Field of Science

Sunday(?) Protist - Eucomonympha

Internet broken at home, and also incredibly busy: lots of research stuff, final this Friday, another summer course just started, and unofficially auditing a microscopy course that's happening right now. Basically, back to chaos as usual.

So out of laziness, a cute Eucomonympha to oogle at:

(Carpenter & Keeling 2007 J Euk Microbiol)

Cockroach gut endosymbiont, eats wood, anaerobe. Scale bars 20um, so this thing is quite humongous. Surface consists of multitudes of flagella interspersed with spirochaete ectosymbionts, and some other bacteria. I'd love to do cell biology on this thing, but that creator made those things anaerobic to inconvenience our attempts to deny his existence. What a sly bastard!

Ok, they're making me ditch protists for the next little while... the cruelty! =(

There's also a recently accepted (but still in advance publication) paper full of absolutely drool-worthy Trichonympha SEMs by the same guys... will save for later.

Memetics - problems with the current state of the field

Someone was wrong on the internet on one of the forums I waste my time at frequent, claiming memetics was 'dead' and unsubstantiated - this lead to a discussion of problems with the current state of memetics, which I will repost here: (an introduction to memetics will follow in a later post...)


I see a few issues with the field as it is today (which, btw, has a freakish number of parallels with genetic theory prior to the discovery/characterisation of DNA):

- legitimate work in the field is being overshadowed by laymen's musings and ill thought out theories. While there are those who treat the field with full scientific/academic rigour (eg. Blackmore, Dennett), the vast majority of the stuff that reaches the general public seems to come from 4chan and the likes (ie. not particularly academically-oriented places).

And here I must make a highly emphasised clarification -- a 4chan 'meme' is NOT a true meme! I'd argue it's more of a memeplex or a memetic organism, if you will... if the meme is to be the fundamental unit of semantic/cultural heredity, 4chan 'memes' are far too complex for that. Even words are too complex to be memes (Dawkins seems to imply words act as memes, but, no offense, his linguistics background is rather sketchy).

- This leads me to the next point: memetics is about as multidisciplinary as one can get; to do work in the field, one must be able and willing to rigorously analyse ideas and knowledge in everything from evolutionary biology to genetics to neurobiology to psychology to linguistics to sociology, anthropology... pretty much sealing that chasm of CP Snow's "Two Cultures". Now there's a bit of a problem with that: The cultures in question seem to LIKE their border, and rather cherish it.

What I consider to be one of the greatest obstacles to a scientific exploration of the humanities is: Cartesian Duality - the mind/body being separate ontological realms bullshit. I HATE it. Dennett goes into this in some detail in Darwin's Dangerous Idea (great book, btw - highly recommended!), and it becomes rather evident those people are 'skyhook' seekers, to use his wonderful term. The dualists, both in the sciences and the humanities, are deeply repulsed by the idea that all we are is a pile of chemical reactions, and that conscious thought is an epiphenomenon of complex biochemical processes inside the brain (not all of them are actually aware of this perfectly natural repulsion...) They want for us to be special -- at every step, science undermines our status as the lords of the universe more and more, from Copernican cosmology to Darwinian evolution (still deeply resented by many) and beyond.

Thus, many people rather NOT touch that great mind/body divide: 'Scientists must stick to their physical realm and those in humanities are to deal with the higher ontological plane -- the Mind. Theology can have the Soul.' Etc. And many people seem to be quite happy with this arrangement -- no wonder discourse between the fields is still rather limited! Our very ideas of how to gather and analyse data are different!

Now it can be argued the humanities cannot be done in a scientific manner because you can't run experiments there. But I really wonder -- have people really tried? Experimental human psychology was ethically off limits until modern technology like fMRI enabled one to view subjects in real time with no harm done. Perhaps there are valid experiments to be done in social science and anthropology as well! The linguists have plenty of experimental stuff figured out... so there isn't that much of a limitation after all.

- As in 19th and early 20th century genetics, memetics is hindered by the fact that we honestly still have no fucking clue how the brain works. Perhaps there is a neurologically encoded semantic unit, somehow. It would be analogous to how genetic information is encoded in mere sequences of atoms -- that also seemed quite ludicrous not too long ago... As soon as we overcome Cartesian duality, we realise that there must somehow be some physical manifestation of thought -- semantic meaning must be stored in some physical/neurological form.

