The article refers to the 3 billion base pairs in the human genome, not 3 billion dollars spent. (I suspect that far more than $3 bil has been spent on the genome project.)

Knowledge of the human genome will be invaluable in the treatment of diseases, understanding the effects of toxic substances, and eventually conquering cancer. Public access to such information will eventually repay our investment a hundredfold.

Private businesses should under no circumstances be allowed to patent human genes or charge for access to human genome information. Corporate ownership of this information would be a recipe for escalating health care costs and genetic discrimination.

Human DNA.... what... is this on? Do we want people like Hitler and Al Capone back?.. Are these scientist gone crazy? What's next... creating dinosaurs....

It appears that the immortals are still with us.

The people who thought cleanliness is an evil thing are still here.

The people who thought vacination is an evil thing are still here.

The people who thought x-rays is an evil thing are still here.

But they are as irrelevant today as they were in the days past when they fought these other advances.

I, for one, look forward to the advances in medicine this study will bring.

I find The Human Genome Project an exciting scientific pursuit. Just think: if we could change color ON DEMAND, it would erase racial prejudice! That cause of fighting would be removed. It would make it impossible to make money off racial hatred. It would get us ready to move on to bigger things, like finding life on other planets.

Andrew LaFollette: "Knowledge of the human genome will be invaluable in the treatment of diseases, understanding the effects of toxic substances, and eventually conquering cancer. Public access to such information will eventually repay our investment a hundredfold."

I agree completely.

"Private businesses should under no circumstances be allowed to patent human genes or charge for access to human genome information. Corporate ownership of this information would be a recipe for escalating health care costs and genetic discrimination."

That is a good way of ensuring that private business never experiments with new and beneficial genes and never offers human genome analysis to the public. Scratch off half the benefits you were hoping for in paragraph 1. Imagine what our pharmaceutical industry would be like if nobody could patent new drugs. And, of course, biotech research will simply flee overseas to any country that does allow it to profit by designing and patenting new alleles.

I believe that each individual should have a property right in his or her own genome; no using or duplicating people's genes without their permission.

This is the best news from the world of capitalism in recent times.

But it is also said that the knowledge gained could be used to synthesize diseases which attack only certain group of people .. similar to the type which killed the native americans.

Complete caution must be taken to avoid misuse of the knowledge.

Daniel Baker-

I don't wish to prevent pharmaceutical companies from patenting drugs. I wish to prevent them from patenting human genes. One cannot patent other pre-existing natural resources such as petroleum or silicon... and yet there has been a world of research performed with these resources. A company can patent a drug which is designed from information in the human genome, or a method for DNA sequencing or modification, or a tailor-made allele which does not exist in nature, but the human genome ought to be a public resource. This is merely a logical extension of the laws which govern the chemical industry. You can't patent oxygen.

Free access to this information will STIMULATE research, not hinder it, because it will allow every research institution, public or private, to pursue any genetic research they choose.

I certainly agree that the US should not unilaterally alter its patent laws. This needs to be a global convention.

Andrew LaFollette:

All right, it seems I misunderstood you. You merely wish to prevent private business from patenting already existing human genes that they did not develop. This sounds reasonable to me, and although I don't know much about patent law, I doubt it would require any changes to the existing law; as you pointed out, you can't patent oxygen, or something else that you didn't develop.

I saw an interesting article the other day - some woman in the UK wanted to patent her own genome, because she had spent 30 years working out who she was, and didn't want to get ripped off.

More power to her, I figure - everyone should patent every gene in their bodies (note there will be a long list of "co-inventors" for the vast majority of them, some of whom will be monkies etc.), and declare the sequences (tho not who they're from) public domain - people who don't like the genome project can stay out of it, and it will prevent big business from seizing control of sequences they didn't invent.

I know it sounds like a joke (and I'm sure that's why she started it) but is this idea necessarily legally invalid? Anyone got any ideas?

Howzat for a crazy idea?

Mark

Since when is it a crime against humanity to be a "capitalist pig" to engage in the business of mapping the human genome? Exactly what authority do the U.S. Prez and U.K. PM have to dictate to private business around the world that they should immediately publish results? Let's get real folks!

These companies through their thousand of stockholders have invested billions of $$$ to get to this point. Now they should hand results over for free for the betterment of humankind? Clinton and Blair live in Fantasyland, where they should both return. Thank God this country hasn't turned completely socialist yet.

Think just one step further. Suppose big brother USA and UK governments come in and confiscate the results. WHO is then going to pay for the next step of developing all this new knowledge about genes to cures for disease and all other human ills? The government? (e.g. you and me?) And tell me exactly why I should trust Uncle Sam to make more ethical decisions about the the use of this knowledge.

No thanks; keep the results in private hands, and whatever profit is to be made from the research belongs to those who earn it - not steal it.

Walt Bishop

Walt B: "Since when is it a crime against humanity to be a "capitalist pig" to engage in the business of mapping the human genome? Exactly what authority do the U.S. Prez and U.K. PM have to dictate to private business around the world that they should immediately publish results? Let's get real folks!"

"These companies through their thousand of stockholders have invested billions of $$$ to get to this point. Now they should hand results over for free for the betterment of humankind?"

Walt, I see where you're coming from, but you're badly misinformed about the Human Genome Project. This mapping wasn't done by private business, with Clinton and Blair then "ordering" the biotech companies to publish their results. The whole Human Genome Project has been a government project from the beginning. The U.S. portion of the project was planned and funded through the Department of Energy and the National Institute of Health. I believe that the British portion of the project has been entirely government-run from the beginning also.

Now if this research had actually been done by private companies, by all means I would say that they could keep the results of their own work secret. But the Human Genome Project is the result of government work, paid for by taxpayers, and it is perfectly appropriate that all the taxpayers get to reap the rewards.

I am somewhat mystified as to why the biotech companies took such a dive on this decision. Did the investors think the govenment was going to spend billions of dollars mapping the human genome and then just lock the results away in a safe somewhere? Or that the feds were going to simply hand the data to them, and not their competitors, in a locked box? The only way I can make sense of it is that some of the biotech companies were hoping to map the human genome first, and lost the race. But the HGP has been going on for something like eight years; the investors had to see this coming.

Walt B.-

The overwhelming majority of the human genome project was completed by university and government researchers using federal funding, with the intent of making the information free to all scientists. Most of the techniques used in the project were developed by university researchers and published freely... which has long been the spirit of academic science.

Somewhat late in the game, private biotech companies started jumping into the research and patenting genes which they discovered first, with the intent of charging researchers for the information or keeping it completely private.

If the events had actually happened the way you portrayed them, you might have a valid point. In reality, however, this was a government project from the very beginning, because it was initially expected to take 20-30 years and nobody was willing to invest in it. The biotech companies in this particular line of research are merely attempting to get a piece of pie for themselves out of a project that would be completed soon with or without their efforts. It will be far better for all humanity (except for a handful of investors) if this information is freely disclosed.

Concerning DNA human genome research. When(intended used in positive ways of course)this seems to be the medical cure-all,or everyones dream come true. If researchers can stop or end diseases and cure human suffering,(by a medically ethical means)of course,no sane person's going to object.

I believe that most wise citizens of the world,always will gladly encourage MEDICAL changes positive. If cures are to be offered/intended USED FOR EVERYONE,only those to afraid to utilize offered options will thereafter suffer in pain .

Definitely, the companies who have sequenced the human genome should be able to profit from it. Afterall, they invested the money and effort to do it. Remember a few years ago when the government announced the human genome initiative, and said that it would cost $3 billion and take 30 years to do? Thats because government beaurocracy is incapabible of innovation. The genone will be complete this summer because start-up companies innovated and developed faster, more-efficient methods to sequence genes, and did it in the last 5 years. Damn right they deserve to get rewarded for it.

There is a problem with medical care being too expensive. Being someone without regular medical insurance, I am well aware of this nasty reality. However, this is due to excessive regulation by the FDA not to mention the "bioethics" jerks on the government payroll (read: your tax dollars) who think they have the right to decide what kind of gene therapy is "morally acceptable" or not.

If you really want to do something about the high cost of medical care, I suggest you cruise on over to the Life Extension Foundation at www.lef.org and join them. They have a 20 year history of bring affordable medical advances to the general public. The LEF deserves any support you can give them.

For those of you who think capitalism is to blame for high medical costs, explain why semiconductors and computing technology keeps getting cheaper and cheaper all of the time? If the same capitalistic principle that drives "Moore's Law" were to be allowed in biotechnology, we would probably have a cure for ageing in the next 10 years and would be able to give the middle finger to anyone who says you have to settle down and live a conservative, boring life, because you have to save for old age or have kids.

Let's say I developed a gene therapy that made it so that you would never grow old that you could live forever young. How big of market do you think there would be for this gene therapy? A big one, right? It'd make me an overnight billionaire. It'd make me richer than Bill Gates! You know damn well that some of these silicon valley entreprenuers are working on the "immortality" treatment right now. Ask yourself, do you think the FDA would approve it. What about the bioethics jerks that live off your tax dollars? Do you think they would approve it?

No, excessive government regulation, not capitalism, is to blame for the excessively expensive medical care in the U.S.

Kurt Schoedel: "Definitely, the companies who have sequenced the human genome should be able to profit from it. Afterall, they invested the money and effort to do it."

I feel like a broken record here. There weren't any companies that sequenced the human genome. It was done by the U.S. and British governments; the U.S. agencies responsible were the Department of Energy and National Institute of Health. If you don't believe me, look at the Human Genome Project link at the top of this page under "Related Sites."

I don't blame "capitalism" for the high health care costs in the U.S. Governmental regulation does play a large role in increasing these costs, as you say. I have long advocated reducing the FDA to an advisory role, with the decision ultimately left up to the patients and their doctors whether to take the risk of a therapy that is not yet FDA-approved. But none of this is any reason why the rewards of the Human Genome Project should be reserved to the biotech companies. The Project was funded by all the taxpayers, not the biotech investors.

Kurt Schoedel: "You know damn well that some of these silicon valley entreprenuers are working on the 'immortality' treatment right now."

No, I don't know that. If you know it, kindly tell me how you found out. I would be intrigued.

Kurt Schoedel: "'bioethics' jerks on the government payroll (read: your tax dollars) who think they have the right to decide what kind of gene therapy is 'morally acceptable' or not."

I am not quite sure what you meant by this. Is it your contention that nobody has a right to decide what kind of gene therapy is morally acceptable? If, for instance, gene therapists altered people's genes without their consent or knowledge in order to gain new data, or altered human ovarian cells in such a way as to cause the birth of deformed babies, has anyone the right to decide whether this is morally acceptable?

I should say that it is debatable whether bioethics should be principally a governmental or a private responsibility, but the importance of bioethics itself is effectively beyond dispute.

Danial, I am saying that noone other than myself has the right to tell me how I may alter my body, with or without gene therapy. There is already a gene therapy that can reverse the effects of ageing on the brain and on muscle tissue. There will probably be a gene therapy for baldness in 3-5 years. My comment is that the individual should have the right to choose whether to undergo these therapies or not. The government does not have the right to deny me the right to enhance myself if I choose to do so. If you read some of the articles in publications such as Time or Newsweek, you will read comments by "bioethics" people questioning whether the individual should have the right to enhance him or herself in this manner. It is precisely these bioethics people who should be fired from the government payroll. They are parasites of your tax dollars.

As far as a medical professional altering your genes without your consent, such an action is legally defined as assault and there are existing laws prohibiting that. My point is that any technology that allows a person to become more than what they are now (for instance, perpetual youth, increased intelligence) should be developed and made commercially available as quickly as possible, at the lowest possible cost. It is the bioethics people who are opposed to this who should be fired.

BTW, Dirk Pearson and Sandy Shaw proposed the "split-label" concept in the early 80's for medical therapies. It is the most reasonable concept of regulation I have heard of, and its time to be implemented has come. Since you also believe that excessive regulation is the cause of high medical costs, I suggest you join the Life Extension Foundation and help us reform the FDA. The LEF is the only organization which has successfully sued the FDA on constitutional grounds. Help us win the battle against the FDA and for consumer choice in medical affairs. Those of us into life-extension are the true "consumer advocates", not idiots such as Ralph Nader and Jeremy Rifkin.

To the negavative responding people I'd like to say. The changing of genetics through medical research is"A GOOD THING".Unless of course you're a perfect genetic speciceman.

We who await the chance to see ourselves cured of diabetes,or heart ailments etc,& extended family changes possible; thank our lucky stars for the opportunities.

Nay-sayers unable to condone or support such medical options,(yes you willing can opt-out);But some of us do want their own family trees medically needed "body up-grades genetically boosted", as I call it.We didn't self inflict or cause these defective genes, but we would willingly,GET THEM FIXED ! ABOUT > Greediness unethically attempted, and any other misuse of this genome information:,(which may or may not ever come to pass):That will be dealt with accordingly,"IF*&*WHEN";Because comon sense proves so few things are truly fail safe.

Friends, As far as Clinton and Blair's statements are concerned, you are missing the issue. The human genome is not new. The companies such as Celera have not created a process or invented anything. Thus a patent can not be issued. It is as simple as that. However, the information obtained can be used to create processes to treat diseases. These processes are patentable. The US government has been clear on its position all along. Basically what happened is Ventner of Celera decided he would force a showdown with the US government. While many government funded programs have been working for years throughout the world to sequence the human genome, a number of companies attempted to do the same in less time. They knew that the governments of the world would never allow the patenting of human genes. The point is to be the first one to know which genes are linked with which pathologies. Then you can sell this information to the big pharmaceutical companies of the world for HUGE amounts of money. The value is in being the first to create new drugs for specific diseases and patenting those. I am sure that if the genome sequencing corporations can also get enough shareholders who don't want to take a hit on the market to yell loudly enough that the companies win some concessions from the US government, then they will consider that a nice bonus. Joe

Not only will mother nature allow us to alter humans, but I think she wants us to.

Close to a quote taken from the movie Gatica.

I think we will be able to accomplish great tasks with the completion of the human genome project. There are though, many concerns that rise due to this new technology. For one, it seems to mainly apply to those that are altered before birth. All those that are not altered, not "perfect", will be discreminated against. Not maybe, its for sure... all you slow minded geneticaly imperfect humans (everyone alive now) will be jobless or even worse. Another concern I have is that there will be criminals that dab into the techonolgy; who knows what they may produce. Most people may think: "criminals are not smart enough to produce anything dangerous."-> WRONG. There are criminals out there right now that produce synthetic drugs...chemicaly inclined talented individuals that will soon have the power to produce humans in the face of evil. We will have a new breed of terrorist. And God, I hope I'm not around for that one.

This is great in many ways but also scary in many other ways. People WILL abuse it regarless of limitations the government may create. Government regulations may deter (questionable) but will NEVER stop anything. Regardless of our discussions here, this will happen, they will complete the project and people will abuse it. I am afraid.

For those of you who question whether we should develop anti-ageing medical technology, I suggest you read last week's issue of U.S. New and World Report. They had an article about the baby boomers turning 40 and about the career as well as health implications of this. Job discrimination due to age is increasing at an alarming rate in the U.S. In the article, a U.S. apellate court judge agreed that it was OK that companies lay off people in thier 40's and beyond, because the ageing process really does adversely affect thier work performance. Furthermore, many high-tech companies find ways to not hire people over 35-40 years old for programming jobs because they think that the ability to learn new technologies and job skills decreases due to the ageing process. In the same magazine issue they described medical breakthroughs that could allow us to live young for centuries (stem-cell regeneration, telemerase therapies, etc.) and questioned whether we had the moral right to do so!

I am 37 years old. I am facing the specter of not only physical decline but the career decline associated with the ageing process, and these bioethics jerks employed by our government and universities question my right to medical breakthroughs that would allow me to be free from the dismal future currently facing me? THIS ENRAGES ME TO NO END.

Consider this: In the past 2 years there have been no less than 3 technologies developed that can reverse the age-related decline the brain. A gene therapy has been developed that can reverse the age-related decline of the muscular system. Telemerase and stem-cell technology offers the potential of being able to completely eliminate the ageing process in humans in the next 10-20 years. Why aern't these technologies being made available to those of us who risk the cogitive decline (and attendant career risk) caused by ageing?

As an American citizen and tax payer, I DEMAND the most rapid development of all biotechnological breakthroughs that can free us from the spector of ageing. I demand that the FDA give fast-track approval of these technologies and I demand that this technology be made available at the lowest possible cost. Finally, I demand that the bioethicist that live off our tax dollars and who question our right to live free of ageing be immediately fired, and thier retirement pentions confiscated from them.

I'm sure that many of you on these boards are over 40 years old. Your financial as well as health future is at stake here! Let's all form a political lobbying movement to force the government to implement the changes I have mentioned above.

I simply cannot understand how anyone can feel any different that I do on this issue.

I am going to write or email Harvard University and insist that they fire Daniel Callahan. He is one of these bioethics jerks who doesn't want us to have access to the anti-ageing breakthroughs that will improve our lives. I urge everyone else to do the same.

Well first of all except for twins (clones) all people have a genome that differs in some ways. There is no "human" genome.

Second when someone develops a non natural gene that is desirable for humans, does that gene become a human gene?

How about a useful animal gene inserted in a human genetic structure; human?

I'm not even sure that there is within the 10% of expressed genes (xons) any that only humans have.

Patents run out in 17 years. That is the maximum length of time the "evil" business men could profit from any invention.

Lets face it we do not possess the religions, (morals) the ethics, the law, or the foresight to have a clue about what is happening now, let alone in the near future.

Science fiction can not even keep up with recent progress.

This board is going to be fun.

Is everybody stupid, stupid, stupid or am I a supergenius??? It's mine, it's mine and let no man mine, what's mine. "Let no man put asunder", what God has given.....it's mine, you hear, it's mine, every last gene. You every wonder what they do with your blood, after you have a blood test??? THEY SELL IT!

RE: Carl Nicolai #27-

"There is no 'human' genome."

The "Human Genome" includes the genes which are common to all humans, all the different variable alleles, and the prevalence of each allele within the general population. Therefore, there IS a human genome.

"when someone develops a non natural gene that is desirable for humans, does that gene become a human gene?"

In this scenario, the gene would not be considered a human gene in the first generation. Once it is incorporated into the genome and passed on to offspring, it becomes a human gene.

"How about a useful animal gene inserted in a human genetic structure; human?"

Same as an artificial gene. Except an animal gene would not be patentable if our patent laws made any sense at all.

"Patents run out in 17 years. That is the maximum length of time the 'evil' business men could profit from any invention."

17 years is a long time. Even after a patent runs out, the business which held the patent holds a tremendous advantage in the market.

"I'm not even sure that there is within the 10% of expressed genes (xons) any that only humans have."

Most human genes are slightly different from our close animal relatives, a few are very unique. The real differences between humans and other apes develop from differences in relative gene expression... which is a topic which will keep molecular biologists busy for many years to come.

"Lets face it we do not possess the religions, (morals) the ethics, the law, or the foresight to have a clue about what is happening now, let alone in the near future."

I (for the most part) agree. I think that's an excellent reason to spend some energy developing the ethics, the law, and the foresight to have a clue about how to deal with technology.

"Science fiction can not even keep up with recent progress."

Science fiction has anticipated much of our recent progress and pointed out some potential dangers. Those who do not read their science fiction are doomed to live through it.

Kurt Schoedel-

"Definitely, the companies who have sequenced the human genome should be able to profit from it."

