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Human Chromosome 22 Mapped
tuck was the first of many to submit this important milestone in arguably the world's most important scientific endeavor. The Human Genome Project has completed mapping its first entire chromosome, number 22. Second-smallest of our 23 chromosomes, some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia and mental retardation." Portion of its DNA which is "junk" (encodes no protein): 42%. Read it at your favorite source:
CNN,
MSNBC,
the Boston Globe,
the Christian Science Monitor,
the AP,
or Reuters.
I could be asking a stupid question here (blame it on my genes), but since everyone has different DNA, how do the scientists decide which genes are normal? I mean, if there is a hereditary disease that only a very few people get, you probably decide that the 'healthy' gene is the more normal gene. But what if the gene f.e. encodes eye-color, how do the scientists decide what gene to map? Or do they simply say that that and that gene encodes eye-color and leave it open what DNA sequence it has?
HGP does it by "clone by clone" strategy. That means, the chromosome is cut in smaller pieces, then again in even smaller pieces, the pieces get cloned (cloning in molecular biology means not the Dolly sheep: it means, a certain sequence is inserted into a epigenetic element called plasmid, which itself can propagate and thrive in bacteria), and then sequenced. This is cumbersome and requires a lot of manual work, but it provides unmatched quality of the sequencing.
TIGR adopted another strategy, the so-called shotgun method. In this strategy, you get a sequence, but you have not the slightest idea where from the genome does it come from. Only you when you have a lot of this sequences you can start assembling - using a lot of CPU, trying to match them one to another, like a puzzle, but trickier: a sequence often contains errors, especially at the end (you can only read a couple of hundreds bases, then the signals are to weak and not clear enough). This strategy requires considerably less highly trained man-power: just a lot of technicians and $$ for expensive sequencing machines (which were provided to TIGR by Perkin-Elmer). However, this method has a serious drawback: there are many sequences in the human genome, which are partly, or totally repeated. This repeat elements can be a royal pain in the sequencing project (been there, done that).
It is really a good thing that there are two sequencing project with two different strategies: the comparison between the two sequences could provide an enormous insight into a) quality of the sequencing b) human variablity. Venter from TIGR is definitely an enfant terrible, but I don't think he is one of those corporate Bad Guys (TM), rather one who was fed up with the slow pace of conventional scientific projects. On the other hand, HGP, representing "the slow pace", shows us also why a slow pace is needed sometimes.
Regards,
January
it has come to my attention that the gene for statuephillia has been sequenced on ch.22 this is a massive breakthrough for statuephiles and sexualists alike in order that we may begin to live in harmony together, at one with each other, the earth, and lovely smooth statues of young girls. may i use natalie portman as an example of the latter.
just as we are beginning to understand homosexuality in the sociological and genetic contexts, i pray to you all that you open your eyes a little to the wonderments of human nature, and the human genome itself.
thank you for your time.
H@AAD.com
Interesting that it compresses so well, compression only happens when there are a lot of repetitions in the code.
And indeed there are a lot of repetitions in the code. But there's also a simpler reason: only 4 characters are used, so the uncompressed data uses only 2 bits for every 8. Naturally, compression will reduce this to 2.25 bits at worse.
I can see the fnords!
I dunno for sure about Sanger, but WashU and Whitehead in the US are working from the same clone library.
At the Sanger we've historically been using the RPC-1 library from Pieter de Jong's lab. I have been told several times that the individual can and has been identified. I was told a name as well. More recently we've been moving onto other libraries based on anonymous panels, such as the RPCI-11.2, from the same lab.
I still haven't read any of the articles and of course hadn't when I wrote the above. Seems that what most people are referring to as "junk" was actually about 97% of what the HGP people sequenced. 42% was things like the repeat regions I mentioned. Those numbers make much more sense (ie, they were expected ;)
Not quite true. Sometimes the presence of a particular gene can cause a problem in an area where most random pieces of noise would cause no problem. Not common, but...
Think of a program that has a statement like:
qwerty = null;
where qwerty is some random string of characters. Most often this will have no effect, but if by happenstance it matches the name of a variable that's in use, then a program bug can arise. Occasionally this may fix a bug, but that's not the way to bet.
I think we've pushed this "anyone can grow up to be president" thing too far.
There is probably a great deal of overlap between what was sequenced. They have sequenced about a billion bases but I'd guess about 1/4 of that is repetitive, which puts them about 25% done. They'll probably have to sequence at least 4 billion bases before they end up with the non-redudant 3 million base pair human genome. (The more you sequence, the more likely that you will be re-sequencing you already did...)
All joking aside, I think you're very close to the mark. But it isn't commentary on the code, I believe it is in fact commented-out code. Or fragments of commented-out code. What happens if a random mutation "uncomments" a section of code comprised of leftover bits of old code that aren't in use anymore? Evolution.
-- There is no truth. There is only Perception. To Percieve is to Exist.
Actually, natural selection ensures that it is an efficient process. The more DNA in a given cell's genome, the more energy and the longer time it takes that particular cell to replicate all of its DNA and divide/reproduce. Therefore, it is beneficial for the cell to get rid of any DNA that is not absolutely necessary. You can actually see this working at bacteria; engineer a run of random DNA into a bacterial genome, and you'll see that after a few generations, the cells that have managed to (randomly) excise the extra DNA will grow faster and more efficiently than cells still carrying around the extra baggage. This is where "survival of the fittest" kicks in," allowing the more efficient cells to dominate the population
In addition to the types you mentioned, you also have DNA that is not only useless to the organism, is also harmful. For example, a virus may insert itself latently inside the DNA of a germ cell, inadvertantly adding itself to the evolutionary pathway of that species. Should the DNA stay latent (or, more likely, undergo a mutation that keeps it from being expressed), it ends up being a "time bomb" waiting for the right time to be expressed.
:) But the thing to remember is that there are also evolutionary pressures for other DNA that doesn't necessarily jibe with our own interests.
Mice happen to have a lot of this viral DNA, which tend to act as oncogenes (cancer causing genes). Mice (just like everything else) accumulate mutations over their lifespans, and as the mouse gets older, the likelihood of a mutation activating an oncogene increases, until one day the mouse ends up with a tumor. This is a common cause of death for mice.
As you pointed out, Eukaryotes are big and complex. They are also still "works in progress". Some people seem to think that evolutionary pressures have created the lean, sleek, perfectly adapted creatures that humans are today
Cheers, Sean, and congratulations once again on this important milestone.
Personally, though, I think public money should go to a myriad of smaller projects instead of one big Manhattan/Apollo style push that sucks money from everywhere else.
If the private sector is willing to plunk the $$$ to sequence genomes, I say let 'em do it and give them patent protection as a quid pro quo.
But that's just my opinion, not like you asked for it or anything. Cheers!
whuppy enjoys smelling like diesel fuel
The appendix is part of the intestinal immune system. AFAIK, it modulates it, and also allows a handy springboard for immune cells into the stream of material that original came from the outside. It also gives a home for some "friendly" bacteria. Without it, people are less well equipped to handle opportunistic infection. It's analagous to the tonsils.
Of course there are some cases when it is known exactly how a genetic disorder causes a certain type of illness - you all know of the Down syndrome, thalassomy, sickle cell anaemia - but there is *a lot* more.
