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A Map to Nowhere?
Aruges writes "It seems as if there some serious doubts about the value of the human genome map. The main thrust of the problem is that since there are far fewer genes than once thought, the old idea of "one gene, one protein" has fallen by the wayside. The upshot of this is that it may be several decades before we see any benefits, if we see them at all.
Check this story on Spectator for more information."
"Upshot" means "a phenomenon that follows and is caused by some previous phenomenon". That was the correct usage.
the amount of data needed to describe the human body could conceivably be quite small.
And in the case of some guys, really really small.
That's an interesting take.
Now, when life is breathed in to an embryo, I guess we can assume that can't happen at conception? Because the zygote, at that point, is decidedly less complex than Win2000. Probably less complex than notepad.
About four months along and now you've got something really remarkable; various organs coming along, a basic shape going there. But nope, while it may be as complex as the Mach kernel, it's still no Win2000.
Another two months and there's a big change; neo-cortical brain activity, where logic and reason and emotion and what-not come from. At about the same time, the fetus becomes "viable" - able to live outside the womb, albeit with assistance, if delivered prematurely. (And this is the current law of the land in the US, BTW.)
All I really want is for you to admit that maybe this "soul breathing in" is the beginning of neo-cortical brain activity. And, if you agree with me, please spread the word.
I doubt it changes much. After all, other than Dawkin's friends, Andrea Dworkin, and sundry Feminist Studies departments, does anyone consider biological determinism anything other than a bag of shit, anyway?
Its interesting how people always believe that it will be easy to understand a very important part of being human once we have enough data, and once they have the data, they found out that things are not as simple as they think. First, AI, now the Genome.
Likewise, everybody in the field knows that the hype about curing genetic diseases is a lie to keep the money flowing. Nobody has any clue about how to do gene therapy. And most researchers don't care: they are interested in basic science, as they should. I think that was one valid point of the article.
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I do think I would add a few comments though. To start with, it seems that the artical really didn't credit how much progress has been made, and it is obvious that the artical is not being written in context of the project. Specifically, I would point out two things:
First, not to many years ago, there were numerous articals that discussed how difficult the project would be... and giving credit to how far ahead of the predictions the Human Genome Project is really.
Secondly, IMHO, no one has given enough credit to how much Moore's Law has really played in the project. It was calculated the length of time to decode the human gene, and deemed impossable. It was only in light of Moore's Law that serious work began. Now, it's at a level that outpaced most estimates.
It's only because of how far we have come that people say things like "map to nowhere." Keep in mind, when people tried to find alternate trade routes to India by sea, finding America was probably considered "a map to nowhere."
The genome's not just any CD-ROM-worth of data, though. There are a lot of things that happen with a sequence other than simply building proteins straight from it.
Consider it like a CD with a DOS filesystem and a Linux filesystem on it in the same places. The contents read each way are totally different, because the reading mechanism reads different things and combines them differently. Then it additionally has things that are both Mac binaries and Intel binaries that do totally different things.
So it's less like a Windows CD than like a best of Obfuscated C Contest CD, where they picked all of the programs that do a bunch of totally different things, except that they interact and include, among them, obfuscated versions of all of the utilities.
The latest news is that straightforward compilation of all of the files doesn't produce all that much of the interesting stuff.
In fact, what breathes life into the genome is the complex set of ways the DNA is used, and all of the ways that the raw data is interpreted, from compiling it with different sections commented out to compiling it with a somewhat different compiler to passing chunks of the source code to the linker as well as the compiler. This set of ways is packaged with the DNA (and can be reconstructed from it later, too).
Well, if one were throughly cynical, one could imagine the following scenes:
Scientist: If you give us lots of money, we'll be able to produce a complete genome, and cure all human diseases through genetic manipulation.
Non-Scientist: OK.
[Some years later]
Scientist: The genome is complete. Thank you for funding us.
Non-Scientist: Why are we still afficted with disease?
Scientist: Although we decoded all the DNA, we still don't know exactly how some genes control other genes. It's going to take many years of study. However, genes encode proteins, and if we can figure out how proteins fold (which is, technically, NP-complete), we can generate a complete proteome. With this proteome, we can cure all known diseases.
Non-Scientist: OK. Here's your money.
Scientist: Thanks. This is going to keep my lab funded for years to come. [sings "I'm in the money, I'm in the money"]...
The genome is only the first step. Now, the role of each gene in the organism must be defined-- a someaht more difficult task that will require the application of computational techniques to accomplish.
Many of these techniques involve probabilistic methods (Baysian, Markov Chains), informed by evolutionary principles to adduce an answer.
In the service packs!
---- "If we have to go on with these damned quantum jumps, then I'm sorry that I ever got involved" - Erwin Schrodinger
Maybe when thousands of humans have had their DNA completely sequenced, the code will be easier to solve.
> When a man impregnates a woman, the Holy Spirit breathes life into the resulting embryo. At least, this is what we were told in school.
Speak for yourself. Some of us had Religious Education as a separate subject not to be confused with biology (or history).
> But really, the Church has known this for thousands of years
Oh bollocks. The Christian Church hasn't _existed_ in a recognizable form for two thousand years yet. Fruit flies, flatworms, and even bacteria are also complicated compared to the amount of genetic information they use. Since when has the Church taught that flatworms have souls breathed in when the eggs hatch? That bacteria have souls breatehd in when they divide?
--
rant
The author makes some strong claims (some of which I agree with) but he doesn't give proper scientific evidence. Instead he refers to press releases, articles by journalists, and other soft facts. For example, he describes the implications of the research on science as being brought to light by the Washington Post. Where were the scientists?