As I, and many others on this board have pointed out, the human genome was overwhelmingly sequenced by university and government researchers. The private sector did not dare undertake such a colossal long-term project. Early goals were exceeded due to improvements in technology developed via public funding. Last-minute efforts by private businesses to grab a small piece of the genome and profit off of it are lamentable, and will hinder medical research.

The information from this project will be available to all businesses to try and make a profit, and to all universities and hospitals to try and find creative ways to benefit mankind. The odds of someone finding a way to extend your life increase exponentially when everybody is able to do the research... not just one company with limited resources. Businesses will still be able to patent the drugs and gene therapy treatments which they develop from the genome information.

I don't think you realize that most scientific discoveries have NOT come directly from private industry... they have come from public-funded research and then been licensed to private industry, or they have come from private industry benefitting heavily from freely published public-funded research.

"As an American citizen and tax payer, I DEMAND the most rapid development of all biotechnological breakthroughs that can free us from the spector of ageing. I demand that the FDA give fast-track approval of these technologies and I demand that this technology be made available at the lowest possible cost. Finally, I demand that the bioethicist that live off our tax dollars and who question our right to live free of ageing be immediately fired, and thier retirement pentions confiscated from them."

As an American citizen and a biologist, I have some problems with your demands. If we want to demand that these developments occur faster than the market is producing them, we have to ante up for public-funded research, which you seem to oppose. Fast track approval might just lead to you getting sick or dying from your anti-aging treatments, as has happened in some gene therapy clinical trials. Oops, sorry, Kurt is dead, but he didn't live in vain because someone else will live longer thanks to his sacrifice!

This stuff is NOT going to be available cheaply unless it is subsidized by the government, which will not actually be cheap to taxpayers. If you want drugs to be cheaper, write your local pharmaceutical CEO and ask him to politely cut his own salary and all shareholder benefits. He'll be very cooperative, I'm sure. Since it won't be cheap, do you mind if all the ultra-rich people keep themselves alive for 1000 years while you suffer and die because you don't have the money? We can't dare to question the morality of the marketplace with regard to health care, can we?

And of course, all bioethicists should be shot because they dare to question how biotechnology affects society, right? Then they won't be there to question whether your treatment is properly administered, or whether clinical trials are conducted with regard to human well-being. What do they know anyway? They're only experts in the field. You go ahead and try telomerase treatment on yourself. Maybe you get cancer and die. Maybe the animal research doesn't work in humans and you just waste a lot of money. Maybe the initial paper on the subject was fudged by a grad student who wanted to advance his career. You willing to take those risks? Those ethicists might be the best friends you ever had.

"I simply cannot understand how anyone can feel any different that I do on this issue."

Some of us have thought it through a little more clearly, and some of us don't live in a little self-centered universe and worry about our own mortality all day long.

Great! We have a player.

There are many genes which do not determine strict viability and therefore could only be passed on as an intron to the first generation. They may sleep until there is a corresponding correctly located gene in the mate of a progeny.

This could account for some of the vast number of introns (90%) that don't work but have all the other qualities of an exon.

"when someone develops a non natural gene that is desirable for humans, does that gene become a human gene?"

Wait a sec. if I have the gene it is not necessarily human but if my child does, it is then human?

"How about a useful animal gene inserted in a human genetic structure; human?"

They don't

"Patents run out in 17 years. That is the maximum length of time the 'evil' business men could profit from any invention."

So not the price goes from 100,000 per cure to $.20 per cure. being rich or educated has always conveyed some advantage.

True the point is how many and what kind are worth considering. BTW there is considerably more difference between "apes" then the average difference between humans. Our structure is not as varied or as old.

"Lets face it we do not possess the religions, (morals) the ethics, the law, or the foresight to have a clue about what is happening now, let alone in the near future."

I claim that there is not enough money to track it. The technology is moving too fast.

"Science fiction can not even keep up with recent progress."

Great twist on an old saying. I love it.

Hello Carl.

"Wait a sec. if I have the gene it is not necessarily human but if my child does, it is then human?"

That's a paradox, isn't it? If, say, Big Evil Corporation develops an artificial gene which allows people to metabolize coal and defecate diamonds, then they have exclusive rights to market this gene and monitor its effects on paying customers. If this gene is incorporated into the germ line and transmitted naturally to the customer's child, then it has become a naturally occurring gene in the human genome and BEC cannot control the rights to it anymore, because it is a HUMAN gene. At least, that's my take on the situation.

If, however, we foolishly allow businesses to patent naturally existing human genes which they discover, then BEC may discover a gene which enables tumors to form, and they can refuse to allow other researchers to use this information to create anti-tumor drugs.

"...being rich or educated has always conveyed some advantage. Always will."

Sure, but we as a society can decide when and how to limit these advantages. When it comes to life, liberty, and the pursuit of happiness, we have an obligation to level the playing field. I think health care falls into the realm of LIFE.

"There are many genes which do not determine strict viability and therefore could only be passed on as an intron to the first generation. They may sleep until there is a corresponding correctly located gene in the mate of a progeny.

This could account for some of the vast number of introns (90%) that don't work but have all the other qualities of an exon."

Technically, there is a difference between introns (non-coding segments within a gene) and the so-called "Junk" DNA (non-coding segments outside of a gene). But that is a minor semantic point. Such segments are still part of the human genome and should be treated as such.

Introns can be differentially spliced in different people. Some of the "junk" DNA may actually be capable of switching on a variety of genes with the right partner, or a single mutation, but that is still just a hypothesis.

With regard to the pace of technology and the pace of ethics and law, I think we would be foolish to allow science to advance unhindered without considering how these advances affect existing social structures. You are correct that this seems to be happening already. It is truly a brave new world in which we live, and I, for one, am both excited and concerned about the prospects.

Andrew, I just might try the telemerase treatment on my own. You know what? I might not work. Thats why I have a trust fund set up to pay for my cryonic suspension in case it doesn't work. You do defend my right to be cryonically suspended AND to be able to take whatever assets that I may have with me, do you not?

Maybe the bioethicists are my best friends, but only those who do believe that the individual deserves a shot at immortality. However, I'm sure that you know of bioethicists who are against physical immortality, these people are who I am angry, and rightly so. My point is that these issues concern one's body and self-image, and I have always viewed anything to do with my body as a personal matter, Not a matter of public debate. I don't think you get it. This is a very personal issue with me. If you approach the issue from a personal standpoint (because it really is personal in nature) you will find that you agree with me. I'm not going down, and I'm not going to let society throw me out like a piece of trash because that same society is too stupid to develop the biomedical breakthroughs that will ensure that none of us get thrown out like trash.

You are aware that people over 40 years old are beginning to suffer job descrimination? I know of several people who have undergone cosmetic surgery in order to look younger in order to pass job interviews. I feel that the reason why we do not have life-extension advances is because of a hostile intellectual and regulatory climate against researchers who either seek funding to do ageing research or who seek regulatory approval for anti-ageing treatments (such as telemerase) in order to market them to the public.

I also know biologist working in this field, and they have told me that if it wasn't for the hostile regulatory climate, that we would have significant anti-ageing breakthroughs on the market today, and the boomers would not be facing the career as well as physical decline that they are facing today.

You are correct that it does take money to do this research. However there is enough private money to do the job in the next 10-20 years, if the government would provide the moral support for it. That moral support is lacking. Since I pay taxes to the government, I insist that they provide this moral support.

I remember those years ago when I heard the folks say, "we won`t mess around with genes--we`re just looking". At what point do we finally understand that if we can find it we will fix it? To the far planets--do we need to go there? Seems there are enough things wrong here that could be addressed with all the NASA money sent off into outthere, than scratching the itch of those who want to climb the stars just because they`re there. To play God with the matrix is foolhardy, and I`m fearful that past prophecy will come into effect sooner than we`d like. I realize this may be wishful thinking, but I feel some deep thinking must be done and not act on emotion. Who should be the enabler of all this? Solomon out there somewhere?

Is it relevant to think of "immortality" in terms of what it is going to do to society? The social fabric we know of is only because a "circle-of-life" exists.

Immortality and a very long life could be the proverbial Midas' touch. Can someone want to live forever? What do you want to do? What do you want to achieve? I think, it is a very near-sighted approach to think eternal longevity is the panacea for self-fulfillment. I dont know anything about genomes, but i do know tinkering with basic human behaviour is going to drastically alter human conceptions of what society is...Its a very frightening thought..

I believe that there is GREAT potential for abuse of this "GREAT DISCOVERY". Just look at what the internet has gotten us. I agree that there are some great things that are accomplished with the aid of such discoveries. I think our society has been hurt, to some degree, by the "opening of these cans of worms" so to speak. I also think when you start to try to improve on what a greater power than ourselves has created, you will only cause more damage than good.

I think it's interesting but there's plenty of room here for abuse. I'm not sure that making it public is such a good idea. I'm just wondering what those not so altruistic could find to use this information for that would cause harm to others... does the word "hacker" ring a bell. Is there anything here that someone could use to create a "virus" that would be not so pleasant for the rest of us to deal with?

Who would not want to live forever young? Unless someone out there can convince me that the human soul is immortal and that we do survive physical death, then physical immortality is the only option for true happiness and fulfillment. Society is simply a collection of free individuals. The concept of society being something more than this is fascistic nonsence.

As far as what I want to do, I've got so many dreams and ideas that it would take me at least a thousand years for me to do them all sequencially.

The issue of immortality is purely a personal matter, not one of public debate. Do you think that what hair-style you wear is a matter of public debate? No, because its your own body and you do what you want with your own body. Immortality is the same thing, no different. Owr bodies are our own property. We should have freedome to do what we want with them.

What is ment by the expression "circle-of-life"? How is this "circle-of-life" relate to someone who wants to live forever and go to the stars?

There seems to be an issue as to who will 'own' the rights to the sequences once they are understood. I'm sure some big company wants to make a lot of money by claiming to own these. For my part, I sorta like to think that *I* might own the rights to my own personal Gene Sequence. Is there any talk going on about this. How to ensure that each of us maintains the rights to this ultimate essense of ourselves?

The real ethical issue here is libertarian. Does the individual have the right to use the emerging biotechnology to alter his/her self for their own personal happiness, or must the individual accept the dictates of governmental or religious bureaucrats on how they may alter themselves. Biotechnological enhancements (including immortality) are simply a form of self-expression, just like body-building or wearing make-up. I think its way off base to suggest that the individual should not have complete freedom to alter themselves anyway they want.Especially for an American. I have lived in unfree societies and the one thing that makes be believe in America is the regards for individual liberty.

As for religion. If god did not intend for us to become immortal or to go to the stars (intersteller colonization), he/she/it would not of given us the ability to imagine and dream of these things. Furthermore, it is the moral duty of any Christian to seek immortality because this religion promotes the sanctity of human life and that suicide is morally wrong. As such, it is un-christian to be opposed to the biotechnological conquest of ageing and death.

Christ himself said that he was on the side of life, and that to be on the side of death is to be on the side of the devil. I think its time that those of us who want immortality reclaim the christian religion as our own. If god exists, he is certainly on the side of the immortalists.

A lot of medical problems are going to vanish. The major social implication is that humans will not be "playing god" they will be practising doing things that previously only "God" could do.

First and foremost do not let the government invest any tax payer (stolen) money in human genetics. If you do, the agents of "the government" will claim that they, and only they, are going to "own" the information and, they and only they, are going to control it.

They have all ready screwed up atomic energy which they had total control over, so bad it will probably never recover.

Carl, I totally agree with you.An open, competitive, free-market system is the only assurance against abuses of this new technology. When all players are forced to compete with each other, they have an incentive to treat us (the customers) well. Its when you have a monopoly situation (such as government or a monopoly business) that abuses of personal liberties occur.

If any business ever treated its customers that say way that governments treated thier citizens, such a business who be bankrupt within a year. The free-market system is the only system that allows for the greatest amount of individual freedom of choice in biotechnological services and products, while reducing the possibilities of abuses from this technology.

Science fiction movies teach us that in the future there will be medical devices that can read our genetic structure. This information can than be used for medical purposes.

I question other use. Will females be donating their eggs? Will we have a president with a "test-tube" offspring?

And, who is presently donating genetic material towards this project? Do they know they are doing this? Secrets imply that this is contrary towards a productive society.

One last word of ethics and law, the US Patent Laws prohibit the issue of "Patents" for NATURALLY occurring substances.

The problem is that how do you prove that a substance is not "NATURALLY" occurring.

C60 Fullerine spheres and so called Buckey tubes had never been observed to occur in "nature" before, but once they were produced further investigation showed that small amounts of them were found in common soot.

With the extreme complexity of DNA and at the same time the extreme commonality of many structures, until we sequence ( de-sequence ) all the life on earth, we will not know what is produced "naturally"

Then there are the possibilities of very minor changes in the DNA that produce, for all practical purposes the same result.

The patent standard that I believe will be more important is "non obvious to someone conversant in the art"

The law and indeed the morality and ethics for DNA manipulation does not now exist and can not be rationally legislated in the near future.

Like the applied anarchy we now see on the Internet the codes of DNA must be left outside the law unless severe repression of the technology is contemplated.

In that case the innovators will just move to countries where they have more freedom to ply their trade.

HUMAN GENOME....WOW what a great idea. Now that we have decided to play god, we shall create creatures half centaurs and half humans, we shall create the mythical gods of Egyptian civilisation for after human genome will come animal genome and so on....

we shall use the technology to create sterile unwanted persons, blue eyed blonde boys and girls , we shall create Saddats and Hitlers we shall repeat the haulocaust when a mad man uses the genome to create biological weapons.. and holds the whole world at a ransom.......wow the thought is disturbing to say the least..

but then we are curious humans, we need to know ..and we need to create things that harm us...........good for us this genome ...it will destroy us surely one day.

who knows if HIV is not a Genome mistake in the making..good work you scientists,,for we shall thank you for messing up this world, Are we not all like the mad hatter in the Alice's Wonderland...........all for finding that key that will call the end of all normal humans as we know them.

Lets have sanity, lets feed our masses good unpolluted food, no chemicals, and lets not spend money to satisfy some nut's curiosity...but to provide better roads, communication, education, new skills, and so on to better the living standards of the poor and deprived of this world..

Over the coming years, the roles of the genes may eventually become understood. Perhaps not all genes will be found to be "good." Possibly, some will be found which actually cause problems and not help the living organism in which they reside. I am curious to know if any such "bad" genes have been found. Can diseases really be stamped out by modifying or eliminating one gene or another? I would love to see the answer to this question posted here. What percentage of the genes found so far are "good," and what percentage are known to be "bad"? Anybody know the answers?

The Genome Project fairly raises many ethical issues, most notably, who owns what.

It is one thing for a company to "use" data derived from genome research, but it is another thing all together to say they "own" the genome too.

The Genome Project should remain a public resouce available to any researcher or company. If Celestra(?) completes research on their genome project does that prevent the orginal work from continuing, I would think not.

I think that there is lot of misleading information out there as to what the HGP is and what it might enable us to do. First of all sequencing one genome is much like photocopying the encyclapedia brittanica while only able to read at a first grade level. The information you will be able to understand and use will be only a fraction of the whole. Just because we know the sequence does not mean much. We must then discover what, if any protien is controled by a sequence fragment, and what if anything that protein does, Also we need to know how it is regulated and what are its implications in life. Take it from someone who knows, this is extremely hard and time consuming. To sequence the genome is no more playing god than mapping the human vascular system. The HGP will result in new medicines, and perhaps even ways to alter potential humans prior to thier conception eliminating some congenital diseases and perhaps even lowering the risk for disease later in life, but this alteration will be extremely costly and beyond the reach of most for a good long while. This technology will not allow us to create another Hitler, or some such other nonsense. A reasonable discussion of this topic is neccissary to allow people to become comfortable with the project and its implications.

And as to CELERA patenting thier genome, that is perfectly legal, and so is it legal for the Government funded project to make thiers public. No two genomes are alike. There is much more money in the private sector, and more drugs and therapies will be brought to market by private drug corporations than by public research, so it is more important to let the private sector develop therapies and the public research facilities to hash out the nuts and bolts of the genome and its implications. Both can work synergisticly to the benifit of everyone.

Tiffany, I agree with your post except for these two sentences:

"And as to CELERA patenting thier genome, that is perfectly legal, and so is it legal for the Government funded project to make thiers public. No two genomes are alike."

What on earth does this mean? Both the human genome project and the private biotech companies are attempting to sequence the genome of the entire human species, including all common variations. The genome is only one body of information. If Celera patents portions of the genome, it would prevent ANYONE from using it without Celera's consent.

Celera most certainly does not have the right to patent this information. Once all of the information is available to the public, then ALL private and public researchers can use the information, and THEN they can patent the drugs and other advances which they create from the genome information.

Look at it this way. If the genome is patented, and you wish to develope something potentially profitable useing the actual sequence of a gene, you would have to enter a licencing agreement with Celera. This would be the case in gene therapy, DNA vaccines etc. This is already happening with biotech companies that hold individual patents on individual genes. Celera would have nearly all of the genes not already patented. How could you legally deny Celera its patent rights without revoking those already held by companies? If such a thing were to occir, nearly every biotech company would collapse. Virtually no public money goes to the actual production of new medicine without licensing agreements between two or more companies. What would be the incentive for a company to develope anything that they would be unable to patent for protection of profits? It is not as if Celera will be hoarding the information. Licencing agreements are made every day. A small amount of the agreements will result in a clinical trail for a new drug, 50 percent of those that make it to trial fail in the level 1 FDA trial, another 25 percent fail at phase 2, and yet another at phase 3. This may give you some idea as to the sheer number of licencing agreements that are made every year. Basicly anyone with an idea and Proof of Principle can pick up a licencing agreement, especially with Celera. the entire strategy of Celera is to let anyone do anything with any of thier informantion in the hopes that a few of them will result in new drugs, and allow the employees to live off those cash cows. One other interesting note. While Celera may recieve patents on the sequence of the genome, it is often not the sequence that turns out to be important, but the protien it encodes. The process of decifering the structures of protiens coded for by the genome is called proteonomics, and is a handy way to get around patent protected gene sequences. If the human protien you are interested is also patented, you can often find protiens with the same mechanism in other species. Believe me, patenting the genome will not appreciably hamper the progress of worth while research, while to deny those patents would harken the end of biotech in the US, not to mention put the info in the hands of every crack pot with a tissue culture lab. Patents mean protection.

Mapping the Human Brain could be next … we now only use a tiny fraction of it & if science figures out how to tap the rest, the resulting human species will be as similar to ourselves as we are to the cave men & women. Carl Sagan’s novel Contact movie made the point that if there is no other intelligent life in our universe, what a lot of space has gone to waste. The same point can be made about our brains.

We will need to be smarter to cope with the implications of population growth.

I believe that patent law, copyright law, etc. needs to be for different time periods based on the speed of technological development … computer related products need protection similar to a multiple of the life time of a computer platform, while other inventions should last the lifetime of the inventor & next generation heirs. Given that Cloning or using Genome to recreate some worthy individual requires 2 decades of loving nurturing like any other human baby, protections should last at least as long as it takes for a new intelligent being to reach maturity, and immediate descendents should have some say over the recreation of their parents.

The reason why medicine is so expensive & computing technology gets so much better at lower prices is that the latter is almost a free market. It has a little government regulation, and a few oligarchies like M$, but the market is open to new ideas starting from a family garage & basement. Anyone who can create a new peripheral, software tool, operating system, etc. is free to join the market. But some industries are heavily regulated, or subject to huge lawsuits, so there is expensive insurance, so that would be entrepreneurs have to have massive $ up-front before product to market. Consider the costs of finding new places to plant oil wells. Consider the road blocks against private enterprise going into space independent of the government.