Imagine hiding easter eggs in junk DNA... Bend the frog's arm the right way and it croaks the genetic engineers' names....
Of itself, the periodic table didn't make any new chemicals. What it did was provide a framework to identify patterns that could be used to predict areas of research. For example, the discovery of helium: the table predicted the existance of the element, and allowed calculation of the spectral lines. The element was then identified in the sun, hence the name (helium, from helios, the sun).
Similiarly, the HGP of itself won't cure any diseases; rather it will allow the mapping of patterns. We'll be able to say, "This gene, which we know does this in wheat, is present in humans. Perhaps it does the same thing?".
Once we get one copy of the human genome sequenced, we'll still need to sequence many others, from [tall|short|skinny|fat|bald|hairy...] people, and start cross-referencing the results.
Think of it as a massive reverse engineering project on a program we only have uncommented object code for.
Unless the "junk" DNA are comments...
www.eFax.com are spammers
The pairs are not identical. Each gene on a cronosome refers to another on the second half of the pair. Some genes are dominant and others are recessive. If a gene is dominant than the behaviour to prescribes is used, recessive genes only surface when bothe genes across the pair are the same ie. brown eyes+brown eyes=brown eyes, brown eyes+blue eyes=brown eyes, blue eyes+blue eyes=blue eyes. It is the differance between the chronosomes in a pair that make us what we are. This also explains why males are more prone to some conditions- ie hymaphilia(sp?) A recessive gene on the X gene is not dominated on the Y chronosome as that gene simply is not there- where as females two of these genes to get it.
J-aims
--
Yo, whatever happened to peas? Join T( H)GS
There I've explained that in a sentence even a fool can undertand. Junk DNA my adenosine. Either sloppy journalism or else the researcher explaining this to the journalist was sloppy.
"I just can't sit while people are saying nonsense in a meeting without saying it's nonsense" J Watson, Sci Am 288:(4)51
It'll be interesting to see if male and female lifespans are equal in another 200 years or so, after sexual equality has been fully established.
According to Desmond Morris' The Human Sexes , recently rerun on TLC, men's life expectancy was several years longer than women's for most of recorded history.
It has been only in this century that women's lifespans have caught up with, and exceeded, men's -- Morris attributes this to improvements in medical care, specifically the dramatic reduction in the number of women who die while giving birth.
DAMNED!!! Why can't I send a cancel message? :-) I pressed the "Submit" button again! Grrr....
Back to the topic. There are cases, when finding one single disorder which causes one specific disease is easy. There are cases, when you can pin down a certain region - by tracing the genetic tree of the family, whose members have the disease. There are cases, where you are able to tell that - well, there *is* a genetic component of a certain disease. In some cases, you can tell two forms of the disease: a genetically inherited and a genetically independent form (e.g. the early-onset Alzheimers and the age-dependent Alzheimers disease).
There is yet one thing you have to keep in mind: there is no "gene causing disease X". It's rather: "a gene, whose malfunction or absence causes disease X". For example, a single nucleotide substitution can result in a non-active enzyme, or an enzyme with much slower activity. The whole metabolic pathway, to which this enzyme belongs, is hampered. In some cases a heterozygous organism will have another copy of the gene, which will do the job, or do the job at least in a part - and the disease shows fully in homozygous organisms.
Regards,
January
My friend says that this is not a real disease. She insists that it would have something to do with the neurons in your stomach and muscles and brain muscles. Doesn't exactly make much sense. I for one believe you, but maybe I am a worthless fool. Please clear this up for us.
Probably a stupid question this but who's DNA is being mapped here? Is it someone alive? Is it one or many individuals?
Hemophilia is an X-linked recessive disorder. The reason why it is much more prevelant among males is that if a male inherits the recessive allele from his mother, he is hemizygous (expressing the trait in both the recessive and dominant condition) This is because a male has only one X chromosome. A female would have to be homozygous (carry both mutated alleles) in order to be affect. A woman's odds of having hemophilia are about 1 in 100 million,but not impossible.
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
I wouldn't mind a 25-pin parrallel port in /my/ head... I'd rather have firewire though. Or at least 2 USB ports. Ok, even UW-SCSI3...
I thought human beings had 46 chromosomes?
certain genes have already been patented by pharmecutical companies, largely the insulin gene. If you have a working insulin gene, it's been patented. Some genetic researches have patented whole fragments of code, and are now working on deciphering it.
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
I would say cleaning up oil spills is a good incentive.
The producer of the bug would have a massive market lead on any competitor who cloned it anyway. Patents were originally intend to /promote/ competition, by encouraging people to release details of their products, in exhcange for a limited monopoly. These days, they work against competition, since the lengths of time the patents are granted for means that by the time the patent has expired, it's useless to competitors anyway. In both genetics and software, the protection period should be 1 to 2 years. The current patent period is calibrated for 19th century steam-powered machines, not infinitely replicating, almost zero unit cost things like software and genetic code.
Another thing is that both software and genetic code are really algorithms. You should not be able to patent an algorithm.
What if a patented software algorithm was used in an academic mathematical proof? Would the whole of the mathematical community ahve to pay license fees each time they wanted to use graboskies theorem (fictional example).
Most genes have a "normal" important function, and when the gene is mutated in some way, and ceases to "do its job" that genetic disorders occur. In cases of genetic metabolic diseases, mutations that cause a loss of function in a single enzyme can have many pronounced effects. In the case of Cystic Fibrosis, the gene that it was mapped to (q31 of chromosome 7) produces a protein that inserts itself into the plasma membrane of exocrine gland cells. This protein regulates the flow of chloride ions accross the cells plasma membrane. With CF patients, this protein is absent or defective. In most cases, mutated genes can not perform their normal functions.
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
Has any experimentation been done on creatures with differences in only their 'junk' DNA.
It just seems a bit iffy to say it's junk because it doesn't do something that we know other DNA does.
To reliably say it does nothing you would have to know how the whole system works, wouldn't you.
-- That which does not kill us has made its last mistake.
um.. yes it does... introns consist of base pairs too you know....
Say I have 5 important boxes.
1 2 3 4 5
I shoot a ball into one of them, with equal probability of hitting any : chances of hitting an important box : 5 in 5 ie. 100%
Now say I put more unimportant boxes in between these boxes
1 a b 2 3 c d e 4 5
The ball still has equal probability of hitting any box. chances of hitting an important box : 5 in 10 i.e. 50%
There. See?
In Science news and Discover, They've had articles about the so-called "junk" DNA found in our Chromosomes.
Some of the genes that have been mapped are very similar to ones related to cancer and other genetic deseise (the posting said that I think).
One of the most interesting sections of "junk" and "leftover" genes are the ones that look almost identicle to Simian Imunno-deficiancy Virus...That would be the version of HIV that Chimps and Gorrillas get in the wild. This would suggest that , earlier in the evolutionary process, that there was an epidemic of SIV in our (humans) predicessors that the species developed an immunity to. SIV and HIV are actually very similar viruses, so if some genetesist could figure out how the SIV gene gave early man an immunity to SIV, an anti-HIV gene/vacceine could be developed from (most likely) a combination of the SIV gene and parts of HIV viruses...
