Friday, July 20, 2007

Updates. 4 dollars in my pocket, a million of dreams in my head:

Greetings from... Colombia!

Finally I begun this trip. I am anxious.

I could not leave Mérida last Tuesday, because the University still had not bought my ticket because the person who was supposed to it wasn't at his office. Finally I got the money for the ticket on Wednesday, but then, it was too late, because of the holidays. There wasn't a single ticket available for the twentieth, the available tickets were for dates like the 26th and the rates the double of the money my university was going to cover, so I was going to miss Chicago, even if could still go to Minneapolis and to Mountain View. I was desperate, but the travel agent did a great job and found an itinerary for today, arriving to Bogotá today in the morning, then waiting 14 hours in Eldorado Airport and arriving to JFK airport in New York tomorrow morning. A little bit far, a lot of time waiting, but what the hell, I was lucky to get a plane and deliver the presentation.

I was worried about the fourteen hours, since I have almost no cash, due to the currency exchange control. I have almost four dollars in cash. In my prepaid credit card (another strange consequence of the currency exchange control, a card that officially is a credit card but works as a prepaid one) I do have money, but I was still worried. But my good luck was beyond belief, I am am beginning to think I am an ancestor of Teela Brown, because due to the lack of seats in the flight to NY, I got a first class seat and then I am allowed to use the VIP lounge at the airport. So, I am writing this from a cozy leather couch, drinking iced mocaccino and eating sandwiches. I am saving my tuna cans for later, three meals I will enjoy without paying. I slept well, I installed Ubuntu again, I am downloading Bioinformatics packages, I sudo-ed, installed the drivers and got functional wi-fi again, which is impossible for me in Windows for strange reasons.

I only spent a day in Caracas, I could not see my sisters, I was pretty sad about it, but I will see them next month. What a hectic day yesterday. I called to my cousin in California and she bought a ticket from NY to Chicago, I will arrive tomorrow at 3:00. Thanks, darling! Human altruism never ceases to amaze me. This trip is possible thanks not only to the people who invited me, but to a lot of people who believes in me and are helping me. Not just my family, but friends and my thesis advisor. I am lucky to have them and I am deeply thankful for it.

I got a grant request for getting my ticket to San Francisco payed refused. Well, I still have chance to get it paid. If not, I'll have to borrow money, but, what the heck. This is once in a lifetime chance.

I am getting sleepy, these lasts days were a constant rush and I did not sleep last night. But the nerves are hard to overcome and I finally do not sleep. At least no yet.

The VIP room is alien to me. An agalmic environment, obviously, but not a useful one. Here you have the basic needs covered, but does that leads to creativity? Maybe yes, maybe no. But the fact that I am writing this entry, downloading bioinformatics packages and studying for the presentation rather than complaining and sited in the floor. The people here is very rich, and often, very old. Some of them are really strange persons, they seem to live in another world. A guy was hitting his laptop and shouting at it because something dropped its value. Some of their kids look like spoiled brats, but not all of them. I am feeling like a field anthropologist today, lol. And this place triggers my interest about the analysis of current agalmic environments: All included-resorts, VIP lounges, the Googleplex?. Can we find some patterns in these temporary situations that gives clues about the development and organization of post-scarcity societies? Or is it a delusion because the current agalmic environments are distorted at core by its scarcity-driven surroundings?

I would love to discuss these ideas with the anarco-transhumanists in Chicago and at the Googleplex.

Well, in 8 hours I would be leaving to NY. Hopefully I won't be rejected at customs.

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Tuesday, July 17, 2007

First they came for my donkey, then, they came for my cow. Now, they are coming for me.

Some people in Kenya are mad at the government because the damn government (Would they be Libertarians if they moved to the US?) wants cleaner streets and want their donkeys to use diapers (I had problems with the word "nappy" until I learned what it meant few months ago).

Mr John Kinyanjui, a donkey owner, said: "The council itself has workers. They can do the sweeping. We are paying taxes." Another anonimous donkey owner said "If we have to put nappies on our donkeys, soon they will say our cows need them too,".

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Tips ( for Open Notebook Science

Jeremiah recently posted some really useful tips about Open Notebook Science, you can see them here:

J's blog: Tips (rules?) for Open Notebook Science

A brief excerpt:

  • include high quality images in your documents; things like agarose gels will need to be zoomed in a lot to be inspected in detail; if you convert your full resolution tiff to low-quality jpeg, it'll just look like pixelated blah. Then again, you can't always use full-size images, particularly from a high megapixels camera, because the notebook will quickly become giant; so here is my suggestion:
    • if the image is small (<1mb)>
    • if it is huge but detail doesn't matter, include a decent resolution image that can be zoomed in 2-4x and still look nice
    • if it is huge and detail matters, include a decent resolution image, but also include a link to the full size image like you would for other raw data
  • construct the document in such a way that it is easily indexed by search engines (otherwise no one will find your results; people probably wont read your lab notebook for fun)

Be sure to check the tips, they are realy useful if you are going that way. I think I will post my thesis and the models before they are released, however, probably I will write almost everything in Spanish and Fortran (Maybe SBML and Mathematica too) code.