Perhaps the great discovery of the 21st century may be the neurological manifestation of the "Mind". Perhaps we're not ready for that, perhaps it's even impossible for one reason or another. But we must keep looking, for that is how science is done -- by poking around in the dark, with only a small candle in hand.

"If you know what you're doing, how long it will take or what it will cost -- it isn't research." - anon. I can testify to that, personally!

Until then, memetics can act as a powerful (and quite rigorous) model for cultural transmission of information. I don't see anything wrong about that idea, save for the few morons who hijacked the term and defiled the public image of the field.

Sunday Protist - assorted Foissner SEMs

It's quite late and I'm lazy... have some Wilhelm Foissner instead:


I'm gonna guess them spiraling clockwise inward, starting from Bursaria (the big thing with the gaping oral cavity); take this with a big grain of salt:

Bursaria - Coleps - some other ciliate - testate amoebozoan (some relative of Difflugia?) - suctorian - amoebozoan (Arcella relative?) - some Tetraselmis-like thing? - another ciliate - filose amoeba - Didinium - Euplotes

Check out more of his SEMs if you can... his stuff is amazing!

Cute Arachnid

Found a cute jumping(?) spider on my wall before Friday's exam:

(the head kinda looks like a spaceship of sorts...)




Anyone wanna key it out?

I have another one somewhere, which I'll post when I find it. 'Somewhere' is a very difficult place to reach sometimes...

Elateridae - click beetle

Have an exam later today - best time for catching up on blogging...

Came across a fairly sizable click beetle while on vacation: (about 2-2.5cm long). Now to compete with Myrmecos in macrophotography:




Ok, perhaps I'm not viable competition quite yet, but look - it's in focus! =D

Quick sloppy search on Wikipedia reveals the existence of bioluminescent clickbeetles. I want one.

Oh look, I have something multicellular on my blog! ^.^ Now I should really get to this exam I have 1.5h left to study for...

(more pictures to follow eventually later soon!)

Going away...

Going on vacation until June... may not be able to post much there. Although it's not like you'd notice the difference anyway...

Lurk ToLWeb and Paleos to get a bit of a protist fix if necessary. Or read a paper by Tom Cavalier-Smith, or two, or three. That shall keep you busy! mwahaha...

Another delinquent Sunday Protist -- Euglenids

Kinda busy this week; going on two week vacation on Friday, so naturally stuff just piles up. Thus I'm gonna parasitise off the ToLWeb Euglenida page and send you guys there.

They have cool pictures:



And possibly nearly everything you'd ever wanted to know about Euglenids and their evolution.

Back to chaos...

Sunday Protist resumed: Acetabularia

I've been thoroughly neglecting Archaeplastida... probably because I see its representatives everyday anyway. Archaeplastida is the superkingdom containing Glaucophytes, red algae, green algae and land plants*. Archaeplastids are characterised by primary plastid endosymbiosis, so most of them are photosynthetic. Hopefully I'll get around to discussing some exceptions later...

Since I like large complicated cells, today's menu features Acetabularia:

(UBC Botanical Garden)

Each of those umbrella-like things is a single uninucleate cell up to 6cm tall. At the base of the stalk is the rhizoid containing the nucleus. This little detail turned out to be extremely useful for establishing the cell organelle responsible for heredity back in the 30's by Hämmerling. A couple species of Acetabularia produce morphologically distinct caps, so Hämmerling cut off the caps and exchanged the stalks between the two species. The morphology of the regenerating cap was determined by the species of the nucleus-containing rhizoid, not the stalk: thereby strongly supporting the central role of the nucleus in heredity and the cell's 'information'.

I'd love to study cell morphogenesis in that thing! There seems to be a bit of work done on it here and there, but it is far from model organism status. Doesn't seem to have its genome sequenced yet, although I may be wrong on that. Being a unicellular organism relatively close to land plants, it could reveal some insights about plant cell development and evolution. The size would be wonderful for studying cytoskeletal dynamics. Acetabularia was at one point used as a model for circadian rhythm studies - it maintains its rhythm in the absence of the nucleus, implying a cytosolic component to biological clock regulations (briefly mentioned here).