All the more reason to let EVERYONE have access to any genetic data of any creature.
~Donald / Just RTFM
You also have to consider environmental factors that have been shown to cause genetic mutations. I guess these genetic muations could be stuck in the subfile titled "s**t happens"
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
I think we all know why the "junk" section is aprox. 42% of the chromosome... this just proves that Douglas Adams has been on to something far greater than any of the rest of us could possibly imagine.
It is not the genes that cause the disease. /.
Its a mutation in on of these genes that cause the disease.
The way it is done is that you screen populations of diseased and nondiseased ppl. If a high percentage of diseased ppl have a cerain mutation in a certain gene you have association.
Next thing you mutate the gene in inbred mice. If the mutants die early of heart disease you have cause.
Its ok that CNN miss out on the facts but you should try to get a basic understanding on how things work before you post your thoughts on
Just basic Mendel(sp?)sonian studies have proved that homosexuality isn't caused by heritage.
I have never seen this answered to my satisfaction. Are they using a particular individual's DNA, multiple DNA samples from many individuals, or does it matter?
The Nature article said that individual human DNA differs from person to person by about 1 base pair in 1000.
If this is true, it seems like having one individual's sequence might be useful, but it is not going to tell you all that much about the variance from person to person. You'll get a general idea of what's going on, but it seems like you would have to sequence quite a few more individuals before you could really say how genetic changes effect a gene's expression.
-josh
The timing is actually entirely coincidental. We've been working on this for several years, and I've been involved in problem-solving in the closing stages. There's no way we'd have been able to time the finishing to match, and there's no way we (or Nature) would have been willing to delay it to that purpose.
I'd agree that it's happy timing, though.
The Sanger Centre's hoping to be able to announce the completion of Chromosome 20 sometime next year, and I understand that the GSC in St. Louis is hoping to do the same for Chromosome 7. Both have stats pages up, if you're interested. The Sanger's is at http://www.sanger.ac.uk/HGP/stats.shtml
The HGP is a joint venture funded by biotechnical outfits. These companies that map this information do so because for the first six months they have patent rights on processes they discover from (or in) this information. These companies only care about "the good of mankind" _after_ the patent window has expired.
-- The constitution may not be perfect, But it's better than what we got.
Hmm, if this DNA-patenting thing gets through, the next thing after the Open Source movement might be the Open DNA movement, where a certain RMS II will fight to regain lost rights of the public to access their DNA... and he will start to license DNA sequences under the DPL (DNA public license) to prohibit corporate entities from taking freely-accessible DNA and making it "proprietary".
(Disclaimer: if your sense of humor doesn't match mine, please don't take this as flamebait... somebody help me, I've been infected by the GPL virus and I can't stop Open Sourcing every topic that comes up on /.!!! :-O )
mikre he sophia he tou Mikrosophou.
So the theory goes.
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While you're at it, please come up with organisms and products that clean up toxic waste spills, produce insulin, kill crop-destroying pests, produce more nutritious food, serve as research tools for developing anti-cancer drugs, and grow new organs from scratch.
We can agree that these are all Good goals. What more incentive do you need? Go to it!
whuppy enjoys smelling like diesel fuel
Rats!
Would have loved to have been a Gattacean rather than a human.
Some employers in the U.S. that sponser employee health insurance already conduct pre-employment assesments using genetic testing. There are fears that this will lead to bias and eventually, an "unemployable underclass".
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
They are the four bases in all DNA. A=adenine, C=cytosine, G=guanine, T=thymidine.
"Sometimes the road less traveled is less traveled for a reason." -Seinfeld
. . . and I do take your point that software patents may be counterproductive, but it is precisely the situation you describe -- low marginal costs for each additional unit, be it organism or software -- that intellectual property law is designed to protect. In other words, why spend all your money up-front if it's just gonna be instantly knocked off anyway?
As for your quote: The producer of the bug would have a massive market lead on any competitor who cloned it anyway. You don't know that. I don't know that. The company who develops it has to assess the risk about whether or not they're going to even recoup their development costs (or if it's even going to work, for that matter), and it's far less likely that they're going to bother without the benefit of patent protection.
Another benefit of patent law: By law, the patent makes the know-how public. Which means that anybody can look at the patent and think of ways to adapt or improve it. Such as developing a bug to eat toxic waste and produce cotton candy. Yum.
Finally, everyone: Please learn a little about patent law before you start spouting the doomsday scenarioes mentioned above. Thanks.
whuppy enjoys smelling like diesel fuel
I know the Christian Science Monitor is a respected paper, and I was very impressed with the quality of the articles when I just browsed through, but I find it ironic that the voice of that sect published news about biology and medicine. Scary that their was the most in depth article too. What does that say about the other media?
************************************************ ***
Being bitter is drinking poison and hoping someone else will die
don't tell me it isn't free!
but I strongly doubt there would be gene that's ONLY function is disease... what sense would that make?
Why should it make sense? Assuming you don't suscribe to Creationism, there's no reason to assume a reason behind any particular genetic coding, any more than you should assume the function of gravity is to make your milk spill. Rather than 'function', which tends to sound like a design with a purpose, think 'effect' or 'result'. So, the effect of foo genes or gene-sequences is bar desease. A mutation has 4 possible results:
1. It helps a creature and/or its offspring thrive and reproduce.
2. It hinders a creature and/or its offspring from thriving or reproducing.
3. It has advantages/disadvantages which don't (yet) affect the reproduction chances.
4. It has no effect at all (or yet).
That's it. No point system other than:
1. You have children.
2. They inherit some of your genes and some of your partner's genes, and perhaps some of the genes mutate.
3. Repeat.
People tend to think that their's some grand design behind everything that is. I'll leave the resolution of this question to the Philosophers and Theologians, but I think we can agree that if there is one, it's not something we're capable of recognising...
Chris
San Francisco values: compassion, tolerance, respect, intelligence
I know next to nothing about DNA but the term junk DNA seems... wrong. First of all contrast the articles in the 6 or so URLs listed. Only one referred to them as junk DNA, this sounds more like the reporters lack of understanding or bias than something the scientist said.
Second, consider a gene as an information exchange mechanism. Most forms of information exchange include some amount of material that isn't essential to the message but can't really be classified as junk either. It may be redundancy, it may be for error detection or correction or it may be for clarification.
Run an estimate of the actual needed text in the average paragraph written or spoken in English. The percentage that is 100% essential is pretty astonishinly small. It's a bit higher for a text but a bit lower for a novel. Mathematical proofs are pretty concentrated information but consider what happens if a little bit of information is transmitted wrong, say a sign is reversed. It's difficult to recover from it.
Likewise I think a 100% essential gene would be very difficult. Any random genetic damage would have impact. Gene replication would have to be absolutely exact and so on.
As I stated, I don't know anything about genes or DNA, but from an information theory standpoint calling 'unused' DNA junk seems wrong.
I would like to learn more about genes though, can anybody recommend a good progression of texts on the subject? Something to take somebody from absolute layman to at least having a general idea of the subject?
Someone correct me if I'm wrong... Are the results of the HGP going to be designated as common public property so everyone can profit from it? Just wondering.