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Monday, July 16, 2007


Today my mother came to see me with my stepfather and my brother.
We had a meal together and they left to Valera, 4 hours from Mérida.
As I am leaving to Caracas on tuesday, they came to say good bye. I should be in Chicago the friday, and I will deliver my presentation on sunday.

I have already packed my clothes, my books and like 10 tuna cans, as I am going to be without much money this coming month. Hopefully, there will be wi-fi in a lot of places. I am lucky I will have a free hotel room in Minneapolis and free food and hotel in Mountain View, I also have a cousin in Anaheim, so Chicago is going to be the toughest place to be.

I am afraid about not delivering a good presentation, but I will do my best.

US, there I go.

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Friday, July 13, 2007

Exposing some quacks

Updating: James the Amazing Randi has replied to my letter and said the Olalde is ellegible for the one million dollar prize, besides he kindly corrected my letter and translated it to proper English.

It's been a long time since I wrote something about my first intellectual passion, Skepticism. I became a skeptic 7 years ago and became an activist on the field six moths later. I founded the only skeptic association of Venezuela and happily, we are still on the road and we even have a weekly radio show of 15 minutes every thursday.

I haven't written about the subject in a while, I have been too excited about the future, and worried abouy MY future. But now it's time to change that.

What would you think about this:

I am not making this up. It is actually a peer reviewed paper indexed in Pubmed, one of the most trusted databases in science. And this crap is in. How can this be?. Well, I have a theory: That happens when peer review is not made by peers, but by quacks. Yes. On the board of the Evidence-based Compl. and Alt. Medicine (eCAM) (no wonder why all the letters are capital but the e) there is at least a person who is neither biologist, doctor or has any training related to Health Sciences, a tycoon of the alternative health who has shown no respect for the healt of his victims and abuse of them, emitting tv spots of "cured" patients who turn to be dead by the time the spot is aired.

I will post here a letter I just sent to several leading skeptics and quack busters:

My name is Guido David Núñez-Mujica. I am the founder of the only sceptical association in Venezuela ( We have been involved for the last six years in promoting scepticism and rational thinking among Venezuelan society. To date, we have dealt with several traditional kinds of quackery. One particular case of quackery in medicine is remarkable not only for its economic success in Venezuela, but also for its virulent, shameless, slanderous promotion, its international projection and success, and -- more dangerously -- its infiltration of the peer-reviewed literature.

I am talking about "Adpatógenos Internacionales," a company founded by José Olalde, a self-proclaimed "Engineer in Artificial Satellites" and a Scientologist. The basic claim of Olalde is that he has devised a new theory of living systems, based on a triangular scheme, a so-called "triangle of life" in which each side represents Biologic Intelligence, Biological Organization and Energy. Check for yourself: They also claim to be able to diagnose "140,000 diseases" with yet another version of an aura-reader, their "energimeter." Unfortunately, all the rebuttals we have produced are still in Spanish and our English is not good enough to attempt a proper translation, nor are our resources enough to get a professional translator.

What is more worrying here, is not the usual quackery. We have seen quacks before and we will see quacks in the future. What is actually dangerous is that this crook has in fact gotten into the board of the journal "Evidence-Based Complementary and Alternative Medicine," despite the fact that he hasn't any training as a doctor or biologist, or in any field related to Health Sciences. If you check closely the first paper published by Olalde, you will find that something smells pretty foul there. At the bottom of the paper you will see: Received January 13, 2005; accepted January 14, 2005.

I have not published any paper yet, but I do work in research and I am aware of the painfully long process of submitting a paper to a journal, of the time the referees need to evaluate it and often suggest new experiments and further research, besides wording and graph issues, and yet here you have a completely new theory of life that quotes L. Ron Hubbard and you have not even a tiny correction to the Author? That is suspicious, but when you see Olalde's name on the editorial board of the journal, the mystery is solved:

I think that is VERY dangerous, since these people claim to cure everything from cancer to arthritis and diabetes, and they often boast about their "paper in Oxford" and point to the people who criticise them, saying we have no papers at all and we are "jealous" and at the service of evil pharmaceutical companies. You know, the usual quack stuff. Even more outrageous, their "papers" are indexed at Medline! I think it is necessary to denounce this travesty of science and make Oxford Journals come to terms with the Ecam, closing the journal or retracting all these papers and expelling the fraudulent people from their board. This is different from most of quacks, since it now is part of the accepted and peer-reviewed knowledge. And this journal has not stopped at publishing this quackery, they have also published other "papers," like the influence of the pyramids on stress in rats. These papers not only give very extraordinary results, but also quote as a fact the existence of a kind of "energy" responsible for the observations. And this rubbish is published as peer-reviewed and indexed in Medline. There is another paper ( published in another magazine that seems more fact-based, however, I see some things that do not fit, but since I am not an expert at interpreting microarrays, I cannot say anything, but, fortunately they have produced a video ( where they boast a lot about heir product Circulat, claiming totally unrelated things, even if their results are correct and fraud free. In the video you can see Olalde's business partner, Anatoly Antoshechkin, is the Director of R+D of a company named Genext (, whose mission is to patent and eventually put on the market tested herbal "adaptogenic" compounds. But wait, those plants were already being used here, before the paper was released! We in Venezuela are the guinea pigs of Genext, Nulab and International Adaptogens, who are not only selling Circulat but scores of other products -- never tested -- that they claim can cure almost everything.

