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Field of Science
Sixty-four years later: How Watson and Crick did it9 hours ago in The Curious Wavefunction
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post doc job opportunity on ribosome biochemistry!2 years ago in Protein Evolution and Other Musings
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Blogging Microbes- Communicating Microbiology to Netizens2 years ago in Memoirs of a Defective Brain
Out of Office3 years ago in inkfish
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in The Biology Files
No, not the annoying kind that secretly restarts your computer in the background because you just bought it and haven't gotten around to deactivating auto-update yet and told it to fuck off the last few times so it didn't pop up the window anymore because it was sad. Or the kind that Adobe's PDF reader mysteriously wants about four times a day. Just a very late bloggy kind.
Apologies for disappearing for a while there. Personal issues came up and didn't really feel like writing about science (or reading much about it for a while). Long story short, I'm may well be a failed scientist at this point (no grad school for me, yay), and the academic career is one of the few where once you fall off the track, it's practically impossible to get back on. And unlike in most other careers, the skills you acquire by that point are nontransferable anywhere else, meaning you're screwed, period. Add to that the worst economy since the Great Depression, and the party starts off with a bang. That said, I'll continue with my attempts to sneak past academia's fortifications under the cover of night, if no other reason than that banging my head against brick walls fucking arouses me.
Anyway, I'm getting back to blogging now. Should at least take advantage of the fact I still have a computer and internet; might be a bit harder to blog when unemployed and homeless ;-)
There are some exciting developments next month: one I can't tell you about yet as it's part of bigger news; the other is that I'll be going to a phycology-protistology meeting (PSA-ISoP) mid-July and will be officially blogging it! There's lots of awesome research going on in the area and I'm happy I'll be able to share some of it with you.
Microscopy Reddit Community - /r/microscopy
Every once in a while a stack of undeciphered micrographs appears before someone's conscience, and every once in a while a resolution of this issue is attempted by approaching yours truly. I'm still a novice to the realm of the small, and usually fail to identify creatures (or artefacts) in question, leaving behind a trail of disappointment and pristine befuddlement. Forwarding those images to friends and colleagues would be awkward, since those people have enough on their plate to begin with. In short, would be nice to have a centralised place where people could share images and others could voluntarily look them over and comment on them. Micro*scope/EOL is a nice image repository, but generally the images there are of good quality and are finished products; furthermore, I still don't know how to work the interface there despite having access privileges. What would be great is if people could host images wherever they like, and then link to them in a centralised place for discussion where anyone could participate. In other words, Reddit.
There already was a microscopy subreddit (a Reddit community), but it was largely inactive and abandoned. Anyway, I'm now a moderator there, and would like to develop it into a community where micrographs of all sorts can be shared and discussed, with emphasis on microbial organisms (but sliced up macrobes welcome too). Creating an account is really easy, as is submitting a link (just make sure it goes to /r/microscopy and not some other area of reddit). We need participants though, so if you have any neglected mystery images, please post them, and if you're in the mood to browse micrographs from time to time, feel free to stop by! Just keep in mind anyone can see the subreddit including the images, so careful with potentially publication-worthy data...
Hope to see you there!
There's a really awesome Russian underwater macrophotography blog I came across a while ago that you should all know about. The photos are stunning, mainly of pretty tiny inverts in the White Sea in northern Russia (and plenty of shots of Northern Lights and white nights and all that).
[Sticky proteins and complex relationships]
[(protein) Relationship drama: promiscuous proteins in small populations]
[Not all is good that sticks: non-adaptive complexity gain through compensatory protein adhesion]
[Man, I suck at titles]
NB: This post can be considered as part 2.5 of my In defense of constructive neutral evolution series; also recommended for some background are part 1, discussing selection, drift and Neutral Theory, and part 2, discussing Constructive Neutral Evolution; to answer a popular question, part 3 *will* materialise
Constructive neutral evolution is one mechanism of complexity increase without any associated increase in fitness – or, in other words, non-adaptive complexity gain. Basically, a random interaction between two proteins can lead to a fixed dependency if this interaction compensates for a mutation that was otherwise lethal – termed 'pressuppression'. In this way, previously unnecessary dependencies accumulate to make a very bulky, bureaucratic system that essentially does the same thing. We've all seen it in our institutions, and evolution is about as efficient.
Fernández and Lynch 2011 Nature paper, from here onwards referred to as "the paper".
