Map of human genome - This isn't another "cold fusion" type scam, is it?

[Deacon]

The following article gives a layman's rundown of an announcement made by a London based research team which claims to have mapped the human genome. http://dailynews.netscape.com/dailynews/cnnnews.tmpl?story=human.genome.030626.html

What makes me uneasy about this is the article states that what the research team released was a "rough draft". Which brings to mind a few years ago when those 2 jokers claimed they found the key to cold fusion, which later turned out to be false.

Does anyone know any more about this human genome map and what they mean by a "rough draft"? The potential of this technology is so promising that it would be a shame if the researchers were announcing this breakthrough prematurely.

[This message has been edited by Deacon (edited 06-26-2000).]

[Wolverine]

I'll try to explain this as I understand it. It's true that they've mapped out the linear sequence of all of the base pairs in the human genome, from beginning to end. It was a big announcement since that project wasn't supposed to be completed until 2002-2003, so they're a couple of years ahead of schedule.

The thing is (and this I think is why they're calling it a rough draft) they don't know, for the most part, where the actual genes are in the sequence. And once they find all of those, they still have to learn which ones do what. The other thing to keep in mind is that a huge percentage of the human genome is never used at all, so there's going to be a whole lot of junk to sift through before they find the important stuff.

So they really have mapped out the entire sequence, which was pretty much the brute force of going through and doing it. Now they have to do the harder part of making that information in some way, shape and form useful.

There's a lot of fear about this information in the medical community. While it does have the tremendous advantage of giving us the tools to cure many diseases which were previously untreatable, it also sets up a lot of problems. The big worry is that insurance companies are may end up being able to use this information to find disease potential in people before we the actual cures for that disease can be found. That's bad. There is also a problem where employers may start using it to decide which employees to take.

Then you can also get into the whole Gattaca, Brave New World, etc type situations. Really the whole issue sets up all sorts of philosphical (and religious) arguments that are going to start popping up a whole lot more.

Dave

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[aLittletank]

Deacon I am just responding to check on you. After I got your email I hve thought about some of my clients and how I would feel in the same situation.

how ya holding up?
did you ge my email?

Allen

[Deacon]

Yeah, I did get your email, Allen. Everything is fine here. I'll email you with some more of the details. Rich

[Rinaldi]

Since we can now talk politics, I "heard" that it is premature, that the project is not yet done, and that the timing is political - i.e., Clinton wants credit for it.

[Wolverine]

That would surprise me for two reasons. One is that the first group to announce it was not from the US. Another is that it's something that was going to just happen eventually. It was brute force type work, and the key was how efficiently that brute force could be done. Really not much has been accomplished, in the big scheme of things.
Basically, we now have the great book of human life; we understand the letters, but we only know a few words, so we're still quite a long ways from really being able to read it.
The other problem is that it was only done on the DNA of a few people (around 12, if I remember right), which means they're still a very long way from having the true feel for what it should be.

So I guess it's possible that Clinton could be trying to get credit for it, but I just think that would be strange since all that's been done is setting the stage for the real work.

Dave

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[dragon0121]

I saw some tv footage a couple days ago about this. Was a government endevour, with usual gov. trappings; lots of manpower, little technology, not enough money... you get the picture. Along comes the private individual, billionare or whatever, he uses the best technology, lots of money, replaces some people with robotics and turns a 10 year gov. project in a 3 year project. They claim that this was a joint venture, but the show claimed that until just recently, months I think, these two projects wouldn't even talk to each other. They were talking to Mr. X (don't remember name) about the human genome project and he said if you read one chromosone pair a second it would take like 100 years to read them all. This project gives science the pairs (might be the wrong terminology here), but not even the correct order. All of the where, what, and why's have yet to be addressed.

[fishonly]

I think it will be a long time before this affects any of us. Like was said, we have the letters but don't know what words they are making. Figuring out the genes is the hard part. Many other genomes have already been sequenced for example, almost every genus of bacteria, but we still don't know what the genes are or do in these genomes b/c it is hard work to figure this out so I think it will be quite a while before we get this accomplished for the human genome as well. Not to mention, after we figure out which genes are of interest, the common public will have to have their DNA sequenced as well to see if they have these genes. I think that people who get all up in arms about this sequencing deal are over reacting. Yes, it could be bad news if it were used the wrong way but so could so many other things in this country. Like the internet for example. I am really glad that the work is being done b/c I know of so many benefits that can arise from this. I'm very excited. The only question I have is how did they decide whose genome to sequence. Everybody is so different from one another. Will we really get usable info from just a few people's DNA?

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[Frisco]

I don't stay too on top of this type of stuff, but I thought that they called it "preliminary" because of the method that they used to determine the sequence.

