Oligo

Genes have a promoter region, which is a stretch of DNA sequence that can bind proteins like RNA polymerases and transcription factors essentially controlling the expression of the gene, and a coding region, which is a stretch of sequence that describes the amino-acid sequence of the protein to be produced. In the knock out tomatoes, the coding region has been truncated so that the gene now expresses just a small bit of trash instead of the spoilage enzyme. But again, think about plant breeding, which has been done for thousands of years without ill effect (and without public outcry and without regulation). In modern plant breeding, ionizing radiation has been used to produce new and exciting variants of plants. Essentially the radiation works so that it mutates either the coding or promoter region of the plant genes, totally at random. Then you just select the interesting variants for further breeding and so on. I could produce the knock out tomatoes purely with this kind of plant breeding (just select the one with the spoilage gene knocked out by the radiation) and nobody would mind. With genetic engineering techniques we can go from random radiation and other breeding techniques to accurate modification of the plant or animal DNA with the precision of a single base pair. With genetic engineering, we actually know what we are doing. Ironically you are now opposing the specific technique and advocating the totally random technique. Interesting link on modern plant breeding (no GMO).

If you're so damn concerned about combinatorics, you sure as hell aren't considering selective plant or animal breeding enough. What about Boysenberry? That's a hybrid between raspberries, blackberries and loganberries. That's a new species with thousands of new genes, it has been around since 1923 and it hasn't taken over the world. No crop in the world is natural, they are all creations of selective breeding and hybridisation with cross-pollination. These species have random combinations of tens of thousands of genes. Yet, there have been no problems. All we have managed to produce are plants more dependent on us, not less. The things I know about genetic processes have convinced me that I could not make a weed that would spread across and suffocate Sweden, even if I wanted to. Seriously, all the outbreaks of species in nature we have seen have been caused by the introduction of exogenous species to some place, not by some subtly altered variant of an endogenous species. You know, we are not really introducing new species, since GMOs (which have only a few new genes at most) are perfectly capable of cross-breeding with the original variant. Thus they should be called GMO variants, since the definition of a species is that it cannot cross-breed with other species. The only new species that get introduced into the environment are new species created with traditional plant or animal breeding schemes and the transport of species from one place to another by humans.

We know for a fact exactly (by analysing the mRNA expression profile of the tomato plant) that this one gene produces only one protein with a certain sequence. In knock out tomatoes, the coding part of the gene has been deleted, but not the surrounding regulatory region. The deletion obviously did not cause production of toxins or carcinogens, since animal tests have proven that the properties of these tomatoes are exactly the same as the properties of regular tomatoes (same lethal dose). Nor did this deletion affect the "DNA validation wetware" as you call it, since we pretty much know how DNA damage is repaired in eucaryotes and the deleted protein had nothing to do with it. Besides, having a high mutation frequency is a competitive disadvantage in nature. You can test this yourself: Irradiate plants with gamma rays (this introduces mutations) and see whether the irradiated plants can outcompete their unirradiated peers. But I can point out the evidence for you: GMO crops are routinely cultivated in U.S. in actual fields. I haven't noticed the eco system crashing down faster than it already did...

The issue of modified plant species escaping into the environment is something the opponents of GMO plants always bring up without understanding a few basic facts: 1. Nothing in this world is truly separate from the environment, 2. GMO species are already cultivated in the U.S. so their "escape in to the world" has happened already and 3. the genes that have been introduced into the GMO plants are natural genes from different species, thus they are already present in the environment. Besides, I know of many experiments done in countries with free legislation, where insane amounts of GMOs have been dumped into the environment without any harmful result, but lots of beneficial results, especially in the area of environmental clean up. About the plants that produce their own pesticide: Into these plants, a gene from an insect virus (Baculovirus) has been introduced. This gene codes for a protein, which can form holes in the surface of the digestive tract of some insects (=dead insect). This gene has been present in the nature for ages, baculoviruses are probably much older than humans. Yet, insects have not developed a resistence to the porin gene. Also, if the insects did develop a resistence to porin producing GMO plants, it would not make any difference, except maybe to the cash flow of the company producing the GMO seeds. Remember that insects becoming resistent to chemical pesticides has not stopped us using chemical pesticides. DDT still saves lives in the third world (and that is some bad shit). And finally, about the motivation of the scientists developing GMO crops: Scientists need money to work (like we all do) and what best funder but a commercial company. If such products as Golden Rice or RoundUp resistant plants are made with such obvious benefits to the whole humankind, I don't care whether the motivation of the scientists is greed, altruism or the will to play god. As a researcher in biotechnology, I find it insulting that our moral values are always questioned. People think that you have to be a greedy bastard to be in biotech...

