Melting in Vancouver...

It is almost midnight and 27 fucking degrees outside, and humid as hell. No fucking way can I write anything marginally intelligent right now, while melting away into a sticky puddle of sweat and anguish. Typing has become a strenuous physical exercise, each keystroke trickling on into a raging torrent of perspiration. This is not supposed to fucking happen in Vancouver! I've spent six long summers in Toronto, and was so glad to have fled the awful, horrible climatic hell that is the Great Lakes summer (not the winter, mind you - I actually enjoyed those! A bit of bone-chilling frost is good for you =P).

And apparently, today was the hottest day in Vancouver/Lower Mainland in recorded history... just 6 months ago, we had one of the coldest, snowiest winters ever. At which time Toronto had +17 in early January. And now, TO is at a tolerable 18C. I think we somehow swapped weather...

I hate heat. I hate it so much it was one of the major factors that forced me out of the east. No point in living in a place where you can't function for 6 months of the year... winters are ok, just wear more clothes and it's quite nice and refreshing even. But the fucking 38 degree summers with humidex way well in the 50's is simply insane.

Which brings me to wonder... why is it that we African primates suck at tolerating heat so much? It's not like people living in the tropical regions fare much better than us; they're just more accustomed to the discomfort, but there doesn't seem to be much fundamental difference physiologically. They too must avoid excess sun and stay somewhere cool and drink lots of water; danger of heat stroke is very real to them as well. So how is it that we are so poorly adapted to what is supposed to be similar to our more-or-less native climate? 40 000 years shouldn't be that much time for substantial change! And even if we did lose the tolerance somehow upon migrating north, that still doesn't explain the aforementioned low physiological differences.

Intelligent design my sorry ass - how incompetent must a designer be to create his chosen species to be poorly adapted to survival on the vast majority of the earth's surface?

This goes for 'evolutionary creationism' (directionalistic hyper-adaptationism) too - perhaps we never have really adapted to live comfortably in the heat, but the discomfort (and the occasional heat stroke) wasn't enough to stop our lineage from continuing. Perhaps our ancestors once originated elsewhere, or, more likely, were better adapted and some later developments/adaptations in our lineage enabled us to lose those features. Eg. no need to devote energy to growing fur if you can obtain it from another animal (NOT saying this is what actually happened! Not particularly familiar with anthropaleontology anyway...)

Anyway, let's see if I can melt into sleep... somehow I doubt it. =(

Sunday Protist - Dinophysis: Whirling teapots...

Since I'm busy with Student Directed Seminar proposal revisions that's due tomorrow (which I naturally left until tonight) this will be more of a 'protist appreciation' post rather than anything educational.

Here's some Dinophysis, a group of dinos with rather interesting morphologies. (though the top left and the very bottom left aren't part of this group, as far as I know) I've first come across these in Haeckel's drawings, and thought he was making this stuff up. Apparently, there really are organisms vaguely shaped like whirling teapots:

(Source: Waller Lab); main page here (with more pretty pictures)

Also, these have undergone a tertiary endosymbiosis event with a cryptomonad. As cool as they are, they're fairly understudied as some have only been cultured fairly recently. Even more interesting morphogenesis questions there...

---
And shit, someone just timetravelled forwards and 'scooped' my ideas. People (zoologists+botanists) usually give me funny looks when I say cell differentiation in multicellular organisms is but a spatial version of developmental stage differentiation in unicellular ones... but I'm not alone! =D

Must be a Russian thing. Привет, братья! ^_^

Sunday Protist - Dinoflagellate eats Chaetoceros (gory) (for real this time!)

(Yesterday's attempts were derailed by having to shred some New Age BS instead)

The media seems to be obsessed with posting pictures/videos of things eating things; apparently that generates a lot of revenue interest. Since I'm neck deep in syntactic trees and X-bar theory (Yes, I voluntarily, by my own will, as an elective, take third year syntax & grammar courses. Also, I dislike Chomsky. Clearly, I am very sane), I'm going to resort to posting gory pictures: (and yes, I mixed up Chaetoceros with Skeletonema in the previous post. Sue me. =P Not that I pursued the topic any further over there)

Following images from Jacobson & Anderson 1986 J. Phycol, unless otherwise stated)

A dino (Protoperidinium) extends its pallium (feeding pseudopod) to devour a sizeable chain of diatoms (Chaetoceros); why bother bringing food to your mouth/gut when you can bring your gut to your food instead?