I am sorry if I am being too vehement, or my language is rude, but I am furious, as a scientist, to see this kind of stupid quackery as relevant and true as real papers – and precisely at this time. Now, when stem cells are said to do marvels, when implants are made that allow paralysed people to move things with their help, when things really astounding are happening in science and technology, precisely now, when a lot of people are confused about what science is, and what isn't, about what science is able to do and what it isn't able to do, because the limit of possible things seems to expand, precisely at this time a dishonest (yes, dishonest, not simply naive) journal has allowed crooks and liars on its pages not only giving them space for their ridiculous claims, but also giving them scientific respectability in the eyes of unaware people who trust in the high standards of peer-reviewed publications and in the self correction of science.

This is not only utterly dangerous and a cruel joke for the general public, as Olalde's company makes a lot of money here in Venezuela, and is beginning to spread to other countries. There are several cases of deaths due to his products or to the lack of proper medical treatment. In one of these cases a woman on a TV spot claimed to be cured from cancer, while in fact, she died 9 months before the date the spot was released. This is also an affront to all of us who try to understand how things work, and for those of us who work hard to turn abstract knowledge into useful products and a better quality of life.

I think that this situation must be acknowledged and we have to do something about it. There must be a strong reaction from scientists to stop this, analogous to cases of fraud in papers. I am writing this to you because I am sure you will be interested in this case and maybe Olalde's claims may win him the $1,000,000 prize if he can prove them, for instance diagnosing diseases with his "energimeter," or maybe you would be interested in "Dr." K. G. Korotkov, who claims that there exists "Evidence of the mind-body activity after death."

In 1993, Dr. Korotkov and his associates obtained strong experimental evidence of human life energy for up to 6 days after physical death. Characteristic patterns emerged according to the manner of death, i.e. peaceful death, sudden unexpected death, suicide. Details are described in the book by K. Korotkov in Russian and English (Email:

Korotkov is the creator of the energimeter and one of Olalde's close allies.

I have already written to Dr. Stephen Barrett on this issue, I hope that you can help us to debunk this dangerous quack and expose him and his partners.

Thank you very much for your time.


Guido David Núñez-Mujica

Undergraduate student of Biology and Computational Physics, sceptic

Mérida, Venezuela

If any of you, dear readers, can help to spread this meme and begin to complain to withdraw this silly "papers" from Mdeline, I will be eternally thankful to you.

Suggestions are needed.

PS: These weeks are hectic indeed. Yesterday I submited my first abstract to a traditional science conference and we are working on a paper in bioinformatics. Nothing edge-cutting, but it is fun as hell. And I just finished the preliminar model of my thesis in Fortran, but as my Ubuntu's X crashed, I have still to check if it runs properly.
Ps: Again, forgive my awful English. I hope it improves next month! ;)

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Thursday, July 12, 2007

My new T-shirt

Something that I just made up. I would like to use this image during my US trip. I will try to get it on a shirt next week. Hopefully it won't be too expensive. Hopefully there won't be any trouble, after all, I will be on the country of Freedom, right?

One about Hellen Keller and Che Guevara is coming soon. You have to be balanced critizicing morons from both left and right wing.

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Monday, July 9, 2007

A dismissed nightmare?

One of my complaints about futurism is that it is mostly done by wealthy older people (often males, but not necessarily) coming from developed societies with very different problems than most of the rest of humankind. I mean, yes, they come from where the wealth and the high technology come from, but they also belong to a tiny but noisy minority. I am among that minority too, even if to a lesser degree. Yes, they are very smart, but that does not means that they have more empathy than your average Joe. Their problems are not the same problems that face people who has not their basic needs covered. They cannot be sure if they are going to starve or not, neither if they are going to die from a nasty disease. To be sincere, those aren't my problems too, even if sometimes I cannot eat properly for a couple of days due to lack of money, but I have a network of friends and a family that supports me.

In any case, the different perspectives of the world that arise from different situations lead to different priorities. And most of the people thinking about the future of the world are from a minority with different priorities. I feel (This is in no way an objective observation) that they tend to be over-optimistic when addressing some of the problems that people in underdeveloped countries face. What is solved for them becomes automatically "easy" for the rest of the six billion of our fellow Homo sapiens sapiens. I was sparked by this to write papers and discuss about the future, as I think that for building a coherent picture of the future we must acknowledge the diversity of human beings that are building it. I think that being born and raised here gives me a slightly different perspective and could be useful to study the unintended consequences of technological developments.

Of course, not everybody is the same and a lot of people from the developed world has done a lot for us in the South, along us, getting their hands dirty. People like Norman Borlaug, who once said: "some of the environmental lobbyists of the Western nations are the salt of the earth, but many of them are elitists. They've never experienced the physical sensation of hunger. They do their lobbying from comfortable office suites in Washington or Brussels. If they lived just one month amid the misery of the developing world, as I have for fifty years, they'd be crying out for tractors and fertilizer and irrigation canals and be outraged that fashionable elitists back home were trying to deny them these things". Unfortunately, people like him are scarce everywhere.

