A tale of enzymes and sun

By Martín Bonfil Olivera

Published in Milenio Diario, august 4, 2010

Sometimes, evolution plays dirty.

Once upon a time there was a planet (ours) where, about 3.5 billion years ago, life emerged. But the first cells confronted a problem: their star emitted, apart from visible light, a respectable amount of ultraviolet rays. And this high energy radiation normally damages complex molecules, like the nucleic acids that store the genetic information. The result: mutations and death. Life was tough in those days.

In the course of evolution, millions of years later, photosynthetic organisms that released oxygen (O₂) emerged. About 2.4 billion years ago, the Earth's atmosphere was became full of this gas. Part of the oxygen, high in the atmosphere, reacted to form the famous ozone layer (O₃), that protects us today – although not fully– from the excess of ultraviolet radiation.

But evolution could not wait for an ozone layer. Way before that, some adaptations emerged to repair the damages that ultraviolet light caused in the cell's DNA. One of the most efficient ones was the enzyme photolyase: a protein that, activated by the visible light from the sun (hence the suffix,"photo"), reverts the damage in DNA (specifically, it breaks thymine dimers: abnormal bonds between two "steps" of of the spiral ladder of the double helix, so that when genetic information is copied into the next cellular generation, it causes mistakes: mutations).

Photolyase was so successful that today it is found in almost every living organisms: bacteria, fungi, plants, fish, insects and some mammals, like marsupials (such as kangaroos, which carry their immature babies in their bags). But -and here comes the cruel evolutionary prank– something happened along the way. One of the branches of the tree of life suffered a mutation that eliminated the photolyase genes. As a result, humans, and all other animals with a placenta (placentals), lack photolyase, thus making us more susceptible to skin cancer. This is why we depend on sunscreens when we go to the beach or when we walk in the street in sunny days.

Fortunately, last week, Nature magazine published the work of a Chinese researcher, Dongping Zhong, and his team, from Ohio State University, in Columbus, where they describe the detailed molecular working of the repair mechanism of photolyase from the fruit fly Drosophilia melanogaster. With this and other studies, it is possible to visualize the use of this enzyme in creams that protect us from skin cancer by repairing the damages that ultraviolet light causes in the DNA of our skin cells (it has been demonstrated that photolyase can be applied to the skin inside liposomes –fat vesicles– in in the form of cream and has protective effects).

Basic science thus gives a possible solution to an evolutionary injustice. All in the name of a good tan.

(translated by Adrián Robles Benavides)

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Dinosaurs for free!

By Martín Bonfil Olivera

Published in Milenio Diario, August 5, 2009

Popularising science is placing scientific culture in reach of the general population: to turn science into a part of pop culture.

One way to do it is through exhibitions and museums, in which many visitors have the opportunity of directly experimenting and getting close, in a special surrounding, to the objects, phenomena and concepts of science.

But this is seldom achieved in such a marvelous way as in the exhibition "Huellas de vida" (life's footprints), which Mexico City's government and the Museo del Desierto (the dessert museum) from Saltillo, Coahuila, together with other institutions, have installed in the city's main square since May 22.

I confess that I approached the exhibition with some skepticism: I am accustomed to visit science museums, and didn't think I'd find something to amaze me. I was wrong.

From the first enormous fossil fish, with its monstrous mouth filled with teeth, that welcomes you in the first chamber, the journey is full with marvels. Complete fossils, some original and some replicas of superb quality, of terrestrial and "aerial" dinosaurs (actually, pterosaurs; among them, the grand Quetzalcoatlus). Robotic models, specimens of "living fossils" and of species that help us compare the routes from which evolution, sometimes, produces similar results in very different species. Actual, live paleontologists showing how they work.

And a really professional museography, in which the specimens can be enjoyed with safety, and the professional and enthusiastic attention of many young guides, perfectly prepared to answer even the oddest questions from an avid public.

Of course, going to the exhibition will not turn you into a dinosaur expert. But that's is not the idea. A science exhibition must only, as Carl Sagan begged, "spark the sense of wonder". This the exhibition fully achieves. Other museums should take it as an example to follow.

Honestly, don't miss it. It opens from 9:30 to 19:30 from Monday to Sunday. But hurry up: it ends on August 31. And if this was not enough, it's free! What a magnificent gift for the citizens of our city.

(translated by Adrián Robles Benavides)

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Darwinian ballots

By Martín Bonfil Olivera

Published in Milenio Diario, July 8th, 2009

In other occasions have commented the similarities between biological evolution and democracy (and economy, and science).

