HIV: genomic confusion

By Martín Bonfil Olivera

Published in Milenio Diario, August 12, 2009

On August 6, the main science note on almost all media was a study of the genetic material of the human immunodeficiency virus, HIV.

The bad news is how this discovery was reported. Some sample headlines: "HIV genome deciphered"( BBC, picked up by newspapers such as Publimetro and radio shows like Hoy por hoy en la ciencia (Today in science), from UNAM and W Radio); "HIV genome, deciphered" ( El Clarín, Argentina). What is the problem? That it is incorrect: the full genome of HIV was decoded about 10 years ago. (A Mexican blog on internet even mentioned that "it has been confirmed that HIV uses RNA -ribonucleic acid- instead of DNA -deoxyribonucleic acid", something that has been known since the eighties.)

Some other media were more precise, though still not so clear: MILENIO Diario mentioned "the first HIV full map", "to create an image, not only of RNA nucleotides, but the forms and folds of the RNA strands". Excélsior, with the information from EFE news agency, used the following header: "AIDS virus genome structure decoded". And Spanish El mundo digital headlined "HIV genome, at bird's eye", and explained that "for the first time, the complete structure of HIV's genome was decoded and they got a clear image of its internal architecture".

Let's explain briefly:

HIV, unlike most organisms, does not have genes made of DNA , the famous double helix molecule, but of RNA, formed by only one chain, not two. The chemical links that form this chain are the "letters" in which genetic information is written, and this is what was deciphered years ago.

The discovery of researchers from North Carolina University headed by Kevin Weeks (and published on Nature magazine) is that the HIV RNA strand folds in a complex way: some parts pair up with others to form double helical stretches, for example.

When the virus penetrates a cell and its genetic information is read, these "knots" and rolls (technically known as "secondary structure") can delay the reading of the genes, and this can be fundamental to control how HIV proteins are manufactured.

In other words, a kind of "hidden code" was discovered on the virus' genome, which can be important not only to fight it, but also to better understand the control of genetic information in all types of organisms.

Unfortunately, to explain this with the necessary detail, more space is required than is normally available in news media. At the very least, we should try to be as precise as possible.

(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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Reflections on scientific culture

By Martín Bonfil Olivera
Published on Milenio Diario, July 22, 2009

Last week I argued in this space against the lack of scientific culture that is so evident in so many aspects of our society.

Among the different responses I received, a letter from a reader from Argentina got my attention.

She proposed that my concept of "scientific inculture" is an inadequate simplification. She asks whether the mystical or magical beliefs of the "native people" of Latin America should be classified among the "absurd beliefs" that, as I mentioned, are replacing science in the minds of our citizens.

A lot of these folk beliefs are based in the respect for the environment, and have survival and preservation value, although they are not science-based. On the contrary, often the environment suffers in the name of science.

So, how desirable is scientific culture; how harmful are absurd beliefs?

I should clarify that when I spoke about absurd beliefs I had in mind things like quackery, horoscopes, indigo children or quantum healing. There are a lot of examples of, for instance, efficient traditional therapies —and others that are completely useless, of course— and folk environmental practices that work better than modern proposals… though not always.

My reader questioned also whether it makes any sense to demand a scientific culture from a population with a high proportion of poor and excluded people, without the means to consult not an astrologer, but a decent health system.

She is right: to foster scientific culture is utopic. But the fact that problems such as poverty or injustice exist does not imply that spreading scientific culture is a worthless task. These are problems that have to be taken in parallel.

I agree with my reader that "the concept of scientific inculture makes reference to a complex and multidimensional historical, political and social process".

Even so, I insist that a widely spread scientific culture in our population can be the first step for the development of a scientific, technological and industrial system that, in the medium term, will help obtain a better life for our peoples.

(translated by Adrián Robles Benavides)

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The moon and lack of culture

By Martí­n Bonfil Olivera
Published in Milenio Diario, July 22, 2009

Last Monday, on the 40th anniversary of the day humans stepped on the moon, the radio talk hosts of El Weso, a popular Mexican radio show on W Radio (of which I'm a fan) showed a regrettable lack of scientific culture.