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Let me be more clear. I agree with your points, but my "make sense" was more like "is propable enough to appear and stay": If there's gene that's there just to make me die, isn't it more propable it will disappear than otherwise? Sure, if it's sickness that comes after I've reproduced, it won't be all like that... but, because people DO live after having spent their age of being able to reproduce, it might imply that old persons would be usable to community. Thus, I don't see why there's still gene that kills us in our gene pool.
- Kaatunut
This is not my idea and I have no specific details for supporting it. But from what I have heard speculated at different places, the "junk-regions" of the DNA could house a chemical history of previous generations for each individual. Don't take my word for it though, it's just a thought to the mind-provoking 'junk DNA'.
- Steeltoe
http://www.debunkingskeptics.com/
These companies did not INVENT the sequence, they (figurativly speaking) picked it off the ground held it up and said "I MADE this" I have no problem with patenting living things as long as you only patent the CHANGE yopu made to that living thing, not what was already there
Of course it's useful. I wasn't saying that it wasn't useful or that it shouldn't be patented. My point is simply that patents are being issued on biological things. Sure, microbes. But can companies really patent variants of human cells? Or patent DNA altogether? Hmm ....
A fundamental assumption of the human genome project is that the genome sequence is "precompetitive" information that is best put in the public domain, to spur both additional basic research and commercial innovation. This makes it an obvious target for public, not private investment.
So far, no company has stepped up and said they intend to make the human genome sequence freely available. Celera is even waffling over their promise to release the Drosophila genome sequence. And somewhat understandably so; a company needs a business model.
His name is Duncan Idahoe.
...and I'm sorry to inform him, but House Attreides is going to make around 10,000 clones of him over the next few years and...
... oh yeah, right. nevermind.
Your Brain + EEG + LEGO Robots = Brainstorms
Additionally, from an evolutionary "fitness" point of view, having a certain amount of "useless" DNA that does, literally, nothing makes a certain amount of sense. Basically, mutations happen for whatever reason, exposure to chemical agents, being out in the sun, whatever-- there are probably plenty of ways that your DNA can become permanently screwed up s.t. your repair machinery can't fix the stuff, and its going to happen with some probability (lets call it p), now in coding regions of DNA you've got some built in redundancy (4^3 == 64 and we only have 20 amino acids + 2 stop codons (UAA,UAG) and a start codon (AUG) (hmmm... 23, but thats a different story :-)) so we've got 41 extra codons), most amino acids have multiple codons that will code for them (if I remember correctly Tryptophan (Trp) only has a single codon-- UGG)), which reduces the chances that some point mutation due to environmental mishap will change the amino acid a given codon codes (this is known as a silent mutation), which is good since if say a Tyrosine (UAC) gets changed to a stop (UAG) then the transcription/translation process stops early and the protein can't be made anymore. Now lets say it was some regularatory region that gets screwed up and causes the cell to go into massive reproduction mode (read: cancer). Wham, you lose-- no gene pool for you.
:-), while Organism 2 (o2) has a genome that is about 50% "junk" (not useful in any way). Now, let's say they've got some regulatory region that, if it gets mutated, will cause uncontrolled growth (cancer) and kill the organism. Now just to simplify things lets say that any change in the regulatory region will cause cancer and the region is 10 nucleotides long. Assuming all nucleotides have an equal chance of being mutated in the event that a mutation occurs then P(Regulatory Region Changes|Mutation Occurs) = 10/n, where n is the number of nucleotides in the organisms genome, BUT o2 is 50% junk, so if 10/n is the probability of the mutation in o1, then 10/2n or 5/n is the chance of the mutation occuring in o2. Thus, o2 is 1/2 as likely to get cancer and die-- an evolutionary advantage.
:-)
But I digress, we are talking about junk DNA. Ok, so lets consider two organisms hanging out on a beach somewhere. Organism 1 (o1) has NO junk DNA in its genome, somebody went through and "optimized" its genome
Of course the amount of "junk" we can have is probably limited by some factors (stability of the DNA molecule or some sort of mechanical constraint-- I don't know) that keeps the amount of DNA from getting out of control (or we just haven't been evolving long enough and having an infinite amount of DNA is selected for). Disclaimer: I'm not really able to back this up with any hard data-- its mostly just my guess as to why we have some much apparently useless DNA, its just a hypothesis so I could be wrong
[Spoiler!!!!] One theory for the purpose of "junk" DNA was included in Jeremy Narby's book, "The Cosmic Serpent". The theory leverages the fact that the DNA chemical is indeed a crystal. Junk DNA contains many repeats and palindromes. One 300 letter sequence can be found 500,000 times. These crystals might allow humans to comminicate (using light) with higher beings. But only when our brain is under the influence of a suitable chemical (e.g. ayahuasca, LSD, MDMA, THC...) to do the translation. Because DNA is the most faithfully reproduced information set on this planet, it would be the perfect place for alien cultures to leave messages, and even communication devices. This could explain how shamans in tribal cultures consume ayahuasca potions to create medicinal remedies far superior to western drugs. When asked how they got the information, the shamans reply: "The plants told me".
unfortunately this is the case. the researchers want patents on all the genes they discover, so they will have exclusive research rights to them (unless somebody else pays for the right). however, there is a French team out there (can't remember who offhand) which is trying to beat the Americans to the sequence so they can *donate* the entire genome to the UN, and people will be free to research what they want without having to pay. research moves slowly as it is, and is terribly underfunded (if you consider everything we are attempting to learn). in this case, i hope the French team wins.
Perhaps the introns are really nature's way of saying, "Hmmm... This isn't useful now, but I might like it in the future." :-) OK, so that probably isn't it.
Perhaps God is using our Intron DNA sequences as a large distributed storage for his pr0n and mp3 collections?
Yeah, I don't really like the idea of open-sourcing the genome. There is always the risk of a fork of the code base, and before you know it, we are two different species! Wouldn't you hate not being able to mix genes with everyone? Eh, I mean, like, 50% of everyone.
Lars
--
Reality or nothing.
Actually, introns != junk DNA . Introns are intervening sequences within genes that are spliced out before the RNA is translated into protein. Introns often contain regions important for regulation of gene expression and serve as a way to generate more diversity in gene products (by the production of alternatively spliced RNA transcripts). Junk DNA refers to regions of DNA between genes with function (if any) unknown. Just want to keep the discussions accurate.
They have collected samples from almost all ethnic groups in the world (not all know this though). Most of it was from volunteers and from donations to medical science. But more than one group of less technologicaly advanced people had blood samples taken and used with out thier consent of knowledge of what it was going to be used for.
They are doing the MDMI (multiple data many individuals) approach. What they get is basically an average genome. And certainly a good map of the genome.
The next step is to hunt for SNP:s, which stands for Single Nuceleotide Polymorphisms. And the race has already started. Both companies and universities are hunting for them. They are expected to be useful for things like identifying inheritedable deseases.
Lars
--
Reality or nothing.
It's possible that all this "junk" DNA still has uses that we haven't seen yet.
The "junk" DNA is a coded message, implanted into the first humans by our creators, passed down through the generations, waiting for us to find it. I reckon that distributed.net will start a project to decode the message.
