead focus your energy on criticising your own discipline and your own misinterpretations of evolutionary theory? Just sayin'.

We should stress that every such case (and we argue in our book that free-riding is ubiquitous) is a counter-example to natural selection. Free-riding shows that the general claim that phenotypic traits are selected for their effects on fitness isn't true.

Free-riding as a counter-example to natural selection? Huh? Followed by a complete non-sequitur. My, Jerry Fodor must have gone senile...

The most that natural selection can actually claim is that some phenotypic traits are selected for their effects on fitness; the rest are selected for... well, some other reason entirely, or perhaps for no reason at all.

Doesn't selection by definition act on fitness? If the other traits have nothing to do with fitness, then, by definition, they are not 'selected for'. Why can't we just say 'evolved'?

It's a main claim of our book that, when phenotypic traits are endogenously linked, there is no way that selection can distinguish among them: selection for one selects the others, regardless of their effects on fitness.

Ooooh, you discovered pleiotropy? Congratulations! =D Although the selection part is still muddled up a bit. But yeah, byproduct of selection do happen, quite frequently too. That doesn't mean there is no fitness involved!

Natural selection has shown insidious imperialistic tendencies. The offering of post-hoc explanations of phenotypic traits by reference to their hypothetical effects on fitness in their hypothetical environments of selection has spread from evolutionary theory to a host of other traditional disciplines: philosophy, psychology, anthropology, sociology, and even to aesthetics and theology.

Actually, despite the drama queen -esque language ("insidious imperialistic tendencies" -- what the fuck?), I must kind of agree. Instead of applying evolutionary theory outside biology, the scholars instead just took natural selection, which is but a part of the overall theory. I have issues with that too. But this isn't so much a fault of evolutionary biologists (communication -- sure, but perhaps not so much the field itself) -- but rather the unwillingness of some rash humanities scholars to actually comprehend evolutionary theory prior to shoving it everywhere possible. Natural selection is a powerful concept that does deserve application outside biology, but in conjunction with other parallel processes!

Accordingly, if natural selection disappears from biology, its offshoots in other fields seem likely to disappear as well. This is an outcome much to be desired since, more often than not, these offshoots have proved to be not just post hoc but ad hoc, crude, reductionist, scientistic rather than scientific, shamelessly self-congratulatory, and so wanting in detail that they are bound to accommodate the data, however that data may turn out.

HEY LOOK, WE'RE DRAMA QUEENS! WHEEEEE! Behold our powaz of teh rhetorik! MWAHAHA! But seriously, the very ideo of natural selection disappearing from biology...just...how? Dear FSM, how is that even supposed to be conceived? Any finite system is bound to have selection, just because you will eventually end up with limited resources, and subsequent competition for said limited resources, which will favour entities that are more stable and efficient at procuring said limited resources. If you agree that biological systems are finite (which they ultimately are, to any sane person), then it must follow that there will be competition and selection! It's inherent in the system!

Of course, natural selection is just one process, and that I'll agree with them on (although I seriously doubt that they really understand what they're talking about), and it may perhaps in some cases even not play a major role in order/change in complexity/evolution overall, but it's still there, lurking in the background, and directing evolution when the situation is right.

So it really does matter whether natural selection is true.

How can it be untrue!? I don't get it -- they mean, there is no selection happening, AT ALL? So I guess competition in the business world also goes by some other model, that has nothing to do with natural selection, despite the concept actually originating there? Like...that sentence...makes no sense, actually. They could've asked "whether natural selection is significant in [situation X]" or "whether natural selection is a prominent force" or anything along those lines, but debating its truth value? Huh?

I guess I'm just too scientistically reductionist to comprehend such lofty topics. Oh well.

(I would've typically been more polite about stuff like this, but Jerry Fodor really pisses me off on some other topics too. Don't. Get. Me. Started.)

Mystery Language #01

Ok, let's start easy.

5 points to whoever can tell me what this is, and another 5 for translating the first paragraph!


Meanwhile, let me procrastinate with serious posts by pretending to study for Monday's physchem midterm... *yawn* never mind!

NOTE: "points" do not constitute valid currency anywhere outside this blog, or even inside this blog.

MM#11 Answer: Rhizochromulina: algal amoeba

Remember this from a looooooong time ago?

