Assorted link roundup

Some links from my epic procrastination foray:

Since I'm supposed to be cramming studying for my developmental biol lab exam (early chick embryology) this Monday (8am, ewww), NOVA's Guess the Embryo was quite fun! And amazingly difficult too... (the bat develops quite cutely, for some reason.)

An interesting application of DNA barcoding: testing sushi meat

Science standup comedy, via MolBio. On that note, lab cartoons, also via MolBio.

Forgot where I found this (was quite a while ago), but How to write consistently boring scientific literature (Sand-Jensen 2007 Oikos; free access) has 10 simple rules to ensure your scientific work never falls into the hands (or mind) of others.

CG animation of Aspergillus conidiophores via MycoRant. Fungal fruiting bodies seem very graceful there!

10 days left for 2009 Open Lab submissions, due 01 December at midnight.

And I guess that's it for now. Should probably get back to drawing embryos over and over and over again. Also, why is mammalian developmental biology literature so bloody hard to read? Plant people are kind enough to provide sufficient background for everyone, even zoologists, to understand what's going on. The mammalian guys assume you know everything already. Hello, some of us actually work with different systems, y'know?

It's kinda fun to be thrown in at the deep end of a completely foreign field though. Too bad we're expected to focus on only one paper for the class presentation thing, and I like to skim over a small pile of reviews before narrowing in on one topic. That seems to be quite discouraged, considering the time alotted to this endeavour. Maybe that's why I seem to get along quite well with TC-S papers (aka Megamonumental Reviews of Life, the Universe and Everything). FUZZBRAIN PRIDE!

When I take over the world, undegrad is going to be run so differently. Also, microbiology and protistology would be the most well-funded fields. Disciplinary tribalism will be banned, and everyone will work together and learn from each other's fields, even arts and science. Engineers will be banished to a deserted island in the middle of the Pacific somewhere. The steady state for a sane social model will be found, and societies will be engineered towards it, somehow. (all previously invented utopias failed to be steady states; this one will be different. Mwahaha) LOLcats will be displayed proudly and ceilingcat will be worshipped on Caturdays, along with FSM and various protist and bacterial demi-gods. And there will be NO bloody sweet meat. Evar. Sweet meat is a freaking abomination - how the HELL can anyone in their right mind pour honey over a delicious beef steak? That's just horrible. A crime against culinary arts, a grotesque malfunction of the human culinome. Seriously, new -ome coinages cannot begin to compare with the abomination that is sweetened meat*.

*Exceptions include: apples and cranberries in duck, turkey et al. And NOTHING ELSE!

And finally, the theft of forceps from microscopists will be a capital offense. I NEED THOSE FORCEPS FOR MY WORK, YOU %$@&$s.

I think I'm ready to quit procrastinating for a while...

Mystery Micrograph #08

Originally posted on 04 November 2009 4:20 AM
17.11.09: Bumping this up before it falls off the first page...
21.11.09: You guys have until tomorrow, unless someone says something. I actually have a reason to procrastinate this time... (waiting for a paper I had to order) So go, guess!

This time we have two organisms. Tell me what's going on here. And yes, you have to figure out both of them. Which is kind of necessary for this one anyway. Unlike some people(=P), I'm not very picky on very fine taxonomy (species, genera), so don't freak out!

(scalebar = 300um; to be referenced later)

Good luck and enjoy!

HINT 05.11.09: Unusual parasitism
08.11.09: Two kingdoms

Ciliate orgies and barnacles with twin penises

Like any other human beings on the planet, scientists too are enamoured with sex and genitalia. After all, procreation (self-replication) is the central theme in biology, and we tend to find it more fun when more than one individual is involved. Especially when these individuals differ anatomically into categories, in our case, two types, since that is what's most familiar to us. As far as I know, no lineage has evolved obligatory triple conjugations of three different mating types, although such a thing can be induced in the lab. But for now, let's have a look at a particularly unusual developmental glitch in an individual barnacle, and an even more surreal publication accompanying it:

An Individual Barnacle, Semibalanus balanoides, with Two Penises (Hoch & Yuen2009 J Crustacean Biol) [NOT SAFE FOR WORK due to images of genitalia. Unless you work in biology...]

I came across this while responding to someone's comment, and chuckled. Then I checked whether it really was a single individual case, and whether it really was published in a real journal. In 2009. Yes and yes. It was a rather entertaining read as well. Now, I would go off on a rant about some of their hypotheses and assumptions, but the type of work and the following accompanying note in the acknowledgements suggest this was actually an undergrad project, and I should be nice to my brethren:

"This work was partially supported by a Student Research Fellowship from the American Microscopical Society to [author] and a Crustacean Society Summer Research Fellowship to [author]."