*has been watching too much Star Trek*
-Stephen
Although the malfunctioning genes were quickly eliminated during human evolution (now it changed, because people with even grave diseases can still live or even reproduce), there are some DNA sequences which are more prone to errors during replication than others, due to the DNA chemistry and nature of eukaryotic replication mechanisms. Of course, theoretically such "weak spots" could be eliminated by natural selection - but in most cases probably the enhancements in the repair mechanisms would cost more then a sporadic mutation. Don't forget that natural selection does not act on organisms, but on genes.
Regards,
January
Imagine this:
You are a computer programmer, faced with the task of decyphering almost a gigabyte of machine code, which was written by billions of programmers making random changes and seeing if the result was an improvement.
And you thought Perl was hard to read...
--
Patrick Doyle
Patrick Doyle
I mod down every jackass who puts his moderation policy in his sig. Oh, wait a sec....
from what i understand i don't think the whole thing will be done until sometime in 2003. at least thats what i heard. now that they know how to do one of them, the rest should be relativlyeasy to map. we will just have to wait and see. hopefully after we have mapped it all then we can start curing all those nasty little dieses that have been killing us off for so long.
Junk DNA is one of the worst misnomers possible, coined back when researchers honestly believed that non-coding DNA had no purpose. I believe what they mean is junk = introns + intergenic space, i.e., all non-coding sequence on chromosome 22.
... "How will what we're learning about our genes today affect medicine X years down the road?" where X = 10, 20, 50, 100.
This is a bad misnomer because the junk DNA is required for the proper expression of all of our genes. We have on the order of a trillion cells, so 100,000 proteins (all combinations of 2, representing gene A regulating gene B) can only differentiate, at best, 10 billion. The complexity, and where a lot of the interesting research will be in a few years, is in how these genes are regulated to properly create all of our cells, each of which "knows" what it is, and what it is supposed to do.
I must also say that I am surprised at their estimate of only 42% non-coding. The usual estimates are of ~3% (at most 10%) coding sequence in the genome as a whole, which gives a greater than 90% non-coding estimate.
So... the interesting question, maybe I should send this to Ask Slashdot, is
-Todd
"I'm almost done with classes! Again!" (me)
Having read them all the Christan Science Monitor has the best/most informative article and AP or MSNBC are the lest informative.
Read it for yourself before you flame
Remember that DNA formed by trial and error. There could be "commented out" code in the genome that is no longer used. If there is no selective advantage in deleting it, it will hang around.
--
Patrick Doyle
Patrick Doyle
I mod down every jackass who puts his moderation policy in his sig. Oh, wait a sec....
Discover had a short article on the so-called "junk" DNA. Apparently, these sequences have served legitimate purposes in our evolution, doing things like enhancing or reducing the effect of other genes.
If anything, these genes with unknown purpose add to the genetic diversity of the species. Who knows, maybe they may confer some immunity for as yet undiscovered virus.
BTW, today on NPR there was a short news piece on genetically engineered crops and their (possible) deleterious effects on other plant species. We've seen articles on Slashdot (?) about glow-in-the-dark Christmas trees too. By introducing these genes to the world (controlled until some bee cross-pollinates a similar uncontrolled species) we are crap-shooting. I am not yet convinced that genetically engineering crops is ultimately economical.
for automated sequencing (on the Perkin-Elmer machines), if you use some of the new Taq dyes, and the new gel methods, you can EASILY get 700+ bases per reaction. also, the repeat sections are more of a problem to the "clone by clone" method - you can't design good sequencing primers that differentiate between the areas being sequenced. with shotgun sequencing, you have a slightly better chance of putting repeat areas in their proper place (this depending on the legenth of the repeat, of course!!)
For those of you who can't stand not having the source code for everything you use , you can download the results of the human genome sequencing project from http://www.ncbi.nlm.nih.gov/genome/seq/ .
(Before you all rush and slashdot the site, please ask yourself whether you really need to download over one gigabyte of what is, to the uninitiated's intents and purposes, a random string of A's, T's, C's and G's.)
There is an interesting article in the December issue of Discover (not yet online), about transposons, which are what junk DNA really is. Transposons create random mutations in our genetic code and may be responsible for the astoundingly fast development of Homo Sapiens (which was faster than random gene mutations would predict) - humans have more transposons than our closest kin, the chimpanzee. Get the magazine - there's a bunch of other stuff in there too.
Visit
dont you mean TPN(telepath networking) address?
Everything has a purpose, even "Junk" DNA. I think that in addition to the other reasons that have been mentioned, it is just there to take up space. Seriously, if a chromosome were only large enough for the "real" genes, there would be less of a chance for the enzymes to bump into it. I'm no scientist, though. Maybe the junk DNA helps to point the enzymes to the right gene or something. But that's not my point. My point is that it has a purpose that we probably will never completely understand. Genetics in the context of evolution is kind of like the monkeys and the typewriters. We will never know what was actually going through their minds when they reproduced Shakespeare, only that they did.
Before you go blindly accepting my opinions, let's propose a few alternatives, shall we?
That's enough! You should have been able to tell that they're all bogus. Well if how much junk DNA you have represents how pure you are, I'm highly adultrated with imperfections. Darn.
Ken
-------
CAIMLAS
~/ssh slashdot.org ssh: connect to host slashdot.org port 22: too many beers
I email them this I wish 97% was finished in other professions like mine. The other 3% of chromozone 22 probably holds the secret to creation of the universe ...they should finish it for real, its just like science to try to round everything off, but in this case 3% of an obviously vital chromozone will lay undiscovered all because they decided it was time to call it quits and go on to the other ones. Oh well and so it goes with grants . . . I guess it was time for a little press to make sure the money spent was justified for 1999 so you could continue the work next year. Keep up the good work,
What exactly does "mapped" mean?
In general it means that the location has been established relative to known markers. In this case, though, the chromosome has been sequenced : the areas have had their composition established base-by-base.
Does that mean they know what all the bases are in the average human?
Roughly, yes. The sequence is a mosaic derived from several people.
Does this imply any knowledge of the pattern of such variations?
Not in itself, no, although other work is continuing to establish this.
Does it imply any knowledge of the function of the encoded proteins?
Again, not in itself. Many of the identified genes have been studied already. Others have similarities to genes already known, either from humans or other creatures. Some have been inferred from features of the sequence itself and are of totally unknown function.
A biology class I took said that human DNA was 96% junk (not protein encoding).
Was this biology class wrong?
No. The vast majority doesn't code for protein, and most of this has no known function. Closely related species have widely differing amounts of this, so (together with other reasons) the current hypothesis is that it doesn't do much that's useful for the organism. Some of it is composed of "selfish" elements such as transposons : it might be the case that in a looser sense a lot of it is.
I extracted the Junk DNA and respliced it so that it would stand without the DNA that is neccessary to humans, inserted it in a cell and watched it grow. 5 hours later to my horror it took a flat retangular shape, black lines appeared on a white surface. They connected to form letters in clear English which read...
"Mr _________ , You have been selected as a final entry for the Publisher's Clearinghouse largest drawing, enclosed is a Check worth $30,000,000 if you have the winning number!!! Please open and send your entry form within the next 24 hours, and get a GUARANTEED prize."
