Field of Science

"[...] that so-called professor who only studies little fish"

That would be PZ Myers, apparently. I had to laugh REALLY hard at that one.

For more exciting (and mildly depressing) Catholic hate mail, see

What about those "so-called" professors who only study little bacteria? Poor microbiologists, for they shall never become real professors! =(


Another gem:

"All of the monkeys ain't in the zoo; the rest are at the University of Minnesota. Even more illuminating is that all the assholes are there too, not to mention the bigots, frauds, perverts, and no-nothings. I think that pretty much covers the spectrum in the educated imbeciles category. But, you stand out a little more than others."

Who knew -- the entire world's population of assholes is conveniently compressed into the University of Minnesota. So that's why I've never seen any assholes before -- they all reside in Minnesota! I guess the author of that note also teaches at U of M? Hmmm...

The Official Creationist Worldview Professional Certificate

Just came across this on Pharyngula:

"They also have a distance learning program in which you can get an Official Creationist Worldview Professional Certificate" Yes, apparently such an abomination exists. From the site:

"The Creationist Worldview is an innovative program of study designed to equip current and future Christian leaders with practical tools to effectively influence their world with the truths of Scripture. A formal science degree is not required, and those who can benefit from the Creationist Worldview program includes, but is not limited to, Christian men and women who hold various positions of influence within the community, educators, ministers and church leaders, business and industry experts, professionals in medicine and law, government officials, leaders in the fine arts, and high school and college students."

OH MY FLYING SPAGHETTI MONSTER, a formal science degree is not required to study creationism? Shocking indeed!

And their curriculum is sad and amusing simultaneously.

Sigh. Why do these people exist so easily, whereas if you want to retain integrity and sanity you may be subject to harassment and BS? We actually have to work to get where we want -- these cretins make a whole giant industry just by

A rant on pluralism...


















Sunday Protist -- Diatom

When UV light bounces off chlorophyll, the frequency is shifted towards red (fluorescence), which can be safely picked up and observed through a UV filter. What is awesome about UV work is that you can view it simultaneously with our own spectrum, since we don't notice when UV light is filtered away. You can't do the same with substances whose excitation frequencies (the incoming colour that later changes) lie within our visible spectrum, since you have to filter out a band of colour - making the filtration pretty obvious. Thus, you can't simultaneously view GFP (green fluorescent protein) and normal light, since you'll have to filter out everything but green, which is the emission frequency (the resulting colour).

Fluorescent microscopy is a powerful tool in cell biology, as it enables one to "colour" certain proteins, and find them via fluorescence. You can do live cell imaging with that, and observe real cellular processes in vivo, as well as creating time-lapse (movies) and stacks (3-D reconstructions).

I wish people were taught about real cells in school, as opposed to that hideous textbook thing (which does NOT exist -- there is no 'typical' cell!) Cells are so alive and dynamic and exciting...all that gets thoroughly lost in those cartoon diagrams. Can't we provide highschool educators with our sexy movies of real cellular phenomena in action? Should be cheaper than textbooks themselves! And much more informative, not to mention memorable!

Now back to our diatom. Since UV light is converted to red upon hitting chlorophyll, what does the image stack tell us? Well, you can see certain compartments emit this red light, indicating the presence of chlorophyll. You may or may not have heard that diatoms are phytoplankton, meaning plant-like plankton. They are actually not particularly close to plants at all -- diatoms are brown algae, the ancestor of which has engulfed a green alga at one point, and incorporated it as an organelle. As a result, the chloroplasts in diatoms have two extra membranes around them, coming from the original green algal host. This is called secondary endosymbiosis -- a host engulfed a host of a cyanobacterial descendant (chloroplast)!

There's also tertiary endosymbiosis -- a host engulfing and host of a host of a chloroplast. Some of things have an extreme number of membranes layering each chloroplast.

I'll discuss endosymbiosis in more detail at a later day, but back to our diatom. I'm a bit dense, so it took me a while to remember that diatoms are phytoplankton, for they don't particularly look like plants or green algae -- they're not particularly vibrantly green like the green algae. But playing around with our UV lamp after a whole day of DAPI imaging (to see nuclei in plant cells), I threw on some seawater samples on the slide, and got views like the following:

And that little thing with a tail near the top may be a dinoflagellate of some sort, perhaps. Catching those things with a camera is nearly impossible...they like to move!

Anyway...most diatoms you find tend to be empty shells, as opposed to the live organism itself. So you often forget that they are in fact photosynthetic. I think the autofluorescence drives that point home quite well. Now we remember. Also, you could possibly identify plastids based on their autofluorescence emission, but I'm not sure how it's done yet... that would be topic for another day.

