Update!

Neglect... so much neglect. Been swallowed up by my move to Indiana and settlement attempts. Haven't really been keeping up with my SciAm blogging either, but I do intend to return here and post the occasional snippet of something random and perhaps even technical, that I don't want to bother with in terms of translating to a human language. That was an awful sentence -- see what a lack of writing practice can do?

For the few who may care about personal life, well... being a full-time researcher takes up a lot of time, it turns out. Particularly when your experiments aren't really shining in glory or anything like that. And when your gentle introduction to a subject you despised all through undergrad happens to be a grad-level course you absolutely have to do well in. In other words, I've been thrown off into population genetics at the deep end. The course was great, actually, and think I learned *a lot*, but a little bit intensive to someone who merely a year ago defiantly ignored claims that evolution involved 'populations'.

In terms of research life, feels like I'm involved tangentially in enough projects to get away with not really doing anything in particular. In addition to maintaining some ciliate and diatom mutation accumulation lines (long, boring and painful multi-year project to ultimately measure the mutation rate and spectrum, which is actually very exciting as a final product!), I'm trying to learn the art of harnessing ciliate growth rates to be able to have them undergo autogamy (recreating their macronuclei, etc etc) at just the right times to gather RNA for sequence data (that is not my project), and figuring out imaging techniques for deciphering the identity of food vacuole bacteria that persist after longterm starvation for some inexplicable reason. In addition, also trying to start up new protist mutation accumulation lines to ultimately get a phylogenetically sounder sense of eukaryotic mutation rates.

As you can see, lots of trying and attempting and figuring stuff out, and not a whole lot of results and data, which gets frustrating after some time. But rumour has it that's not unusual when starting in a new lab.

Another shift was going from a protistology haven to being some sort of a sole regional expert on protist diversity, entirely for lack of anyone else in the field around here. It's rather alienating, and you can't argue with people about arcane topics in protist phylogeny and taxonomy as they'll just go with whatever you assert. Which renders argumentative assertion a lot less fun. On the other hand, there's an exciting challenge to convert locals to the dark side, and I'm trying to do anything I can in that department, mwahaha! After all, Indiana U used to be quite a bustling centre of protist research, back in the days of Tracy Sonneborn, his deciples and Paramecium genetics. A handful of us in this lab are all that's left of IU's proud protistology tradition...

So that's what I've been doing lately, leaving little productive time for blogging (but, of course, plenty of time for unproductive procrastination). Not easy getting started after a long break either...

Anyway, enough rambling, and onward with moar protists!

Big Announcement: New blog -- The Ocelloid

After several months of contained excitement and preparation, the embargo has been lifted and I can finally announce the unveiling of the new Scientific American blog network, of which I am honoured to be a small part at The Ocelloid, my new blog -- focusing, like this one, on protists and evolution, although with a stronger attempt at reaching the lay audience. I will continue blogging here at Skeptic Wonder as before, and since I already don't blog as frequently as I should, not much of a difference should be noticed. Basically, my goal is to have The Ocelloid more general audience friendly and introducing people to the protist world from a more superficial 'wow' angle, while Skeptic Wonder will be cater more to the current crowd that seems to consist mostly of people more qualified than I am about this stuff. It has been a bit awkward trying to reach both types of audiences from the same blog so I think this may work out well for everyone. I'll also keep more raw discussions here and The Ocelloid should be more polished up. We'll see where this goes. From time to time I'll cross-post between them but perhaps it's better to keep the recycling to a minimum.

Bora has an amazing detailed introduction to the SciAm network which discusses its purpose as well as awesome overviews of the individual blogs. The official launch press release is here, as well as a welcome post from the Editor-in-Chief and a post on The Observations. More once I get home, am out of town right now until tmr with crappy internet and no control over own time...

EDIT 23:30 05.07.11: Just to clarify things: I am keeping Skeptic Wonder and staying here at FoS as well! And there may be another change here coming up, for the better!

An update!

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 ;-)

News
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!

Random link
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).

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...

Back from Science Online 2011 and the east coast

*brushes off a layer of dust* Long time no see! Done travels for the time being, am here to stay in one place for a while. ScienceOnline 2011 was absolutely fantabulous, as was my little trip up the eastern states to Massachusetts (look, I even learned how to spell that!). Never been to eastern or southern US before, which is embarrassing for someone who's lived on this continent for two decades. Well, I guess the North Carolina Research Triangle barely passes for 'south', but it was definitely different already, enough to pique my interest in further exploring the southern US someday. Passed by New York City on my train ride north, and was a very obvious hick, glued to the window in total awe – so big! I really don't get out much these days, and seeing a little bit more of the world, of only briefly, was quite necessary at this point. Hell, it was my first time in Seattle since passing through there c.10 years ago, even that was worth the effort of flying out from there (well, that and the substantially cheaper tickets, of course).

Apparently people don't mind us bloggers revealing random oddments of our personal lives, like travel. At least a couple people found the preceding snow camping post interesting, so I'll do something with my east coast photos too. The ones without people in them, since we don't want any careers terminated prematurely due to the context of those photos and the ethanol-rich atmosphere ;-) (for some idea, look up the hashtags #DSNsuite and #TheGam, at your own risk). You can also read the potentially incriminating records of the #scio11 tweets here, sorted by days of the conference. And yes, that hashtag is still alive and well because we just can't stop, and #scio12 is up and running already too...