Protein 'stickiness' can be enhanced by biochemical means. Proteins vary in stability, and themselves come in populations – generally, most are in the optimal conformation that is presumably functional, but some individuals are messed up. This happens well past the sequence and folding errors, and some perfectly 'normal' proteins can be in a suboptimal state at any given time. Clearly, this affects the overall efficiency of the protein – even if it's enzymatically awesome, the overall 'protein' as we biologists understand it (sans population aspect) would decline in efficiency if a large chunk of its population is in a misfolded state.
One aspect that pushes around the proportion of the protein in the 'right' conformation is how well it plays with water. It shouldn't be too surprising that hydrophobic regions induce instability. What was new to me, but perhaps old news to those who actually understood chemistry, is that the exposure of the polar(hydrophilic) protein backbone to water also has a destabilising effect – and not only that, but often more significant than that of exposed hydrophobic regions! This may seem counterintuitive – doesn't water like hydrophilic regions? And there lies our problem.
Water molecules are attracted to polar groups, and the amino acid backbone is quite polar. This means little water molecules wander in towards the backbone and form hydrogen bonds with it. The problem is twofold: first of all, the protein, like all molecules, likes to 'jiggle'. The more it can jiggle in its given conformation, the more favourable that conformation is thermodynamically since its satisfied by more states. Entropy, etc. (now we're *really* entering territory I know nothing about, since my phys chem experience is locked away by PTSD...). Hooking up this backbone with water molecules reduces its 'jiggle' room, and makes it less thermodynamically stable – making change to other conformations more probable, therefore possibly leading to more errors in the protein population.
Secondly, as detailed further in the paper, water likes to hang out with more of itself. Water molecules are happiest in foursomes, sharing four hydrogen bonds with their neighbours. When a creepy protein backbone emerges and lures an unsuspecting water molecule away into the protein's murky depths, the water molecule cannot form as many bonds with its fellows (or as many hydrogen bonds, period), and is really sad and lonely. Or, in proper terms, the system becomes less stable, since thermodynamics will favour an arrangement where these water molecules are all happily coordinated with each other, and not being molested in a corner by an amino acid polar group. In other words, exposing the polar backbone (Solvent-Accessible Backbone Hydrogen Bonds, SABHBs in the paper) to water induces what is called Protein-Water Interfacial Tension (PWIT).
One way this tension can be released and the backbone exposure ('coded for' by genes, by the way) can be compensated for is if a random other protein (or more of its own kind) are recruited to cover that exposed backbone. This would help stabilise the protein conformation, and allow this potentially deleterious drawback to be tolerated (and get fixed in the population). Ultimately, the second (and third, etc) protein can become exapted for something useful, although just an eventual dependency is good enough to make sure these proteins stick together permanently. The crazy web of interactions gets crazier.
Fernández & Lynch's fig1a suffices perfectly but I like making diagrams, so I made one anyway. See text.
Now I'm about the last person to willingly blog about biochemistry, and this seems to have little only a distant relevance to evolution, particularly the non-adaptive kind that fascinates yours truly. It will make sense in a bit. Recall from a few seconds ago (hey, already difficult for some of us) that protein instability leads to reduced protein efficiency. This reduction is generally tolerated, however, until it's bad enough to have a higher chance of being removed. Recall from [what should be] introductory population genetics that selection acts probabilistically, with true slightly deleterious mutations have a lesser, but still significant, chance of fixation than strongly deleterious mutations, which selection has a higher chance of taking care of before drift quietly fixes it. (more detail in older post here) Since proteins are, quite unsurprisingly, also governed by fundamental principles of population genetics, drift becomes involved there too.
As populations get smaller, drift becomes a more dominant force relative to selection, and the window of 'effectively neutral' mutations – slightly beneficial and slightly deleterious, but unlikely to be dealt with by selection – increases. More mess is tolerated. This means more protein inefficiencies are allowed to fix in the population, those induced by backbone exposure among them. Since there are now more proteins that are no longer happy with themselves (or, rather, have an increased Protein-Water Interfacial Tension), they are more likely to stick together for biochemical stability. And here Constructive Neutral Evolution can come in too, allowing further deleterious mutations that are now presuppressed by the recruited proteins. In a way, this greases the presuppression process, rather than competing with it as this BBC news piece made Ford Doolittle appear to suggest.
