Field of Science

Vacation

Going to be mostly absent from the internet until the 4th. Happy holidays, everyone!

Probably won't be able to post protists until then, but expect more, much more, in the new year. We are celebrating evolution in 2009, after all!

Apologies for vanishing for the last two weeks -- finals can do that to you! (I think I survived...)

Moss Microforay

Occasionally, I do go out. In anticipation of such an unlikely event, I usually have an eppie tube or two and possibly a ziplock bag in my pocket. In that case, I collect random samples of whatever I'm in the mood for, and abuse my work-related scope access privileges engage in highly legitimate microscopy practice. I like to take pictures, and although I have a long ways to go to reach the professional protistology levels, I try...anyway... <_< So here was one such foray, where I collected a wet moss sample, and added a drop to a slide. Turned out to be teeming with life:



As for identification, I only have a faint idea for the most obvious ones. The rest stump me clueless. But I'll try. Any real protistologists out there, feel free to help out!

Plate I:
A - Test of some sort of amoeba. Euglyphid?
B-E - green algae of sorts
F-H - ? algae...
I - a young hypha emerging from an fungal spore (awww, so touching!)
J - ???
K - green algal like thing again
L - amoebozoan test?

Plate II:
A-C - green algae, although C may be some sort of photosynthetic excavate for all I know...
D - fungus?
E - generic round biflagellated algal thingie (probably as far as one can get without molecular analysis)
F - a spore?
G-H - amoebozoans
I - too small for a nematode I think... so perhaps a euglenid of some sort?
J - timelapse of some non-photosynthetic motile flagellated thingie
K - Euglyphid!
L - green algae of sorts
M - ??? Algae. Of sorts.

Someday I hope to fail less epically at this kind of thing. Perhaps is some protistologist out there is willing to train me. As a grad student. Or something... /explicit self-advertisement

Sunday Protist -- Xenophyophore

Possibly the world's largest cell:


Source

A deep-dwelling marine foraminiferan (Kingdom Rhizaria) that is one large multinucleate cell. They can grow up to 25cm in diameter!
More information here.

What is a protist?
The Eukaryotic Tree of Life

There seems to be lots of confusion as to what a protist really is. This is quite understandable, since the chaos has deep historical roots.

The definition (guideline) that most protistologists tend to follow is:

Any eukaryote that is not a plant, an animal, or a fungus.


ie., the other ~98% of eukaryote diversity!

Let's take a look at this diversity: (Keeling et al. 2005, Trends Ecol. Evol.) (free access)




Assignment: Find animals and land plants. Note relative significance and diversity!

And before a microbiologist wanders by and launches a massive attack on my eukaryocentric ego, I'll put things into perspective: (Ciccarelli et al. 2006, Science) (free access)


K, now that this is over with, back to ignoring prokaryotes...


Why is Protista such a cladistic mess?

Historical reasons, mainly. Only a couple centuries ago, people still classified life into things that were motile (animals) and sessile (plants). Fungi were plants because they didn't walk. (molecular evidence shows they're actually the sister clade to animals). Microscopic life was unknown at that point, so there was very little reason to suspect any of those strange organisms even existed. And seaweeds were plants as far as anyone was concerned. Not like it's actually obvious without examining the cell structure and molecular data.

Eventually, this system failed, and attempts at patching it up eventually led us to a tangle of taxonomic chaos. Thankfully, molecular biology has allowed the eukaryotic phylogeny to be resolved quite a bit better (but still with plenty of vagueness).

Another problem is convergent evolution screwing up morphology-based taxonomy. Before molecular biology became possible, organisms were sorted by their appearance and special structural features. Unfortunately, some of those features tended to evolve independenly multiple times. A good example is the heliozoa -- sun-shaped microorganisms. Turns out the group actually was spread over three kingdoms -- chromalveolates, rhizaria and the green algae! (Nikolaev et al. 2004, PNAS)

Actually, the entire non-photosynthetic stramenopile group mostly consists of stuff that were confused with something drastically different:
- Labyrinthulids and Oomycetes -- thought to be fungi
- Blastocystis (can cause disease in humans) -- thought to be yeast (fungi) -- looks like yeast morphologically!
- Actinophryids -- a remnant of Heliozoa
- Opalinids (amphibian gut endosymbionts) -- used to be confused with ciliates
- Bicoecids -- easy to confuse with generic small things with two different flagella. The fact that there's a genus Pseudobodo might hint at something... (Bodo is a kinetoplastid in the Excavate kingdom, relative of the trypanosome with its awesome kDNA)

I'll elaborate on this at a later date... exam season is near!


Main points:
- Protista = Eukaryotes that are not Plants, Animals or Fungi
- Multicellularity arose several time independently and is therefore not a relevant trait... kelps are huge and multicellular, but are still protists (brown algae)
- Size does not matter: aside from seaweeds, there are plenty more macroscopic protists. Some unicellular ones get quite huge!

Hope this clears up a little bit of confusion...


And apologies for irregular updates... too much stuff going on at this time of the year!

Sunday Protist -- Saccinobaculus

If you're a unicellular organism, chances are you might want motility at some point or another. Being able to move helps escape predators, find food, find better sunlight access if you're photosynthetic, find a partner for some nice quick steamy sex; as well as entertaining easily-amused cell biologists.