So I intend to have two posts, one summarising the conference and my thoughts on things, and another on my rapid 'tour' past 8 states (and Washington DC) in 24h. Behold, I even have blurry photos of the Washington Monument in the distance, at night!

Before embarking on attempting to write something marginally passing for coherent and maybe even intelligent about Scio11, I must point out that the organisers of the conference, Bora Zivkovic and Anton Zuiker, are fucking awesome, and we in the science blogging community are really lucky to have them around!

To be continued.

Why I did not blog this weekend...

Happy New Year, everyone! (hey, it's still January...) While I did only get back a week ago, with plenty of urgent offline matters to attend to, I was totally going to dust off the blog this past weekend. But I didn't. As much as I enjoy protists and writing for you, I just had to take the liberty to sneak off from the internet and enjoy THIS:

That's right, I actually went outside and explored those pointy things outside my lab window up close and personal. (have I mentioned being able to see snow-capped mountains from the lab pretty much year-round, except for maybe late August-early September? ;p) Tried out backcountry skiing (telemark) for the first time, though that didn't work out too well due to a combination of an impressive sheet of ice, steepness, busy trail with ruts and holes everywhere and bindings that didn't want to fit properly...so the skis were mostly carried. Uphill and downhill. Ah well, will actually check snow conditions next time (some seasoned skiers also resorted to carrying them so we didn't feel so bad).

Went with a pretty large group (university-affiliated), the point was actually winter camping. In snow caves. Igloos too, but those are freaking impossible to build, it turns out. If Canadians really did all live in igloos, we'd all be structural engineering geniuses up here. My friend and I resorted to a simple cave to start with:

Yes, you really do wake up to that shade of blue. Does the ceiling look thin? There's a good half a metre of snow up there. Amazing how much light it lets in. It had pretty good insulating properties, kept things warm - at around 0˚C. The other option was -12-15˚C outside...oh yes it was freaking cold. Meanwhile, in the distance lay the city with it's non-freezing temperatures and sane people who got to sleep without worrying about hypothermia and frostbite. Without their hair freezing to snowy walls even!

Sure they had the warmth and luxurious comfort, but did they have this to surround them when they woke up?

Did they get harassed by these rather bold birds as they tried to eat breakfast? Seriously, that little grey bird (apparently a jay) would approach you to about 20cm away and not care. Even the ravens were a little more cautious...

And where there is ice, there are ice sculptures. Natural or man-made. (neither of them are mine)

One of the wonderful things about camping is that you get a rush of euphoria from the simplest things. Like hot tea. Or getting home with all your toes still intact. Somehow, those things become much harder to appreciate back in the city.

Apologies for total off-topic-ness and protist-less-ness (was going to sample but it was waaay too cold), but it's kinda fun to step back and look at a different scale from time to time, especially for a microscopist. And I'm ashamed for not having taken much advantage at all of living in such a beautiful place. Anyway, protist blogging shall return later, after I get back from ScienceOnline 2011, which should be after the 19th. Also, there may or may not be some exciting announcements to make. Watch this space...

Happy holidays to all, back in January!

I totally meant to do a kick-ass end-0f-the-year post, but that'll have to wait until January... was swamped with everything. Promise to return to regular, proper blogging in the new year! (after ScienceOnline2011!) Mostly away from internet until 05 Jan.

Almost late for my flight... so a happy and relaxing whatever-you-celebrate (protistmas? =P) to everyone!

Personal Update

Dear readers-who-haven't-abandoned-the-place-yet,

You may have noticed that calling my recent blogging as 'spotty' would be a bit of an understatement. And it is. I don't like resorting to excuses, but the truth is, there's some agonising deadlines coming up, many of which are kind of important to my life after graduation. That is, if I want to have food(=instant ramen) to eat and occasional internet access (for blogging! =D) after the university kicks me out in May, these deadlines must be addressed. After all, one must work hard to deserve a life of academic poverty and eternal job insecurity. The good news is, many of these deadlines will pass, hopefully having received appropriate attention beforehand, around 01 Dec, after which I may have a sliver or two of free time to share some epic protist awesum with you.

Thus please don't think I've forgotten or have become too lazy to blog – the guilt eats me alive day and night, if that makes you feel any better. But there's scarier guilt competing with blogging guilt at the moment. In case it's not entirely obvious – I'm applying to graduate schools. Since the average PhD lasts longer than the average marriage in North America, this is a bit of an important decision.

For now, here's some amazing crafts (surface scales) created by a 'lowly' amoeba, Cochliopodium (second from left in my blog header images), arguably putting Haptophyte coccoliths to shame:

(Kudryavtsev 2004 Acta Protozool)

PS: If any of you are going to ScienceOnline2011 in January, I'll be there!

Room D - “But it’s just a blog!” – Hannah Waters, Psi Wavefunction, Eric Michael Johnson, Jason Goldman, Mike Lisieski and Lucas Brouwers
Many young people are eager to communicate science despite their lack of scientific and/or journalistic credentials. While all science communicators face challenges, this subgroup has their own set of challenges including cultivating a following of readers from scratch, and high levels of self-doubt, often referred to as "imposter syndrome." What value does this rapidly-growing group of science communicators bring do the field? How can the science blogging community encourage and mentor young bloggers? How can we hold these individuals accountable to the high standards of science and journalism while simultaneously allowing them to make mistakes as part of the learning process? In addition, established and successful science communicators will be encouraged to share their tips and tricks with their newer colleagues. (Source: program)

Research proposal ramblings – Eukaryotic cellular evolution

Have a research proposal to do in a week for a graduate research fellowship (which also contributes to my spotty blogging as of late). Figured I'd try out Rosie's strategy of blogging to generate ideas and sort things out a bit. Would really appreciate feedback + discussion, particularly criticisms. This is my first time doing one of these, so I'm a total clueless n00b. This isn't my proposal, obviously, but rather a pre-draft of a pre-proposal draft, to lay out some thoughts ;-)

And this stuff needs to be narrowed down A. LOT. I'm well aware of that!

