Free ImageJ Macro -- for citing images

(of course all IJ macros and IJ itself are free...)

So I got sick of constantly clicking away just to resize an image and add some citation text to the bottom and then name the file that exact thing; in fact, it was a deterrent to blogging -- yes, I am *that* lazy, apparently. At 4 in the morning today, my latent inner yet-unexplored codemonkey decided it needed an ImageJ macro for doing that, and it needed it then, at 4 in the morning, the day before I fly for holidays, and therefore a very busy day. After a couple hours of failed negotiation attempts between brick walls and my head (and much profanity), I finally produced a piece of code that not only does something, but does what I want it to! Being an utter failure at anything technical (engineering aptitude turns out to not be particularly heritable, as my parents' experiment demonstrates), I get soooo excited when something I slap together out of copy+paste and single-finger typing on the keyboard actually works, that I absolutely have to share it with the world. Even if it's pathetically minor and useless. Shhh.

World, behold -- an ImageJ macro for adding citations to images!

// This macro creates citation (or other input) text by adding a 20p strip to the bottom of the image, aligned right

// Image is saved in Documents as the ref input text

// WARNING: saving several images with same citation input WILL result in overwrite!

ref=getString("Reference", "ref");

var width = getWidth();

var height = getHeight();

height=height+20;

run("Canvas Size...","width=&width height=&height position=Top-Center");

var textwidth=getStringWidth(ref);

var textmargin=width-(textwidth+5);

drawString(ref,textmargin, height-5);

var path="C:\\";

var name=path+" "+ref;

saveAs("Jpeg",name);

Hopefully this means I'll get back to regular blogging soon, as one more Gate of Laziness has been removed from the path. Now if only IJ could also upload and link those images...

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).

Protists gone motile! (and a Euglenid metaboly video)

So I caved and got me a Youtube account, partly inspired by a comment in the previous post. Accumulated half a metric shit ton of random protist videos by now, and compressing them for Bloggers crappy video sharing system would take way too much time, and I barely have the time to grab stills and post them here. So finally there's a suitable outlet for my raw video data – maybe someday when I'm not going completely insane and falling behind on a million things I didn't really have time for in the first place, I may put together a properly edited video. But don't hold your breath for it...

We have some pretty awesome microscopy and video equipment in the lab, and I'm lucky to have a PI nice enough not to mind some of us using it to fuck around with random samples in the middle of the night. I hope it may help bring the microbial world a little closer to you, and add a whole new dimension of time to our protists.

Let's start off with some euglenid metaboly, since it's quite hard to talk about without seeing it. Actually, the true reason is that it's about the first thing my cursor landed on when I opened my pile of videos for file conversion. But just as we ascribe purpose to evolutionary happenings, we can likewise ascribe purpose to my selection here ;-)

Since I'm lazy and behind on about a million things (to the point where I must mention it twice), just gonna copy the short description I wrote for this bug on the YouTube page. Enjoy!

This is a heterotrophic euglenid, perhaps a Peranema sp., exhibiting metaboly in all its splendour. The cell might be slightly squashed or otherwise damaged, keeping the flagellate conveniently in one place. The clear vesicle near the base of the flagellum that grows and shrinks is the contractile vacuole, the flagellate's analogue of the animal secretory system. At the tail end are refractile starch granules used to store energy.

Metaboly is a form of cell movement that is most famously exemplified by ciliates, but also known in some other flagellates. It appears to be caused by the specific arrangement of microtubule (cell skeleton) bundles at the cell periphery, and greatly enhanced by the 'armour plates' of the euglenid surface, which is lined with long pellicle strips going from the flagellar insertion all the way to the tip of the 'tail' -- as the cell twists about, the strips slide against each other and result in this movement. Euglenids with fused pellicle strips, like Phacus, are incapable of metaboly. The function of this movement is unknown, and there may not be any in particular.

The hairy thing next to the euglenid is a badly mangled ciliate.

Freshwater, Apr 2011, Vancouver

And please let me know if you have any requests, comments or suggestions for these videos. I'm new to the world of moving pictures (instead I see videos as image sequences, like any proper cell biologist ought to...), so I'm in an even greater state than usual in not knowing what the hell I'm doing.