In an ideal democracy, a group of citizens, who are supposed to be rational and to possess the information necessary to make thoughtful decisions, selects from a group of candidates the one they think is best. The analogy with natural selection, in which the environment selects the best adapted individuals for survival, is clear.

The same happens in an ideal economy, where "the market" (buyers) select products or services, and thus companies, that offer the best quality/price balance: the selected ones survive, the less efficient go extint.

In science, selection is made by a sort of "elitist democracy", in which a group of specialists (the scientific community) choose, among the great variety of theories proposed, the ones that turn out to be more convincing.

In all cases there's a variety of candidates and a system that select which will survive at the end.

The difference lies in the criteria used for selection. In evolution, anything that gives an advantages to an organism will increase its survival. In science, the factors that determine if a theory is accepted by the community vary, but there's one that stands out: the rational judgment of the facts and arguments presented to support it. Although deviations may occur, science tends to make rational decisions.

On the other hand, in economy and democracy, decisions -even though politicians and economists hate to accept it- are often far from being rational. In extreme cases, the decisions are made based on emotional factors, which are easily manipulated through marketing strategies (in Mexico's elections on july 5th, the "null vote" was a very successful protest, in the face of a system that is not working).

The point is that, unlike what happens in evolution, in human affairs the blind selection processes do not always produce the most desirable result. It would bea good idea , at least, to try to make electoral decisions more rational. What a shame: in Mexico we have a long way to go until then.

(translated by Adrián Robles Benavides)

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Predictive microbes

By Martín Bonfil Olivera

Published in Milenio Diario, July 1st, 2009

According to Wikipedia, it was Dutch cartoonist Robert Storm Petersen who said: "making predictions is hard… especially about the future."

True, but those who can predict the future with some reliability have better chances of surviving. That's why a lot of animals have developed the capacity of making predictions about their environment from information they obtain through their senses. (Science itself is a refined descendant of these biological survival mechanisms.)

Predictions can vary from the complex phenomenon of learning —what to do to obtain certain results— up to the conditioned responses discovered by Ivan Pavlov in the XIX century, which explains how dogs can "learn" to secrete saliva to the sound of a bell, even when there's no food near.

But to learn that when the sky gets cloudy I need to find cover, or to hate any food that has sometime made me sick, I need a nervous system.

Species that lack this system have to resign to "learn" more slowly, through natural selection: the environment eliminates individuals that react in the wrong way, and maintains the ones that get it right. Unfortunately, this form of "prediction" is not flexible, and big environmental changes exterminate a large part of the population, which are incapable of adapting quickly.

Amazingly, scientists of the Weizmann Institute of Israel have just published (Nature, June 17) that some microbes, such as intestinal bacteria Escherichia coli and brewing yeast Saccharomyces cerevisiae can "predict" changes that have not yet occurred in their environment, and activate in advance the genes they are going to need.

They achieve this through evolution: through natural selection, as experimentally confirmed, such microbes "learn", as a species, to associate environment stimuli with gene activation.

Of course, the trick only works in environments that present regular changes (such as the ones the bacteria encounter when passing through the various zones of our digestive tract, or the ones that the yeast causes when changing the temperature of its environment as they ferment the available sugars).

Even so, the lesson is clear: even brainless microbes can learn to predict, thanks to evolution.

(translated by Adrián Robles Benavides)

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On second thought…

By Martí­n Bonfil Olivera
Published in Milenio Diario, June 17, 2009

Two science news items published last week make us wonder.

One is the discovery that the star Betelgeuse, the brightest in Orion constellation (if observed on infrared, not in visible light), one of the most studied stars, has shrunk 15 percent in the last 15 years. In 1921, Betelgeuse was the first star to be measured. It's a red supergiant; its diameter is around 40 million times that of the sun, and it's on the last stages of its life. It would not be strange that one of these days —or years, or decades— it will become a supernova: it will be a magnificent show.

How is it possible that a star shrinks? Scientists don't know. There are stars that pulse, but until now, it is uncertain whether Betelgeuse's size will increase again.

What confidence can we have, then, in the knowledge of astrophysicists, if they can't even assure that their data will not change any other minute?

The second news item reinforces this sensation of distrust: two researchers from Oregon University reveal that their studies regarding the anatomy of birds and dinosaurs appears to refute the theory, held by decades, that birds are direct descendants from those reptiles.

The special structure of bird bones, necessary to give them the lung capacity they require, is not present in the alleged ancestors. Most likely, they must have evolved in parallel.

