Diagrams that make me cry, part LargeNumber

I was calmly blogging about real content, of course procrastinating simultaneously by writing pieces of stuff for work, as well as planning on possibly contemplating actually doing the readings for tomorrow's paleontology class. In the intro chapter titled "Fossils and Evolution", we get shown the following figure as The Taxonomic System, with a mention in passing the there have been some minor adjustments in the past, such as Three Domains, etc. Of course, such trivial taxonomic nitpicking is apparently of no use to paleontology students, so we'll use the horribly outdated Whittaker 1963 classification which should never be seen outside history of science lectures...

Aaaaaaaaaaah! Gotta love the 3:2 vertebrate:invert ratio too. Apparently bryophytes and 'pteridophytes' don't actually exist either. My own kingdom makes me weep. Also, for personal sanity, ignore the "Protoctista". That's just Margulis trying to feel special. And somehow succeeding outside her own field. (Levin 1999 Ancient Invertebrates and Their Living Relatives. Prentice Hall, NJ)

'Oh but the textbook's from 1999, cut 'em some slack with the volatile ever-changing taxonomy mess!' If they had used the Woese tree, which I have other personal issues with, I'd be fine with it. Of course, Woese tree in 2010 is a bit irritating, but I can still live with that. But...what truly adds insult to the injury, and rubs various salts even deeper into the bleeding wounds of my inner soul – THAT FUCKING PIE CHART!

"Proportions of members of each kingdom living today"

Hang on, gonna go break some furniture with energetic *headdesk* maneuvers. And my forehead with epic *facepalming*. BRB.

...ok, back. Lab benches are quite sturdy, it turns out. I'll just let Star Trek and internet memes take care of this:

Source: The Internets. All of them.

And they teach this as an uncontroversial, neutral fact. When, in fact, reality looks more like this:

Proportions of total marine biomass and abundance occupied by the only noticeable taxonomic groupings. Also, anyone who replaces "eukaryotes" with "protists" must be pretty freaking awesome. And/or actually understand biodiversity. (Suttle 2007 Nature Rev Microbiol)

I don't mean to bash the textbook itself. Aside from the little taxonomical issue there, the rest of the book seems quite interesting and perhaps a great source for paleontology (not being of that field, I have little idea). It just bothers me when something so cheap and simple to fix is left ignored and perpetrated on and on as students fail to learn any better, and teach what the learned, and further students learn that, and so on, ad infinitum, until we're left wondering why modern anthropology graduates seem to think evolutionary biology progressed little since Darwin's time. It's kind of annoying. And detrimental to efficient progress in all relevant fields. Not even asking for a new section in the book; just fix what's already there!


Ok, my blogging spirit is back now. Time to write up actual posts, relying on the creative writing juices (if any) unlocked by the power of RANT.

Conflict of Interest is not unique to corporate blogging

You may or may not be aware of the major kerfuffle on ScienceBlogs recently. If not, consider yourself lucky. Seriously, it's not that important. In a nutshell, SB launched a new blog on food science operated by someone in PepsiCo, SB readership exploded, SB withdrew blog, several very important bloggers left over it, and yeah. Basically, a scheme devised to remind me of how nice it is here on Field of Science, where we are truly independent, mostly blog about actual science (with apologies about this post) and have yet to see any drama *knock on wood* =D

Well, since all the big kids are doing it, I'll chime in too =P partly to procrastinate with take a break from writing about foraminiferan pseudopodia.

I don't really have a strong opinion on corporate blogging either way. It should be clearly labeled as such, just so we can estimate what the bias would be. On the other hand, it'd be nice to know what our brethren in the private sector are doing. They have labs and scientists and science over there too; one doesn't need a medieval institution for that. But again, there is a real potential of such a blog turning into a PR campaign. Which, actually, isn't too different from an independent blogger pushing a particular opinion or ideology. On the other hand, ScienceBlogs did fail public relations, and quite miserably too. From the looks of it, its bloggers weren't well informed. But still, that's a poor excuse to act like a cage full of rabid howler monkeys on caffeine tablets and low-grade acid.