Cell motility tends to fall into two (crudely-defined) broad categories:
1. Amoeboid -- cell extends pseudopodia ("false feet") and pulls itself into a particular direction along a surface.
2. Flagellate -- cell uses whip-like flagella to propell itself through a fluid. The flagella can be short and numerous, as in the cillia of a Paramecium, or long and few in number. You'd expect the flagellum to originate in the back of the cell, pushing it forward. Our sperm do that. However, interestingly enough, the majority of eukaryotic life voted against posterior flagella. Animals and their closest relatives, fungi, form a group called opisthokonts -- Greek for "posterior tail". Almost every other eukaryotic organism has anterior flagella -- and at least a couple of them. We're just weird.

There's also adhesive-based motility, where the cell is like a rock climber -- it anchors itself to the surface, uses cytoskeletal motors to move ahead, and then abandons the anchor. Diatoms and the malarial parasite use such technique.

However, there's something even weirder. (this is Protista -- there ALWAYS is something weirder!)

Imagine you're floating around in fluid, and you just can't be bothered to whip things around on the outside. Nor do you feel like protruding pseudopodia along a surface, like some lowly amoeba. Nor do you want to associate yourself with the brown algae because you're racist like that. Or rather, imagine that evolution does weird things. It really does...

What would you do?

This creature decided it wants to be a snake-in-a-bag:


(source)

Meet Saccinobaculus, an anaerobic resident of the gut of the wood-eating cockroach Cryptocercus. The stiking feature in the middle is the axostyle -- a think bundle of microtubules (cytoskeletal structural elements) that functions in a similar way to the muscle tissue... of a snake in a bag, which is what the name really means! This axostyle is highly motile and wriggles around inside the cell, causing it to move. This seems to be a rather inefficient mode of motility, but the creature hasn't gone extinct yet, so it can't be that bad.

But you have to see it in action:

video

I searched all over the internet for a movie of a Saccinobaculus moving about. Unfortunately, I failed to find any. Either my search skills suck or there just isn't any publically available out there yet. So I'll have to make do with a crappy clip I shot in class. Appologies for the shitty quality, and half-deteriorated specimen. As soon as I have legitimate access to a professional scope with a decent camera, and acceptable specimens, I'd try to fix this...

So next time you catch a harmless snake and throw it in a plastic bag, for whatever awkwardly surreal reason, be sure to remember that there's an organism that moves like that for a living. And please don't hurt the snake -- they're beautiful animals!


This advice is serious: If you have access to a microscope, and some wood-eating roaches, or Zootermopsis termites nearby, please remove the gut of one and examine it under the microscope. You'll be amazed by what you find! Unfortunately, the organisms tend to die quickly upon contact with air, so you can't really culture them for your enjoyment...

(delinquent) Sunday Protist -- Chaos

A genus that sums up my life perfectly:

Chaos (Amoebozoa)

source

We were looking at amoebae today. This one is quite huge -- a couple milimetres across, multinucleate and slow as an...amoeba.


Good site with background info on amoebae

(Chaos is the reason I'm falling behind on this Sunday protist thing -- midterms, research, time management issues, general loss of sanity, etc...)

And no, next entry will not be Phallus

I'm ashamed of you, California!

Having practically grown up in Bay Area (9 years of my childhood), I'm quite disappointed to hear about Prop 8, and the anti-gay marriage vote. I've always considered California as a special civilised part of the US, a shore of liberal sanity next to the shamefully fundamentalist South and Midwest.

I simply cannot comprehend: why on earth could anyone, anyone, be offended by legalised gay marriage? I mean, is anyone forcing you to have one? Does the encouplement of gays hurt anyone? Do you seriously get physical injury from seeing two girls kissing or guys holding hands? If so, perhaps you should take greater care when playing with yourselves. If your mentally-demented deity will send people to hell for it, why not let them go there? There will be more chances of you getting into your heaven of choice -- think of the gays as your competitors. If the applicant admission average is lower, more chances of you getting in. How in the hell could you have a problem with that? I can't even understand why fundies would oppose such liberties. I cannot understand how any harmless liberties could be opposed.

Including weed. Weed only makes people mellow and benign, how could that be of any harm to society? If anything, alcohol is a far more vile substance. But I guess the Christian god says booze is ok, thus we'll allow it. He said nothing about Cannabis sativa though, therefore it's bad. Also, teh paganz smoke it. Therefore it should be banned.

How much longer must we be governed by medieval laws based on the customs of a developmentally-challenged bronze age society in modern-day Israel? Why the hell should the ancient shepherds of the Middle Eastern deserts have a say in how we live our lives today?

It's not like the ancient Palestinian civilisations were worthy of any admiration, even back then. Intellectually and technologically behind their own peers, exceptionally misogynistic, racist, xenophobic to the extreme... viciosly intolerant even to their own original thinkers. I simply refuse to admire such a society -- even Rome, with all its problems, is far more pleasant. The Waorani are far more attractive -- at least they had the humility and honesty to admit they were tired of their endless bickering and spearing raids.