Science Online 2011 ramblings

By now, about every aspect of Science Online has been thoroughly blogged and overblogged, so for a comprehensive review, see the Science Online 2011 website, namely the Blog and Media Coverage page. I don't think I have much to add, but I'll ramble anyway. After all, this is why I have a blog, right? Plagued by an epic writer's block lately though, so lower your expectations accordingly. Even more so than you should normally when approaching this place. In fact, since this has been sitting in my drafts folder for about four five six days, I'm just going to hit random parts of the keyboard and hope the result resembles English somehow, while torturing you with a sequence of cumbersome, poorly linked clauses, so I can get back to regular blogging, ideally with readable sentences that time.


Cheesy as it sounds, the highlight of the conference was definitely the people. In a way, it's more of a 'reunion' than a conference sensu stricto, as some put it. A major aim of the conference is to humanise the blogosphere, as knowing each other personally should make the environment more pleasant and less aggressive, and I think it works. Without knowing the physical entity behind an online alias, it is sometimes easy to find yourself carried away with something they wrote, as opposed to evaluating the person as a whole. We all have our quirky opinions, and we all write stuff from time to time that can piss off someone, somewhere. Sometimes it's too easy to get fixated on a single idea you find personally irritating, and forget that there is more to the poster than that one comment. Knowing each other in a more personal manner could diffuse some of those conflicts.

I was pleasantly surprised by how little of the general blogosphere drama carried over into the physical conference. People generally seem more chill offline. Maybe I was just oblivious to the real picture, as I usually am (drama usually passes by me without even acknowledging my existence – I guess that has its own perks), but everyone was really friendly and full of energy. Combine that with Deep Sea partying and North Carolinean hospitality*, and great times were had!

*I'll ramble about 'surprising' non-homogeneity of North American cultures in a later post...

The group of attendees was surprisingly diverse in the professional/occupational sense, including a range from students and scientists to full-time writers and journalists to PIOs and librarians and some people behind things like PLoS and Mendeley. There were those with various artistic talents, from science illustration (eg @flyingtrilobite/Glendon Mellow) to music (eg. Adrian and Kevin's GFAJ-1 Arsenic Blues – though that recording does not do it justice) and comedy (@sciencecomedian/Brian Malow). Being somewhat locked up in the ivory tower by this point, it was great to meet people with real jobs who actually talk to people outside academia. Science Online is also unusual in that everyone was on a fairly even level, regardless of professional rank. Your professional hierarchy and reputation were irrelevant since there was hardly anyone from your own field. Thus, faculty, students, librarians, writers, postdocs, etc all spoke on equal ground, which was a wonderful experience in itself. As much as some try to suppress hierarchy at traditional academic conferences, it's still clearly there, and your rank in the field does matter. At Science Online, your online presence was more important, but that hierarchy is, thankfully, less rigid, and still rather nebulous in concept.

The use of Twitter at the conference was rather surreal...it's as if between all the smaller discussions and conversations in the physical realm was a broader conversation in the electromagnetic waves of Twitterland. The badges had a place for one's Twitter handle, along with a QR code for the website. It's as if we had multiple identities, and I did for sure. I went by my blogger alias (shocking plot twist: Psi Wavefunction is not my legal name ;p) since that's how people know me online. Given that, I still preferred by real name in offline conversations. Which made it even more awkward. Some people insisted on calling me Psi – I don't mind at all, but it was odd to be called by something other than my real name!


I won't even try to go over all the highlights regarding people and events, but I'll just casually mention some snippets, in a totally random manner and order. Mostly my own reactions to them, since others have already discussed the topics in greater detail (and insight).

First off, our keynote was Robert Krulwich, a journalist and co-host of Radiolab. In attempting to attract an audience who typically think they don't care about science, they have a very interesting approach to explaining complicated topics: acting stupid. Stupider than their listeners. We like feeling smarter than others, so it often works better when the teacher (sensu lato) speaks the language of a novice rather than an expert, and asks such questions of the guest experts that the audience would never 'stoop' to. Ie, very basic questions, prodding for very basic answers in return. That way, the audience doesn't feel like material is dumbed down for them (which may feel somewhat insulting, and definitely distanced), but rather for the host, ie Krulwich. Of course, there is also much humour involved, and the programmes are, as a result, entertaining. It's amazing what these people can do, as it is incredibly difficult to convince someone a topic is interesting once they've made up their mind it's not. Making it relevant is not enough – making it relevant and fun, without the feeling of distance (and definitely not lecturing!) is an art, and one we really need more of.