I tried the Junk DNA of other chromosomes and got ads for term life insurance, timeshares, and then the Junk DNA materialized in front of me into a pushy Amway distributer!!!! The horror!!! Cellular SPAM!!! AGHHHHHHHH
It hasn't just been mapped, it has been fully sequenced (with a few small gaps). According to the original article, only about 3% of the sequenced DNA is actually 'exonic' (i.e. stuff that ends up as 'spliced mNA', the final step before 'translation' into protein). The 42% figure presumably comes from "the 41.9% of the sequence that represents tandem and interspersed repeat sequences" (not exactly 42, so no need to consult the Hitch Hiker's guide!). But there are various other kinds of noncoding DNA too, including some sequences that are known to be required for expression and regulation of the genes (promoters, enhancers, etc.), untranslated sections of exons, introns (sequences which are 'transcribed' from the DNA into RNA, but are spliced out before the RNA is translated into protein), and intergenic regions. Apart from the protein coding sequences and regulatory elements, most of the rest (including the introns) is of uknown function, and usually classified as 'junk'. It's interesting that some organisms (including Fugu, the 'Puffer Fish'), have 'compressed' genomes containing a much lower proportion of 'junk' (presumably because God remembered to strip the comments from his source code :-)
. html
For information on diversity in human genomic sequences see:
http://www.stanford.edu/group/morrinst/hgdp/faq
One sentence from the original article that is worth quoting to Slashdot readers -
"Making the sequence of human chromosome 22 freely available to the community early in the data collection phase has benefited studies of disease-related and other genes associated with this human chromosome"
which sounds a lot like 'Release early, release often' to me. At least this part of the genome is now Open Source.
How many people had the word, "Gattaca" pop in their minds when they saw the mention of finding the human gene that could lead to heart problems?
-Vel
You don't have to do the complete sequence of many people in order to find out how the DNA varies from person to person. Once you know the rough sequence of a length of DNA, you can read the exact sequence of that length from any sample of DNA. Think of DNA as content-addressable memory: you can't access it randomly, or even sequentially, but if you know the sequence of a couple of small lengths, each a dozen or so bases long, and seperated by a few hundred bases, it's easy to read the few hundred bases between them. To find out what a length of DNA from any person looks like, find the same piece of the Canonical DNA sequence you just downloaded from the HGP, use it to design the two short primers (and make sure that they're unique over the whole genome), yank out the bit of interest from DNA sample and sequence. There are projects going on currently to do just this sort of thing on large scale. They are only possible because we already have a large fraction of the Canonical sequence.
I read an very interesting book in college last year called the Biotech Century about gene technology. I don't know much on the subject but this brought alot to my attention.
I highly recommend this book if interested in knowing of what has been developed and patented and topics like the such in genetics: engineering and technology.
The 42% doesn't include all the noncoding DNA, just the stuff in tandem and inverted repeats. Only 3% of the Chromosome 22 DNA is exonic (& some of that will also be noncoding).
"Is it just me or is there not a big difference between causation and association? Seems to me along the line of correlation vs. causation."
I'd go ahead and say that association vs. causation is exactly the same thing as correlation vs. causation. However, while a causitive relationship implies a correlative relationship, the reverse is not true. Two phenomena can have a high correlation between them, but not have a one be directly causing the other. They might both, for instance, be caused by an unknown third variable.
Anyway, this has been hashed and rehashed forever...statisticians and behavioral scientists have had this indoctrinated in them forever. Sometimes the media screws it up, however, when they go and "report" the results.
"UNIX" is never having to say you're sorry.
Of course, that would be awful, but what about the installation process? Everyone would want to improve it.
:-)
Currently, parents are forced to accept all the default values, and many are clamoring to get at least an installation menu, to be able to choose hair color, IQ and IP address
now that they know how to do one of them, the rest should be relativlyeasy to map
In fact all chromosomes are now being sequenced. Check this page for details.
I doubt having finished one will make much difference. It's just an interesting milestone.
I'll do it for cheesy poofs.
Well thats one theory that has some really big clues behind it. It seems that these junk DNA may contain all the "subtle" differences needed to make a human different than say an orangutan. We share about 95% of the same DNA with our closest evolution cousin and the difference may be in what the junk dna does (i.e. turn on certain enzymes, proteins, etc. at specific times). Damn, I just read something about this....
The article I read eluded to a "war on the molecular level" if that rings a bell. I'll
post more later when I get home from work if anyones interested.
Does that make it "holy writ"?
Bantam Dominique roosters crow a four-note song. Once you've heard it as "Happy BIRTHday" you can't NOT hear it that way
Reminds me of a story by Phillip Dick called the Minority Report. It's in production for a movie now. Tom Cruise plays a guy who is arrested because the authorities calculate that he will commit murder soon.
Be insightful. If you can't be insightful, be informative.
If you can't be informative, use my name
Many guys have asked questions the answers to which can be found in a good book. Here's one .. I got this book recently and IMHO very well written. Informative and clearly written. (It does not assume that the reader has a college degree in genetics or molecular biology.) It is Everything You Ever Wanted To Know About the Human Genome Project ... Peter Sudbery, Human Molecular Genetics HUMAN MOLECULAR GENETICS Addison Wesley Longman 1998 It even has a webpage that provides updates to this fast moving field. http://www.awl-he.com/biology/sudbery/molecular/ho me.htm
This is pretty much obligatory here, so...
Check out the Human Genome Project's website at http://www.ornl.gov/TechRe sources/Human_Genome/home.html
------
If a tree falls on an anonymous coward yelling 'first post' in the forest, does anybody hear?
Congratulations to all who participated in its sequencing. We look forward to the first draft of the human genome by spring 2000.
I'll do it for cheesy poofs.
Gab
"unemployable underclass".
That "underclass" will strive to become as large as possible.
Remember at the end of 1984, the fake society is falling apart. The proles, being the vast majority, are poised to take over.
If "most" people are in this underclass, they have
the opportunity to organize and the sheer size of the class makes them predominate.
As long as they are the minority, they haven't a chance.
-fb Everything not expressly forbidden is now mandatory.
it reminds me of space exploration and atomic power: huge sums are spent to make few richer and more powerful, while driving billions of people into misery. why not pursue causes that really can make more people happy and live a dignified life, instead of spending unimaginable sums and energy for projects that endanger our freedom ? if you want to stop patenting of life, join a mass movement, fight these patents directly. there is no other way, in the long run. kind regards philippe, http://StopLifePatents.org/
( ...Global agreements being discussed by WTO trade ministers in Seattle this week include the Trade Related Aspects of Intellectual Property (TRIPS) that allows private ownership of commercially valuable knowledge such as software, agricultural innovations, and pharmaceuticals. WTO members are currently reviewing clauses of the TRIPS agreement related to the patenting of plants, animals, genetically engineered organisms and other forms of life. ...)
I forget what it's called, but what if those fragments of DNA are "leftovers"? Wonder if some of that 42 percent junk dna is something like that, and has no proteins as it doesn't do anything *anymore*?
Disclaimer: IANAGR (I Am Not A Genetic Researcher)
Also, I must admit I don't trust mankind in general... I hope this knowledge of ourselves doesn't get misused/abused. I know any advance is a double-edged sword, I just hope this sword is handled with wisdom to do the right thing with it.
David
bash: ispell: command not found
This sig left intentionally blank.
TPN? What's that?? Telepath networking? My searches found nothing.