Needless to say, yesterday's results made me quite happy! I'm not an American, and therefore had no say, but luckily sanity won (even if barely). The Democrats will be far from perfect, and are plagued by plenty of problems ranging from the Bush's awesome legacy to their own incompetence. But at least they're not theocrats. Oh thank god for that. I would not survive a day in a theocracy, for I cannot keep my mouth shut. I suck at censoring myself... would run into so much needless trouble. Also, if I happen to be quite certain I'm right -- I am right. Until proven wrong. The fundies are right... until sufficient therapy and medication. Stalemates are boring...


Although I must admit, this feeling of hope...it beckons irresistably, akin to some mind-numbing drug. You know it's not real, you know times ahead will suck (economic crisis, etc.)... but, so tempting for your mind to shut down the skeptic faculties and enjoy the party.

Yesterday was a joyous day for many who have lived to see the day a slightly more pigmented member of our species be able to hold office. Perhaps we may live to see the day where posessing a Y chromosome is no longer a strict requirement.

Perhaps, (this is a wild fantasy) one day... we could live to see an atheist elected to office! What if there will be a time when a presidential candidate does NOT have to end every single speech with "God bless" and the likes. Perhaps, a day will come when we will no longer be America's most mistrusted and hated minority! Further yet...perhaps, someday, freedom from dogma will become a cherished goal embraced by the whole society! Perhaps a day will come for us all to embrace intellectual liberty and pursuit of happiness in truth, a day of healthy balance between skepticism and wonder. A day when the majority appreciates life as it is, living it to the fullest rather than awaiting an eternal heaven that will overwhelmingly most likely never come.

We have a long way to go. Can we?

I'm cynical. Prove me wrong, and I will gratefully succumb to euphoria. Please help me reject my null hypothesis...

On the 7th day of creation...

...god took a few hits of LSD and created Protista.


This solves the great mystery of why the Bible neglects microorganisms... the ancient priests realised the dangers of letting imagination run wild and tried supress hallucinogens as much as they could. Lest you get another protist-ful of madness out there!

Some evidence supporting my hypothesis statement of profound enlightenment:

1. Kinetoplasts

Srsly, WTF?

You know how normal people pack their genomes into a few chromosomes in a nucleus, and then transcribe and translate at will?
Said normal people also have little anucleate bacterial friends within them, mitochondria, who stored away most of their genes in the host nucleus, and kept a few for themselves. They have circular DNA, which is then transcribed and translated like a normal bacterial genome, more or less.


Well, these things decided that was simply too boring for them.

Instead, let's string about 5000 varieties of circles together with a couple dozen large circles thrown in for extra fun. And by 'string together' we mean: make chainmail.

What an epic idea! DNA chainmail! Can you imagine how much hallucinogenic chemistry you'd have to experiment with to generate such ideas?

And then we're gonna pack this chainmail into a very tight disk, and shove it right below a flagellum, in a mitochondrion. And yeah, rotate it during replication...


Crithidia fasciculata
(http://www.biochemsoctrans.org/bst/033/1409/bst0331409f01.htm)
The arrow points to one of the few dozen large circles.

('normal' mitochondrial DNA:

The circular string in the sea of junk (suspension medium)
www.bios.niu.edu/core/)


But those are no ordinary circles of DNA.

They are required in order for the mRNA transcript from the gene on the large circle to code for the right protein. If you sequence the large circle genome, you'll find lots of gibberish and very little gene-like content. Those 5000 tiny circles are involved in a process of editing this mRNA transcript to code for something marginally sensible. In fact, the resulting proteins correspond quite well to their conterparts in the saner organisms...

Expect more details on this sometime eventually later... (when I learn some more about it myself)


2. Algal vision
And this thing:


(Photo: Haruyoshi Takayama)

The spherical thing there is an ocelloid. Basically, camera eye entirely out of subcellular components: lens and retina. It can likely form an image on said retina. Great -- but Erythropsidinium is brainless! What does it do with the image? Why does it bother?

There's quite a few other examples of algal vision, although I think the ocelloid is the most elaborate seen so far.


3. Cortical inheritance (Paramecium)
(Beisson & Sonneborn (1965) Cytoplasmic inheritance of the organization of the cell cortex in Paramecium aurelia. PNAS 53:275-282)



Take a row of cilia in Paramecium, revert it so it points backwards... and watch them divide -- copying the backwards row of cilia into the next generations! In no way was the genome altered in this process -- likely during cell division the original cell is used a bit like a template, thereby prompting this weird phenomenon of epigenetic inheritance...somehow. To my knowledge, precisely how this works is yet to be understood, still... over 4 decades later.

---

The creator had some good LSD or crack or shrooms or whatever... if only he/she/it could share some with us... sigh.

Actually, it did. Evolution gave us coca, Psilocybe, Cannabis, Ayahuasca, opium, Tobaccum... a perhaps a vast unexplored realm of even more drugs out there awaiting discovery!

(One wonders if smoking a certain protist could yield similar effects... )

Woes of broken internet

Had spotty internet connection at home for the past week or so. That was compounded by the usual midterm madness at school, thereby resulting in slight neglect of certain blogging duties. Appologies... I really shouldn't do that!


So to redeem myself a little... ciliate diversity! Pretty and quite trippy:


(Finlay and Esteban: http://members.magnet.at/p.eigner/Diversity.html)

Why are chromalveolates so damn sexy?