So far I have tried to add what I see as a perspective form the South to my research, trying to make our problems widely known and thinking local what-ifs for new technologies. I do not know if I have been successful, but I have tried. I plan to use my forecoming trip to do exactly that, to shout to the world "Hey, we've got this problems!". On that subject I wrote a paper last year about the possible negative effects of perfect recycling. Yes, you read well. The problem would be not the perfect recycling and nanotechnology, but the exclusive use of that technology by the developed world, that from that point would not need any more raw materials for its industry because it would be able to fetch them from its huge junkyards, leaving us without our main income source.

Countries with a moderately developed industrial infrastructure could cope with that making huge efforts, but the ones who totally lack that infrastructure certainly would return straight to a pre-industrial society. No more fertilizers. No more drugs for curing diseases. No more fancy electronics. Those things would be impossible to manufacture anymore, and without anything useful to exchange we would be at the mercy of the developed world. Not a pleasant situation to live as you know. And without those things we would have to rape and destroy the environment with primitive agricultural techniques in order to live and many of us will die. No matter what the organic movement says, organic are not environment friendly when you have to feed several billion people from wasted land. I thought a lot about this and I arrived to the conclusion that a group of policies should be implemented in order to ensure that a minimum of technology is shared with us to prevent us from ravage whatever woods and resources still are existing by that time. However, I was not sure if the scenario I depicted was plausible, maybe this perfect recycling will always be SF, or nanoassemblers will never become true. Or suddenly the world is going to turn a better place and technology is going to be shared (yeah, right).

Preparing to attend the Scifoo I stumbled on a project by one of the attendees:
They say is about “wealth without money”, a macro universal assembler (OK, another name for a huge 3D printer, but still rocks!) that will be able to autoreplicate and construct a great diversity of things, with models you can create or download from the Internet. The models will tell the assembler how to create from bicycle helmets to chairs. Of course, some designs will be proprietary if the idea takes off, but eventually those proprietary designs will be back-engineered and copied. What will happen to global economy? I wish I knew, but fear mongers are talking about the destruction of it I do not think so, FOSS clearly show that people is still able to create good, professional and reliable products when no money is involved. For the sake of the creative process. Sure, a lot of people will say that they are not playing this game, and they have the right to refuse, but if with the RepRap we improve the living standards for billions, we would raise the numbers of potential creators, since well-fed healthy and happy people with the right tools is more prone to think on other things that survival (I am speaking from personal experience, my grades rose around 30% once I got my first second hand PC, when I was 20).

What I love about the RepRap is that is totally OS, you can improve it, you can create you own machine (well, you will once it is finished), your own designs, suited for your needs and problems. Maybe this will be a major milestone for an agalmic society and an example of the wild changes that are waiting for us in the case nanoassemblers become possible. But what I like the most about RepRap is that it takes off the clouds above my head. Maybe the nanoassemblers of the future will be OS and released by wealthy humane people that understands that helping to develop intellectual abilities is the best venture capitalism feat that they could ever do. You are skeptic about that? OK. Let’s calculate what’s the value in dollars of the Indian market and how much it saves to American companies thanks to outsourcing. now, tell me, how much of it would have been that way if Green revolution would have not existed?.

Sure, Green Revolution is not a Panacea. Even Borlaug acknowledges that. It is a patch that will work while the population is not too high and it also has undesirable side effects, but it’s better than the alternative. We need alternatives, we need to create new methods to stay alive, to live comfortably, to avoid catastrophe, and we would be far more successful if we had a few million people more working on urgent issues, rather than starving to death. Thanks to RepRap and its OS replication the environmental nightmare I foresaw might never come true.

But I still wonder...

PS: Now that I know that I have at least two Indian readers, I would like to ask them some questions, if they don’t mind.
1) Do you think that most of the policy making and planning on a global level and the scenarios about the future are biased and based on a US-EU point of view? Would it be a good thing if those studies included people from more diverse grounds?
2) What do you think about the RepRap? Do you think it would make a huge change or not?
Thank you very much for your comments!

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Sunday, July 8, 2007

More strange fusions: This time is Kraftwerk

Two year ago, shortly before I began to travel (yes, that was a milestone in my life and I refer to that frequently) I discovered Kraftwerk. I was in love with those pure sounds, sometimes a fast beat, but mostly paused notes, flowing, building a fresh, unadorned, but beatiful music. Besides, their lyrics, simple, but appealing, were something I liked, with mostly an optimistic and cheerful attitude to technology. And I was learning to code, my first useful (but very clumsy, as they are still now) programs are from that date.

And I dreamed about a better existence when I heard:

I program my home computer

Beam myself into the future


I'm the operator
with my pocket calculator

I could say my dreams have become reality in a certain way (I am real geek, I guess).
I liked a lot Kraftwerk's fusion of their electronic music with the Yodel in their song Autobahn, blending the old and the new. But now I have discovered an even more wild mix, featuring latin rythms, electronic music, Kraftwerk and colorful clothes.