"So, what did you do this summer?" "Found a barnacle with two penises, and you?"

Damn, I wish my summers were as exciting. They usually get spent in a dark room staring at blue [DAPI] dots all day. Sometimes I surgically rape a tiny flower with a pair forceps. Other times I drown my poor seedlings in nasty cytotoxins, and wonder why how they die. This guy got to measure barnacle genitalia. And infer about its sex life.

Here are the two penises in all their glory:

Lemme paraphrase all the scientific lingo: "OMG, TWO penises!" (Hoch & Yuen 2009 J Crustacean Biol)

So why barnacles, of all things? Thing is, upon reaching maturity, they glue themselves to the rock. And become stuck there. And then they get horny, but they can't go out. Kind of like that basement-dwelling 4chan crawling internet loser nerd stereotype. With one key difference: in the barnacle case, size does matter. A lot. Maybe that's not such a key difference, and we won't go there in this polite company (LOL!), but the barnacles can do it without ever going out. All they need is really loooooong penises, long enough to reach the next mother's basement-dwelling geek barnacle. And those beyond it. You can see how this particular sticky situation can lead to evolutionary peddling of male organ enlargment solutions*.

*My horrible, horrible mind is trying to imagine what molecular spam would look like... alas, my imagination does not stretch as far as barnacle penises If only they were immersed in some serious horizontal gene transfer...

They've proposed that at least one of the penises is fully functional, as the sole nearby barnacle has been fertilised. Then they wonder whether this was a genetic or developmental accident. Well, when your sample size is...ONE...it becomes very difficult to separate the two. Especially when you terminate the sole specimen by chopping its penises off. A regularly inherited twin penis trait would be rather unlikely; it's quite improbable for a genetic change to result in the doubling of an entire organ in the metazoan version of multicellularity. So it's likely just a chance developmental glitch. I've seen a photo of a tulip with half its leaf converted to a petal, but only one tulip and a single leaf -- another example of an entertaining, but biologically unimportant, developmental glitch.

So, to summarise:

Lab slave: Holy shit guys, this one has two penises!
PI: OMG, let's see if we can publish that!
Slave: LOL nice joke, buddy!
PI: No, seriously!
[...]
Reviewer: So what's the scientific significance of this work?
Authors: It has two penises, lol XD!
Reviewer: *giggle* Ah what the hell, we need our [juvenile] entertainment too! *accept*

So what is their actual stated conclusion?

"The result is significant because it shows that the mating ability of the barnacle is resilient to developmental instability and able to overcome extreme departure from normal morphology."

For a sample size of ONE. Remember guys, this isn't a mutant line or anything, this is ONE single freak case. But they had to write something ^_~ Still amused by this getting published though...

And now for another anomaly:

Ciliate orgies
Ciliates are obligate sexual organisms. If they don't have sex within a certain number of generations (~50 for Paramecium), their somatic nucleus basically rots away. Thing is, they actually have two different nuclei - one the pass on, and one they use (ie transcriptionally active). The transcriptionally active 'macronucleus' (MAC) is essentially a giant bag of linear plasmids, sometimes having upwards of ~9000 copies of a single unigenomic, or just really short, chromosome. A problem with having so many chromosomes is evident at mitosis -- how do you attach a bundle of microtubules to every single chromosome of the thousands there are? Well, you just...don't.

Ciliate MACs undergo a special form of nuclear division termed 'amitosis', where the nucleus is more or less pinched in half (ciliates do closed mitosis where the nuclear membrane remains intact the whole time), more or less evenly. Sort of. This is roughly compensated for by some rather crazy DNA replication regulation stuff, but eventually the organism may start losing genes. (how it corrects for the ever-changing gene copy numbers is beyond me...*)

This is were sex comes in -- the ciliate exchanges its germline 'pronuclei' (haploid gametes, if you will) with that/those of its partner (in some species, it gets complicated...), and makes a new MAC. Actually, the making of a new MAC heavily depends on the preceding one, which gets destroyed just as the new one is formed, yet its information can still influence it...basically, a paradise for anyone obsessing over epigenetics! In fact, I've done an essay on that stuff for a class: Ciliate genome rearrangements pdf (not my best writing as I spent way too much time reading stuff and not enough time constructing sensible sentences...)