I don't think automatically treating anyone with private funding as a 'corporate shill' and 'non-human immoral braindead moron' is a particularly wise or constructive thing to do. In other words, it's fucking moronic. Corporations are technically just a legal shell, and can't really write or do anything. They themselves don't have a physical presence. Corporations consist of people, who do have a physical presence, and are capable of writing and doing stuff. They're people like everyone else. Being employed does not suddenly make one a braindead zombie. In fact, can't the other side call academic bloggers "academic shills" and accuse them of merely parroting what the grant officers want to hear?

As all people, corporate employees have personal interests, desires, goals, demands and worldviews based on which they try to deal with all the former. These interests are not evil, nor is the 'pure' pursuit of science a saintly task. Sometimes – nay, often even – other people's interests conflict with our own. Who the fuck are we to judge our own interests and worldviews as 'morally superior' to anyone else's as if we, alone, have some god-ordained divine access to 'Higher Truth'? Sure, some views (hypotheses, if you will) stand up to facts (ultimately, sensory input) better than others. Which is why creationism is not on equal footing as evolution. At all. But one must remember that those people will act in ways that are founded on their beliefs and worldviews, as well as extrinsic restrictions. In other words, they're doing the best they can. Soulless* corporate 'shills' included.

*In the literal sense.

We all have conflicts of interest. Starting with the very basic fact that a lot of our blogs are known to friends, colleagues and *gasp* employers. I'm affiliated with a certain lab (and still sort of affiliated with another), I am funded by a specific university and have an employer. Obviously I'd have a conflict of interest whenever I write something potentially sensitive, like blogging about my department's research. That's little different from somebody in the private sector blogging about their industry with all the associated concerns. We all have political, social and financial interests to consider. (unless you're some isolated hermit in the middle of the tundra somewhere in Nunavut with a satellite connection)

Furthermore, people who actually do research (unlike those of us who just write about it, heh) generally need $$ for their activities. This $$, generally, needs to come from somewhere. Where do you think it originates? Siphoned off the Flying Spaghetti Monster's personal chequing account? Magically created in the lab of some mad scientist? If only. It comes from the evilest source of all: the bloody economy. Ok, perhaps you [wisely] stay the hell away from Big Science, and subsist entirely on federal grants. Where did you think that money came from? That's right: taxpayers. Ie, ultimately, the very private sector we all love to hate.

From the little I understand (still a long ways away from grantwriting), grants aren't exactly a no-strings-attached affair. You have to report your results eventually, having not only done something productive but also something very relevant to what you wrote in your grant application. I may be wrong, but that's the sense I'm getting. Please correct me if grants actually are free gifts of shiny money you can then spend on a giant fully-catered university-wide orgy with an open bar, on a boat cruise in the Seychelles. Not that federal grants can cover even a tenth of that...

If it's the former, then, presumably, your next step is to work towards securing the next grants. That is, your results should probably be of a kind that would encourage further funding in your field. Presumably, if you get funding for environmental topics, you'd be better off with results stating your Cute Fluffy Animal is on the brink of extinction rather than 'oh it's doing fine'. In that particular case, who the hell is going to dump more money into Cute Fluffy Animal research if it's not under some sort of threat? Conflict of interests much?


Even blogging about research papers is sensitive, especially within your own field. You have to balance opinion, factual accuracy and style without offending the authors. Some bloggers find it perfectly sensible to unleash a tirade against some paper they don't like, but I'd prefer not to sever potential relationships with people I've never met, even if I do think their paper is a piece of crap. Primarily for selfish reasons: at this point, I'm in no position to start collecting enemies in academia. Or anywhere, really.

If I were a truly independent blogger, that wouldn't fucking matter, and I'd probably make a point of devouring every crappy paper I come across for shits and giggles. Again, this isn't all too different from a corporate blogger generally speaking well of their employers and perhaps being more critical of their competition. Naturally, I'd be more inclined to publicly rip other labs' papers to shreds rather than my own.

This wasn't really about the ScienceBlog 'Pepsigate' incident much; drama fluff comes and goes. I think there's a bigger problem: too many people, including academics themselves, live in this magical bubble where conflict of interest and the bias it drives somehow fail to exist in the bastion of rational thought that is academia. Research, as soon as it's peer-reviewed, is automatically politically-neutral and scientifically-accurate. That sort of thinking is outright delusional, and dangerous. We are humans. And, like all humans, we are just trying to make ends meet in this distinctly unfriendly world, handicapped by the eons of accumulated evolutionary garbage and imperfections in our bodies, brains included. We are biased and selfish. We are also diverse and varied. And not a single one of us knows the 'Truth'.