Now, this is all great in theory, but is there any real data in support of this? For one thing, there is a clear increase of interactome (set of all interactions in an organism) complexity correlating with decrease in effective population size, suggesting a link between lax selection and accumulating complexity. Furthermore, the proteins in organisms of these smaller populations have more blistering backbone exposures to water. Supporting the relationship with population size further yet with the advantage of more phylogenetically independent events (but less interactome data), bacterial intracellular endosymbionts consistently exhibit higher protein backbone exposure (hydration) than their free-living counterparts. Selection appears to disfavour not only polar backbone exposure (also described as 'poorly wrapped proteins' in the paper), but once again, the rise of interaction complexity as a whole. (Fernández and Lynch 2011 Nature, in case you somehow managed to miss that)
Obviously I like this paper because it adds another mechanism to the arsenal of evolutionary processes happening independently of adaptation. But moreover, I don't think one can find too many examples of biochemistry mixed with population genetics. You hardly find cell and developmental biologists thinking about population genetics, and perhaps many biochemists have never even been exposed to such a subject. When fields that should never come that close together do, some really nice explosions of insight can occur (my sad attempt at chemical metaphors). We really need to talk to other more, and maybe even wander over to other departments from time to time. It's sometimes (often) frustrating to communicate with those strange ones from afar, but just like ethnic xenophobia, its interdisciplinary counterpart must also be overcome.
Figure 2a annoyed me a little as it ignored phylogenetic relationships, which is a big no-no when comparing properties of taxa. The figure is technically fine, especially since there aren't any correlation analyses there, but it's hard to discount phylogenetic history as being the cause behind the correlation of the traits without actually the characters on a tree. Anyway, since I like playing with data and running statistical analyses on things, especially when I didn't actually have to go through the pain of obtaining the data myself, I mapped some characters (interactome complexity from fig2a) on a phylogeny:
Unfortunately, even the most basic statistical operations become an epic headache when trees are involved, and very quickly things become painfully complicated, for the human as well as the computer. Especially when you're handed a dataset of mixed categorical and continuous characters, as I learned the hard way last night. After fighting Mesquite for a good many hours, I finally had to resort to extracting the Ne*µ (effective pop size * mutation rate; roughly put, both lead to increased selection efficiency) estimates from Lynch & Conery 2003 – relying on an intersection of two datasets meant that our taxon sampling was quite sad by the end of this enterprise. Anyway, I ran a pairwise comparison test (Maddison 1999 J Theor Biol) on the data, which probably isn't the best thing ever, but I got something resembling significance: p = 0.019. Depending on how statistically noisy your field is, you may even deem this acceptable. In any case, not too bad given my crude (and somewhat clueless) analysis and limited taxon sampling:
I mostly did this because I thought it'd take a couple hours max. If hours meant days, that wasn't too far off... but hey, I learned something!
Acknowledgments: thanks to Lucas Brouwers for helping me wade through the heavy biochemical stuff, and to Mike Lynch for explaining the key idea of the paper a while earlier. Otherwise I would've probably been too daunted to even read it, let alone blog about it...
Oh, and my Twitter people for random phylogenetics advice ;-)
Fernández, A., & Lynch, M. (2011). Non-adaptive origins of interactome complexity Nature DOI: 10.1038/nature09992
[will add some supplementary refs once I return to internet on Monday...]
*Or perhaps something happened to both that made them prone to evolve this bizarre system.
Genomic quirks are not just interesting in their own right as some arcane oddities, but can reveal a great deal about the dynamics of genomes in general. The dinoflagellate splice leader system turns out to yield a very crisp illustration of the power of ratchets and the toll of reverse transcription on genomes.
To reiterate, every single nuclear gene transcript in a dinoflagellate must be spliced with the 3'cap-bearing 'splice leader', or else it simply won't work. This means that the dino is full of mature transcripts with splice leaders attached to the transcribed genes. Enter reverse transcriptases, which are prevalent in probably most, if not all, eukaryotic genomes, thanks to viruses and their partners in genomic parasitism crimes, transposons. When they're not busy moving transposons around and helping viruses move in, they reverse transcribe random gene transcripts for fun, that may then, on occasion, be successfully recombined back into the genome. This process probably doesn't happen [successfully] every day, but over thousands or millions of years (and countless individuals) is rampant enough to leave a noticeable trace in the genome.
So we have a load of transcripts floating around with an extra sequence stitched onto them from the splice leader. Do the reverse transcriptases care in the slightest? Of course not: to them, a ribonucleotide is a ribonucleotide, give or take some trace biophysical stuff that might make a couple people cringe at what I just said. (meaning, I wouldn't be surprised if there could be some slight but ultimately detectable biases there too) This means that splice leader, on occasion, actually makes its way back into the nuclear genome attached to the beginning of the gene.