Yes, it eats that whole thing! Super Big Macs and 12" subs would be no problem for Protoperidinium, although this fine diner probably actually has standards.

More gore:

So cute, yet so voracious! NOM NOM NOM /memeplex

Detail of feeding apparatus:

(Jacobson & Anderson 1992, J Phycol)
The pallium can be described as a 'feeding' veil, a feature found in some thecate (armoured) predatory dinos, which cannot devour large prey as their expansion is limited by the thecal plates (an alternative is myzocytosis, or 'drinking through a straw'). The dino then proceeds to digest its prey much like a fungus - by secreting digestive enzymes and consuming the useful products (from ToLweb Dino page).

Diversity of dining etiquette among knightly armoured dinoflagellates:


Dinoflagellate feeding is a fascinating topic in itself, but I should probably abstain until after the upcoming final. Added to post topic queue.

I honestly intended for this post to consist of one picture; then I got carried away. Scholarly literature is addicting (that's normal, right? *crickets*)

/massive procrastination foray

Jacobson, D., & Anderson, D. (1986). THECATE HETEROPHIC DINOFLAGELLATES: FEEDING BEHAVIOR AND MECHANISMS Journal of Phycology, 22 (3), 249-258 DOI: 10.1111/j.1529-8817.1986.tb00021.x

Jacobson, D., & Anderson, D. (1992). ULTRASTRUCTURE OF THE FEEDING APPARATUS AND MYONEMAL SYSTEM OF THE HETEROTROPHIC DINOFLAGELLATE PROTOPERIDINIUM SPINULOSUM1 Journal of Phycology, 28 (1), 69-82 DOI: 10.1111/j.0022-3646.1992.00069.x

Also see: Gaines & Taylor 1984 J Plankton Research "Extracellular Digestion in Marine Dinoflagellates"

Dinoflagellate eats Skeletonema (prelude)

I was looking for a particular picture (of a dino chomping on a filament of Skeletonema if I recall), and came across this very insightful abuse of marine protists: Frequensea - The Ionic Whole Food Tonic.

Normally I would just snicker to myself and move on with business. But I'm rather cranky lately, and a vigorous ego-stroking demolition of worthless crap would be quite nice! Also, this stuff touches on way too many of my personal pet peeves ('natural', 'organic', 'wholesome', 'healthy' foods, New Age bullshit and general white upper-middle-class cultural refuse - I live in Vancouver, you see... At least they're not offering some spiritually-cleansing energy-harmonising dinoflagellate Tantric yoga, yet...) so let's see what they got there:

"The elements and electrolytes in plankton are almost tailor-made for the human body

Yup; the Intelligent Designer thought it'd be really funny to hide our best source of nutrients amidst tiny microscopic floating crap in the ocean. He also thought it'd be hillarious if we have practically no means of tapping into that perfect food source. He's a funny guy, ain't he?
Oh, and electrolytes aren't composed of elements? I knew I suck at chemistry, but didn't know I sucked that much...

It's no coincidence that the composition of human plasma is similar to that of seawater.

Of course, life originating in the oceans has nothing to do with it. And what's this 'plasma' you speak of anyway? Me no animal biologist, me metazoan vocabulary no good!

Over reliance on land-based food sources often leads to deficiencies in micronutrients and trace elements.

Fuck, millions of years out of seawater and still can't cope with those land-based food sources! Hey, what about eating whales? Those are no longer land-based, and are actually sort of filling compared to sea scum... oops, sorry PETA, just joking, you can go back to firebombing medical research labs =D

Our bodies need these elements to perform as nature intended. Left to its own devices, the human body has a marvelous system called homeostasis which keeps all systems in balance. Take away some critical component and the body experiences malfunctions that cause suboptimal performance. Too many malfunctions cause disease.