Automated equipment makes it easy to both replicate DNA strands repeatably and and chop them up in repeatable ways. But figuring out how to put the pieces back together is another story. So say you take a strand of DNA and chemically cleave it every time CACATAGA is encountered, and then you take a copy of the same strand and chemically cleave it every time AACCTTGG is encountered. If the strand stays in one piece, you know that none of the pairs are in this order. But if it cleaves, you can count the number of pieces and determine the number of occurences of this AACCTTGG (or the other one) sequence. Then if you repeat this cleaving process for every possible sequential combination of 8 base pairs, you're on your way to mapping the original piece of DNA. Then you just program a computer to compare subsets of the 8 pair sequence, take all these numbers and use statistical information to piece them back together. At least that's the way a molecular bio buddy explained it several years ago.

Incidentally, I had a chance to take a trip over to one of the companies that makes PCR (DNA replication) and electrophoresis (DNA "chopping") equipment a couple years ago. Very cool stuff.

[Wolverine]

fishonly, I agree completely that it's a long ways off before any use will come of this information, especially since it took so many years to just do this on something like a dozen people. We're not quite to the Gattaca stage yet.

Frisco, I spent a long time in undergrad doing PCR, electrophoresis, and all the others. I was a lab tech (aka peon) in two different genetics labs (the man who runs one of them is on the short list for the Nobel right now, and should win in the next few years). It was pretty interesting, but I don't think I'd be able to be a lab tech for my whole life.

Dave

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[Wolverine]

Bigben, actually, the majority of DNA is not just in the introns of the genes, but is between the genes and ends up playing no role whatsoever except for space filler (that we know of, of course).

As for the private vs public thing, most doctors right now (at least that I've been in contact with about this) would much prefer this to be a private venture right now. If all of the detailed information gets public, that will allow both insurance companies to raise premiums and deny people coverage before they have any evidence of having problems. It will also allow employers to discriminate based on whether or not someone has enough of the intelligence genes", for example. Of course, that kind of thing is pretty far down the road, but it's still a very real possibility.

I agree that most MDs who were trained in the past don't have a whole lot of knowledge about genetics, but there's been more and more teaching in that in medical schools lately.

As for the small number thing, it is true that most of that unused DNA is conserved, but it's the part that isn't conserved that we care about, since that's where we'll find the keys to diseases and all the other traits that we'll be concerened about, and this is where we'll need to find the concensus sequences. Using only a few people will not allow us to do that.

Just my thoughts,
Dave

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[bigben]

Hey yall,

Just thought I'd comment on the idea that many people think the majority of our DNA is "junk". Well, that's just an easy way of saying that we don't know what most of it is good for. Only a very small percentage of human DNA codes for proteins that will have some basic function (enzymatic, structural, etc). So far, most of the other repeating "intronic" sequences, etc, have been shown to display regulatory functions (I have made this VERY simplistic). So, don't pay attention when people (even the masses of misguided professors) tell you that most of our DNA is junk. We just don't know yet.

BTW, I'm waiting on our collaborative (non-private) version of the human genome to come out. I think I speak for most of the scientists in saying that we're not really all that pumped about this private venture. The reason is that the private folks are rushing through it, using less accurate techniques, and don't have the advantage of collaboration with a lot of people. Personally, I put very little faith in the results of this private firm. These folks don't care about anything but becoming famous. They've lost sight of the real reason the project was begun...kinda ****es me off!!

By the end of this century, we should start having a decent grasp of the human genome. Until then, it's just gonna be a bunch of mutational studies, microchip arrays, etc to screen large numbers of oligonucleotides.

While I'm on my soap box, remember that when the news media mentions all the "medical doctors" doing the work, please ignore that statement. Remember that the vast majority of the work is being done by scientists who don't earn the dollar that MDs do. I may get flamed for this, but I know very few MDs (especially ones that have gotten their degree before the the mid 80s) who have a CLUE about genetics. This is the scary truth.

Ben

PS--To comment on the question about using very few people: Since about 95% (we think) of DNA does not code for a product and is very conserved between all humans, it is feasible to use a small sample for the experiments. However, one must always keep this in mind. There is no "magic" number of people to use.

If you must, then flame away!!

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--Police Chief Wigham

[This message has been edited by bigben (edited 07-02-2000).]

[bigben]

Dave,

Just so you know: I didn't claim that the majority of the DNA is in the introns of the genes. I simply said this: So far, most of the other repeating "intronic" sequences, etc, have been shown to display regulatory functions. I'm not an idiot!

The genome publication offers a tool for us to find homologous proteins, etc, to study functionality as compared to animals models. I don't know why folks are so concerned about the abuse of the genome to create mutant people or sh*t like that.

It is true that this little private venture is producing data that is much less reliable (wait and see) than what will be released later. The stuff being cranked out right now is all out of order and has bits and pieces of ORFs all stuck together--pretty frustrating when doing searches!!

BTW, your previoius statement in another thread, "The main animal resevoir for it [V. colerae]is shrimp and oysters, but you probably don't need to worry about it unless you're eating them uncooked" is inaccurate. Fecal/oral transmission is the primary route.

