Genetic Stone Soup

It's the scientific achievment of our generation; what can you say about the mapping of the human genome? But here's a story behind the story. parvati turned us on to this NYT article about James Kent, who wrote the gene assembly program GigAssembler last June. It turns out that, thanks to his code, the public Human Genome Project had actually finished its work three days before the private effort by Celera Genomics -- a feather in their cap and a boon to public science. The head of Celera was "astonished" to learn of this grad student's genius -- ten thousand lines of C in a month, and why? -- "because of his concern that the genome would be locked up by commercial patents if an assembled sequence was not made publicly available for all scientists to work on." (The debate over public vs. private science continues to rage; see this Seattle P-I article, which discusses among other things the ethics of NDA'ing scientific data produced for profit.)

Update: 02/13 02:26 PM by J : Thanks to tlunde for finding the link to GigAssembler and thus clarifying which language it was written in.

Comments

Re:What about the anti-genetic backlash?

[rlk]

What happens is they set up one or two of the richest farm owners with thier patented grow twice as fast corn or wheat. These farmers then have a large advantage over all of the family farms that did not get the mansanto handout. The monsanto farmer then buys out the smaller farmers. When the mansanto farmers own most of the farmland mansanto then raises the price of thier grain (which by the way cannot reproduce) and the large farmers are forced to sell out to a large agricorp.

Why? They could always buy their grain from a different supplier. And if they've managed to get themselves locked in to a contract which allows Monsanto to raise their prices at their whim then that's a foolish move and these farmers are reaping what they have sown.

This reminds me of Pastor Niemoller's words. If Monsanto drives out the local suppliers, then the farmers don't have a choice who to do business with. As for their "foolish moves", I don't think it's either a stretch or unfair to say that farmers in developing countries lack the business acumen and strategic foresight that Monsanto has, and it's not realistic to expect that they can do business on the same playing field as Monsanto. Remember that a "free market" assumes good knowledge on both sides of the transaction; if one side has all the knowledge and the other doesn't understand what's going on, it's not a free market any more, but rather a scam.

The same applies to Chinese farmers buying GM food. You talk about doing research on issues such as disease resistance. Precisely how, pray tell, are they going to do such research? Assuming they even know about the genetic basis for disease resistance, and that crop diseases in the US differ from those in China, you're assuming that they have the resources to do this kind of investigation.

It's not only governments that can oppress. Anywhere that there's an excessive concentration of power there can be oppression. It's not a matter of duly constituted laws and sovereign states (most dictatorships have neither; Saddam Hussein rules by personal whim and doesn't have too much respect for borders of neighboring states). If Monsanto's doing this kind of divide and conquer in Latin America, it's no better than if it's a government doing the same thing.

In Germany they first came for the Communists and I didn't speak up because I wasn't a Communist.

Then they came for the Jews, and I didn't speak up because I wasn't a Jew.

Then they came for the trade unionists and I didn't speak up because I wasn't a trade unionist.

Then they came for the Catholics and I didn't speak up because I was a Protestant.

Then they came for me and by that time no one was left to speak up.

Possible Slashdot interview??

[moonboy]

How about trying to get an interview with this guy? Could be very interesting.

His previous animation work

[jfoust2]

Jim Kent was once known in the mid-80s for writing Zoetrope, a 2D path-based animation system for the Atari ST, not unlike today's Flash technology. Zoetrope also became Aegis Animator on the Amiga, and Autodesk's Animator Pro for the PC, which begat the .FLI/.FLC animation format. I believe Kent also worked on the first DOS generations of Autodesk's 3D Studio, too.

Re:Grad Student?

[KaRll]

I am more concerned with this kind of projects being run by commercial enterprises. Just because you can make money out of it doesn't make it right.

Re:What about the anti-genetic backlash?

[Zara2]

Man you chose a really bad company to base your argument on. Mansanto is very well known for a lot of underhanded tricks re: frankenfood. On the surface I am not agianst GM food. Actually I see a lot of good things coming from it. However Mansanto will go down to a small south american country and completly bankrupt it. What happens is they set up one or two of the richest farm owners with thier patented grow twice as fast corn or wheat. These farmers then have a large advantage over all of the family farms that did not get the mansanto handout. The monsanto farmer then buys out the smaller farmers. When the mansanto farmers own most of the farmland mansanto then raises the price of thier grain (which by the way cannot reproduce) and the large farmers are forced to sell out to a large agricorp. Much like the ones mansanto owns a lot of stock in. Now all the local farmers are reduced to basically being wheat pickers.

Also on top of this GE food has never had to pass any serious tests of it. Whole crops were wiped out in china because the GE food had disease immunities from the western world. China has a slightly different set of crop diseases and *poof* there goes the rice. Please do your research into how things are done and not just hope that people are doing the things that they should be. While this is a "anti frankenfood" site it does have some good info in it. http://www.purefood.org/monlink.htm

Gene Patents value overhyped?