I find it odd and annoying that neutrality/centrism tends to be universally politically unfavourable, sometimes absurdly so: people often think higher of their opposition than of anyone neutral. Neutrality is not necessarily symptomatic of indecision or indifference (although sometimes is, and for good reason), but rather often an admission of the intense complexity of the issue at hand. I think it's better to abstain from taking sides at all than make ill-informed ones based on oversimplified cases. For some reason, that view is surprisingly unpopular in some circles...

Anyway, I'll get back to actual science posting. Now you know why I rarely discuss controversial/political stuff here -- too complicated for my tiny little brain. Besides, protists are way cuter =D

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

Public service announcement: animals-fungi-plants != eukaryote-wide

Was just perusing some high impact factor journals before going to sleep, and every other week or the following little detail makes my blood boil:

Someone claims to have done a eukaryote-wide analysis, or something pertaining to eukaryotic evolution, in the title; excitedly, I click, only to find out the eukaryote-wide analysis was metazoa-wide with some yeasts thrown on, maybe Arabidopsis if we're really lucky.

Since I'm in a rather grumpy mood today already, finally slapped together this quick little announcement I've been meaning to make in a while:

(yes I'm lazy and just modified the Tree of Roots published earlier...sue me.)

That's all. Just had to let it out. How can trained biologists be so ignorant about basic biology!? Shouldn't you know at least a little bit about the relatives and evolutionary history of the organisms you work with; shouldn't you be even a little bit curious, at least enough to actually know a thing or two about something as basic as the general scope of eukaryotic diversity? Is that asking for too much?! If an undergrad with a 2.0 GPA can swallow this, why can't tenured faculty at high-ranking famous instutitions?

At least I don't see implicit (animals,plants),fungi too much lately, only once in a blue moon. Maybe because I don't read as much hardcore cell biology literature anymore...

I hate Macs.

So. Much.

Please, are there any sane people left out there? Am I really alone? Is anyone else sick of getting owned by a stupid white/light grey box every 5 min because some morons are obsessed with making their products 'sleek' rather than something that actually works in a sensible way, and is compatible outside the small special cult they formed???

The only reason Macs are 'safer' in terms of viruses is because Apple has such a small percentage of the total market share that one would have to be a total idiot to write viruses for them. Although considering the arrogance of many Mac fanatics (bordering on religious fervor), it is somedays really fucking tempting to write one.

Can't wait to save up enough to finally get my own computer again. It will definitely be a PC. And all you mac users will save your files in sane formats to accomodate the other 99% of computer users. We are not inferior to you.

Maybe I should just go ahead and install GNU/Linux everywhere in the lab. MWAHAHA. Too bad I probably don't have sufficient computer skills to do so =(

Ok I think I can proceed with my work now. Writing this from a Mac right now... how does one autoclave a blog? Ewww the cooties...

Pwned by Euglena* earlier and now by a Mac. My day really sucks...

*I think I just discovered the first strain of those fuckers who are NEGATIVELY phototactic. That's right, they consistently move AWAY from the light, or ignore it altogether at lower intensities. Photosynthetic organisms displaying photophobia. Oh yeah, makes so much sense. Maybe tomorrow the laws of nature will hate me a little less...

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...

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

"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.)

Yet another Woese Tree rant

o_O OMG, I'm getting infected by You-Know-Who's writing style...

I just sent this to my cell physiol prof:

The tree in slide 9 of the first lecture powerpoint is absolutely awful and grotesquely outdated (apparently based on Woese 1990). First of all, it is well-supported that the root is more likely to lie either between Eubacteria and Archaea+Eukarya, or within Eubacteria (I'm partial to the latter). It's rather murky in that particular diagram. Secondly, the eukaryote side of the tree makes one want to cry/punch a giant hole in the wall: Trichomonas and Giardia aren't exceptionaly likely to be the basal eukaryotes, and group reasonably well with Trypanosoma+Euglena, forming what may well be a monophyletic group. In any case, Trichomonas and Giardia seem to form a clade.