Mmmm, actual data! Note how the oldest SL piece closest to the gene (on the right) is the most degraded. (Slamovits & Keeling 2008 Curr Biol)
Splice leader trans-splicing not necessarily promoting reverse transcription – only makes it easier to detect. In other words, it inadvertently makes for a wonderfully convenient system where you can actually track what happens to a gene after it gets reverse transcribed. Once the gene makes its new home, the old gene copy is still present and they generally would be functionally redundant, so the dual-copy state is extremely unstable as ultimately the loss of one of the copies will be tolerated. If the newly transcribed copy is lost, we never see it and thus don't talk about it in the first place. However, once the clean original is lost, only the gene with the crap from the splice leader remains, and reversal to the original state is so improbable it's practically impossible. In other words, this process is a wonderful example of an evolutionary ratchet.
This ratchet example is therefore an elegant case of evolutionary direction that's not particularly well explained by the central dogmas of Modern Synthesis or (neo)Darwinism, where selection is the force that crafts order and directionality, with mutation a mere passive provider of material to be molded. I will go into a deeper discussion of this in another post (there's a cool paper coming out soon), but I think it's worth briefly mentioning here too while we're at it. The "mutation" step (to which, I guess, this trans-splicing and reverse-transcription process can be awkwardly attached) here is what provides a drive, a push in a certain direction, and towards increasing complexity, no less (although that last detail is irrelevant). While selection is present and provides constraints (if both genes are lost, for example, the organism dies), it does not do the 'driving' or 'forcing' in this system. Very crudely put, selection here is the passive phenomenon, and mutation is at the wheel.
Another case of intrinsic directionality, but where reversal is allowed, is your garden variety directional bias – where proceeding in one direction is more probable than going backwards. A very basic example of that is if the replication machinery favours a certain type of nucleic acid – left to its own devices, the genome base composition would be skewed in that direction. Boundaries can also induce an apparent directionality, but in this case it's no longer intrinsic... that's, again, a topic for another day.
This idea was a part of the Mutationism theories in the early 20th century, which were a little extreme and perhaps premature, since mutation was far from being even marginally understood at the time. In the usual melodramatic manner characteristic of academia and the scientific community, the pendulum swung far to the opposite extreme, and Modern Synthesis was born. It became heresy to think that mutation itself can actively contribute to direction and order. The field became engulfed in a false dichotomy, where either selection or mutation can actively provide direction, with the modern folk siding with the former. That is a serious mistake and an unnecessary waste of great explanatory potential – you can go so much farther with selection, drift, mutation and recombination all at the wheel, each pulling with different magnitudes in various directions. Well, technically, you wouldn't if you were the thing being pulled – which resonates so well with the absense of 'ascension' or general active directionality in the evolutionary system as a whole. Evolution is a slow, painful, inefficient and rather stochastic process, partly because the cart is being pulled in so many ways.
(The latter part, concerning directional biases and Mutationism, is based on various publications and conversations with Arlin Stoltzfus and Dan McShea, whom I gratefully acknowledge. =D)
McShea, D. (2001). The minor transitions in hierarchical evolution and the question of a directional bias Journal of Evolutionary Biology, 14 (3), 502-518 DOI: 10.1046/j.1420-9101.2001.00283.x
Slamovits, C., & Keeling, P. (2008). Widespread recycling of processed cDNAs in dinoflagellates Current Biology, 18 (13) DOI: 10.1016/j.cub.2008.04.054
Stoltzfus A (2006). Mutationism and the dual causation of evolutionary change. Evolution & development, 8 (3), 304-17 PMID: 16686641
Protistology Q&A on Reddit
And now to randomly show off a random Haptorian ciliate – meet Litonotus, a vicious predator armed with terrifying toxicysts, which you can see as long narrow things in its cytoplasm. Also note the two prominent macronuclei visible as clear-ish round areas in the cell. Litonotus is cool and all, but the bastard preys on creatures like Euplotes, which are kind of adorable (imagine Litonotus eats kittens...that's how bad it is). Nature is red in
Apologies for the delay – am behind on pretty much everything and frantically trying to tie up loose ends of my degree, fun times. Also, it's kinda awkward to write up a carnival post with only THREE submissions – you guys really need to submit more and/or write more MolBiol posts!
It seems molecular biology doesn't get blogged about specifically as much as evolution and diversity – perhaps because molecular biologists are usually busy troubleshooting their PCRs and RNA work for weeks on end, and have little time left over to write. In fact, judging from recent woes experienced by some of my lab buddies, I'm beginning to doubt the existence of RNA and believe it may all be a giant elaborate hoax invented to enslave more grad students. Have any of you ever *seen* RNA? That's what I thought...