*Hmmm, just thought of this: overexpression lines might be a problem in a ciliate model, no? It may well be that just like what seems to be happening with the polycistronic gene situation in trypanosomes, may be also happening here: namely -- highly emphasised post-transcriptional and post-translational regulation of gene expression levels rather than direct regulation of the promoter... thus would mean that driving a gene with a highly expressed promoter might be compensated for by some pathways specific to regulating that gene (or its class), thereby screwing with your overexpression attempts. Any thoughts?

So, before I get too carried away with this, ciliates need sex. Furthermore, I'll argue that sex was a prerequisite for such a ridiculous genomic system to evolve in the first place -- frequent sex allowed their genomes to get loose like that, for it could be easily compensated for by more sex. Perhaps this is what fundies fear under 'sex addiction'? In a way, sex does a wonderful job at screwing up otherwise perfectly self-sufficient organisms. So yeah, they're right, sex is a sin. Remember the poor barnacles? Divine punishment.

On the topic of impure deviations and dirty sex, ciliates have been observed having orgies. Like the more familiar fungi, ciliates too have multiple mating types, and avoid breeding with their own. If you have a culture with, say, three mating types, you may, occasionally, see orgies of three (rarely four) organisms. Even when such orgies do occur, most often they feature a pair of ciliates conjugating, while the third kind of sits there sadly and has sex with itself. Literally (autogamy)*. (Chen 1940 PNAS)

The big solid black things are MACs, the things undergoing meiosis are the smaller germline nuclei, which are about to be exchanged. Don't you feel sorry for the poor little guy who got left out? =( (Chen 1940 PNAS)

However, sometimes they can arrange themselves into a circle and pass around the pronuclei in a circular fashion. A true triple conjugation where all the participants can get their fair share:

Wheee - a circular orgy! I suspect there may be enough material for a ciliate Kama Sutra out there... (Preparata & Nanney 1977 Chromosoma)

They also had ways to induce massive group copulation (I guess also orgies, to some extent) using a sex-inducing mystery fluid; which caused massive autogamy sprees in populations of a single mating type -- Chen (1945) proposes it was actually a 'killer', toxic substance secreted by bacterial endosymbionts which render their host immune, and kill off everything else (I don't think they knew about the endosymbionts yet at the time). Basically, their defense response to the threat of death seems to be...having sex.

I think I've just ruined ciliates for you too. You're welcome ^_^

Note: Nice picture of ciliate triple conjugation on its way when I finally scan this Russian paper I 'had' to order through the library...

*When it gets too old and still solitary and mateless, the ciliate can also cure that by having sex with itself. Ciliate microbial sex life would be an awesome topic for a popular book...

References
Chen, T. (1940). Conjugation of Three Animals in Paramecium bursaria Proceedings of the National Academy of Sciences, 26 (4), 231-238 DOI: 10.1073/pnas.26.4.231

Chen, T. (1945). Induction of Conjugation in Paramecium bursaria Among Animals of One Mating Type by Fluid from Another Mating Type Proceedings of the National Academy of Sciences, 31 (12), 404-410 DOI: 10.1073/pnas.31.12.404

Hoch, J., & Yuen, B. (2009). An Individual Barnacle, Semibalanus balanoides, with Two Penises Journal of Crustacean Biology, 29 (1) DOI: 10.1651/08-3037.1

Preparata RM, & Nanney DL (1977). Cytogenetics of triplet conjugation in Tetrahymena: origin of haploid and triploid clones. Chromosoma, 60 (1), 49-57 PMID: 870290

Rule 34: Proteins

(alpha-helix, beta-barrel)
The reader is now encouraged to go out and find real examples of protein Rule 34 in action. There must be some suggestive protein interactions out there somewhere! And we shall never view biochem the same way again...

Inspired by this comment...


PS: In light of Jonathan Eisen's 'competition', shall we hereby coin 'pornome'?

How about genomeome, a set of genomes? "The genomeome of this phylum suggests..."
And then genomeomeome "A comparative analysis of genomeomes in multiple phyla led to the assembly of a larger genomeomeome..." I can keep going. But now we're getting off-topic...

Pond Microforay encore part 2 - Amorphous amoebae of ambiguous affinity

Part 1 featuring both familiar and mysterious types of flagellates found here.

These suckers are amoeboid and potentially amoeboflagellate, thereby leaving me rather clueless with regards to their identity. Help would be much appreciated! And I know some of you real protistologists read this. You're not as anonymous as you think =P So go help me ID some of this stuff, so we can have more excuses to learn (and blog) about obscure organisms. Please? ^_^

A few tiny blobs with crap (pseudopodia) oozing out:

Seriously, what the fuck are these things!?