* This happened around hour 56** since I last had sleep, so I shamefully admit to not processing much information at that point

**let's see, got up around 9ish on Tuesday, hung out + packed all night, went to Seattle on Wed, hung out, flew out Wed night, horribly packed flight with stopover at Washington DC, too short to sleep much, arrived at RDU on Thu around 9am, couldn't check in or sleep, keynote around 8pm...yeah. Must've been a zombie by that point.

Went to the history of science panel, where we underlined the importance of understanding the context of scientific discoveries, and the richness that the extra dimension (time) adds to scientific stories overall. And historical context provided properly, not crudely mocking the past thinkers for coming up with such "ridiculous" hypotheses. Probably most of the stuff we think today will be laughed at in a couple centuries or so, if we as a species make it that far. The historical aspect includes not only the history of one's field, but also the sociopolitical context of the time, since science is not this purely 'objective' holy thing independent of human thought; science is a human process, and thus carries with it the stamps of every generation's worldviews. It can only make more sense that way. Where possible, good science writing should happen in four dimensions.

With John Logsdon and Julie we directed a discussion on improving public outreach for small and/or obscure "micro"-disciplines, with emphasis on internet presence. I'll make a separate post on this topic later.

I was also on a panel my awesome co-moderators on beginning blogging and issues like the impostor syndrome, which was a great lot of fun. Others have blogged about it already, and I'll add the links once I find them (soooo many #scio11 posts to catch up on...!).


There is currently some talk about compromised diversity in the blogosphere, but we must keep in mind that we are biased by being an anglophone blogsphere, and the conference was in North Carolina, which was difficult to get to even for those of us on the other coast, let alone from overseas. I personally doubt pushing labels could help much, and think the problem, where it truly exists, lies deeper than online presence. Yes, some races/ethnicities/groups are underrepresented in the English-speaking blogosphere, but that may have something to do with the same races/ethnicities/groups being underrepresented in the educational system in general, and not with the internet or the community.

When I read blog posts, I pay very little attention to the background of who writes them, aside from their field of expertise/activity. If I find the stories interesting, I'll read them regardless of the gender of the author, and I don't feel particularly obliged to read a story I wouldn't otherwise touch simply due to their background. On the internet, it is especially easy to be truly 'colourblind' (in the metaphorical sense too), since you don't even see the author unless you look. So the issues with diversity online are probably a direct result of the problems offline, which are much harder to fix with online means. Maybe instead of focusing on the skewed diversity of bloggers, we should first look at how blogging can help the problem closer to its root. Eg, are underprivileged groups even reading any of our stuff in the first place, and if so, what can we do to be more useful to them, etc.

But I'm not sure it's entirely helpful to start shelving ourselves into categories like "female blogger" or "white blogger" or whatever. I don't particularly care for being read as a "female immigrant Russian atheist blogger". I would prefer to be read as some person whose writing people occasionally find interesting. My background would be a digression, perhaps interesting for my regular readership, but far from necessary for the main goal. But then again, maybe as a scientist I underestimate the average reader's desire to understand the blogger's character – would love for my readership to chime in on this!

Anyway, those were my [somewhat obligatory] two cents on the diversity issue, and I'll probably leave the discussion there. It's not that I don't care, but rather that such topics are not my forte, so I prefer to lurk quietly. But, by all means, feel free to discuss here!


And lastly, before I forget, some nebulous panel ideas for #scio12:
- Online presence of non-English languages
- Issues/specifics of niche blogging
- Dealing with "writer's block" (successfully, unlike Upper 1974 J Appl Behav Anal)
- Making the most of course blogs

Next up, eventually I'll put up some pictures from the overall east coast journey. And post some fucking protists, at last! =D

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)

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!