Government exists to protect us, but in some cases we do not want to be protected. Consider people dying from diseases for which there are no approved cures – shouldn’t they be allowed to gamble with experimental cures? Don’t we all want to gamble with immortality? However, how about the people who gambled & lost, with sexually transmitted diseases? The cost of keeping AIDS patients alive is catastrophic.

If the citizenry of advanced nations cannot trust their own governments to manage this, what does this say for the future when this technology enters the realm of weaponry … we need to stay current with it so that defenses can be developed as fast as those against computer viruses today.

Kurt Schoedel – I am aged in my mid 50’s & I am a computer programmer. I am now working for a company that has several employees in their 60’s who work 4 days a week & a guy just voluntarily retired who was over 70. He had been working a few less days a week & was down to 2 & instead of going down to 1 day a week he retired. The company has made no promises to me whatsoever, but I find the prospect promising that whenever I have to slow down, provided I can stay reasonably healthy, they can put someone into the high pressure operations role & let me do programming via telecommuting. You need to shop around for companies like my employer that recognize the worth of people, irrespective of their age. Be willing to accept less pay for traditional job security. There still are firms that honor loyalty.

Science is not ahead of Science Fiction … Cloning implications were thoroughly explored long before Science developed it. The problem is that many people, who never believed it possible, react to some scientific breakthroughs with speculation that belongs in a B-rated movie or comic book, when a Masters degree in understanding the implications of the topic can be found in the literature of Science Fiction. Where the news media could perform a service to non-SF fans, would be to provide a directory of SF novels on the topic that suddenly exited the realm of SF … what books & authors should you have read before you can call yourself an expert on this topic?

Al Macintyre

Mayur Shah … although I cannot cite a link to this, I have read a bit on where HIV came from & my understanding is that it was a natural mutation in Africa which has now killed half the population & is one of the reasons why the nations of Central Africa seem to be in a continual state of self destruction. They have lost most of their youth & intellectuals, leaving babes & old folks & barbarians. We have to find a cure, or the whole world may suffer like the plagues of the Middle Ages. Human Genome research could save us.

Early on the disease was before the fall of European Communism & our adversaries crafted a story, that many in the 3rd world believe to this day, that AIDS was a disease crafted in bio weapon labs by the CIA. If you read Science Fiction, you might be introduced to the notion that we humans have very little experience with mutations. Contemporary theory is that mutations occur only once in a million years, so we’re safe … AIDS was the latest event of God throwing dice. But an equally valid view within Science Fiction is that a disease that has mutated once is more likely to mutate again than one that has never mutated.

This is like the notion that rocks in our sky killed off the dinosaurs & have been missing us for 6 million years, so we’re safe. In Science Fiction we are playing a game of Russian roulette with long odds but no certainty of continued survival. God gave us the ability to look into the sky & see the threat & do something about it. Currently we have the scientific ability but not the political will to protect ourselves.

Andrew LaFollette & Tiffany Winburn – I think a useful parallel might be the use of computer languages & operating systems. There is precedence in someone writing software using resources that someone else has intellectual property rights in, such that the original creator is paid a portion of the profits from the person using the tools. This is not as common as it used to be, but it was perfectly legal under contract law.

I am not happy that the rights to one click internet shopping has been awarded to one particular site, so that all the others have to either use two click or pay for the privilege of offering their customers similar convenience. But we now live in a world driven by business interests who think of us as their consumers. Be thankful we do not live in a world driven by interests who think of us as their slaves.

I am thankful that there are some checks & balances out there. Government regulations & an electorate that has the power to effect changes.

Al Macintyre

Tiffany-

"Believe me, patenting the genome will not appreciably hamper the progress of worthwhile research, while to deny those patents would harken the end of biotech in the US, not to mention put the info in the hands of every crack pot with a tissue culture lab."

While patenting the genome MAY not greatly hamper the progress of research, I beg to differ with the rest of your statement. You are fear-mongering. Denying Celera the right to patent the genome will not harken the end of biotech in the US anymore than it would harken the end to the Atlanta Braves' pennant streak. All it does is prevent them from skimming money off of everybody who wishes to do research in molecular biology.

Everybody who wishes to can use the genome information, perform research, develop drugs and other products, and patent them. You just can't patent the genome information and limit the access of others to it. All this does is prevent Celera from hoarding the information and either delaying medical research or increasing its cost through unnecessary licensing agreements. The Human Genome Project provides this information, free, on their own website. Which system do you think is better?

How many crackpots have their own tissue culture labs? Other than my boss, of course. :)

Seriously, who the Hell are Celera et al to decide which scientists are worthy of performing research? Even the NIH doesn't have this power--it can only stop crackpots from doing research with government money. If scientists are violating the law it is the duty of law enforcement officials to stop them. It is not the duty of your local biotech company.

Al Macintyre #56-

Where did you get the idea that mutations only occur once every million years?

Mutations occur constantly. They cause most birth defects, and they are the root of genetic variation within species. Odds are that every one of us carries a mutation that occurred in the past few generations. The cold and flu viruses have mutated hundreds of times, which is why they are virtually impossible to effectively vaccinate against.

The AIDS epidemic is believed to have been caused by mutations in the HIV virus that turned a harmless bug into a killer, NOT a mutation in humans. (Is that what you were implying?)

That being said, however, you are absolutely correct that a highly contagious worldwide plague is, and always will be, a very real risk.

Whoa yual. This is dog bone simple.

All .gov or any private foundation has to do is fund a group of concerned scientist to file some "defensive letters of publication".

They have the effect of a patent in that no one else can get one on that art, but give the rights to everyone.

I can not beleive that all the really sharp minds in this field have not thought of this.

(Actually I can not beleive I did not think of it until now.)

Eventually we will develop the "medicine" to cure all genomically ills. Of course, the "medicine" may eventually cause a form of literal genocide. By knocking out genes or replacing mutants with "normal" types, who knows what this will do in 10k years? Mostly, this kind of genocide is not a bad thing. I think of this more like plastic surgery that can be passed to your kids.

There should be a panel of ethics to determine whether or not theraputic uses can come from research on a strand of code or a region. More specifically, a panel to watch and report what research with what goals are out there.

I would like to see what genetic approaches are being persued for Alzheimer's disease. Are there groups working chromosome 1, 12 or 19? Or diabetes, are there groups working of the 3-Adrenergic Receptor? Its this kind of research I want to see fully supported now.

10,000 years? I do not think anyone can predict what will happen in 10 years.

We have no law, we have no morality, and we have no ethics to handle this technology.

Bio engineering is going to make all other human advancements pale by comparison.

We are becoming "self evolving" beings.

By the definitions of the past we are not "playing God" we are are practising being gods.

Or so we have deluded ourselves to think... We have no idea what we are doing. It is more like- well we don't know what this will do, but let's try it and see what happens.... like Adam & Eve biting into that apple.

Deluded? No, we are moving along slowly. A bit too slowly in that we should have made much more progress in the time we have been working at it. However bureaucrats and people whom don't understand the science at hand and its implications, fear it. They fear it and impede its progress like the church making Copernicus recant his claim that the Earth wasn't simply another planet rotating about a star. Embrace this emerging science and support it. There are cures to diseases on the horizon, that otherwise will continue to haunt the world. Imagine being capable of curing the world of diabetes, most forms of mental illness, Cystic Fibrosis, and a slew of abnomalities that otherwise soak up resources and bring pain and suffering. Some of these diseases are in a liminal state of being cured.

So would you rather spend half of all medical dollars on the treating of diabetes or a fraction to find a cure? This isn't playing God, this correcting the mistakes that do occur.

What we do need is peer review to determine what is and what is not a genetic disease. I would not approve of genetic research dollars spent on "curing male pattern baldness". However, with as many as 120,000 genes... it would be a while before research were to have to sink to those depths. Better just leave that to the cosmetic industry (which probably has a great deal more money anyway...).

hello people, I have just joined this board.

I would like to say that it is a very good thing to be able to know exactly the cause of every problem in the human being, so we can in the future find a cure for it. This is a revolution in medicine. But on the other hand, it is scary because having such information in the wrong hands can prove catastrophic...Imagine your genetic code is used to make another you, but stronger for example. Genetic manipulations are dangerous to society. They should only be used with good intention, which is unfortunately not guaranteed on this earth.

You must do something more then just "discover" or "map" the sequence - you have to genetically alter or cause an organism to express a new (exogenous) nucleotide sequence, or somehow inhibit, eliminate, augment, or alter the expression of an endogenous nucleotide sequence or express a specific physiological characteristic not naturally associated with the organism, or produce a new cell line that expresses a specific protein, such as a new monoclonal antibody. This is much more then merely elucidating the sequence of a naturally occuring gene or genome.

As a health care provider I can't help but think that "cracking" the genome would be anything but good for our society. However, the implications for society and indiviuals are overwhelming. Policies safeguarding the public need to be addressed NOW. Ethical issues need to be addressed NOW. There are plenty of discussion, plenty of research, but few policies that can be found protecting consumers. DOE and NIH have established budgets but is that money doing anything other than raising more questions. Politicians and healthcare workers get cracking!!

It may sound like a line from MEN IN BLACK the movie, but it's true: 1500 years ago Ptolemy said that the universe revolved about the earth. At and for the time the belief was mandantory. 500 years ago everybody just knew that the earth was flat and mostly for the time it too was gospel. And less than 100 years ago everybody knew that a heavier than air device could not fly and space travel was impossible.

The existence of a GOD for many years was also a mandantory belief. Rene DeCarte wrote a rather interesting dissertation of the existance of GOD. He concluded finally that GOD did indeed exist. This is a great conclusion, BUT did he concluded the existance because in his mind he truly believed or did he conclude the existence because of the very real possibility, at the time, of being the star at a burning at the stake.

Throughout history men of curiosity, vision, and the innate desire to know have always battled uphill to produce for the good of man. It is the individual seeking self aggrandizement at the expense of the innovators that constantly invoke religious admonitions and dire warnings of impending doom. In the very distant future our sun will expand into a red giant consuming the earth and all on it, so if you can't help, for yours and everybody else's at least get out of the way. Let those that can solve every puzzle nature has proposed in cluding the human gnome.

Most of the important discoveries eventually boiled down to a very few items that had to be understood to grasp the idea.

The trouble with the genome is that while some of the structure codes for simple things like thousands of proteins the vast majority of the code has completely unknown functions. This 90 to 95% represents perhaps some so called junk DNA but it is hard to believe that such a large quantify has no uses.

Also a small part of the DNA, 47 genes, are located outside the nuclear membrane in the cytoplasm, an area that might be called the "factory" of the cell.

There is still a lot of discussion of how many genes an average human has.

The questions multiply at this time much faster than the answers. The "men of curiosity" will continue to create more questions than answers for a long time. Maybe long enough to stave off the "warnings of impending doom" for a while.

Even as you read this GM plants are interacting with wild ones.

There is no way to know what is going to happen or to stop it if we did in some cases.

No doom necessarily just more complexity in our local universe.

We still havent really started on humans yet, or even most animals.

Carl Nicolai

I couldn't agree with your statement about creating more questions than answers, more. Everything new always presents complexities that must be understood. But without pun being intended I qualify it by injecting understood in a relative way. Briefly, Aspirin comes to mind. It was introduced in 1899 but discovered much earlier. Our esteemed FDA says that a drug cannot be released until we understand how it works. We didn't understand its pharmacology till the late 1980's

Einstein released his general theory of relativity in 1905 and 40yrs later we got the message of what it was all about.

It has been my experience that most truly earth shattering discoveries were discovered by accident and someone curious enough to examine it further.

It's nice to have productive accidents. Some of the ones we have on purpose don't always have happy endings

In the commercial realm, it means tons of money for pharma companies and private sequencing companies. We have the ability to CURE CYTSTIC FIBROSIS NOW, however since there are only a few ten's of thousands of people afflicted with it, there is no interest in curing it. Since the cost of commercial research would not bring in enough PROFIT to make it attractive. Diabetes will probably be the first commercial cure to come of the genetic diseases.

What can you do to a private company?

In the commercial realm, it means tons of money for pharma companies and private sequencing companies. We have the ability to CURE CYTSTIC FIBROSIS NOW, however since there are only a few ten's of thousands of people afflicted with it, there is no interest in curing it. Since the cost of commercial research would not bring in enough PROFIT to make it attractive. Diabetes will probably be the first commercial cure to come of the genetic diseases.

What can you do to a private company?

Calista

You are very correct about what pharmaceutical companies can do and will do and you have hit on the absolute reason for them following the policies that they do.

The have a long list of ORPHAN DISEASES and they do, in part, schedule their projects along the demand issue.

There are only 9 cases to my knowledge in the world of Progeria. The nearest cases are in Canada. Drug companies are in business for a profit and to devote company treasure to cure 9 cases wouldn't be a prudent use of shareholders money even if it would be a humanitarian act of immense value.

There is great hope in the medical field that some how genetic engineering will answer a few more of life's most perplexing problems.

Fear, such as generated by AIDS, Fear such as in the 50's of POLIO or in the late 1800's of YELLOW FEVER, or Fear of the FLU in the early l900, all of these fears generate vast quanties of money for research. Whenever a disease can generate FEAR in the populace, you will get action and until there is an epidemic of CYSTIC FIBROSIS it will be treated as an orphan and financed accordingly

I won't totally demonize pharma companies for wanting to go after the profitable diseases. I mean, if they cure Diabetes, AIDS, various cancers, etc... Then great, a lot of people can be helped. The big pharma companies still pay for research on disases that affect smaller numbers such as CFTR.

Quite often the research generated for the less visible diseases is critical in some of the larger projects. A gene transference method used in the treatment of CFTR proved viable when used in CFTR patients. This viral carrier is now being used for other disease research. However I have not heard anything about the progress of CFTR research.

The original study took a group of late term CFTR sufferers. They put a corrected gene in a viral package and distributed it via nasal sprays. I remember one patient had improved something like 25% of breathing function, however being in the late stages of CFTR it was too little too late.

There is one overriding trait in the medical profession and quite probably in most professions and that is ARROGANCE.

It seems quite often that PhD's, MD and doctorates in general convey a air of pure unadulterated arrogance that, while moderate amounts of skepticism is healthy the possession of an advanced degree is no guarantee of excellence.

We tend to grant deference to those with those degrees and subjugate our own good sense to their professed expertise.

Each time I see that deference given I'm reminded that Pasteur nor Curie nor Huntington were possessors of these degrees, yet Huntington is really the father of modern day surgery and the others are well known for their contributions.

Ideas, such as those genetic advancesy you discuss, regardless of who presents them, have merit yet a vast number are discarded by those making the decisions and later claiming them as their own. Jealousy is rampant regardless of its position on the academic ladder.

I think that its important to remember that pharaceutical companies and the medical community is working hard on pretending they are looking for cures for diseases not actually finding them. Just think if the ACS or the NCI actually found a cure for cancer? What would happen to the millions of corporations, hospitals and the the doctors and scientist who are paid to look not find? Entire organizations are built just to look for a cure. If a cure is actually found what would happen to those jobs and research funds?

Too much financial loss!.. That's why a cure is never found nor are funds for educating the public on prevention or health ever considered...let's just pretend we are looking for a cure. If we find any real valuable data that prevents cancer let's bury it...unless of course we can make a drug that we can use to profit from the discover.

It we even get close to finding a cure let's change direction quickly...especially if this information would offend pharma companies or big polluters.

Henry Baugh--Marie Curie had a doctorate in physics. Pasteur graduated from the Ecole Normale Superieure, which qualified him to become a university professor. And if you are referring to George Huntington (of H's disease), he was an MD.

June Blake--I'm a cancer researcher, and I would love to find a cure for cancer, although because of its wide genetic variety there isn't likely to be a single cure. In fact, genetically speaking, every cancer patient has a unique disease. The human genome project has already allowed us to distinguish between two forms of lymphoma that pathologists thought were the same. 40% will respond to therapy, 60% won't. Now we can give the standard therapy to the 40% and try new drugs on the others. Drugs designed to hit specific molecular targets are already being used in clinical trials, and some are working very well. STI-571 for myelogenous leukemia is a terrific success story, as monoclonal antibodies for breast and colon cancer. Within 10-15 years most cancer may be treated as a chronic but controllable condition, as diabetes is today.

There are plenty of other diseases that I and others could apply our knowledge to, if cancer were conquered.

Dawn,

As a researcher do you think that it is at all important provide the general public with information about cancer prevention?

I think that we should start providing research study results to all citizens.....even if these result have a negative affect on drug profits or corporate growth.

People need to know what to avoid in the air, water, soil consumer products, food and the workplace.

I wonder why most studies never get published to the general public? Why not publish the human studies that prove the clear connection between saccharin and bladder cancer? studies that prove the connection between birth control pills and estrogen replacement therapy and cancer? and on and on and on..

Also, most of the cancer funding today is spent on genetic research for finding that "cancer susceptible gene"...even though genetic factors are only involved in less than 10% of all cancers.

As a research have you ever studied prevention or non-drug options for treating cancer?

Don't you think it would be a better use of the 5 billion dollars a year that the NCI and ACS collects to educate the American public on cancer prevention instead of spending 90% of the funds on gene research and drug only treatment options?

June, I think that ACS and NCI do provide information about prevention--smoking causes one-third of all cancers, skin cancer can be prevented with proper precautions, evidence for diet is a little less clear, but alcohol is a risk factor for breast cancer and a Meditteranean diet of fish, veggies and olive oil greatly reduces the risk of many cancers. Exercise and keeping your weight down help a lot.

The evidence that sacharrine, pesticides, etc., in the concentrations most people are exposed to is less obvious, and very difficult to prove. For every epidemiogical study showing an effect, there is another equally good study showing no effect. My guess is that there are gene-environment interactions, and that some people just can't detoxify carcinogens as well as others. Epidemiologists understand why studies vary when the risks are small to overall populations (but not to specific individuals), but it is hard to get that message across to the public, though we certainly try. Not all published research is absolute truth! Experiments need to be repeated and verified before major actions are taken.

As for hormones, I think most women today are aware of the studies showing the risks and benefits of hormone replacement therapy. HRT is not indicated for some women, but--at least short-term--can vastly improve quality of life for most. OCs actually cut the risk of ovarian cancer in half, and have only a slight risk of breast cancer which disappears after one goes off them. The major reasons for an increase in breast cancer can be almost totally attributed to not having many kids at an early age, starting menses at much younger ages than in the past (overweight girls), and maybe hormonal influences in utero. Most women who get breast cancer never took hormones of any sort.

Both NCI and ACS spend looking for ways to prevent cancer, but so far only the chemicals--tamoxifen, which has reduced breast cancer deaths by 25% over the last ten years, and NSAIDS like aspirin and celecoxib have shown any promise. Please remember that people were getting cancer eons ago, it isn't all a modern Western phenomenon. We are just not dying of other things first anymore.

Only 5-15% of cancer is inherited, but it is 100%genetic and involves mutations and alterations in genes and their activities that occur over a lifetime. So studies of genes are crucial to understanding the disease. Drugs targeted to specific genetic alterations are working in early trials. I think researchers should try to prevent cancer if they can, but we still have to do something for the people who get the disease.