Topic: Eukaryotic cellular evolution

Or "cellular evo-devo"; of protists, obviously ;-)

Possible subtopics:

- The role of non-genomic ('cellular') inheritance in the broader context of evolution

- The relative extent of cellular inheritance in various unicellular and multicellular examples, in relation to size/"complexity", effective population size, mutation rates, whatever. (no idea how I'd do that yet though)

- Tracing the path of individual components in eukaryotic evolution, such as specific protein families, etc. Comparative work.

- ?

Background

Early evolutionary biology focused on the macroscopic level, such as general morphology of an organism and its behaviours in relation to its ecology. Later developments in molecular techniques have largely shifted the focus of the field towards the molecular scale, focusing on genes and proteins. In doing so, the organisms have been reduced to mere genomes – their cellular and developmental contexts largely forgotten. While evo-devo aims to revive the developmental aspect of evolution in multicellular organisms, little has been done to approach evolutionary biology on the level of individual cells, particularly in unicellular lifeforms. Cellular biology is crucial to a properly holistic understanding of evolution, and since the vast majority of organisms on earth, both in quantity and in diversity, are cells, time is ripe to investigate the role of extra-genomic cellular hereditary processes and their role in organismal evolution as a whole.

The first requirement of studying cellular evolution is good sampling. This demands a good phylogeny, and well-understood cell biology among non-Animal/Fungal/Plant organisms. Phylogeny together with cell biology must then be used in attempt to reconstruct ancestral states in order to seek out potential patterns and correlations. These patterns must arise several times independently, in order to have a decent independent sample size. However, at this point it's still only comparative biology; to make it to the level of evolutionary theory, predictive models must be inferred and tested from these patterns – this would ultimately require tying it in with the entire range of biological topics, from biochemistry to population genetics and ecology.

Of the above steps, only the phylogeny has begun to more-or-less solidify, at least enough to begin doing comparative work, if enough well-developed model systems exist in the attention-starved areas of the tree. However, the organismal & cell biology side does not fare as well: of the non-Animal/Fungal/Plant eukaryotes, only the medically important intracellular parasites like Plasmodium, Giardia and Trypanosomes have been well-studied (in the molecular cell biology sense), as well as cellular slime mould Dictyostelium due to its assumed significance in the evolution of multicellularity. To a lesser degree, ciliates Tetrahymena and Paramecium have been studied, as well as diatoms and oomycetes. This leaves huge swaths of phyla severely underrepresented, including practically all of Rhizaria. It must first be established whether anything is salvageable from what has been done to date.

(It would be unwise to rely on developing a novel model system for a PhD project, as potentially awesome as some candidate species may be. Maybe on the side, somehow (I really want Allogromia!))

As an aside, the close relatives of a potential model system should be examined to evaluate how well this model represents the group – picking at outrageously derived system would not be preferred for comparative work, although it would be quite biologically informative in its own right. Some of model candidates may have annoying quirks for certain types of things – eg. Paramecium undergoes autogamy every couple of weeks and destroys its somatic nucleus, thereby being ill-suited for molecular work.

To summarise, studying cellular evolution would require further development of protistan model systems, as well as extensive comparative work between them. Project could focus either on using what's already there for widescale comparative and theoretical work, or picking a single system and working on it specifically.

Relevant examples

- directed assembly of ciliate cytoskeletal elements (Grimes & Aufderheide 1991; Sonneborn & Beisson 1965 PNAS; Frankel 1989) A substantial body of work exists on the topic of ciliate development and how a chunk of the cytoskeletal organisation and morphogenesis seem to depend on non-genomic factors; eg the vertical transmission of a surgically inverted row of cilia independently of genomic inheritance. Furthermore, during encystation, hypotrich ciliates lose all basal bodies, and morphogenesis must happen anew. Some altered traits are lost after encystation, some are not. A mysterious 'organising centre' seems to exist in Oxytricha that determines defining features of the new morphology.

- endosymbiotic bacteria (eg. Görtz 2006 The Prokaryotes) of ciliates as a model for cytoplasmic inheritance of more tangible/quantifiable things.

- organellar inheritance, but that's been done to death already. Relative to above two cases, I mean! (before they kick me out of the lab for saying that...)

Potential projects

A lone tumbleweed rolls across the vast expanses of the chilling mind desert as the ruins of a derelict ghost town stand as a ghastly reminder of the Mind's complete and total absense. A slanted cracked wooden door of the saloon creaks softly in the winds of confusion, seemingly bemoaning the long-gone days of vibrant endless drinking...OH, THERE, I GOT IT! I need beer, the cause of and solution to all research problems!

- Continue the ciliate morphogenesis work of the 60's-80's. Look for general evolutionary principles, if feasible. [something specific goes here]

- Cytoplasmic inheritance of endosymbiotic bacteria and their genomes; effects of various things on that; comparing patterns between different [independent] clades? [something specific and intelligent goes here]

- mapping known cell biological traits onto modern eukaryotic phylogeny, look for patterns. Protein trees, for starters. Eg, Jékély and Cavalier-Smith type of work.