Well, after a couple minutes of digging I figured out what was wrong. This is an editorial by Tom Bethell, who is the senior editor of The American Spectator.
The American Spectator is a news magazine with an openly ultra-conservative agenda. My guess is that the intent of this article was to show the profligate spending of the US government. The author, Tom Bethell, is asking, "Why did the US government spend billions on research which (it now turns out) might not have direct medical uses for decades?"
It's a reasonable question. If it was my question to answer, I would say that it is precisely because this research is a long term investment in science that the government should be funding it. If Mr. Bethell is correct that human genome research isn't directly applicable for medical use, then what company would tackle it? Twenty years is a long time for a company to bleed money waiting to become profitable.
In general you should take anything you read in the The American Spectator with a grain of salt. The current issue includes articles that make even moderate conservatives queasy such as More Money in Politics, Now! that ends with the following mind bender:
Twenty years ago, when Sen. Moynihan accused the Reagan administration of deliberately lofting the deficit to push down spending, it occurred to many Reaganites that he had a heck of an idea. It is time for the creative faction in American society, otherwise known as the top one percent, to reach a similar conclusion about the charge that unlimited citizen donations would allow them to buy elections. It's a heck of an idea.
Another good one is an article where they try to recycle the old "Cigarettes Don't Cause Cancer Because Scientists Haven't Proven It (Yet)" argument and apply it to (of all things) DDT.
Ben
That the human genome tells a human how to make another (usually differnent) human. Your huge store of additionally information is the human egg. Pretty much every biologist and geneticist under the sun and a few subterranean ones agree, the genome only tells a cell of that species how to make another of that species. Thus you get projects like the mammoth cloning, where your going to take generations and generations to 'massage' the elephant cell into something like a mammoth cell. Geesh, even that crappy movie Jurassic Park got it partially right. You use a cell base that differs from the gene base and you get some zany hybrid. Part dino, part frog in the movies case. (Of course this leaves out mitochondria, but everyone forgets the mitos, cept Parasite Eve. MUHAHAHAHAHAHA!)
USA-Democracy is 270 million YESes and NOes a day, not one every four years.
All those patents running out before they ever see a use, so sad.
My personal Buddha is laughing.
USA-Democracy is 270 million YESes and NOes a day, not one every four years.
given the evolutionary origin of the genome, it seems likely that it is full of garbage. It would be surprising if the genome was optimised for space, which in my agnostic mind would be enough to start me going to church or something.
Surfing the net and other cliches...
Surfing the net and other cliches...
(Who Meta-Meta-Moderates the Meta-Moderators?)
Z = Z^2 + C
The above equation, when iterated over each value Z on the complex number plane (where Z is decomposed to X + Yi), produces the Mandelbrot set.
An amazing amount of complexity is evident in the Mandelbrot set. Yet, the basis is simply that one-line equation.
The genome is similar to that equation, in that it is relatively simple when viewed as a string of bases, an abstraction that ignores the existence of the cell that surrounds it. However, in terms of a biological system (DNA is near-useless without the complement of chemical reactions that work on it), the genome becomes a basis for the generation of life processes--much like the equation becomes the Mandelbrot set when iterated.
Mind you, this does not discount the possibility that some deity may have originally set these processes in motion. But I feel that whatever the origin of these processes, the amount of information that can be derived from the human genome should not be underestimated.
-W-
"Is it all journey, or is there landfall?"
-W-
Is it all journey, or is there landfall?
--Ellison & van Vogt, 'The Human Operators'
When these "do nothing" portions are removed, though, the system does not function properly-- showing the evolution worked to take advantage of all possible types of "interaction" within the substrate of the FPGA (quantum effects, possibly?).
Try parasitic effects. There's a lot of "unwanted" capacitance, resistance, and inductance in integrated circuits. This causes crosstalk between lines and devices close to each other (physically or electrically close), and leakage of signals through parts of the device where they wouldn't propagate with ideal (perfect) components.
There's plenty of opportunity for communication here. Invoking quantum effects isn't necessary (at the relatively large feature sizes involved, quantum effects show up as low-level noise and not much else [other than the quantum effects that give the material properties in the first place]).
While showing that there isn't a 1:1 mapping between genes and proteins makes it a lot harder to figure out what proteins are present in the body, it *does* make it a lot easier to figure out how the proteins work.
If proteins are made of several modular components, then by understanding the relatively few component proteins we have a terrific foothold for both understanding the vast array of proteins found in nature, and on easily constructing our own.
It also raises the possibility of tricking the body into generating new proteins just by insering a couple of new "job orders" that use existing parts, instead of having to insert the blueprints for entire proteins designed from the ground up.
I look forward to seeing the research that results from this.
I see plenty of people dismissing the parent as a troll and wonder if they are being fair or not. True there has been more than the average amount of trolls written in the past couple days or so. But I think that Christian Soldier has a valid point here. The human genome is complex, yes, but I think that it is correct to say that "who we are" cannot be fully attributed to the genome. There is an awful lot of complexity to our very existences (and I'm getting a bit metaphysical here so I apologize.)
Of course who we are isn't fully definied by our genes - we're exposed to a vast, almost infinitely complex environment that varies greatly from person to person. As far as I can see, this provides ample source for variation between people with the same genetic material.