If any cancer researcher stumbled upon even step 1 of 5 in putting together a comprehensive treatment to cure even 10% of the world’s cancer, he would be immediately so famous that his company going out of business wouldn’t bother him. The research grants given to him to continue research along that vein would so overshadow his measly salary that his boss threatening him with "the pharmaceutical companies won’t like that" would cause him to laugh so long and hard that he might actually roll to the bank to cash his billion dollar check. Now that’s assuming he’s unscrupulous enough to even be tempted to "bury it" if the right offer came along. Besides, you are forgetting that large corporations outside of the medical field contribute heavily to the cause. And Dawn is quite right, if we found a cure for leukemia, it would likely not be a cure that everyone could enjoy. We would likely still have a lot of work to do. Then whichever company found that cure would have one under it’s belt, and the fame that follows. Guess who would be getting more donations next year.

Lung cancer accounts for about 1/4 of the overall cancer rates since 1950...20% of lung cancer is caused by factors other than smoking.

I'm not saying smoking isn't a big factor but most of the incidence of cancer are non-smoking related such as prostate cancer, multiple myelon, and non-Hodgkins lymphona, rates have gone up 200 percent for each. Brain cancer is up 80%, testicular cancer up up 300% in men ages 20-35,breast cancer and colon cancer up 60, and childhood brain cancer up 40%.

The cancer situation in this country is a crisis. Our current efforts have failed.

I think it's time to start shifting our funding to something that will actually improve this situation.

I think educating the public about cancer prevention is critical.

The biggest madical problem of all is the ageing process. Curing cancer would only extend the human life-span by one year, and you would still have the physical and mantal decline caused by ageing. If we're not going to try to cure ageing, then we might as well shut-down all medical research, and spend the money on something more worth while. Trying to cure deseases without trying to cure the ageing process is the biggest waste of tax-payer's money that I can think of.

Dawn

Marie Curie nee Manya Sklodowska studied at Sorbonne and did in fact assume the chair of her husband , but no where I can find that she received a doctorate in any field. Even if she did or did not receive a doctoral degree in no way distracts from her acomplishments.

Louis Pastuer never received a doctorate from any college or university, but held academic posts at Strasborg, Lille and Paris.

If I remember my post, I believe that the theme was that ARROGANCE seems to accompany the possession of the advanced honor and often it is this arrogance that causes the ones that could and should discover the great cures often are the reasons for its delay.

If any of the aforementioned personalities received advanced degrees it was after their discoveries, not before nor during. I just read some short bio's on them and no mention of any degrees beyond those in their possession at the time of their discovery were mentioned.

Speaking of arrogance, should we expect any cures anytime soon? What does it speak of a civilization where a sports figure earns more in one year than a person who may find the cure to diabetes, cystic fibrosis, or aids could possibly earn in a lifetime? When society values its entertainers more than its researchers, something is seriously wrong.

The medical community hasn't found a cure for most of these diseases because it is more profitable to not find cures.

If we educated the public on prevention or found cures we might actually work towards creating a nation that was healthy. We can't promote health. We need a nation dependent on billions of dollars worth of drugs, surgery and radiation every year. That way everyone working in the medical community can stay employed. Hospitals, doctors and clinics will have an endless supply of sick people that need more drugs, surgery and radiation. Talk about generating your own income!

Our health care model is a very profitable set up but has nothing to do with promoting a physically or emotionally healthy nation.

June, ACS Facts & Figures estimates 161,900 deaths from respiratory cancers this year, making tobacco-related cancer deaths way ahead of colorectal cancer, in second place with 56,300. ACS also states that 85-90% of lung cancers are related to smoking, direct or second-hand. So smoking cessation is the #1 preventive measure to push in terms of public health. Sunblock or sun avoidance for skin cancer, monogamous sex for cervical cancer, maybe Hepatitis virus vaccination for liver cancer. It doesn't hurt to eat well and exercise. Also, one should follow guidelines for early detection of those cancers where this is possible--breast, prostate, colon, cervical. Yes, lymphoma and liver cancers are increasing, and we need more research into why this is. But they haven't increased nearly as much as lung cancer, paticularly in women, and melanoma (which may be due to ozone depletion, but is compounded by the attitude that a good tan is healthy).

There just isn't enough good science to support any other prevention strategies at the present time. Unless there is a 3-4 fold difference in the risk of exposures (as in smoking and lung cancer, which is 9-10X, or estrogen and endometrial cancer, which is 4-7X) epidemiological studies will be inconsistent. There are no good biological markers for most exposures, and patient recall after 10-20 years is unreliable. Neither are animal studies where animals with short life spans are given massive doses of a chemical to come out with the same dose-years as humans. Under those conditions, even broccoli can cause cancer.

The exciting thing about the human genome project is that it will allow us to look at the complete set of genes and how they are switched off and on in every cancer patient, and perhaps identify those combinations of genes that might predispose someone to develop cancer when confronted with a specific exposure. Only about 20% of smokers die from lung cancer--what is different--genetically or in their lifestyle--about the smokers who don't? Other than that they die earlier of heart disease and emphysema! Is it their immune systems, their carcinogen metabolizing systems, their DNA repair systems? I can hardly wait to find out!

Ok it you don't want to support prevention but I don't want to support a medical establishment that does not promote health and in fact does promote ill health and often death.

Medical procedures in this country, when performed properly, are the 2nd leading causes of death. I am not talking about medical mistakes. I'm talking about standard drugs and surgery intervention and "care".

Even adverse drug reactions account for over 100,000 people a year. I think this number is underreported.

(JAMA April 16th 1998)

http://www.ktv-i.com/news/nn04_16_98.html

Dawn

I don't doubt your bio research into the lives of Pasteur and Curie.

Women of Curie's time had a difficult enough time getting the opportunity to even compete let alone actually earning advanced degrees.

I've often speculated that when ever the academic heirarchy is literally embarassed by academic peasantry, conferring, acknowledging, and offering even honoary doctorates is a face saving ploy to bring those who dared challenge the establishment to the upper levels avoiding the embarassing event of dealing with academic inferiors.

Uh... What about roses?

June Blake - Monday, 06/12/00, 5:05:57pm (#86 of 88)

I read the article you linked, and it certainly indicates that there is a lot of improvement in the health care system by addressing adverse drug reactions. I hope the researchers continue, and find the changes that will do the greatest good.

Your link, however, does not support either of the two statements you made.

"Ok it you don't want to support prevention but I don't want to support a medical establishment that does not promote health and in fact does promote ill health and often death."

While I agree that a philosophy aimed more at prevention and less at cure is desirable, I have to admit that I and a lot of members of the general public bare a large share of the blame. I do not exercise much, and my diet isn't great. Many other people smoke, drink, drug, and engage in high risk sex. Most people choose to remain stressed out much of the time, rather than learning to let go. All these things put life and health at risk, and anyone who reads, thinks, or watches TV knows this. In fact, most of the drugs people have adverse reactions to are administered in response to a situation that the patient could have avoided by applying knowledge he or she already had.

"Medical procedures in this country, when performed properly, are the 2nd leading causes of death. I am not talking about medical mistakes. I'm talking about standard drugs and surgery intervention and "care"."

I did not find that referenced in your link. Is it in some other article? In fact, the article cites cancer as the number 2 leading cause of death.

On top of these comments I would like to note that prevention requires understanding of the cause. For many of the biggest health problems knowing more about the cause requires knowing more about how the body works. I see the greater understanding of the genetic code as a research field that is likely to greatly improve our ability to prevent health problems, and perhaps even fundamentally change the way we live.

The DNA contains many meaningless sequences which have no function. If we learn to edit these out, and reduce the length of the molecule, will cell division occur more quickly?

Will it be possible to grow a 20-year old body in only 5 years?

Could we engineer a cow with blood that's compatible with humans? Could we engineer a cow or a pig capable of hosting a human embryo until the fetus is ready for birth?

Might we engineer companions, soldiers or slaves? I'm looking forward to anencephalic clones that can be used for spare parts. No brain, no guilt. Just organs. Basically a "meat puppet", if you will.

And with the coming technology of molecular computers, maybe we could mass produce several lines of anencephalic supermodel clones retrofitted with nanocomputers to control movement, speech, facial expressions and sexual behavior?

We could call them "genies". They'd be perfect toys, with perfect flesh, and perfect personalities. But there'd be no guilt about abusing them, since their brains will just be inanimate computers interfaced to a spinal cord. Essentially, they'd have no more rights than hamburger or steak, since they'd just be warm meat with no real feelings.

And with our knowledge of gene editing, we could grow a 5' 10", 36-24-34, completely sexually mature love slave in only 5 years or so. You'd have to order one for your teenager when he's only 8, so she'll be ready by the time he reaches puberty.

I wonder if her eyes and smile and laughter will be as clear and bright as those generated by real brains? I suppose it all comes down to the molecular computers, and how well they have stored the patterns of behavior of their trainers.

If we're truly to be freed from work and hardship, we'll need a class of mass produced expendible herculian heavyweight soldier clones and service worker slaves to perform laborious tasks like baggage handling and nuclear power plant maintenance. And when we're really bored, we can use them for food.

Just tissue cultures. No harm done.

Kurt Schoedel: "The biggest madical problem of all is the ageing process"

Why would anyone want to halt the aging process? The resources to support an ever-increasing population are not limitless. Without disease and aging to limit population growth, we would all just starve to death. Or kill each other in the pursuit of food and shelter. At what age would you want to "stop" aging?

I have no problem with aging or dying, i do believe in life after death, so aging and dying do not bother me. People are "living" longer now than society's resources are prepared to handle. People are just being warehoused and fed until their brains and bodies become useless.

If people had no fear of dying, the aging process would not be a concern. And a better quality of life would be what you make yourself, not a product of science.

Jack Clark:

Extending lives wouldn't be too much of a problem, except that many more people would have to avoid having children (or, as much as we might not like it, adopt a child policy similar to China's).

Actually, I think the real problem we need to figure out in genetics is in how to extend the YOUTH of people, not so much the raw numbers. At this point in time I'd rather have the body of a twenty-something for twenty more years than to live an extra twenty years (although the former would probably cause the latter).

Imagine what sports would be like if a football player didn't consider retirement until his 50s or 60s! How about actors and actresses who can still play the lead role in their blockbuster action film series when they're 40 and not look as if they've aged a bit?

Hopefully the expression "youth is wasted on the young" will become a relic of the past. :)

J Fingas

Yeah my wife would love to have me as a twenty something- 80 year old! And i would not mind having her in perpetual youth either, you know how gravity affects women. Please no flames from the feminists, it is only an observation, not meant as a derogatory remark.

But when do you tag out of the game of life?

As a technically minded person, I was startled at my own reaction to this article. For the first time in a long time, I was somewhat frightened by the news today. I have followed the Human Genome Project happenings for some time now, and for the most part I have been rather excited about the possibilities it affords. Now that significant strides are being made however, I am alarmed of the overwhelming responsibility that this technology forces on the human race.

The human genome seems much like the atomic research of the early 40’s. When Robert Oppenheimer saw for himself the weapon he had created, he could only ask, "What have we done?" After the revelation of nuclear weapons, it seemed America, and indeed all of mankind, had suddenly added a great burden to their collective shoulders. Granted, it is difficult for me to judge, as my mere 21 years on this planet have not given me a first-hand account of the happenings of the time. However, from what I have gleaned from textbooks and records, there was a change in the human condition at that time.

My question is: are we really ready or willing to shoulder another such responsibility? As complex as our lives have become, do we really want to bring about another issue that threatens the very nature of our existence?

I could be wrong though. The human genome may give us the answers mankind has sought since the foundation of civilization. Perhaps we can cast off our million-year-old forms, and emerge as beings evolved to match the complexity and severity of our future.

The government Human Genome Project (HGP) has been a waste of taxpayer money. They spent 3 billion dollars doing what Celera (CRA) accomplished in private industry for 300 million. PE Corp (PEB) did it for 1/10th the price.

I've read a number of the posts on this site and a few have mentioned the fear of creating another Hitler or similiar evil person from the past. This is just not possible. They might be able to create someone who looks the same, but the person inside will be quite different. All one would be doing is to create a twin after the fact. Identical twins are quite different. (I'm not one, but I know of a few.)

This breakthrough is going to be looked upon as one of the greatest moments in the history of our society, if not the greatest.

It is true that there will need to be standards of some kind placed on the use (or abuse) of the knowledge gained, but the benifits outweigh the drawbacks 1000 to 1. I would like to think that fifty years from now hospitals will only be necessary for the repairing of injuries sustained from accidents and the like.

And as for the opportunity of engineering offspring, I'm not so sure I would be against it. I might not do it myself if it were available today, but to remove the option of ensuring that our children receive all the benifits that we may be able to provide for them is a bit unsettling.

Before we adopt laws to prevent the use use of some of these new things, maybe we should wait to see how this new technology evolves...

The news about the human genome sequence is great, but not unexpected. There is still a lot of data mining to do before the information becomes useful. As I understand it, about ten people were used in the government project. Celera is rumored to have just used one person, probably Craig Venter the CEO. I don't think Celera is planning to patent the genome, but sell the sequences to other researchers and ask for a cut of whatever drug or gene therapy is derived from the gene. We'll know on Monday when they make the joint announcement.

A lot of research groups will now dive in and sequence many individuals to determine all the variations, or polymorphisms, that exist and what effects they may have on a person's disease susceptibilities and drug reactions.

Calista, researchers are still working on CF. The virus vector works temporarily, but then the patient develops immunity to the virus. A way needs to be found to get the correct gene into the stem cells of the lung that repopulate the epithelium as the older cells shed off. It is doable, and I am sure it will happen in a few years. It is the sort of research the government can and does fund, and the ultimate treatment probably won't be all that expensive.

Kurt, do you have children or grandchildren, as I do? I suspect not. If you did, you would realize that they are the true form of immortality. I don't mind the idea of getting off the planet and making way for new people with new ideas. I hope I have another 20 years of good health, but that would be about right (and yes, I'd like to have had 20 more years as a 30 year old, but it is too late for that!)

As for the junk DNA, I believe it would be very difficult to edit all of it out, since it probably contributes to space and size of chromosomes that affect cell growth and division in ways that aren't immediately obvious. In any event, the amount of DNA doesn't control the rate of cell division or an organism's life span. Many smaller organisms have quite a bit of DNA and don't live very long, although I don't think the reverse is true. Maybe redwoods don't have as much DNA as humans, but I don't know.

One thing I am hoping is that the human genome sequence and the DNA sequencing of many "lower" organisms will definitively reveal the evolutionary tree, for example how the genes for gills and tails have mutated and changed as you go up the phylogenetic tree. Most of the junk DNA is probably evolutionary leftovers from millions of years ago.

The technology for producing designer humans ("genies") is 20 years away, at least. Your concern about privacy, however, is valid today.

Eventually, ubiquitous portable instant identification will be inevitable. The upside is safety. The sooner each citizen is easily identified by DNA, the sooner we can throw away our wallets (meaning cash and banks), credit cards, driver's licenses, passports, car keys.

A cashless society will be easier to manage. Granting credit, social security or welfare payments will be instantaneous and discrete. There will be less reason for crime or poverty. The monopoly game (global economy) will be based less on scarcity, and more on abundance.

Now that's commerce!

I look forward to the completion of the genome sequencing. Once and for all the basis of human life will be revealed. Also to be revealed are those aspects of personality that are more highly dependant upon biology than most would care to admit. I foresee genetic engineering not only being used to reshape physical bodies, but also the minds within those bodies. My greatest concern is how these new technologies will be handled by the powers that be.

At the outset, it should not surprise anyone to see these agencies move to try to restrict the scope of engineering, allowing only what "experts" deem to be harmful genetic conditions being subject to modification. In this instance, one has to wonder what agencies will use as criteria for determining such harm.

Let me posit that the least amount of governmental restrictions will serve the greater good. Just as a government can allow certain changes, it is only a short step for it to mandate those changes. Further, why would any society allow a panel of experts to restrict these procedures, using the experts' value systems as a gauge rather that the person who desires therapy?

Does the idea of what is essentially government controlled eugenics disturb anyone else?

Dawn, I think the difference between you and me is that I have a more brain-centered concept of identity than you do. In otherwords, I view kids as other people, separate identities. Hence, they cannot represent any form of immortality for me. I think, perhaps, that you may view your genetic programming as the basis of your identity. Since your genetic code is passed to your kids, it can be said that they are immortality for you.

Of course, the real issue whether the political system will respect my choice to live forever young if I so choose. If the American system truely believes in individual liberty, then it must include the right for people to live forever young, when it becomes technologically possible. Immortality goes together with entreprenureal freedom and individual liberty.

James Hogan, your not the SF writer, are you? And yes, government controlled (or sponsored) eugenics does bother me.

Also, I do think that we need to have personal medical information protected from both governments and companies (employers and insurance companies). Of course, the sooner we get rid of the FDA and get the technology to transform ourselves, then these medical issues will disappear from the business culture.

In regards to Mr. Larson's post about the government's project being a waste of money, you are completely incorrect. From a matter of principle this should be a public project. But more importantly, what Celera did was completely useless. The Human Genome Project went along and sequenced each chromosome as a whole, hence the extra time and cost. Celera chopped it up into smaller pieces and used super-fast sequencing machines to sequence these fragments. What the the Project did is in effect going through the Library of Congress and cataloged each piece in order. What Celera did was take all the books, rip all the pages out throw them all in a pile on the ground, and now they have to try to put them back in order. Good luck, it's not going to happen without too many significant errors. Additionally, I agree with a professor of mine who said that the government and health care industry have no idea what this information is gogin to do. It's going to force the implementation of a socialized system. There is no way not to have one now.

Having the sequence is not enough. Data mining of human genome is not enough. Experimental protein based drugs discovery is not enough. That what we need are analytical methods and theories to invent or discover the n-tier coding scheme embedded in the genetic code. No less than formal (analytical) language of bioogical life. GEENOR will do it, if others will not.

Cloning is pretty far off, and no one will want to get cloned because people value uniqueness.

In any case, whatever the cost, and whoever accomplishes it, the genome sequencing project is a great scientific undertaking in biology. This is a first real breakthrough since the discovery of DNA itself in '53. The more we know about our own biology the better. Aside from the possible medical applications, we'll know what all those genese are doing and perhaps this will shed light on our past and future evolution.

Jack:

I don't know if that's possible, or even a good idea. Death evolved in animals for some reason. On the other hand, theoretically, the body can repair itself forever, if given enough resources. Maybe in animals death has a purely ecological reason, and if we colonize other worlds, longer lifespan won't alter our quality of life. In any case, I see 200 year old people on the horizon. I certainly hope to be around 100 years from now.

I think that this is a significant achievement - but it is also a humdrum achievement. We've known how to sequence DNA for quite some time now. The breakthrough was made long ago. All we have done is devoted the time and effort required to parse the DNA and delineate the words. Now the work begins - figuring out what the words (genes) mean.

I don't mean to belittle the achievement - it marks the beginning of the beginning.

The implications of genetic engineering smells strongly of nazism...the perfect species. What about the less perfect humans whom have made this very discovery possible? Will others like them be eliminated simply because they don't fit the mold of perfection. Will some unscrupulous manager of genetics find a gene in his sequence that indicates something other then what is deemed acceptable, and put into his ubiquitous file only to to be rejected when his first sign of the end appears. I don't have confidence in the human laws of science. The laws of nature are not random, but very carefully evolved rules of common and symbiotic relationships within nature. When we change specific areas, without regard to the relationship of those changes with nature, we're not only playing with fire, we're playing with white flame. "To live forever young"is utopian. How about being denied medical treatment because of a genetic flaw. Or being labeled a killer because of specific gene. The potential for good is balanced equally with the potential for disaster. We should understand, and be very critical of what's happening before we embrace such esotoric break throughs.

