Clearing up eukaryotic life histories

I can still vaguely recall the horrid hell that was my second year "non-vascular 'plant'" course (valid contender for most polyphyletic course in existence...) - amid the poorly explained phylogenetic clusterfuck, we also had to cram life cycle diagrams from hell. Ever thought red algae looked cute? Not quite so much after realising you get three fundamental life cycle phases to plow through...the night before a final, as it always is. In hindsight, it actually makes a lot of sense, once you grasp some basic principles. Somehow, I missed those the first time around, and then wondered what the hell went wrong.

Warning: This is a bit of a rant. For the meat, skip to the figure.

The damnation

One of those key concepts is the haploid-diploid variation found in many, if not most (if not, secretly, all) eukaryotes. You know the whole thing with syngamy and meiosis and gametic vs. zygotic vs. sporic life histories. You may even wish I hadn't reminded you. Click here if you'd like to experience the wonderful feeling of intense confusion again. So basically, eukaryotes can be haploid or diploid. Typically they have ways of switching between the two phases: diploid --> haploid = meiosis (typically), haploid --> diploid = syngamy (again, roughly). To make things more fun, there may also be several distinct diploid and haploid stages, but let's ignore those for now. Now, it logically follows that there may be variation in how 'prevalent' a certain stage is for various organisms. Let's call it the 'dominant' stage, just for kicks.

Now, how do you define 'dominant'? Well, for humans, it's obviously the part of your life you're an 'individual'. Ok this gets weird when said 'individuals' can clone themselves; also, a bit too philosophical. Let's reword that: It's obviously the stage in your life you're multicellular and big and stuff. Baker's yeast, for example... hang on, what's the big multicellular stage in yeast? Errr... scratch that. Ok, the stage an organism spends most of its time in. Great, works so far. Yeast is most usually haploid. What about moss? It's roughly equal (for the sake of the argument) in both haploid and diploid stages. So it's sporic.

I admit to being a little slow at times, but that seriously confused the fuck out of me -- it seemed arbitrary! How exactly do you decide whether an organism has one or multiple "dominant" stages?

We've been told to "look where meiosis happens". Now this is where it becomes absolute and total mindfuck, on steroids and LSD. Remember the 'gametic', 'zygotic' and 'sporic' life histories? You know what else they're officially(!) called? Gametic, zygotic and sporic...MEIOSES. That's right. We have gametic meiosis, zygotic meiosis and sporic meiosis. Now, sit back and savour the absolute chaos that this naturally incites in young minds yet to be protected by the hard-ass defensive shell your brain produces from years of bitter academic cynicism.

Done? Borderline mental abuse, ain't it?

Of course, while none of those terms have a single redeeming quality besides being physically pronounceable, the worst, by far, is 'gametic meiosis'. Last time I checked, there are no documented case of haploid cells consistently/normally undergoing meiosis. (allowing it has somehow been induced artificially in haploids - who knows) So that's absurd. Even speaking from a field where biological "laws" need not apply. I'm happy to know that someone with qualifications agrees with this, and also has a nice rant on the topic. Of course, I'd say we should do away with 'gametic', 'zygotic' and 'sporic' altogether, but more on that later.

We've also been told "the big, obvious stage [presumably, multicellular] is dominant" Again, last time I checked, Chlamydomonas doesn't exactly jump out of the culture medium and grow before you into a giant... SuperChlamy... or something. That would be really cool for a cartoon character, but most life doesn't exactly strive to be visible to the human eye or anything. In fact, it's much better to not be...

A slightly more sensible point was "look where feeding happens". Great, so sperm are now a dominant stage? If I recall, they do absorb nutrients. Are we gonna go as far as define what manner the nutrients must be obtained in? The lesser known life of Dictyostelium involves cuddling up with a mate, fusing, forming a cyst and then baiting unsuspecting haploid dictys with cAMP...to devour them!

How about "the stage that can live freely"? Well, then many parasites now have no life, and are very sad. Or "the stage that lasts the longest". Well, many things can fuck, encyst, and hang out for what is an eternity compared to their mitotic cycles. Some organisms can spend more time in resting stages than in active ones - ever wondered how a puddle can come back to life as quickly as it dries up?

In the end, I figured this was more of a fuzzy philosophical question, with ultimately everything being somewhat sporic-

Salvation at last!

-until randomly wandering across this neat little diagram today:

A sensible summary of a) Haplontic, b) Haplodiplontic and c) Diplontic life histories. ( Houdan et al 2004 Syst Biodiv based on (and greatly improved from, IMO) Valero et al. 1992 TrEE)

Do you see the difference? At last, a clear, crisp definition! The dominant stage is the one where mitosis occurs, duh! Perhaps it'd help to add 'reproductive' meiosis, to take care of those pesky little exceptions (some multicellular lineages). And personally, I prefer 'haplontic' vs. 'zygotic'. Zygotic sounds very diploid to me. That term owes me a nice chunk of my grade for that 'non-vascular plant' course. 'Haplodiplontic' is wonderful too as you don't have to sit there wondering what a 'spore' is. It's straightforward, concise and universally applicable.

Humans? Diplontic - sperm and eggs don't reproduce mitotically. Dictyostelium? Haplontic - diploid stage quickly followed by meiosis without any mitotic divisions. Moss? Haplodiplontic - both haploid and diploid forms divide mitotically, in this case to form large multicellular organisms. Our favourite beer-making Saccharomyces? Haplodiplontic, actually - it can happily reproduce mitotically in haploid and diploid stages! Red algae? Don't ever remind me. But haplodiplontic as well. A very convoluted form thereof. Pfiesteria-aka-lets-cram-every-possible-eukaryotic-way-of-being-into-one-organism? (yup, that was [reportedly; some doubts RE amoebae] 24 distinct life cycle stages) Appears to be haplontic as a typical dino.)

The original source of the above diagram still makes the usual mistakes of skipping stages taken for granted and relying much too heavily on metazoa, fungi and land plants for explanation (and using Margulis' 'protoctists', ewww...) As per usual, a protistologist comes along and makes everything better! =D

Ah the legacies biology's phylogenetically myopic traditions have left us!

