Field of Science

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,
-Psi-

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
Blog: http:blogs.scientificamerican.com/ocelloid

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();
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!

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.

References
A shit ton (see image). But ResearchBlogging.org 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 ;-)

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).

Sticky proteins, complexity drama and selection's blind eye

*For your entertainment, rejected titles:
[Sticky proteins and complex relationships]
[(protein) Relationship drama: promiscuous proteins in small populations]
[Not all is good that sticks: non-adaptive complexity gain through compensatory protein adhesion]
[Man, I suck at titles]

NB: This post can be considered as part 2.5 of my In defense of constructive neutral evolution series; also recommended for some background are part 1, discussing selection, drift and Neutral Theory, and part 2, discussing Constructive Neutral Evolution; to answer a popular question, part 3 *will* materialise eventually once I get off my ass and write it.

ResearchBlogging.orgConstructive neutral evolution is one mechanism of complexity increase without any associated increase in fitness – or, in other words, non-adaptive complexity gain. Basically, a random interaction between two proteins can lead to a fixed dependency if this interaction compensates for a mutation that was otherwise lethal – termed 'pressuppression'. In this way, previously unnecessary dependencies accumulate to make a very bulky, bureaucratic system that essentially does the same thing. We've all seen it in our institutions, and evolution is about as efficient.

Now, one bottleneck in this model is waiting for proteins to actually interact. Proteins are quite sticky and non-specific by nature, but usually not too much as that can be quite deleterious. Piling up a bunch of proteins on each other has a non-negligible chance of interfering with their function, and one would expect for chance interactions to not be excessively promiscuous, although those who have done regulatory genetics and protein work are probably aware just how annoyingly non-specific some of the protein binding can get. Luckily, there is now a possibly mechanism boosting these chance interactions, and thus alleviating that particular bottleneck in the Constructive Neutral Evolution process, rapidly accelerating complexification and protein network obfuscation to the extent where the interaction map looks like a web; not a finely organised web of an orb-weaver but rather one of those clumpy webs that are a clusterfuck of stickiness and silk. Enter this week's Fernández and Lynch 2011 Nature paper, from here onwards referred to as "the paper".

Protein 'stickiness' can be enhanced by biochemical means. Proteins vary in stability, and themselves come in populations – generally, most are in the optimal conformation that is presumably functional, but some individuals are messed up. This happens well past the sequence and folding errors, and some perfectly 'normal' proteins can be in a suboptimal state at any given time. Clearly, this affects the overall efficiency of the protein – even if it's enzymatically awesome, the overall 'protein' as we biologists understand it (sans population aspect) would decline in efficiency if a large chunk of its population is in a misfolded state.

One aspect that pushes around the proportion of the protein in the 'right' conformation is how well it plays with water. It shouldn't be too surprising that hydrophobic regions induce instability. What was new to me, but perhaps old news to those who actually understood chemistry, is that the exposure of the polar(hydrophilic) protein backbone to water also has a destabilising effect – and not only that, but often more significant than that of exposed hydrophobic regions! This may seem counterintuitive – doesn't water like hydrophilic regions? And there lies our problem.

Water molecules are attracted to polar groups, and the amino acid backbone is quite polar. This means little water molecules wander in towards the backbone and form hydrogen bonds with it. The problem is twofold: first of all, the protein, like all molecules, likes to 'jiggle'. The more it can jiggle in its given conformation, the more favourable that conformation is thermodynamically since its satisfied by more states. Entropy, etc. (now we're *really* entering territory I know nothing about, since my phys chem experience is locked away by PTSD...). Hooking up this backbone with water molecules reduces its 'jiggle' room, and makes it less thermodynamically stable – making change to other conformations more probable, therefore possibly leading to more errors in the protein population.

Secondly, as detailed further in the paper, water likes to hang out with more of itself. Water molecules are happiest in foursomes, sharing four hydrogen bonds with their neighbours. When a creepy protein backbone emerges and lures an unsuspecting water molecule away into the protein's murky depths, the water molecule cannot form as many bonds with its fellows (or as many hydrogen bonds, period), and is really sad and lonely. Or, in proper terms, the system becomes less stable, since thermodynamics will favour an arrangement where these water molecules are all happily coordinated with each other, and not being molested in a corner by an amino acid polar group. In other words, exposing the polar backbone (Solvent-Accessible Backbone Hydrogen Bonds, SABHBs in the paper) to water induces what is called Protein-Water Interfacial Tension (PWIT).

One way this tension can be released and the backbone exposure ('coded for' by genes, by the way) can be compensated for is if a random other protein (or more of its own kind) are recruited to cover that exposed backbone. This would help stabilise the protein conformation, and allow this potentially deleterious drawback to be tolerated (and get fixed in the population). Ultimately, the second (and third, etc) protein can become exapted for something useful, although just an eventual dependency is good enough to make sure these proteins stick together permanently. The crazy web of interactions gets crazier.

Fernández & Lynch's fig1a suffices perfectly but I like making diagrams, so I made one anyway. See text.
(Disclaimer: I'm horrible at chemistry, this may all have been thoroughly wrong...read the paper.)