This month we have a very biochemical (post-translational, if you will) MolBiol Carnival featuring enzyme spec, cyanobacterial biofuel precursors and some sweet diastereomer metabolism regulation.
Christopher Dieni at BitesizeBio has a nice write-up on measuring enzyme kinetics using UV spectrophotometry, complete with procedure, tips and troubleshooting – the kind of thing you wish accompanied every assay you've been assaulted by. Not being anything close to a biochemist, I had no idea you could actually observe enzyme action using something as simple as a spec, so this is quite cool!
Cyanobacteria and biofuel production
With growing concerns with using land plants for biofuels (for one thing, kind of odd to use food to power cars when not everyone has enough of it...), increasing attention has been turned towards algae eukaryotic and not. For one thing, algae are already quite good at photosynthesising and are vastly more abundant than plants, and arguably have the largest contribution to global photosynthesis – not surprising given the earth's surface is 70% ocean. Michael Scott Long at a NASW.org blog explains recent developments in genetic engineering and domestication of cyanobacteria for fatty acid production.
Diastereomers and regulation of metabolism
Stereoisomers are the beginning chemistry student's worst nightmare – they're so similar and easy to mix up, particularly if you're like me and can't tell left from right to begin with. However, a bacterium (rather, its enzymes) would have little trouble with the stereochemistry portion of a intro biochem class – to them, stereoisomers are day and night (and other things). Glucose and galactose are 'close enough' to each other for a biochem student, but a flipped arrangement at just a single stereocentre is enough to require a whole new set of enzymes and drastic changes in the pathway. E.coli prefers glucose, but can also process galactose (compromising its growth rate) by embellishing its metabolic pathways a little – the products of galactose digestion are sent to the tricarboxylic acid cycle via the glycoxylate shunt. Becky Ward at It Takes 30 discusses how sugar type availability affects the transcriptional regulation of this glycoxylate shunt, among other things, featuring a galactose-loving mutant.
This was fun. Wish there were more submissions – having to write up random blog posts forces me to revisit forgotten subjects and explore new ones: I'd never brave a post on metabolic regulation on my own! By not submitting, y'all are having a deleterious effect on my education... ;-)
The next edition will be hosted by our resident microbiologist @labratting at Lab Rat, and she better get more than three submissions... come on, we do so much molecular biology in almost every field of biology! Write 'er up, dammit!
We have some pretty awesome microscopy and video equipment in the lab, and I'm lucky to have a PI nice enough not to mind some of us using it to fuck around with random samples in the middle of the night. I hope it may help bring the microbial world a little closer to you, and add a whole new dimension of time to our protists.
Let's start off with some euglenid metaboly, since it's quite hard to talk about without seeing it. Actually, the true reason is that it's about the first thing my cursor landed on when I opened my pile of videos for file conversion. But just as we ascribe purpose to evolutionary happenings, we can likewise ascribe purpose to my selection here ;-)
Since I'm lazy and behind on about a million things (to the point where I must mention it twice), just gonna copy the short description I wrote for this bug on the YouTube page. Enjoy!
This is a heterotrophic euglenid, perhaps a Peranema sp., exhibiting metaboly in all its splendour. The cell might be slightly squashed or otherwise damaged, keeping the flagellate conveniently in one place. The clear vesicle near the base of the flagellum that grows and shrinks is the contractile vacuole, the flagellate's analogue of the animal secretory system. At the tail end are refractile starch granules used to store energy.
Metaboly is a form of cell movement that is most famously exemplified by ciliates, but also known in some other flagellates. It appears to be caused by the specific arrangement of microtubule (cell skeleton) bundles at the cell periphery, and greatly enhanced by the 'armour plates' of the euglenid surface, which is lined with long pellicle strips going from the flagellar insertion all the way to the tip of the 'tail' -- as the cell twists about, the strips slide against each other and result in this movement. Euglenids with fused pellicle strips, like Phacus, are incapable of metaboly. The function of this movement is unknown, and there may not be any in particular.
The hairy thing next to the euglenid is a badly mangled ciliate.
Freshwater, Apr 2011, Vancouver
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:
To save loading time, the rest are below the fold.
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)
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...
|A grocery store still life, primarily Brassica oleracae|
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.