Amoebozoan (most likely) with what appear to be acanthopodia. Probably not a cercozoan, right?

Another random small amoeba...

And another. Was trying to stalk it to see it eat, but no success.


I'd ramble off some stories about them, but again, I have no idea what they are. Probably could make up some cool 'factoids', but that's not really why we're here, is it? As appealing as academic fanfiction seems in principle...

I know I have some comments to respond to here, as well as VERY LONG OVERDUE posts. Ummm, they're in preparation, seriously. Unfortunately, there's some more high-profile 'submissions' queued up as well, such as lab exams (labelling crap in chick embryos o_O) and multitudes of assignments, and an eternally data-craving PI (aren't they all?).

Looking forward to tomorrow evening though: Carl Zimmer's talk on evolution of disease!

This sounds like a great idea for a grant proposal

Mark Liberman over at Language Log proposes we should go hunt for the Hat Gene*! =D
(sums up the average humanities major's understanding of genetics quite nicely)

*In case you didn't click the link, before you lynch Liberman: he's mocking poor reporting. Intelligent humanities majors (especially in linguistics) do tend to have a decent understanding of genetics. Although the artsci cross-talk still needs a lot of work...

Sunday Protist - Assorted forams

I kind of got distracted while writing up a long post about ***** (you can wait until it actually comes out, probably next week! =P), so I'll do another short one for today. Also, a giant hint for the Mystery Micrograph, since y'all are taking so long. (another hint - I first heard of it in Ball GH 1968 "Organisms living on and in protozoa", in Research in Protozoology (ed. TT Chen); ok, I'll stop bragging about my fledgling old protistology book collection- hey, have I mentioned AC Stokes 1888? Got that for 2$ at the library discard sale... /derail)

Here we go, some random foraminifera (basic intro here):

Inspiration for a sci-fi novel spaceship? Tubulogenerina; source here, along with more forams among other things

I may do a more thorough write-up on forams later, but I don't have AO Roger's books here (and the library is still closed), and it's practically impossible to write anything intelligent about foram biology without them. Most of the literature on forams, which is quite large by protistological standards, tends to be from a paleontological/geological perspective. It's not so easy to find information on their biology, especially on the cellular level (people seem to prefer treating them with some gas or metal or confiscating a nutrient, and then measuring population-level responses; perhaps because that way you can avoid dealing with the microscopic level of things)

So a few more pictures instead:

Fossil Amphycoryna scalaris, Uni Southampton gallery of foram SEMs

Calcarina hispida; foraminifera.eu site contains really a really awesome gallery, the best I've seen so far!

Some can get quite large (bar = 1mm) like this Psammatodendron arborescens from Foraminifera.eu

Nature's concrete? Psammosphaera fusca, again from Foraminifera.eu

A really nice pic of a foram shell (~1mm wide) from Snail's Tales (which you should all visit, btw. At least to remind ourselves from time to time that slugs and snails actually exist o_O)

Before we forget that these things were once alive too. The 'needles' are thin pseudopodia (filopodia) extending from the organism in its shell. Some keep symbiotic algae with them; in some species, during the day, the algae are transported to the tips of the filopodia where they can photosynthesise, and drawn back in for the night (aww!). And some have even bothered to make little 'windows' in their shells to allow light to reach inside. Here we have Globigerina, from here.

Lastly, I found us the coolest apple pie ever made in the history of mankind:

Forams made out of marzipan (and there is not a single word of that I don't like!) (Hannes Grobe at Wikimedia Commons)

PS: You know how searching for information on one thing can lead you to come across interesting tidbits on something else? I randomly came across this paper:

JO Corliss 1974 Taxon Time for Evolutionary Biologists to Take More Interest in Protozoan Phylogenetics?

"Darwin, as someone has recently commented (H. Sandon, unpublished MS), wrote "On the Origin of Species" without any mention of protozoa, and evolutionists ever since have followed his example. Scarcely a decade ago, Simpson (1961) matter-of-factly concluded that for the protists "evolutionary classification is not yet practicable. . ." and thus "they do not concern us in this book," his volume on principles of animal taxonomy and classification." (p497)

Things don't change very quickly in academia, do they? (even in the era of a relatively well-sorted protist phylogeny!) Funny how what Darwin wrote, and failed to write, has such an impact on evolutionary biology even today, [almost exactly] 150 years later. Not that I have any issues with Darwin, but should we really base much of our research planning on 19th century work?