In reference to the Human Genome Project, just announced and recalling some of the discoveries,progressive movements and social changes of the past: Galileo's solar system, organ transplants, automobiles, women's rights, civil rights, to name a few: they all came with dire warnings about the adverse effects on the human race, to say nothing of mankind's relationship to God. I would think that a thinking, rational person, regardless of religious convictions or political affiliation would conclude that the very human qualities of curiousity, need to challenge, and sense of wonder will lead us to astounding places, unexplored. Over time, the need for limits and laws, restraint and evaluation will be obvious. Some , if not all will be constantly evolving, as progress and experience dictate. There will always be those who abuse any technology, gain unreasonable financial benefit or attempt to misuse the fruits of our intellect. Hopefully, we can go into the next age of discovery, wiser, yet hopeful that we've learned from the past and need not fear the future.

There is the real possibility that insurance companies and potential employers could use one's genetic profile as leverage to deny coverage or employment. Hence, the need to enact strict and binding laws preventing the release of private individual genetic profiles to outside parties is absolutely paramount if we, as a society, are to avoid the creation of genetic underclasses.

Fortunately, we have some time: there are only a few tests currently available that can correctly determine a particular individual's susceptibility to diseases traceable to a certain genotype. But be uncomfortably assured - that situation is going to change very soon as every run-of-the-mill, upstart biotech firm in the world races against one another to find genetic tests that would determine everything from an individual's potential for acquiring airborne-illness to an individual's ability to retain their suntan (I'm not kidding about the latter - in the course of hunting for jobs in my field of chemistry, one lab director spoke about that pursuit as if it were the cash cow for the 21st century.)

Finally, be very wary of statements along the lines of "this new technology reminds us of the need to deregulate the pharmaceutical industry", or "it would be now better if we just abolish the FDA." Take these statements with a huge grain of salt: believe me, the consequences of a genetic testing industry running rampant with no authority to oversee their abuses (and abuses there will be) are too huge to ignore. Given leeway, genetic profiling can create a a whole new system of genetic "haves" and "have-nots".

Jacek--right you are. A whole new field of systems biology is opening up with this achievement. At last we will learn how all of the myriad numbers of metabolic pathways interact, and how interfering at one step on a pathway may have effects you can never guess by looking at that single path.

Bobby A: Sure people will want to clone themselves. Remember Richard Seed! I wouldn't mind being able to give a replica of me all the advantages I think my parents overlooked. But that would put phenomenal pressures on the little clone, so I probably wouldn't do it. Americans value uniqueness more than most other cultures, I suspect. Some value conformity. I don't know that all biological processes, such as death, evolved "for a reason." Did polio evolve to paralyze little kids, etc.? It just works out that way.

Kurt, it is okay with me if you want to live forever, but if everyone chooses that route the world will be a very dull place and not much progress will be made after a few centuries. It would definitely change the character of human relationships. I can't imagine being married to the same person forever. Part of what makes life so precious is the knowledge that it isn't going to last forever. I'm still ready to check out around 85, or sooner if I become seriously ill. I don't see that the human genome data will help people in my age group (60) very much, since the benefits are still a long way off.

The mapping was inevitble and the promise of better treatments for diseases/disorders is certainly welcome.

I can only hope that in the future, anti-discrimination laws and rights of privacy will be used to prevent corporations from taking advantage of this knowledge.

"Gattaca" was an interesting movie, but it pointed out the potential horrors of a corporation's complete access to genetic info, a family's manipulation of the healthy unborn, and a society's genetically elite discounting all others.

History has proven that when man plays God, then God destroys man. Judgment Day is just around the corner folks!

It is appointed unto men once to die, after this the Judgement. Hebrews 9:27

Diane wrote:

I guess the question I have is Who makes the laws and How do they arrive at these limits? There is a great clamor about how HMOs determine whether a particular procedure should be covered. Imagine the uproar if the government refuses to allow some genetic treatment based upon sort sort of arbitrary rationale.

In Canada, there is legislation proposed prohibiting physicians from disclosing the gender of a child before it is born absent some chromosomal-related imperative (i.e., for males offspring with potential X-chromosome-related disabilities). So, if you want to find out from an ultra-sound if it's a boy or a girl, too bad. The powers that be have determined that you can't be trusted because you shouldn't be allowed to make an abortion decision based upon gender.

The proposed Canadian law is a good example of legislating in the negative. Instead of prohibiting abortion decisions on the basis of gender (more common in places like China and India), the government simply won't allow you to have that information. Ignorance is bliss.

The ideal seems to be to have no laws whatsoever and let individuals make decisions based upon their own consciences and concerns.

BTW, I am NOT the Science Fiction author. we have different middle names. :>

This is pretty much bang on. A monkey could have sequenced the human genome if you gave 300 million dollars. It was only a matter of time and effort. No new science here (yet). The big hoopla is only in the news media.

I'm not sure if this equilavent to landing a man on the moon. It's more like inventing a bottle rocket and figuring out that you may be able to some day invent a really big one that can get you to the moon. The real science is yet to come.

It seems that the DNA that codes for proteins is less than 10% of the total. The remainder has been termed "Junk DNA". I have seen no writing on the function of this DNA, other than evolutionary debris. To me, it is obvious that this is the region wherein instinct, behavior, and personality are coded. A baby suckles at birth, and my cat does very "cat-like" things, even though the last time she saw another cat was age 3 weeks old. We just have no idea how a base sequence is translated into a synaptic structure. Does anyone know of any references on this topic?

So now we may now understand how our bodies are madeup, but this has nothing to do with our intellect or that essence that truly makes each of us unique. To place this in the realm of religion or theology is an indication of just how much those that try to merge this together don't know about religion or science.

Jealousy. That is a word to describe the recent (is it really over?) ire with Craig Venter. Venter has been groundbreaking. While the NIH researchers decided to rub two sticks together to build the fire, Venter cooly came along with the lighter and put them to shame.

So what if Venter is to charge for the information. Scientists have been paying for information for as long as anyone can remember. Subscriptions must be bought to scientific journals. Scientific meetings charge a hefty price for attendance. What is new here?

JUNK DNA- May Not Be Junk After All

To Chris Woodhouse, message #130:

Junk DNA according to current state of knowledge is really a trash, a trash that constitutes 97% of whole human genome! Why trash? Because it is not translating into proteins. So it seems to be useless.

But I do think that it serves some purpose. Statistical analysis has showed that there are some regularities in this part of genetic code of humans. Nobody understands however what could be function of this part of this 97% of DNA there is saying that it is trash. I think that at least some part of this Junk DNA has some very important functions.

We need to conceive software or theory which would make us possible to understand Junk DNA as well, not only the standard code, which is used as template for building proteins. Any ideas how to do this?

"Junk DNA" probably plays a regulatory role.

Thanks, Jacet, those are great links. I am compelled by the theory of "spread spectrum" radio, and error-correction coding, where information is spread out as much as possible, so large chunks can be damaged, but the message still gets through. The data itself looks just like noise, even though it is dense with information. Even the brain is similiar, where strokes can take out big pieces of cortex, but function is minimally impaired. So, as far as this topic is concerned, we have accomplished the easy part. Yea! Let's go make some good medicines. Now comes the subtle and mysterious part.

With respect to "junk DNA," there is some evidence to sustain the belief that these are inactivated portions of the genome that humans have evolutionarily outgrown. I believe supernumerary nipples along the bodies' milk line are the outcome of junk DNA that becomes activated (likely as a result of a mutation). This was a feature of humans that predate even the earliest hominids.

Phill Gonzales:
Monday, 06/26/00, 11:23:08am (#121 of 137)
"The laws of nature are not random, but very
carefully evolved rules of common and symbiotic
relationships within nature."

Interesting, yet this view suggests that any human activity is somehow outside the laws of nature, as if we aren't natural. Well, we are. And we are doing what humans do, just as trees do what trees do, and dogs do what dogs do... well, you get the point.

Arguments that state the "thing" we do is somehow not par for the course tend to fall in on themselves.

No matter, really, because we will do what we do, whether we like it or not. Our awareness is the only reality we have anyway.

We can enjoy what there is to enjoy, and suffer what there is to suffer. Or not.

I'm very excited about the mapping of the human genome, and I look forward to hearing about the advances made in medicine, using this technology. I would like to hear more about the people involved in sequencing the genome and less of the political rhetoric. These are fascinating, complex and highly intelligent personalities!

While I am not saying anyone is or is not highly intelligent, why do you say they are "highly" intelligent? Do you think sequencing DNA demands high intelligence?

We actually cannot waste money; it is either used, or not. In the case of the HGP, it was used. Barring a time machine, forward motion is what we experience. Therefore, all effect comes about through effort. Money helps to facilitate this. *Something* happens, which is all existence is... awareness of effort. So, in light of this, there really can be no waste, IMHO.

Guess what,mapping the human gen system is great because it will finally let white racist know for sure that they have Black blood running through their veins. Wait until they relize they are part Black, and have African ancestry. This will do a lot for race relations among white people. How will they hide the fact that they are part Black from their neighbors,ha. ha. ha. Because of this fact, gene mapping will be stopped by white people that are afraid to know the truth, damn,another thing for white people to fear, ha.ha.ha.

The genetics race and the mishandling of genome information might turn this into something like "Brave New World" ( read Aldous Huxley ). Won't we have different genetic classes and people being labeled "better" than others because of advances in this technology? Who is to say that developed countries won't have the rights to most of the genome, and who knows what the governments will hold for the rest of us? Scientifically, it's great. But the what about the social and ethical aspects of genetics?

Agreed with Brad that man should not play God. However, we need to face realities...

Man is rapidly changing nature. Man is becoming nature (perhaps Adam was banished from God's presence because man cannot and should not play God).

When it comes to biology, the term "complexity" is appropriate. From here on there are not going to be simple black and white answers. Just as much as the workings in biology are rather complex, the decisions that affect humans and human wellbeing will also become complex... very complex (as they should!).

Concerning Mr. Taylor's Comment:

Yes, white racists may have something to fear along with black racists--imagine their shock when they find out their lineage contains Jewish blood. But this type of racial munbo jumbo is not new. The nazis made use of an "Ahnenpass," a record book which verified the owner's racial history through the use of baptismal records--a necessary prerequisite for a marriage license in the 3rd Reich.

But nowadays, who is going to force the issue that each citizen receives a blueprint of his/her genetic makeup? If there is a "don't ask, don't tell" policy in the armed forces concerning homosexuality, why would one believe that there would not be something similar regarding genetics. How well it would work is entirey another matter. One can look at the way in which AIDS has been handled by the insurance industry to get an idea of where the situation is headed.

Garnie Taylor - Monday, 06/26/00, 4:58:35pm (#142 of 144)

Guess what,mapping the human gen system is great because it will finally let white racist know for sure that they have Black blood running through their veins. Wait until they relize they are part Black, and have African ancestry. This will do a lot for race relations among white people. How will they hide the fact that they are part Black from their neighbors,ha. ha. ha. Because of this fact, gene mapping will be stopped by white people that are afraid to know the truth, damn,another thing for white people to fear, ha.ha.ha.

It's practically on the verge of being mentioned, but no one seems to really be mentioning it: the movie Gattaca (GATTACA is a DNA sequence if you didn't know) touched on the whole issue of genetics determining your fate in society in addition to your physical health.

Personally I don't see genetic screening happening except in situations where having that knowledge could be very important - if you're planning a manned mission to Alpha Centauri that will take 40 years, you don't want someone on the crew who you know will die in 20. Yes, it would definitely be scary to know the particular time frame you could die in, but it could also mean the difference in some situations. I wouldn't prevent someone from taking a job at a company outright, but obviously it would be a good idea not to base any long-term plans around someone who will most likely not survive that long!

Mapping the DNA of human life is certainly a breakthrough which will revolutionize the practice of medicine by paving the way for new drugs and medical therapies and determine our susceptibility to illnesses like cancer or diabetes. Would it also be helpful to determine the right treatment for other illness,which are still under research, like - Migraine Headaches?

As a budding genetics student, my professors have taken pains to instill the inherent problems associated with vast genetic knowledge. Until recently, humans have been forced to assess the value of a man on a social or economic status. While not necessarily divine, this does leave room for equalization over generations, or even lifetimes. Genetic science however, is relatively static, being predetermined at conception, and remaining throughout our lifetime. The only way to "assess" the genetic value of a person is to test them, most likely at an early age.

This assigns a valuation to the most intrinsic construction of a human being, something I don’t think a human society will ever be responsible enough to deal with. So while markers for the "genetic flaws" that we all possess will be detected, improving the quality of life with early treatment, I do not believe any lifeform should be reduced to its Dinucleotidyl composition. Even as a student of science, I feel that I am not privileged to have absolute knowledge of another life, only something greater then man should do that. This is not anti-progress, I just hope that my great grandchildren still feel awed at the complexity of life, and never feel possession of it.

I have been reading the posts on this message board and would like to comment on some of them. Some of the messages seem to stem out of a sense of fear that knowing the genome sequence in some way is 'playing God' I would attribute that fear to ones need to have something to lean onto in times of distress. I think the current spate of fearful emotions have existed since time immemorial. I believe the first doctor (prehistoric times) claiming that a disease could be cured raised similar fears amongst its people. It is well documented that the claim that earth was circular raised a lot of chaos and commotion in the society of the times. What I am saying here is that the thought of a breakthrough which makes us question our pre-existing beliefs makes us uncomfortable and fearful. Personally I feel that the more we know about ourselves the more we will be closer to God. And the knowledge about what we are made up of is just a step closer towards the ultimate enlightenment that we want to achieve. The Nirvana!

There are a lot of posts which talk about 'Junk DNA'. The word Junk DNA is a misnomer, since scientists couldn't attribute any function to a major part of DNA they 'canned' it for the time being by calling it Junk DNA. It is now known that the so called Junk DNA plays many important functions, some of which are listed below:

1) It contributes towards the chromosomal architecture or chromatin packaging so that we can have many meters of DNA packaged into a minute sized chromosome. A very important function if you want to keep the DNA from getting tangled.

2) It probably acts as a mutational sink: soaking up deleterious mutations and thereby protecting the coding part of the genome.

3) It probably serves as a raw material for evolution of new genes or new gene combinations or in other words it confers on a species the ability to evolve beneficial gene combos.

Lastly I would like to say that the discovery is without a doubt a major breakthrough of this century. It opens up many possibilities. Provides us with the tools which we can use to tackle diseases and thus better the plight of human beings. What one needs to exercise is caution and making sure that these tools don't fall into the wrong hands, for if they do they have the potential of causing great harm too!

I wish to extend a heartfelt thanks to the mass media for managing the release of the Genome Project progress in a bold, sustained and carefully courageous manner.

The scientific elite are carefully educating and reprogramming the general public. The majority of the world's citizens are highly indoctrinated by very unscientific religious belief systems. The media and academic communities have their work cut out for them in terms of the difficulty of conditioning the populace to accept modern scientific realities.

I find that often controversial disclosures are made simultaneous to distraction and misdirection. I am amused to see CNN's visual messages: 5 minutes of robotic genome robotic sequencing followed by 7 minutes of jubilation at the opening of Paul Allen's Experience Music Project in Seattle. Make it look good, as they say.

While the spoken message may be impartial, the more powerful visual message is clear: we are very happy at this moment in history. The public is being responsibly trained by the mass media. I'm pleased that the conspiracy favors advancing science and technology.

Ajay writes "There are a lot of posts which talk about 'Junk DNA'. The word Junk DNA is a misnomer, since scientists couldn't attribute any function to a major part of DNA they 'canned' it for the time being by calling it Junk DNA. It is now known that the so called Junk DNA plays many important functions, some of which are listed below: "

Reminds me of a home repairperson who tosses out all of the "extra" parts when fixing an appliance.

I wonder if a caterpillar has genetic code that causes the transformation into a butterfly? If so, what transformations could be hidden in our code? Also what "memory" could be in our code? It seems like lots of information could be there if you count it as bits or bytes.

As a science librarian I know only enough to getmyself in trouble. Perhaps someone will be kind enough to help me out.

As far as "playing God" is concerned - I think our job is to "play people" and realize that science is what people do.

Regards,

Gary Masters

Well.. I guess the days of the Church and its worldwide equivalents are definitely numbered. Pretty soon it will be farewell to preachy sermons, dictations on how we should all live our lives as per whatever the God of the country decides, and (thank God (excuse the pun)) goodbye to the poor throwing their hard earned cash at grotesquely rich church organisations in order that grand cathedrals can be built. Hello, instead, to a world where those in power could create master races, where past sci-fi/horror entertainment becomes fact and the human race itself could undergo horrendous physical transformation should this new info fall into unscrupulous hands (politicians..dread the thought!) Such unchartered territory must be trodden on with absolute caution. Unfortunately, those doing the walking are only human.

I ask you kindly to listen to my personal opinion.

Thank you, Mr. Venter. Genetic engineering will never forget you.

Jacek, Thank you for your link to junk DNA.

About 7 years ago I got my genetic engineering friends to give me a sample of some dna which contained both exons and introns so I could play with them on from Information Theory background.

I used running compression algorithms to plot the difference or similarities in a informational sense.

Being a cryptologist I reasoned that I might be able to find out something the biology people had overlooked.

Upon my presentation of preliminary results they commented that to their knowledge no one had ever taken this approach before and so encouraged me to pursue this avenue to intron (non expressed) research.

After I retire from my job running an Internet station I intend to attack this "spike" narrow and weird approach to discovery. It may not find the "pot of gold" but it conceivably construct a rainbow. ; )

As I am now accumulating many Linux machines and the ability to interconnect them into what would be just a few years ago considered a super computer I plan to, at least, have some fun.

Again my thanks.

Dawn you are an awesome human being.

If you die at the tender age of 250 you will undoubtedly have the mind and sprit of an 18 year old.

It was because of you that I again joined the AAAS and restarted my "Science" subscription.

Now I have to contend with a bio vocabulary that reduces my normal ego mania to pure humility.

Wife and "bun in the oven son" are doing well. 6 year daughter is besides herself at maybe getting a chance to be a "sister", and I still intend go save some umbilical blood for stem cells, although with all the advances going on it probably will not be necessary for long. Quite a thrill after several implantation problems. One more and I was seriously considering carrying the fetus myself. Really makes us males appreciate the structure of the female body. Sure did not want my wife to endure another D & C.

I'll have to go rustle up Cliff who has been his usual ecumenical self on the contentious Science and Religion board.

All the time that these scientists figure out that they COULD decode this genome, then never bothered to think if they SHOULD decode it...

At the risk of being repetitive, and redundant, I think the information and structure involved in the myriad of instinctual neural activities is staggering. Just think of GI tract processing, spinal cord reflexes, cortical reflexes, food seeking and reproductive activities, language skills, vision and other senses, cranial nerve structure and functions, etcetra. These are obviously coded in DNA, and surely could not be held in a 100,000 proteins and their promoters and regulators. With all due respect to Ajay, and encouragment to Carl, we haven't scratched the surface yet, have we?

Couldn't agree more. If any Nobel comes from this (I'm not sure it's really warranted), Venter is the only deserving one. He's the only one to pioneer something new (i.e. shotgun sequencing). The governemnt guys were and still are in the stone age.

With that said however, politics runs rampant in science and I'm sure Collins will get his so-called "fair" share.

Well, since Al Gore is vice-president during this, I guess it won't be long before he claims that he sequenced the genome just as he invented the internet :-)

Well, since Al Gore is vice-president during this, I guess it won't be long before he claims that he sequenced the genome just as he invented the internet :-)

Are you kidding?