As for the physical complexity of the human body, see my other post. We know that complex-looking systems can arise from simple rules and simple building blocks. Until a compelling reason to believe that something more is going on is given to me, I see no reason not to think that our DNA (identified and unidentified portions) and our growth environment are solely responsible for the human physical structure.
This has been beaten to death elsewhere. The upshot is that many people argue that the complexity of the human mind and body prove divine influence in their creation, while as far as the scientific community's concerned, it's perfectly consistent with nature taking its course.
The reason why the original post is being called a troll is that, while the strong of faith still drag out the complexity argument now and then, it is far more likely that it was posted as deliberate flamebait. Back when trolltalk was still active, people would *brag* about posting plausible-sounding messages like this.
In summary, while they're not being nice about it and not contributing much to the discussion, the troll-bashers are probably correct in their assumptions.
Well, the entire genome can be fitted on a CDROM. That isn't very much data at all. Are we really saying that the human body is no more complex that a copy of Windows 2000?
Obviously, it is.
Not so "obviously" at all. A complex-looking object can easily arise from simple rules and/or simple building blocks.
When I build a house, I don't have to specify where every brick is laid. I just have to tell you how bricks fit together to make walls, and where I want the walls to be.
The Mandelbrot set is another example, for the math geeks among us. It looks infinitely complex, and it _is_ infinitely detailed, but the algorithm that produces it can be stated in one sentence.
In summary, the amount of data needed to describe the human body could conceivably be quite small.
This intrigued me:
I'm not sure whether to agree with the author that this is a bad thing for would-be gene therapists. For one thing, it offers a bit more of a safety net for highly speculative treatments.As far as figuring out causality, this is actually probably helpful. Protein synthesis is reliable despite noise in the system. Accidental conformational tweaks (this coil of RNA happened to be a couple angstroms to the left, instead of to the right, and therefore failed to bind with that site on the ribosome) are somehow rendered insignificant in the final outcome.
From an analytical standpoint, it would be great if the one-gene-one-protein doctrine worked. But we don't need to fear the analytical worst case, where molecules bump and grind willy-nilly with no discernible pattern, and the reliable production of correct proteins is just some kind of well-balanced accident. There will be a pattern, just not the nice simple one we hoped for. Despite the article's analogy, this will be an easier problem in principle than cryptanalysis. There is still work worth doing here.
In fact, there will be plenty of work, and much of it will be work to which computer geeks are well suited. Long healthy life available soon would be preferable, but an increase in employment is way better than a poke in the eye with a sharp stick.
There is one more good consequence of all this. Earlier, it looked like there would certainly be a quick race to lock down the entire genome as intellectual property in the private sector. Now that genome information isn't so immediately profitable, it will migrate to the public domain much more easily. And that will be good for everybody. Unfortunately the complex causal phenomena will become patent targets instead, but with luck that's another battle for another decade.
WWJD for a Klondike Bar?
They were decoded a long time ago in the 1980s. Fairly simple too- only about 17 proteins. However very devilish in controlling- resisted billions of dollars and decades of efforts.
We know so little about biochemistry, really.
Hey, this is this first animal more complicated than a worm to be sequenced. It turns out that indvidual gene complexity is more significant than number of genes when you get to mammals.
I do technical support for genetics researchers, and I can pretty confidently say that few if any of the oh-so-shocking revelations in the article are anything new.
Some -- probably most -- genetically-based diseases can't be traced to one simple gene. Old news. Some are based on multiple genes, and/or may be a combination of genetic factors and environmental ones. Old news. It will take more work and time -- much more, for many things -- to turn what knowledge we've gained so far into treatments and cures. Old news.
Science research is sometimes over-hyped by the people involved and/or by people trying to sell magazines. And sometimes the people who write articles for the public just don't understand the topic very well. Old news.
Bethell is either seriously lacking in clues, or is heavily spinning things to sell copies of American Spectator. Feh.
Have you read a grant proposal lately? [grin] But, yeah, a lot of the time it's sloppy and/or over-pumped reporting.
On the other hand, there's scientists like Venter. Ugh. Granted, these days he's less a scientist than he is a corporate droid, but he's not unique, either.
wtf? You might as well start citing Reader's Digest...
If I remember right, one of the ways they found genes "fast" is by killing a cell and looking at what genes were active at that moment.
However, what if--to use a computer analogy--
those 30,000 genes are merely the "working set"
of a much larger program?
Put another way, what if there are a great many other genes which are inactive for the vast majority of the time, but which DO matter?
Do they have other ways of finding genes
than I described above, and have these methods been used to cover the whole genome?
PeterM
Holy smokes, one of the first good comments on genetics that I have seen on Slashdot EVER! *clap*
Hey, when is God going to release a Security Update to disable virus propagation by default? And while He's at it, I could use a wireless networking protocol update.
I agree. I also believe it makes obvious the fact that "directed" research, opposed to "pure" research, is not all some would want it to be. Some may have viewed the genome mapping project as "directed" research towards the goal of finding simple mappings from genes to proteins; however, we have not gained so much the goal of this "directed" research, but we have discovered a lot more about how our genome really does work. It's a complicated mess, but we wouldn't have know this if we had not tried to decode it. Setting expectations on any project is quite important so that those who like to poo-poo scientific research are not armed with arguments of the ineffectiveness of even "directed" research.
end of line
I would hardly consider the genomic map as a "map to nowhere". What the article and the initial poster assumes is that this idea of one gene one protein is gospel. Well it's not folks. There are lots of genes that may be present with no discernable function whatsoever. Furthermore there are other genes that encode proteins at different times with different interactions of their protein products. And additionally, through the magic of alternative splicing, it is possible to have multiple gene products expressed from any one gene in a group of genes revealing many more possible protein products from the presence of a limited number of genes. It is easily conceivable that more "emergent" properties begin to occur in genetic systems than we are currently aware of. For example, start thinking of the number of permutations that can occur from a group of say twenty genes. For simplicity sake, lets say that they can produce thirty gene products that can have effects on each of the other gene products and on the original genes. Right there you have several tens of thousands of possible interactions that can occur. Also lets throw in metabotropics. This is where real life happens, at the small molecular level with amino acids and small molecular communications systems. This complicates matters even more. My point is that this article is falling seriously short of facts and borders on sensationalistic.