Yet another rant about teaching...

I'm slowly beginning to believe in the following principle: If [caring] students don't understand something, it's either wrong or taught poorly. Usually, but not always, the latter. Science is seriously not that complicated. At all. Just that we humans are fucking abysmal at explaining it. And since most teaching seems to be vertically inherited, poor approaches to certain topics are often maintained due to purely historical reasons. All too often it is perpetrated in the same form the teacher once received it as a student; and since those who make it in academia tend to be those who can grasp concepts despite the poor teaching (sigh...doesn't bode well for me =( ), they are perhaps somewhat oblivious to how cumbersome their inherited approach is.

As much as I love research, I still think teaching is a more pressing priority for academic science.

(Personally, I tend to think of everything from a cellular perspective. Furthermore, if you tell me something that only applies to a small polyphyletic assemblage of conspicuously sized organisms, I tend to file it away as an exception and forget. (I like exceptions, but only when aware of the general principles that go along with them) Furthermore, that 'non-vascular plants' course revolved predominantly around terminology, most of which I immediately forgot after the final. Or even before the final. Hell if I remember what an 'archaegonium' is, and how it differs from a 'sporocarp' or whatever. Especially when the same things get different names depending on who studies them. In fact, don't expect me to remember taxon-specific terms for general things even for organisms I actively study (and like!). I won't. Even though everyone claims to 'know' this, students (and conference attendees, etc) tend to take away concepts, not terminology. Seriously. We all have our favourite jargon, but please pity the uninitiated!)

Now, food for thought: how did a student just plow through four years of biology courses without properly understanding eukaryotic life histories? Our education system is truly scary...

References

Houdan, A., Billard, C., Marie, D., Not, F., Sez, A., Young, J., & Probert, I. (2003). Holococcolithophore-heterococcolithophore (Haptophyta) life cycles: flow cytometric analysis of relative ploidy levels Systematics and Biodiversity, 1 (4), 453-465 DOI: 10.1017/S1477200003001270

Valero, M. (1992). Evolution of alternation of haploid and diploid phases in life cycles Trends in Ecology & Evolution, 7 (1), 25-29 DOI: 10.1016/0169-5347(92)90195-H

On coordinate systems and polarisation in science

While reading and writing about neutral evolution, the theme of polarisation in science (pitting of ideas against each other) comes up a lot. Coincidentally, today I had a discussion with someone about group selection and the tendency of issues in academia (and elsewhere in life) to get grotesquely hyperpolarised. A frequent tactic used perhaps almost subconsciously is to pick the most extreme nutcase example from the side you argue against, and use it to represent the entire subfield. Also known as strawman arguments.

This is done almost ubiquitously in academia, and is often not even recognised as a common phenomenon. Perhaps it's some effect of our tribalistic tendencies, I don't know. Government politics is also quite similar. But at least one could be better informed about how their discipline works to be able to correct for some of it on the individual level. I think these practical aspects of philosophy and sociology of science (real fields, btw -- there are people out there who go into science labs and study labrats...very meta.) should be taught along with basic stats and hypothesis testing. Knowing how your field -- and academia in general -- works is arguably more important than memorising Rho GTPase associated pathways.

Curiously, perhaps some of the vicious arguments in science, such as group-level vs. individual-level selection, are actually similar to arguing over the superiority of cartesian vs. polar coordinates in math, rather than using the optimal one for the given circumstances. That is, if you have a flat plane to model, you'd probably go with cartesian coordinates where it's very easy to describe; defining a plane by polar coordinates is cumbersome and absurd (in most cases). Conversely, describing spherical objects would probably favour polar coordinates which simply work better for that type of thing. Similarly, depending on what you're trying to model, you can pick whether group selection or individual selection best fits the situation. Just like both polar and cartesian coordinates exist in the same reality and are ultimately interconvertible, group and individual selection are also both extant and suitable for different situations. The war is utterly unnecessary.

I like that analogy so much I'll breech my own policy of avoiding exposing who I happen to interact with and attribute it to its author -- Wayne Maddison. Now I wonder how many other raging wars in evolutionary theory and beyond are actually arguing over the existence of polar vs. cartesian coordinate systems... selectionism vs. neutralism is one such area that comes to mind.

People in science seriously need to stop obsessing over having a single all-encompassing model for everything, especially in messy fields like biology (fields that deal with real world data, that is). Theoretically, it all does boil down to quantum physics+relativity (or whatever the hypothetical unified version of that would be), but almost any biologist will tell you we actually could care less. Some models are more practical in given situations than others. That doesn't mean one is absolutely superior to another. In order to get anyone, one has to be rather pragmatic. Unless there are actually people in science who think our business is dealing with The Truth. I sincerely hope only undergrads can be that deluded...

PS: Neutral evol part II on its way, not tonight though: really tired and test tomorrow =(

Biology education needs less knowledge, more curiosity

(RANT ALERT)
Of course, we've all heard about how any system with rigid requirements can be manipulated by the undeserving and crush those who rightfully belong. Ultimately, some balance must be found between rigidity and flexibility to enable creativity and true learning while keeping out various manipulative "quick" elements, all while remaining resistant to subjective biases and 'unfairness'. This problem actually runs even deeper, and seems to be an integral element to many, if not post, political debates plaguing humanity: should every individual have an equal starting point, or an equal end point? In very crude terms, capitalism favours the former while socialism favours the latter. This debate has raged on long before those concepts were even conceived, perhaps as old as communicating structured society itself. Education and academia are no exception.

So to sum up my views on rigidity of rules and regulations: Hell if I know. I'll get back to you once someone definitively and unarguably proves the ultimate superiority of either the capitalistic (equal at start) or socialistic (equal at finish) approach. We've got plenty of time...

But aside from that, there are still plenty of other issues that need attention. And perhaps they are actually much less controversial, and would therefore yield a rather productive pursuit to solve them. Among the many, I can point out two somewhat related problems: the obsession with knowledge, and the failure to encourage or even enable personal curiosity in the students.