Rhizochromulina. Mischievously looks like a chlorarachniophyte... [source]

As a warning, about the only marginally comprehensive ochrophyte phylogeny I found was in TC-S & Chao, J Mol Evol. It looks like this, and makes me want to cry:

[no comment needed] (TC-S & Chao 2006 J Mol Evol)

In case those names look simply alien to you, you're not alone. In fact, I wouldn't be surprised if they'd stump some phycologists. Ochrophyte phycologists. This, my friends, is where we enter the bottomless pit of chaos that is Cavalier-Smith Taxonomy. It's a special kind of taxonomy, so I capitalised it.

So Rhizochromulina belongs to Actinochrysia in Alophycidae in Hypogyristea in Marista in Ochrophyta. I wonder if the latter is the only one of those which human beings actually use. Eikrem et al. (2004 Phycologia) put Rhizochromulina and co. in Dictyophyceae, which seems to be the taxon used by the world outside Tom's head. Seems like Dictyophyceae = Actinochrysia exactly; save for a milirank difference. That way, Tom gets to take an old, well-accepted group and liven things up with a fresh name. And get his own attached to it. Damn good deal he's got there...

Anyway back to algal amoebae...Rhizochromulina's fellow Dictyophyceans include the silicoflagellate Dictyocha, a 'heliozoan' Ciliophrys and a loricate flagellate Apedinella[photo]. And Pteridomonas, which appears to be a wannabe Choanoflagellate. Such a small group, such morphological diversity. Although, I don't know whether I can say that yet...

Initially I wanted to do a big overview of Stramenopile (fine, "Heterokont", happy?) amoebae, and take a look at their phylogenetic distribution to try to guess how easy it can be for cells to switch between amoeboid and flagellate forms through their evolution, and whether the easier direction would be from flagellate to amoeba or vice versa. This has some implications in cellular evolution, as well as the overall eukaryotic tree and its much-contested root. TC-S 2009 JEM(free access) argued (sigh.) for an important aspect of the unikont-bikont split being cytoskeletally amoeboid vs. flagellate cell morphologies (see my Naegleria post for further info), as well as evoking lateral transfer of myosin II (a motor protein [mostly] unique to unikonts, that is, opisthokonts like us and amoebozoans(Richards & TC-S 2005 Nature)) to Heteroloboseans (bikonts), enabling their complete transformations between amoebae and flagellates. Ok, take home message: I wanted to have a closer look at the EPIC MESS that is eukaryotic cellular evolution.

I wanted to fix this mess with a group that's well-known, relatively well-studied (or so I thought), with its phylogeny all sorted out. Ooops. Ochrophytes, despite being home for kelps and diatoms and such, do not qualify, apparently -- their phylogeny is a mess, many of their groups completely understudied, and...yeah, my little amoeba exercise kind of failed miserably as I fell deeper and deeper into confusion.

Furthermore, I need to figure out how the various ways of being amoeboid, flagellate, and amoeboflagellate really differ from each other, and how best to classify them to analyse the situation properly. At best, this will take A LOT of reading. But this is overly optimistic -- it assumes that there exists proper reading material in the first place! This story might actually have to wait until we learn more protistan cell biology.

Now that Rhizaria also seems to be among Chromalveolates, things get even weirder. Rhizaria is full of amoebae, full of flagellates, and everything in-between. Although as far as I know, most Rhizarians have at least some flagellate stage, even the Chlorarachniophytes. Rhizaria is also a huge mess, and even more obscure than the Ochrophytes. There's just SO MUCH untapped diversity and opportunity for biologists of all sorts to truly study eukaryotic evolution as it ought to be studied...which is why I get so livid over how cell biology is generally taught -- from this dull, lifeless zoocentric "This gene is linked to cancer" perspective where they seem to think that memorising signal transduction pathways is a worthwhile activity.

No, learning about just how many ways a cell can be is far more worthwhile and educational. It's much more informative to learn biology from a perspective of diversity. I'd argue this is even true for the biomed-oriented spawn of Satan researchers: any kind of biology without comparative work is blind and shortsighted, and to understand how a particular cell type responds in a particular form of cancer, one must first understand how eukaryotic cells work, period. And it's shameful and stupid to foresake the rest of the Eukaryotic Tree when any help is so desperately needed in comprehending the mess that >3 billion years of evolution have left us in.

Enough of my ranting (taking a cell physiol course at the moment, feeling rather sore about the obsession with macrophages and cancer cell signalling)... have another Ochrophyte amoeba:

Chrysamoeba. (Hibberd 1971 Eur J Phycol)

Some Rhizarians look vaguely like that too. Hmmm.

Yeah, I really hit a brick wall with this post. Don't really have the time to sort out messy fields at the moment, as much fun as it is. Anyway, right, midterm...