:-) Did you know that IPv6 promises an address to every human on the planet, and also to their pets ?
:-)
Is this proprietary technology? Are you trying to reinvent the wheel, lock us in your technology and decommoditizing the best communication protocol for parents and children, the ol' trusty IP? Did you know that if any member of the family stonewalls for any reason, IP can route around it ?
OK, you can send samples, but make sure to include the source too!
Will this finish a task? No, it is just a beginning - having the sequence, the real work starts: searching ORFs (Open Reading Frames - sequences which could possibly be genes), running database searches, and slowly passing to the most exciting fields of modern molecular biology - from genomics to transcriptomics and proteomics. Transcriptomics is looking for genes, which actually got expressed, and proteomics - similarly, looking for expressed proteins. Making transcription / translation (translation is the process in which proteins get synthetized) profiles can lead us to 1) function of proteins (e.g. protein X. is expressed under this and this conditions, so it must take part in this and this metabolic response) 2) regulation - DNA is a single strand, but various enzymes are present in various copy numbers under various conditions.
Those are enormous projects. A lot of work has to be done before the raw sequence will actually be of any use; nethertheless, it is a milestone of molecular biology and will be a fine achievement for the end of our century.
Another project will be to determine the variability of human genome: screening for different gene allels, mutations etc. This will be one of the most important goals in human genomics in the next few years.
Whats on the catch... erm, chromosome 22? 22 is 33,400,000 bases long (Mycoplasma pneumoniae, one of the smallest bacteriums, has about 816,394 bases). It contains several already known genes responsible for various genetic disorders, and possibly a gene responsible for certain types of schizophrenia.
By the way, a much better source of information is the Nature science update page - the original scientific publication has been published today in Nature.
Regards,
January
Let's see, how many things can we find that are amazingly 42. Let's see the constant that explains universal expansion. The % "junk" in chromosone 22 the answer to the question "how much is seven times 6?" Come on people, let's find some more
I wouldn't start systematical study from 1. chromosome so I presume it was the one they knew most of, how's study for others doing?
- Kaatunut
Oh just remembered, (after posting article) the constant is known as "Hubble's Constant" and yes it == 42
It is far away from Open Source. Many companies are applying patents for the gene diversities they found whcih are good or bad to human health. And this is the biggest money pool ever in the world in some people's eyes. It is scaring
Mmm resistant to malaria... well there's the good side I was looking for. Also, does this mean that most of mankind was prone to malaria back then? We don't see lots of malaria here north... Heh yeah, I've understood it's common misunderstanding of evolution, also, that people think it makes what's "good": it does what's propable, which leads into kludges like this.
- Kaatunut
Are they using a particular individual's DNA .. ?
:-)
After we finish mapping some DNA we can go munch on some grindage, buuuuuuuuudy!
We're going down, in a spiral to the ground
I heard somewhere that the sequence "GATTACA" actually appears at least once in every single human gene (this being why they chose it for the movie title). Furthermore, it's the only sequence that does that.
I'm no genetic researcher, and neither is the person who told me this, but I suppose it's possible.
I'd be careful calling it that. Someone proposed the idea that it's mutation fodder (that is, a safe place for mutations to occur). That's a possibility.
But there've also been posts talking about a lot of redundancy and such. It's possible that all this "junk" DNA still has uses that we haven't seen yet. I guess we won't know until we've mapped out the whole thing.
Who knows... maybe someday we'll all have something like a mini-RAID coded into our DNA.
The human genome project is funded in the US by the National Institutes of Health and the Department of Energy, and in Britain, by the Wellcome Trust, a charitable organization.
Every base that we sequence is put in the public domain.
We strongly oppose the patenting of sequences. Some of our strategies are designed to preempt attempts by companies to patent sequences from the human genome.
Undoubtedly, the mapping of the human genome will revolutionize medicine during the 21st century. But it opens at least one can of worms... Will individuals have rights to their genetic map? Like any information, if this gets out, could this information be used against a person.
Say, if you carry the gene predisposing you to some form of cancer, could an insurance co. deny you coverage for that condition? Could an employer not hire (or fire you) because you have a genetic tendency toward alcoholism? Could police or the FBI tag you as being a potential criminal because of some combination of traits in your genes?
Stuff like this worries me sometimes.
Mike Eckardt meckardt@yahoo.spam.com
Yup, we put everything in the public domain.
This is slightly off-topic, but I remember reading about how a genetic algorithm (am I thinking of the right thing? I'm talking about the programs that write themselves) that was made to design some kind of circuit layout to do some task came up with a design that was totally convoluted, but it worked.
My point is, in this working design, there were parts of the circuit that weren't connected to the rest (i.e. didn't affect the input/output). What's more interesting is that there were other disconnected parts of the circuit that *did* affect the input/output.
Could this be a case of man-made technology imitating nature?
The thing about cycle cell anemia is that it has advantages for people with one normal and one cycle cell gene. Oh and it is less common in people who's ancestors come from locations without malaria. And based on mitochondrial DNA the human race has been traced to one female proto-human. All evidance puts this individual in Africa (most evidance) or in Asia (less evidance)
Whoever patents the X chromosome will make bank. No reproduction without a license.
--
"I was a fool to think I could dream as a normal man."
Several people seem to be wondering how are the rest of the chromosomes doing. The completion of the 1st billion nucleotides was recently announced in Nature, so approximately 1/3 of the whole thing is done. Expect more complete chromosomes in near future. BTW I'm participating in organizing a bioinformatics conference, which in progress right now. The person from the Human Genome Project will only speak tomorrow though, so I'll be a bit wiser after that. The billionth base was G (= guanine). How that was agreed on between the dozens of labs doing the sequencing, I have no idea.
AFAIK, most of the genome sequence being produced by the HGP is from a single male individual. (Male, because we need to see a Y chromosome too.) I dunno for sure about Sanger, but WashU and Whitehead in the US are working from the same clone library.
The identity of this person is a closely guarded secret, as well it should be: this person's genome sequence will be available on the Internet. We'd like to avoid a nightmare scenario where a well-meaning "genome hacker" discovers a fatal disease gene in the sequence, and calls this guy up out of the blue to tell him.
That's just an extreme example. Basically, there's serious privacy and confidentiality issues. We consider the genome sequence to be a "reference sequence" or a "typical example", and we don't need (or want) to know who it came from.
Portion of its DNA which is "junk" (encodes no protein): 42%
See? 42 has to be the answer to Life, the Universe, and Everything! Even our DNA knows it!
You should never take life too seriously - You'll never get out of it alive.
Now it all becomes clear..
42% of our this chromosome is "bloatware". Poor Microsoft engineers can't be helped.. they've been battling this urge to include stuff in their code that does nothing and just takes up space. Kinda like salmon feeling the urge to return home to spawn.
Well, this should take care of some of the lawsuits against them.. "This bloatware, it's not our fault! Quit picking on us! We're products of our GENETIC HERITAGE and we can't be blamed for it! Help, help, we're being oppressed!"
Soon we will be Open Source. I fear that the temptation to develop and try patches will be irresistible to many.
From the CNN article:
More than 30 human disorders are already associated with changes to
genes of chromosome 22. These include a form of leukemia, disorders
of fetal development and the nervous system, and schizophrenia.