He invented the gene.

As a free enterprise advocate I hope you can imagine how painful this is for me to say but:

"Shotgun Sequencing" was invented when Crags mothers milk was still wet on his lips.

The essential argument revolved on the computational effort to achieve reliable results using this method.

Venter understood better than the .gov scientists how fast the bang for buck was improving and that he could raise a lot of capital to amplify this effect.

It is a classical conflict in two dimensions. Known vrs. unknown and quantify vrs, quality.

Venter was rejected because of quality. In return although he used every ounce of .gov sponsored data for his plan he did not release his results publicly but made economic hay and pushed .gov to alter the concept of patent in respect to true invention vrs. discovery.

Right now it is a push, but like Bill Gates this son of a concubine will bring down the wrath of the public against free enterprise.

I'm not sure which I despise more. I am concerned that freedom and clarity of law will suffer.

I wonder what the impact of this titanic discovery will have on the more fundamentalist religions.

If woman is created in god's image then woman is now capable of shortening or lengthening life, eliminating disease and avoiding predispositions in human life.

How does that impact on those who believe that only their interpretation of God's will is correct?

There are two aspects of considerations about human genome in particular and genetic engineering. One is moral/ethical and second is scientific.

There’s no reason to bring religion into it. I think we ought to have as great a regard for religion as we can, so as to keep it out of as many things as possible. Sean O’Casey

From moral point of view we should take care that advancements in genetics will not destroy our moral values, religious included.

I am an ethnic Pole, as Pope John Paul II is, and I know that religion has high value in humans life and is a worthwhile and needed.

Truth is a pathless land, and you cannot approach it by any path whatsoever, by any religion, by any sect. Jiddu Krishnamurti

on a lighter mood,

What we have been able to decode is the genome for Humans.

It may take a few centuries more , if ever, we will ever be able to decode the genome for the GOD and hence religion.

Perhaps, even this big step is an act of His great play!

Let's go on watching the show!

Thanks, Carl, for introducing me to this board. In particular, I wish to thank you for providing a link to Dawn's post. Like you, I have an enormous amount of respect for Dawn, and I enjoyed her post enormously. I think this will be my new home after I have read all the posts submitted to date.

Cheers, friend.

Here's a prediction for a movie that should be arriving at your local cinema in the near future:

Religious zealots steal the Shroud of Turin. Fossilized DNA samples are extracted from the fabric and turned over to the Richard Seed-like biologist for cloning.

For the music, I suggest the same guy who did the score for "The Omen." I even have a suggested title:

"Second Coming"

Should I copyright this or is it too late?

While this mapping is one of the greatest discoveries of the modern age, we should steer the course carefully. I feel that no one person or Corporation should own any part of this mapping, maybe the technology that does the mapping but not the cells themselves. Isn't it bad enough that drug companies gouge us with their prices and then claim that it's the cost of R&D when in my case this was done by our own government and I paid for that through my taxes then! There are many variables when it comes to genetics, things we still do not know about, and things we may never know that may in the long run hurt us if we tamper with them. On the other hand, the day that I learned that this technology has broken through and the genetic code was mapped, I cried! simply because there are so many illnesses that will be unravelled so that we will finally be able to treat and even cure them. Medicine as we know it will be changed forever and if all goes well we will have a healthier future because of it. My only hope is that nobody messes things up by doing something stupid. Scott E.

deleted

On the other hand I am tempted by the enquiries and offers which have started pouring to me. Please help me resolve this matter.

Thanks, Davinderpal S Bhatia [email protected]

Just for the record, Carl, in recent years, the period for a US patent has been modified. It used to be that patents were issued for 17 years starting from the date of issue of patent. Now it is 20 years from the date of the application.

I think we should first see if Dr. Venter follows through on his promise to publish, and, also, we should see how his patents affect innovation in this area. Do they stimulate innovation or do they stifle it?

Hi, Carl and Cliff! I checked out to see if there was any news on the Cloning Board RE: the fantastic announcement today in Nature that scientists can "knock-out" and replace genes in context in sheep clones. Immediate application will be in knocking out pig transplantation antigens and replacing with human. And this really does suggest a GATTACA possibility of having a kid that is the best of his/her parents with a few little extras thrown in as desired. This is a much more important achievement that knowing the sequence of 3 billion base pairs without knowing the functions...why hasn't the press picked up on it?

Carl, delighted that wife and baby-to-be are doing well. When is the due date? I'm sure you will be ecstatic, even though you didn't control his complete genomic makeup. Shotgun sequencing was invented in the late 70s, so Venter was a little older than a baby then. I can't see that he deserves a Nobel prize at all--the people who deserve Nobel prizes for cloning and sequencing have already gotten them--Watson, Crick, Hamilton Smith (who is a senior researcher at Celera), Daniel Nathans, Paul Berg, Walter Gilbert, Fred Sanger. I'd like to keep the Nobel reserved for conceptual breakthroughs, not technological tour-de-forces.

There is an article in today's NY Times by Andrew Pollack about gene patenting. I recommend it highly. Ten big drug companies formed a consortium last yeat to study the most common polymorphisms--individual variations, not mutations, that make us different from one another. Obviously if a person can be exonerated from a rape through DNA, sequencing one human genome, or five, doesn't tell the whole story. Anyway, they plan to put these variant sequences (known as SNPs, for single nucleotide polymorphisms) in the public domain so they can't be patented. What can be patented are the uses of the information to design diagnostics, drugs, etc. That is where the money is, after all.

Well I just received my free CDRom From Science Mag. and Celera.

Now if I can wade through the conventional mappings of the genome and get down to the base code I can try to see if my running compression tricks will yield anything of value.

As some are aware, the code is a single dimensional four element string that encodes for three dimensional molecular structures. While there is the two dimensional CCITT compression algorithm, it is not applicable because it depends on a fixed frame conventions which is just not inherent in structures with this variability. There is a poly dimensional method of linear predictive encoding but that is incredibly computationally intensive.

As far as I know there are no compression algorithms that are optimized for genome DNA data compression.

My ignorance of what is already known is so vast that in no way will I be doing research, what I am going to do is "search", probably best described as "stumbling".

Maybe this is good. Having less preconceived ideas means I don't have to carry a lot of baggage around and can just look with an open mind.

In any event I am grateful for the vast amount of effort that has been expended to bring this data to me.

Good point. I would guess the reason that the press appears to be ignoring that is that the ability to modify the genetic structure of plants and animals is, by now, considered old news. And cloning has been around for sometime now. How quickly the phenomenal becomes commonplace :)

However, knowing the "complete" sequence of five individuals is significant also, holds significant promise of future discovery, and is something new.

I wonder what the economic value of the study of polymorphism might be. Individual treatments to specific individuals may have significant benefit to the individuals involved, but I would think that small scale special treatments of the few is not likely to have a significant financial reward for the large drug companies.

Is it possible that this is mainly a public relations effort that may yield significant benefit to society, but will have little economic impact to the drug companies, if any--and the reason for forming the consortium was to spread the cost of an effort unlikely to yield significant financial benefit?

However, I would have expected Celera to delay the release as long as reasonably possible. The longer the raw data is withheld from others, the longer they have to get a jump on possible competitors in the design of diagnostics and drugs. (But I have understood Carl correctly (below), they have already released the the raw data.)

If I read this correctly, Celera is immediately giving it's competitors equal access to the information from which diagnostics, drugs, etc. may be created. My understanding was that Venter planned to publish his data in a peer-reviewed scientific journal once he has sequenced the genome. I expected that that would probably take a year or so during which time Celera could continue to work on possible diagnostics and drugs.

Have I understood this correctly?

Sorry Cliff I should have been more specific.

The Mar 24th issue of Science had an issue dedicated to the complete mapping of the Drosophila genome. ( fruit fly )

There was a cut-out to send for a free CDRom of the Genome and a large map in Science.

I ordered it by e-mail and just received it. You can e-mail to [email protected] and they will probably send you one too.

It is something to hold a CDRom in your hand that has the "blue print" of a living creature inside.

I kind of feel like "OK here are the instructions, but where do I get the rest of the Fly Kit". Juvie feeling I know but just holding it strips away about 45 years in my mind. See! genetic engineering is all ready making me feel younger again. ; )

To tell you the truth, from a coding theory standpoint I would rather study the DNA of the cockroach.

It is substantially the same as it was some millions of years ago I understand. As you might know we use electronic coding for 3 reasons.

* Error detection and correction

* Compression

* Cryptography

Cockroaches are supposed to be extremely resistant to radiation and this implies a number of things including "error correction" via redundancy, and maybe dynamically as "error detection and correction".

It seems pretty certain that our immune system uses killer T cells to correct for errors in human cells by killing the ones that have certain types of errors in them.

Perhaps Dawn can illuminate us on this.

Okay if you say so :) Actually, I am just relieved that Venter hasn't totally taken leave of his senses. (I had the understanding that he was giving away some pretty valuable information a lot sooner than he needed to.)

Obviously, the optimum PR/cost ratio would be to get the release of his data in within the next couple of years (typical for peer review). Actually, this is about perfect because it will be before the public sector project completion, but after release of most of the public sector data. That way he doesn't lose much that he wouldn't lose anyway. And, also, he can appear to be "doing it right" in a peer reviewed scientific publication.

Carl, I'm not clear from your message what you want to find in the Drosophila genome. I'm sure you understand how linear DNA results in 3D proteins. Do you want to make DNA-like electronic codes? I don't know that the cockroaches inability to change is such a big advantage. They are still cockroachs, after all. While look where we mammals are! I'd rather be flexible myself, even if it means I'm susceptible to cancer and other genetic mishaps.

Killer T-cells kill cells that they recognize as "foreign," which includes many virus-infected cells and some cancer cells, but not every cell with genetic errors for sure. Most cells with DNA damaged by chemicals or radiation are thrown into apoptosis, or programmed cell death. This requires that several genes make functional proteins, notably p53, the so-called "guardian of the genome." Cancer cells, the ultimate example of Darwinian mutation, selection, and survival of the fittest, acquire mutations in many critical genes to by-pass apoptosis.

Cliff, I think the SNPs have considerable economic value, as it is in this 0.1% of our genomes that all of the multigenic disease susceptibilities occur. Correlating SNPs in multiple genes with disease and drug efficacy or side effects will eventually lead to individual profiles that can predict disease risk and drug action. Obviously predicting disease risk has ethical problems when it comes to insurance and other forms of discrimination (job, mate selection). But I would like to know if eating creme brulee is likely to lead to the diabetes type II that is common in my family--if not, I'll quit passing it up! Drug companies can save money by knowing which drugs will work best and which might be useless or dangerous. Anti-smoking efforts can concentrate on those who are most at risk from smoking, or who will have the hardest problems with addiction.

There is a difference between data and "information", defined in the scientific sense.

Information is the data that can be used to change the a priory probably of a well formed question.

Normally we select a coding mechanism that uses a small amount of data to carry the true information.

If we were using english we know in advance that the letters in order of usage run e t a o n r i s h d l f c m ...... with the first letters being much more probable than the later ones.

Thus rather than use 8 or 7 or even 5 bits of data to specify a letter we can measure the probability of the use of each letter and combinations of letters to devise a code that on average only uses 2.3 bits per letter. English is that redundant.

If I wanted to write Chinese in an english ":roaminization" the probability of letter usage would be different and the compressibility would be different because the languages are coded differently.

Just by measuring the ability to compress a large amount of data I could separate the Chinese from the English without having any idea what was being written.

Rather than use correlation to measure how close various strings of genetic material are I use compressibility similarity to indicate where useful combinations might exist.

Like I said before it is a weird way of looking at data. I am pretending that DNA is a man made secret code and will apply cryptanalysis concepts to see what I can find out.

In re-reading you prior post, I believe I misunderstood your reference to SNPs and supposed that they were the same as Venter's reference to "random [DNA] sequences," referring to the human genome in general, that he said should not be patented. I see now that that was probably an erroneous assumption. In any case, my current assumption would be that if they plan to put SNPs in the public domain, as you indicated it is their intention, it is probably because obtaining a patent on an SNP is problematic.

These are clearly things which can not be kept secret and even a mere application for such a patent creates all sort of bad publicity for the patent seeker that can have a significant effect on a company's stock price. I think I can see why "they" are putting some pretty valuable information in the public domain.

I do not believe I ever appropriately expressed my appreciation for your role in giving me cause to quit smoking a couple of years ago. I think what really did it for me was when you mentioned that most smokers do not die from lung cancer, and thus I probably wouldn't die of lung cancer even if I continued smoking. That and Zyban. Thanks.

About this human genome project and its potential use in cloning (which is the other similar subject on these pages and should actually be read together, I think) don't you think the entire ethics issue involved in having this unfortunate Danish woman discovering that some of her genetic material was used without her knowledge nor permission -- in the cloning of the latest batch of "Dolly lamb clones". The mind boggles: would this Danish woman somehow be considered a parent or a sibling -- and could she claim any kind of ownership to those odd chimera? How can humanity stop these scientists from actually using anyone's genetic material to create clones with? This news story opened up a whole new can of worms to me -- and gives the word "morality" a completely new meaning, too..

And I was losing the time by reading (and posting) on other CNN boards. When the most serious discussion is going on here.

I have to say first, that I mostly agree with Kurt and admire Carl's insight. Some others have points also. Some jerks ... I will ignore.

Before say anything more ... I will do some thinking! :)

Adriana, I haven't seen the article about a Danish woman's DNA being used for the latest lamb clones. The source of the DNA wasn't mentioned in the scientific article in Nature. However, her actual gene was not used, but a DNA copy made from the messenger RNA transcribed from that gene. Also, I don't think there was anything novel about this particular gene, and an identical gene could have come from any number of people, probably even the researchers. Hers just happened to be more convenient and sitting around in the test tube ready to go.

I don't know what informed consent is like in Britain or Denmark, but when you donate tissue for research in the US, you sign away your rights to any product developed from it. At the same time, you are guaranteed anonymity and all personal identifiers that link you with the sample are destroyed. Sometimes the informed consent is confined to a specific project, but there are forms in which the signee agrees to research in general, since future discoveries may make additional research worthwhile, and people are notoriously difficult and expensive to find after a few years.

Cliff, I am glad that you quit smoking, and am gratified that I might have influenced your decision. But why did the knowledge that you were probably NOT going to get cancer persuade you to quit? Maybe we are going at our education programs all wrong! Of course, emphysema, stroke, and heart disease aren't very pleasant either.

I think you are right that SNPs and ESTs would be impossible to keep secret. The interesting information is not the sequence itself but the function of the gene product, and how that function can be manipulated. And that is definitely patentable, as it should be.

Carl, I don't know if it is relevant to what you are doing, but the triplet nucleotide codons for the amino acids are redundant. There are two or three possibilities for each amino acid. Drosophila doesn't have as much "junk" DNA as mammals do. And bacteria and viruses make the most efficient use of their genomes. Just about every nucleotide in bacteria and viruses has a role.

To: Carl Nicolai.

Carl, don't be offended, but you have no idea what are you talking about! Sorry, but your trying to apply "Error detection and correction, Compression, Cryptography" on genetic code is nothing else then pseudo-scientific technobabble. OK, maybe you are a kind of professional in these areas but stright application of them to genetics has not relevance whatsoever! What have you done, where have you published it? Could you please be more specific and stop pretending that here you are with great scientific value. Don't let us deceive please !

As you maybe remember: I am very much for creation of software analysis tools, which would in analytical (not statistical) way (by means of formal language) enable us to understand how genome is operating. So that we would not need to rely solely on experiments. But statistical analysis of genetic code is not the answer. The answer is to find out models of operation of DNA (creating proteins, operation of proteins, intra- and inter-cellular communication) and ways how to put these models into work in some simulator framework.

Sorry to destroy your illusions, but your approach is a dead end.

------

Apart from that please undestand that DNA or genetic code is only a part of a bigger replicator : the cell. If we speak only about DNA in abstraction of cell operation, communication through cell's membrane, etc. then we really are missing the point. DNA is only pure information but not replicator itself. Like memes need our brains to replicate, DNA needs cells to replicate. We need to understand whole picture to get breakthrough in analytical discovery of genes.

Sorry Jacek, but it is you who is wrong here. Wrong in the sense that you apparently can't grasp the whole matter of the information approach to the genome.

This angle of view - on the information theory based analysis of the human genome - could lead us very far to the understanding some crucial questions, of just how this machine is working. Not to mention to clean the errors out.

To say that this is technobabble is the same argument which was used by "officials" against the Ventor's approach. Or many, many historic parallels.:)

I am very much convinced that an "software" analyses of the genome structure is as important as it was the data gathering now finished!

We have the data now. But it MUST be checked for errors, must be interpreted, must be understood. I see no other way, than to use computer power, to do it.

Here exactly is, where you are wrong. The statistical analysis of the data - is the possible way. When that is done - completely ... the

- just emerges!

Think about it Jacek.

That is just wrong! The holistic approach pops up time and time again. But it seldom leads us to any valuable conclusions.

If we go holistic, why don't demand to know what "are relations between the cells and the stars". In fact some do that ... but as I said ... those I will ignore. :)

Well I suppose you could read my paper on Non Deterministic Cryptography in the series Advances In Cryptology / Proceedings of Crypto 82. You could also get in touch with Ron Rivest , Whitfield Diffie, or David Kahn. I am indexed in the New York Times, received Patent of the Week, and had several pages in Science devoted to my work and it's implications. If I am deceiving people at least I am reeeeelllll. good at it.

No, but it may enable one to ask the right questions.??? Please remember that matching up the cut strands of DNA is a statistical process and involves a lot of non deterministic philosophy. The results only become more and more certain over time. This is still the fastest method to get a "mostly correct" result.

Well you are probably correct. I think I will just stumble along though and see what comes up.

If you read my posts you can see that I am painfully aware that I am completely out of my field in molecular biology.

Since you are of a critical bent, and I intend to "publish as I go" perhaps you would do me the honour of trashing my ideas so that I can correct, either the work, or my explanation of it.

Thanks.

Jacek, I think you are being too hard on Carl. I am an MSEE and MD and I think he may be on to something.

Viruses are little more than their constituent proteins, and mammals have tremendous complexity, over and above that of the individual cell.

I would like to see a plot of percentage of "junk DNA" versus a metric of the organism's macrostructure. I would bet there is a high correlation. There might be a few problems, such as the African Lily, which has a huge genome, mostly "junk".

Perhaps the information content of the genome (in some sort of Nyquist sense) could be compared to the information contained in the "complexity" of the organism. Just a thought...

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Dawn, I strongly suspect that you are right that both the relative risk of disease from and degree of addiction to tobacco products is genetically related. I understand that the correlation between genetics and certain cancers is well established. The correlation of genetics and the degree of addiction caused by nicotine is not as well established, but I nevertheless believe it to be the case. In answer to your question specifically, I did not mean to imply that it was the knowledge that I would probably not get cancer if I continued to smoke or not that persuaded me to quit. But your statement to that effect certainly surprised and interested me, and it caused me to think about the subject more than I would have otherwise. I was thinking about what you said specifically when my doctor walked to give me my physical, and on a lark, more or less, I asked him for a prescription for Zyban although I rather doubted that it would work. Otherwise, I am sure I would not have done it. Do I think I am healthier? Not sure. I tend to cough much less, but I have put on about 30 unwanted pounds. My teeth are much whiter than they used to be since I had them bleached, but I tend to get cavities now from all the candy I eat. The really big thing for me is that my grandchildren don't smell tobacco on my breath anymore.