Citing papers from the future

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

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

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

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

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

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

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

Random question: Does evolution require selection?

Got a midterm tomorrow, so should must be studying tonight, and may well be undergoing EtOH treatments tomorrow night (haven't dared to drink'n'blog yet...), so I've got a question for you guys to ponder over/discuss:

Does evolution require selection?

(context can be found in this comments thread on Sandwalk)

Go!

---

Update 16.11.09: I've mentioned this in the comments, but it's kind of a new question so I'll repost it here:

An evolutionary system, regardless of its medium (biological, linguistic, cultural, etc), has finite resources, and must abide by laws of physics. The former necessitates some form of positive selection eventually, the latter invokes negative selection right from the start, provided variation exists. Some forms will end up being unable to self-propagate, regardless of which system we are dealing with. In the biological system this is very obvious - fuck up DNA replication, and the organism's lineage ends there.

My question was invoked partly by the commonly accepted statement that evolution fundamentally requires three things: Heredity, Variation, Selection. As much as I like fighting commonly accepted statements, this one seems strong thus far. Also, I've heard strong proponents of Neutral Theory use these preconditions as fact, so it's not in any way conflicting with a more neutral view of evolution. So I referred to it in the discussion on Larry Moran's blog, and the selection component, to my surprise, was shot down entirely.

So I often hear that evolution is change in allele frequencies (or their equivalent in non-biological systems) over time. Can this change occur without positive selection? Well, yeah, we've got genetic drift. But what about negative selection? Surely, for allele frequencies to shift, the population size must be finite; else the proportions would remain the same (ignoring positive selection). Stuff must die. Even if we assume no selection at that level, the new variation must be 'proof-checked' via negative selection, especially considering many changes are actually deleterious.

I guess if we remove all mutation, then we could have a system devoid of any selection, where stuff just randomly dies and then the allele frequencies would drift, and evolution can be said to occur.

But then, would weather patterns be an evolutionary system? They can be argued to be heritable in a non-discrete sense. Say we have each sq km being rainy, sunny, foggy or whatever. It inherits its next weather state partially from its previous condition (and obviously influenced by neighbours; lets call it LGT). The percentage of sq km in a given population experiencing rain or shine changes randomly selection-wise (although non-randomly if we consider it from the physics perspective; but the same applies to biology).

I'll argue here that, unless I've missed something, the weather system is akin to the biological system minus selection (the variation and heredity are still there). Does it still evolve?


(and thanks, this discussion is really helping me wrap my head around certain things! I don't learn well by just listening and digesting; I have to constantly prod at stuff until I'm ready to accept it!)

Pond Microforay encore part 1 - Bicoecids and mysterious flagellate blobs

About a month ago I've done a second microforay -- same sample a week later. Amazingly, stuff was still alive.

I'll start off with more familiar things. A bicosoecid of sorts:

Another one:

What may well be another one: (I think)

I like imaging loricate Bicoecids - they're nice and sessile and don't swirl about the slide uncontrollably. Thus, they're stationary enough for the camera.

A euglenid (not sure which kind though; but I think you can almost see the pellicle strips in the first one!)

Pretty sure this one's a cryptomonad of sorts: (sitting atop a bacterial thing; spirochaete maybe?)

As an aside, spirochaetes can make pretty much anything appear motile and flagellated. They can really confuse inexperienced microscopists (like me, admittedly...). I can see where Marguilis gets her crazy "flagellum = spirochaete" ideas from...

Ciliate (Cyclidium again; they have this jumpy, peculiar (for ciliates) movement, where they actually stand still for several seconds -- quite convenient for snapping reasonable pictures)















And now for the completely unknown. Please let me know if you know anything about any of these!

(we're bordering on the resolution limit there)

A blob with a blob. (aloricate bicoecid?)

A blob in a diatom. A cyst of some sort? (note the outline)

A blob with a flagellum with a thick base.

Similar blob to the one above?

A blob in a dead algal filament:

Another colourless flagellate.

And a bigger colourless flagellate thing (I'll complain yet again about our painfully slow CCD camera)


Perplexed by the mysterious flagellates? Don't you worry -- the next installment shall include mysterious amoeboflagellates, which tend to make normal flagellate ID appear to be a piece of cake in comparison. I mean, they're flagellated like almost everything else in Eukarya, but also have a rather, malleable, cell morphology. And that's not very helpful for morphology-based identification. Unfortunately, I can't quite make out their SSU sequence from looking at the pictures...