Field of Science

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
The arrow points to one of the few dozen large circles.

('normal' mitochondrial DNA:

The circular string in the sea of junk (suspension medium)

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:

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 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.

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 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



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...