Another cool thing about diatoms -- when they divide asexually, the top shell separates and forms a bottom, which is smaller than the top. The bottom shell becomes...the top, and forms and even smaller bottom. Consequently, several generations later you end with a population of very tiny diatoms, so they have to somehow get bigger again. So they enter the sexual cycle, fuse and dissolve their old shells entirely, forming a new, large, pair upon separation. That's why you find a gradient of sizes within the same species.

Happy diatom worship!

Free ciliate

Here you go, enjoy! XP

(40x, Namarski phase contrast)

And then it suddenly... EXPLODED!

An image sequence of a cilliate I got today, while taking optical sections:

(40x, Namarski phase contrast)

The heat from the light source must've got to the poor guy... =(

Sunday Protist - Labyrinthulomycota

Cute little marine protozoans that run around through 'tunnels' of their ectoplasmic net. Featured above are Aplanochytrids, which glide along the ectoplasmic net without being enrobed in one. (Leander at al. 2004 Eur. J. Prot.)


On the other hand, labyrinthulids (above) travel right through the ectoplasm they secrete. They form those elaborate nets they crawl around and use to catch floating debris/prey.

Biblical Microbiology

This randomly popped into my head while I was doing E.coli transformations today:

(From: Microbius 1:01-1:33)

She sayeth onto the chosen Tribe of E.coli
"Taketh upon thee my Holy Construct,
For it shall heal your soul and spare thee from the devil."
And she blessed the great tribe with a heat shock,
Hoping to instill faith within them for all eternity,
Faith in her Holy Construct.

But some E.coli refused the Holy Construct,
Preferring instead to believe in their own pagan plasmids,
Neglecting the holy plasmid of God.
This insolence angered Her deeply,

And her neurons fired in wrath,
And She inundated the E.coli culture
With a great Flood of hygromycin;
And thus were smote in fiery wrath,
The heathens who failed to place faith in the Holy Construct.
And from the Flood their souls unsaved,
For they have not receiveth the Resistance Gene.
And lysed their membrane were in hell,
Damned to an eternity in the autoclave.

And She sayeth onto the good E.coli:
"Get thee to my pipette tip ark,
And I shall carry thee to the land of plenty,
And ye shall call this land the Test Tube,
And may the LB broth save ye from starvation."
She commandeth to the good E.coli:
"And while ye flourish on my sacred LB,
Dare not forsaken my next commandment:
Be fruitful and multiply,
For in a forthnight ye shall find thy souls,
Preserved in -20C heaven, in a stock of glycerol,

And blessed thy genomes shall be Saved,
As my Holy Constructs is delivired to the Holy Plants,
In the Growthchamber of Eden."


May your DH5α be forever blessed! =D
(And GV3101 as well; why not?)

Yes, the Growthchamber of Eden has GFP-expressing plants. The sun shines 488nm wavelength there. No wonder it's so green, eh? You should, like, totally see the tubulin:GFP-expressing tree -- it's a freakishly fluorescent green cytoskeleton! And the Forbidden Fruit is forbidden due to being stained with DAPI -- DAPI is bad for ya, y'know?

This is getting out of hand...I think I need to get out more often or something ^_~

21st Century -- The Battle of the Memes



(this reminds me strongly of the terrifying documentary Jesus Camp)













Sunday Protist - Tetrahymena thermophila

(Definitely not totally ripped off of Pharyngula's "Friday Cephalopod")

Since [putative] readers of this blog are unlikely to be in church on Sundays, we shall celebrate by looking at cool little organisms instead. Worshipping protists is so much more rewarding!

(from Wikipedia)
( Robinson R (2006) Ciliate Genome Sequence Reveals Unique Features of a Model Eukaryote. PLoS Biol 4(9): e304 doi:10.1371/journal.pbio.0040304 )

Tetrahymena thermophila (fluorescently tagged, of course).

It's an aquatic cilliate -- a microscopic organism covered in little hairs (cilia) it uses for swimming.

Those creatures have two types of nuclei -- the micronucleus which is the germline, and the macronucleus which is used during the organism's everyday life (ie. somatically expressed). Upon conjugation, the old macronucleus is destroyed and the micronucleus is doubled, with one of them being modified into a macronucleus. The macronucleus genome is then duplicated multiple times -- up to 45 copies -- and the non-coding DNA is spliced off. (

What a brilliant strategy: keep a copy of your genome safe and unmolested by transcription enzymes (in order to actually use it to make proteins), and have another copy amplified and optimised for everyday use.