The futility of pursuit of knowledge
We all know that universities are centres for the pursuit of knowledge, and that knowledge is priceless, long-lasting and leads to power. However, I'll argue that is not actually the case, or what the case should be anyway. For one thing, knowledge is highly perishable - for example, can you remember what you so desperately crammed (or even wisely accrued gradually over the whole term) for your organic chemistry final? Calculus? Even an exam from your own field? Doesn't it get rather fuzzy? I like to think of stocking up on knowledge as being similar to buying 10 years worth of groceries in a single trip -- would be rather useless as food is perishable. Knowledge too is highly perishable.

That said, there are aspects of knowledge that seem to last. While you probably forgot all the intricate equations and reaction names from o-chem, there may be some foundational relics lingering on in your memory: resonance, or the mutorotation of sugars (had to google to remember the exact term...), or the concept of how electrons can move. The nomenclature probably all but vanished (unless you are a biochemist), although there are some basic concepts that may remain -- the backbone goes last, for example. Now, this is still very unproductive for the countless hours that were spent slaving over the subject. Beyond those very primitive concepts, I can recall very little usable information. It's pretty much impossible for me to read and understand an organic chem paper, which indicates that despite the courses, I'm still embarrassingly illiterate in the field.

I'm no model student (by FAR...heh), nor does my chemistry talent shine particularly brightly (in fact, I REALLY suck at it), but I find it difficult to believe that a better student has a brain that is fundamentally different from mine in what it prefers to retain. Thus, in our above grocery store analogy, what is important is not to grab a crapload of food, nor even remember where all the food is sold (every store is a bit different), but rather to get an idea of the type of food that exists, and how it tends to be organised, and how to find it.

I [used to?] consider myself a cell biologist, and have been involved in research in that field for three years now. I'm not claiming to be anywhere near an expert in ANY of it, but I feel I've been acquiring some 'sense' for how cells work. In any case, I can read cell biology papers with a certain degree of confidence, especially once I look up a few obscure gene names. So I was quite excited for this cell physiology course: I was even prepared to tolerate its anti-comparative 'phylogenetically-uninformed' approach.

Curiously enough, the course is turning out to be a bit of a disaster. Despite my experience in the field, I find it extremely difficult to focus on the content, and feel rather overwhelmed by the sheer volume of stuff. For example, I've actually worked quite a bit with microtubules, doing all sorts of fun (reads: destructive) stuff with them and reading quite a bit of literature. I find cell shaping and the molecular processes behind it simply fascinating. Don't get me started on MTOCs and nucleation and regulation of dynamic instability, etc. Oh, and unlike quite possibly every other student in the class, I've actually watched microtubules grow in real time, in vivo, with my own eyes, and made my own timelapses. And we're going to talk about them -- what could possibly go wrong?

Turns out, when presented with slide after slide of info on various molecules and their interactions and all this data about them, I simply blank out. The material magically becomes beyond me (somehow, it makes A LOT more sense in a dry research paper...), and even a bit...boring! When I first read about gamma-TuRCs (microtubule nucleating complexes present in MTOCs, and regulated in potentially very interesting ways to control cell shape!) in a Nature paper for a lab meeting, I could devour the material rather smoothly and quickly, and it all made sense, and was awesome, and I just couldn't wait to get the time to look up more papers on gamma-TuRCs in various systems and contexts and OMG IT WAS VERY EXCITING! It helped that at the time, we were working on an endomembrane trafficking mutant that showed cell shape defects, so it was interesting to see how this could relate. And we were going to cover this stuff in class!

First off, the whole approach to the cytoskeleton seems to be very bottom-up: first we will examine the chemistry of tubulin polymerisation, and only afterwards [rather briefly] look at how any of this is relevant to cell biology. I prefer a top-down approach: We have a problem -- how does the cell exhibit the necessary cytoskeletal form/organisation and switch between them? Eg. Take plant cells -- the microtubules must go from a fairly chaotic cortical array to then form a band of 'tubes perpendicular to axis, then mitotic spindle (parallel to axis), then phragmoplast (perpendicular), then back to cortical arrays (as in this diagram). Basically, a crapload of moving around. How the hell does this work? First off, these changes require some instability, and yet a fair degree of stability at the same time. This must be regulated. Then properties of tubulin polymerisation, then microtubule-associated proteins, then organisation by nucleation, etc. Rather similar material is covered, but in the latter case we have context. We students know why we should care!

Those generalities are what stick, not mundane specifics. Seriously, am I expected to remember 10 years (or even 10 days) after the final how exactly gamma-tubulin looks like and where the alpha and beta tubulins bind it? No? Then why the hell does the stuff get tested? Even presenting it as an aside is questionable, as it may be distracting despite being potentially cool. I can always look up those details myself. Meanwhile, the question of how cytoskeletal organisation may be regulated by these gamma-TuRCs (eg. adaptor proteins regulating where those TuRCs localise) remains unexplored. Personally, I find the latter a much more memorable and interesting topic, to a cell biologist anyway. And note, much less specific.

(Again, not to pick on this cell physiol class -- despite its fallbacks, it's actually quite a reasonable course compared to some others I've taken. I know the instructor tries; I'm just using this as an example to illustrate issues with the overall prevalent approach in undergrad biology, at least here. I do not intend to slander the course!)

So I think there are roughly three points to make:
- necessity induces relevance, induces better learning
When you have some sort of own particular problem to solve (either research-related or out of personal interest -- artifical problem sets do not work, in my view), you crave any piece of information that can even slightly help you solve the problem. This is why lab research doesn't actually have to be particularly narrow -- a researcher must scour many distant fields in hopes of finding data or ideas that may come in handy with their own problem. And the more distant fields an investigator explores, the more material they have for some potentially awesome idea. Of course, this must be balanced with the requirement to focus, creating a bit of a scale between what I heard being described as "fuzzbrain vs pinhead" mentalities. (you can probably guess what end I gravitate towards...)