Dicty is WAAAY more closely related to Humans+Yeast than either Maize or Paramecium -- the later two are on a fundamentally different branch of eukaryotes -- the bikonts (eg. Cavalier-Smith 2009 J. Euk. Microbiol) or the corticates (Cavalier-Smith 2010 Biol. Lett.) Dicty, Humans and Yeast are members of a quite well-supported group (Unikonts), and this tree erroneously suggests that multicellularity evolved in the common ancestor of Plants, Animals and Fungi, which is completely wrong. Multicellularity evolved in each of those lineages independently, and in quite a few other lineages as well, up to ~16 times in the Eukaryotic kingdom (King 2004 Dev. Cell) and arguably a few times among prokaryotes as well (eg. Streptomyces).

I can't believe this is in a 2008 edition of the textbook! This tree has been outdated for at least a decade! How does one go about formally complaining with things like this? I refuse to let any suggestion of "crown/higher eukaryotes" vs. "stem/lower eukaryotes" go by unnoticed. The very notion of higher/lower organisms is thoroughly wrong and must be abandoned. Even in an introductory diagram. ESPECIALLY in an introductory diagram. Especially when they have the nerve to HIGHLIGHT Maize, Yeast and Humans as if they're some special enlightened life forms.

The era of Woese 1990 is over. We can move on anytime now...

The diagram comes from the "Big Alberts" text, 2008 edition. They should bloody know better by now! >.<

Candidate for the Twisted Tree of Life Award?

Also, their 'interesting' spelling of eukaryotes is in itself a rantworthy topic for some other day...

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...

It's probably time to take a break when...

I just failed to realise pAP3::GUS is a transcriptional fusion reporter and therefore only expresses if and only if there is transcriptional activity of its promotor (hence pAP3); thus 35S driven expression of the same protein would not necessarily result in GUS activity, unless shit exists to activate it, including itself, if it is thus inclined. Should I take a break from my slides and go home now?

(this is for a class. Will never look at goddamn flowers the same way every again. I hate you, ABC genes. Past 3am the morning a talk is due about them anyway...)

PISTEFUCKINGLATTA*! SEPALLATA! (those look really scary about now...)

Also, Nature papers become unbearably dense when you have to present about every single fucking sentence in them...

*grumble grumble*

*Does the FUCKING insertion have to be italicised too? What do gene naming conventions say about expletive inclusions?

PS: For those of you who have absolutely no fucking clue what I just rambled on about -- lucky bastards!!! [ok the HTML got fucked; I'm not rewriting that, no fucking way] is AP3 expression, but that's just shitty wording and is getting me really bloody confused at this hour. Grrrrrr. I was like "WTF won't it show GUS if the fucking same thing is constitutively expressed via 35S!?" and then hung my head in deep shame and embarassment. And profanity.

5am update: Screw this I'm off to bed... been working on this for the past 12h pretty much non-stop... can totally wing it tomorrow if I have to. Actually, I'd do a lot less preparation if it wasn't a group project. Other people seem to have phobias of 'winging it'. Too bad, because all you really need to do is sound convincing. I mean, it works for me in lab meetings... isn't that how science really works anyway? (oh shit, the secret's out now!)

And yes, I made all the slides myself despite it being a group project. Did I ever mention groupmates can actually somehow manage to slow you down rather than help sometimes? Even if they're willing to help, they can still be fucking useless? Well, now I have. Grrrr.

Windows is evil!

In other news, water is wet.

But srsly, you're sitting there, writing stuff, and suddenly... THIS FUCKING WINDOW RANDOMLY POPS UP SAYING YOU'VE GOT 15MIN TO LIVE SAVE ALL YOUR SHIT BEFORE THE COMPUTER AUTOMATICALLY RESTARTS TO INSTALL A FUCKING UPDATE YOU NEVER ASKED FOR IN THE FIRST PLACE!!! And the best part of this: YOU HAVE NO OPTION TO STOP IT!

Don't they have principles of some sort in compsci and robotics where the user must retain rights to override the machine at any time, ever? Isn't it a bit of an ethical (not to mention, PRACTICAL) violation to deprive an intelligent user of a dumb fucking machine the right to control when and if it does things? I mean, seriously, this is like IN YOUR FACE rude -- for no necessary reason, it randomly tells me, without any warning, that the computer is going to shut off. No, not because of a software glitch, or some safety concerns, no. It's just randomly going to restard. To install a fucking update. And you have no choice. Ever.

And I just lost like 20 tabs of papers I took all this time to find... fuck you, whatever idiot decided this automatic restart without override thing was a good idea. IT'S NOT.