Another thing that we need to consider is that we have only roughly mapped out the genome, it will take many years to actually figure out what each gene is, what it does, if it does and how it does it. Also the human genome will serve as a sort of proof of concept for the many other genomic, proteonomic, and metabotropic explorations of other biological systems that will be examined in the coming years.
Visit Jonesblog and say hello.
Nova on PBS is airing a show abotu this right now. It's pretty good. Also see the show's website.
License: By reading this you are agreeing that you agree with me.
Hah ... if you think that sighting the coastline is the same as colonising a new continent then I've got hidden city to sell you. *FUNCTIONAL* genomics where you want to map out the pathway from genome to the protein sequencing to the biological pathways to the symptoms is not just a mere <A HREF="http://cbcg.lbl.gov/ssi-csb/Program.html"> ;supercomputing crunching job</A>. We're talking Petaflops and petabytes here, not your average desktop word processor. <P>
... who would like to put some venture capital into this black hole?
Early research indicate that blind similarity comparison needs to be intelligently directled as the combinations can be daunting. This is the difference between random chess permutations and a quality alpha-beta pruning. To do the algorithms you need smart biostatisticians, bioinformaticists, cellular experts, and probably enough bureacratic gravy to keep NSF afloat for the next century or two.
<P>
Now question
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LL
You may be correct, however I tend to think that people dont pay enough attention to emergent properties of itterated non-linear systems, of which growth is certainly one.
It is amazing the amount of information that can be "pulled from thin air". When in fact its not any information at all but just the manifestation of a simple itterated system. A great if overused example is the IFS Fern. I admit it dosn't exactly mimic its natural counterpart, but its quite a bit more complex "looking" than the set of three or four affine transforms that make it up.
Another piece of the puzzle comes from chaos theory, that (forgive me everyone) basicaly says that small changes in the initial conditions of chaotic systems result in drasticly different outcomes. So alot of the diversity we see in humans I would claim comes from our environment (nature vs. nurture). These (not so subtle) differences in our upbringing lead to very different people, even if they start as identical twins.
In reality, our makeup is a combination of both out genetic foundation and our environment as we grow up.
In conclusion, I claim that we are more complex than a copy of Windows, not because we start with more information, but because we learn as we age, and our mind changes with what we learn.
As many people will probably mention I didn't even scratch the surface of meme's and thier role.
I must be missing something. Having just completed a Ph.D. in Immunology, there was nothing surprising about the genome map. Alternative splicing has been known for awhile (at least 10 years, probably longer but I am lazy and don't want an exact date right now), which is essentially what they are all talking about. Gene therapy will work just as well in this environment as any other, as the problem of fixing a single defect remains the same. The problems with gene therapy right now are delivery and targeting. Once those are solved (IF those are solved) then whether it was one gene=one protein or not doesn't matter. You fix the point mutation and get on down the road. Don't change the sequence surrounding it, and you don't have a problem.
The article is misleading as well in regards to what affymatrix and others sell. They sell clones dervived from mRNA, which is just as valuable whether it came from alternative splicing or from individual genes. You just adjust your thinking, but your data remains true and valuable. Proteins come from mRNA, and then can also be modified for another level of control, so you know you aren't at the end of the story, but you do have to start somewhere.
The control of splicing will involve control proteins, that will be made by mRNA, that will be turned on and off by other control proteins...etc... going backwards in an endless loop of feedback loops.
This is why the field of Bioinformatics is taking off. You can't hold it all in your head, even for a simple pathway.
Gavin Fischer
Because it's fashionable to bash religion for several reasons.
The majority on people in the US probably still believe in god to some extent. It's always fun to feel intellectually superior by bashing the (mentally inferior) majority. You see this in a lot of areas (microsoft bashing being good example)
As with most any arbitrary group of people, a non-insignifigant percentage of religous people are idiots and are also very vocal. It's easy to think of all the stupid things done by people in the name or defense of religon and assume that anyone who believes in the existance of god is also an idiot.
I also submit that a good number of people also feel as you do, but don't bother to speak up. It is much easier to say nothing and keep browsing rather than defend an unpopular position. I know that I have clicked on the "Reply to this" link many more times than I have actually posted, just because I decided that going to all the trouble of replying wasn't worth it. (I'm incrediably lazy...)
the value of genes & disease I don't want to speculate about, but behavior analysis showd years ago (see e.g. behavior analysis web that genetic knowledge would contribute very little to understaning human behavior.
-- Rolf Lindgren, cand.psychol
I do note that these are mathematical exercises. Just because a molecule can be derived from genetic sequences does not mean that it does something, perhaps because evolution has not created a receptor for it. Or a receptor might usually be blocked by another molecule which fits in a nearby receptor and the 3-D shape of the nearby molecule blocks the one of interest to the molecule being studied. We have a lot to learn yet.