Now I'm about the last person to willingly blog about biochemistry, and this seems to have little only a distant relevance to evolution, particularly the non-adaptive kind that fascinates yours truly. It will make sense in a bit. Recall from a few seconds ago (hey, already difficult for some of us) that protein instability leads to reduced protein efficiency. This reduction is generally tolerated, however, until it's bad enough to have a higher chance of being removed. Recall from [what should be] introductory population genetics that selection acts probabilistically, with true slightly deleterious mutations have a lesser, but still significant, chance of fixation than strongly deleterious mutations, which selection has a higher chance of taking care of before drift quietly fixes it. (more detail in older post here) Since proteins are, quite unsurprisingly, also governed by fundamental principles of population genetics, drift becomes involved there too.

As populations get smaller, drift becomes a more dominant force relative to selection, and the window of 'effectively neutral' mutations – slightly beneficial and slightly deleterious, but unlikely to be dealt with by selection – increases. More mess is tolerated. This means more protein inefficiencies are allowed to fix in the population, those induced by backbone exposure among them. Since there are now more proteins that are no longer happy with themselves (or, rather, have an increased Protein-Water Interfacial Tension), they are more likely to stick together for biochemical stability. And here Constructive Neutral Evolution can come in too, allowing further deleterious mutations that are now presuppressed by the recruited proteins. In a way, this greases the presuppression process, rather than competing with it as this BBC news piece made Ford Doolittle appear to suggest.

Now, this is all great in theory, but is there any real data in support of this? For one thing, there is a clear increase of interactome (set of all interactions in an organism) complexity correlating with decrease in effective population size, suggesting a link between lax selection and accumulating complexity. Furthermore, the proteins in organisms of these smaller populations have more blistering backbone exposures to water. Supporting the relationship with population size further yet with the advantage of more phylogenetically independent events (but less interactome data), bacterial intracellular endosymbionts consistently exhibit higher protein backbone exposure (hydration) than their free-living counterparts. Selection appears to disfavour not only polar backbone exposure (also described as 'poorly wrapped proteins' in the paper), but once again, the rise of interaction complexity as a whole. (Fernández and Lynch 2011 Nature, in case you somehow managed to miss that)

Obviously I like this paper because it adds another mechanism to the arsenal of evolutionary processes happening independently of adaptation. But moreover, I don't think one can find too many examples of biochemistry mixed with population genetics. You hardly find cell and developmental biologists thinking about population genetics, and perhaps many biochemists have never even been exposed to such a subject. When fields that should never come that close together do, some really nice explosions of insight can occur (my sad attempt at chemical metaphors). We really need to talk to other more, and maybe even wander over to other departments from time to time. It's sometimes (often) frustrating to communicate with those strange ones from afar, but just like ethnic xenophobia, its interdisciplinary counterpart must also be overcome.

-----
Figure 2a annoyed me a little as it ignored phylogenetic relationships, which is a big no-no when comparing properties of taxa. The figure is technically fine, especially since there aren't any correlation analyses there, but it's hard to discount phylogenetic history as being the cause behind the correlation of the traits without actually the characters on a tree. Anyway, since I like playing with data and running statistical analyses on things, especially when I didn't actually have to go through the pain of obtaining the data myself, I mapped some characters (interactome complexity from fig2a) on a phylogeny:



Unfortunately, even the most basic statistical operations become an epic headache when trees are involved, and very quickly things become painfully complicated, for the human as well as the computer. Especially when you're handed a dataset of mixed categorical and continuous characters, as I learned the hard way last night. After fighting Mesquite for a good many hours, I finally had to resort to extracting the Ne*µ (effective pop size * mutation rate; roughly put, both lead to increased selection efficiency) estimates from Lynch & Conery 2003 – relying on an intersection of two datasets meant that our taxon sampling was quite sad by the end of this enterprise. Anyway, I ran a pairwise comparison test (Maddison 1999 J Theor Biol) on the data, which probably isn't the best thing ever, but I got something resembling significance: p = 0.019. Depending on how statistically noisy your field is, you may even deem this acceptable. In any case, not too bad given my crude (and somewhat clueless) analysis and limited taxon sampling:

Moral of the story: the inverse correlation between interactome complexity and effective population size is unlikely to be a mere artefact of shared phylogenetic history. In other words, Fernández & Lynch's hypothesis stands strong.

I mostly did this because I thought it'd take a couple hours max. If hours meant days, that wasn't too far off... but hey, I learned something!

Acknowledgments: thanks to Lucas Brouwers for helping me wade through the heavy biochemical stuff, and to Mike Lynch for explaining the key idea of the paper a while earlier. Otherwise I would've probably been too daunted to even read it, let alone blog about it...
Oh, and my Twitter people for random phylogenetics advice ;-)

Reference
Fernández, A., & Lynch, M. (2011). Non-adaptive origins of interactome complexity Nature DOI: 10.1038/nature09992

[will add some supplementary refs once I return to internet on Monday...]