- excess information overwhelms, inhibits learning
One of the ways to induce one to seriously loathe Powerpoint is to flash those ridiculously complicated slides with MASSIVE GIGANTIC BLOCKS OF 8PT TEXT. Even if you don't use blocks of text, but instead use 20 concise bullet points per slide, the situation is still rather loathesome. And ineffective. There is a reason for this: the brain actually has limits to how much stuff it can process at once. If you're going at 20 bullets per slide, most of your talk will be a blur to the audience. When cutting down your slides, you often feel very attached to the pieces of information you intended to present. But it helps drammatically to ask yourself: Does anybody actually care? Is it absolutely essential for the main point? Does it really matter how many species are in Phylum Porifera if you're discussing their evolution? This may seem pedantic, but those tiny excess bits of information pile up, and overwhelm.

This applies even more strongly to course lectures. For some reason, all those great skills the research profs must have in presenting at conferences seem to evaporate instantenously in front of a lecture hall. Much irrelevant information is crammed into an already-long (and attention-taxing) lecture, such a protein structures in a cell biol course. As a result, it's hard to keep track of the central ideas, the things that are much like likely to persist past the final.

- understanding is closer to modelling, not knowing facts
Ultimately, we can't really know anything. We can only create models to make predictions from. Luckily, not all models are equally good at making accurate predictions, and thus we have science. Understanding that science -- nay, the very attempt to comprehend our environments -- is essentially an optimisation algorithm (Bayesian MCMC, anyone?) rather than makes it so much more alive and dynamic and interesting! Thus, it is the modelling, even the optimisation seeking algorithms themselves, that must be the focus of education, not memorising the underlying data!

Thus, the point of education is not to fill with knowledge, but rather to provide the tools for acquiring further knowledge (eg. literature research skills) and provide a conceptual outline of where stuff fits, particularly interesting questions and basically providing ideas for further [personal] investigation, which is the topic of my next point. To me, science is more about asking questions than having answers, since seeking the latter invariably leads to the former. And that's what's exciting about it -- if you want to know things, perhaps theology is the better way to go!

I realise I'm not being too concise here myself, but this is a rant, not an article or anything.

The value of pursuit of curiosity
We taught from a very young age that curiosity is dangerous. Children run around asking questions about everything, much to the great annoyance and suffering of their parents. Curiosity leads to nasty things, from injuries to social failures. Unrestrained curiosity is dangerous, and to a large extent, curiosity isn't really a necessity for a good life. In fact, it seems curiosity tends to lead to a poorer quality of life, especially where it results in rather stupid career choices, like academic research. But just like curiosity leads to awful career choices, those careers provide an opportunity for one to achieve fulfillment and gratification from its pursuit. In fact, that's probably the only gratification you can get from an academic job -- it seems to really suck in all other regards.

Most science students will probably eventually wisen up and make good career choices and run the hell away from science, and that's great because they'll be productive and make lots of money and pay taxes and ultimately fund our research. However, while they are in science in whatever form, I think curiosity is essential. Without passionate interest in the subject, the entire degree is just a waste of time. Maybe that's a bit extreme, but I stand by it. I don't understand why someone would suffer through four years of generally horrible classes with dry material just to get a Bachelor's degree if they don't give a flying fuck about the subject. (ignoring the premed problem for now; North Americans really need to start medschool straight from highschool like they do everywhere else in the world...) Diligent studying does not contribute to the giving-a-flying-fuck index (that is, passionate interest), but is instead an execution of one's duties as a student (something I admit to failing miserably at). In fact, I'm gonna get extreme enough to make this statement:

A 'true' biology student must, from time to time, peruse scholarly literature at their own leisure, for fun.

In other words, being a fucking nerd, right? Well, if you chose to study science, being nerd-o-phobic is rather weird, if not just plain dumb. In my eyes, you are not a student of your discipline unless you read relevant materials for your own enjoyment. At the very least, reading popular literature in your field is a start, especially in first and second year. Otherwise, you'd just be flotsam as far as your majors program is concerned.

What would be really cool is if the programs that exercised those awful things called internal admissions (that is, bottlenecks after you start attending the university -- borderline fraud in my opinion, but no one cares...) actually considered the give-a-flying-fuck index when choosing applicants. I think that's more relevant to the program's mandate -- [supposedly] training biologists -- than how well a student performs in the coursework. In other words, the admissions programs should seek out 'nerds', for those are the people who may actually become scientists.

Otherwise, you end up with practising biologists with several years of real research experience and a few hundred of read papers and impending publications of their own locked out of a program full of dull flotsam drifting by oblivious to the awesome wonders of the very fields surrounding them. This may sound quite arrogant, but the onus is on the student to be honest to themselves whether they truly care about their discipline, and then decide whether they should really spend time there. And I once naïvely thought the university would like to educate its future crop of academics. Hah. They'd go after the easier choice even at the expense of their own kind. Which kind of makes sense -- do they really need more competition? Judging from the quality of some of the research out there, probably not...

"The anus was a prerequisite for intelligence" TC-S quote anthology 01

Still working on the Sunday Protist; it's the last week of classes, finals start next week, and I have to sort out some last minute stuff for the seminar we're running next term (finally got it officially up and running in terms of registration!). As you can see, I'm rather swamped here. Also, staying up till 4am working on the Sunday Protist last night was definitely not a splendid idea. I blame TC-S for distracting me with his elaborate hypotheses...

Speaking of which, I've started my very own personal collection of TC-S (Cavalier-Smith, for ye strangers) quotes. When you read most papers, there's just information being spat out and chewed up in more or less mechanistic technical language completely devoid of any human voice. Sometimes the monotony can be interrupted by a burst of "Holy fucking shit did they seriously just write that!? Who the flying fuck gave them a faculty position?" or "This sounds fishy". In contrast, Tom's stuff goes something like:

Looks interesting, let's do this! Ok, so this paper reviews...everything. *cringe* arggghhhh...dense...massive...life-changing hypothesis...crammed into...half a paragraph... OMG ROFLOLOLOL!!!! ...how could you postulate that? Eeeeek, shaky evidence there... dude, you just cited yourself like 10 times in a row!... omg, DEAD ON, YOU GET 'EM TOM! aaaahh....what is that supposed to mean... LOL!!! Wait, did he just write that in a research paper? You cheeky bastard you! ...wow, he reads paleogeology papers!? aaaah ANOTHER DENSE PARAGRAPH OF DOOM! o_O

And so on. See, it's never boring. Which is why despite being notoriously difficult, I actually find his papers easier to work through -- they appeal to my rather-easily dulled attention span. As soon as you begin drifting off somewhere, either you realise you actually needed to thoroughly understand every single sentence to follow along and get hopelessly lost, or you come across something like "The anus was a prerequisite for intelligence", and definitely pay more attention. Which is why he gets an entire label to himself here.

