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a crack in the ice - First simulation of a life form.

Mar. 28th, 2006

11:16 am - First simulation of a life form.

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In the journal Structure (doi:10.1016/j.str.2005.11.014) five researchers from the University of Illinois, Urbana-Champaigne report "the first all atom simulation of an entire life form, satellite tobacco mosaic virus, albeit an extremely primitive one with an artificial nucleotide sequence." This is an exciting announcement; my own simulations, however, predict this story will undergo rapid inflation when exposed to journalism.

Tobacco mosaic virus is the reason many gardeners who smoke do not smoke in their garden. Humans, even smokers, cannot 'get' tobacco mosaic virus, but in smoking and handling tobacco products, they can 'give' tobacco mosaic virus to their plants -- particularly to tomato plants (tobacco and tomato are both in the Solanaceae or nightshade family.) One reason many researchers study the virus is the big plus that the virus poses no threat to researchers (tomato gardens aside). Another is that it is really easy for researchers to make more of it, whenever they want, from some infected plants. It is an extremely simple 'life form', apparently made up of 61 proteins and a pamphlet-sized string of RNA.

It appears that what they simulated was the structural properties of the viral body in water under different temperature conditions. You can think of it as being akin to a computational reconstruction of the collapse of the World Trade Center, that takes no account of the interactions of the people or stuff inside. Of course, this *is* a virus. Presumably there isn't a bunch of stuff inside, the virus's protein coat and RNA payload are pretty much all it has got. (There are illusions in the article to a single 'mystery protein', though; hopefully some reader expert in virology can tell us more about that.) And anything that helps us learn more about viruses is a good deal, because it certainly seems that most viruses are not on our side.

Still it should be recognized that the simulation of the internal workings of any whole organism -- all the activities and interactions of proteins and metabolites; all the internal work and signalling -- is still quite far off. According to one of the team members, Klaus Schulten, "it could still be a long time before scientists can simulate a digital dog wagging its tail." (quote from LiveScience.com) Understated humor. It will still be a long time before scientists can deeply simulate a protozoon wagging its flagellum...

Comments:

From:(Anonymous)
Date:April 26th, 2006 03:14 pm (UTC)

Genetically Modified food

(Link)
Farmageddon, Frnakenfoods, and the FDA: The Dangers of genetically Modified Food.

Would you mind reading and commenting on this article? Thanks!

http://www.drstevebest.org/papers/vegenvani/farmaggedon.php

Snippet from article:

In May 1999, entomologist Dr. John Losey from Cornell University published a shocking study in Nature. In a laboratory setting, he found that 44% of monarch caterpillars died within four days when they consumed milkweed plants -- the staple of their diet -- dusted with pollen from "Bt" corn genetically engineered with a bacterium (Bacillus thuriniensis) to kill the European core borer. Other butterflies were stunted in their growth, but those who consumed regular crop pollen survived unharmed. What will be the fate of butterflies in a world planted by Monsanto and Novartis? What will be the environmental consequences of the genetic drift of Bt corn pollen (which could contaminate not only milkweed plants but also "organic" crops)? What might be happening to human beings who already are consuming a steady diet of Bt corn crops? And why was this study done after the government approved the use of Bt genes that were fused into a third of the U.S. corn crop?

In October 1999, Dr. Arpad Pusztai and Dr. Stanley Ewen published a more disturbing report in Lancet. Their controversial study showed that over a period of 110 days (equivalent to 10 years in human time), rats fed potatoes genetically engineered to produce an insect-repelling chemical (a plant-derived compound called the "snowdrop lectin") and using a common vector (the Cauliflower Mosaic Viral Promoter [CaMv]), suffered damage to their vital organs, immune system, and digestive tract, results which did not occur to rats fed ordinary potatoes. The researchers concluded that the viruses used in the gene-altering process made the potatoes toxic. Another study found that CaMv "has the potential to reactivate dormant viruses or create new viruses in all species to which it is transferred. This transgenic instability increases the possibility of promotion of an inappropriate over-expression of genes to the transferred species" which could lead, among other things, to cancer.


From:tdhoufek
Date:April 26th, 2006 10:34 pm (UTC)

Re: Genetically Modified food

(Link)
I did take the time to read Dr. Best's article,
Farmaggedon, Frankenfoods, and the FDA: The Dangers of Genetically Modified Food".
My own position on the genetic modification of food is somewhat more ambivalent. I am certainly skeptical of blanket assurances by the FDA. Modern methods of genetic modification do substantially differ from more trusted selective breeding practices, and I do not doubt that significant dangers could await us here.

The hitch: it is not always possible or desirable to avoid danger. Driving an automobile is dangerous in a very personal and obvious sense, but rapid transport is so desirable that almost everyone tolerates the danger. It is possible that benefits of genetically modified foods could outweigh the dangers, even if the dangers sometimes include illness, death, and irreversible and undesirable effects on the environment. After all, this is food we are talking about. Significant increases in yields, and concommitant decreases in costs, can improve the lives of billions of people. We accept the risks of fatal food allergies in many natural foods (shrimp, fava beans, etc); note also that genetic modification might be used to address serious natural food allergies.