There really is no other explanation.
Rubbish. I can easily give you an excellent explanation, and a demonstration to the contrary.
The genome contains a set of simple information. It is then expressed using a series of decoding rules. The 640MB of info is then turned into several GB/TB/PB of information, which is used to build a human/dog/etc.
As an example, consider the Mandelbrot set. It is based upon a very simple piece of information; the repeated iteration of the rule z = z^2-1.
This rule can be stated as a few mathematical symbols; alternatively, it could be coded in just about any language and still fit in a few kb.
However, the expression of the Mandelbrot set is infinitely detailed - and I do mean infinite. It would require an infinite amount of information to uniquely encode the detail in the Mandelbrot set in a point by point fashion. The Mandelbrot set contains all sorts of interesting patterns, repeats of patterns, unique bits and bobs; yet it comes from a simple expression rule, applied to a single complex number.
If you look at a cloud, and see a fish, it doesn't mean that there is a fish in the sky. It means there is a cloud in the sky, which might bear some sort of resemblance to a fish. Please resist the temptation to declare that magic and jiggery-pokery is the only reasonable explanation for a complex phenomenon. Sometimes a simple explanation will do the trick.
Russ %-)
... and never, ever play leapfrog with a unicorn.
This genome map thing is useless. And it's not the only one. When I was in high school the chemistry teacher tried to show me this 'periodic table' thing. It was totally useless. All it did was tell you where certain elements were. It didn't do anything useful, like showing you how to create a bomb in your basement. I don't know why scientist waste their time on things like "genome maps" and "periodic tables". They should all get real jobs, like studying how to give me gills like Kevin Costner in that movie where he was a fish.
Aah, change is good. -- Rafiki
Yeah, but it ain't easy. -- Simba
I think the common assumption that introns are junk may well turn out to be one of the most glaring fallacies of turn-of-the-century genetics.
I'll go out on a limb and bet that within the next 20 years we discover that not only is the protein coding of the exons immensely more convoluted than we ever dreamed, but that the "junk" introns are indeed information carrying and serve a vital and useful purpose. (There is some speculation that the information that tells the coded information *how* to develop (*something* tells undifferentiated tissue to become a heart) could reside in the introns.)
Remember, if we're at all intellectually honest on this subject, the first thing we have to admit is that we don't even know how much we don't know. Unfortunately, this attitude is rare amongst genetic researchers.
God is an awesome engineer, so doing the reverse engineering is likely to take quite a while...
"The future's good and the present is nothing to sneeze at." - Roblimo's last
People have portrayed the task of unravelling the human genome as a Herculean task. Well, the entire genome can be fitted on a CDROM. That isn't very much data at all. Are we really saying that the human body is no more complex that a copy of Windows 2000?
Obviously, it is. So where is this extra information located? It is obvious that there must be some other mechanism at work. I would posit that the mechanism is supernatural.
There really is no other explanation. The Church has known this for many thousands of years, and now the scientists are realising it too.
Really? Well why the hell didn't The Church (which one? I know of thousands throughout history) tell us so that we didn't have to waste so many dollars? The Church could have just said "Oh there ya go... we had this medicine thing and this genome thing licked years ago... this is what we found out... and here's all the data we amassed on the way".
Ignorance is not bliss - except for the religious. It's just ignorance.
Simon
Coming soon - pyrogyra
The rest of your comment seems sound enough, but there is no way scientists can know what a mouse's perception is. They can observe behavoiur, measure neuron activity or in some other ways discover things indicating the mouse's perception has changed. But there is no way anyone can tell how (ot iven if) anyone or anything else perceives anything!
Naive question here: would we even know there are only 30,000 genes without having mapped the human genome? If not, I fail to see what sort of point they're trying to make.
Ah yes, a true troll would NEVER claim to be troll. Well done moderators!
Before you break your arm patting your religion on the back, look into the origins of the dead guy on a stick and then bakc further, into the religions and societies that existed before and during the corruption of Constantine. Take a peek at their mythology and method of reasoning out the universe, and realize that your "god" is about as original and omnipotent as Windows for Workgroups is to Kernel 2.4.
I'm the center of my Universe. You're the center of yours- why you'd want to give that level of power and responsibility up to a corrupt, aeon-old second-hand deity is beyond me.
Overall this article seems to be more a demonstration of the ability of journalists to blow scientist's claims out of proportion than the ability of scientists to make important, but incremental, discoveries. I think the article tries to be provocative, and it's not completely off-base.
However, there are number of factual details that the author leaves out here:
The number of genes predicted by these programs varies wildly (Incyte claims 100k+, Celera says ~30k). This is because these different organizations use different software packages to find the genes. But the reality is that no-one really knows yet. No one has actual studied all these genes, yet. No one has purified the actual protein molecules that they are supposed to encode. Very few (less than 1000) have been extensively studied, and in almost every one we've learned more about what makes a gene.
The sequencing of the genome is a hugely important achievement. But, as other have said, it is just a first step. It gives us the substrate upon which many many years of research will be based. It's clear that there is a lot of work left to be done. Already many research labs are moth-balling their DNA sequencers and replacing them with NMR magnets to examine the 3D structure of these gene-products. The protein folding problems remains one of the most studied, unsolved questions remaining in bioinformatics.
Hope this was somewhat useful.
-c"If you are an idealist it doesn't matter what you do or what goes on around you, because it isn't real anyway."-R.P.W.