- ?

- lock self in a dark closet microscopy 'room', grab Allogromia or Stentor or Oxytricha or something, work on its molecular cellular biology, screw the whole broad research questions thing. Play with new protists on the side. Be a real hardcore protistologist. Shun everyone else. Damn, so bloody tempting...

Considering the cytoskeleton is the best part of the cell, and tubulin kicks actin's sorry little ass, my hands are seriously itching to do some in vivo fluoresent labelling on various cytoskeletal components in foram reticulopodia, and...well, that's a career right there. Especially when their microtubules grow 10x faster than those of any other eukaryote. (not sure how foram genomes go – could be a pain to work with)

But ciliates are cool too. And Warnowiid dinoflagellates with their awesome 'camera eyes', and radiolarians, and all these other things that aren't even culturable yet. Damn.

Broader impacts, justification

...heh. Should probably have something vaguely resembling a faint outline of a potential project before even considering these. Content first, embellishments after, even if the latter can appear to be more important at times.

---

Problem with cellular evolution at the moment is that we don't even have a decent grasp of cell biology yet, even in multicellular model divas like Arabidopsis and C.elegans. Not even getting into the phylogenetic sampling issues and lack of extant theoretical framework.

And we haven't even mentioned the prokaryotic cells yet. Yes, they have cell biology too, not just bags of biochemistry. No, most people haven't realised that yet, and/or don't care. Yes, we're fucked.

The very idea of cellular evolution almost looks impossible at the moment. So I really want to do it!

Ok, now sink your teeth in and demolish my very dream of making it in my foolish career choice. Start discussion. I need ideas. My mind is full of arcane protist taxa to think straight anymore (did you know Pseudospora was reported in 1905 to produce uniflagellate gametes? Did you care? Lookie, I'm soooo employable! Transferrable skills galore!)

Scaled protists and bloated distractions

Ok, I was gonna just post this picture as filler, and then suddenly got sucked into the microbial biogeography debate – you know, "is everything everywhere?" etc. So I was going to write up a quick blurb on that, but it somehow grew out of control. As I don't have time for such epic digressions at this moment, esp w a promised post quite overdue, amidst other stuff, I'll just shelve that for later and simply post the pretty picture instead. Enjoy this lineup of protists scaled to the size of a pinhead:

How many protists can dance atop a pin? (Finlay 2002 Science)
I'm going to try to vaguely identify them, from left to right: Chaos sp.; Stentor sp.; some random amoebozoan; Amoeba sp.; Loxodes? man I suck at this; Bursaria sp.?; Paramecium sp.; Mayorella sp.?; a euglyphid; another bloody ciliate; Strombidium; Difflugia-like thing; Euplotes; Ophryscolex-like; heterotrophic euglenid; heterotrophic euglenid again (Peranema); het eugl (Entosiphon or Petalomonas), Chlamydomonas? too small; ?, pedinellid-like thing?; Bodo, non-descript small unknown flagellate? Bodo., last two look like those tiny non-photosynthetic stramenopiles everyone ignores.

This tangent was initiated by working on that long overdue post, by the way. Apparently, one graph is enough to lead me on a massive multi-window-tab-explosion journey into the wild unknowns, even if it involves ecology. Maybe this is why it's taking me like four months to write a single freaking chapter. I'm not sure the free version of Mendeley was meant to handle hundreds upon hundreds of references. Let's see what it does once I hit a thousand, which will be soon. At least researching flagellar root apparatuses doesn't typically lead me to Hooke's description of the first cell, unlike one particular reader here =P (who needs to update, by the way...)

Oh, and submit to the carnivals! The more posts I have, the lest posts I'd have to fake, and the less I must rickroll you with fake links...

Cute Peritrich and random update

As alluded to earlier, I've been swept away by midterms and applications. Now that the midterms are done, got the rest of the ever-growing to-do list to take care of. Oh dear. Currently working on: a chapter, research proposal for fellowship, applications and that long-overdue write-up of Mike Lynch's seminar. Fear not, I have not forgotten. Just haven't figured out a way to reproduce by fragmentation yet...

So enjoy a random pretty Peritrich ciliate (think Vorticella) - Apocarchesium, a sizeable clump of vorticella-like bodies atop a single contractile stalk:

Forest of trumpets, on a single stalk. Scalebar - 100µm. (Norf & Foissner 2010 JEM)

And since this paper is by the great Wilhelm Foissner, it includes the obligatory sexy drawings:

Everything you need to know to identify Apocarchesium. (Norf & Foissner 2010 JEM)

That one's actually modest by his standards. There's some truly amazing descriptive drawings by him out there. Possibly worthy of a whole post. Eventually. Especially since he has described a freaking insane number of various ciliates, and possibly other protists. But before that, prior obligations.


Meanwhile, I like to recommend this awesome NAS Sackler Colloquium talk by Julius Lukeš accompanying Lukeš et al. 2009 PNAS on convergent evolution between Alveolates (namely, dinoflagellates) and Euglenozoans. Go watch and savour the amazing genomic evolutionary madness contained therein.