A new community is born -- come join us!

Some drama on a forum I used to frequent (will elaborate on and analyse eventually) has led to the birth of new site with a forum:

Atheist Refugees

We intend to make it a friendly community of free thinkers with a front page articles on science, history, news, atheism, etc. Feel free to join us -- we don't bite! (especially after we've JUST been all chewed up)

We're at the fresh, friendly part of the community life cycle. Seems they have a limited lifespan, the end of which ends up plagued with censorship, dirty politics and general utter chaos... hopefully we'll get to last a while before that happens!

RD Forum Censorship Drama Part I

This goes beyond a simple forum.

I'll elaborate further if needed at a later date (seminar talk to give tomorrow), so I'll just post some of my responses from the forum instead:

"This is a policy update from Richard [Dawkins] and Josh [site admin].

The purpose of this forum is to encourage discussions on topics related to reason and science. We will reserve one forum for off-topic discussions, but it is not a free-for-all forum. This forum is still to be regulated for appropriate content.

OFF TOPIC
Off-topic discussions will be allowed in the designated forum, but content must be appropriate and all-ages. If it wouldn't fly on the Discovery Channel (standard cable television), it doesn't fly on this forum. All threads containing inappropriate content will be removed from the site immediately.

SEX
Discussions on sexuality are limited to professional scientific studies and topics. No discussions of personal sexual issues, desires, or problems. No images, descriptions or discussions of sexual acts."


-----------

I'd like to add that there's MANY things that won't fly on the Discovery Channel -- controversial ideas would be a large part of that. Can one go on Discovery and announce "I dislike democracy for the following reasons"? Can one go on Discovery and discuss Christianity in a negative light? Does that mean we must now avoid controversial ideas as well?

Ok you say I missed the point there. Well then, pray tell, how is sex any different from criticising Christianity or Democracy? Sex is taboo in our society largely due to religious influences; if you look at it objectively, there is absolutely no reason we should not discuss yet another part of our daily lives -- so sharing your sports or hobbies is ok, discussing eating is ok, but mating is some sort of special action now? Objectively-speaking, that is. I know societal norms currently dictate something different, but those are so abstract and irrelevant to an intellectual discourse!

Now you would probably say "How the hell does smut constitute intellectual discourse?"

How doesn't it? If one looks beyond elitism and snobbery, how is a discussion of a nightly activity any different from one on the fine art of cooking or sports tips?

"Well, SOME people find it offensive. And it is their right to not have such views forced on them."

Many Christians find atheism offensive. Must we all tiptoe quietly around them?


I find some instances of rusophobia mildly offensive due to my nationality; however, would I ban it, given the power? Of course not! First of all, that would weaken my own points. But more importantly, supressing those views does no good to me -- they still remain, and I know I could still do something about it! [i]That which is censored does not simply vanish, it merely vanishes from plain sight. [/i] If I'm seriously objectively offended by that (that is, with justifyable logical reason), I'd engage in an intellectual discussion. Let's convince the other party they are mistaken. This is how scientific discourse works (for the most part)! And if I can't be bothered to care enough, then I simply ignore it.


Eugenics of ideas is a dangerous field. Let's assume some ideas can be vile. Let's make an analogy to virulent diseases. So to stomp out a certain disease -- let's say, smallpox, because it has been done, for the most part -- we have, say, three options:

1. Eradicate the virus itself by isolating and killing each infected individual
2. Eradicate the virus by designing a special drug that only targets this virus (practically impossible, I know, but that's irrelevant) and kills it off
3. Vaccinate each and every individual against the virus, thereby essentially starving it to death.

Perhaps some of you may already know which of these was done and was successful in practically eradicating the disease off the face of our planet. You may also be aware of the serious threat we now face after not having faced it for decades, while armies still have stocks of the virus sealed away... but I digress.

It may be rather evident that attempts to eradicate the disease by drugging every single virus would be epically futile. Killing off the infected is also quite futile, as there would always be an infection leak one way or another. So what do we do? Vaccinations! Let's be exposed to a mild form of the virus in our early age, let the body realise it's bad stuff, and therefore immunise ourselves against the disease for the rest of our lives!

So what does this have to do with anything?

Censorship, dear friends, is akin to #2. Extreme censorship (eg. Stalin era purges; Gestapo in Nazi Germany; N.Korea) is similar to #1. Allowing exposure to all ideas (albeit not acted upon yet -- hence, weakened), is like #3. It allows us (assuming we have the proper immune response -- SKEPTICISM and rational thought) to foresee potentially bad ideologies to pursue, and avoid them, even combat them fiercely. It allows us to understand WHY an idea is wicked -- simply censoring it altogether does not mean people won't agree. This applies to racism -- many people would say bad things about it, but ACTUALLY PRACTICE IT because they never investigated WHY racism would be a vile activity to engage in. It's politically incorrect to discuss that.

So even if we assume sex is a vile topic for discussion (I strongly disagree but whatever), one must still allows discussion thereof. If people genuinely want to discuss it, they definitely see some worth in the discussion. This means the idea is not yet dead.