However, for all I know, it may be hard to culture, do genetics with, etc.

(personally, I still prefer ciliates... ^_^ )

*Archaeplastida is also alternatively called Plantae, but I resent that naming. After being taught for so long that plants are the terrestrial multicellular green stuff, and being proud of recognising that 'seaweeds' aren't plants after all... they suddenly decide to name the whole freaking group Plants. Sorry, no. I find it rather unsettling when some protistologists refer to red algae or prasoniphytes as 'plants'. The conventional plants are refered to as 'land plants' (which I'm fine with to avoid confusion; although botanists give me funny looks when I do that...) Furthermore, the name Archaeplastida makes sense, since this group is defined by having plastids from primary endosymbiosis. Everything else got their plastids from them via secondary and tertiary endosymbiosis.
S
orry, but your Chlamydomonas is not a freaking plant, kthx.

Pipet FAIL

When you set up PCRs, often you first make a master mix and then aliquot it into smaller portions to which you add template DNA (the stuff you need copied). Often you do one extra reaction more than you need, since you tend to run out due to pipeting error. But you don't need that much extra normally...

For the last few months, I kept on running low when aliquoting - often not having enough for the last tube. I would make 10 reactions when I really needed 8, so about 36μL extra, for 18μL aliquots. And STILL I would not have enough for all reactions. I calculated my recipe numerous times in numerous ways, and it should have worked. I tried the most careful pipeting technique I could manage, although it would be a rather exquisite accomplishment for pipeting error to be THAT bad!

I suspected the pipets, but my labmates were all like "Oh don't blame the pipets now!"

So I got sick of this. I grabbed water, and went to the analytical balance. I check the p20 - everything more or less fine. Then I grab my p200...



Yes, it only pipets ~75% of the set volume. FOR THE PAST FIVE MONTHS.

So yes, when all fails... check your pipets. Their calibration could be way off by now... (after changing all the water and buffers and stock solutions, that is.)

Now, my burning question:
How the hell did my PCRs work for the past five months despite all my concentrations being absolutely RANDOM!?

So much for molecular biology being an exact science, hahaaa!
Actually, molecular biology is voodoo. Seriously. You can make things exactly right and they don't work. You can leave your DNA out on the bench for a couple nights and completely screw everything up while pipeting... and it magically produces the bands you want. I think it depends more on the star alignments or something...

Homage to RefWorks...

I wish Blogger had RefWorks citing capabilities... I've gotten spoiled by clicking the 'cite' button to cite stuff. Here I actually have to write out the full citations. By hand. The horror.

Luckily, I can preformat stuff there and just copy it over here. Blogging has just got a ton easier.

Sadder than my newfound dependency on citation managers is that I actually think they're like the coolest thing ever. There was actually a rush of euphoria when I discovered cursing the process of typing bibliographies is a thing of the past! I even investigated all the various citation styles and...yes, found my favourite one.

I have a favourite citation style: of the Current Opinion series. I even have a rationale for liking it. Look how neat and easy to follow it is:
Cavalier-Smith T: Predation and eukaryote cell origins: A coevolutionary perspective. The International Journal of Biochemistry & Cell Biology 2009, 41: 307-322.
The bold formatting option exists to be used, either for the author or the title. The author is usually first anyway, so it makes more sense to bold the title. The numbered in-text citations [1] make it easy to follow review papers without the clutter of full in-text references. (although the full format comes in handy at time too...) The only issue I have is the year appearing at the end. I prefer the pub year to appear right after the author, since in biology it's fairly important to know when stuff was said/done. I hate that about the wretched MLA: they don't even use year in their in-text refs!

I randomly blogged about citation styles.

I think I've just reached the epitome of geekdom. To beat that, you must argue for YOUR favourite citation style.

However, in this post is a preview of paper I will be working on translating into English for you guys, from the TC-S dialect of academese... it's on the evolution of eukaryotes from prokaryotes. Fascinating stuff!

Now I'm actually gonna do it...