Sunday Protist - Ciliate-in-a-basket: Dictyocysta

Crazy days this week (and possibly next), so a short one. This tintinnid ciliate has a particularly beautiful lorica:

SEM of Dictyocysta in its lorica. Scalebar = 40µm (Agatha 2010 J Euk Microbiol)

Tintinnids construct their loricas out of proteins and polysaccharides, and some species attach matter from their surroundings. There's a few interesting stories involving them, but I still need to finish the post on that. Tintinnids are only very distantly related to Folliculinids, and both evolved their loricae independently from each other. Several other lineages of ciliates also construct tests, but Tintinnids and Folliculinids are the most prominent ones. And have cool names.

---
Two midterms this week, midterm and lab exam the week after, writing my GREs in three weeks, blankly staring at grad school apps and trying to find a way to justify my existence in 500 words or less for the personal statements (You must be so jealous of me, I know). Also need to finish a bunch of stuff for work – was too distracted this past week.

Blogging-wise, I'm hosting the upcoming MolBiol Carnival; you should submit early and often so that I don't have to fake data posts. Faking posts is baaaad. Don't make do it. Here's the link to save me from immoral temptations: LINK. <-- click there and submit to the carnival. (intentionally ambiguous, mwahaha) I'll also be writing up a very interesting seminar talk involving molecular biol, mutation, genomes, introns, popgen and really cool evolution stories. The topics are a bit intense, so it may take me a while to understand it in a way that's not outright wrong, but very soon there'll be a continuation of my non-adaptive evolution series. To get you more excited, the speaker in question is Michael Lynch!

Oh, and I will finish Part III of In Defense of Constructive Neutral Evolution as soon as I can get around to it. Apparently some of you actually do care, so I must return the favour =D

Not enough time in the day to get everything done. Damn you, physics! (I'd imagine that slowing down Earth's revolutions would have drastic side effects wiping out all cumbersome macroscopic life in an instant. Prokaryotes, and possibly even unicellular protists, wouldn't mind much though).

Hiatus until 01 Sep + MORE random doodles!

Flying out very soon, for an underserved vacation smack in the middle of "OMG I don't have "all summer" anymore!!1! *flailing arms*" season. This is what happens when you let parents buy tickets for you. On the other hand, I really need the extra money so I can blow it all on my GREs. Yay.

So before I go and ditch you guys for a week and a half (really, I'd rather be here, blogging and working! =/), I'd like to share something from...my bedroom ^^. I know, how risqué...! This naughty piece is a part of my...wall. That's right, my wall is covered in very shameful things, like even more protist doodles:

No, I don't actually need a life. It's all over my wall anyway.

Anyway, I'll be back 01 Sep. Hopefully the blogging will pick up then, as I'm beginning to discover that regardless how nicely undergrad-free it is, summer is just not conducive to extreme productivity or anything. Quite annoying, actually. Must compensate in fall.

[rant] Some asshat recalled the two specific books I was gonna bring home and read on my vacation to get two major sections of the chapter finished before it becomes evident how little I got done this month... and those aren't books of which you find many similar works lying about -- one of them is the ONLY book on the subject since the 1800's, and I absolutely cannot get by without it. So yeah, thanks, whoever it was. Not that they were supposed to know or anything. But I still retain the right to be irrationally pissed off about it. So much for catching up over the vacation. Now I'm really screwed come September. [/rant]

Must head off to airport soon... have a happy end of August, everyone!

Microfieldwork and a couple mystery critters

My work-related productivity ran aground lately, and thus I feel too guilty to blog. I should probably sort out the stuff I get paid to do first, and until then, do not qualify for having "spare time", especially since I already did too much of that this weekend by going on a random sampling foray:

My friend apparently saw a bubbling pool with a nice stench of sulfur on a local beach, so we went hunting for extremophiles. She had just borrowed A Field Guide to Bacteria, and finally realised that microbial life is many orders of magnitude more awesome than anything easily visible to the naked eye. Far more exciting than her sticklebacks anyway =P (joking! please don't lynch me, fish people!)

Anyway, naturally our fieldwork had to be accompanied by the first rain in over a month, and we got soaked while wading through salty mud in search of the elusive bubbling pool. Unfortunately, the pool seems to have disappeared. Furtunately, the stench of sulfur hasn't. Nor has the blackish-greyish unappetising-looking gunk, or the patches of bright green algae. Being biologists, the yuckier and smellier the gunk, the more excited we got, and the more happily we sampled away. Now I have a plate of anoxic goo sitting on my bench -- could be a great teaching tool for training one not to open random plates and sniff them. Biologists are immune to such lessons, of course, especially microbiologists, who seem to be irresistibly attracted to nasty smelly stuff.

Anyway, gunk hit the slide and on the scope it went (the slide, not the gunk). It was AMAZING. I have found an excavate paradise! At least four varieties of diplomonads I could see! Swarms of bodonids and heterotrophic euglenids! For the saner people, there were loads of bacteria to oogle at too. For some reason, many assume all prokaryotes are too tiny to be detected by a light scope, but that is entirely not true -- you can see bacteria swimming around, even under low mag. Resolving inner structures is obviously nearly impossible (except for Epulopiscium), but you can definitely watch the cells themselves swimming around for hours, and see plenty of morphological diversity.

On the topic of bacteria, next time you put a coverslip on a rich anoxic sample (at least of the very surface layer, but maybe planktonic/benthic samples work too), wait a bit and go towards somewhere in the centre of the slide on medium mag. With phase contrast, you can even go to low mag. Somewhere on the slide, there may be a giant swarming ball of bacteria! The ball gets bigger and bigger as more bacteria accumulate inside, and becomes slightly visible to the naked eye! After a few minutes, the ball collapses into an ever-expanding ring, which keeps growing until it reaches the edges of the coverslip, by which point many of the bacteria die.