GRRRRRRR!!!

I've deactivated that shit on my own computer, but lack privileges/desire to fiddle with the innards of the one in the lab. Perhaps that's a mistake. Sigh.

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.

Two rants on endosymbiosis

First off, quick point: Can we please stop using headlines like "Darwin was wrong about [x]"!? Srsly, big deal, some dead dude from the 19th century was wrong about something. Well shit. Evolutionary biology as we know it is now fundamentally flawed. Because Darwin didn't have PCR or fancy sequencers or GFP-tagged whatever. Tragic. What about all the shit Mendel was wrong about? Are we gonna ignore him now? /rant #01

Sometimes when writing up a post on something, I come across 'interesting' sites and papers. I mention my reaction in brackets, and find more crap to rant about. I then move the contents of the brackets to a footnote and unleash an off topic at the bottom of the post. But sometimes, this rant would be -really- off topic, and would be rather distracting if it becomes longer than the post itself. Today, we have come across one such case.

Warm-up - (excessive endosymbiosis)
Before embarking on a little journey of "Did he seriously just write that/get a faculty position/get a degree", a warm up paragraph from this week's Nature:

"In the former, the peptidoglycan layer is sandwiched between the outer and inner membranes, so that it surrounds the inner membrane: in contrast, in the latter there is no inner membrane, and the peptidoglycan layer, located outside the cell, surrounds the outer membrane." (Lake 2009 Nature) (via Catalogue of Organisms, who beat me to it, grrr XP)

That, my friends, is a wonderful example of epic semantics and topology fail. What he's talking about is that double membraned bacteria in question have cytosol-Inner Membrane(IM) - murein wall - Outer Membrane(OM) - outside. Single membraned bacteria have a cytosol-OM-murein wall-outside arrangement [sic]. Ie, somehow OM-M became IM-M-OM, raising the question of how the outer membrane end up on the other side of the murein. Thus, Lake invoked endosymbiosis to explain this 'conundrum' - an OM-M endosymbiont entered another OM-M prokaryote, and the endosymbiont OM became the inner membrane, while the host lost its murein wall. Very complicated stuff.

It may be quite evident at this point what the real 'conundrum' is there. Instead of comparing biochemical properties of the membranes to each other, he compared their relative positions. There is a very interesting topological property where if you have an double membrane and lose the outer layer, the former 'inner membrane' becomes the outer one. I think I may be onto something here...anyone wanna collaborate on a Nature paper? Any mathematicians out there wanna contribute a proof?

So how could someone who's probably a decent scientist fall for something like that? In fact, this seems common as soon as you put the 'hype' into 'hyp[e]othesis' - in this case, the guy seemed desparate for endosymbiosis, to the point of overlooking this very simple point in semantics. The reviewers and editors were no better - they too were getting carried away with the endosymbiosis hype (of course, they've still got ways to go to reach Margulis levels thereof...) For some reason, the fact that there's only one confirmed case of prokaryote-prokaryote endosymbiosis in the literature seems to worry no one...

(Coming from the TC-S camp of eukaryotic evolution, it was probably the double membrane state that was ancestral, with the loss of the outer membrane leading to what TC-S calls 'negibacteria', which eventually gave rise to us Neomurans. Even if you propose that single membraned bacteria came first, there's still no need for endosymbiosis, for they could have perhaps devised a way to form the outer membrane on their own. That would still be more parsimmonious, and more likely, than Lake's hypothesis above...) /rant #02

The big rant - (insufficient endosymbiosis)
We have some major endosymbiosis people in our department, so I never really came across any skeptics of mitochondrial endosymbiosis. The endosymbiotic theory of mitochondrial and plastid origins is pretty much beyond dispute these days, and the evidence is simply overwhelming. However, there always has to be someone to blow against the wind gale. Very rarely, they happen to be right; but even in those cases, their argument tends to be well-reasoned and supported by at least some data from the start. The other 99% of crackpots remain just that - timeless testament to our innate irrationality.