Here's some lines that made me chuckle:
"There was no spinach in the Archaean." (2006 Phil Transac R Soc B, p995 last paragraph)
"But it is not." (concise disagreement) (2006 PTRSB, p997 first paragraph)
"Assumptions that such a neomuran prokaryote existed for hundreds of millions of years are science fiction." (ouch!) (2006 PTRSB, p997 second last paragraph)
"Very likely this anal breakthrough ca. 550 GYr ago stimulated the long-puzzling Cambrian explosion." (2006 PTRSB, p998 second last paragraph)
"The anus was a prerequisite for intelligence; without it, heads and brains would not have evolved." (2006 PTRSB, p998 second last paragraph)
"I consider Brachiozoa, bivalves, Bryozoa [...] were not secondarily beheaded." (2006 PTRSB, p998 second last paragraph)
"Overstatements of gradualism asserting that megaevolution is simply the accumulation of large numbers of small mutations of the same kind as predominate at lower evolutionary levels are simply wrong and must be abandoned." [emphasis mine] (2006 PTRSB, p1000 first paragraph)
"[...] but have been partially forgotten and need restating each generation." (isn't that how science works?) (2006 PTRSB, p1000 last paragraph)
"When I spoke frequently on skeletal DNA over 20 years ago, a common reaction was why not make the nuclear skeleton of protein? One sometimes felt that one's critics would prefer any material but DNA - protein, chitin, even steel, or teflon." (and yes, he refers to himself as 'one' here...) (2005 Annals of Botany, p152 second paragraph)

And a line that makes me feel all warm, fuzzy and happy on the inside: "Understanding microbial megaevolution requires cell biology -- not just biochemistry." (2006 PTRSB, p1000 second last paragraph)

And 'one' must agree with this nice summary of how science academia the world works:

"[...] is not that we do not understand mutations well enough, but that the solution I have offered, and develop further here, is a synthesis drawing upon cell and molecular biology, population and evolutionary biology, developmental biology and ecology; evaluating such a complex synthesis is tough to a specialist in just one area. Population geneticists might prefer to be able to solve evolutionary problems strictly in their own terms and ignore detailed cell biology; cytologists might prefer to do the same and ignore abstruse population genetic arguments; molecular biologists might prefer to sequence DNA and ignore both the cell biology and population biology. But for a deeper understanding we must make the effort to combine the explanatory modes of all relevant disciplines." (2005 Annals of Botany, starting last line of p147)

Despite come across as a bit arrogant there (probably not his intent), he does have a great point. There is so little interaction and integration between the various clans and tribes of biology that one guy can go ahead and monopolize a nice chunk of an integrative field just like that. People complain, but what are they doing about the little issue of each department/discipline burying themselves into a nice comfy hole somewhere, never to venture outside and explore the world beyond. And then the occasional traveler ventures into a foreign burrow, only to be appalled at how horribly their own field gets abused there. Forget the monkeys, a ground squirrel can engage in better interdisciplinary integration =P

Anyway, enough for the first installment. I'm aware some of you guys also have nice TC-S quote collections -- feel free to contribute! There was one Opisthokont had that was oozing Tom-ness all over, can't find it at the moment... *nudge*

And this is definitely getting filed under ResearchBlogging =P

And the Neomuran eukaryogenesis post will be underway after I finish a couple more 70-page reviews of Everything. Well, actually, I should just start writing, probably. Although I did want to read some competing 50 page reviews of 'everything' by other people, although theirs are much more focused.

EDIT 18:26 03.12.09: If you think about it, the "anus was a prerequisite for intelligence" quote actually does make sense: The anus allowed Bilateria to evolve, since the input and output no longer had to be in the same place, thereby drastically altering the fundamental body plan. This freed up one end of the organism to specialise in obtaining food, which is aided by rather elaborate sensing systems. The mouth-containing head end was the focus of increasing cephalisation, eventually resulting in brains. Thus, in a way, the anus is responsible for allowing heads and brains to evolve. Just adding this in to point out that there IS good substance to that quirky TC-S quote, it's not just him going insane or anything (not this time anyway) ^_~

References:
CAVALIER-SMITH, T. (2005). Economy, Speed and Size Matter: Evolutionary Forces Driving Nuclear Genome Miniaturization and Expansion Annals of Botany, 95 (1), 147-175 DOI: 10.1093/aob/mci010

Cavalier-Smith, T. (2006). Cell evolution and Earth history: stasis and revolution Philosophical Transactions of the Royal Society B: Biological Sciences, 361 (1470), 969-1006 DOI: 10.1098/rstb.2006.1842

Citing papers from the future

Ok. I'm getting rather annoyed. SOMEONE keeps on citing papers from the future. HIS OWN papers from the future. Now I know that it's common practice to cite "Bob accepted" or "Bob in review", but "submitted for publication"?! What the fuck? What next, we're gonna have "Smith et al. in preparation" or "Smith et al. writing grant proposal"!?

I really really REALLY want this paper. And I've been waiting for it. Almost the entire year. This one:

Cavalier-Smith T. Intracellular coevolution and the origin the cell nucleus and sex, submitted for publication.

It is only mentioned in ONE PLACE IN THE ENTIRE UNIVERSE: The references section of this wonderful Review of Everything: TC-S 2009 Int J Biochem & Cell Biol Predation and eukaryote cell origins: A coevolutionary perspective. A really nice paper, by the way, except for the whole 'citing papers from the future' drama. Heavily referring to that non-existent paper. Kind of like "Hang on a sec, I'll explain that in the next paper...sometime...eventually..." Note that it was published online in October 2008; I wonder if his Giant Review of Sex, the Universe and Everything has been rejected, considering it's been a year. Anyone happen to know of any updates on that paper?