References:
CAVALIER-SMITH, T. (2009). Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations Journal of Eukaryotic Microbiology, 56 (1), 26-33 DOI: 10.1111/j.1550-7408.2008.00373.x

Cavalier-Smith, T., & Chao, E. (2006). Phylogeny and Megasystematics of Phagotrophic Heterokonts (Kingdom Chromista) Journal of Molecular Evolution, 62 (4), 388-420 DOI: 10.1007/s00239-004-0353-8

Eikrem, W, Romari, K, Latasa, M, Le Gall, F, & et al (2004). Florenciella parvula gen. et sp. nov.(Dictyochophyceae, Heterokontophyta), a small flagellate isolated from the English Channel Phycologia, 43 (6), 658-668

Hibberd, D. (1971). Observations on the cytology and ultrastructure of Chrysamoeba radians Klebs (Chrysophyceae) European Journal of Phycology, 6 (2), 207-223 DOI: 10.1080/00071617100650231

A stats question RE T-tests and U-tests

So I'm in the midst of the "Oh fuck, must get actual numbers and graphs for publication" stage of my project. This means I must not only generate piles of data, but also make it talk, and speak the truth. Which means I get to interrogate it with statistics, mwahaha. I actually enjoy this part of the process, since you can magically convert piles of numbers into pretty p-values and sexy graphs showing how earth-shakingly significant your data is...oh, well, statistically significant anyway. That is, if your stats is being done correctly, otherwise the whole activity is a futile waste of taxpayer dollars, more so than it usually is.

So I noticed that for situations where I'd expect some sort of significance (they're bloody obviously different, but I never thought/said that because I'm a 'good scientist' and all that...), the p-values were...well, maybe a little bit too high. Like, they were kind of insane -- 10^-45? Oh come on... it would be awesome boring if biological data were so clean! But both the t-test, and the Mann-Whitney U test showed extreme significance, with the latter being more trustworthy in my case, or so I've been told (I have a prominent shift in distributions rather than means; that is, cells in the drug treated case get really big, while in the mock they don't get really big.)

So I decided to test the data I know shouldn't be significant -- treatments of two wild-type ecotypes, and another case where the drug had no effect. So here's my data that SHOULDN'T be significant:

The first graph shows means and st dev errorbars, second graph shows quartile box plots of the same data (that is, no obvious shift in distribution either). Then I have t-test results from Excel, which show significance regardless of whether we assume equal or unequal variance, although F-test shows equal var. The Mann-Whitney U-test, while not being as striking as the results for the data that should be significant, is still somewhat... acceptable-ish. That is, 'significant'. But that doesn't correspond well with the data in the graphs, does it?

Would anyone know what the hell is going on here? Could the difference in sample sizes come into play? All involved data has a normal distribution, but under some conditions (not in the data above though), there is evident shift in skew in the data. I was told a U-test should sniff out differences in skew and kurtosis. I ran my data by a stats-ish guy (ok, ecologist...) a while back, and he said there's no doubt my significant data (not shown), is actually significant, but I can't trust my tests if they show 'significance' between wild types (not shown) and treatments that don't make any noticeable difference whatsoever (above).

This is really REALLY frustrating because I have a total of like 10 different lines, each treated and untreated, with massive sample sizes considering the work it takes to get the data (microscopy and measurements and all that), and I'd like to wrap up very soon with a complete graph with significant results pointed out, and finally start writing. This will be my first time writing up a part of a manuscript, so it's really exciting (and scary), but right now I've got damn stats in the way!

And I am aware Excel is not a stats program. We don't have anything else though...

I'd really appreciate any input, thanks! =D (even if it leads to rediscovering that I'm actually a huge idiot...)

UPDATE 07.02.10 2am

Ok, so Aydin recommended PAST, which turns out to be quite a nice stats program =D Thanks!

But it shows the same thing.

Actually, looking at the confidence intervals (and repeating the calculations back in Excel), the 95% CIs don't overlap, nor do the 99% ones. What's even more frustrating, is that the drug that generally causes cells to get bigger (ploidy, etc), in this case "significantly" shows smaller cells. Which is weird. And rubbish.

Ok, fine, this isn't really a proper control. Let's compare our wild type ecotypes -- the ultimate negative control. There's no bloody way Col-0 and Ler (ecotypes) should have different responses in this situation! Right?

Amazingly, it baaaarely scrapes by for 95% confidence! We use 99%, so we can call it non-significant, but still... it shouldn't be anywhere near barely scraping by! I mean, the damn p-values should be like 0.5 or something, no? Again, these are two WILD TYPES! Sketchy...