New carnival in molecular biology and CoE#25

Sorry for the delays in posting - was out of town and away from internet, and then frantically scrambling to get back into the writing zone and get work done. Only half a month ago, another edition of the Carnival of Evolution went out: #25 at Culturing Science. Go check it out, she even has drawings for each heading!


Coming up soon is the first edition of the new MolBio Carnival, headed by Alejandro at MolBiol Research Highlights, where the first edition will happen (posts on the first Monday of each month). We need submissions (form here), and after a couple months, hosts. From the the carnival's main page:

We encourage the submission of posts discussing peer-review articles, techniques, books and related topics. Specific areas of interest include, but are not limited to: structure and function of proteins, nucleic acids and other macromolecules, gene expression and its regulation, signal transduction, apoptosis, developmental biology, cell cycle and cell growth, microbiology, biochemistry, structural biology, membrane dynamics and many others. Systems and synthetic biology-related posts are also welcomed.

So go on and share anything molecular biology related, which is perhaps the bulk of modern biology anyway ;-) (except my stuff -- really need to crank up the molecular details here someday...) Feel free to double or triple post or whatever to multiple carnivals. The more linkage action going on, the better.

Ok, the carnival's gonna be waaay better than my miserable failure at advertising it. So go hit that shiny submit button *sparkle*. And please help spread the word!


Finally, I find many old illustrations to be quite beautiful. This one is from 1938 (Myers, PNAS) discussing the sex life of forams:

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!

Skeptic Wonder has joined FoS! (and new header!)

In case you haven't yet left the comfort of your feed reader and noticed the changes, Skeptic Wonder has moved from Blogger.com to FieldofScience.com, hereafter known as FoS. The founder, Edward, has invited me very kindly and thus persuaded me to join. I feel quite honoured to be among the wonderful bloggers here, and hope I can pull my weight. Thank you, Edward!

Please let me know if anything's not working as well as it should, or if some element of formatting is tempting you to throw a sharp heavy object against the monitor. Or even if it only bugs you slightly. And, of course, speaking of which, various bugs too. The blog looks a bit funny via Safari on a Mac for me, does anyone else have the same problem? Or is that computer generally fucked? Via Firefox on PC seems fine though...

To celebrate the move, I finally set out to take care of a problem that has plagued this blog since conception, namely the long overdue customised header. I have spent many mL of brain juice pondering how to make the header several months ago, and never quite got anywhere. Today, I scrapped all prior planning and simply assembled some of my own micrographs together, intended to represent the eight major eukaryotic supergroups:

From left to right: Opisthokonta (nucleariid), Amoebozoa (Cochliopodium?), Excavata (Trichonympha), Archaeplastida (Eudorina?), Hacrobia (centrohelid Raphidiophrys), Rhizaria (euglyphid), Stramenopila (bicosoecid) and Alveolata (ciliate Cyclidium).

Ha, I have images for every supergroup! Would be nice to have one for each subgrouping, and then refine further and further until I get the whole tree covered. And then my plans for world protist domination shall be complete, bwahaha!

I've posted the Trichonympha image before, but haven't shared the whole stack. Admittedly, the poor creature is kind of bloated and dead, but I think the piece of undigested xylem lignin helix makes it all worth it:

I don't have any half-decent pictures of other parabasalians. Yet.

Also, the full picture of what I think may be Eudorina:

It's one of my earlier micrographs, and thus the DIC sucks badly. The colonies are still adorable though!

The other images hang out elsewhere on the blog, except for the euglyphid, which will be blogged about eventually soon. I've got more where that came from.

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!

Hiatus until March

Due to the extended reading break resulting from the abomination and massive waste of taxpayers' dollars that is the fucking Olympics (I guess that's where Genome Canada's funding went instead? Great allocation of resources we've got there!), I will be mostly internetless at my parents' house for the next two weeks, until 01 Mar.

I didn't have any time to schedule posts or anything (INSANE week), so for now just enjoy the blogroll on your right, lurk around the tree, google random protists or whatever. Gonna try to resume half-decent posting after the break. This term just hasn't been very kind to blogging time thus far...

And the next Tree of Eukaryotes release should happen after the first week of March too. There's a few spelling errors in need of attention, and some taxa.

Anyway, have a good two weeks!