59th Carnival of Evolution up at DNA Barcoding

Clicky here. Lots of interesting stuff, with a Dr. Who theme to boot. Reminds me of those times when I taught biology of fantasy and sci fi movies, except the cultureless students didn’t recognise most of the movies and series I was talking about. Anyway, my post on randomness in evolution is in there too, but I won’t link to it so that you’re forced to go read.

Carnival of Evolution 58 at Synthetic Daisies

Long carnival, a lot of stuff to get through. Good thing all of it is pretty interesting. Check it out! (My Lamarckism lecture made it in there too.)

Comprehensive update on my current situation

Because I’m constantly taken aback by the support I get from the subscribed readers, I thought I should give a final update on my situation in relation to the self-caused meltdown of Cyprus, and my plans for the short-term future (which will hopefully stick).

It’s obvious that we’re in dire financial straits. In view of that, I have cancelled just about every single one of my ongoing projects, including the palaeontology exhibition I’ve spent the last 2 months painstakingly creating exhibits for, several book chapters, and all my research projects. Reason is that I don’t have the luxury to spend time and/or money on things that will not provide me with the direct benefits that are needed now. The only thing I keep doing is my various educational duties – work with schools, public lecturing, this website.

Instead, I take up my time by whoring my skills out to the internet for whatever money people will pay me. Need a drawing? Need your homework done? Need someone to write your thesis? Need texts translated? Need a phylogenetic tree built or tons of data analysed? I’m your guy. $5 and I’ll do all of that. So far, it’s just been ghostwriting, proofreading, translating, tutoring, and drawing storyboards, but I’m fairly versatile.

In addition, I have kept one software project going. It’s a phylogenetics-based media recommendation system that I hope to sell off for a life-changing sum, or however it is that software people get rich. It will allow the user to enter their favourite film/series, director (or other prominent staff member except actor/actress), genre, or theme, and the program spits out recommended movies or series based on the magic that I am programming. Atm it’s limited to anime and East Asian cinema because that’s where the bulk of my film knowledge lies, but the system is flexible enough to allow for any media, as long as you can provide a comprehensive database.

Of course, this is only a temporary situation. For the short-term future, my plan is the following:

• Complete an education degree, most likely in teaching English.
• Move to Japan for a university position interview.
• If I get it, great, I’ll most likely be on Ph.D. track.
• If not, then I will not have enough money for a two-way ticket, so I will use my English teaching degree to get a job at a school, or maybe even get a job teaching biology in English at a school or even at university. (If any Japanese readers have some help in this area, contact me!)

Why Japan? Because I firmly believe that the best scientist is the one who broadens his horizons and visits as many schools of thought as possible. I got educated in a specific brand of German evolutionary thought, and am well acquainted with the various schools of Europe and the USA through my colleagues. So the next logical frontier for me is Japan, since I already have a basic functional knowledge of the language, plus my multilingual skills make me an appealing prospect there, a distinct advantage that I do not have in Europe or the USA.

However, I’m also acutely aware that beggars can’t be choosers – and I am most definitely the beggar here – so while my mind is set on moving to Japan, I realise that the reality of the situation points to either a future of atrophication in Cyprus (suicide would be a better option if I had no family), or moving to Europe once more (acceptable), or maybe a move to a Middle Eastern country (which I would rather not do due to social reasons).

Shameless Self-Promotion

I live in Cyprus, a country inhabited by reactionary, short-sighted morons with a victim complex, an over-inflated ego, and rampant xenophobia, and governed by a Parliament more interested in populistic pandering than reasonable action. If you have read the financial news over the past week, you’ll know that Cyprus has been killed by its own populace and politicians, of their own free will. Banks are now closed, and will probably be dissolved soon.

So, in a pathetic act of desperation that I will probably regret soon enough, I have to resort to shameless self-promotion in the hopes that someone influential might perchance read this and give me a chance to leave this shithole out of the goodness of their heart. I was planning to leave of my own initiative, but the money I needed to set up a job for myself overseas got locked up in this disaster.

I will take any job, or an internship if accomodation is provided. I will even clean your toilets, as long as they’re not toilets in Cyprus. I have Cypriot (EU for now) and Lebanese citizenships, for VISAs. By the by, I have an Iranian microbiologist friend who is in a very similar position, if that’s more what you’re looking for.

What follows is simply a listing of my talents and skills. My training is in invertebrate palaeontology and zoology, and my main interests are in phylogenetics and macroevolutionary processes, so you have an idea of  my basic toolset that I will not mention in the listings. My knowledge-base comprises the above subjects, as well as a hefty dose of history of biology. My e-mail’s marcsrour@gmail.com.

Scientific skills:

• Phylogenetic methodology:  constructing and interpreting trees from multiple sources of data; emphasis on morphological cladistics;
• Applications of phylogenetic methodology outside of biology, e.g. linguistics, categorisation algorithms;
• Dissections;
• µCT and volume rendering;
• Histology, including serial histology for 3D rendering;
• GIS;
• Statistical analysis with R;
• Entomological sampling, storage, and curation;
• Collection databasing;
• Identification expertise: fossil molluscs, beetles, Hymenoptera, spiders;
• Programming languages: R, C, python, Ruby, Perl.