When the question of whether the moon landing was real popped —you might have heard the nonsense that it was filmed in a TV studio—, they answered "we'll never know"! And singer Fernando Rivera Calderón added that going to the moon was "useless" (I wonder, my admired Fernando, and what about poetry? Do you think it serves any purpose? These are the wrong questions to ask). It had to be Rodolfo Neri Vela, the first Mexican to go to outer space, who amended them for good.

The problem is not that our lack of information and our tendency to believe in complots carry us to be unsure even of one of the greatest scientific-technical achievements in history. What's alarming is to confirm that science is still absent from the average Mexican popular culture, and that it is being suplanted by all kinds of absurd beliefs.

More examples: astrologer Amira, also in W Radio, announces "Did you know that the positions of the stars can directly influence your health, your finances and even love? No lady: we know perfectly that the position of the stars does not directly nor indirectly influence that at all, and to propagate these false ideas and on top of it charge for them is a fraud. Why can't the Mexican consumer protection agency do something about it?

On Friday, a columnist from MILENIO Diario published that on "December 21 of 2012… there will be an astronomical phenomenon that occurs every 26,000 years: the sun will align with the center of the milky way… where there is a black hole, manufacturer and deestructor of stars". He adds that the Mayas mention this specific day as the final date in their calendar". (It's a shame that to be able to speak of an alignment you need at least three points, that black holes don't manufacture stars, and the supposed "end of the world" announced by the Mayas is another nonsense story).

As a final offense, just outside my house there was a sign: "Loose weight with laser. 100% natural" (a 100 % natural laser??)

There's no doubt: the lack of scientific culture of Mexicans is galloping. We science communicators could very well double our efforts.

(translated by Adrián Robles Benavides)

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Still, Influenza

By Martín Bonfil Olivera

Published in Milenio Diario, July 15th, 2009

Science does not reveal absolute truths, but it does have a commitment to reality.

A good example is the pandemic -started in April in Mexico as an epidemic- caused by a swine A/H1N1 influenza virus.

Mexicans remember how, after the emergency stage that forced Mexico City and other places to shut down schools, restaurants, cinemas and other gathering places, there was a curious reaction. It was said, through email and as gossip, that the epidemic was a sham. That the virus did not exist, or that the epidemic was planned by the current panista government of Mexico (or bye the American government) to influence Election Day on July 5 (or to reactivate world economy).

There were multiple versions of the rumour, but all of them had something in common: it was a way of denying reality. The traumatic experience of those secluded and inactive days, and the economic, but also social and psychological harm they left, created a fertile field for rumours that everything was a complot.

The efficacy of the health authorities was questioned, as well as the science behind their decisions. Today we can see that the epidemic, already spread around the world, is a reality that affects many other countries. Argentina and Chile in their full austral winter, already have 137 and 33 deaths, respectively, and thousands of infected people. Also, Cuba is reporting cases, and the Mexican states of Chiapas, Tabasco and Yucatan have detected an important spike, up to the point that Tabasco has decided to cancel its annual state fair.

In the meantime, research about the virus advances: a group lead by Yoshihiro Kawaoka, from Wisconsin University, reported last Monday on Nature magazine that the swine virus -which is actually a result from mutations and combinations from other already existing viruses, human, bird and swine- causes more harm to the lungs of experimental animals (mice, ferrets and macaques) than the common seasonal influenza virus, and that it can asymptomatically infect pigs (maybe that's why the epidemic was not detected until it jumped into humans).

They also found that people born before 1920 and therefore exposed to the massive epidemic of A/H1N1 influenza in 1918 (spanish flu) have antibodies that can react against the current virus, unlike people born after (thus maybe explaining the anomalous behavior of the epidemic, which affected mainly younger people).

Currently, the virus is still sensitive to tamiflu, but it is very likely that in the short term some resistant varieties will arise. Soon, we will have a vaccine, but it will take time to produce it in enough quantities to respond to the World Health Organization's request for "all countries to have access to the vaccine."

The reality of the pandemic imposes itself, beyond any belief or rumour. The countries should better pay attention to what science reveals, and they should act united in consequence.

(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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