I thought leaving the body to its own devices leads to starvation? Feeding yourself upsets some innate natural balance? Actually, there is a lot of truth to that. Feeding yourself does keep you away from nature's little balance chemical equilibrium. The little problemo here lies that chemical equilibrium = death, but never mind...

Also, germ theory was wrong I guess. It was those disbalances after all.

What is Marine Phytoplankton?
Phyto = "Light" Plankton = "Floating/Suspended"

Wow, major etymology fail! Quick fumbling with own memories and an online translator reveals that: phyton = plant (also look at bryophyte, chlorophyte, pteridophyte, etc); light = photos (eg. photon, photograph, phototoxicity) You don't really need to know anything about science or the scientific method to at least get your classical Greek etymology sort of right! I mean, seriously, is Wikipedia even too advanced for the writer of that page?

Also, planktos = wanderer/drifter; but there's much easier prey in this website, so I'm not gonna nitpick, for now...

Scientists at NASA theorize that some 3 1/2 billion years ago, the world was changed forever.

Yes, those astronomers at NASA sit in their armchairs and wonder about the origins of life. They 'theorise' feel the answer to be 3.5 bya. And...really, I can't say anything more. Next.

The appearance of tiny organisms with the ability to convert sunlight, warmth, water and minerals into protein, carbohydrates, vitamins and amino acids marked the beginning of life.

Protip: if you're gonna randomly bold and change the colour of something, link is generally expected. Also, first life wasn't photosynthetic; that appeared fairly late, IIRC. They're not creationists, so I won't nitpick any further there...

Marine Phytoplankton, the single-cell plants are the basis of all other life forms on planet earth, they are the 'vegetation' of the ocean. Marine Phytoplankton are responsible for making up to 90% of Earth's oxygen.

THEY'RE NOT PLANTS! /phylopedantry Also, 85.3% of statistics are made up on the spot.

Marine Phytoplankton are the food utilized by the worlds largest and longest living animals and fish. Blue whales, bowhead whales, baleen whales, gray whales, humpbacks, and right whales all eat plankton. These species live between 80 and 150 years old and maintain great strength and endurance throughout their lives. The largest fish a plankton eating whale shark lives for over 150 years, grows up to 14 meters long, weights up to 15 tons, and is sexually active until it dies.

Whales eat plankton and grow big and old and horny, ergo, clearly humans should too.

Ok, I've only taken one ecology course in my entire life, and hated it, but this picture makes my eyes bleed in so many ways. SINCE WHEN DO ARROWS POINT FROM PREDATOR TO PREY!? HAVE YOU EVER SEEN A FUCKING FOOD WEB, EVER??? Those arrows represent flow of energy; drawing them backwards loses all meaning! (to be fair, USGS.gov got it wrong too...)

With this patent pending technology, spring bloom conditions are reproduced in a controlled environment, and this diversity of species is represented in these products which make our marine phytoplankton more powerful. Also the exclusive extraction process allows us to combine the benefits of phytonutrients with a natural and balanced composition of sea minerals. Phytonutrients are natural plant-based chemicals that promote proper metabolic functions.

You can get a patent for culturing mixtures of diatoms? Hang on, have some friends I should probably notify... also, wtf are 'phytonutrients'? How do they differ from 'zoonutrients'? Is there an unnatural/unbalanced composition of sea minerals? Which specific region do you sample?

Until now mankind could only dream of obtaining significant quantities of microscopic plants.

Yes, mankind's deepest philosophical and scientific questions were all about how to grow those little bastards. Actually, I bet there must've been some Eridu or Harappan dude who left a jug of water out in the sun. And then it turned green. Magic!

Through years of research, the Sea Farms can now grow these in quantity. This state of the art facility allows us to produce something unique in the world for your benefit. Many manufactures call cyanobacteria algae. Our marine phytoplankton is not cyanobateria but true micro-algae in its many forms and species.

Ouch, cyanobacteria got shafted! "Our marine phytoplankton is not cyanobacteria but true cyanobacterium-containing eukaryotes in their many forms and species"

Seriously, is anyone else reminded of sewage treatment facilities by those pictures of algae growing tanks?