There's some guy who seems mildly annoyed by mitochondrial endosymbiosis. To the point of dedicating an entire website to the topic: http://www.origin-of-mitochondria.net/

So there's a whole page 'critiquing' the endosymbiotic mitochondrial origin theory. I know this is only half a step up from bashing creationists, but it got me a little irritated. Not because I feel threatened, but because it seems to be so easy to get employed as a crackpot, and I'm a little envious of their capabilites. See, if you actually try to abide by proper reason and the scientific method and all that crap, you'll be dirt poor and socially marginalised for the rest of your life. Thus, I shall enjoy one of the few advantages we do get - the feeling of intellectual superiority as you rip into some crackpot's drivel with a barrage of citations and proper data. It's a sport.

"The extensive gene transfer that is needed in the endosymbiotic theory would wreak havoc in a complex genome since frequent insertion of random pieces of mitochondrial DNA would disrupt existing functions."

Uhhh...heard of transposons, by any chance? I'm sure those are a few orders of magnitude more plentiful and more violent than the occasional piece of mitochondrial DNA. Yet they still...happen. And genomes have generally been able to deal with it. Random gene insertions do disrupt functions, but then you've got a few million other genomes to take their place! Isn't evolution awesome?

"Most pictures in textbooks of mitochondria resemble bacteria, but in reality, mitochondria form a dynamic network of interconnecting tubules (reticulum)"

May we introduce you to bacteria that don't look like 'bacteria'? Say hi to Streptomyces and Planctomyces, for example.

I'm just making shit up hypothesising here, but it seems like the stereoptypical bacterial morphology may be limited by the fact that it swims. There are certain shapes optimal for a flagellate lifestyle, and netlike/mycelial/branching forms are not among them. Once a bacterium has become commited to living exclusively in the intracellular environment, it no longer needs to be hydrodynamic, and can start taking on whatever other form it likes. I'd imagine that >800my is plenty of time for drastic morphological changes, considering eukaryotes managed it quite well.

"It is said that mitochondria, like bacteria, divide by fission, but the mechanisms are completely different and mitochondria use mainly components of unique eukaryotic origin."

Ever heard of intracellular parasites? An intracellular lifestyle does some weird shit in terms of intense reduction - microsporidia (fungi which shoot their cytoplasm into the host cell, where it takes over and lives off the host's resources, until forming new spores) have highly reduced genomes that have been harsh to introns due to space limitations(eg. 13 introns in an entire genome (E.cuniculi)), as well as a great purge of proteins for nucleotide+amino acid biosynthesis (Keeling & Slamovits 2005 Curr Op Genet Dev)* This makes sense - you don't have to make your own amino acids if you can just steal them from the host! So any degeneration and subsequent loss of previously essential genes is now tolerated, and thereby bound to happen.

*Ok, when you come across a paper with the following introductory paragraph, you just have to read it:
"At the bottom of the rabbit hole, Alice found a bottle labeled, ‘‘Drink Me’’. When she did, Alice shrank to a perfectly functioning, ten-inch miniature of herself. In reality, shrinking can be more difficult than simply drinking a potion, because the component parts of many systems are not themselves shrinkable, and so the system fails to function properly. In the world of eukaryotic nuclear genomes this is probably true, despite the fact that they vary in size by factors of hundreds of thousands (Figure 1), much more than all of Alice’s many transformations combined." (Keeling & Slamovits 2005 Curr Op Genet Dev; free access)
Classical studies geek really shows here...
(I'm quite bothered by the desolate desert around Rhizaria in fig.1 =( )

Similarly, the early mitochondrion no longer desperately needed to maintain its own division machinery, which eventually became transferred over to the host or lost. In a way, it has been able to hijack the host cell to take care of its own division. (so who's 'enslaving' whom here?) Through extreme evolutionary 'laziness', some lineages have been able to lose all genomic DNA entirely, and reduce to tiny membrane bound compartments essentially for specific parts of the host's metabolism. They basically 'disolved' into the host over time! (of course, de Roos' theory would probably claim those lineages as an ancestral state, eventually increasing in complexity. Too bad phylogeny king of stands in the way. Oops.) Just because an organism isn't capable of free life now doesn't mean it ancestrally wasn't either. Again, parasites support that very well. de Roos seems to have fallen for the 'evolution aims to gain complexity' misconception, and had difficluties with it 'going backwards', as it often likes to.

"So, although we see some characteristics that are shared between mitochondria and bacteria, we see many more examples where mitochondria are actually quite different."