It is Señor Coconut y su conjunto, these guys (Or this guy) remix Kraftwerk and blend it with latin music in turly innovative and funny ways. I even found to actually enjoy their music rather than just finding it amusing, as is often the case with these kind of covers. Anyway, this blend is unique, exciting and strange, but enjoyable, and it makes me feel at home, mixing the tropical rythms of my native culture (of one of my blend of cultures) with the high tech elements of other cultures that I crave for, giving birth to an astonding and creative synthesis.

Anyway, I have to go, gotta finnish the presentations and some code I am working in, but I leave this for those of you who are curious:

PD: Yes, it is more fun to compute!

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Saturday, July 7, 2007

I must say I am amazed

I have always liked Freeman Dyson. Well, at least his books.
His visions are poetic in a way I really like, mixing science and beauty in such a way that is mind blowing but intuitive at the same time.

Now, he has done it again:

Our Biotech Future
By Freeman Dyson
in The New York Review of Books, July 19, 2007

It has become part of the accepted wisdom to say that the twentieth century was the century of physics and the twenty-first century will be the century of biology. Two facts about the coming century are agreed on by almost everyone. Biology is now bigger than physics, as measured by the size of budgets, by the size of the workforce, or by the output of major discoveries; and biology is likely to remain the biggest part of science through the twenty-first century. Biology is also more important than physics, as measured by its economic consequences, by its ethical implications, or by its effects on human welfare.

These facts raise an interesting question. Will the domestication of high technology, which we have seen marching from triumph to triumph with the advent of personal computers and GPS receivers and digital cameras, soon be extended from physical technology to biotechnology? I believe that the answer to this question is yes. Here I am bold enough to make a definite prediction. I predict that the domestication of biotechnology will dominate our lives during the next fifty years at least as much as the domestication of computers has dominated our lives during the previous fifty years.

I see a close analogy between John von Neumann's blinkered vision of computers as large centralized facilities and the public perception of genetic engineering today as an activity of large pharmaceutical and agribusiness corporations such as Monsanto. The public distrusts Monsanto because Monsanto likes to put genes for poisonous pesticides into food crops, just as we distrusted von Neumann because he liked to use his computer for designing hydrogen bombs secretly at midnight. It is likely that genetic engineering will remain unpopular and controversial so long as it remains a centralized activity in the hands of large corporations.

I see a bright future for the biotechnology industry when it follows the path of the computer industry, the path that von Neumann failed to foresee, becoming small and domesticated rather than big and centralized. The first step in this direction was already taken recently, when genetically modified tropical fish with new and brilliant colors appeared in pet stores. For biotechnology to become domesticated, the next step is to become user-friendly. I recently spent a happy day at the Philadelphia Flower Show, the biggest indoor flower show in the world, where flower breeders from all over the world show off the results of their efforts. I have also visited the Reptile Show in San Diego, an equally impressive show displaying the work of another set of breeders. Philadelphia excels in orchids and roses, San Diego excels in lizards and snakes. The main problem for a grandparent visiting the reptile show with a grandchild is to get the grandchild out of the building without actually buying a snake.

Every orchid or rose or lizard or snake is the work of a dedicated and skilled breeder. There are thousands of people, amateurs and professionals, who devote their lives to this business. Now imagine what will happen when the tools of genetic engineering become accessible to these people. There will be do-it-yourself kits for gardeners who will use genetic engineering to breed new varieties of roses and orchids. Also kits for lovers of pigeons and parrots and lizards and snakes to breed new varieties of pets. Breeders of dogs and cats will have their kits too.

Domesticated biotechnology, once it gets into the hands of housewives and children, will give us an explosion of diversity of new living creatures, rather than the monoculture crops that the big corporations prefer. New lineages will proliferate to replace those that monoculture farming and deforestation have destroyed. Designing genomes will be a personal thing, a new art form as creative as painting or sculpture.

Few of the new creations will be masterpieces, but a great many will bring joy to their creators and variety to our fauna and flora. The final step in the domestication of biotechnology will be biotech games, designed like computer games for children down to kindergarten age but played with real eggs and seeds rather than with images on a screen. Playing such games, kids will acquire an intimate feeling for the organisms that they are growing. The winner could be the kid whose seed grows the prickliest cactus, or the kid whose egg hatches the cutest dinosaur. These games will be messy and possibly dangerous. Rules and regulations will be needed to make sure that our kids do not endanger themselves and others. The dangers of biotechnology are real and serious.

If domestication of biotechnology is the wave of the future, five important questions need to be answered. First, can it be stopped? Second, ought it to be stopped? Third, if stopping it is either impossible or undesirable, what are the appropriate limits that our society must impose on it? Fourth, how should the limits be decided? Fifth, how should the limits be enforced, nationally and internationally? I do not attempt to answer these questions here. I leave it to our children and grandchildren to supply the answers.