Free thought and censorship are antagonists to each other. Please decide which side you lean towards. This isn't a with-us-or-against-us statement, but rather a plea to avoid blatant hypcrisy. Especially when we have a public image to mind."








And another one:

"What isn't explained? This isn't a forum for sex. It is a simple policy decision made after viewing many threads with content that was not appropriate for this website. There will be an area for off-topic discussion (I'm leaving this in the admins and mods hands), just not discussions on sex. I believe the admins are dealing with the off-topic section now. Everyone who has become so vocally angry about this needs to take a serious step back. This is a forum for issues relating to reason and science. The statement is very clear relating to sex: If it wouldn't fly on The Discovery Channel, it isn't going to fly here. If the only reason you were on RichardDawkins.net was to discuss sex, then I won't miss you when you're gone. Take it elsewhere, it's that simple. Come back if and when you want to discuss something related to either Richard Dawkins or the themes of his website.

Josh Timonen" [site admin]
-----

You know, I feel kind of insulted by that. And I don't get offended very easily.

First of all, none of us are here just for sex. As a matter of fact, I rarely ever engaged in the discussions, although I did enjoy the liberal atmosphere after a long day in a research lab, after which I prefer to relax my mind a little. I wouldn't even be that outraged if you outright banned all explicit sexual discussions -- annoyed, yes, but not outraged.

Josh, I see you may have missed a point or two on social dynamics. I'm the farthest thing from a sociologist, but those are just things you learning by watching the social environment you're immersed in on a daily basis.

First off, when people engage in some sort of communication long enough, be it online or offline, they tend to form special bonds amongst themselves. Inside jokes emerge, the traditional social barriers of subject matter melt down, and the groups begin to unconsciously develop 'home' bases where they tend to congregate. This results in a positive feedback loop which leads to a tighter and tigher union between the group members. This, in turn, results in an even more liberal and open discussion atmopshere, which creates tighter bonds, and so on. Sometimes this closeness may lead to socially inappropriate topics, and a slight warning is usually enough to put things back in order and keep going.

You cannot expect people to constantly stay on topic and discuss serious matters like science all the time. I work in cell biology research and I definitely go off topic and desire a break sometimes. Since you say this is a forum for discussing science, atheism and Prof. Dawkins, let me give you a simple analogy of a lab. In any given lab, the topic is unquestionably whatever research topic is being investigated. At the very least, it will definitely be science.

Yet, do lab members occasionally have group chats about non-science related items?

Of course! We'd all lose what's left of our sanity otherwise! Of course there's a time and place -- we wouldn't be discussing favourite restaurants at a lab meeting or in the middle of a conference session. But occasionally we'd congregate around some coffee and talk about...well, random crap. That's life -- regardless of profession, or lack thereof, groups of people would engage in off-topic shallow talk. The brain needs to relax sometimes.


So the second and more important piece of social dynamics you seem to have neglected is that said groups eventually become close enough to feel at home in some place. This location can be completely arbitrary -- yes, a forum board does suffice. Even as hunter-gatherers, we set up bases around which we would congregate and share food and data, and be in protection from predators. It's an innate instinct.

Ok, let's say the conversations may have gone out of hand (I disagree but that's irrelevant). What would happen if you simply cut off one of those instinctive home bases? Something akin to walking up to a tribal encamptment, and blowing out the campfire because you think their dress is indecent. That very similar feeling too. Sure they can leave and set up camp elsewhere -- but they had been evicted without warning. The result is a feeling of cold and darkness indeed.

This is why this band is slightly enraged at your decision. You could have banned any future sexual discussions, and openly merged OT with GOT. Ok, not too nice, but we can live with it. You led us to another campsite where we can enjoy our evening festivities. And we understood we may no longer wear our strange dress. Disappointing, but at least we're not refugees.


Of course a forum is a very small part of life. I'm not traumatised -- I have quite an active offline life to keep up with. But even online, there's some sort of instinctive tribal mentality going on, even to the extent of the 'home' or campfire concept (in older Russian, 'hearth' and 'home' are the same thing -- for a reason). Naturally, we get as offended at a 'cyber' hearth being blown out as if a real one were. This is why we found your actions highly objectionable, and...insulting.


Please read and understand this before accusing me of being yet another irrational sex-obsessed drama queen.

Thank you."

--------


More on it later, but for now:

That which is censored does not simply vanish, it merely vanishes from plain sight. If the material is dangerous, why let it thrive in privacy? If the material is benign, why bother hiding it in the first place?

Plant skins enlarged

I was down with a cold lately, along with a couple midterms, so appologies for crappy posting. Since I don't have time or energy to write anything thoughtful at the moment, I'll shower ye with some random pics from my collection:



Liverwort leaf surface -- one cell layer thick, round cells



Bladderwort (aquatic plant) with permanently closed stomata -- relics of the plant's terrestrial ancestors.


Arabidopsis leaf; UV fluorescence: DAPI (binds to DNA and stains blue) and chlorophyll (red) autofluorescence. Those two huge things are... drugged up mutant stomata! The tissue was overstained and too old, thereby sucking for science, but it made some pretty nice desktop wallpaper material!

And just because I love how UV imaging makes everything seem surreal :



It's almost a bit nebulous, isn't it?