And, hang on... F-test comes out significant? Owww, headache!

Do I need more data then? It'll take another couple of months to double the sample sizes, especially for these ones, where there's much lower count per view, so I'd have to image waay more specimens. Grrrrr...

OMG, IT DOES HISTOGRAMS? And in a HUMANE way, unlike Excel? Aydin, I owe you for PAST!
So here's the obviously significant case:

The non-significant (histograms can be really misleading when the sample sizes differ, I find...)

And now the really weirdly 'pseudo-significant' case: (again, n = 280, 352)

I can see how there's a bit of a shift, but significant? Really???

Great. So while the phylogeny course has beaten out any faith in phylogenies out of me, now goes my faith in statistics. I mean, this is the thing we're supposed to rely on to avoid introducing our own biases and judgements... but if done wrongly, it can really make a mess. And I suspect I'm not doing something right.

Or am I just being too paranoid?

The long-awaited TC-S paper IS OUT!!!

OMG, yes, it's finally out, in February, just like he said...! Wheeeeee! Featuring that very famous heartwarming diagram style of his! *drools*

*does a happy dance*

The paper I've been dying to read since no less than a YEAR ago...
(TC-S 2009 Biol Direct: Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution) (Alternative title must be "Sex, the universe, and everything")

No, seriously, I've even ranted about it before -- who the hell cites papers from the future?

(TC-S 2010 Biol Direct) My two great fetishes in one diagram -- cell biology and evolution. See, at least someone understand me! Well, would understand if he were even half-aware of my existence... that latter part really needs to be fixed ASAP. Maybe if I magically wake up one day at an ISEP meeting. One can dream...

And I'm late to class. And other obligations. *sob* I won't be able to get to it until tonight. I mean, I'm gonna tend to my actual obligations tonight, yeah, totally...

But today is going to be a great day! The first thing I saw in Google Reader was that paper, so it must be a good sign, right?

Anyone wanna read this along with me, and then we can chat about it? Lab Rat, I'm looking at you =P

Oh and I'm really late to class now... I doubt the prof knows TC-S (or has read his papers anyway), and would therefore be unable to understand and sympathise with me. Sigh, such depraved souls they are, those non-evolutionary biologists. Poor things. If only they'd read from the Book of Tom, and see the light...

Carnival of Evolution #20!

Welcome to Carnival of Evolution #20!
The time has come to analyse and describe the environmental samples that piled up in my inbox throughout the month, kindly donated by my esteemed colleagues. Some of the samples were clearly inorganic matter pretending to be evolution-related, and thus had to be discarded (sorry, but we are trying to stay on topic here...), but the rest of it consists of some intriguing and exciting posts organisms.

Sequence data was extracted using the Copy+Paste Protocol (CPP) devised by [citation forgotten], and then analysed in a sophisticated combination of Notepad, MS Word and Mesquite. My first analysis involved the URLs of the submissions, as they seemed to be at least somewhat conserved. Since this was my first time actually building a tree from scratch (cell biologist here), and since I'm just learning about NNJ, SPR, treelength, maximum parsimony, etc in phylo class, my data is obviously very reliable and makes sense. Clearly, I should now go ahead and reconstruct the history of life, the universe and everything. Without further ado, here are the latest Nature-worthy phylogenies:

MY FIRST PHYLOGENIES EVER! ^_^ Left: Colours mark submissions from the same blog: Yellow - Phylogenomics, Blue - Grrlscientist's blog, Green - Evolving Mind, Red - Pleiotropy. Oh and a clade I missed: (sea-slugs,hi-resolution-evolution) - Adaptive Complexity. Right: Second analysis, a consensus tree of the post 'content' sequences. See text. Blue - omg, a clade! =D With support of... 0.52. Whatever that means, exactly -- doesn't feel too comfy though.
(Blog URL 'sequences' converted to a protein character matrix (fig. S1), gaps removed and tree found via SPR searching for minimum treelength in Mesquite (Maddison WP & Maddison DR 2009)

So Bjørn Østman apparently has a paraphyletic blog. Learn something new every day...

But one gene is never enough, so I went ahead and PCR'd some of the post contents. EVOLUTION was used as primer, and the 40 letters (including gaps) following the first instance of the primer were used in the alignment matrix. No proper alignment was actually done as the data was utterly random, and the non-existant grant did not provide for any extra work. In a couple cases, no instances of EVOLUTION were found, so other primers were picked completely at random. Ignorant and unskilled parsimony-based tree reconstruction was used haphazardly, revealing a rather large clade (fig. 1, right; in blue) that clearly has long reaching scientific significance.