A New Biology for a New Century

Carl Woese is the world's greatest expert in the field of microbial taxonomy, the classification and understanding of microbes. He explored the ancestry of microbes by tracing the similarities and differences between their genomes. He discovered the large-scale structure of the tree of life, with all living creatures descended from three primordial branches. Before Woese, the tree of life had two main branches called prokaryotes and eukaryotes, the prokaryotes composed of cells without nuclei and the eukaryotes composed of cells with nuclei. All kinds of plants and animals, including humans, belonged to the eukaryote branch. The prokaryote branch contained only microbes. Woese discovered, by studying the anatomy of microbes in detail, that there are two fundamentally different kinds of prokaryotes, which he called bacteria and archea. So he constructed a new tree of life with three branches, bacteria, archea, and eukaryotes. Most of the well-known microbes are bacteria. The archea were at first supposed to be rare and confined to extreme environments such as hot springs, but they are now known to be abundant and widely distributed over the planet. Woese recently published two provocative and illuminating articles with the titles "A New Biology for a New Century" and (together with Nigel Goldenfeld) "Biology's Next Revolution."[*]

Woese's main theme is the obsolescence of reductionist biology as it has been practiced for the last hundred years, with its assumption that biological processes can be understood by studying genes and molecules. What is needed instead is a new synthetic biology based on emergent patterns of organization. Aside from his main theme, he raises another important question. When did Darwinian evolution begin? By Darwinian evolution he means evolution as Darwin understood it, based on the competition for survival of noninterbreeding species. He presents evidence that Darwinian evolution does not go back to the beginning of life. When we compare genomes of ancient lineages of living creatures, we find evidence of numerous transfers of genetic information from one lineage to another. In early times, horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time.

Whatever Carl Woese writes, even in a speculative vein, needs to be taken seriously. In his "New Biology" article, he is postulating a golden age of pre-Darwinian life, when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer.

But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell, anticipating Bill Gates by three billion years, separated itself from the community and refused to share. Its offspring became the first species of bacteria—and the first species of any kind—reserving their intellectual property for their own private use. With their superior efficiency, the bacteria continued to prosper and to evolve separately, while the rest of the community continued its communal life. Some millions of years later, another cell separated itself from the community and became the ancestor of the archea. Some time after that, a third cell separated itself and became the ancestor of the eukaryotes. And so it went on, until nothing was left of the community and all life was divided into species. The Darwinian interlude had begun.

The Darwinian interlude has lasted for two or three billion years. It probably slowed down the pace of evolution considerably. The basic biochemical machinery of life had evolved rapidly during the few hundreds of millions of years of the pre-Darwinian era, and changed very little in the next two billion years of microbial evolution. Darwinian evolution is slow because individual species, once established, evolve very little. With rare exceptions, Darwinian evolution requires established species to become extinct so that new species can replace them.

Now, after three billion years, the Darwinian interlude is over. It was an interlude between two periods of horizontal gene transfer. The epoch of Darwinian evolution based on competition between species ended about ten thousand years ago, when a single species, Homo sapiens, began to dominate and reorganize the biosphere. Since that time, cultural evolution has replaced biological evolution as the main driving force of change. Cultural evolution is not Darwinian. Cultures spread by horizontal transfer of ideas more than by genetic inheritance. Cultural evolution is running a thousand times faster than Darwinian evolution, taking us into a new era of cultural interdependence which we call globalization. And now, as Homo sapiens domesticates the new biotechnology, we are reviving the ancient pre-Darwinian practice of horizontal gene transfer, moving genes easily from microbes to plants and animals, blurring the boundaries between species. We are moving rapidly into the post-Darwinian era, when species other than our own will no longer exist, and the rules of Open Source sharing will be extended from the exchange of software to the exchange of genes. Then the evolution of life will once again be communal, as it was in the good old days before separate species and intellectual property were invented.

I would like to borrow Carl Woese's vision of the future of biology and extend it to the whole of science. Here is his metaphor for the future of science:

Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow.... It is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as stable, complex, dynamic organization.

This picture of living creatures, as patterns of organization rather than collections of molecules, applies not only to bees and bacteria, butterflies and rain forests, but also to sand dunes and snowflakes, thunderstorms and hurricanes. The nonliving universe is as diverse and as dynamic as the living universe, and is also dominated by patterns of organization that are not yet understood. The reductionist physics and the reductionist molecular biology of the twentieth century will continue to be important in the twenty-first century, but they will not be dominant. The big problems, the evolution of the universe as a whole, the origin of life, the nature of human consciousness, and the evolution of the earth's climate, cannot be understood by reducing them to elementary particles and molecules. New ways of thinking and new ways of organizing large databases will be needed.

Green Technology

The domestication of biotechnology in everyday life may also be helpful in solving practical economic and environmental problems. Once a new generation of children has grown up, as familiar with biotech games as our grandchildren are now with computer games, biotechnology will no longer seem weird and alien. In the era of Open Source biology, the magic of genes will be available to anyone with the skill and imagination to use it. The way will be open for biotechnology to move into the mainstream of economic development, to help us solve some of our urgent social problems and ameliorate the human condition all over the earth. Open Source biology could be a powerful tool, giving us access to cheap and abundant solar energy.