Scientists are in general pretty good about not overhyping things. The press on the other hand... Usually when you read a quote by some scientist apparently hyping some project or finding, read the whole transcript of the interview and she or he will sound a lot more resonable. I can think of a few exceptions, however, especially regarding supposed miraculous energy technologies discovered in the late 1980s. Note also science-publisists ("Scientists" who long ago gave up research and now just write books for the masses and do the news-talk circuit) do not fit into the above description.
In Capitalist America, bank robs you!
The authors slant seems to be pretty harshly critical. He bashes some pretty fundamental ideas of genetics without giving much reason or counter arguement. Especially the bit about skin pigment being multiple genes but we haven't found the genes. He seemed to be implying that the genes mix or something else outside of our current understanding. If thats true, which no one seriosly suggests, then our current understanding would have to be waaaaaay off, and there would need to be some other genetic material other than DNA.
But his most basic arguement is that finding the genetic cause for disease is pointless because we haven't cured the disease yet. Well we identified bacteria as the cause for most illness long before penicillin was discovered... there is no knowledge that is not useful, and unless this guy totally believes that genetics research is useless, then his suggestion that having a transcript of the human genome is "useless" is complete and total fallacy.
Scienctific practices often deserves critisism, but not from ignorant hotheads.
In Capitalist America, bank robs you!
doesn't know inside from out?... I won't bother with that part, but I feel I must contest the second law thing. There is NO second law problem with reproduction or evolution. The 2nd law of thermodynamics states that the TOTAL disorder of a closed system (here the whole friggin' universe) will increase, not local disorder. Local disorder decreases all the time in very common chemical reactions, such as the freezing of water. Life is a local decrease in disorder, but if you think about it, with food consumed + broken down, waste released, environment degraded, and ultimately body decomposed, plants and animals contribute greatly to the DISORDER of the universe. Remember kids: universal disorder does not prevent local order. I'd listen to creationists a lot more if they didn't use such twisted and purposefully ignorant science.
In Capitalist America, bank robs you!
Exactly! We need the whole documentation, program comments, etc! It must be *somewhere*, why can this Church organization not provide it if they're so smart? Or did somebody do a sloppy job and hack it together in a one-nighter?
All this reverse-engineering is fun for some time, but when you want to do serious work, you really need the docs.
Oh, and besides: Wouldn't the genome project be illegal under the DMCA?
EagerEyes.org: Visualization and Visual Communication
The key is that the cell is an emergent system.
Moreover, the genome is wholy the product of evolution. We've seen, in a very simplistic way, the types of "optimizations" that evolution creates by using the genetic algorithm and such ilk to "evolve" programs.
It's silly to think that the genome is going to be anything but highly "optimized", incredibly "interdependent", and something that I can only express as "multidimensional". I'd liken reading and understanding the genome to disassembling highly optimized machine language back to assembler source code except I think that it's orders of magnitude more complex than that.
We are aware, in the case of a processor and machine language, exactly how all the interactions and processing occur. Though we have a lot of knowledge about protein folding and the spatial interaction of proteins, I daresay that we're not aware of 100% of the "rules", and will miss nuances in the "code" as a result.
This makes me think about the article posted a few days ago concerning the "evolved" FPGA systems, and the comment that the resulting systems were "strange", and were filled with structures that appear to "do nothing" and were not wired to surrounding parts of the systems. When these "do nothing" portions are removed, though, the system does not function properly-- showing the evolution worked to take advantage of all possible types of "interaction" within the substrate of the FPGA (quantum effects, possibly?).
I've often heard the observation that a large portion of the genome is "garbage" or is not used specifically for coding proteins. I would submit that we cannot dismiss any of the genome as "garbage", given that we aren't 100% sure of all the "rules" of the genetic system. Not at all unlike trying to understand the strange systems evolved on FPGA's.
The Attitude Adjuster, I hate me, you can too.
The "nurture" side of the nature vs. nurture argument (the argument over what makes a person: genetics or environment) have certainly been losing out recently in the media coverage over the human genome project.
R.C. Lewontin has a very elegant short book titled Biology as Ideology that includes discussion on the subject of why the project may not be as useful as it seems.
I see a lot of folks throwing around terms like "information" and "complexity" without really understanding the further-reaching concepts of context and meaning.
First off, syntax != semantics.
All of us programmers ought to understand this fundamental statement. It is naive to say "z=z^2-1 (Mandelbrot) is/represents infinite complexity:"
1. It "is" not infinite complexity. It is 7 characters in your web browser.
2. Is does not "represent" infinite complexity.
The semantics you are (subconsciously apparently) attaching to it are a formulaic image, that can be said to represent infinite "complexity". Still, this image (in your mind) cannot exist without an algorithm interpreting and displaying that function. Even here, "complexity" is up for debate, because:
High visual complexity != high information content
Mandelbrots are not complex simply because they do not contain very much information. However, the human genome is HIGHLY complex, with lots of information; moreso than even any human scientist has yet to comprehend (the point of the article). This is because we do not understand the contextual and semantic meanings of the genome sequence. The first step to look at, according to the article, is the context of proteins, but since humans aren't just a bunch of proteins, I doubt it will end there. This will carry on until they begin understanding enough at some level to do some kind of useful work.
And of course, it is nonsensical to compare a human to Windows 2000. Neither can exist solely on a CD-ROM. Windows is not an operating system until it has an operating environment/system to run on (a computer). Humans aren't human until they are living inside a body, have material, etc.
Remember that when you evaluate some object or concept, you are always subconsciously attaching some level of your own subjective interpretation. This interpretative shell can be a significant amount of attached semantics.
