19 November 2009

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...

18 November 2009

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!

17 November 2009

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...

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

16 November 2009

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...

13 November 2009

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!)

12 November 2009

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...

11 November 2009

Quick ImageJ Tutorial: Scalebar calibration

Due to popular demand, I'll sporadically write up a series of posts on some ImageJ basics. For those not in the loop, ImageJ is a popular open source image processing program for microscopy; due to the availability of some rather sophisticated plugins, it can be a very powerful tool in the right hands. Also, the customiseable shortcuts are a blessing (and a curse for one's muscoloskeletal system, especially in the wrist region). I'm by no means anywhere near an expert with ImageJ (and don't do anything sophisticated, like macros or even much 3D/4D work), but there's a few basic things that I had to learn, and would like to share with anyone interested.

I put the rest of the post under the fold as most of you probably don't care...

10 November 2009

Live Hypermastigote clips

To compensate for crappy blogging as of late (and the delays in the Great Review of Heterolobosea aka 'cruel and unusual punishment'), here's some random parabasalian swimming around: (Trichonympha methinks)
video
And a Spirotrichonympha?
video
Since I'm too lazy to ID this thing for sure at the moment, it would be great if some resident extreme excavate experts (XXX for short...?) could perhaps blurt it out. You know who you are. Also, are those Monocercomonoides, the little things swimming around?

I lack video editing software, so apologies for random background noise.
Got plenty more clips of Saccinobaculus, by the way. Should show up when I have time to re-blog about that wonderful organism (I think it deserves a much better post...) For now, enjoy the suspense =P
(and go hang out at the Mystery Micrograph - should be more interesting now that we've established it's a case of a multicellular parasite of a unicellular organism. Hint: As far as I know, there's only one documented case of that. )