Field of Science

Marine Microforay – foram and a thecofilosean party

Apologies for disappearing for a while – had an interview, finals and then my arm decided to temporarily rediscover RSI-like symptoms just when I had a term paper to write, so I had to lay off extraneous typing for a while. Then I realised just how much of my life depends on typing, and losing that ability would not only make me worthless and unemployable, but also unable to communicate with many of my friends who happen to be inconveniently dispersed around the globe. So yeah, I should probably stop casually dismissing ergonomics about should you, if you haven't already!

I've accumulated another batch of microscopic findings, this time from marine samples. By the looks of it, I might be moving to the Midwest soon, and thus be deprived of my ocean (and mountains *sob*), so I figured that focusing on marine protists while I have the chance would be a good idea. Swampy pondwater is available pretty much anywhere anyway.

From time to time, you can be lucky enough to find a foram shell in the sediments around here. Live forams can be found too, but much more rarely – I have a couple, but still need to process the videos. This is not a snail:

Foram. Wreck Beach. 20x obj, DIC except for last image, which is in phase.

To save loading time, the rest are below the fold.

Adorable velvet worm composite

Too busy to write a proper post these days, but just happened across a cool Current Biology quick guide to onychophorans(=velvet worms), with a pretty picture showing their diversity (and really pretty textile-like patterns):
Australian onychophorans (Blaxter & Sunnucks 2011 Curr Biol)

The guide itself is quite interesting, recommend reading it if you have time. To entice you, they talk about the diversity of breeding behaviours found in onychophorans:
"Some are fully live-bearing (viviparous), with well-developed placenta-like, extra-embryonic structures that attach to the mother's uterine wall and nourishes growing embryos until the birth of sequences of self-reliant, mini velvet worms."
Onychophorans are way cooler than arthropods ;p

And they can be social with dominant/submissive behaviours, which I talked about in an earlier post (which happens to be one of my most visited, probably because it's not about protists =( ).

And with that, there may or may not be a surprise while I'm away, so stay tuned. In any case, I should engage in some form of proper blogging sometime after the 20th... (finals, shoot me)

Personal army of diplomonads (doodle)

Accidentally discovered the Symbols tool in Illustrator, and had a little too much fun creating a personal army of swirling multi-coloured diplomonads:
They really remind me of diodes. Incidentally, they can also invade diagrams and make them barely legible:
Aren't you glad I haven't gotten around to making cartoon-y spiders and cockroaches yet?

In other news, I'm rather swamped for the next week and a half (as if I wasn't before), as laws of the universe mandate that right between classes and finals not only do you end up with a [potentially awesome] trip across the continent but a particular obscure somewhat rare flagellate you've been searching for throughout the past 5 months or so randomly decides to announce itself unexpectedly. Not only are protists sentient and exceptionally intelligent, the sly little bastards are also evil as fuck.

I do have a couple posts in the making, but don't guarantee anything until after the 20th (this includes replying to comments and emails too)...

May this round of finals be my last...! For this degree anyway...

RQ#03 Is there really a non-natural selection?

I haven't done a random question in a while. This is the third one, apparently.

A grocery store still life, primarily Brassica oleracae
Lately I've been involved in some fairly theoretically discussions about evolution, which tend to push one to pay more attention to terminological precision. Or get very confused And get very confused regardless. Additionally, I hang around some biologists with minority opinions on certain aspects of evolution, and ultimately end up talking about evolution differently, to the point of using different words or same words differently. The usual side effects of specialisation. This becomes particularly evident in heated argument with someone outside your tribe – you start speaking slightly different dialects, if you will. Of course, where there's variation, there's opportunity to pick the variant that suits you better. Ideally, that has something to do with accuracy, since we are, hopefully, still attempting to do science and what-not.

Let's start with the easier of the usage and terminology discrepancies – the term 'natural selection'. Is it useful or does the simpler 'selection' make it redundant? I tend to drop the 'natural' part; laziness and word limits may help, but I think there may be valid theoretical or philosophical merit in doing so:

1. 'Natural selection' was initially proposed in contrast to 'artificial selection', which was used as an effective pedagogical/explanatory move. It got the point across, particularly in an age when humans were unquestionably special and distinct from the natural world. Nowadays, few scientists would seriously make a distinction between human and non-human nature in the context of biology, and thus there really is no artificial selection per se. 'Artificial selection' is 'natural selection' performed by humans to pressure their organisms towards traits the humans find favourable. In this case, the humans are part of the environment, playing a similar role to predators, except they breed the variants they like instead of instantly culling them. With no need for an 'artificial selection', is there still a need for 'natural selection', since there no longer is a valid contrast?

2. 'Natural selection' is often equated with adaptation. This isn't to say 'selection' by itself isn't, but 'natural selection' is the variant used most often in popular writing, some of which can be careless and inconsistent with its terminology. While presumably many of the authors do truly understand that selection and adaptation are different things, adaptationism has led some to consider the difference irrelevant. If adaptation is the sole phenomenon responsible for all the observable or cool things in biology, does it really matter if it's used interchangeably with natural selection? When a term is learned and frequently used incorrectly, it is extremely difficult to fix even in an individual, let alone a population. While 'natural selection' is not meant to be conflated with adaptation, it is, and has thus been tainted.

