Bloody cataract

by Martín Bonfil Olivera

Published in Milenio Diario
April 22, 2009

The mistery started on 1922: Australian explorer Thomas Griffith Taylor discovered on Victoria's land, Antarctica, a blood-colored waterfall that emerged from below Taylor's glacier (named in his honor).

Initially it was thought that the color was caused by algae, but today we know that it's due to iron oxides. What produces them?

The current sprouts at certain times of the year from a sub-glacier water deposit: a little buried lake 1,300 feet under the ice. The glacier, an ice river that flows with geological slowness, covered the lake of sea water, encapsulating it two million years ago. In its inside, today hiper-salty, there is no oxygen nor light.

Although it's not possible to enter the lake, by analyzing the water that flows in the waterfall Jill Mikucki and her team of researchers from the Land and Planetary Science at Harvard University (Science, April 17) have found, with support from NASA, genetic evidence of different types of bacteria ("a bacterial consortium") that use sulfur compounds to oxidize iron present on the rock under the glacier as medium to survive in a cold environment that lacks light and oxygen.

We are accustomed to think that life only exists if there is oxygen, but this is only true for modern organisms. Microbes like bacteria and their cousins the archaea are much more ancient, and have more versatile metabolisms.

Plants use solar energy to manufacture food from carbon dioxide from the atmosphere (then we, the other living beings, oxidize this food, combining it with oxygen, to obtain the energy stored in them). But there are other ways to survive. Antarctic bacteria obtain energy through sulfur compounds and in the process they produce iron oxides.

What's fascinating is that the same thing could have happened 700 million years ago, when the seas were covered in ice. And the same thing could be happening in other worlds, like Jupiter's moon Europa, under whose cold surface there may be a sea housing microbial life.

The moral of this story is: you never know what can be discovered when investigating a bloody mistery.

(translated by Adrián Robles Benavides)

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Me, myself and I

by Martín Bonfil Olivera

Published on Milenio Diario, April 15, 2009

Wisely, when many philosophies seem to seek its disappearance, my fellow columnist on Milenio Diario newspaper Braulio Peralta says, last Monday "Hurray for the self"!, since, whatever his followers say, "Buda could be nothing but his own self".

"With a self", Braulio says, corruption, for example, can be fought. If we deny it, it becomes impossible to defend "honesty, ethics, human rights".

The question of the self has fascinating facets also from the scientific point of view. How can a brain made of cells, in turn made of molecules, originate the subjective sensation that allows Descartes, and all of us ith him, to say "I think, therefore I am"? How can a material mass of tissue generate consciousness, a sensation of self, a soul?

The easiest answer is the dualist one: to suppose that something external, a soul or spirit, "enters" the brain and animates it. The brain is only the vehicle; the soul is immaterial and, since we're at it, immortal. Sounds nice.

The alternative, known as materialism, monism or naturalism, is more sensible, but has problems. One can explain how sensory stimuli are processed in a very complex way, in parallel, by different brain systems. But the problem really starts when explaining to whom the result of all of this processing is presented, giving us our subjective experience of the reality that surround us.

To postulate a "homunculus" that lives inside the brain is a return to dualism. Philosopher Daniel Dennett - whom I have mentioned a lot lately - proposes a stimulanting explanation in his book Consciousness explained: consciousness, the self, is a virtual phenomenon. It is not material, nor spiritual: it’s a consequence of the working of the brain that emerges in a superior level of organization. (Life is another example of an emerging phenomenon: it only exist in and above the cell level, not in atoms).

In some level of this processing, the brain starts to perceive itself, and that gives rise to the - virtual - sensation of conscience.

Sounds complex, but trying to understand the self, as difficult it may seen, will always be better - and more useful - that to deny it or to renounce to explain it. "Long live the self; and long live the naturalized soul!

(translated by Adrián Robles Benavides)

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The paradox of species

by Martín Bonfil Olivera
Published on Milenio Diario, April 8, 2009

The human brain tends to simplify. We like to understand things in terms of black and white, good or bad… And we also like to think that things can be defined with clarity: that they have an essence.

A problem when understanding Darwin's theory is the definition of biological species. Although Darwin himself avoided defining it ("…I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that ...does not essentially differ from the term variety"', he wrote in The origin…), he didn't deny the existence of species. Nobody confuses dogs with horses, after all.

The usual criteria to define a species is "reproductive isolation": if two animals or plants cannot mate, or they produce sterile descendants, they belong to different species. But if, however, no matter how different they look, they can mate (like dog breeds), they belong to the same species.

But the reproductive criteria is not infallible (there are canine breeds that don't mate just due to reasons of size), and does not always apply: there are many asexual organisms; bacteria, for instance. Besides, as mentioned here in last week's post a lot of these organisms exchange genes "laterally" (not from parents to progeny, but by a mechanism similar to a "contagion"), so even a more modern criterion, such as gene analysis, does not always allow a clear distinction among species.

On the other hand, saying that "species evolve" is confusing: if a species changes, it turns into another one. So, do species change, or do they just disappear to leave room to other species?

The problem, philosopher Daniel Dennett explains in his revealing book Darwin's dangerous idea, is that what characterizes a species is not the presence of a certain essence that defines it, but the absence of the intermediate forms between one species and the other.

Species are not collections of identical organisms: they are more like clouds of individuals with almost identical genomes, but with little variations. We say that there are two distinct species when between two of these genome clouds there is an empty space; in the opposite case, we talk of varieties. As always, in science things are not as simple they are said to be.

(translated by Adrián Robles Benavides)

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Darwin's little tree

by Martín Bonfil Olivera
Published in Milenio Diario, April 1, 2009

In 1837, returning from his five-year travel on board of theHMS Beagle, and starting the two decades he would spend thinking about the "transmutation of species", Charles Darwin wrote in his notebook the phrase "I think", and then he drew a little branched outline: the first evolutionary tree.

In 1859 he published The origin of species, and the only illustration he included was a more elaborate tree. Since then, the tree is evolution's dominant metaphor: a ramified process in which new species appear from pre-existent ones.

But attacking Darwin is a hobby few can resist, from fanatics that try to banish it to restless biologists that pretend to jump into fame by proving that some of his ideas are wrong.

And of course, there are a lot of aspects in which Darwin was wrong (his theory of heredity, for example, was way out of line). With time, the Darwinian theory of evolution by natural selection has been corrected, completed and fine tuned. Still, it remains as the backbone of modern evolutionary thinking.

Recently, New Scientist magazine published an article that caused an upstir, because it declared that the discovery of "horizontal gene transfer" (not from parents to descendants, but like that which occurs when two bacteria exchange antibiotic resistance genes, or when a virus injects genes from another species into us, as has happened lots of times in human evolution) is the downfall of the image of evolution as a tree.

But gene evolution is not the same as species evolution. Of course, evolution is not as simple as Darwin thought, and in some aspects it looks more like a confusing web than a tidy tree. There are branches that are weirdly connected one with another (like when some bacteria entered old cells to become our mitochondria and chloroplasts). Maybe the tree has more than one root (there is evidence for several "origins of life" that later became connected).

Maybe the tree metaphor will change, or will be substituted by a web. But from that to proclaiming "the end of Darwin" or biology's next great revolution, there's a long way to go.

(translated by Adrián Robles Benavides)

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