Yeah, shit diverges over 850my. Just because they're 'different' doesn't mean they can't share a common origin, even a fairly recent one. Again, microsporidia were considered to be very ancient due to their apparent 'absense' of mitochondria and a highly reduced structure (wiser people were a bit alarmed by the latter detail; parasitism is almost universally a secondary trait (looking back far enough, it always is; first life must have been free living, otherwise we get the chicken-and-egg problem)). Turns out, they're fungi, like the mold in your fridge. We're not well-equiped mentally to deal with such timescales, but a lot can happen in just a few million years.

Thus, as long as we do not have a clear picture of the last common ancestor and its relationship with eukaryotes, it will be difficult to interpret gene similarity as evidence for the endosymbiotic theory.

This is where parsimony helps. Sure phylogeny is fallible (again, see microsporidia), but if an endosymbiont and a free living organism share a significantly large chunk of genes, it takes a lot less explanation and hand waving to invoke endosymbiosis than to craft elaborate hypotheses of weird massive lateral gene transfer stuff. That alone doesn't make it right, but definitely much more probable. And we're really working with probabilities here to begin with.

The mitochondrial genes could be derived from transposable elements, plastids or viruses and could come from either the nuclear genome or a bacterial genome.

'Domestication' of transposons is not as easy or probably as we may like it to be. Also, much of this would have to happen between the proto-eukaryote and the last common ancestor of most eukaryotes alive today, which is an epic question mark at the moment, although it does seem like that time period may not have been that long after all ('short' paper here: Cavalier-Smith 2006 Phil Trans R Soc B; free access). Cell structure, on the other hand, seems to be more malleable than large-scale gene organisation. Also, has there been at least one case of genes randomly congregating into a de novo genome in a random compartment? That would be quite ridiculously unlikely! How did the replication and maintenance machinery get in there then?

And plastid origin of mitochondrial genes? Ok, maybe once or twice that could, in theory, happen (has it?), but we're talking about mitochondrial genes in primarily plastid-less organisms! Does this guy propose a plastid endosymbiosis as ancestral to all eukaryotic lineages with mitochondrial genomes!? He seriously needs to explore something a little outside his metazoa. He needs to take one good look at a proper tree of eukaryotes (one without the 'crown eukaryote' abomination, kthx), and read a TC-S paper or two on eukaryogenesis. Or perhaps we should cross him with Margulis, and the result would have an intermediate phenotype, and perhaps even be a decent scientist!

Intermediates exist in the form of hydrogenosomes and mitosomes from amitochondriate primitive eukaryotes.

Hey, let's pull a little prank! How about we introduce him to Blastocystis and the ciliate Nyctotherus with mitochondria-like organelles (Stechmann et al. 2008 Curr Biol)? Actually, the table in that page, if you can access it, is a powerful demonstration of the dangers of relying on a single morphological for reconstructing evolutionary history. Essentially, if you follow organelle complexity, you'll get something like: Microsporidia, Giardia, Trichomonas, Nyctotherus, Blastocystis, and us. Let's draw that as a tree, mentally (let microsporidia be basal to the rest). So far so good. Ok, let's pull out a certain tree I tend to [ab]use a lot:

(Keeling et al 2005 trends ecol evol)
(I went for quite a while without pulling that out! Did you notice? See, self-restraint works sometimes! Until it doesn't...)

Let's do a little exercise. Grab a mental marker, and let's find Microsporidia. It will be among the opisthokonts, close to chytrids and zygomycetes. Done? Great, now find Giardia. It's a Diplomonad, close to Malawimonas in the Excavates. Trichomonas is a trichomonad, close to hypermastigotes (remember Trichonympha?), again in the Excavates. Now head over to the Chromalveolates, the alveolate neibourhood, for Nyctotherus, a ciliate. And then go down to the Stramenopiles, where you'll find Blastocystis between Actinophryids ('heliozoans') and Bolidophytes. And then point at pretty much everything else. And now look at our single-trait tree, which was built keeping de Roos' hypothesis in mind. So...how'd that go? I think someone needs to read up on basic eukaryote diversity before making shit up about the origins thereof...

See, while both de Roos and Cavalier-Smith like to make up grand hypotheses that tend to contradict the mainstream theories, Cavalier-Smith is actually good at it. He thoroughly reads astounding volumes of literature, formulates rational, testible hypothesis that make sense, and backs off his theories when evidence definitively proves them wrong (as with Archaezoa). de Roos has ways to go to even dream of such level.