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 ;-)
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)
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
5-8 Dermamoeba going about its business (n – nucleus, cv – contractile vacuole). 9 – Dermamoeba lounging about in cysts (c) upon devouring some algae (chain-forming diatom or some Trebonema-like thing). Nom nom nom. (Smirnov et al. 2011 EJP)
Dermamoeba's fine coat consists of thick bi-layered glycocalyx (a covering of fluffy sugar-proteins), sometimes with additional 'dense matter' lining the cell membrane. Upon encystation, an extra layer, the cell wall, is formed, but the contraption is thick enough without it already, at about half a micron.
EM sections through the intense Dermamoeba cell coat. m – cell membrane, gl – glycocalyx, adm – 'arrangement of dense material' (ie, "we don't know"). The glycocalyx often forms pretty patterns when sectioned. (15 is part of a Golgi body) (Smirnov et al. 2011 EJP)
Diagram of Dermamoeba's unusual feeding procedure. After the algal prey (al) is contacted by the amoeba (am), the glycocalyx (gl) is digested and the prey is drawn in by thick actin microfilament bundles (mf). The resulting food vacuole (fv) is conveniently devoid of coat material. (Smirnov et al. 2011 EJP)
And here the food cup is 'live', or was before some electron microscopist brutally murdered it in osmic acid and sliced it up:
EM sections through prey (al) being engulfed by the amoeba (am). Note the disappearance of the glycocalyx (gl) at the centre of the invagination. (Smirnov et al. 2011 EJP)
How do some of the other coat-bearing amoebae get around their irremovable clothing? Without going into much detail (amoebozoan surface coverings are really cool...), the glycostyle-bearing Pellita simple sticks small 'subpseudopodia' through it for both moving about and feeding. In fact, some propose that the glycostyles may help it move by reducing the surface area in contact with the substrate – keeping the sticky cell membrane away on stilts.
Top left: Pellita walking on stilts of glycostyles (depicted at the right). Bottom: extruding sub-feet across stilts for feeding. (Smirnov & Kudryavtsev 2005 EJP)
PS: My committee* has voted to remove "Sunday Protist" from Sunday Protist titles, since:
a) They seldom come out on Sundays anyway (lulz); and
b) Takes up too much valuable headline real estate. Since we bloggers are supposedly playing pseudo-journalists or something, might as well play it right... ;-)
(and c) Structure and I aren't the best of friends.)
* Given how inefficient my brain is at accomplishing anything, I've concluded it can only be composed of a close neural approximation of a committee. Explains the indecisiveness as well. Probably requires a double majority to pass any major decisions, and hence is about as effective as the Californian government. Without the sovereign debt crisis, fortunately.
SMIRNOV, A., & KUDRYAVTSEV, A. (2005). Pellitidae n. fam. (Lobosea, Gymnamoebia) – a new family, accommodating two amoebae with an unusual cell coat and an original mode of locomotion, n.g., n.sp. and comb. nov European Journal of Protistology, 41 (4), 257-267 DOI: 10.1016/j.ejop.2005.05.002
Smirnov AV, Bedjagina OM, & Goodkov AV (2011). Dermamoeba algensis n. sp. (Amoebozoa, Dermamoebidae) – An algivorous lobose amoeba with complex cell coat and unusual feeding mode European Journal of Protistology : 10.1016/j.ejop.2010.12.002
Cover slip floated ~ 1wk on marine sample from intertidal silt at Stanley Park. (40x obj, DIC and phase, resp.)
EDIT: Confirmed Filoreta.
Almost overlooked it thinking it was just slide gunk. Amoebae suffer all too often from that fate – apparently Parvamoeba, one of the most common and ubiquitous amoebae, was only described in the early 90's (Rogerson 1993 EJP) because it was tiny and no one noticed.
Could be something like Filoreta sp. (Rhizarian), but something feels off about it. Filoreta doesn't seem to stretch cytoplasm between filopodia like this specimen does. Maybe it's more like the amoebozoan Corallomyxa and Stereomyxa, or stramenopile Leukarachnion. Then again, amoebae are notoriously dynamic in their morphology. Something that's a far bigger issue in the microbial world is the necessity of getting a sense of the morphotype range of a species; one specimen doesn't quite cut it as it does for animal taxonomy.
In fact, perhaps instead of the ridiculious (for us) ICZN and ICBN requirements for submission of material for curation (many species neither like being cultured nor preserve all that well on a slide), for microbial species there should be a requirement for additional images of different specimens, if possible, to try to capture some of the morphological range. But then again, I'm not a taxonomist, so what do I know.
Right, midterm... (hey, at least I procrastinate productively!)