Hellfish6, here are some points: Me saying "greenpeace sucks arse" just reflects my frustration and like you noticed, it was written under the clause "in my opinion". I used to like greenpeace, but then I realized that they oppose everything new just for the sake of opposition, since their arguments are always designed to make the average Joe alarmed. Their opposition of the Golden Rice for example is ridiculous: They say that since you can only get about 8% of your daily recommended intake of vitamin A from Golden Rice, it is not worth eating. Answer me this, is it better to get 8% than nothing? About Pierre down the road, well, where do you think Pierre gets his seeds? Since nobody anywhere I believe is farming the natural variants of edible plants, but the variants produced by thousands of years of selective plant breeding, Pierre buys his seeds from seed companies every once and a while in order to keep his plants maximally producing. So Pierre down the road could buy his seeds from Monsanto and farm away, thus enabling you still to buy your veggies from Pierre. Remember that if Pierre uses glyphosate resistant GMO seeds he can use environmentally friendly pesticide which does not screw up nature like the other pesticides do.

I'm not being sarcastic and yes, there are theoretically two ways such transfer could be possible: 1. If cross-pollination of for example a weed with pollen from GM plants were to produce viable offspring, this offspring could have the extra gene in it. Such offspring would probably be sickly as compared to the parent plants (conflicting genes and such) and would probably lose in competition in nature. Also, if genetic exchange with cross-pollination would be commonplace in nature, there would be a lot of cases of food poisoning (people eating plants with toxin generating genes transferred from toxic plants). 2. Some plant viruses and bacteria can pick up DNA from their host and transfer it to a new host as they infect a new plant. This is probably also quite rare, since genetic exchange between plants seems to be quite rare in nature (see above). You also have to remember that nature is a master of adaptation to competition meaning that the species we find in nature are pretty damn well optimized for survival. It is my personal opinion that we could not (currently) generate an überplant even if we tried our damnest to do it. We can only improve on areas the nature is not interested in improving, like suitability for human consumption and farming properties.