Jesus lives.
it's maybe 10Mb (libraries and all) yet given enough RAM to work with the number of different C programs it can compile successfully almost certainly cannot be counted ....
I'm kind of curious as to why you think a CDROM is not much data at all. Are we that blown away by the whiz-bang of PC gadgetry that we can't turn our perspectives back 20 or 30 years to see how mind-blowing 700 megabytes is especially in such a small disc?
That being said, making biological statements on mechanical objects is kinda silly. Would you be more comfortable if it fit on a DVD or a 8mm tape? Am I allowed to use compression?
As someone already pointed out this is the "god of the gaps" argument, which I'm sure is fun to play but scientific advancement usually wins out. Not that there aren't huge problems with the materialistic cosmology, but its a popular working model explaining lots of natural phenomenon to a high degree of accuracy.
Also, picking one religious viewpoint and assuming that specific one is truth kinda kills any credibility you might have had with this crowd.
At the same time scientific materialism really has little to say about issues religion focuses on like morality or nature of self, consciousness, existence, etc. The problem of gaps of knowledge isn't about quickly filling them in, but shows you the limitations of current knowledge.
I don't think we have enough reliable information, or information enough to pick extreme sides like "card carrying atheist" or "creationist troll" and calling it quits. I see both groups as people with a deep need to believe in *something* as agnosticism doesn't seem to do it for them.
Now we return to the hackneyed arguments of those who have all the answers.
Hogwash. The insulin gene (no responsible for the commercial production of all insulin) is a direct byproduct of study of the animal genome. Of course it is more complicated that they thought. So what. It doesn't mean there wont be major breakthroughs soon.
Someone you trust is one of us.
There is no excuse for the vast majority of software systems to be as complex as they are except that, in the paraphrased words of Pascal: "I haven't had time to make it shorter."
Seastead this.
A lot of optimism assumed that a single gene had a single function, for all time through the life of the cell. But as one would expect with a biological system, things are far more complex. Geners are "turned on" and "turned off." Multiple genes interact indirectly.
The key is that the cell is an emergent system. It exhibits extremely complex behavior as a result of vast numbers of interactions of simpler parts. Thus we may never find a "gene" that "codes for" the shape of a nose. The fact that a nose arises at all from a bunch of protein specifications is itself a clue that things are extremely complicated.
The decoding of the genome will indeed be extremely valuable. But it won't "solve" biology anymore than the understanding of the laws of gases "solves" the weather forecast problem!
The only good weather is bad weather.
Really? The Church, which is less than two thousand years old, has known about genetic complexity for many thousands? Apparently in the supernatural world anything can happen.
Does this create problems for Dawkins' "the gene is the unit of selection" theory? If there is such a nonlinear relationship between genotype and phenotype, how is it possible to ascribe evolutionarily desireable or undesireable qualities to any /particular/ gene? The best we might hope for is that perhaps small subsets of genes have predictable qualities. If "fitness" must be assigned to the /combinations/, we may be talking about such large numbers, that such a theory has almost no predictive capability whatsoever. Such a theory is merely tautological.
But IANAEB (I Am Not An Evolutionary Biologist).
--Lawrence Lessig for Congress!
"Interesting"?! "Funny" maybe. A new category for "Chock Full of Nuts" might be in order.
--Lawrence Lessig for Congress!
"I don't know (or particularly care) if gods, jesuses, devils, spooks, bunnies, or fairies are behind them, but I am at least honest enough to admit they can't be ruled out. Why isn't the rest of Slashdot like this?"
Because we didn't go to school in Kansas.
--Lawrence Lessig for Congress!
"I don't know (or particularly care) if gods, jesuses, devils, spooks, bunnies, or fairies are behind them, but I am at least honest enough to admit they can't be ruled out. Why isn't the rest of Slashdot like this?"
/aren't/ honest enough. You're the only one who's that honest.
Let me try again.
Because we
--Lawrence Lessig for Congress!
I wonder, though, if there wasn't the slightest suspicion of such a possibility until after the funding for the mapping research was cashed out.
/am/ a cynic. Yuck...)
(Eeesh, I
--Lawrence Lessig for Congress!
My theory is that the Kansas board of education cracked Slashdot's slashcode.
;)
That would explain a lot of things.
--Lawrence Lessig for Congress!
Well you cannot tell a mouse's perception, perhaps I used the wrong word. However, we can measure how much an animal detects the presence of a bitter compound. Quick Neurophysiology lesson:
Rats and mice (especially rats) can be completely decerebrated (take away all higher processing, brain dead), and they will still respond to bitter taste. How do we know? Well, if one of these brain dead animals is presented with a bitter taste, it will reflexively withdraw its head. This is a very basic primitive response that goes beyond any perception and is located in the brain stem of the animal (with things like breathing and heart control).
So, they knew that certain mice had this mutation that affected its response to a bitter compound, cyclohexane (I think it was cyclohexane anyways) and caused the mouse to not respond. The reasoning is that the mutation effected the receptor in a way that caused it to no longer respond, or not respond as strongly, to the stimulus.
I don't believe they specifically tested this, but I am sure that if you ran specific tests to test for the products of the reaction of cyclohexane with the taste receptor, you would not see the products of the reaction (Calcium influx and neurotransmitter release).
I am writing a paper for Molecular Biology about this right now interestingly enough. For a long time we have had little information about bitter, sweet, and umami (monosodium glutamate... meat! (well mostly)) taste receptors.