A plant is a creature that uses the energy of sunlight to convert water and carbon dioxide and other simple chemicals into roots and leaves and flowers. To live, it needs to collect sunlight. But it uses sunlight with low efficiency. The most efficient crop plants, such as sugarcane or maize, convert about 1 percent of the sunlight that falls onto them into chemical energy. Artificial solar collectors made of silicon can do much better. Silicon solar cells can convert sunlight into electrical energy with 15 percent efficiency, and electrical energy can be converted into chemical energy without much loss. We can imagine that in the future, when we have mastered the art of genetically engineering plants, we may breed new crop plants that have leaves made of silicon, converting sunlight into chemical energy with ten times the efficiency of natural plants. These artificial crop plants would reduce the area of land needed for biomass production by a factor of ten. They would allow solar energy to be used on a massive scale without taking up too much land. They would look like natural plants except that their leaves would be black, the color of silicon, instead of green, the color of chlorophyll. The question I am asking is, how long will it take us to grow plants with silicon leaves?

If the natural evolution of plants had been driven by the need for high efficiency of utilization of sunlight, then the leaves of all plants would have been black. Black leaves would absorb sunlight more efficiently than leaves of any other color. Obviously plant evolution was driven by other needs, and in particular by the need for protection against overheating. For a plant growing in a hot climate, it is advantageous to reflect as much as possible of the sunlight that is not used for growth. There is plenty of sunlight, and it is not important to use it with maximum efficiency. The plants have evolved with chlorophyll in their leaves to absorb the useful red and blue components of sunlight and to reflect the green. That is why it is reasonable for plants in tropical climates to be green. But this logic does not explain why plants in cold climates where sunlight is scarce are also green. We could imagine that in a place like Iceland, overheating would not be a problem, and plants with black leaves using sunlight more efficiently would have an evolutionary advantage. For some reason which we do not understand, natural plants with black leaves never appeared. Why not? Perhaps we shall not understand why nature did not travel this route until we have traveled it ourselves.

After we have explored this route to the end, when we have created new forests of black-leaved plants that can use sunlight ten times more efficiently than natural plants, we shall be confronted by a new set of environmental problems. Who shall be allowed to grow the black-leaved plants? Will black-leaved plants remain an artificially maintained cultivar, or will they invade and permanently change the natural ecology? What shall we do with the silicon trash that these plants leave behind them? Shall we be able to design a whole ecology of silicon-eating microbes and fungi and earthworms to keep the black-leaved plants in balance with the rest of nature and to recycle their silicon? The twenty-first century will bring us powerful new tools of genetic engineering with which to manipulate our farms and forests. With the new tools will come new questions and new responsibilities.

Rural poverty is one of the great evils of the modern world. The lack of jobs and economic opportunities in villages drives millions of people to migrate from villages into overcrowded cities. The continuing migration causes immense social and environmental problems in the major cities of poor countries. The effects of poverty are most visible in the cities, but the causes of poverty lie mostly in the villages. What the world needs is a technology that directly attacks the problem of rural poverty by creating wealth and jobs in the villages. A technology that creates industries and careers in villages would give the villagers a practical alternative to migration. It would give them a chance to survive and prosper without uprooting themselves.

The shifting balance of wealth and population between villages and cities is one of the main themes of human history over the last ten thousand years. The shift from villages to cities is strongly coupled with a shift from one kind of technology to another. I find it convenient to call the two kinds of technology green and gray. The adjective "green" has been appropriated and abused by various political movements, especially in Europe, so I need to explain clearly what I have in mind when I speak of green and gray. Green technology is based on biology, gray technology on physics and chemistry.

Roughly speaking, green technology is the technology that gave birth to village communities ten thousand years ago, starting from the domestication of plants and animals, the invention of agriculture, the breeding of goats and sheep and horses and cows and pigs, the manufacture of textiles and cheese and wine. Gray technology is the technology that gave birth to cities and empires five thousand years later, starting from the forging of bronze and iron, the invention of wheeled vehicles and paved roads, the building of ships and war chariots, the manufacture of swords and guns and bombs. Gray technology also produced the steel plows, tractors, reapers, and processing plants that made agriculture more productive and transferred much of the resulting wealth from village-based farmers to city-based corporations.

For the first five of the ten thousand years of human civilization, wealth and power belonged to villages with green technology, and for the second five thousand years wealth and power belonged to cities with gray technology. Beginning about five hundred years ago, gray technology became increasingly dominant, as we learned to build machines that used power from wind and water and steam and electricity. In the last hundred years, wealth and power were even more heavily concentrated in cities as gray technology raced ahead. As cities became richer, rural poverty deepened.

This sketch of the last ten thousand years of human history puts the problem of rural poverty into a new perspective. If rural poverty is a consequence of the unbalanced growth of gray technology, it is possible that a shift in the balance back from gray to green might cause rural poverty to disappear. That is my dream. During the last fifty years we have seen explosive progress in the scientific understanding of the basic processes of life, and in the last twenty years this new understanding has given rise to explosive growth of green technology. The new green technology allows us to breed new varieties of animals and plants as our ancestors did ten thousand years ago, but now a hundred times faster. It now takes us a decade instead of a millennium to create new crop plants, such as the herbicide-resistant varieties of maize and soybean that allow weeds to be controlled without plowing and greatly reduce the erosion of topsoil by wind and rain. Guided by a precise understanding of genes and genomes instead of by trial and error, we can within a few years modify plants so as to give them improved yield, improved nutritive value, and improved resistance to pests and diseases.