3. Use of 'natural selection' implies that phenomena like sexual selection and kin selection are somehow distinct, or special. These are secondary phenomena, special cases or manifestations of selection. That is, sex and kin selection are subtypes of 'natural selection' and do not lie on equal hierarchical level as it may first seem. While most of the scientific community has no problems understanding this, it is perhaps not the clearest delineation of the terms for the general public or students. This way, we can also keep 'artificial selection' to refer to domestication (although I don't see the necessity in doing so) without it contrasting with the 'natural' kind.

4. This is the least important point, but rather a more personal one. I dislike Darwin-worship; I'm not a 'Darwinian' (nor a "Neo-Darwinian), don't know what that means and frankly don't consider this question relevant now, over a century after Darwin's death. While history of science is indeed fascinating and undeniably worthwhile to learn about, we shouldn't trap ourselves in our history. In fact, I think equating evolution with Darwinism is a bit offensive to all the hard work and frustration of subsequent researchers that have contributed to the field – do they not matter? They work for evolution, not Darwin. 'Natural selection' has been too often tightly associated with 'Darwinism', and often plays a part in Darwin-worship. In other words, the term has acquired some baggage; mind you, not through Darwin but rather through his fervent supporters afterwards.

5. Population geneticists seem perfectly happy with just 'selection'. They're the ones who actually study the mechanisms of this stuff, so if it works for them, perhaps it should be adequate for the rest of us?

I don't mean to nitpick on words and 'mere semantics', but given the difficulty of conveying ideas to those outside your field and the general public, any site of potential confusion is worth trimming if we can. Those on the writing end are also prone to sloppiness and mistakes, so we too are susceptible to the confusion potential. That said, 'natural selection' has stuck around for this long – perhaps there is a beneficial reason I missed out on? This is an honest question – I've never really been formally trained in evolutionary biology save for a basic first year level, and may thus miss large chunks of theory. As I mentioned before, I'm being 'brought up' in some minority circles of evolutionary thought.

Why should we still use 'natural selection'?
Your turn. Just be gentle with the philosophy – I'm rather slow at following complicated abstract theoretical discussions, which is why I do experimental science ;-)

"Just another ciliate" – importance of sexy descriptions

ResearchBlogging.orgThere are species descriptions, and then there are species descriptions. All too often, you come across a mention of some obscure but ridiculously cool-looking organism, with only a very scant description of what it looks like and what it does. Much less often, you can come across yet-another-new-species (usually of a ciliate), but a particularly nicely described one. Again, those super nice descriptions tend to be of ciliates, largely due to the likes of Wilhelm Foissner and his academic offspring. Descriptive detail can only make species more interesting, and eventually of great potential to be useful for science. (Conversely, many a taxon has been rendered invalid due to poor description)

A sexy description is also a great way to lure readers into noticing your otherwise garden variety new species. Case in point – I see this random IJSEM paper on a couple new marine ciliate Frontonia species – nothing too earth shattering. Being rather compulsive about skimming over any mention of a protist I see in the literature, I click. Being rather lazy and a shallow-minded picture-loving type, I head straight for the figures. Unexpectedly, they dazzle me with sexiness. Desperate for something easy to blog about for the next little while (impending interview, exams, end-of-term chaos, etc), I suddenly find your otherwise-routine new species description quite exciting and blog about it. Here, Frontonia mengi and F.magna get screentime largely thanks to their authors.

Some of us in science are that simple minded. If more people realised that and preyed upon our ilk with shiny pictures, think how much more presentable science as a whole would be!

(That said, no amount of gloss and shine can make your data more or less wrong. But it can, and does, dazzle some of us into overlooking a flaw or three...)

Actually, the above was just a long-winded elaborate excuse to post ciliate porn. Ah, check out the kineties on that ass!

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Well, those were mostly just shots of its oral ciliature, but close enough. The root structures of the cilia are highlighted with silver nitrate and carbonate staining, yielding the pretty staining effect. a-c section through the 'mouth'; d shows the "membranelle" around the 'mouth'. e shows the area behind the mouth; arrowhead points to the cytopyge. 'Cytopyge'? Well, a cell's gotta get rid of its waste somehow, and ciliates actually have the cellular analogue of an asshole. Not the socially dysfunctional kind. So yeah, look at that ass. g shows detail of the cortex, h is the overall view of the ventral ciliature. At i, the rows of cilia "stitch together" at the 'anterior suture'. k shows the germline micronucleus (Mi) and somatic macronucleus (Ma).