Communication skills:

• Languages: English (native), French (native), Arabic (native), Greek (business), German (business), Japanese (basic, self-taught).
• Lecturing and teaching experience: undergrad teaching assistant (evolution, invertebrate palaeontology); monthly public lectures, extracurricular biology project advisor for schools; webcam lecturing for overseas undergrad and grad journal clubs and discussion groups; lecture database now at 22GB; worked as English teacher at language school (B2-C1 level);
• Scientific outreach online through this blog and through Quora, where I was one of the Top Writers of 2012 and included in the Best of Quora book;
• Zoology and palaeontology museum tour guides;
• Educational fieldtrips for nature-lovers;

Miscellaneous skills:

• Research paper curation: see a screenshot of my 100000+-paper collection as an example, or my Papers of the Week posts;
• 2D illustration, analog in pencil or digital vector-based;
• Scriptwriting and storyboarding;
• Basic macro photography;
• Basic web design, e.g. my NGO’s website;
• Basic electronic engineering, mostly for fixing computers and modifying electronic equipment;
• Considerable budgeting skills: living at €5/week for several months, running entomological research programs on shoestring budgets.

I am not dead

Just a personal note on why even regular updates have been nonexistent: I’m pretty busy with several projects and sudden workloads.

• I’m going full-steam ahead with my palaeontology exhibition, and besides the negotiating and trying to find sponsors and places to hold it in, I’m designing and writing all the exhibits (making infographics is far out of my league) and setting up advertisements for a crowdfunding campaign soon (because finding sponsors on this island is impossible). And making a website too, although I just remembered this now while writing…
• I’m juggling the writing of five quite different papers and the analysing of the involved data is requiring writing new scripts and programs, which also takes some time.
• I’ve spread out into e-lecturing. Some colleagues are asking me to guest lecture for their classes, either a full class or just journal club meetings, or just interviews with the students about my research. I prioritise these because I love lecturing but don’t get any chances to do so in this wretched land of apathy. They’re fun affairs but easily suck up 3-4 hours at least with technical set-ups, preparation, and the actual lecturing time. (If any reader is interested, I will never refuse an offer to do a talk in meatspace or cyberspace, so do get in touch. My knowledge base can be gleaned from the post history, the about page, or the talks page.)
• And my work with schools has ramped up to the point that I have at least one meet every week. And there are field days with them on the horizon, so that means I will have to cobble together some field guides because none exist for this island.

So yeah. These are the main reasons why I’ve been pretty silent. Sorry, but it’s the trade-off involved in being an unemployed scientist: CV needs to be boosted, and so there is no free time to slack off.

Here’s a fly getting ready to shoot lasers from its front legs.

I got interviewed!

Over at The Genius Salon (very flattering). The two meaty questions are “You have a very scientific and logical mind, tell us how to think like you to filter the sensible scientific content from the rest,” and “What are the biggest obstacles toward intellectual enlightenment?” (answer to that one: educational systems). Read if you’re curious about my answers. There’s also a picture of me holding a beached jellyfish on a Danish coast while the wind blows my hair. It’s not quite a sexy as one would imagine though.

My Research: Biomechanics of insect sex

Mammalian sex that we’re all familiar with is amazingly simple. You have a gaping vagina to be penetrated by a shaft-shaped penis. Sure, there are variations on the theme, but it all boils down to that.

On the other hand, the mechanics of most insect sex is more complicated, since the penile and vaginal apparatuses are composed of multiple interlocking parts. Besides studying the structure of the reproductive parts (which is species-specific most of the times), looking at how sex actually proceeds is also a legitimately interesting question.

Of course, for the most part, insects are too small to film having sex close-up without very good video equipment or high-speed cameras. So what needs to be done is close observation and behavioural recording, then standardised interruption to discern what is courtship and foreplay, and what is actual mating movements.

The way to do this is simple: observe a couple copulating completely and record all the distinct phases and movements (e.g. thrusting, leg tapping on abdomen, antennal touching). Then have more pairs copulate, and interrupt at each phase you identify by pulling the male away. Immediately anaesthetise both male and female and put them under the stereoscope and check the status of the genitals. If there is sign of opening or entry, then check for ejaculate in the female by dissecting her.

This may all seem like much work for nothing but satisfying a juvenile sense of humour. But such research forms the basis of studies on sperm storage and sperm competition, which then informs the study of sexual selection. My interest here extends to endemism.

As I make clear here, I consider Cypriot endemics to have evolved due to geographical isolation and rampant microevolution rates driven by geology. But there is also reason to suspect that the isolation may not just be geographical, and that it is in fact impossible for sister insect species from the mainland and from Cyprus to mate because of changes in primary sexual characteristics, i.e. the shape and mechanics of the genitals. It’s certainly common enough for this to happen in insects, and linking it with my master scheme provides another interesting dimension – I’ve concentrated so far on linking genotypical changes with gross morphology, but the same can be done with genotypes and sexual morphology. This line of research will involve attempting to mate subspecies from the mainland with the endemic Cypriot subspecies.