Okay, here is my rant on GMO plants. I'm trying to make it an objective one. Typical multi-celled eukaryotic organisms like humans and soy beans have around one billion base pairs (bp) of DNA, give or take a few orders of magnitude. A typical gene is a stretch of sequence of about 500 to 10000 bp in length. The chemical structure of DNA in all organisms is the same, it's the sequence of the four bases (A,G,C,T) that is different. However, the sequence homology between different species is astounding, especially in the case of "household genes", the most numerous of genes, which are responsible for basic metabolic processes. Furthermore, since the genetic code is degenerate (many different words can mean the same thing), the functional homology between different species is even greater than the sequence homology. One big happy family. Now, what we do in genetic engineering is take one or a few of those 500-10000 bp genes and transfer them from one organism to another or we destroy one or more genes to make the organism function better for us. Examples: Tomatoes spoil easily, because tomatoes have a gene, which codes for an enzyme which hastens the spoiling of the tomato. Obviously the tomato needs this gene in order to compete better against other plants or it wouldn't have it. We humans surely don't want rapidly spoiling tomatoes, so we have engineered a tomato called "FlavrSavr" in which that one gene has been deleted. So this species is better for us, but weaker in competition against other plants. No risk of übertomatoes developing here, right? Rice does not have vitamin A. People who mostly exist on rice diets have a lot of vitamin A deficiency (ceuses blindness). By introducing three new genes to rice (two from a flower species, one from a species of bacteria), researchers have been able to get a species of rice which has A vitamin in it (Golden Rice). Unfortunately it currently does not have enough of it to make a major nutritional impact (it can only provide 8% of the daily recommended intake), but research is ongoing. These three new genes offer the plant only an extra energy expediture, so Golden Rice is at a competitive disadvantage in nature. No chance of überrice developing, right? Plants can get frostbite and die, every northern farmer knows this. Frostbite is caused by the crystallization of water (ice) inside plant cells in low temperatures, which causes disruption of the cell machinery. With genetic engineering we can introduce one gene from certain fish to certain plants. This gene codes for a protein, which, when present, inhibits water crystal formation in cells. Thus the cold tolerance of these plants is better than that of the normal plants (but not infinite). Therefore these plants could fare better against other plants in nature in very cold areas. However, producing the protein in every cell consumes a lot of resources, which is a competitive disadvantage for the plant. Could überweeds take over if they got a hold of this gene? Weeds are killed from fields by the use of pesticides, which do not harm the plants being cultivated, but also do not rapidly break up in nature. Glyphosate is a pesticide, which kills all plants and breaks up in nature very rapidly (soil bacteria eat it). With genetic engineering researchers have introduced a gene to some plants (like soy beans), which makes them resistant to glyphosate. Thus fields can be treated with glyphosate and only weeds are killed. The gene, of course, is a metabolic burden to the planty that carries it. Could überweeds take over if they got a hold of this gene? In order to better judge the last two questions, you have to consider such thing as antibiotic resistance of bacteria. When subjected to antibiotics, some bacteria pick up antibiotic resistance genes from the environment or get them by mutations of their own genome. But once the antibiotics are taken out (and this has been proven several times), the bacteria start kicking out the resistance genes, since having them in an environment free of antibiotics is a waste of energy better spent on outbreeding the competition. This is why antibiotics resistant infections often happen in hospitals, which are environments rich in antibiotics. Having useless genes is a competitive disadvantage, people! To conclude, in my opinion regulating genetic engineering with regulations that make sense is a good thing, but the witch hunt we have been seeing especially in Europe is downright idiotic. Greenpeace sucks arse. Thank you.

Denoir, you don't seem to know all the facts behind GMO plants and animals. However, I don't have time to write a reply now, but I'll get back to this tomorrow.

Does it really matter whether the Galileo fuel canisters went nuclear or not? I'm sure nothing as small as a nuke would cause any trouble for Jupiter, which shrugged off a huge cometary impact by Shoemaker-Levy. A nuke is but a small fart compared to the impact of each of the 1-2 kilometer fragments of Shoemaker-Levy. The biggest impact by Shoemaker-Levy fragment G released energy equivalent to 6 million megatons of TNT, which is roughly 600 times the estimated arsenal of the world. The biggest nukes tested on Earth were in the 100 megaton range. So if Jupiter did not go sun from that impact, why would a small nuke cause that?

Yeah, even in the finnish army we had to clean our rifles and mortars all the time. And we were not in a war. I cannot imagine how much cleaning would be done if there was actual combat. Besides, I would be totally jumpy if i knew my weapon might not function in a combat situation.

The particle accelerators have a use in biology as well. Esquisitely accurate three dimensional pictures of biomolecules can be generated with them. And since in protein chemistry form IS function, these three dimensional pictures of proteins help us understand molecular biology.

The line between NBC weapons and "conventional" weapons is pretty blurry at best. I mean, if DU rounds spread toxic aerosols, is it a chemical weapon or not? Was Agent Orange a chemical weapon just because it did not kill people outright? Is DDT, a common insecticide still in the third world, a chemical weapon, because it causes infertility in animals (and humans)? The reason for the U.S. love of DU is the fact that DU has ideal properties for a penetrator: 1. High density. 2. Easily obtainable (for U.S.). 3. When a DU penetrator hits a target and fractures at the tip it forms a sharp point. Tungsten penetrators form a blunt end as they fracture. So DU penetrators ARE better than tungsten penetrators. Then again, currently U.S. is shooting obsolete tanks fielded by almost defenceless small countries, not russian state-of-the-art tanks. So why use DU when tungsten would do as well. Hell, you could have killed Iraqi tanks with LAWs...