Post Taxonomy
Now that we have a couple utterly nonsensical curious phylogenies, we must sketch a basic taxonomy before we proceed to species descriptions. I will act as an old-fashioned traditional taxonomist and completely and utterly ignore phylogeny in my classification scheme altogether.

So, Cavalier-Smith style: (Note: not approved by ICZN/ICBN, yet)
KINGDOM Evolutionary Biology

INFRAKINGDOM Animal Evolution
SUPERPHYLUM Non-Mammalian Evolution
SUPERPHYLUM Mammalian Evolution
Microphylum Human Evolution

INFRAKINGDOM General Evolution Topics
SUBKINGDOM Genomics
SUBKINGDOM Selection
Phylum Cooperation
Phylum Group Selection
Phylum Evolvability
SUBKINGDOM Symbiosis

KINGDOM Science Communication

PHYLUM Combatting Creationism
PHYLUM Public Education of Evolution

Note: Only some of these will actually be used... I really don't care for ranked taxonomy.

And in case it's not obvious, I am not actually an evolutionary/phylogenetic/systematic biologist. I colour cell structure with GFP and stare at them all day. Also, I pour microtubule-disrupting drugs on my plants and wonder how they die so quickly. So apologies if you're a real phylogenetic biologist/taxonomist and the above made your eyes bleed =P

The Carnival
Let's now describe and analyse our 'samples'.

Since spring shall be on its way eventually soon, we've got cryptochromes and the biology of monarch butterly migration patterns. Turns out that monarchs can actually 'see' the earth's magnetic field! Speaking of which, Grrlscientist also talks about how egg predation has driven the evolution of bird migration patterns. Furthermore, it turns out that colourful feather colouration may be used as an indicator of the male Tit's ability to resist oxidative stress due to increased carotenoid uptake and secretion, in Grrlscientist's "Colourful tits produce speedier sperm". Still on the topic of birds, the Pacific Dunlin employs a weight loss strategy not for cosmetic purposes but rather to avoid predation by Peregrine Falcons, while over on the Galapagos some Darwins finches have developed an immune response to the pox virus while their neighbours on a nearby island have not.

Meanwhile over at Observations of a Nerd we've got a discussion of dog evolution, including a case of stray dogs of [my native] Moscow learning how to navigate our rather elaborate subway system! Furthermore, they've adapted well to coexist with humans, and even keep out the wilder strays from the outskirts, earning some favours from the local politicians. Another wonderful illustration of the power of natural selection! (which, we must remind ourselves, is not the only driver of evolution...) Heading over to coastal wetlands, we've got a post on Terrapin evolution and their adaptations to brackish seawater.

We have a critical discussion of brain size vs. body mass, the evolution of the two, and why one must be careful to note whether the brain size decreased along with body size (retaining proportion), or on its own. The story of Homo florensiensis and brain size evolution depends on which H.erectus ancestor it descended from. In another post on human evolution, we have a discussion about human uniqueness and whether rank insubordination may be something we're particularly good at.

What do the unicellular Hacrobian Hatena and the multicellular photosynthetic sea slug have in common? They are both partners in crime, engaging in kleptoplasty (plastid theft from algae). Furthermore, the sea slug has been found to acquire some plastid genes through lateral gene transfer through viruses! Speaking of genetic evolution, turns out the Y chromosome has a much higher evolutionary rate than other human chromosomes, and David Winter ponders why that may be. Now that we have the tools to fairly cheaply trace evolution and variation on the level of genes, there's been work done on stickleback skeletal evolution showing how they have on several separate occasions happened upon very similar genetic solutions to pelvic reduction.

Another major event recently has been the publication of the first batch of Genomic Encyclopedia of Bacteria and Archaea(GEBA) genomes, featuring a rather awesome tree. Then, we have an interview by Jonathan Eisen of several cichlid researchers about behind-the-scenespublication stories of their research.

Bjørn has found a couple interesting group selection lectures, alluding that perhaps the controversy around it is far too hyped up. (personally, I've avoided the topic altogether because of how polarised it is...) We also have altruism and helpful chimps, suggesting that helping out upon request may well not be limited to humans. We also have a couple posts on the subject of evolvability -- bacteria 'hedging bets'; and mutational robustness not necessarily being a hinderance to the organism's ability to adapt to changing environments, but in fact may even help promote it.