The suspense is horrible. It's like watching part I of a movie, leaving off at a cliffhanger, and not knowing whether part II will ever come out. Of course, there's always fanfiction. o_O Academic fanfiction. TC-S fanfiction*...oh god, I think I've just discovered a genre that was never meant to exist. What have I done?

As for my Sunday Protist...it's, well, in preparation...

*That's right, I can write MY OWN damn TC-S Reviews of Everything. Ooooh, this could be kinda fun! I could heavily refer to events that would happen in the sequels. And then never write them. Prompting more fanfiction...

Scientists: glorified bureaucrats?

I found this a while ago, but no one, to my knowledge, seems to have blogged about it:

Real Lives and White Lies in the Funding of Scientific Research
The granting system turns young scientists into bureaucrats and then betrays them
Lawrence PA (2009) PLoS Biology 7(9): e1000197 (open access)

Go read the article. It's scary. And seems accurate enough even to an undergrad with limited experience. (Shit, I've been jaded already before even going to grad school...)

Within the article is this quote:

“Scientists might have had a Hippocratic oath of their own. They might have promised their gifts to mankind. But instead, I have fathered a race of inventive dwarfs who can be hired for anything.”—Bertolt Brecht “The Life of Galileo,” version by David Hare

To be fair, doctors aren't exactly saints these days either, being tied up by the madness of insurance policies and a culture that deems it acceptable to SUE(!) a doctor for trying to help a patient. But at least doctors can have their own practice. You pretty much cannot set up your own business as a researcher, unless you're an engineer of sorts. Or if you blatantly contract yourself out to some organisation somewhere, which makes the research even more obviously not objective. There is hardly any real freedom or self-employment. A scientist must become a minion of their funding sources just to make ends meet.

You know how we scientists are fundamentally different from artists, how we hail from different universes and all that? I'm deeply amazed by the parallels between us! It is also nearly impossible for an artist to survive as a self-expressing independent individual - they too must subscribe to fads and funding sources (commissions, etc). They too spend most of their time freaking out over funding rather than actually practising their art. And just like our research, their art is also skewed to please the sugar daddy commissioner. We are just artists who use a different medium with different rules. But many of the common stereotypes used to ward people off foolish career choices (such as those of the fine arts) are eerily as applicable to us. After all, most of us do embark on our chosen foolish careers to satisfy some absurdly naïve inner yearnings and desires; only to find the world absolutely indifferent to our dreams.

We are all but artists-turned-businessmen.

PS: What keeps me trying to stay on this path is the realisation that I'm absolutely worthless for any other kind of job. It's been observed that having limited options often forces one to be quite happy, since there's no point in constantly reflecting upon your choice, so you adapt to it. Yay! =D

Lawrence, P. (2009). Real Lives and White Lies in the Funding of Scientific Research PLoS Biology, 7 (9) DOI: 10.1371/journal.pbio.1000197


EDIT: Speaking of academic issues, we're not so hot on the data sharing either...

I've wondered about this too...

In this week's Nature:

"Overzealous use of decimal places has wrong kind of impact"
by J. M. D. Coey 23 Sep 2009

"Scientists teach students to evaluate critically the significance of their measurements, and to eschew meaningless decimal places thrown up when pocket calculators work out a quotient of two integers. So what are we to make of the recently released impact factors, including Nature's much advertised rating of '31.434' (see also http://www.nature.com/nature/about)? Has Thomson Reuters discovered a protocol that allows it to measure the impact of a journal with an accuracy of 32 p.p.m.?

Quoting this figure conveys the wrong impression — that innumerate marketing is trumping common sense at the heart of science's leading journal."

So what does a thousandth of an impact factor rating look like anyway? Also, how much does Thomson Reuters charge per point? ^_^

Butterfly = Worm + Insect (2009, PNAS)

Shit, is it really that easy to get published? Seriously, what the fuck:

Caterpillars evolved from onychophorans by hybridogenesis
PNAS 2009 AOP

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals. “Caterpillars,” the name for eruciforms with thoracic and abdominal legs, are larvae of lepidopterans, hymenopterans, and mecopterans (scorpionflies). Grubs and maggots, including the larvae of beetles, bees, and flies, evolved from caterpillars by loss of legs. Caterpillar larval organs are dismantled and reconstructed in the pupal phase. Such indirect developmental patterns (metamorphoses) did not originate solely by accumulation of random mutations followed by natural selection; rather they are fully consistent with my concept of evolution by hybridogenesis. Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants. I present a molecular biological research proposal to test my thesis. By my hypothesis 2 recognizable sets of genes are detectable in the genomes of all insects with caterpillar grub- or maggot-like larvae: (i) onychophoran genes that code for proteins determining larval morphology/physiology and (ii) sequentially expressed insect genes that code for adult proteins. The genomes of insects and other animals that, by contrast, entirely lack larvae comprise recognizable sets of genes from single animal common ancestors.

This? In PNAS of all places?

Basically, worm hybridised with insect to make grub-like larval forms. Yeah. I thought "k, maybe the paper itself may have some data, or something", and even VPN'd to get it. It actually wasn't really worth it. At all. There was nothing of substance there .I expected some grotesquely misinterpreted data. It was disappointing: a few drawings pointing out the visual similarities (very robust methodology, especially for constructing phylogenetic trees. Absolutely failproof.), some rather sketchy-looking tree I was too lazy to figure out in the 2min I could spare for that paper. And discussiony-looking text. Kinda reminiscent of a certain creationist 'journal' we do not speak of in fear of death by laughter...


Via Musings of The Mad Biologist, wherein the paper is gently chewed up (could be worse). I really like the phrase 'clusterfuck of genes'. I'll be sure to steal it when necessary. Because that's really the only argument you need against this paper. And also, genes don't work like that. Really, they don't.

Come to think of it, neither does evolution. Or decent science.

A plea to bridge a chasm Why should cell biologists care about evolution?

Our department seems rather heavy on molecular biology, and thus I get plenty of opportunity to hang out with with the molecular evolution and phylogenetics folk. They taught me to appreciate good phylogeny and the importance thereof to work in other fields of biology. Developmental/cell biology is becoming increasingly more 'interphyletic' as the findings in other clades often turn out to be quite relevant throughout the distant tips of the tree.