The problem with the DU rounds is not the radiation (which is minimal as pro-DU people always point out). The problem is that DU dust which results from impact with targets is toxic, which is not at all surprising since many other heavy metals are toxic to life as well. But I also know that with the U.S. defence lobby behind DU rounds, they will never be banned, regardless of how toxic they are.

Nice essay. I'm sure you will get a nice grade for that. It's funny, though, how your "marine corps -obsession" shines through the text.

Hehe... I was just in a scientific conference, where a 28-year old scientist from UK was telling me how terrible it was when Hitler's Germany invaded Finland during WWII. Needless to say, I had to educate him about the history of WWII. I think Iäm worried about the education system in UK.

To me, the "American Dream" is essentially about control. It is a brilliant way of keeping the peace in society instead of control by Gestapo tactics. Let me quote: "We have been told that one day we will all be millionaires and movies gods and rock stars." We believe that simple slogan, so we toil away to realize that dream. We toil and eventually we die of exhaustion or old age, accomplishing almost nothing. But because of our belief in the American Dream we made no trouble, we lived a quiet life. Our belief in the Dream kept us realizing that life is bleak and simple and that we are just parts in a machine designed to produce more people and more wealth. And that machine, by the way, has no purpose whatsoever, it just is. No, what we should say is: "We have been told that one day we will all be millionaires and movies gods and rock stars, but we won't. We are slowly learning that fact and we are very pissed off." But who to be pissed off at? (The above quotes are from the novel Fight Club by Chuck Palahniuk)

As far as I know Estonian economy is humming along pretty nicely, considering that they have very few business limiting laws in place and lots of highly trained personnel. The problem I see is all companies escaping high taxation and strict corporate laws to Estonia. Maybe that will force the dissolution of the scandinavian social-democrat welfare state.

You're absolutely right. However, only a fraction of the people in this world realize this. Most people think you can have both freedom and security. Anyway, what I was trying to say with my earlier post is that I am not at all surprised by the fact that some dimwit imitated Grand Theft Auto or Jackass. Whenever a new idea is presented, some monkey will imitate it, it is inevitable. This is just something we should accept, hell, at least it weeds out total morons from the society. But of course society has to try to assign blame. Nobody is responsible for what they do anymore, it's ridiculous. If I poured gasoline on my head and lit a match, I wouldn't blame anybody else for getting burned. That kid knew perfectly well that if you pour flammable liquid on yourself and light it, you will get burned. Yet he is blaming Jackass, which is by the way quite educational since it actually shows what happens to real people when they do stupid shit (it's not like a cartoon where nobody ever gets hurt).

Yeah: America, love it or leave it.

Ideas are dangerous. If monkey is presented an idea, monkey will make it happen. But should we ban all ideas because of that?

Service of flying things is a nightmare.

Living in a country with really rough terrain I can also point out that bigger size means greater weight means bogging down becomes easier.

US doesn't pay but pennies to the UN, because for some reason they don't want to. Anyway, in order to prevent huge conflict in the world, it is best to keep the (militarily) strongest country in the UN. That way other countries can at least try to control the flailings of the wounded giant.

About those anti-materiel micro-organisms: According to that report posted above, it seems that the genetically engineered anti-materiel bacteria are supposed to have a suicide-gene, which is supposed to kill them off after suitable food in their immediate area has been eaten. However, since those bacteria are living entities, they can very easily mutate and thus inactivate the suicide gene and/or they can donate the anti-materiel genes to other bacteria living naturally in the target area. I would be very concerned about contaminating the world with metal/plastic/tarmac eating bacteria. Normally I am not concerned about releasing genetically engineered organisms to the environment, since the modifications are always chosen so that they are beneficial for humans and thus usually not beneficial for the bacteria that carry them. In case of bioweapons, however, the modifications are very useful for the bacteria (new food source available).

You know, religious people often assume that since they would be lonely without their god, godless heathens are lonely without a god. But that is simply not true. As a godless heathen I can say that I find the absence of god to be a very liberating thing: I would not like to be a helpless puppet torn between the conflict of two supernatural beings fighting for supremacy (god and satan). Instead I prefer to make my own destiny and one day watch my final sunset.