Lastly, we've got some posts on communicating evolution and fighting creationists. Quite shockingly, Texas is still fighting reason and good sense. Who'dathunk? And how can creationists get so fixated on evolution when developmental biology is similarly complex and 'unlikely', as Bjørn points out. All is not well in undergraduate education (I can testify...), and we need to note the frustrations resulting from some major issues with the way it's run, including underfunding and worst of all, students who are ill-prepared from highschool and generally not too curious about topics like evolution (failed by their past education), discussed by an instructor about to approach an into biol course (good luck!).

Sadly, even some proponents of our own side are guilty of miscommunication and outright errors. Dawkins can get so caught up in being defensive about evolution that he misuses words like 'proof' and 'fact', being a little too emphatic for good scientific taste. Evolution is not a 'fact', it's currently the best explanation we have for explaining, well, all of biology, and I'd argue the only framework currently seriously worth considering, by far. Fundamentalists have the facts and certainty, we've given up such luxuries in pursuit of better understanding.

Luckily, we have protists to the rescue. A JEM paper by Mark Farmer and Andrea Habura points out how thoroughly wrong some of the protist-related anti-evolution 'proofs' are. Furthermore, protists have are a wonderland of good examples for supporting and teaching evolution -- unicellular organisms are easier to analyse in large sample sizes, easier to illustrate some points with, and also more familiar to our eukaryotic biases than bacteria. Not to mention really hawt and sexy. To quote something I wrote elsewhere: 'not only should protists be used to ward off some creationist claims, but also to teach biology undergrads, and to promote public interest in biology overall. Sure cancer has its place, but I, perhaps naively, believe that at least some of the public has a latent, untapped fascination with just how weird biology can be. Creationists are far from the first of our concerns -- adressing misinformed biology students and the scientifically-curious public should be a top priority!'

Since you're currently standing on protistophile territory, I'd like to welcome those of you who have sadly been deprived of the wonderful world that is concealed within ~99% of eukaryotic diversity. Furthermore, I think it would be effective to approach some of the aforementioned problems (creationists, but much more importantly, undergrad biology students) by employing some of those wonderful stories, rather than ignoring them for the sake of memorising the insulin pathway MAP kinase cascades. I believe protists (and prokaryotes; basically, a thorough appreciation of diversity) can not only teach a lot about evolution and organismal biology, but also stretch the limits of our wildest imaginations. And that is my main purpose here, which I hope to at least somewhat attain from time to time, despite still just learning about both science writing and protistology (and the rest). All life is wonderful, and it is truly a shame that we tend to ignore the vast majority of it.


In case there's any glaring blatant errors, or if I completely misrepresented your post -- it's 4.30am, I'm getting tired, and stuff happens. But please let me know anyway!

The next Carnival of Evolution (#21) will be hosted on Mauka to Makai; you should go check it out to get ready for the next open season on evolution blogging! Speaking of open season, it's never too early to submit your February posts to the next Carnival of Evolution using this form. Take care and hope to see you around again!

Supplementary Data
Fig S1:

Submitted posts' URL sequences. So pretty!

Mystery Micrograph #14

Apparently the last one was too easy, at least for our resident micropaleontologist. I'll explain it later, but before I bury myself in the bitter products of procrastination (known as work that could've been done much earlier at leisure, but instead will be done in a rush of madness right now... the story of my life, pretty much. Sigh), have another mystery micrograph to play with. These are a single genus.

To be referenced later; all scalebars = 1mm

Apologies for CoE delay!

I'm sorry but I'm gonna have to delay the CoE post by a day... had it planned for tonight, but a whole bunch of other stuff popped up that's actually sort of more important (no offense), including a test worth 10% and a talk I completely forgot about. Oh and some revisions to finish because they were promised today. And it's 10pm already, and I've had more hours of class than sleep, by a factor of 2 -- so my blogging was gonna suck anyway. Would rather attempt to do something actually nice -- expect it tomorrow night! (Pacific Time; that is, morning of the 3rd for most of you...)

Again, really sorry!

Here, have a desmid =D

Micrasterias radiosa. These things can be quite huge (100-300um), even visible to the naked eye as little aquatic green snowflakes in the water...! [source] (Archaeplastida: Charophyte)

Mystery 'Micrograph' #13

This one is more of a macrograph than a micrograph, and for once it may or may not involve a non-protist. This one is actually pretty weird. This is to give some of the sane people non-protistophiles a chance =P Bonus marks for telling me why this organism is weird/interesting.

Distance between lights -- 10cm