Now for some delicious DIC:

Frontonia mengi. See text. (Fan et al. 2010 IJSEM)

Crisp DIC intoxicates me. The seductive allure of polarisation-derived faux-3D relief is nearly impossible to resist, especially when you have the fine complex cell of a ciliate. In fact, good DIC is often better than staining, since you don't have to fix (kill) anything. Unfortunately in the case of some larger ciliates, some degree of squishing must be done otherwise the sample is too damn thick for crisp DIC. I think the gist of microscopy can be summarised as the never-ending compromise between care of specimen and care of the optical setup. The most powerful microscopy generally requires total destruction of the specimen, whereas the most natural and undisturbed data can only be attained with simple techniques and weak optics. It's like the Heisenberg principle of microscopy: the more accurately you determine the state of your specimen, the more mangled your specimen gets.

I digress. In the above plate, a-e show general views of several individuals of F.mengi. Remember my rant a couple posts ago about the usefulness of depicting morphotypical (shape type) variation? I hope it is evident here how that can be useful. For example, if only figure a was published, one could be mislead to consider that large vacuole a characteristic feature of this particular ciliate species. The other four images, however, show that to be a feature of just that specimen instead (non-contractile vacuoles, in this case). Furthermore, the authors even invluded a table of morphometric data, measuring the body dimensions and some visible subcellular details (like numbers of kineties and nuclear size) of 23 individuals.

The arrow in 1b points to a contractile vacuole – one could just make out the channel leading to the cell's exterior for expelling its contents. f-g show sections of the mouth, live. h shows detail of the cell surface, the oral apparatus quite visible (as is the cytopyge). i details the cytopharyngeal rods, which are specialised structures this genus of ciliates employs to devour long strands of algae. The characteristically massive ciliate nuclei are visible in j – the arrow points to the macronucleus while the arrowhead points to the micronucleus. No staining necessary, fuck yah.

Frontonia, like many ciliates, is also armed and dangerous. The surface is loaded with extrusomes (k), which can fire leaving a trail, much like the cryptomonad ejectisomes (l). m and n show the contractile vacuole and its exit pore, respectively. The contractile vacuole is necessary for osmotic regulation, especially in freshwater species, and is somewhat analogous in function to our kidneys.

The second species, Frontonia magna, is also well-described. In these specimens, one can make out the algal filament and its constituents – particularly in b, e and f. Like F.menga, it's also loaded with extrusomes (h). I particularly like i, which shows the ciliature of the anterior suture. It's quite hawt.

Frontonia magna. See text. (Fan et al. 2010 IJSEM)

Of course, no description is properly complete (in my opinion) without drawings to accompany the micrographs. Drawings highlight the important features observed by the authors, and are useful in combining information gathered from multiple sections and imaging techniques in a convenient summary. Making an accessible visual summary of a huge pile of microscopy data is no easy task, and is very much an art.

Continuing with F.magna, a summarises the ventral view of a typical individual. b provides a sketch of the sutures, without the distracting detail. c shows the side view, along with the contractile vacuole. d shows the relative sizes and positions of the nuclei. e, again, emphasises variation – it shows the various ways a cell appears after overeating with algal filaments protruding all over the place. It's amazing how hard prey can try to make their predator look like an entirely new freaking domain of life, by stretching it out and colouring it in all sorts of funny ways. A similar phenomenon has been responsible for an entire mistaken genus, Ouramoeba, in the otherwise totally awesome Leidy 1874 work on amoebae. The algal prey is detailed in g, while h details the cilia around the oral apparatus.

Frontonia magna See text. (Fan et al. 2010 IJSEM)

Of course, no species description these days is complete without a healthy phylogeny, and Fan et al. got that covered too. I feel I've stolen more than enough figures already, so I'll just say their Frontonia spp. fit snugly within Peniculia, a group including the famous Paramecium, and the two species are sister to each other. There's also a composition of drawings from multiple sources for other members of this genus, so this paper is a nice current reference for Frontonia, if you ever wake up one morning needing one. Believe me, these cravings may strike at the oddest hour.

Anyway, I just thought these figures really deserve to see the light of day, and not just remain buried away in what will very soon be just the back issues of a microbial systematics journal. While some may look down on routine-seeming research like basic species descriptions for they do not provide a fancy high-level synthesis or anything, but ultimately, these fancy high-level syntheses are built on lower-ranking papers like these, and cannot exceed the quality of their constituents. It is primary 'basic' literature like this that forms the foundation of science; without species descriptions, without "yet another gene/genome/tree/whatever", there will be nothing to base the more glamorous studies on. This is why impact factor is a load of bullshit, and anyone whose hands itch to oppress "low impact" science should be kept the hell away from research funding strategies, for they obviously have no fucking clue how research works in the first place. Grrr. How can anyone vote against a species description as awesome as Fan et al. 2010 above?

Fan, X., Chen, X., Song, W., Al-Rasheid, K., & Warren, A. (2010). Two new marine Frontonia species, F. mengi spec. nov. and F. magna spec. nov. (Protozoa; Ciliophora), with notes on their phylogeny based on SSU rRNA gene sequence data INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY DOI: 10.1099/ijs.0.024794-0