Where does that beautiful story, that dinosaurs did not go extinct but turned into hens, stand now? Can we trust, a creationist would ask, in a supposed science that does not even guarantee that the information it generates is true?

Of course, the answer is that science does not reveal absolute and unchanging truths, but useful knowledge, that constantly evolves when subject to testing, discussion, analysis and correction.

It is this capacity for change that gives science its power.

It is difficult to accept science as a human process of trial and error, fallible, yes, but very reliable. Too bad: an infallible science sounded nicer… even if it was just a fantasy.

(translated by Adrián Robles Benavides)

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Darwin and death

By Martín Bonfil Olivera
Published in Milenio Diario, June 10, 2009

The game of linking concepts that at a first glance look unrelated can be a good way of keeping one's mind in shape. I was invitated to give a talk about "the death of Darwinism", and that's a good excuse to explore the relations between the life and work of Charles Darwin and the subject of death (since Darwinism is alive and evolving).

Darwin's encounters with death are not few. His mother died in 1817, when he was only eight years old; that forced him to be admitted in a boarding school. Years later, already married to Emma, his cousin and then wife, he had ten children, of which two died very young (not an unsual thing in those times). But the death of his favorite, little Annie, at the age of ten, was no doubt the most traumatic encounter of Darwin with death. So much that it is believed that this put an end to whatever rest of religious faith he had left.

Darwin's own death was not unusual: he was buried in with honors at Westminster Abbey, the place reserved for the great men of England. The excessively austere grave on the floor that marks his resting place contrasts with the nearby grave of Isaac Newton, a kind of mini-Disneyland.

Darwin's ideas are too related to death: they help us to understand, for example, how it emerges.

It turns out that the oldest organisms, composed of only one cell, are immortal. They feed, grow and, when the time is right, they divide in two, but they don't die. Only with the emergence of multi-cellular organisms and sexual reproduction do phenomena like ageing and death emerge; they are the price we have to pay for the capacity of forming more complex organisms.

Apart from helping us to understand death, if Darwin's ideas are used in the wrong way, they can cause death: at the beginning of the 20th century, the development of the pseudoscience of eugenics, which intended to improve human race through Darwinian selection, was a global trend, and gave way to the excesses of Nazism. Even today, the application of Darwinian thinking in social contexts bears this stigma.

The moral of the story is that Darwinism, as any other knowledge, can be used for good or bad. That's why it is convenient to have a good understanding of it.

(translated by Adrián Robles Benavides)

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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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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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Natural wonders

by Martín Bonfil Olivera
Published on Milenio Diario, March 25, 2009

I have just been to one of the 13 wonders of Mexico: the basalt prisms of Santa María Regla, in the state of Hidalgo.

When he came to Mexico in 1803, Alexander von Humboldt visited these impressive 30 meter basalt columns, of perfec hexagonal shape, that border a ravine as if God had arranged them like giants pencils. They're breathtaking.

But for a naturalist such as Humboldt, and for a relentless atheist like this columnist, the divine explanation is not satisfactory: it doesn't really explain anything. Could there be a natural process that allows hundreds of hexagonal prisms to be formed and carefully stacked ?

Basalt prisms, although rare, are not unique. There are 10 or 15 sites in the world with similar structures: the “giant's causeway”, in Ireland; the “Devils postpile”, in California; the “organ pipes”, in Australia… The formation of these structures doesn't seem to be that difficult.

A second hint is the hexagonal shape of the prisms. There is an old saying in northern Mexico, "as the wagon moves, the watermelons arrange themselves", that accurately applies to this case: spheres tend to accommodate spontaneously so that each one is surrounded by twelve more: it is the most compact arrangement. In the case of circles, the most efficient arrangement is hexagonal: the most compact form to arrange cylindrical columns is so that each one is surrounded by other 6. The hexagonal shape of the prisms is the result of this arrangement. They weren’t constructed and then arranged: they formed in their actual position.

And how could melted lava —basalt is solidified magma— form individual vertical prisms? The answer relies in the existence of self- organized structures in nature. "Bénard cells" are example : when heating a liquid from below, the convection movement —hot water goes up and cold goes down— can form hexagonal columns of water that keep circulating as long as there's a temperature difference. Prisms are fossilized convection cells that were solidified when they quickly cooled down.

The mineral world can form marvelous and arranged structures. The same thing occurs, but augmented, in the living world. Darwin, another naturalist, saw it and explained it. Because of this, and more the basalt prisms of Hidalgo are really worth visiting.

(Take a look at my pictures of the basalt prisms here)

(translated by Adrián Robles Benavides)

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