What's going on there? I've been told it's probably aerotaxis - microaerophilic/anaerobic bacteria scurrying the hell away from the poisonous oxygenated slide edges (while their aerophilic counterparts often form borders along the edges, if you look carefully after a few minutes). Thus, the bacteria eventually congregate in the local minimum of oxygen concentration, and form a ball. What is interesting is why this ball then collapses into a ring -- do some anaerobes produce oxygen waste, and thus poison their immediate vicinity? Alternatively, could they be secreting some other toxic product and fleeing from it? Seems like this is something that should have been well studied (and well-modeled - mathematical biologists love this kind of stuff, don't they? They get to whip out their gradients and differential equations and other fun stuff), but my unproductivity guilt stops me from looking it up myself ^^

Anyway, plenty of cool stuff has been seen, including a particularly weird flagellate that swims around in a corkscrew fashion and has a warped cell body morphology too difficult to describe at the moment. Might anyone know what it is? It's not too common, around 1-2 cells/slide, and seems to enjoy lower planktonic/benthic areas more than the surface. Roughly 10-15um, I'd say. Anyway, I grabbed some pics:

Sorry for the awful quality -- they're crude screenshots of stills from video, as the scope in question lacks a normal camera and I've yet to figure out how to use the software...those pixels have been through a lot. Be nice to them. The resolution abuse really bothers me though, so I'll try not to look at them myself...

Any ideas? Anoxic dense marine intertidal sediment, ~10um big, swims in a corkscrew fashion. Slightly more refractile than nearby bodonids and diplomonads of similar size. Two cells depicted above.

I'll get more images from the anoxic samples once the unproductivity guilt issue gets taken care of, but that flagellate has been nagging me too much. But in addition to excavates and this mysterious thing, there's also loads of cool ciliates, Naegleria (I think!), dinoflagellates, amoebozoans, and cercozoans. Speaking of which:

In addition to the anoxic wonderland, I also went on a grueling field work expedition to a nearby stagnant ditch-pond thing, an arduous journey that took me 10min including stair-climbing and door-opening. And the potential threat of being bitten by a feral stickleback or some roaming drunk undergrad. I almost sympathise with the field biologists - it is dangerous and difficult work, after all. Especially once the beer runs out.

Anyway, got loads of sample, dumped it into a petri dish, floated coverslips on it. I heard of this technique where coverslips are floated for a while and stuff grows on them, so I had to try it out. Was sort of relevant to my work too, to see how well it would work for an undergrad lab. Fairly quickly, you get 'benthic' ciliates crawling all over it. Curiously, the neuston (air-water interface layer) is full of benthic-looking things growing upside down on it. Amoebae crawl under the water (air?) surface, hypotrich ciliates 'walk' on it. While neuston has been studied a fair bit lately (under the glamour word "biofilms"), the protist component has, as usual, been entirely ignored, save for a couple old papers. Upside-down forest of stalked choanoflagellates, bicoecids and various ochrophytes? Hard to believe, eh?

This doesn't simulate the air-water interface per se, but the cover slips do show how easily small floating life can grow upside down and not even care. After about 4 days, you start seeing some really cool stuff, like this peculiar cercozoan:

Peculiar cercozoan. Freshwater 'pond' sample, collected in early August, cover slip floated on sample for about 4 days. Organism growing on the cover slip glass.
The doughnut-shaped thing is the nucleus with the large nucleolus (I think - plenty of cercozoans do that anyway), the large circle beneath that is the contractile vacuole. From the cell body proper to the shell/test/lorica opening leads some strange 'neck' structure with longitudinal striations. From the shell extend numerous branched filopodia exhibiting bidirectional streaming of granules (extrusomes?) and what appears to be bacterial prey (the large-ish lump in a filopodium near the shell)

I doubt this is a freshwater foram, as the foram reticulopodia look quite different (less thin, and fuse together a lot). There are apparently freshwater gromiids (remember the giant track-leaving Gromia in the news a couple years ago?), but something feels off about its pseudopodia -- they don't appear to anastamose (fuse together) in the ones I saw. Alternatively, I thought it could be a Granofilosean cercozoan, like Limnofila(Bass et al. 2009 Protist fig 5) or something, but those lack tests, so that's stupid. And now I'm all out of ideas. Would appreciate some help from anyone into this kind of thing =D (could also be an stramenopile amoeba, not a cercozoan...a thraustochytrid, perhaps? Cell body structure doesn't seem right; also, do thraustrochytrids do bidirectional streaming of granules and prey?)

I probably lost most of my readers by about there. Sorry about that, but I really want to know what these things are! They nag me! In my sleep! (seriously -- never read a detailed taxonomy paper, especially a Cavalier-Smith taxonomy paper, along with a beer just before going to sleep; so many gliding amoeboflagellates went through my head last night...creepy. Unless you like that kind of thing. Looking forward to my bedtime beer + Cavalier-Smith paper tonight =D)

Anyway, my guilt is back, so I must go and read stuff so I can finally make progress in writing stuff. I'm still alive and blogging though, and hopefully will get back on track soon ^^ And you have some more protist pictures (and maybe even videos!) to look forward to!

Intermission [hopefully] over...

Hey guys,
Sorry about the lack of posting lately. Discovered that actual writing (ie not rambling blogging in my style) is kind of slow and painful and difficult, at least at the start anyway. First thing that happened when I got my chapter assigned was one hell of an epic writer's block. I spent hours staring at the damn outline. And being miserable. Thus I had to make up for it on the weekend...