Image you had your favourite film on a VHS tape (those ancient casette things, in case a reminder is needed!). Every time you play the tape, you damage it little-by-little, eventually ending up with loads of scratches and poor sound quality. Now you need to copy the film for a friend. The scratches will still be there when you copy it, since that particular data is permanently lost. You friend watches it few times, and the next copy is even more damaged. And so on.

So that the data is not completely lost, you can build some mechanism that edits and fixes the tape each time you play it. It notices the minute scratches, and patches those holes in the data while it can still guess what must be there. This mechanism would be fairly expensive, difficult to set up, and prone to malfunctions. This is what we animals do. Also, we have millions of cells, most of them not in the germline (ie. will not be passed on to the next generation). Mutations in those cells are usually benign and don't matter in the long run (even cancer itself is not transmitted to the next generation; although susceptability to it may be). We try to protect our germline DNA to the best of our ability, albeit in a very unnecessarily complicated, inefficient way.

The poor little Tetrahymena doesn't have a place for germline cells to be stored. Everything must be enclosed in one cell. And it's a bit too small to experiment with low efficiency complex strategies. Every joule of energy counts in its life.

When you first get your film, you could also make a copy of it right there, lock it away in a cupboard somewhere and use the other at your discretion. Hell, you can even keep it out of the box if you'd like -- if you damage it too much, you can always make a copy of the one in the cupboard. If a friend comes to you and asks for a copy of the film, you just make them a copy of the cupboard one, so the damages you've inflicted on your viewing copy do not propogate any further. Your friend also makes a viewing copy and a storage copy.

That's exactly what the Tetrahymena does. It leaves a copy of its genome for storage, locking it away in the micronucleus. The other copy is optimised for reading and is later destroyed upon conjugation.

In a way, that's kind of what we do, albeit in a rather complicated manner. Once the zygote is conceived, the male's somatic cells can all but disappear. We don't care if he dies. Oh, and after gestation and childrearing, the female can die too. Your gonads are micronuclei; the rest of your body consists of macronuclei.

Yet another example of convergent evolution between multicellular and subcellular structures?

Tetrahymena has more cool features, but I'll leave them for later. Since Tetrahymena is a convenient model organism, I'll probably return to it quite a few times.

RETRACTION(18.08.2009): The tangent about the 'adaptive advantages' of nuclear dimorphism is fundamentally flawed and therefore retracted. The reasoning is backwards, and ciliate nuclear dimorphism is in fact a testament to the generation of complexity by neutral forces. The micronucleus is almost completely packed with transposons and other toxic DNA that must be excised for proper nuclear function. Most other life simply takes better 'care' of their genomes...

Cypress Bowl Mushroom Foray Part II: Slime Moulds

We found about 5 species of slime moulds on out foray. Unfortunately, as explained previously, I fail at remembering names. I'm a cell biologist. We only know model organisms... ^.^

Again, photos by Achiru.

A very common species -- Physarium sp. -- same one as in the older slime mould entry.

Still can't figure out what kind this is...

This, apparently, is also a slime mould. It looks like someone rolled up balls of gum and stuck them on a log... (Lycogala epidendrum - thanks, Emma!)

I think this is Ceratiomyxa sp.?

So yes, I found a very useful site for looking at hawt sexey pictures of slime moulds, and also for their identification:

And that made me late for Ecology...gotta run!

Cypress Bowl Mushroom Foray Part I: Fungi

Yesterday Achiru and I tagged along with a bunch of fellow fungus/slime mould/botany freaks on a hike up Mt. St. Mark (I believe) in Cypress Bowl part on the north shore. The frequent stops to admire some of Earth's little aliens at the beginning were soon followed by a grueling hike to the top. Grueling, at least, to someone who tends to live in the lab, and cyberspace.

Since there's lots of pictures, I'll split this up into three parts: Fungi, Slime Moulds, and Views + Misc. Appologies in advance for my failed attempts at retaining taxonomical data -- I cannot remember all the names, whether scientific or common, to save my life. Seriously. I SUCK at taxonomy. I think it's a bit overrated anyway, but that's a rant for another day. So I'll just use whatever I've remembered of some of their common names, or just refer to them descriptively. Even mycologists have coined LBM - Little Brown Mushroom. I think that's a valid taxonomical categorisation. It makes life easy for me. Maybe because I'm not a mycologist...