I could go on a multi-page rant about how all this vitamin and nutrient bullshit ignores the fact that more =! better, and we've coevolved with specific food sources that would perhaps be in our bests interests to continue using... but then that'd be treating this crap too seriously.

So I guess this post really does entail a tiny dinoflagellate devouring a chain of Skeletonema in some ways ^_^


A post doc working with dinoflagellates once moaned about how easy it would be for her to quit research and open up some New Age algal face mask business, using her expertise to sell to people the 'rejuvinating wonders' of...well, anything. So tempting. Damn, honesty is such an annoying nagging bitch sometimes...

She wasn't really the first to think up such ideas. By far. Sad thing is, our fact-checking and research skills are utterly useless and unwanted out there in the dreaded 'real world'. Yeah, we know a bunch of crap about random protists - but who the fuck cares? And the public actively supports those folk over those who do real science. The authors of that website are a few orders of magnitude more employable than I am, even if they are lying and/or ignorant scammers. I'll be the one with glorified welfare, if I even make it that far...

Sigh.

"Sunday" Protist - Trichonympha returns!

Finally published today: Extreme Trichonympha sexiness:
(Carpenter, Chow and Keeling 2009. Morphology, Phylogeny, and Diversity of Trichonympha (Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus. J Euk Microbiol 56:305-313
I stole these while the manuscript was in advance online publication, before the images were shrunk and butchered to fit print quality:




The little rod shaped things in 12-15 are some bacteria on the posterior end of the cell. 26-28 - after removing the anterior 'cap' (operculum). Scale bar is 10um in #2, for size comparison.

Trichonympha is this giant and utterly adorable wood-eating gut endosymbiont of early-branching dictyoptera (cockroaches and termites). Sadly, it's anaerobic and thereby difficult to play with unless you have a steady supply of termites going on in your lab, like those guys do. As for the wood roach from which these particular critters come from, it has to be ordered. This roach also has the amazing Saccinobaculus...Trichonympha can also be found in basal termites; we're lucky to have some native ones here in Vancouver (alas, devoid of Saccinobaculus =( )

It seems like cockroaches and termites formed endosymbiotic relationships with the protists before the two diverged - both groups have endosymbionts in their basal lineages, and lose them later on. The protistan endosymbiont diversity is wonderful: you have the aforementioned and much beloved 'snake-in-a-bag' (Saccinobaculus; can you tell I'm obsessed yet?) and fellow oxymonad companions like Streblomastix - a long cell with 'docking' for even longer episymbiont bacteria on it; Trichomitopsis and its protruding axostyle when it curls up into a ball; accompanied by loads of symbiont and parasitic bacteria.

The wood-eating dictyoptera require endosymbionts to digest cellulose, since we metazoans suck at it. The more derived termites can get by with bacteria it seems; but interestingly the protists are actually doing the digesting themselves in the basal termites - killing off the gut bacteria does not prevent the termite from being able to digest the wood, if I recall correctly from class... (was a while ago since we sliced up some termites and cockroaches). Either way, you end up with this complex society with protists of all sorts with bacterial endo- and episymbionts, as well as free-living forms. I find it amazing how this system survived locked inside the termite/roach guts for millions of years; it would not survive without them!

Most of the protists are anaerobic and lack conventional mitochondria, instead carrying highly reduced relics as mitosomes or hydrogenosomes; the latter produce hydrogen gas as a byproduct of their metabolic pathways. It was once thought those organisms were primarily amitochondriate, thus shoving them to the base of the eukaryotic tree, also known as the
Archezoan Hypothesis, put forth by Tom Cavalier-Smith; later this hypothesis was rejected as relics of ancient mitochondrial gene transfers were found in some of the host nuclei and the evidence accumulating for one of the prime archaezoans, microsporidia, being found to branch smack in the middle of fungi (beginnings of demise of Archaezoa discussed in Keeling 1998 BioEssays; free access).

It's 4am and I should stop procrastinating with my assignment... but here ya go. Aren't protists so cute and awesome? ^.^

CARPENTER, K., CHOW, L., & KEELING, P. (2009). Morphology, Phylogeny, and Diversity of Trichonympha(Parabasalia: Hypermastigida) of the Wood-Feeding Cockroach Cryptocercus punctulatus
Journal of Eukaryotic Microbiology, 56 (4), 305-313 DOI: 10.1111/j.1550-7408.2009.00406.x

A bit of a break...