Not digitally altered in any way -- looked just like that in the eyepiece!


Sigh. I am married to microscopy... can't help it!

Sunday Protist -- Trichonympha


(http://www.microscopy-uk.org.uk/mag/artmar03/rhtermite.html)

Trichonympha

Termite gut symbiont, 200-300 microns long (huge for a protist). On the inside, bottom half, are pieces of wood -- termite gut protists digest cellulose for the termite, who feeds on the metabolic byproducts. The round thing in the centre is the nucleus (with permanently condensed chromosomes), and rows upon rows of flagella. Being a parabasalian, this creature lacks mitochondria like ours -- instead, they have been reduced to hydrogenosomes, which produce hydrogen gas.

The termite gut is a lush ecosystem FULL of cool things, more of which will be posted later. You also have episymbiotic bacteria covering some of the symbiotic protists, resulting in an ecosystem-inside-an-ecosystem type of environment.

Hard to resist the compelling urge to start slicing open random insect guts in hopes of finding protists...

"[...] 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 http://scienceblogs.com/pharyngula/2008/09/i_am_a_very_naughty_boy.php#more


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 lying...cr

A rant on pluralism...

Perhaps it really does seem thus far that I'm obsessed with have a research interest in protistology. Unfortunately, I don't have too much time to discuss much else at the moment. Perhaps around midterm time I'll hang out here more, due to alotting more time to procrastination. I can be surprisingly productive during exams, accomplishing a multitude of trivial crap with a blatant omission of study time.

I could rant about that Sarah Palin cow, and her interview of epic fail , but it's a bit depressing, so I won't. Actually, it's mildly terrifying...


Actually, this past Friday I had the opportunity to attend a discussion panel on the integration of sciences and humanities, starring Prof. Steven Pinker (which is the main reason I went...), Richard Shweder and Steven Stitch. Prof. Pinker's talk was awesome, as expected; however, since praise and agreement rarely constitute good writing material, I'd like to share with you the following piece of verbal bowel movement produced by the Shweder guy:

http://www.sci-hum.pwias.ubc.ca/media/pdf/Shweder_prep.mat.II.pdf


His talk was read off a paper pretty much identical to that one, albeit with all the condescending intonations perfectly intact. Though I shall concede that excessive use of Latin-English pidgin does a great job at obscuring vacuous inanities. Unfortunately, too many in the humanities practice this sly art, thereby sadly undermining the rest of the field of any credibility and respect. Examples include postmodernism and the Sokal Affair. Another thing those pidgin Latin fetishists tend to obsess over is contempt towards anything materialistic and scientific. They are fairly wise to do so -- for in proper rigorous 'materialistic' inquiry lies their demise.

I must admit that I had tremendous difficulty following Shweder's talk, even though the two other speakers were very clear and easy to understand. Shweder relied extensively on -isms of all sorts to obfuscate his point further. Essentially I think he was trying to convey that sciences and humanities could never be reconciled because they 'lie on different ontological planes' -- i.e. there some sort of different metaphysical 'realities' of the body, mind, morality, and beyond. And apparently those metaphysical 'realities', whatever they're made up of, are separate, and cannot be examined by the 'monist' methods of inquiry.

Shweder went on and on about the apparent mind-body duality, claiming it is impossible to unify the two, and going as far as criticising collegues for not having read some ancient work of Déscartes himself. I admit I've never even heard of that book; and old writing is practically in a different language from its modern counterparts, thus I'll pass on the commitment to digest archaic French. We do not yet have a clear understanding of what consciousness is, but I insist: when we do, that understanding will be wrought by psychologists and neurologists rather than philosophers!

So then he went on this childish tantrum against 'materialist monists' (I guess I would be one?) and filled the room with enough straw to sustain a small pastoral tribe for a year. Essentially, he accuses us of 'arrogantly' dismissing the worldviews and ideas of the 'natives' and their 'realities'. And yes, he called the traditional tribal people 'natives', possibly implying we don't fall under that category somehow. Please, I'm a native of Russia. Does being white deny me of the privilege to consider myself a native now?

That, to me, is true arrogance. This "oh they don't know any better so let's pretend we believe in their silly games" attitude of most cultural relativists towards fellow humans. Do they seriously feel sorry for the people and assume they're intellectually impoverished, thereby deserving some special sanctum in our ontology? In One River Wade Davis quotes Lévi-Strauss saying "The people for whom the term cultural relativism was invented, have rejected it." (p.290) For some reason, those people don't think they ought to have a special 'ontological realm' for themselves; they see the rest of us as part of theirs.

Perhaps it's the 'pluralists' and cultural relativists who are dismissive and condescending towards differing worldviews? We at least try to comprehend and integrate their knowledge and wisdom in our worldview; albeit there's much improvement to be had, we don't shove them into some separate 'ontological reality'!

Furthermore, why bother creating separate realities when one is more than enough to deal with? Shweder starts off with a quote by Woody Allen: "“Can we actually ‘know’ the universe? My God, it is hard enough finding your way around in Chinatown”, alluding to the common argument that since science cannot know everything, there must be an alternative realm of metaphysics/energy/deities/spirits/woo . So why then, Shweder, are you trying to create a second Chinatown to navigate simultaneously, if one is hard enough?