I will be concentrating on beetles since I’m most familiar with their genitals.

One further potential, if I ever get access to a 3D printer, would be to do 3D models of the genitals, then print them out and play. But this  would be speculation until actual observed evidence of how sex actually proceeds.

My Research: Antlion larvae in a disturbed environment

Antlion larvae are some of the more vicious predators among the insects. They build pit traps in sand. These are context-dependent contructs: the steepness of the pit and its diameter are influenced by several factors, including sand properties and hunger level of the larva. Regardless of how large the pit is, it’s a very sensitive structure: as soon as an ant steps on the edge, the sand will collapse into the hole dragging the ant with it, and straight into the waiting open mouth of the larva.

The work I’m doing with antlion larvae isn’t actually my idea. The study design was done by colleague, who also gathered the data a park trail near his house. The data sedimentated in his office for a couple of years and now he handed it over to me. I’m only responsible for data manipulation, statistics, and interpretation (he’s a coral freak who did this on a whim, not an entomologist).

What he did was every day, on set points along this long path (using distance markers and numbered light fixtures to make sure he was at the same place every day), he recorded the distribution of antlion pits across the path using a quadrat. 27 different lines were done at different points along the trail, and all this every day for a bit over 3 months (with only a couple of days missing).

This is a mammoth dataset recorded on paper. Besides the pits, puddles, larval tracks made by moving antlion larvae, pedestrian footprints, and tyre tracks were also recorded. My first job is to convert all this analog data into a digital format. I’ve played around with some sort of image recognition script that will do it automatically if I scan the pages, but I have no experience with this stuff (if any reader does, e-mail me and we can strike up a collaboration!), so it’s manual data entry for 30000+ points. Maybe I can get one of those monkeys that are busy trying to randomly put together Shakespeare’s works to do it for me.

Once the data is in, I will initially be working it as spatial data. This will allow me to plot the points in each plot and see how they’re distributed: is there preference for one side of the path, do the pits cluster in the middle, do these attributes change on different points along the path (if so, why?).

Once that is done, I can then implement the time axis and visualise the change through time, allowing me to see if the pit distributions along the path change as the rainy season progresses in response to increasing rainfall, for example. This will be the tricky part, as I have very little experience with such analyses, so I’ll have to learn some more R. It can be done on a very local scale, examining the effect of single events (e.g. the decimation and gradual recovery of antlion abundances after a particularly rainy day), or it can be done generally.

One additional goal is to find a way to automate the tracking of individual antlions. I can do this manually by looking at the data, but writing a script that can do it would provide a new depth to the analyses – it would allow us to quantify the responses of all individuals rather than the group as a whole. This can probably get coopted from some other program, I don’t know. If you want to give it a shot, e-mail me, this is an easy publication, and there could be an opportunity to develop a full-fledged program useful for behavioural biologists/ecologists.

There are two points to this research. The first is urban planning. We have this comprehensive dataset showing the behavioural responses of antlions to anthropogenic disturbance (walkers and bikers on the path, construction) and environmental disturbances (rainfall). The general feeling from the data is that antlions are pretty damn resilient – even after a huge disturbance, the same individuals start popping back up in a couple of days. This will thus provide data for use in urban ecology.

The second point, and where I am most interested, is biological. Lab observations of antlions give us a lot of knowledge… but they don’t quite jive with what is observed with this data from the wild. For example, pit sizes don’t seem to be associated with hunger level here. I have a weird, consistent pattern of antlions being more dense where there is most destructive disturbance – this is contrary to what one would expect, and I’m tentatively hypothesising that maternal effects have a role to play in where the antlion larvae settle. There is also an exceptional trail recorded that’s longer than predictions based on how much energy we think antlion larvae have. Either this was a superpowered antlion larva, or we’re just underestimating them.

In any case, I’m still midway through raw data entry right now, so all of this will have to wait a while until I can start analysing.

Small Site Update: A new benevolent money-making scheme

According to the site stats, almost nobody ever visited the Books page, where I listed all the books in my possession, as well as my wishlist, for the sake of anyone looking for new books. I also offered to review books, but nobody requested anything.

So it’s been changed. The page now links to a brand new Amazon store I set up, where those books are sorted into categories and available for purchase. It’s nicer to browse (although lots of tabs are needed), and since I get a commission, it’s also helpful for me financially (yeah, I still am unemployed). The books are mostly undergrad- to grad-level, with several pop. sci. and überexpensive textbooks in the mix.

It’s on Amazon.co.uk, best for Europeans (and hence me), but a US version can be set up if the shipping prices are too high for you readers across the ocean. Let me know.

Due to WordPress limitations, I’m not allowed to embed the store in my sidebar, so I can’t do a “Featured Book” thing. Sorry.

PS: No interesting papers of the last week due to stuff I had to do, so I’ll lump them in with this week’s papers.

53rd Carnival of Evolution

It’s up at Sorting Out Science. Lots of interesting stuff to read about diverse topics, as usual. (My quickie Pikaia and synapsid posts are stuffed in there too.)