Field of Science

Update: Tree of Eukaryotes (parasitology edition)

There arose a need for a new tree for a parasitology meeting, so after almost five years, I finally updated the tree of eukaryotes. There are still things that need to be changed, and new orphan lineages that should be added, but here's an updated version showing predominantly parasitic lineages in bold, and lineages known to contain parasites and/or opportunists marked with an asterisk. Since the citations box from the older editions is hard to keep updated, I've removed it, and hope to replace it with references and further reading on this site, where it can be easily modified.

Once again, note that this tree, which incorporating real data, is an inherently subjective synthesis, and should be used with caution. As always, comments and suggestions welcome.

References and further reading to be added shortly, once I have more time ;-)

(The first edition was half a decade ago... time flies!)

Return home from SciAm Blogs

Greetings and welcome to this particular pond of microbes.

I'm back! My wonderful time at Scientific American at The Ocelloid has come to a close, as I am currently not in the right place in life for semi-professional blogging. The pressure of having someone else's brand name associated with the blog actually made it hard for me to write, as all sorts of anxiety issues crawled out of the woodwork at the sight of that. It may take me some time to get back into regular blogging again -- while adjusting to graduate school -- but this is my primary online home again, for now. You know you've been away for a while when Blogger's interface is entirely different.

Hopefully, the more flexible commenting system here will help re-establish some of the readership and conversation that was lost in transition... well, over two transitions and a very long stagnant period, that is. It may be wishful thinking to expect anyone to remain here, but someone's gotta start sweeping up the dust!

This is mostly to ensure people coming from my last post at SciAm that I do, in fact, still have the keys to this place. Let's ignore that this is the first post of 2014... (whereas that last SciAm post was the... third post of 2014. Sigh.)

Anyway, I'll lay down this vaguely Christmas-y image of a red alga as a front door mat. Red algae are so vibrant under good optics that all too often the camera doesn't quite do it justice. Charismatic megaflora, if you will.

To those who have returned with me -- thank you for sticking along this far! And for those who are new -- welcome! Let's see where this particular leg of my blogging adventure heads to. (the leg must be quite confused as to why it suddenly gets a head, but that's besides the point)

Best wishes,

Live coverage of Big Protist Conference (ICOP) in Vancouver, 28 Jul -- 02 Aug

There's a big protist meeting in Vancouver starting tomorrow, and I've been generously supported by ICOP and ISOP to attend as a reporter. I'd like to invite you all to follow us during and/or peruse the results afterwards -- further information is here. In summary:

Twitter: @ocelloid
Hashtag: #ICOP13

Cheers, and hope to see y'all there, in some form! =)

Ongoing page for protistology resources

(Yes, I still exist!)
I've been prompted to compile a collection of suggested resources on protist diversity and biology, and quite frankly, I'm getting a bit too lazy to look things up and send the links again and again. So I've made a page on Protistology Resources -- it's still raw, but I hope it can help some people get started. If there's anything you'd like to contribute, including own lab pages, papers, etc -- please feel free to comment or email me!

If anyone wonders where I hang out these days: I've a blog with Scientific American -- The Ocelloid. And yes, I definitely really really need to blog more, both here and there.

Cheers, and hoping to be around more often.

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();
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;
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...


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!

New paper on Constructive Neutral Evolution

Don't have time to blog this right now (off to protistology conference today -- will bring back lots of goodies!), but there's a new review paper about CNE out a couple weeks ago. It's paywalled at some rather obscure journal that an institution as big as UBC doesn't have access to, so here's a pdf y'all can [hopefully] access!

Lukes et al. 2011 IUBMB Life: How a Neutral Evolutionary Ratchet Can Build Cellular Complexity

See, if this was published in a proper (ie, open access) journal, I wouldn't have to do this. As taxpayers you all have the right to see this, outdated publishers be damned.

I'm taking off to ISoP in Seattle - I might attempt to live tweet parts of it (as @ocelloid), so do follow us on twitter using the #isop11 hashtag! And for those of you who are gonna be there... let's see if you can find me ;-) (spoiler alert: Psi is a pseudonym. Seriously! o.O)

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!

A Tree of Eukaryotes v1.3a

ResearchBlogging.orgTime for a new tree, finally. Some groups have been fixed and the diagram has moved from Powerpoint to a real vector art program (Illustrator), so hopefully it looks a bit nicer now and has slightly fewer glaring errors. Have yet to fix all issues, the biggest (and hardest) being the proportions taken up by the various groups -- the tree appears dominated by Excavates for some reason. Due to lack of convenient taxa for the heteroloboseans and euglenids, I expanded them to the genus level in some cases to attempt to capture some of the diversity better, but that screwed things up for the rest of the tree. Since fixing that would require some hardcore structural changes to the whole tree, I'll do that later, in the next edition (which will not take over a year to come out this time). Given some conferences coming up this summer, and that people have asked, I'll release what I have done now as v1.3a.

Enjoy! (And do complain if you spot anything awry...)
Previous versions and discussions, along with trees by other people, can be found here.

A shit ton (see image). But doesn't allow indexing 'shit ton', so I'm gonna be pathetically lazy and just cite this:
Keeling, P., Burger, G., Durnford, D., Lang, B., Lee, R., Pearlman, R., Roger, A., & Gray, M. (2005). The tree of eukaryotes Trends in Ecology & Evolution, 20 (12), 670-676 DOI: 10.1016/j.tree.2005.09.005

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 ;-)

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).