Rather swamped with stuff right now - research, class (final next week x_x), other misc stuff. Probably would be best to stay away from the internet as much as I can for the next week or so... that may prove to be difficult. Oh well...

Oh and to top it all off, I think the star alignment is incorrect for PCR these days. May have to wait for them to shift a little so that the PCR prayer waves can reach their destination and make my Taq do its job. Or perhaps its governed by Chaos/Quantum whatever theory stuff BS. Srsly - exact same primers, reagents, temperature, program, machine... similar samples, and one day they work perfectly, the very next round there's no product. WTF? HELP! I need this to work like 3 days ago... argh.

For now, here's a random preview of a post I will finish eventually very soon ^.^

I de-Cavalier-Smithified and combined a couple of his diagrams into what may hopefully be read and understood by a normal human being. The protistology TA instructed me to avoid ever using Tom's diagrams in talks, even after I redrew it.

Here's one of the originals (very typical TC-S):

(Cavalier-Smith 2009 Predation and eukaryote cell origins: a coevolutionary perspective. Int J Biochem & Cell Biol 41:307-322; can't find free access pdf anywhere yet =( )

His phylogenies are even better...!

Hopefully explanation will soon follow...

PS: Just noticed something weird... why does Tom have animals and fungi branching out of 'Choanozoa'? Do 'Choanozoa' include nucleariids and ichtyosporeans too? What do those have to do with choanoflagellates anyway? As far as I know, that region looks something like this:

{Nucleariids + Fungi} {Ichtyosporea [Choanoflagellates + Animals]}; 'Choanozoa' would be a rather awkward group, no?

/pedantry; Damn, now I sound like a cladist...

Down with the "Gene for X" nonsense already!

So how do I properly respond to a question like "Wouldn't putting fish genes in a tomato make it fish-like"?

I could go on explaining how genes don't actually carry any mysterious 'quality' of the organism they're found in, and generally just code for some protein that merely catalyses a specific chemical reaction. For example, jellyfish green fluorescent protein is just a fluorescent protein that gets most 'turned on' by blue light and changes it to green. It has nothing to do with jellyfish stings or tentacles or an aptitude for drifting behaviour. It was simply isolated from a jellyfish, and there's nothing fishy about it. Basically, GENETICS - UR DOIN IT WRONG. But in a more verbose and less condescending manner...

But then they respond that they don't believe you. That it just doesn't seem right. Ok, what do I do now? Not only have they got so much wrong I don't know where to begin fixing, they also have their faith, and information from someone who works with transgenic stuff on a daily basis is not going to be enough to change their minds.

First off, what the hell is the point of asking if you then don't 'believe' their response? If they had an argument of some sort against my story, or if they didn't understand some part, then by all means, ask away! But simply stating you don't 'believe' is a bit of a conversational cul-de-sac. Besides, it doesn't seem that genetics itself cares very much about what you believe.

Next, this leaves me wondering: where has public education gone wrong? How did the 'fish gene' concept emerge in the first place?

Perhaps this is an extrapolation of the "height gene" that permeates introductory genetics classes. Intro genetics is full of problems like "You cross a homozygous recessive short (tt) plant with a heterozygous tall plant (Tt)..." It seems that while convenient pedagogic tools for the study of heritability, problems like this distort the perception of how genes actually work. Genes do not code for qualities or traits - they are just A,T,C,G,N* strings that eventually make their way to being translated into amino acid language to become [hopefully] functional proteins. Playing around with this string of A,T,C,G can result in different phenotypes or physical appearances, starting from the shape and functionality of the protein and sometimes reaching all the way to physical appearance, such as height.

Seeing the gene as coding for a certain phenotype is messy and...well, wrong. Often one locus (gene) has several alleles (variants) which were found in screens for different things by different labs. For example, Arabidopsis rsw2 (radially swollen) was found along with rsw1 when screening for root swelling defects. This same locus was found by a lab studying the plant vascular system, and named irx2 (irregular xylem); dec (deffective cytokinesis) and acw (abnormal cell wall) by some other groups.