(again, photographs by Achiru)

L - Jelly fungus R - Bird's Nest fungus with an unexploded spore capsule

L - Forgot the name...but really strange black mushrooms! R - Witch's Cap mushroom

L - Bracket Fungus (Polypora) R - guttation on a bracket fungus - water droplets secreted by the actual mushroom, not condensation as dew droplets.

Some cup fungus ( ascomycetes)

That's all for part I, I'll put the residual fungi in part III as I have to run...

A post of filth

Have to run to class soon, but feel as if I should drop in my two cents on the politics of the Land to the South (i.e. US), since everyone is yapping about it.

I'm definitely not a fan of politics, and will not dedicate excessive keystrokes to the subject. It's all a sticky tangle of lies, self-interest masked by a false concern for the electorate, more lies, even more lies, and (with appologies to slime moulds), filthy slime. Republicans are abysmal, but the Democrats aren't far behind. Obama is what we call in Russian "проходимец" -- someone who slithers his way around any situation, usually in a dirty cheating kind of way. I won't even think about the alternative -- not a healthy way to start one's morning.

So in a way I could just say I don't care, and move on with life. Like your average exemplary citizen of a democratic society. But on the other hand... I'm innately selfish (and so are you), so there's certain issues that mean a lot to me, even to the point where I'm compelled to follow at least a little bit of the foul political sewage. One of those issues, for me, is science.

Back around the 60's, US used to be an amazing place for science and engineering. There was good science education in the compulsory school system, good universities, plenty of funding, and most imporantly, a pretty decent rapport between science and the public. People respected what science brought, and had great interest in it. Same thing on the other side of the sea in the USSR: good education, good science fuding, good public interest. Scientific advancement thrived. Religiosity was kept aside in the quiet, letting people do their jobs safe from bullshit ideologies, for the most part.

Then something happened. The public stopped caring much about science. Scientists became viewed as something of pure evil. Science education plummeted. Religion triumphed. Education eroded away further yet. We get creationists. Research funding is on a steady decline. Despite the ever-growing gap of knowledge we see before us (each scientific advancement reveals more and more of how much remains unknown), work in the field is made more and more difficult.

People feel some obscure right to impale others with their oft ill-founded moral convictions. "I believe abortion/gay marriage/stem cell research/atheism/cracker desecration is bad, therefore no one should be allowed to do it." They start demanding the government to achieve their goal of submitting everyone around the, to their own personal beliefs. They start infiltrating the government. Then we get Louisiana, with an approved stealthy creationist bill to pressure science. There's many of them. They have power. REAL power. They have money.

They have infectious memeplexes on their side.

At least the Democrats are a little itty tiny bit potentially more liberal than the Republicans, and the general agreement in the scientific community is that Obama might cut NSF funding a little bit less than his competitor. If the Republicans return to helm yet again, more money will be dumped into the pointless stupid war in Iraq in the midst of a recession at home, and science will be assaulted both in schools, and in the budget. As soon-to-be grad student, post-doc, etc within the next 15 years, with the possibility of starting my own lab eventually, some day... I'm worried. As a human who sees the dangers of dogmatic faith devoid of any self-correcting mechanism, I'm frightened.

Fundamentalism is not funny. Any sort of it -- be it nationalism, political dogma, religion, some school of philosophy -- is dangerous and degrading to the collective human intellect. Yes they say amusing things, but I can't read them without feeling a mixture of fear and sadness. We find them funny -- they believe they're right. And they have power.

I've heard somewhere that the 21st century will be an era of fundamentalist conflict, both in the Christian and Muslim worlds, and also in terms of nationalism. With the vastly overgrown human population that exceeds the carrying capacity (at least that of psychological sanity), the world is growing more and more competitive and desparate. When people are desparate and threatened, they form tightly-knit groups of similar kin. Religions pray on that -- that's how the memeplexes thrive. Some clever people surface and use these factions to their own advantage, abusing the frightened people convived in their superiority. You get violence, be it ethnic or sectarian tension...or something bigger.

If those people were not united by a conviction of superiority, they would probably be substantially less receptive to arms. If the people were less threatened and desparate, they would be unwilling to fight. One doesn't need much to feel unwilling to fight -- a home, a family, some food...and general political stability. Wealth is irrelevant. We have too many destitute wanderers furious at their past. That is a volatile environment -- not to be ignored. But solving this problem requires long-term thinking -- something capitalism, at least in its Western execution, fails at. One only cares about a couple financial quarters ahead, few bother with looking beyond that.

I think a new political party is in order down south. The Rationalists. Definitely would be a hit... (not). Ah well. Time to work on counter-memeplexes to the creotard filth...

Back to chaos!





And they have better marks than me.