I agree with anyone who says science cannot solve everything. Scientific inquiry has its limits. Eerily enough, so does the human mind itself. But if even the scientific method, the most powerful tool of acquiring and verifying knowledge we have, is limited in understanding the universe, how can blind belief systems work any better? The underlying principles of the scientific method, I insist, are innate; and have been selected for throughout the millenia of our existence. One who failed to make an accurate prediction was overcome by someone who succeeded. One who fell victim to unverified personal assumptions was on the losing side of competition.

Now we have this data acquisition method, which is far from completion or perfection, that has so far been the best tool we have. We use it on a daily basis -- some more aware of it than others. And as of any other naturally evolved instrument, we must be aware of its strengths and weaknesses, and try our hardest to compensate for the latter. This is where the formal scientific method comes in. Training as a researcher demands a good understanding of how our mind can fail. We extensively use statistics for precisely that reason -- we must have a way of checking and correcting for errors in our reasoning.

One of our bad glitches is the attachment we tend to share with our pet ideas. This blocks the self-correcting mechanisms of skeptical inquiry and sends one straight into the clutches of dogma. The further one strays from the sensical path, the harder it becomes to correct the course, due to the growth of emotional attachment. This is precisely why dualism (and pluralism) are, in fact, dangerous.

You can probably imagine by now an obvious example of dualism -- religion. Many religious people tend to separate the world into the physical, and the spiritual. It seems harmless, but renders the victims vulnerable to manipulation by those with alterior motives. Many are willing to die for their religion, and can be persuaded to commit a plethora of hideous acts. Reason cannot speak to these people, for they can create a sanctuary from logic in their alternative realities. 'I'm killing people to serve God, for it is God's will for these people to be killed' makes perfect sense if the related religious stories are perceived in the mind as reality. Suicide bombing makes perfect logical sense in the mind of an Islamic fundamentalist. Killing doctors makes perfect logical sense in the mind of a Christian anti-abortion fanatic. If we assume they are all right in their own way, we will have sheer chaos! Dualism (and pluralism) is dangerous!


On the first page of his talk, Shweder compares E.O.Wilson's Consilience: The Unity of Knowledge to a "monotheistic sermon". Prof. Wilson, the great sociobiologist and entomologist, is apparently a preacher. If so, then I hope I have convinced you, dear reader, that Shweder is a full-out religious fanatic.


After the talk I had a burning urge to pick a vicious fight with Shweder, but decided 5 min of conversation with Prof. Pinker would be worth a few orders of magnitute more than arguing with an arrogant, empty, fanatical academic. It definitely was! =D

And now that I've had a wonderful evening ripping apart some high-ranking academic, sleep is in order.

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.)


(http://www.botany.uga.edu/zoosporicfungi/labyimages.htm)

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)

01
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,

11
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:
21
"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,

31
And blessed thy genomes shall be Saved,
As my Holy Constructs is delivired to the Holy Plants,
In the Growthchamber of Eden."

RAmen.

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

It seems the 21st century will oversee a climactic decisive battle of memeplexes. We are entering the era of violent clashing between fundamental ideologies both new and old. The ones with the most succesful highly viral memeplexes will win.

Take a look at this clip there: http://richarddawkins.net/article,3121,n,n

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

Look at those people involved. Look at their convulsions, both physical and verbal. Are these people sane? Are they normal?

I maintain that those fanatics are, in fact, perfectly normal people. However, they are also batshit insane. The point to stress is the fanaticism and madness do not arise due to some fault or blemish in those particular people -- the insanity invades perfectly normal minds, much like a cold invades normal bodies. For whatever reason, the viral ideas of their particular church happened to invade their minds at a vulnerable time. These viral memeplexes are now gradually gnawing away at the victim's brain, modifying them to suit the needs of the memeplex itself -- much like the Cordyceps fungus chemically alters the victimised ant's brain to force it to go high up and cling to a twig, while the fungus kills it and sporulates from up high. The Cordyceps is truly a terrifying parasite for the ant it preys on.

And that is the terrifying part. Genetic illnesses, although sad and grotesque, do not terrify the rest of us lucky enough not to have them -- for they cannot spread upon contact. Viral epidemics, however, are terrifying -- even mild sicknesses like colds. Furthermore, when an ant is infected by the Cordyceps, other workers of her colony carry her as far away from the nest as possible, and even remain there to die themselves to spare the colony from infection. Some of our parasitic memeplexes have an even better strategy, however. They modify the environment around the affected to disable any potential ostracism of the victim. The parasite portrays itself to the outside as benign, thereby escaping much of the scrutiny that would otherwise bring forth its end. And there are more potentially vulnerable individuals to come in contact with.

This brings us to a rather interesting way to model and analyse many of the world's events: Human minds are highly malleable, regardless of how much we try to resist. We are much like the molecules a DNA molecule uses to perpetrate itself to the future generations -- they may be thermodynamically resistant to such enslaving, but the genes that have mastered the technique are highly succesful in continuing it further (the other genes just die.) The memes use us to live out their own evolutionary stories, and manage to enslave humans to behave at their whim. Nationalism, political ideology, religion - look how many human lives were lost to the fierce battles between them! Humans are trashed around like socks in a washing machine: innocent, vulnerable people simply trying to live can be converted into vicious irrational killing machines ready to destroy the others who are exactly like them -- albeit parasitised by a different ideology.