Does this gene code for forming a proper xylem, mediating proper cytokinesis or to prevent root swelling? Is this a 'Xylem Gene' or a 'Root Swelling Supressor'? What if I tell you defects in this gene result in substantial dwarfism? Is this yet another 'Gene for Height'? If you cross a short plant (homozygous rsw2) with a tall plant, your F1 progeny are all tall. Selfing the F1 results in 1:3 segregation of short:tall, respectively. Determine the genotypes...yadda yadda. See how useless and confusing this way of seeing genes can be?

The gene in question results in a protein chemically known as an 'endo-1,4-beta-D-glucanase' called KORRIGAN1 by biologists. It's believed to hang out near the cellulose synthase complex and cut the crystalising cellulose strands to relieve tension. (Reiter 2002 Curr Opin Plant Biol; pdf) All those mutants are results of point mutations and insertions in various parts of the same locus - many of the phenotypes actually overlap quite a bit, but the labs were focusing on different areas of plant biology, thus naming the allele as it was relevant to them. Yes, it can get quite messy!

Interestingly, different point mutations in this gene can have different phenotypes - implying there are several protein domains with different functions. Perhaps this thing acts in some sort of complex - the story is rather sophisticated at this point. But let's say it results in weakened cellulose fibrils due to crystalisation defects. Celluse is important in plant cell morphogenesis; essentially a plant cell expands like a balloon in a cage, with the cell wall acting like the cage in directing the expansion. Break the cage, and the balloon will tend to swell spherically. Thus the affected plant would end up with cell swelling. This disrupts growth in many tissues, eventually leading to problems with the vascular system and a severely dwarfed sick-looking plant. This gene doesn't 'code for' any of that, but defects thereof have far reaching consequences in the massive tangle of pathways that is life.


Of course, when you first find a gene, you don't know what it is yet, and thus name it after the mutant phenotype. This can lead to comical results - we have a 'Retinoblastoma-Related' gene in plants! No, plants haven't 'mutated/evolved eyes' (like 'evolve', 'mutate' should NEVER ever be used as a transitive verb...it is a strictly passive, non-volitional, non-directed event!) ... this gene is named after a homologous Retinoblastoma (RB) gene in the human system, where it may have been first isolated when studying the retinal cancer. While this gene does act in human eyes, this is not its 'purpose' or funtion it all. It carries no 'eye' qualities - its actual function is to supress DNA replication genes to prevent extra rounds of DNA copying out of turn. When it's broken, cell cycle problems follow, among them retinoblastoma in the human eye. Plants experience increased ploidy levels (number of copies of the genome) and hyperplasia in proliferating tissue. (reviewed in Inze & DeVeylder 2006 Annu Rev Genet; Gutierrez 2009 in The Arabidopsis Book) I hope it's clear by now that RB and RBR don't code for supressing retinoblastoma, but rather code for closely related proteins with very strictly defined chemical activities and precise functions affecting a multitude of pathways downstream.

Actually, the whole idea of genes having any function at all is an artefact of human reasoning (namely the intentional stance) - Dennett (1995 Darwin's Dangerous Idea) argues that while artefactual, the intentional is a powerful tool in inquiry as long as we acknowledge it doesn't actually imply a real 'purpose' encoded anywhere.

Population biologists (grrr) and evolutionary ecology folks ain't helping either. They intend to use the 'gene for blah' concept metaphorically, but that can easily mislead both the public and even some research in the field itself!


So if genes don't code for qualities or characters, how do you get from genes and proteins to organisms? We're working on that. The complexity of this problem will be enough to sustain many a developmental biologist with a lifetime of work (funding is whole other question altogether =( ) I intend to eventually share some snippets of the stories in that field... some of the mechanisms are truly elegant, others truly outrageous!

But hey, it works... otherwise you wouldn't be able to read any of this!


I do need to think up a simpler way of explaining 'how genes work'...

*Ah, the N, the phylogeneticist's worst nightmare and greatest blessing =P Freedom and ambiguity in one nice letter. (N stands for 'any' in FASTA format - ie A, C, T or G)
It's a bit creepy to watch phylogeneticists change 'edit' their sequences "Oh, that T shouldn't be there... *delete*" ...