[Alien54]

On theNewsHour, PBS had a story on this the past day or so. They have a large webpage with many links dedicated to the whole issue. One thing that is interesting is that there are fewer genes than had been first imagined. The end result is that the genes are more often like a multi-purpose module, and that much of the functionality of the system is in the proteins system such as enzymes, etc. As it was noted:

What's going to happen is we have to go into the protein world to really understand where the genome is taking the next level of biology. That's ten times as complex at least.

What is also noted is that the combination of these protein interactions is staggeringly more complex. I can imagine that the system interactions may be a million times or more complex.

So in my mind, patenting a gene might wind up being similar to patenting the management system of a nuclear power plant, and thinking that therefore you understand nuclear physics.

Re:What about the anti-genetic backlash?

[SubtleNuance]

Im a Tree-Hugger of the highest order. Although I do know that Monsanto's GMOs are getting a 'bad rap'.. let me assure you: Most people's concerns w/ Monsanto are not only the idea that you have 'Frankenfood'. There is a whole group of ideas about why 'Monsanto' is evil:

1) Produce GMOs that rely on Monsanto produced chemicals. Further enslaving the Farmer to ecologically unsound farming methods and Monsanto's pocket book. Read: Roundup Resistant Crops.

2) Being a generally massive producer/marketer of Farming Chemicals. Closely related to Item #1, but worth mentioning in a broad sense.

3) Actively participating in the 'mono-culture' momentum that will produce the next Irish Potato Famine & contribute to the general degradation the biodiversity of the planets food supply.

And more generally - Tree Huggers like myself are generally in favour of a broad, local, varied sources of food as apposed to the Monsanto Backed "New Age of Industrial Farming".

When MadCowDisease reaches The Americas which method will be more likely to preserve our food supply? A) 'Industrial' Farming B)Broad, Scaled, Varied, Local Farming... For many reasons this is a Good Thing(TM). Monsanto is the epitome of the industrialization/commodidizaion of the Planets Food Supply. They operate for the benefit to the Bourgeoisie who own stock - not the good of the planets people (which should be pretty relevant when talking about *FOOD*. Their growing strength represents a general 'problem' with our future (not completely described above).

I am not a Luddite by any sense, but I do not see the value in a 'for profit' company producing GMOs for the benefit of their pocketbooks... this 'unholy' motivation will *NOT* lead to the benefits most of us understand will come from GMOs... it is a matter of motivation. They are more likely to risk our food supply based on profit returns - its not simply a concept of people scared of GMOs.

I have no problems with responsible, open, IP free GMO research/production by people with without compromised motivations. That is *NOT* Monsanto.

Things are not as easy

[jw3]

As many of you probably know, the actual work hasn't started yet. The schedule of a genome project looks like that:

a) sequencing, that is -- getting the actual sequence. This is almost purely technical work, and definitely not very interesting for a scientist, although you can get a lot of credits for it.

b) annotating the sequence: finding out where are the genes, what are the similarities between them and between the genes known from another organisms, and what can be suggested about their function based on those similarities. This is pure bioinformatics stuff: first finding the "open reading frames" (ORFs), that is -- anything that can be a gene at all: it has to start with an "ATG" (codon for metionine) and stop with a so-called stop codon. This is only the most basic criterium.

Whatever comes later is called "postgenomics", and it is probably the most exciting stuff in this whole area of reasearch.

1) in most of the genome projects which were done until now, as much as half of the proposed genes had not even a rough function assigned to them. (the group I'm working in sequenced a bacterial genome back in 1996, and during that time the situation hasn't changed much). Experimental work and more biocomputing is needed to find out what those genes do. The problem with biocomputing isn't the lack of CPU, but the lack of good strategies / models / theory (or, not lack of "good", but lack of "better" strategies etc.).

2) knowing what a gene does is, contrary to the common belief, only very little information. You need to know how it is regulated, and this means a lot of tedious and complicated experimental work: two hole areas of postgenomic science deal with that -- transcriptomics (regulation on RNA level) and proteomics (on protein level). You have to understand that each gene is regulated on many levels -- transcription of the gene from DNA to RNA, turnover (that is, the speed of degradation) of the mRNA, speed of translation, amino acid composition of the protein, protein turnover. Moreover, the genes are interconnected into networks rather then pathways. Creating a functioning model of an eukaryotic cell will be probable impossible during the next twenty or so years. That is -- among other things -- my group works with a little bacterium, which has only +- 700 genes. And even though it is a couple of orders of magnitude more simple then the simplest eukaryotic cell, it is very, very, very complicated.

Take-home lesson: don't be too enthusiastic. This is not the flight to the moon. This is only the first Sputnik.

Best regards,

January Weiner