This view places no blame on the common folk who are parasitised, regardless of how vile their crime. They were weak, perhaps mentally unhealthy for whatever reason. They became sick. Now their sickness imposes its raging symptoms upon the lives of others.

There are the smart crooks who take advantage of these ideologies, and despite not being aware of the formalisms of memetics, are masters of the field. To the disadvantage of the rest of us, of course. Some of these people are politicians, people of great power. Many of those politicians are parasitised by vile memeplexes as well. Now that is truly scary, for the ideology can express itself to its fullest foul capacity.

The destructive ideologies are evolving along with the beneficial ones. They're getting better and better at what they do. And perhaps this century may be an age where their battle rages greater than ever before.


I'm afraid the only way to combat this would be to launch a memeplex as a counter-offensive. Some benign ideology that self-destructs after a certain timeframe, immunising its victims from future viruses that may not be so benign. Basically, memetic vaccination. The child's mind is particularly malleable, and must be protected from diseases by a proper education.

We face today a slippery slope downwards from anything that can be even marginally considered 'proper education'. Perhaps we are at the lowest level of education and social intelligence in many centuries. Perhaps we have never been as dumb, naive and gullible as we are now, especially in the west. This compounded by the fact that never before have the ideological diseases been so good at what they do, is a very scary detail. I am genuinely worried. And terrified.


We should be careful not to attack the inflicted, but rather attempt to cure them of the infliction. Of course, many of them view us as inflicted (in the religious sense; we definitely all are inflicted by one thing or another in other ways), and that is one advantageous adaptation of their parasite. Imagine a viral disease that made you feel great and also feel the need to spread it to everyone else! If such a virus ever evolved, even if it killed off the host in drastic manners, it would thrive!

Well, that virus is here. It's been here for millenia, and is now more advanced than ever before.

We are on the losing side. Let's get our acts together and spread the antidote of skeptical rationalism as well as awe and adoration of that which truly is, as opposed to that we wish would be. If we wait much longer, it might be too late...

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. (http://www.ciliate.org/genetics.shtml)

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: http://pick5.pick.uga.edu/mp/20p?see=I_UARK/0001

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!

I came back a couple days ago, but failed to blog due to excessive chaos of the first week of school. Busy busy busy...

Hopefully I'll have more time to blog little pieces by this weekend, when I should make a proper post with some intelligible content. At least try to.


I do have to share some amazement though from a first class I had yesterday: in my Protistology class, which consists mostly of biology major 4th years, most of them didn't know what a...protist...was. Generally, when I sign up for a course whose title eludes me, I'll employ my dictionary search powers and look it up. Apparently that ability dies down by year 4 of university. Also, people who have specialised in biology for four years should generally like...be moderately aware of the kingdoms outside their immediate concern. General knowledge. An animal cell physiologist should remain informed about plants, fungi, eu- and archaebacteria, as well as protists. You know, just as a physicist studying EM should have at least a vague idea about optics and mechanics; an organic chemist should know the basics of the transition elements; a carpenter should know approximately how the plumber and the electrician need to work after him, etc. General knowledge. Being reasonably curious and informed.

Oh wait. I forgot. They're just there for a degree. Right.

And they have better marks than me.


I just wish my peers in science were actually interested in the subject, rather than blindly memorising their way through. A healthy dose of curiosity is good for everyone, but essential for work in science.

"Hi - bye" Maneuver - Episode I

You know when you bump into someone you haven't seen for a while, so you're like "OMG HI!", and then you realise you're rediculously late for something, so just before the other party has a chance to respond, you suddenly say "OH CRAP GTG BYE!" and run away?

This is somewhat similar. Hit-and-run blogging.

Thing is...I'm flying home to my parents' house for a week tomorrow...and will sever all internet access until 01 September so I can properly relax.

Relax before my two hellish semesters of 6 courses each, that is. On top of research work. Despite my abysmal study habits. Despite warnings from several profs against such acts of madness. I know I'm doing something incredibly intelligent, thank you! Might as well die gloriously or something.

This brings to mind a quote from Salinger's Catcher in the Rye: "The mark of an immature man is to die nobly for a cause; the mark of a mature man is to live humbly for one." (paraphrased edition, by the way) Instead of humbly accepting that I'm behind and submitting my pride to the Five Year Program, I'll just kill myself with 6 courses. Yup. Expect rants on the subject matter later. Or diatribes, rather. I'm no longer a teenager:

I don't rant.

Instead, I 'unleash diatribes', ie. sesquipedalian ranting intensified by academic references. Citing Nature or The Congolese Journal of New Age Psychology (note: the latter is not a real journal) always makes one's ranting sound quite sophisticated and well-founded. Especially when it's not.


Anyway, I digress. I write in gradients sometimes, never knowing how the hell I jump between rather unrelated topics. Vectors do that, sometimes. I haven't touched calculus in ages...even though I actually enjoy math when I sorta understand it.

The Better Blogs list should keep the potential imaginary reader occupied in my absense, which should be followed by a real début.

Cheers!

-Psi-