From the introduction:
some of 22's genes can cause "heart defects, immune system disorders, cancers, schizophrenia
and mental retardation."
Is it just me or is there not a big difference between causation and association? Seems to me along the line of correlation vs. causation. Anyway, I believe that scientists have still
a long way to go before they find the genes that cause certain disorders. And then they will still have to prove that these genes are in no way responsible for any other functions in the human body to safely alter them. Seeing all the good possible uses for medicine it still gives me the creeps how through the use of genetics and monocausal argumentation a new "scientifically backed" racism could emerge again. Now don't scream technophobe but how would you all react once the genes allegedly causing things like alcoholism, homosexuality, autism, criminalism, lazyness or whatever unwanted psychic or physical trait you can think off where identified? Have we got our ethics ready to handle this or will it be "what can be done will be done"? On whom will we test genetic engineering for a better race? The inhabitants of prisons, mental institutions, military institutions or just unwanted embryos? Will we allow babys to live with these disorders? Will we allow people to work without mandatory testing of genetic normality?
History has shown that scientists have often produced technology that was later misused by the
willing. Hopefully this time they think more before they hand this Pandoras box to the masses.
And do you know why I want to see this on the news?
It is because I would really like to see reporters try to get their mouths around diseases such as Myoneurogastrointestinal encephalomyopathy and Lysosomal alpha -N-acetylgalactosaminidase deficiency.
They aren't that hard, but still... I want to see it.
------
If a tree falls on an anonymous coward yelling 'first post' in the forest, does anybody hear?
Now we can use this new information for the good of humanity!
Just think. Now you can hack your friends genetic information and make them cancerous! (nmnot really) But seriously, this could help prevent alot of problems later in life and stuff.
Your mouse has moved. Windows NT must be restarted for the change to take effect. Reboot now? [ OK ]
Saying that a chromosome is "mapped" means that you know the location of some identifiers on the chromosome. Thats a far thing from sequencing something. Also not putting up the link to sanger proves someone has not been checking their facts. Bad journalism!
It is still an open question what role the junk DNA, technically called introns plays in organism development. Unlike the simple unicelluar critters (prokaryotes) such as bateria, all higher level organisms (eukaryotes) have these long non-coding sequences which have been retained across evolutionary generations despite the extra energy/space required. The whole area is akin to the physists search for all the various subatomic particles after the cracking of the atom. We can see the bits and pieces, we can assemble the various sequences, but there's no unifying standard model of how or why. With Nobel prizes and new killer apps in the air, it is not surprising that universities and institutes are throwing money into the research.
:-). Fun times ahead.
The 19th centure might have been the dominance of physics and engineering but there's a lot of speculation and anticipation (especially by the empty hands of the biologists and zoologists) that the next century will be their turn at the gravy train
LL
There's an entry in their FAQ that gives an answer to the question. Is the FAQ correct?
Sure, microbes. But can companies really
patent variants of human cells? Or patent DNA altogether?
Yes, if these things are useful and articles of manufacture.
For example, if a company patents a "variant of a human cell" that can regrow tissue, why on earth would you want to deny them patent protection?
Another example, if a company expends a great deal of effort locating a gene associated with a disease, why shouldn't they be afforded protection?
If you have a problem with living things being tinkered with, well that's your own Luddite opinion (IMHO). But it's exactly this sort of tinkering that has and will continue to confer great benefits to humanity. Incentives for this (expensive, time consuming, filled with dead-ends) tinkering, in the form of patent protection, is a Good Thing.
IMHO, of course.
whuppy enjoys smelling like diesel fuel
in this case 3% of an obviously vital chromozone will lay undiscovered all because they decided it was time to call it quits and go on to the other ones.
Work isn't entirely finished on 22. The analysis and summary has to be published at some point, and that point is when all the routine work is finished, and all the usual techniques have been tried. A few remaining problems are still being worked on, and I imagine that new techniques will be tried for remaining areas as they become available : this has happened before to bring previously-covered areas to a higher standard. The goal is still to cover all euchromatic parts of the chromosome if reasonably possible.
First of all, "junk" is a loaded term, which is certainly evidenced by all the nonsense it has spawned in this discussion. So let's do this by enumerating the different types of DNA a typical eukaryotic genome contains:
1. Coding Regions. DNA that gets transcribed to RNA. RNA transcripts in turn have exons, which get translated into proteins, and introns, which get spliced out before translation. Why this added level of complexity? Many reasons. In sexual reproduction, new chromosomes are produced by mixing and matching old chromosomes at random. It's more likely for the new chromosome to be functional if the crossover point is in an intron because crossovers can introduce mutations, especially a nasty sort of mutation called a frameshift which would render everything downstream unintelligible. Exons also allow for a certain modularity of function, evolutionary mutations can involve entire exons being combined instead of having to try changes on a base-by-base level.
2. Regulatory regions. DNA that turns other bits of DNA up or down. Mainly used to control transcription, but also used to control DNA replication.
3. Structural regions. Eukaryotic DNA is a huge, long, string requiring a certain amount of overhead to prevent it from becoming an unmanagable tangle. Lots of the chromosome is dedicated to binding to structural proteins, generally known as histones, around which the DNA is wound. Also centromeric and telomeric proteins.
4. Repeats, cryptic genes, etc: In order to avoid overloading the term "junk," let's call this category "cruft." Cruft arises for lots of reasons. For example, sexual reproduction produces gametes, and it's far from perfect: Regions get repeated, regions get dropped. So called cryptic genes are probably the result of a spliced RNA being reverse-transcribed back into DNA and reinserted into the genome without introns or regulatory elements. What's useful about the cruft is that it provides fodder for further evolution.
In summary: Eukaryotes are big and complex, which means that you have to allow for a certain amount of overhead and slop.
I hope this has helped.
whuppy enjoys smelling like diesel fuel
You know that patented organism that eats oil spills? That's a pretty darn useful organism, wouldn't you say? Well, guess what: That organism was made by humans. Admittedly it was made from parts found in nature, but the manufacture of these bugs took a tremendous expenditure of time, money, and human effort. They didn't just magically appear.
So I ask you, what, exactly is wrong with patenting these useful bugs?
Or let me put it another way, what is the incentive to expend vast amounts of time, money, and human effort to produce these useful bugs in the absence of a patent system?
P.S.: Jeremy Rifkin has no grasp on science or the law. I strongly suggest you ignore his nonsense.
whuppy enjoys smelling like diesel fuel
Douglas Adams should be worshipped as a prophet.
Proteins need to fold up in characteristic ways because they do so many different jobs in the cell, both as builders and as structural materials themselves.
DNA needs to be able to fit nicely into chromosomes that don't have sharp edges that might puncture the nuclear wall. Maybe the DNA would give before the wall did, but then you'd have chromosome damage which isn't a wonderful thing. There may be other constraints on how DNA decides to fold, I don't know what they are.
WWJD for a Klondike Bar?
A biology class I took said that human DNA was 96% junk (not protein encoding).
Was this biology class wrong?
Is there an enormous devation in percentage of junk from chromosone to chromosone?
Or did a Douglas Adams fan do some subtle hack on the results?
Bottom line: human chromosomes may be patented. Fight it.