Ben

[Wolverine]

Bigben, I didn't call you an idiot (and don't think that), so don't worry about that; I just misread what you wrote.

I've never seen or read anything giving evidence that most of the extra-genomic DNA has any regulatory function of any kind (I know that's not what you're talking about with the intronic sequences). Most of what I've read suggests that we simply don't know what it's function, if any, is (you mentioned that yourself a few posts ago). Actually, as I'm reading back over this, I think that you and I may be arguing the same side here, but from different perspectives.

As far as the concerns, the people I've talked to are not worried about creating mutants or anything like that. People are much more worried about the discrimination that will most likely be brought about by this information. And, it's a good bet that we'll be able to interpret what's in the DNA long before we can actually do anything constructive changing it, so this danger about discrimination is much nearer than any problem with making mutants. That's what many people in the medical community are worried about. Consider the test for the Alzheimer's genes, as an example. As I'm sure you know, there are a few genes that come up more commonly there, and people can be tested for them if they have a family history of the disease and want to know. Well, people probably shouldn't get any of these genes tested for. If it's positive, then the insurance companies will up the price a little bit for both health and life insurance. And if the rest of the genetic information is known, this kind of problem will likely be much more rampant. That's the concern.

As for the comment on the other thread, I'll not doubt your knowledge on the subject, since your field is obviously more involved in that subject than mine, but I will say that the information I provided on that thread was from three separate microbiology textbooks that we've been using for school and for studying for the Boards, so it's not like I was making any of it up. I know that fecal/oral is the primary mode of transmission, but the animals I mentioned are the main resevoir. I don't remember the entire context of the conversation, so I can't completely argue in support of what I was saying at the time (and I don't have time right now to go back to it).

Dave

Editted to remove some incoherent rambling (but leaving plenty of others).
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[This message has been edited by Wolverine (edited 07-03-2000).]

[Dan]

Like any new technological advance, the sequencing of the human genome can be used for good or bad. Most of the criticisms I have heard come from people worried about discrimination based on genes. While that certainly can and may occur, there is an easy solution --- don't let anyone sequence you. It isn't anyone's business what your genes are. This is the information age. We must become more proactive to protect our privacy. It is already known that certain genes (or mutations in genes) are directly related to certain diseases. On one hand it may be beneficial to have genetic knowledge in order to properly diagnose and treat disease (or prevent it). On the other hand, that information can be misused if it gets into the wrong hands (i.e. insurance). It will be up to each of us to protect that information. As usual, the law lags behind the technology. I would be wary of "medical databases" sold to us as "tools to help doctors and patients". Remember Bill Clinton holding up that medical card containing your personal medical history? How would we protect that information from being misused? It in my genes not to trust big, bad central planners. I would not want my medical history in some central database. Maybe I'm just a cynic, but there are scrupless people who would pay money to have that information on potential employees or clients.

As far as the genome goes, don't be surprised if functions are linked to genes in a shorter time frame than has been speculated above. The reason private industry moved so fast on this is because the genome is like a gold mine or a vast forest. Its just asking to be exploited. And lord knows, us capitalist pigs love to exploit things. The speed at which private industry outpaced the government genome project is because private industry developed new technologies to do it. Competition drove this. From a biological perspective this was like the race to the moon. New technologies had to be created. Private companies hoped to gain patent protection. But it looks like the patent office is pushing to have functional information linked to any gene in order to patent it. So........ new technologies will be developed to link function to genes as quickly as possible. Don't underestimate the power of capital venturists. What a great country!

Dan

P.S. When will we have the clownfish genome mapped? I want to know which gene causes them to bite me every time I reach into the tank.

[This message has been edited by Dan (edited 07-03-2000).]

[bigben]

Sorry yall, I've just been really stressed with this grant proposal that was due today, and it's affected my attitude. Just gonna have sit back, relax, and let my tank take over my mind. Sorry if I was cross, Dave. I hope I haven't given anyone a bad opinion of me :) Have a good 4th yall!!

Ben

BTW--I just saw the patriot tonight, and it was pretty dang good!!

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--Police Chief Wigham

[Joez]

They are already sequencing us!!

Every time you go to the dentist or barber, even at the restaurant where they collect backwash from your drinking glass.

[Wolverine]

Ben, don't worry about it. I know what a pain those things can be, since I was involved lightly in a couple, and I've seen my wife go crazy a few times writing hers. For me the sad thing is that, if I end up going into research after I get my degree, then I'm going to have to be writing them too.

Dan, I agree about the medical database thing, there are a lot of people I don't trust out there with that kind of information, and a lot of them work for the government (no offense to gov't employees; though, ironically, it is the 4th as I write this). And I'm guessing that's a maroon or clarkii clown you have, since they seem to have more of those mean genes than the other clowns I've dealt with.

My hope is that maybe with this the laws will try to jump ahead of the technology to stop the potential problems and keep the benefits (yeah, I know the odds of that one).

Dave

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