And finally,

"In order for an evolutionary theory to be considered a scientific fact or a valid scientific theory, there are some basic requirements. First, it is necessary to have a reasonably detailed mechanism that explains the basic steps in the endosymbiotic scenario. [done] Second, this mechanism should be placed in the context of current Darwinian evolutionary theory and should contain no fundamental problems or falsifications[huh...?]. Third, a substantial body of empirical evidence that directly supports this scenario should be present.[nope, no evidence whatsoever... I know of a lab where people just sit around on their asses all day because there's simply no data in that field. Also, they don't publish any ridiculous number of papers, thereby making us cell biologists very jealous.] Fourth, no credible or logically sound alternatives should exist[huh? Since when is that a requirement for a valid theory?]. If these criteria are not met, the endosymbiotic theory cannot be considered to be a scientific fact that has been proven beyond reasonable doubt. Remarkably, the endosymbiotic theory fails all points." [bolded edits mine]

Yeah, to all my friends working on endosymbiosis: IT IS A LIE! OH NOES!!1!

Seriously, how can people argue that bullshit, and SOMEHOW be employed in biology?! This guy is apparently an actual biologist (although more of a biochem/bioinformatics background; As a devoted cell biologist, I have an obligation to hate them a little...you see, the academic community has ascended far beyond the primordial practices of stone age tribalism.) After a brief search, I found another interesting abstract, although we don't have access to this paper (and I can't be bothered to ILL it):

"Current theories about the origin of the eukaryotic cell all assume that during evolution a prokaryotic cell acquired a nucleus. Here, it is shown that a scenario in which the nucleus acquired a plasma membrane is inherently less complex because existing interfaces remain intact during evolution. Using this scenario, the evolution to the first eukaryotic cell can be modeled in three steps, based on the self-assembly of cellular membranes by lipid-protein interactions. First, the inclusion of chromosomes in a nuclear membrane is mediated by interactions between laminar proteins and lipid vesicles. Second, the formation of a primitive endoplasmic reticulum, or exomembrane, is induced by the expression of intrinsic membrane proteins. Third, a plasma membrane is formed by fusion of exomembrane vesicles on the cytoskeletal protein scaffold. All three self-assembly processes occur both in vivo and in vitro. This new model provides a gradual Darwinistic evolutionary model of the origins of the eukaryotic cell and suggests an inherent ability of an ancestral, primitive genome to induce its own inclusion in a membrane." (de Roos 2006 Artificial Life; emphasis mine)

Huh? Umm...this...just...like...errr...no! NO! Does not compute! AAAAAH! My eyes! I can feel my brain liquifying and oozing out of all sorts of orifices! See why the computery bioinformatics folk must be kept away from any mention of an actual organism? (ok, admittedly, some can manage it well, but that doesn't mean I shouldn't stereotype for personal fun =P )

I'll fix this sometime within the coming week, and 'translate' for you a real hypothesis on eukaryotic origins.

>Psi Wavefunction casts lvl10 TC-S Attack on lvl8 Crackpot for 500 damage.
Lvl5 Crackpot sustains 500 damage; HP 130/630
>Crackpot uses Copy Attack to cast Psi's lvl10 TC-S attack.
Psi sustains 0 damage due to TC-S Immunity.
>Psi casts lvl40 HAHAPWNEDLULz! on Crackpot for 1000 damage.
>Crackpot defeated!
*cue Final Fantasy victory music
>YOU gain 2000XP

Now back to working on this week's Sunday Protist ^.^

References
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

KEELING, P., & SLAMOVITS, C. (2005). Causes and effects of nuclear genome reduction Current Opinion in Genetics & Development, 15 (6), 601-608 DOI: 10.1016/j.gde.2005.09.003

Lake, J. (2009). Evidence for an early prokaryotic endosymbiosis Nature, 460 (7258), 967-971 DOI: 10.1038/nature08183

STECHMANN, A., HAMBLIN, K., PEREZBROCAL, V., GASTON, D., RICHMOND, G., VANDERGIEZEN, M., CLARK, C., & ROGER, A. (2008). Organelles in Blastocystis that Blur the Distinction between Mitochondria and Hydrogenosomes Current Biology, 18 (8), 580-585 DOI: 10.1016/j.cub.2008.03.037