The public and private efforts to sequence the human genome simultaneously allowed this project to be completed years ahead of schedule at significantly lower cost than originally expected. Originally this sequencing milestone was scheduled to be completed by 2005. Also instead of just one sequence, several human genomes have been sequenced and can now be compared. The most interesting conclusion by comparing the sequences from different races is that the genomes are the same regardless of race. Therefore, the view expressed by racist organizations, that some races are genetically superior, has no scientific validity.

Chris Woodhouse has written:

Jacek, I think you are being too hard on Carl. I am an MSEE and MD and I think he may be on to something.

After second thought I have to admit that statistical and cryptographic analysis of DNA is also needed. But we should keep in mind that having full blown simulation of cell operation, running fully in computers, simulating also switching on and off of individual genes and their operation in production of proteins, is that what we need to get ultimate tool for gene therapy, drugs discovery and fighting all major diseases, AIDS and cancer included.

We need that simulator, together with theory behind it. It is that simple.

Of course we do. But I suspect, that this task is just too demanding for a bunch of human brains. A machine inteligence is needed to build a model.

Carl, although molecular biology is or was my field, I know next to nothing about cryptology, so I can't judge whether your efforts or valid or not. Venter is planning to sell a lot of sophisticated analysis software along with his genomic sequences, I believe. And I have heard Leroy Hood, who has started his own genomic analysis institute in Seattle with the help of the Gates Foundation talk about the need for new alnalysis systems in biology, so there is a need for someone to make sense of this stuff.

Cliff, since you are interested in Science and Religion, I read a brief article on slate.com that said Dean Hamer of NIH, who found a controversial recessive X-linked association of male homosexuality a few years back, is now looking for a "God gene," figuring that religion must be genetic as well. Although I think a lot of behavior is genetic, I don't think this will be an easy association to find. And there won't be any animal models! (But there weren't for the gay gene either).

I read a grant recently where a researcher proposes to isolate the gene for nicotine addiction in rats. He has a strain of rats that drink nicotine-laced water like crazy, and another strain that is totally indifferent to it. If he finds the gene, then it will be a piece of cake to locate the human homolog on the sequence map. Researchers now need some mouse and rat genome sequences to be completed, since it is very hard to do breeding and gene knockout experiments in humans :)

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If he finds it, I am sure that some atheists will score a 10.0 on the religious scale. :)

Thanks. Maybe I can look him up when I go back to Seattle for the birth of my child. (Sept. 13 dd) I would like to hear what a real professional thinks of my ideas.

In the meantime I will start by just publishing some simple facts about the data in the Sequence Files.

The first thing is that I have been reading for years about the size of the genome files in terms of bits of data and was blown out that the data they are talking about lacks even simple coding.

I now question all the press figures about what people mean when they talk about how much "information" is contained in a genome.

I also expected that only a very small fraction of the data would be missing not the 1.22% that I encountered on the ARM2L Sequence File.

Thanks for your "heads up" on Drosophila concerning the lack of "junk DNA" in insects. My earlier work had examples of known xons and introns.

I may have to fetch up the C Elegans genome if I hit the wall.

I feel like a cave man that has just flung himself into the ocean when a small fresh water pond is all he ever knew before. ( Now what was it that grandfather said about how to swim? )

Carl!

Do you mind that I try to compress-decompress this data? :) I would give you the result back!

Cracking the human genome, heh?

We have four letters in the code: G, A, T and C. They constitute the first layer is this code, i.e. DNA. Second layer is RNA, which is generated, or rather translated from DNA. The encoding is of type 1 to 1 like this:
G -> C
A -> U
C -> G
T -> A
Third level are amino acids which are 20. The encoding is like this: ACU -> Threonine
LYS -> Lysine
GAA -> Glumatic acid
... where first column is three letter codon and second is the name of the amino acid. During the process proteins are created out of DNA by such operation:
DNA -> RNA -> amino acids -> proteins.
Proteins are built out of amino acids. Let us take a look from binary coding point of view:
G -> 00
A -> 01
C -> 10
T -> 11
So we need 2 bits per letter. We have 4 to power of 3 = 4*4*4 = 64 combinations of codons. 3 of them are for stop signs and 61 codes for amino acids. In binary code if we need to store 64 combinations then we need 6 bits (2 to power of 6). Having this we can make think of binary encoding of codons like this:
ACU -> 000001
LYS -> 000010
GAA -> 000011
etc.
Well, we have 2 bits also for DNA or RNA letters so no big deal: 3 times 2 gives 6. But please note that different codons code for the same amino acid or for stop sign. The encoding is of type 1 to many. For example: UCU, UCC, UCA, UCG code for Serine, and UAA, UAG and UGA code for stop sign. Since we have intogether 21 types of codons we can put them into 5 bits, because with 5 bits we can code 32 combinations (2 to power of 5). In this way we obtain compression ratio of 83% (5/6).

My point is that this, what should be analysed is not DNA itself but some preprocessed and compressed code resulting from convertion of genome sequence to some encoding (like for example above mentioned 5 bit coding for 3-letter codons).

My hypothesis is: we can (hopefully without need to call artificial intelligence for help) conceive yet higher layers of encodings, maybe immensly complex, and by this operation start creating the model... (or to start discovering the native language of God - depends from the point of view)

Sure no problem. The shareware version of PKZIP is on my ftp site (I'll check to make sure the version is the same ) I think the sequence files are public property so I can put them on the the web site, or you can get a free CDRom like I did. (total is only 128 M bytes or so)

I will describe the exact procedure in the log of the web site, and release the (now don't laugh) "Basic" source and object code for the utilities.

This is an entirely "open endeavour" of mine.

Anything you can do to add, or for that matter detract, from my work will be appreciated by me.

Now if I could find a really good linear predictive compression algorithm like the one used to make the Speak and Spell product of some years ago that would be really cool. (did good recognizable voice at 1,000 bps)

Heck that one took a "super computer" some serious time to do the compression. The good news is that it is easy to build such a computer today with just a few kick a$$ linux machines today. (I've got 10)

Do you have better compression technology that you can share?

It has been said that the day of doing fundamental Science by using "string and sealing wax" is over. My friend Ron Geballe who retired as Dean of Sciences at the University of Washington said "All the easy Science has been done"

I would like to point out that 2,000 years ago the Chinese had silk and bamboo, they constructed a kite that carried a man aloft. They could have invented at least a "hang glider" if not a parafoil aircraft. The means were there.

We have some really cute toys.

I agree. I deliberately disassociated the cordons from the compression by using 4 rather than 3 for the compression. ( well at least somewhat better )

Using 3 would basically just duplicate the amino acid sequence that has all ready been studied in some depth.

By cutting out the N's I further distance myself from correlation studies.

I am now debating whether to replace the non resolved bases by random numbers. This would dim the variation but preserve the 2D to 3D spatial properties. I guess I'll do both and compare them. ( cripes I don't even know whether the data is any good )

By some kind of "Scientific" reasoning I should get a "fallout of significant" deviation from the norm if there is anything to what I am doing.

I do have expertise in generating pseudo random numbers which are if not unconditionally, are at least computationally secure as well as having the ability to generate truly random vectoring and shuffling to make sure what I do is not a fallout of the deterministic machines I am using. Error propagation in a complex deterministic function has been pretty well studied and used.

There is no question that time will allow me to compare my results with known good deterministic thinking.

If "The Code" is as simple as some think it is I will waste a lot of time dinking around with this. Some of it obviously is. I think however that the majority is subtle and transcends what is easily desirable even in simple life forms. (what ever simple means)

Just the observation that some so called "higher" life forms seem to require more junk DNA that others is an indication of some capability exists that has, as of yet, been unrecognized.

In other cases we have really seemingly simple life forms that are more DNA complex than our "higher" ones.

Does this yield a higher possible rate of evolution when times get tough?

Thanks for your post. You make me think.

Please do it.

Please not. Have some negative experience with the custom here - delay.

OK, very well. (Who will laugh - some jerk maybe, but don't put any attention. I love Basic too!)

OK.

I think I have something a little more to offer: A program which will search for the most appropriate algorithm ... in another words: it will try to find out, what is going on inside that data. I can guaranty you nothing. But the result (algorithm) will be public and transparent. Whatever will be. I used that program before (in computer games programming).

We shall see about that. :)

Interesting discussion.

Keep up the good work, guys.

Be cause I don't have a clue ... I can only take your word for that. And I do.

But ... but that is in the eyes of the human beholder. The grouping is always biased. Subjective. It could be defined some other way. However ... the biased view of the human is not bad at all. Usually.

Now what we are going to do here: we will accept the coding

G A T C

Acid is packed in a byte. That way the file is 26 megabytes long and very random it looks for a compressor like PKZIP. Due to the fact that each byte holds only two bits of information, PKZIP can squeeze it to about 6 MB - 1/4.

The program I have "GENERator ALgoritmov" in my native language or "The Algorithm Generator" in English, or the GENERAL for short, will do the following:

1. Randomly will create a pseudo assembler program PAP - 64 bytes long in binary coding.

2. It (GENERAL) will interpret PAP, which has access to the data and GENERAL will monitor how often the correct "next value" is in the A register of the PAP - (before actually reading it)

3. The next version of the PAP will be created by combining 100 top predictors (PAPs) and by a occasional random change

4. Goto 2!

The top predictor after millions of generation can be quite good, but strange to understand how does it work! So it was in many cases. We shall see now what will be. :)

The ASCII code of PAP is the result - algorithm. Public it will be.Compress algorithm or prediction algorithm - as you wish. It is the same thing for me. :)

I will only wait Carl to put the data on his ftp.

Well you certainly have my undivided attention. I have been fascinated by predictor algorithms ever since the advent of artificial music was constructed that sounds like a particular composer.

Well I have all the files in the raw form they came in and individually compressed on my main server.

And I have all of them compressed into one large file.

I am in the process of expanding my FTP site by adding 2 Gigs to it in a separate directory on a separate machine. That way it will be totally publicly accessible without compromising my main server security. I should be operational in 2 more days. ( I am waiting for my, busier than a one armed paper hanger, ftp wizard to tell me why it doesn't work now. )

The combined PKZIP compressed file is 33.8 M bytes so it isn't going to come down in a heart beat. Not at least from here in Taiwan. The total package will only be 205 M bytes with all the subsets.

Carl!

OK. It is not a problem for me to ftp 200 MB. I have aprox. 88 KB per second ftp download - on average. Ten times slower is still good enough, because I have a computer connected 24/7 to the Internet.

Sorry. I guess I did not make myself clear.

All the raw A, C, G, T, N, data of the Drosophila DNA files I have compressed using standard PKZIP into one 33.8 M byte file.

The others are for people who are local or want to inspect the uncompressed files on line or just want to get a part of the Genome in compressed or uncompressed form and not the whole thing. ( 7 files total )

Perhaps you could give our site a trial download at ftp://ftp.transend.com.tw .(with a browser)

I usually have about 200K bits/sec extra download capacity locally but this is Taipei not May West.

If you are in Europe you will have to go through a lot of hops and probably some network congestion to reach me.

I can usually down load about 700 M bytes/day (13 hops) from a fast server in the US. Uploads to the West Coast of the US run maybe 1.3 times faster.

BTW where in the world are you?

24/7 indicates that you are a serious Internetter and should be running a server. (if there was any justice in the world)

Running an open collaboration in plain sight of the public CNN community is a lot more work but who knows maybe some 12 year old will join us.

The Human Genome Project has gone to a lot of trouble to make all forms of Genome research available to the world community. This will probably cause some trouble, but hopefully in the long run will allow more people to feel included in the awesomely complex future that is unfolding before us.

Woops!

screwed up.

I downloaded from your ftp site "netscape6.exe" - 16 MB file. 6 KBytes per second. The 34 MB will not be a problem, when will be available at your ftp site.

I live in Slovenia. A small but quite highly developed country between Austria, Hungary, Croatia and Italy. Europe.

That is! :)

Carl, as a biologist I must admit to being mystified by what you are trying to do. Is there any reason you did not want to do it (whatever IT is) with a more simple genome, such as Hemophilus influenza? Bacteria don't waste extra letters on introns and junk DNA, so their coding capacity is more efficient. I'm not sure humans "require" the junk DNA, except to have the chromosomes line up properly with another member of the same species in sexual reproduction. But most of it doesn't code for anything, or are inactive pseudogenes left over during evolution. Since the pseudogenes aren't active, they mutate at a faster rate than coding DNA, in which deleterious mutations might be lethal.

Drosophila genomes contain movable P-elements, or transposons that can move genes around the fly genome. The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, but there is a possibility that they carried genes across species or within species in the very distant past.

I have to admit I'm a bit lost here, too. Perhaps Carl or Thomas can better explain what they wish to accomplish. All I see is changing ACGT to bits and then ?????? I'm completely baffled.

Well I did a fast hack and put it on my e-text machine.

With a browser you can download it from ftp://ftp1.transend.com.tw/gene/ or you can do a strait ftp to galaxy.transend.com.tw do a guest login with user name ftp and an e-mail address (anynamd@ will work) and go to the gene directory.

and

Dawn:

Well the whole thing started with an argument I had with Linus Pauling (sp?) about 16 years ago. He was explaining that a mould which made its own tryptophan (sp?) could not compete in growth rate with an identical one that was dependent on an environment that supplied it.

I advanced the idea that since diabetes seems to have been with humans a long time it must convey some kind of positive survival trait also. (less functioning genes for a worse regulated system but you survive starvation well )

He said he did not think the argument could be extended that far.

About 5 years later someone showed that a tendency towards adult onset diabetes allows people with the trait to metabolize fat much more efficiently than norms under starvation conditions. Since our ancestors came from a feast and famine existence the ones with the bad trait would live while others starved. Kind of like the sickle cell trait in a way.

A lot of things we possess involve engineering trade offs. With living things these get real complex.

Now the known DNA producers of proteins are being discovered at a great rate, and while the professionals are busy mining gold from the rocks I think I'll just look at the dregs and see if there is any platinum there. (ok maybe just silver)

Real randomness with compression tools (or any others) looks identical with Pure information, but DNA is something like 1000 times less efficient than "Pure". (most information technology we invent is about 17 orders of magnitude from the wall so DNA is real good.)

I will look at known carriers of information (xons) and compare their "compression signature" with so called "junk" DNA. (introns).

Now compressibility is not as well known a tool as correlation but you can measure languages with it. DNA is a kind of language.

Is that like jumping genes?

Do you mean heterogeneous as in originating outside the body?

Whoooa! I am seriously snowed. How big are these HERVs? If large I might be able to get a signature on them.

Are these some of the things people are worried about when we use pigs to host cloned organ growth?

When you say very distant do you mean pre human or pre mammalian?

I would think that they could not survive genetic fading if not reinforced somehow. Even with mitochondrial DNA there is a mutation limit which prevents error propagation of some types of damage.

Sorry for the barrage of questions. I think your field is much more complex than mine or at least has a lot more elements in it.

I guess what I mean is that the theory of complexity is not that complex.

This is the answer:

If I recall correctly, was Lisa Mayer who introduced Watson&Crick into the X ray crystallography when they were on the hunt for DNA structure. Those pictures obtained by X rays were mess at the first glance, but in fact that was a new insight, which helped to gave the double helix answer. So is the compress. A tool which could give us some valuable information, what structure is inside of the genome data.

Permit me to say, that with the kind of the "data customized compress", my program might find, the picture may be even "cleaner".

The weekend here begins in about eight hours. I will download Carl's file then and immediately run the "GENERAL" program on that data. In less than 48 hours I will post the first result HERE. Also a failure to get any.

File has ben downloaded, the program is underway. Far to early to conclude ... but it seems it already found some structure ...

Still may be a mirage only. :)

Carl, genes and mutations can persist if they are neutral, or if they don't become harmful until after reproductive age (diabetes type II and cancer susceptibility). They don't all have to have a survival advantage. It is a little different with bacteria and mitochondria, since all of their genes must count for something due to the physical limitations on their size. Human DNA is full of repetitive DNA and pseudogenes, as well as the HERVs, which entered the germline some pre-human, some later. The HERVs (~ 8-10 kbp)are distantly related to the Drosophila P-elements (~2-3 kbp), and more distantly related to McClintock's "jumping genes" of maize. Yes, this is what we are worried about with pig organ transplants, but with the new Roslyn Institute knockout technology, they may be able to knock out the Pig ERV (PERVs, I suppose). There was a recent report that HIV, which is an exogenous retrovirus, can recombine with some of the human endogenous retroviruses to produce a novel enzyme. Yes, life is complicated!

Drosophila doesn't have nearly the numbers of pseudogenes, repetitive DNA, etc. as mammals do. I think C. elegans may have more, not sure of that. Here are a couple of links on :

<A:href=http://www.chronicillnet.org/reports/ci_report_1_ToC.html>HERV

<A:href=http://www.talkorigins.org/faqs/molgen/>pseudogenes

In light of the Pauling tryptophan argument, it is interesting that humans (and guinea pigs)have inactive pseudogenes for vitamin C synthesis, whereas all other mammals can make their own.

Thomas: I think Lisa Mayer is a reporter for CNN. Rosalind Franklin (deceased 1958)is the X-ray crystallographer who introduced Watson and Crick to the 3-D structure of DNA.

Hmm--the part of my html link didn't carry over. Sorry! I guess the URL was too long.

Oh so I didn't recall correctly - the name! ;-)

Albert Einstein once said something like this:
God does not play dice

But he was wrong: presence of random junk in our genome is the proof. He is outdated genius, like concept of genes is outdated: we need bigger view and working model able to be running in simulator.

Why concept of genes is outdated? Because genes interact with each other and with environment and rarely they operate alone. Just imagine that by our mood we are able to switch on and off some genes (yes! it denies the principle of genetic determinism). Just imagine that we have in our genome some DNA sequences of plenty of other biological organisms. Who knows, maybe some day even HIV (this : villain, who causes AIDS) will be incorported in our genome as a reminiscence of former fight with it.

We need new geniuses like Stephen Hawking who said such things as:

But with the human race, evolution reached a critical stage, comparable in importance with the development of DNA.
...

But we are now entering a new phase, of what might be called, self designed evolution, in which we will be able to change and improve our DNA.
...
genetic engineering with humans is going to occur whether we like it or not

Hello 21st century! You can forget all former achievments of mankind: the real adventure begins just now with genetic engineering. Of course there will be next achievements of human science like nanobots (miniature robots), quantum communication and computers (based on subparticles), artificial intelligence, etc., but genetic engineering alone will have biggest impact on us... You can do nothing to stop it, so better join it! "brave new world" is already now.

Hehehehehe Jacek, I agree with that, but why do you insist that the compress scanning of the genome is something out of any importance. That I cannot understand.

In fact I do. A point of conservationism almost anybody have.

But the compress scan of the junk DNA could show us, that it is not that random after all. Simply if exists an algorithm which compresses it - than it is NOT random.

What implications that would have?

(attributed to Stephen Hawking)

Human-directed evolution has been a reality since prehistoric times. When humans shifted to a hunter-gatherer society to one dependant upon agriculture, there began a purposeful breeding of domesticated plants and animals. Later, when social structures developed, human evolution would be controlled by war and social stratification.

As much as I respect Professor Hawking's opinions, I can't help but feel that the engineering of the genome is not a revolutionary event, but evolutionary. Since the formation of civilization, humans have used genetic manipulation to control environment. What we are discussing now is refining that approach to a molecular level.