Becoming easier, but still full of headbanging and frustration in places, especially where the field gets a little messy. The annoying thing about protist writing is the massive holes in the literature and instances of absolute chaos that no one's bothered to resolve since it transpired half a century ago or so. Like phantom species. And phantom cellular structures. And other phantom factoids. Being obsessive compulsive in a way, I feel obliged to investigate. Which eats up a lot of time, etc. Am trying to learn the art of ignoring not-quite-so-relevant literature. And the art of containing browser tab explosions...

Anyway, I should probably get back to blogging to keep my other stuff from getting too dry (or that's the idea anyway). Otherwise my other writing reads like ultrastructure descriptions. Middle ground between my style here and there would be awesome. (Right now I only have two settings of formality: bloggy and research papery. Grrr. Or, more accurately, zzzZZ.)

Anyway, some of you are probably sitting there snickering at this n00b. Meh.

Feel free to ask me anything about Hacrobians/"Craptophytes". Come on, I dare you =P


Just to keep track of what I need to do here eventually, in no particular order:

- reduce percentage of posts being about lack of posting...
- update Tree of Euks (prerequisite: learn shiny new toy Adobe Illustrator)
- finish part III of Constructive Neutral Evol series
- new Mystery Micrograph
- write up the 10 or so neglected past MMs
- Sunday Protists (maybe even on Sundays! *gasp*)
- Haptophytes (started writing up a mini-series on them)
- Neomura and Eukaryogenesis (Hahaha. Ha. Must read a couple more TC-S novels "papers" first...)
- Bacterial evol: comparing TC-S stories with trees and so on. Leaving that for later. Much later.
- Stomatal development + diversity (related to my old lab project; might as well share some cool tidbits before I forget completely)

Anything I missed? Hard to keep track of blogging obligations on top of everything else...

Coming up next: Dinos mugging ciliates for their stolen algal plastids. Which the latter dismembered and packaged up into neat little compartments.

Carnival of Evolution #24 is up at Neurodojo

Go check it out (I'm in it, uncategoriseable as any true protistologist ought to be...). Vandalised logo included

(I think those black things around the brain are Toxoplasma afflicting Dr. Zen's rational decision-making, driving skills as well as design sense...=P Just joking!)

In personal/blogging news, I just got back from a random trip to Calgary (where it snowed and hit -2C on the 29th of May... wonderful variety of climate!), and for no comprehensible reason volunteered myself to write a chapter in a week and a half. Felt like I couldn't ask for too much time from someone who's rumoured to be fully capable of writing an entire paper within 24h... anyway, since this blog is not that said chapter, won't be able to do much aside from a Sunday Protist or two, and maybe some random post if something comes up.

Hmmm... or maybe I should write parts of the chapter here first? Anyone wanna hear about Hacrobians (cryptophytes, haptophytes, centrohelids, telonemids, katablepharids and biliphytes)?

Oh, and does anyone have access to Cell Motility and the Cytoskeleton, eg. this article? Every once in a while I come across interesting- and relevant-sounding papers from there, and we apparently don't subscribe to the archives, but not sure I'm bothered/desperate enough to order them through interlibrary loan...

On the non-Sunday-ness of Sunday Protist

Even at the very beginning, I sensed trying a regularly scheduled weekly anything wouldn't work well for me, as I tend to be rather haphazard like that. Furthermore, writing depends a lot on time and inspiration, and the two seldom operate on a regular weekly basis. Sometimes things like those pesky offline obligations (aka 'life', apparently) pile up. Gonna have to keep my blogging slow for a while as I currently have two bosses to satisfy and kind of failing at both. Apparently leaving a lab is no easier than getting into one...

So that's why Sunday Protists come out on random weekdays. The name kind of stuck so I don't really feel like renaming the series; the regulars are well aware of the non-Sunday-ness aspect by now, and the n00bs respected newcomers can suffer mwahaha pick up soon enough.

That said, here's a glimpse of the upcoming post, to keep you in suspense and guilt trip myself into hurrying the hell up to finish it:

(to be referenced later)

Maybe from now on they will start happening on actual Sundays, and that would be creepy and hilarious.

Also, pay absolutely no attention to the loads of Mystery Micrographs I still have to explain and write up. Speaking of which, we still have an outstanding Mystery Micrograph and a Mystery Flagellar Root Apparatus to resolve, both at the free beer* level of difficult by this point ;-)

*If/when budget and geography allow it.

Now if only I could get enough results to satisfy everyone. Science is not cooperating with me lately...grrr. Nor are my writing juices. (Must. finish. results *yawn* section...zzZZZ) Annoyingly enough, annoying complications exciting new data tends to come along just as you're writing up and leaving. Oh gamma-tubulin, why do you insist on getting yourself involved in our already ridiculously complicated plot? *sob* Just gonna pretend that experiment never happened, lalala... actually, just gonna sleep and deal with all this crap tomorrow. Maybe even stop whining about it, but that may be asking for a bit much. But afterwards -- Sunday Protist!

Slow Blogging Alert now level Orange

It was Level Red last week, although somehow still managed to write the onychophoran post. (also, I think I've spent too much time at SFO Int'l over the last few years; they keep playing that 'security threat level orange' thing over and over so much that you're guaranteed to heed no attention to any real threat warnings. Anyone know how the cichlids in Terminal 1 are doing lately?)