Because Echinoderms are cool too...

Apparently there's a deep dwelling sea cucumber thing called a 'sea pig' (class Holothuroidea). It looks like something from an alternate universe:

Go read more about it on The Echinoblog! (via The Artful Amoeba)

Now I wonder if that thing has some cool protistan symbionts or parasite to share with us. I wish they actually reported more on microbial diversity in those deep sea explorations... although considering how surreal and obscure some of the bigger things are, it'll probably take some time before we zoom in...

[insert lame pork-related puns here]


PS: On a slightly related note, if anyone needs to satisfy a craving for pretty pictures, just came across a database/gallery of marine organisms of the Pacific Northwest. There's some bizzare and colourful life outside my cage campus...

(http://www.elasmodiver.com/BCML%20cnidaria.htm)
I think this nudibranch got covered in some marine plasmodial slime mould* fruiting bodies!


*Do those exist at all? I guess a fruiting body would be a rather pointless structure in water...

Dennett just made my day...

Fragment of Dan Dennett's priceless musings during a Templeton-funded session at the Darwin Festival, via Pharyngula:

"I had an epiphany at the end of the session, but I kept it to myself: The Eucharist is actually a Recapitulation of the Eukaryotic Revolution. When Christians ingest the Body of Christ, without digesting it, but keep it whole (holistier-than-thou whole), they are re-enacting the miracle of endosymbiosis that paved the way for eventual multi-cellularity. And so, dearly beloved brethren, we can see that by keeping Christ intact in our bodies we are keeping His Power intact in our embodied Minds, or Souls, just the way the first Eukaryote was vouchsafed a double blessing of earthly competence that enabled its descendants to join forces in Higher Organizations. Evolutionary theology. . . . I think I get it! I can do it! It truly is intellectual tennis without a net." - Dennett

(although, a very minor correction: Prokaryotes too have achieved multicellularity; eukaryogenesis is merely a likely prerequisite to our type of multicellularity. If that. But we can still honour the event by eating crackers and reading Tom Cavalier-Smith's massive 2002 review of Eukaryogenesis and the Neomuran Hypothesis...)

The Tree concept is quite alive and well, thank you

To all you people* claiming the tree of life concept is now obsolete due to lateral gene transfer:
*(eg. 1,2, 3, etc; oh, and this pile of shit that erupted in the media recently)

Did you forget about cells???

There is more to organisms than genome sequences. ie. there's this whole world of cell structure that is vertically inherited along with the genome, and that is a very well-defined solid tree. Especially among prokaryotes, where cellular conjugation is practically nonexistent (never mind the pili). A few genes getting thrown around from time to time doesn't suddenly invalidate the very identity of those organisms!


I argued on a forum once with this...strange person...who insisted unicellular life were all 'one species'! (Seriously, what the fuck!?) Apparently biology stops shortly outside the metazoan clade, since there's only 99% of total biodiversity outside. But see, they're 'pre-animals', and thus don't matter.

Ok, he had the argument that the biological species concept (the only one worthy of recognition, according to the zoophile zoologist in question) was inapplicable to unicellular organisms (which is now a natural class, apparently). Oh. Ok then. But... many of them, if not all, have sex (In many of the previously 'asexual' groups, evidence for sex is rapidly accumulating...eg. in Tryps, Giardia, Trichomonas). There probably is some sort of reproductive isolation happening between groups of organisms? So even the biological species concept still holds there. Even among bacteria, where conjugation seems to be an epiphenomenon of other things, I imagine not all of them are mutually compatible for 'sex' (or selfish plasmid propagation anyway)?

But then the biological species concept doesn't hold for all animals... Bdelloid rotifers, some insects and lizards, to name a few. Are those now all 'one species' too? Oh right, they can't be... because they're animals, and it's bloody obvious whether two animals are the same type or now, duh!