However, there is no question that GM food is immensely profitable, and that the companies involved in producing and purveying them are immensely powerful. As such, I think we would be prudent to hold the producers and purveyors genetically modified foods to higher regulatory standards. I am not sure we can trust regulatory standards administered centrally by a federal government with oligarchical tendencies. Perhaps the simplest satisfactory answer IS to slam the door on commercialization of genetically modified strains. But can the door even be slammed? Will not genetically modified organisms just become an active line of black market activity?
From:(Anonymous)
Date:June 26th, 2006 02:57 pm (UTC)

Re: Genetically Modified food

(Link)
Eeek. That one again. We covered that first paper as required reading in a graduate genetics course. It has several significant procedural flaws. I am not familiar with the second paper, but even if completely valid, it doesn't address the basic issue. Genetically modified foods are a line-drawing issue. Where do we draw the line for presumed safety and where do we require testing.

Government regulated testing is not without cost. It provides a huge barrier to anyone except the largest corporations from developing products, and it provides rules which, if followed, essentially prevent legal recourse if a problem does occur. It also delays innovation, which in the realm of food stuffs genuinely means people starve and die. Likewise, unregulated industries are not actually unregulated. Because of general regulations on providing harmful products, no company will provide a product that is dangerous, unless they feel the benefits outweighs the risks. The real question is: Who is better at finding the best line between benefit and cost. A single large government body, or the distributed optimization performed by businesses. I think the drawbacks for large government management is clearly shown by the suffering that exists in many countries that rely only on the government for economic development.

That said, I do believe that some general guidelines are necessary. I'm not sure what actually exists, but I think it should be something like the enforcement bodies that police meat packing, restaurant sanitation, etc. Not product by product review, but a "code of ethics" that gets rated, allows buyers to make an informed choice, and if broken make it obvious that a company is behaving badly. This body should have the authority to step in if evidence accumulates that a product is dangerous and a company is not taking appropriate action. Without freedom, an individual has no value. The same applies to a business entity. Some level of trust is required. But never blind trust. Human nature being what it is, there always needs to be somebody carrying the big stick.

I do think there are problems with the way business are allowed to use their patents in predatory ways, but that is a separate rant.

Stuart Jefferys.
From:(Anonymous)
Date:June 26th, 2006 03:30 pm (UTC)

Re: Genetically Modified food

(Link)
Upon rereading my previous post, realize I left a poorly justified criticism hanging. I don't want to imply that the monarch larvae paper was wrong in its details, but I did mean it was incomplete.

You can kill rats by feeding them enough of almost anything. The amount of pollen consumed by the monarch larvae was "visually comparable". That has the same problem as saying our results "looked" significant. Given the ability of people to fool themselves, one of the basic principles of science is measurement! Risk assessment is based on (hazard X exposure). Given the level of litigation in our society, this is something done every day for almost everything. Nothing is free of risk. If its hard, it can fall on someone's head and kill them. If its soft, you could suffocate on it by stuffing it down your throat. Silliness aside, most things have only a low hazardous potential, so even with high levels of exposure, little risk ensures. Some things have a high level of risk, but low exposure. Giant meteors plummeting from the sky. A huge nuclear explosion that is occurring right now, thankfully 92 million miles away. Some things that have both high levels of risk and lots of exposure are allowed anyway because it is so important to our society. Using the car example from above, I know several people with life-long injuries from car accidents. But I'll keep driving.

The paper did not address issues of exposure. What about the distribution of the pollen, or selective feeding by the monarch larvae. Pollen is surely more concentrated in plants on the edge of the corn field, but what about 200 ft away? 2000 ft away? How much of the monarch food plants are within the high density range? Maybe they only grow within 10 feet of corn fields. That would be bad for monarchs. I doubt that, but without an investigation, I can't say. On the matter of choice, if given both highly pollen covered leaves and cleaner leaves, do the monarch larvae still eat the highly pollen covered leaves? If they avoid them unless faced with starvation, this is surely a mitigating factor.Someone should (and probably has) checked these and similar issues. Only after both risk and exposure are evaluated can a full risk assessment be made.

Finally, I believe (although I do not remember for sure) that the version of bt modified corn tested was not the final product. I think there was a different version driven by a promoter that produced less of the toxic compound in the pollen anyway.

The process of science is based on a careful examination of all the aspects of an issue, or at least should be. The above quoted papers are both from 1999, which was when the flurry of scientific papers published on the health and environmental consequences of genetically modified foods started appearing. Being quick to publish potentially important information often overrides in the short term the need for completeness, although there is some responsibility on the part of the early publishing scientist for stressing the tentative and unconfirmed nature of their findings. In the long term, only complete and careful considerations should be used for long-range decisions, not the first tentative investigations. These can't be the only papers in the field. Why are they still the ones being used as discussion points. What is the state of the art now? Seven years is a long time.

Stuart Jefferys
From:calebzwick
Date:October 17th, 2008 10:17 am (UTC)
(Link)
But they don't want that. They just want the Gold Card, and they want someone else to make the payments.
From:elihins
Date:October 17th, 2008 08:42 am (UTC)
(Link)
But if we broke it, doesn't that mean we can fix it too. So we're going to solve our problem, and we're going to start by saying "yes" to the notion that government can be better than it is.
From:marlinmorche
Date:October 17th, 2008 04:57 am (UTC)
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What will be the environmental consequences of the genetic drift of Bt corn pollen (which could contaminate not only milkweed plants but also "organic" crops).