Within a few more decades, as the continued exploring of genomes gives us better knowledge of the architecture of living creatures, we shall be able to design new species of microbes and plants according to our needs. The way will then be open for green technology to do more cheaply and more cleanly many of the things that gray technology can do, and also to do many things that gray technology has failed to do. Green technology could replace most of our existing chemical industries and a large part of our mining and manufacturing industries. Genetically engineered earthworms could extract common metals such as aluminum and titanium from clay, and genetically engineered seaweed could extract magnesium or gold from seawater. Green technology could also achieve more extensive recycling of waste products and worn-out machines, with great benefit to the environment. An economic system based on green technology could come much closer to the goal of sustainability, using sunlight instead of fossil fuels as the primary source of energy. New species of termite could be engineered to chew up derelict automobiles instead of houses, and new species of tree could be engineered to convert carbon dioxide and sunlight into liquid fuels instead of cellulose.

Before genetically modified termites and trees can be allowed to help solve our economic and environmental problems, great arguments will rage over the possible damage they may do. Many of the people who call themselves green are passionately opposed to green technology. But in the end, if the technology is developed carefully and deployed with sensitivity to human feelings, it is likely to be accepted by most of the people who will be affected by it, just as the equally unnatural and unfamiliar green technologies of milking cows and plowing soils and fermenting grapes were accepted by our ancestors long ago. I am not saying that the political acceptance of green technology will be quick or easy. I say only that green technology has enormous promise for preserving the balance of nature on this planet as well as for relieving human misery. Future generations of people raised from childhood with biotech toys and games will probably accept it more easily than we do. Nobody can predict how long it may take to try out the new technology in a thousand different ways and measure its costs and benefits.

What has this dream of a resurgent green technology to do with the problem of rural poverty? In the past, green technology has always been rural, based in farms and villages rather than in cities. In the future it will pervade cities as well as countryside, factories as well as forests. It will not be entirely rural. But it will still have a large rural component. After all, the cloning of Dolly occurred in a rural animal-breeding station in Scotland, not in an urban laboratory in Silicon Valley. Green technology will use land and sunlight as its primary sources of raw materials and energy. Land and sunlight cannot be concentrated in cities but are spread more or less evenly over the planet. When industries and technologies are based on land and sunlight, they will bring employment and wealth to rural populations.

In a country like India with a large rural population, bringing wealth to the villages means bringing jobs other than farming. Most of the villagers must cease to be subsistance farmers and become shopkeepers or schoolteachers or bankers or engineers or poets. In the end the villages must become gentrified, as they are today in England, with the old farm workers' cottages converted into garages, and the few remaining farmers converted into highly skilled professionals. It is fortunate that sunlight is most abundant in tropical countries, where a large fraction of the world's people live and where rural poverty is most acute. Since sunlight is distributed more equitably than coal and oil, green technology can be a great equalizer, helping to narrow the gap between rich and poor countries.

My book The Sun, the Genome, and the Internet (1999) describes a vision of green technology enriching villages all over the world and halting the migration from villages to megacities. The three components of the vision are all essential: the sun to provide energy where it is needed, the genome to provide plants that can convert sunlight into chemical fuels cheaply and efficiently, the Internet to end the intellectual and economic isolation of rural populations. With all three components in place, every village in Africa could enjoy its fair share of the blessings of civilization. People who prefer to live in cities would still be free to move from villages to cities, but they would not be compelled to move by economic necessity.

[*] See Carl Woese, "A New Biology for a New Century," in Microbiology and Molecular Biology Reviews, June 2004; and Nigel Goldenfeld and Carl Woese, "

I really, really find this piece provocative, disturbing but profoundly beautiful at the same time.

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Tuesday, July 3, 2007

India is exposed to moral degradation

From BBC:

A vibrating condom has sparked a fierce debate in India, over whether it is a sex toy - which are banned - or a means of birth control.

The controversial condom has caused outrage in the state of Madhya Pradesh, because a government-owned company is involved in marketing it.

The pack of three condoms, branded as Crezendo, contains a battery-operated ring-like device.

Critics say it is in fact a vibrator, and should therefore be banned.

Sex toys and pornography are illegal in India.

It seems that hypocrisy and the obsession about controlling sexuality are monopoly of the west.

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Well, here I am.
I should be sleeping or working, not posting.
But I am indeed connected.
I have only two weeks to prepare a lecture about the maths I am already using for my thesis, the presentation for the student meeting associated to TV07 and the one(s) for Scifoo, besides taking care of my brother and finishing a preliminar model that I shall show to my thesis advisor before I leave for the US.

These will be two very busy weeks, but they will be worthy.

I feel I am on a roller coaster tonight.

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