Looking back on these past efforts to alter the environment, the inertia more often seems to point to increased uniformity. A pig raised in the United States is not that different than one raised in China or Egypt. The same is true of corn, sheep, rice and other commodities. With the advent of the eugenics movement earlier in the century, there was even a thrust toward human uniformity.

At the same time, there has been a lesser thrust toward creating more variability; the prime example is the dog, a creature that has become infinitely more variable in its outward traits.

Inevitably, the question of genetic engineering comes always to humans. A thousand years from now, will humans be more varied and specialized, like dogs? Will they be more uniform, like farm animals? Will nothing much be changed from what we have nowadays?

What are the social, political and practical forces that will control the evolution (or lack thereof) of humanity?

Post humans, strings of flipping bits in the virtual worlds inside some giant quantum computer. That is the most likely outcome in a thousand years time. And how that would look like? Incredibly pleasant and fulfilling, I think.

This gene tempering is just the beginning.

Great that gives me a hint as to how wide to set the scanning filters on my compression analyses. I have done a test run at 2 Kbp on the "out of the box" ACGT coding (without Ns) and got differences on the ARM2L file of only a few %. I now have the entire genome coded more efficently and should do better.

Thanks for your help with the english word coding.

If pig ERVs can not become active and transfer to human cells and as far as I know conjugation doesn't occur what is the real concern?

I know active bird viruses that can not infect humans can mutate in pigs and then attack human cells but could a viral code we already carry in our gene structure be somehow released?

The most interesting thing I know about HIV is that there are a few people who have carried the virus for many years without treatment and never had any symptoms of AIDS. I still wonder if this trait would be passed on to their children.

Yeah. He was a real "mega vitamin" promoter particularly with vitamin C. He use to cite a study which said that rats produced an equivalent of 9 grams/day. { That is one heck of a lot of orange juse : ) }

The concept was further reinforced because there is a form of mental illness called pellagra which mimics schizophrenia but which vanishes if you take niacin. (vitamin D)

Nobels or not, I think he got into some trouble with the Scientific establishment because of his strong advocacy.

I am sure some budding genetics engineer will find out if any humans can make their own or could carry a gene to do so. One wonders what the trade off might be.

Thanks also for the links. I'll check them out.

I have enough not justified censorship practicized by CNN employees. I leave this forum and I am not going to post again.

jpzr.

This is the pseudocode of quite statistically succesfull predictor after 848315 generations

000 NOP

001 NOP

002 NOP

003 DEXL= - [218]

004 NOP

005 NOP

006 NOP

007 NOP

008 NOP

009 AEX = <DEX>

010 NOP

011 XOR AEX,BEX

012 NOP

013 NOP

014 AND AEX,BEX

015 DEX = <AEX>

016 NOP

017 AEXL= - [097]

018 AEXL= - [124]

019 NOP

020 MOVE (DEX),AEX

021 NOP

022 NOP

023 NOP

024 NOP

025 MOVE BEX,(DEX)

026 MOVE BEX,(BEX)

027 AEX = <BEX>

028 NOP

029 NOP

030 NOP

031 NOP

Details with explanations will be post later ...

----------------

And I agree with Jacek ... he was not a very friendly guy toward me ... but his latest CNNsored post was tottally ontopic ...

Now that is what I call abstract.

Would you like a web site to post your work on? If so click on my name at the top of this post and e-mail me with a user name and password and I'll set one up for you.

I finally broke down and read the Science Drosophila special issue of March 24th.

I am now contaminated by the way the heavy weight investigators think. : )

My next run will be a compression of 3 bases per output byte and the "Ns" filled with random data.

That way I can see how my compression's line up and compare with the gene map in Science magazine.

Because of the links Dawn posted I now realize that there is a fair amount all ready known about the introns or "junk" DNA.

If any of this is interesting we can move to the published human DNA and look at some of the genetic disease structures that have been uncovered.

It is a little less than the abstract even. I will prepair it for publishing very shortly.

The main point is, that some sequencies of the DNA, which appears to be random - even for a general type of compressor like PKZIP - are NOT random after all ... that means a "structure" is inside. What that can tell us? Some expert may find that fact - as a new information source.

I will go to check and dublecheck it now.

I will send you my complete results. Put it somwhere on that site of yours if you will be able to repeat my results, that is. :)

P.S. my name of course must be seen. :)

Agree on that.

As the American CBers are want to say "I read you 5 by 5 good buddy. That's a wall to wall and tree top tall"

Jacek Rutkowski wrote

That certainly was not my intention. I have no doubt that Prof. Hawking said those words. The term "attributed to" was used to denote that part of your text was from Hawking to alert the readers as to whose observation I was commenting upon. Nothing more than that.

With respect to the balance of your comments, I believe "evolutionary" is still the correct categorization. We have been moving to this point since the invention of the microscope and the discovery of DNA structure. Modern technology accelerates the evolution.

I can recall several years ago in grade school how teachers told us that knowledge, absent historical upheavals, doubled exponentially. What we are seeing now is the byproduct of that acceleration with a lot of the technology coming together to greatly increase the possibilities.

Thomas, I'm a molecular biologist and not a computer expert, so perhaps you could clue me in on how these compression programs work. I ask because if they work by recognizing "repeated" sequences that then can be represented by a shorter "sequence", then I wonder what size "repeats" you are looking at. There are only four bases, as you know. Thus, if you wanted to find a sequence of four bases (say ATTC) it would randomly appear every 256 bases. Or taking a longer sequence like GATTACA, it would randomly appear every 16384 bases. Given the size of the human genome, even a sequence like GATTACA would appear 200,000 times.

That of course is for purley random seuqences so one must look at codon preferences and G/C content of the organism you are looking at. But since we are dealing with "junk" DNA, one would expect some sort of "pattern" even if the junk is completely random.

I now have a graphic display of the running compression of 9,000 wide gases over all of the ARM2L file and most of the ARM2R file.

The download files with software in source and object code are stored in both .zip and a self extracting .exe files. There is also a read.me file that explains the procedure so that anyone should be able to duplicate it or understand what is being graphed.

On a browser the site is ftp://ftp1.transend.com.tw/gene.

The original 40K base/slice file is also there but it did not compress real well and is only raw data.

Thus ends my fast flash peek at the compression of the genome.

Now I will check all the results and build supplementary files that flag specific areas with traits the that indicate where the pros. are interested like stop codes.

I can also do statistical runs tests and of course do smaller and larger windows.

Looking forward to using your compressors which should have more resolution particularly with the smaller windows.

Any criticisms or suggestions are of course most welcome.

Yes, that is absolutelly correct. If just randomly appears. To see, if that is the case, Carl suggested compreesion.

In the case of no compression - that is the case.

In the case of a (significant) compression of the (junk) DNA - the randomnes is only in our eyes. The compress sees the structure. That is a very basic and very fundamental informational fact - holding in biology also.

To rephrase myself: If the data is "true" random, no compress will do. If an effective compress is found - the structure is present! (My compress has an advantage to say which one it sees)

Or I will put another way. If you have the data of the last 10,000 roullete numbers and you are able to compress that data - beyond the so called optimal coding - you are a rich man!

And if Carl and I will be able to compress (junk) DNA - something even better might happen. :)

Carl!

I am trying to make my software a little user friendly before I send it to you. :)

Thanks.

To amplify your points on your previous post:

Data is not "Information:. Information has a very precise definition and is a "real" a measure as say a "meter" of distance.

Information reduces the uncertainty of a problem that has several or many possible answers.

Most of what we see as "information" is in fact just data. It can take many bits of data to encode one bit of true information. It can never take less.

We develop efficient coding to store the most information that we can with the smallest amount of data.

This gets interfered with when the data must also be human language readable.

We first coded our names for the four bases that make up DNA by just using their first letter, and storing that letter (A,C,G,and T). This is still grossly inefficient however as convention dictates that we normally use 8 bits (binary digits) of data for each english letter.

We can in fact store four bases in a single byte (8 bits) of data with just simple further coding.

Given the nature of the "factory" of the cell, DNA coding can be used to manufacture all of the exceedingly complex chemicals and build them into structures that are required for life to exist. (including other cells)

This efficient DNA code however is not optimal, even in a self contained sense.

In that this code is so general purpose that it can serve to encode for all forms of life from the smallest and simplest to largest and most complex beings we know of, we can apply processes that produce even less "data" bits to contain the "information" in its structure.

This is particularly true if we are considering the genome of one creature.

I have been using a general purpose program that compresses inefficient coding to use less data to store information.

Thomas Kristan however has access to an interative compression program that changes itself depending on the results of each "pass" over the data and keeps becoming more and more efficient as it goes. It thus uncovers "structure" that is increasingly invisible to our eyes by just looking at the raw data. It progressively removes and records the elements of the fixed structure to uncover more and more of the less obvious sub structures.

Thus it can help to "Crack the Code" of all but truly random data or data that has been deliberately made cryptographicly secure. Heck it can even penetrate many previously used forms of cryptography. (modern forms are based on math problems of a known intractable nature)

This forms the conjecture upon which we labour.

Okay. But somehow I get the feeling that things don't quite apply here. While on computers you may be able to compress ACGT, you can't do that in life because ACGT stand for chemicals. They are not bits and bytes that can be compressed. Therefore, I have to wonder how one can conjecture that this coding is not optimal.

So perhaps you could better explain compression to me. Aren't you just looking for sequences that can be reduced to something smaller. In that case, how big (or long) does something have to be for a "good" compression.

Correct. the chemicals however are not used with the same frequency, and the combinations even less so.

For instance the "stop" codon (3 bases) appears very infrequently where xons (expressed genes) occur.

Thus I can gain coding efficiency by using "words" or groups of chemicals and assigning a smaller word to stand for the frequently used larger one.

Now I have transformed the language of the names of the chemicals to one that depends on how often various words are they are used.

We can measure the entropy, or degree of disorganization, that occurs in the real world use of any language as opposed to a truly random selection.

The number of possible "organic" chemicals is unimaginably large compared to the much smaller number that are used in life forms. We have a coding system for all discrete chemicals we know of that is published by the International Union of Pure and Applied Chemists (IUPAC).

These rules and conventions allow us to assign an english name to any chemical that is likely to occur. In fact if you know "The Definitive Rules of Nomenclature" you can say the word for a new chemical and a good chemist can see the correct structure in their minds eye and draw it on a piece of paper.

Thus we can compress the information of all the individual chemicals by compressing the data of the words that are used to describe the chemicals.

If we could do perfect compression the resultant data would be indistinguishable from truly random data.

The compressed genetic information bits can always be decompressed and fed to a sequencing machine to recreate the original DNA chemical. (Actually the DNA just is a code for the RNA which produces the usable proteins inside the cell.)

Any DNA that does not have 0% or 100% compressability is suspect of containing some kind of structure that either does now, or in the past may have, contributed to the design of a form of life.

Sorry I should have said" Thus we can compress the data describing of all the individual chemicals by compressing the data of the words that are used to represent the specific chemicals."

Michael!

The "reducing to something smaller" is just one way. If there is a subsequence which appeared before, that is another way. If that previous sequence is rotated then that is another one. If it is somehow deformed (but not to much) then there is another. The point is, if we can describe the sequence on a shorter way than it already is, that fact can be used for a compression. But more to see what is inside.

Now I will tell you a little about my compress searching program:

At first step, a completely random program is crated. It consists of 32 instructions and arguments chosen randomly from 234 possible. For example:

NOP ;do not do anything

MOVE AEX,<DEX> ;move a value from that address DEX points to the AEX (two variables are AEX and DEX)

BITT BEX,22 ;set the 22nd bit of the BEX variable to zero if it is 1 and vice versa.

and so on ...

(a pseudo assembler that is)

Now what the main program called general is doing?

1. He checks the value of AEX and the Nth byte of the concerned data. If they match the general sees it as a guess!

2. He interprets the random program.

3. Increases the N and goes to the first step if not end of data, else he proceeds to 4.

4. He checks how many lucky guesses there were. If there were enough guesses, he enlist it among the TOP 100.

5. He combines the codes of enlisted (randomly but with some tendency to prefer the bests) to a new one.

6. Set N=1 and goes to the step 1.

The general maintains the whole game. He kills any program which wants to make infinite loop or see the data before it guesses it ... and so on.

An evolution is going on among those predictors. The general is just a judge, which are the best predictor and consequently the compressor.

Yesternight I run general on some sequence an the result was a compress program which differently predicts the next base if the current was "A" then if it was not. That was the outcome of the evolution pressure on the pseudo assembler code. Currently the guess rate is around 30 to 40 %. It would be 25% if the data was random.

Very soon the general will be friendly enough for to send it to Carl. Soon for the others also to play with it.

Great post (at least for me) The delusion that I know what you are talking about is getting stronger.

I'll see if I can explain it in terms of a known language like English.

1. English is only correlated with any accuracy over a span of eight characters. (this is a measured fact) This means that if I start with a letter and consider the past 8 letters I can perform the best guess on what the next one will be. More than that does not help.

If the letter is "t" for example the next best guess will be another "t" and so fourth if the last 3 letters are "let" then the probability increases that "t" is the next one.

2 .Scanning a lot of english text will establish a set of rules to make good predictions. We record these rules.

3. We then start by looking at a letter and guessing what the next one will be given knowledge of the last 8.

4 We record a 1 if the guess is correct and a 0 if incorrect and guess again using the next most probable correct answer recording as we go until we get it correct.

5 We wind up with a file of ones and zeros that is much smaller than the ones and zeros required to code the message directly even when combined with the information that records the rules.

6 We refine the rule structure until the smallest set of rules yields the best results.

7 We record the rule structure and the data.

Now some possible results.

The fact that the predictor could not find correlation beyond 8 tells us that the language may be english (each language has it's own limits).

The rules that had to be established tell us something about the structure. (if english it was newspaper english)

The compressibility when taken over a small sample of this newspaper english tells us something about the complexity of the subject matter. (got to have been a science article)

The order of the letter guesses tell us more about the subject. (the letter g which is the 10 most used letter was 5th in the guess list.) (lets look at how many of the words that had g in them like genome.)

And of course

Applying the rule structure to all the "guess data" reconstructs the original message.

------------------------------------

Again I say: "DNA is the language that the cell uses to tell it what to do"

It is just a language; like the chemical pheromone that attracts the moth to its mate, the howl of the wolf, or the dance of the honey bee.

Yes, this has been known for decades. Nothing new in saying that the coding regions are not random. I thought the quest was for the "junk" DNA.

Yes, but nothing new is learned. I can call adenosine 5'-triphosphate ATP but it still is the same and I've learned nothing new. This seems to be nothing more than shorthand.

Yes, that example made things more clear to me. Thanks.

So my next question is how are you distinguishing the known coding and "thought-to-be" coding regions from junk? Since the coding regions are known to be non-random, how are you determining that any compression of the genome is not from the coding regions?

Well Michael ... to locate the junk DNA maybe ...

Well first there is a lot of randomness even in a expressed gene. The most obvious example is that there are more that one way to code for the same amino acid with some of them.

It is conceivable that one way is more efficient and therefore would have different statistical properties due to natural selection. It could also be that this redundancy has an advantage.

This is still in the exon region however. To get back to introns:

Well there is junk, garbage, and refuse, to make the analogy more accurate.

The trick here is to recognize the difference. We are saying that compressibility is one thing that should be looked into.

Exactly correct. Shorthand is a way of compressing data while retaining information. It is a way that is very easy for humans to learn to do on their own.

Short hand can be applied to many of the lengthy but common words that we use in science.

If I look very quickly at a piece of paper with a lot of shorthand words on it I gain the knowledge that common words are being used without having to "read" the whole paper.

I can also surmise that the paper was intended to be written for someone who knows this shorthand and not perhaps the general public.

Gaining information by statistical means, even very complex ones, is not the same as by gathering information in a serial fashion one word at a time. It is often much faster though.

The "shotgun" method of sequencing the genome is itself a good example.

There is an inherent limit to how long a piece of DNA can be before a sequencing machine becomes contaminated with all the chemicals it uses. Lets say 100,000 bases. We use cutting enzymes to break up the DNA and can sort it by length. and sequence it one piece at a time. Then try to find the next piece to sequence.

By using a shotgun approach we can take the raw DNA and do several batch cuttings with different cutters and get sets of DNA that overlap. We then mass process this DNA and let a computer match up the overlapping parts to determine the structure.

The problem is that there can be gaps in the sequence so you may have to repeat the bulk process several times with different cutters to make sure to span all the gaps and further check that the other matches were correct.

We also hope to save time by pre selecting and separating different types of junk, garbage, and trash by statistical compression methods. It is also possible that we can use compression to find exons that while producing different protein make 3D structures that are similar.

IBM has just started building what will be the largest computer in the world to predict the 3D folding of complex molecules. They are doing it by analysing all the electric fields along a molecule and applying the forces generated to understand how this folding works.

There may be a less computationally intensive method to do this or to eliminate whole classes of searching by compression probabilities, or this idea may be total nonsense.

I will post my second charting attempt on ftp://ftp1.transend.com.tw/gene for your inspection. I have made the compression window 9999 bases long rather than the 9000 on the present chart so as to more closely match the genome map published in Science magazine and that is also on the free Drosophila Genome CDRom from them and Celera. The total "out of the box" genome is also posted there in standard PKZIP format. I will also include all the data reduction programs in "grade school" Turbo Basic open source and object code.

True, but it is already established that organisms have biases for certian codons.

The structure of the protein or the DNA? DNA structure is not dependent on sequence.

he he Come on. Of course I mean protein structure.

I mean there is a chromosome structure but the relationship to final protein production is very unknown I think.

Dawn,

It was really great for me, not only because it answered a lot of my questions, but because it defined a lot of complex words and concepts as it went along and even provided examples.

Ordinary dictionaries are useless and my large unabridged ones are in storage in the US.

I'm going back to the US for a few days and will drop by the local University book store and see what if available.

Mulling over the Science gene map contuse to contribute to delusion that I may be learning something.

I find the color %GC scale interesting in that it is statistical in nature. I also understand your concern with the Paling argument and marvel at how I could have so completely misunderstood what you were saying.

With so much "extra space apparently available" in the mammalian genome why don't we make our own vitamin C and indeed all the amino acids we require rather than just some?

Is it possible to modify the design of a mammal so that it could exist on a diet of only carbohydrates and maybe a few minerals?

I guess the color bar scale that records the similarity of DNA structure to mammalian, C.elegans, and S.cerevisiae relates to areas of possible active gene location but don't have a clue yet about what Gene Height:EST coverage does.

Thomas Kristan sent me his first rendition of a user friendly predictor algorithm and it is totally fascinating to watch it munch data. Preliminary studies show something like 10 times more resolution, and utility on much shorter lengths of DNA than my primitive PKZIP compressor allows.

It is like being use to dissecting dead mice with a hatchet and then being given a scalpel to use.

Again my thanks for your links.

Matt Ridley's new book, "Genome," is an excellent, not too scientific exposition of the information encoded in the human genome. He uses a literary device of discussing in detail one gene per chromosome, and it is very effective.

Carl, I'm sure humans could be designed to synthesize all the amino acids and vitamins we normally get from food. We probably contain the genes coding for a lot of them already, in the form of pseudogenes that have mutated from lack of use. Man, apes, and Dalmatians are the only mammals that have uric acid rather than urea as the end product of nitrogen metabolism. The gene for that final step is probably still with us, but inactive. The inactivation obviously occurred before man split off from apes. As for the Dalmatians, they will have a different mutation leading to the same effect. So those three species tend to have gout and form urinary stones on a high purine diet. But high uric acid may protect against multiple sclerosis, so I suppose that is what gave that mutation a selective advantage.