Now, endosymbiosis is an interesting point, but not sufficient to destroy the tree of life. Yes, there is a few fusions of branches (around 3 times overall it seems, once of alpha-proteobacteria (mitochondria) and twice of cyanobacteria (plastids in archaeplastid ancestor, and in Paulinella)). However... even some real [botanical] trees have branch fusion! It's not big deal if it happens a couple times here and there, we can still follow.

I think the diagrams like the one below may be a bit misleading:

(Doolittle WF February 2000 © Scientific American; the trained reader will probably see another reason this makes me cringe. (the 'crown eukaryote' positioning of Animals, Fungi and Plants. Although this was still during the age of Archaezoa...))

Those lateral transfer lines aren't all of one gene; and even if this were a single gene tree, there are thousands of others out there. This diagram represents some well-documented lateral gene transfer events among all the organisms and all the genes we know of; if one were to represent all the genes that didn't undergo a transfer event of any sort, the importance of LGT would quickly be put back in its place. It's not as if entire genomes have been shifted around! (except in the case of endosymbiosis...)

Don't get me wrong, I still think LGT is important and awesome, but do we really need to chop down the entire tree because of a few loopy branches?

Sunday Protist - Choreocolax: Shooting nuclei into foreign cytoplasm

The cell, the fundamental unit of life, consists of a package of information-bearing molecules (DNA) wrapped in some material that delineates it from the outer world (lipid membrane). Basically, a cell is a highly organised and compartmentalised bag of fat and acid. Nothing much to see here...

The story is not so simple however. Multiple nuclei occupying one cytoplasm is a fairly common situation, as are holes (channels) between cells in multicellular organisms. This has even led to discussions about using an alternative "Cell Body" concept instead of the conventional cell (Baluska et al. 2004 Annals Bot. (free access)) - although perhaps it's not worth the bother to panic over redefining everything.

Apparently, some coenocytic algal nuclei can survive plasma-membrane-less upon release from a wounded cell. The nucleoplasm is then surrounded by a gelatinous envelope and subsequently forms a plasma membrane and cell wall. (Ram & Babbar 2002, BioEssays). That could be just a special case, a byproduct of coenocytic wound repair mechanisms.

But there is an organism that specialises in firing its nuclei into the host to take it over! (kinda like installing trojans on your computer...) Meet Choreocolax, a filamentous red algal parasite that leeches off Polysiphonia (another red alga).

(Goff & Coleman 1984 PNAS; free access)

It forms 'planetic' nuclei which are then injected into Polysiphonia by forming pit connections. These planetic nuclei then multiply vigorously in the host cytoplasm and 'take over' the cell:
(PN - planetic nucleus; HN - host nucleus)


The molecular aspect of this process must be pretty awesome -- would love to see that thing's genome sequence (sadly unlikely; this thing isn't particularly popular or well-known. Yet.) and hear about the various pathways involved in taking over the host... and how the nucleus can survive in a foreign cytoplasm in the first place!

There's only one lab studying Choreocolax, it appears. That needs to change...

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.

Naughty nomenclature + Deconvolve This!

Taxonomy can actually be fun sometimes:

Tubifex longipenis

heehee... somehow there's this public image of academics being all mature and serious. In reality, those are rather hard to find...


Recent disappearance was due to leeching off a 2wk 3D live cell microscopy course that happens at UBC every year; they were nice enough to let local students attend lectures... and even leech off the food a bit... Great course, highly recommended for those who think microscopy is just putting shit on a slide and looking at it. Microscopy is a high art and a rather sophisticated science. Course is likewise quite recommended for those who realise that already...they have pretty toys cutting edge microscopes to play with test out for your research purposes.

So yeah, practice safe microscopy -- always use deconvolution on 3D data*! ^.^

Also, physics (and even chemistry) becomes surprisingly interesting when presented by the right people in the right context! Or maybe I'm just crazy... (but so are the course faculty and many students so no one noticed...)

*There is a debate on whether deconvolution works at all on plant material, which is rudely autofluorescent and absurdly packed with spherical aberrations sufficient to utterly destroy your PSF into a disturbing calculation-intensive mess. Our stuff is apparently notoriously shitty for decent microscopy, especially in confocal and multi-photon. And guard cells are among the worst in plants... so decon may not work there (Sorry, Prof. Pawley! >_> )