Chancing upon this many evolutionary protistologists and the likes has led me to read a bit of literature in the field and familiarise myself with some of the works. But being a cell biologist, I've also wandered across some rather interesting developmental/cellular protistology stuff; strangely enough, the evolutionary protistologists seem much less familiar with it.


I've spent the last couple of weeks in the company of cell biologists, mostly metazoan but some fungi, plant and protist people as well. Strangely enough, the protistan cell biologists seemed unfamiliar with many of the evolutionary protistology literature and people! We're talking about what is quite possibly one of the smallest fields in biology in population -- protistology! Shouldn't they really get to know each other and work in an integrated manner?

Furthermore, I had a chat with a prof working on yeast who had the misfortune of revealing himself to be of the crown eukaryote camp (the animals-plants-fungi vs. unicellular organisms model). I politely informed him animals-plants-fungi were not a natural monophyletic group by any means, and that multicellularity evolved upwards of 16 times in the eukaryote kingdom, at at least one other time among the prokaryotes... his response was along the lines of: 'Why should I care? I'm a cell biologist'

Grrr. I am too! Why should we care??? Well, let's see:

- Perhaps we could avoid publically embarassing ourselves by comparing homologous genes between animals, plants and yeasts in that order, and then wondering why the fuck the outter genes share more homology than the crap in the middle!? Every time I see a chart like that being published, I wonder if anyone could please bring those people up to date by about 30 years? It's messy and confusing to use haphazardly organise genes... the subject is a mess by nature, why not use every tool available to clean it up a bit?

- Those of us in the less popular fields often get ideas from the yeast and animal people. Working on the plant cell cycle, for example, requires one to read plenty of opisthokont literature, and even cancer research papers, since much of the work was done in those fields. We're finding some fundamental differences from the opisthokont system, but many principles and gene pathways still apply. Wouldn't it be rather crucial for a plant biologist to be aware that we're more distant from yeasts and animals than the latter are from each other?

- Some of the lesser-known organisms conceal a goldmine of genetic and cellular data. Some of them present us with the special cases we couldn't even dream of. Germline and somatic nuclei within one cell? Ciliates. Unicellular vision? Chlamydomonas, Warnowiid dinoflagelates, Euglenids to name a few. Cells alternative rapidly between amoeboid and flagellate forms with de novo centriole formation? Heteloboseans. A capsule with a coiled up tube that shoots outward at extreme speeds to penetrate the host? Microsporidia. A Martian creature with cortical plates that are opened up by subcellular muscle tissue to engulf prey? Acanthometra. A 'dispersing' 'multicellular' 'colony' of amoebae? Cellular slime moulds. Oh yeah, and a thing that goes plasmodial and then turns inside out to let out dinospores - Amoebophrya (Grell 1973 pp.143-146). Chainmail genomes with RNA editing on crack? Trypanosomes.

Let's stop there. The prof claiming irrelevance of evolution works on post-transcriptional mRNA processing. He should really care about Trypanosomes. Some of their genomes have polycistronic gene clusters, with one promotor to express them all. Well, within a cluster anyway. Traditional promotor-activation focused gene regulation mechanisms more or less fall apart there - the regulation of Trypanosome gene regulation depends largely on mRNA-level and protein-level control. Post-transcriptional mRNA regulation seems to be largely ignored by most, but perhaps it may play a large role outside the Trypanosome clade?

Now, one must be aware of Trypanosome evolution and where the are in the tree to be able to properly generalise and hypothesise from there. If the tree truly does root between unikonts and bikonts, then plant mRNA processing would be expected to be more similar to that of Trypanosomes than that of animals. Or if Tryps were rather distant from everything, then there may be a high likelihood of their regulatory mechanisms being unique...

- Evolutionary biologists need cell biology!!! Organisms are more than just genomes in a lipid bag... cytoplasmic/cortical inheritance (and therefore evolution) happens too, although it is much harder to trace than genomic evolution. So far eukaryotic cellular evolution seems to be dominated by Tom Cavalier-Smith, and that's a sign that it's wild territory desperately in need of hard core research! (According to sources (former student of his), TC-S makes outrageous claims just to make people investigate the topic for him...)


So, in short, cell/developmental and evolutionary biologists - TALK TO EACH OTHER SOMETIME, K?

This gaping chasm is a detriment to progress in both fields. Tribalism has never been of much use to anything but itself, and academic tribalism even more so...


Now there's also medical 'biologists'... but that's a rant for another day.

Homage to RefWorks...

I wish Blogger had RefWorks citing capabilities... I've gotten spoiled by clicking the 'cite' button to cite stuff. Here I actually have to write out the full citations. By hand. The horror.

Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.

Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.

I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:

Cavalier-Smith T: Predation and eukaryote cell origins: A coevolutionary perspective. The International Journal of Biochemistry & Cell Biology 2009, 41: 307-322.

The bold formatting option exists to be used, either for the author or the title. The author is usually first anyway, so it makes more sense to bold the title. The numbered in-text citations [1] make it easy to follow review papers without the clutter of full in-text references. (although the full format comes in handy at time too...) The only issue I have is the year appearing at the end. I prefer the pub year to appear right after the author, since in biology it's fairly important to know when stuff was said/done. I hate that about the wretched MLA: they don't even use year in their in-text refs!

I randomly blogged about citation styles.

I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.

However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!

Now I'm actually gonna do it...

"The Dead Grandmother Problem"

The Dead Grandmother/Exam Syndrome and the Potential Downfall Of American Society

Enjoy!

A rant on pluralism...

Perhaps it really does seem thus far that I'm obsessed with have a research interest in protistology. Unfortunately, I don't have too much time to discuss much else at the moment. Perhaps around midterm time I'll hang out here more, due to alotting more time to procrastination. I can be surprisingly productive during exams, accomplishing a multitude of trivial crap with a blatant omission of study time.

I could rant about that Sarah Palin cow, and her interview of epic fail , but it's a bit depressing, so I won't. Actually, it's mildly terrifying...