Turns out that the universe doesn't suddenly get all calm and manageable immediately after finals. Who knew. Working in two labs simultaneously is not helping. Nor is wrapping up loose ends from the last term, nor is freaking out over super-urgent course planning as summer classes start - OMG - next week. I'm only doing one a term, but still. Also, seems like everyone and their mother needs me to write various things at the moment, thereby draining my 'writing juices' (I'm sure some MRI machine can be tweaked enough to verify their existence...) Strangely enough, not actually procrastinating all that much these days, so I think I may actually be genuinely busy, as opposed to just failing time management 101. Wow.

Blogging should pick up shortly once things settle down a bit. After all, this week I just rediscovered what it's like to be a n00b in the lab again, and don't have any 'lower-ranking' undergrads to abuse anymore. Damn. (conversely, I don't have to train n00bs either, and that can be quite energy-draining as well...) A lab is very much like one of those social onychophoran groups, albeit too antisocial to actually cuddle. And less cute.

I will write up a cool paper or two tonight though... stay tuned for the next post!

PS: I just started my very first culture! Wheeeee! It's Euglena, so shouldn't die off too quickly... it better not, considering how I spent the bulk of yesterday morning searching for exotic salts to appease their complicated appetite...

Oh, and I did not forget about Part III of Constructive Neutral Evolution. That will happen...soon...


By the way, if you haven't done so already, there are new editions of two carnivals to check out:

Carnival of Evolution #23 - at Evolution: Education and Outreach
Next issue at: Neurodojo. Submit posts here

Scientia Pro Publica #28 - at Mauka to Maukai
Next issue at: Maniraptora. Submit posts here

Slow blogging alert...

As you may or may not have noticed, it's April. April is a very special time for some poor fucks students. This is where this wonderful bi-/tri-annual hazing ritual occurs wherein a tribesman is placed before a patterned sheet of paper and scribbles along for a predetermined duration of time, Subsequently, a tribesman of a higher rank employs these scribbled sheets of paper in a peculiar ritual of divination rite, wherein markings (usually in red ink) are splattered all over to determine the worth (and fate) of the tribesman in question. A certain number of these rituals must be committed over 4-6 years before the tribesman has accomplished the initation rite successfully, upon which he or she dons peculiar medieval robes and is said to now be of a higher rank. These robes seem to reflect the colouration scheme of the respective clan the tribesman belongs to.

Long story short, I haz finals looming ahead. April isn't as bad as December (we actually get to see sunlight, which is kind of cool), but I must also wrap up my current project and write everything up, and as you may know, wrapping up one's research can be an epic pain in the ass. Why does it seem easier to write up other people's research rather than your own?

Also, there's like term papers and presentations and stuff. And taxes. And other gov't paperwork. And holy crap I don't wanna think about how I'm gonna survive this month. Thus, blogging will probably be reduced, and happen [even more] in sporadic bursts (procrastination is sort of quantised...). Kind of stressed at the moment, and the more stuff I have to do, the less I can focus on any given item in the list. Really annoying, to be honest.

That said, Sunday Protist and the continuation to the Neutral Evolution posts are on their way, and apologies for the delay. Actually, I think I'll wait until Wed to finish the next installment on Constructive Neutral Evolution, as Ford Doolittle is giving a talk on that at a dept seminar (sooo excited!) Would make sense to blog about that after his talk.

But yeah, apologies in advance for sub-par blogging until May. And why do I have to absorb the Canadian obsession with incessant apologising despite not actually being Canadian? Grrr...sorry about that! =P

Back! (almost...)

Glad to be home on the internet!

Apparently, much drama has happened in my absense (damn, I can't leave you guys for a week without the whole internet seeming to explode in flames!), which may be expanded on later (disclaimer: if/when I feel like it); also a few interesting papers out, including a phylogeny of Noctilucoids, that may also be covered later, if I get around to it.

By almost back, I mean there's a bit of a problem with regards to blogging this week:
- Catch up on seminar course stuff... o_O (esp. marking schemes, assignments, etc)
- Dept seminar talk by this guy =D
- Midterm #1
- Midterm #2
(above three events on the same day, immediately following one another!)
- Make a poster. For Saturday. This is my first time ever. I usually do talks. Shit.
- Prepare a talk. For Saturday. Completely unrelated to poster.
- Freak out over the entire panel for aforementioned talk, since we're doing it together as the seminar class. As a coordinator, everything and anything will be automatically my fault...
- I have a job, apparently. Right. Try to remember what the hell it is they pay me to do at said job... and srsly catch up on my research. I can't fall behind any further!!!
- Guest lecturers for aforementioned seminar course.
- Readings for said seminar course. Which means, find them again, distribute them, and read them myself too.
- The loathsome coursework thing.

And of course, extracurricular plans + obligations, which all seem to congregate at the same time as 'intracurricular' plans + obligations.

Oh, and all those emails I've been rather abysmal at replying to in a timely manner. Sorry!

Then I'll post some protists, and update both the Tree of Eukaryotes, and the Foram Expansion Pack. I haven't been ignoring the comments, honest!

Oh, off topic: I own Grell's (1973) Protozoology now. It cost me an arm and a leg, but well worth it! Also, someone can get his copy back now, after I've been hoarding it for about a year... ^.^ But yeah, I can now blog about the awesome stuff in that awesome book! =D

Ok, back to remembering what it is that I do here. Must. Not. Look. At. To-do list... AAAH!