Actually, this past Friday I had the opportunity to attend a discussion panel on the integration of sciences and humanities, starring Prof. Steven Pinker (which is the main reason I went...), Richard Shweder and Steven Stitch. Prof. Pinker's talk was awesome, as expected; however, since praise and agreement rarely constitute good writing material, I'd like to share with you the following piece of verbal bowel movement produced by the Shweder guy:

http://www.sci-hum.pwias.ubc.ca/media/pdf/Shweder_prep.mat.II.pdf

His talk was read off a paper pretty much identical to that one, albeit with all the condescending intonations perfectly intact. Though I shall concede that excessive use of Latin-English pidgin does a great job at obscuring vacuous inanities. Unfortunately, too many in the humanities practice this sly art, thereby sadly undermining the rest of the field of any credibility and respect. Examples include postmodernism and the Sokal Affair. Another thing those pidgin Latin fetishists tend to obsess over is contempt towards anything materialistic and scientific. They are fairly wise to do so -- for in proper rigorous 'materialistic' inquiry lies their demise.

I must admit that I had tremendous difficulty following Shweder's talk, even though the two other speakers were very clear and easy to understand. Shweder relied extensively on -isms of all sorts to obfuscate his point further. Essentially I think he was trying to convey that sciences and humanities could never be reconciled because they 'lie on different ontological planes' -- i.e. there some sort of different metaphysical 'realities' of the body, mind, morality, and beyond. And apparently those metaphysical 'realities', whatever they're made up of, are separate, and cannot be examined by the 'monist' methods of inquiry.

Shweder went on and on about the apparent mind-body duality, claiming it is impossible to unify the two, and going as far as criticising collegues for not having read some ancient work of Déscartes himself. I admit I've never even heard of that book; and old writing is practically in a different language from its modern counterparts, thus I'll pass on the commitment to digest archaic French. We do not yet have a clear understanding of what consciousness is, but I insist: when we do, that understanding will be wrought by psychologists and neurologists rather than philosophers!

So then he went on this childish tantrum against 'materialist monists' (I guess I would be one?) and filled the room with enough straw to sustain a small pastoral tribe for a year. Essentially, he accuses us of 'arrogantly' dismissing the worldviews and ideas of the 'natives' and their 'realities'. And yes, he called the traditional tribal people 'natives', possibly implying we don't fall under that category somehow. Please, I'm a native of Russia. Does being white deny me of the privilege to consider myself a native now?

That, to me, is true arrogance. This "oh they don't know any better so let's pretend we believe in their silly games" attitude of most cultural relativists towards fellow humans. Do they seriously feel sorry for the people and assume they're intellectually impoverished, thereby deserving some special sanctum in our ontology? In One River Wade Davis quotes Lévi-Strauss saying "The people for whom the term cultural relativism was invented, have rejected it." (p.290) For some reason, those people don't think they ought to have a special 'ontological realm' for themselves; they see the rest of us as part of theirs.

Perhaps it's the 'pluralists' and cultural relativists who are dismissive and condescending towards differing worldviews? We at least try to comprehend and integrate their knowledge and wisdom in our worldview; albeit there's much improvement to be had, we don't shove them into some separate 'ontological reality'!

Furthermore, why bother creating separate realities when one is more than enough to deal with? Shweder starts off with a quote by Woody Allen: "“Can we actually ‘know’ the universe? My God, it is hard enough finding your way around in Chinatown”, alluding to the common argument that since science cannot know everything, there must be an alternative realm of metaphysics/energy/deities/spirits/woo . So why then, Shweder, are you trying to create a second Chinatown to navigate simultaneously, if one is hard enough?

I agree with anyone who says science cannot solve everything. Scientific inquiry has its limits. Eerily enough, so does the human mind itself. But if even the scientific method, the most powerful tool of acquiring and verifying knowledge we have, is limited in understanding the universe, how can blind belief systems work any better? The underlying principles of the scientific method, I insist, are innate; and have been selected for throughout the millenia of our existence. One who failed to make an accurate prediction was overcome by someone who succeeded. One who fell victim to unverified personal assumptions was on the losing side of competition.

Now we have this data acquisition method, which is far from completion or perfection, that has so far been the best tool we have. We use it on a daily basis -- some more aware of it than others. And as of any other naturally evolved instrument, we must be aware of its strengths and weaknesses, and try our hardest to compensate for the latter. This is where the formal scientific method comes in. Training as a researcher demands a good understanding of how our mind can fail. We extensively use statistics for precisely that reason -- we must have a way of checking and correcting for errors in our reasoning.

One of our bad glitches is the attachment we tend to share with our pet ideas. This blocks the self-correcting mechanisms of skeptical inquiry and sends one straight into the clutches of dogma. The further one strays from the sensical path, the harder it becomes to correct the course, due to the growth of emotional attachment. This is precisely why dualism (and pluralism) are, in fact, dangerous.

You can probably imagine by now an obvious example of dualism -- religion. Many religious people tend to separate the world into the physical, and the spiritual. It seems harmless, but renders the victims vulnerable to manipulation by those with alterior motives. Many are willing to die for their religion, and can be persuaded to commit a plethora of hideous acts. Reason cannot speak to these people, for they can create a sanctuary from logic in their alternative realities. 'I'm killing people to serve God, for it is God's will for these people to be killed' makes perfect sense if the related religious stories are perceived in the mind as reality. Suicide bombing makes perfect logical sense in the mind of an Islamic fundamentalist. Killing doctors makes perfect logical sense in the mind of a Christian anti-abortion fanatic. If we assume they are all right in their own way, we will have sheer chaos! Dualism (and pluralism) is dangerous!


On the first page of his talk, Shweder compares E.O.Wilson's Consilience: The Unity of Knowledge to a "monotheistic sermon". Prof. Wilson, the great sociobiologist and entomologist, is apparently a preacher. If so, then I hope I have convinced you, dear reader, that Shweder is a full-out religious fanatic.


After the talk I had a burning urge to pick a vicious fight with Shweder, but decided 5 min of conversation with Prof. Pinker would be worth a few orders of magnitute more than arguing with an arrogant, empty, fanatical academic. It definitely was! =D

And now that I've had a wonderful evening ripping apart some high-ranking academic, sleep is in order.