But one day someone found that a genetic mutation at a specific allele can cause changes in a mouse that effects perception of a specific bitter taste. When they researched the area around the mutation with the genomic database, they found an entire bitter receptor. When they searched for similar bitter receptors across the entire genomic sequence, they found an entire array of bitter taste receptors! This goes for humans too. With so much less work, we've found a whole class (the T2R) of bitter taste receptors.
Now you all may say "WHO GIVES A FUCK?!?", but this is actually important. Since we never knew how sweet receptors worked, we've always guessed about what compounds will substitute for sugar. For example, all the artificial sweetners that I know of were found accidentally, with a chemist tasting the substance during lunch or dinner after working with it for something unrelated. Now that we're gaining more information about receptor function we could conceivably find the perfect artificial sweetner... BILLIONS OF DOLLARS.
Besides, if you can't see by now that finding new receptors and quick searches for similar (consensus) sequences in the genomic database isn't going to herald all sorts of scientific advances, you're pretty dense... While it's true that there are alot of different ways the genetic code is used (substitution of polyadenylation sites in leukocytes, different intron splicing in cochlea frequency detectors), we know about alot of them, and with more analysis we will continue to learn more about ourselves even faster than we ever have before.
Actually that is not what they are saying. Lets not think of this in terms of life for a moment as in souls. Rather, realize the human body is just a system, that has almost endless ways to have things change (in terms of health and appearce) or just go wrong (disease). The system grows thanks to its ability to absorb nutrients from consumption. I am not trying to belittle humans here, but really, as a matter of infinite complexity, we could surely view our bodies an infinite number of ways, but that does not change the fact we are compose of a limiited number of systems with a limited amount of variation (even though its considered substantial, mainly because we don't know what correspondes to what, genetically speaking yet on a whole.)
You are a bitch, Mr. Anonymous Coward. At least troll with dignity like I do sometimes :-D
"Dancing is the vertical expression of a horizontal desire" --Robert Frost
Or as D.A. puts it. God promptly vanishes in a puff of logic! I always liked that one...
"Damn fools are going to break their necks!" observed one bystander, R. Dvork. "And what for? I could walk faster than that thing. They will never replace my horse."
Rumors are circulating about the craft being used by the Army for observations. The craft's frailty stands against it. In fact, the first one blew over and broke.
Friends don't help friends install M$ junk.
I'd have to disagree. As the author points out progress has been made - some pretty basic assumptions about genetics - namely that one gene codes for one protien - will need to be changed as a result of this research. The author explores quite nicely how Mendel's "Gene" was not in any way physical - while we have reduced a gene to a sequence of amino-acids his meaning for them was much broader and more abstract (and apparently more correct). The author also points out how a serise of incremental discoveries, while each one correct in it's self, can lead you a bit off track - which I believe is the case here. I don't think the author is slamming the genome project, rather saying that those who thought that simply decoding it was going to tell us everything were kidding themselves, the public and the government who had to foot the bill. He also points out that "knowing that gene X codes for condition Y" has not brought us any closer to cures or treatment for Y. Also, the number of condition Y's that can be conveniently mapped to a single gene are quite small, and (if there was a benefit for knowing that X caused Y - which thus far there has not been) that only a small proportion of the population would benefit.
A1B2C3D4E5F
Cells use a mechanism called alternative splicing to generate different proteins from within the same gene. So to use the example gene above, the cell can make ABCDEF, ACDEF, ABDEF, ABC, AEF, etc.
Further, the same protein expressed in a different context can have different functions. For instance, protein A, when present together with proteins B and C, may have a different function than when proteins D and F are present as well.
The label "supernatural" has been proven time and again to simply indicate something that's not completely understood.
NO CARRIER
Sorry but its nearly all are wrong:--
1.) Ball point pens were invented circa 1942 by a Hungarian? guy named Biro.
2.)Syntehetic fibres go way back at leat to Rayon in the 1930s.
3.)I am sure there were fairly advanced aircraft before 1965?
4.)Noise reduction was amust for Radar in world war two.
5.)Bar codes came from early sixties reasearch sponsored by railroad companies looking for ways to make freight cars machine readable.
6. ?
7. Thermocouples circa 1920.
8. I am sure we had batteries before 1965.
9. The Joystick -- Wasn't that Wilbert Wrights breakthrough! It made all the complex controls surfaces of the Wright Flyer easy to manipulate (He may have got the idea from somewhere else).
10. Well only Teflon and that see through stuff begining with C they use on motorcycle visors.
Old COBOL programmers never die. They just code in C.
Science cannot explain religious loonies therefore God must exist.
P.S. Send money now to my tax exempt church of the unexplainable expense account.
Old COBOL programmers never die. They just code in C.
I am not really arguing about the basic point which seems to be "spend a lot of money on research and you get unexpected spinoffs".
It was just that most of the examples given were factually wrong.
P.S. some of the things the space race was was really responsible for:-
IBM mainframes.
Databases.
Old COBOL programmers never die. They just code in C.
Maybe the nucleic genetic force is only for the physical body, giving a shell for the soul to live.
"Are we really saying that the human body is no more complex that a copy of Windows 2000?"
You are making the false assumption that since two pieces of data can fit in the same space they are equivalent in data content. The most intuitive contradiction to this assumption is that I could just as easily fill a CD-ROM with "0"s. Does that make my CD-ROM a "data equivalent" to Windows 2000? I think not.
Another far more interesting answer is that many natural phenomena can be fully described in a short mathematical form, yet exhibit behavior that is unpredictable, always changing and essentialy random (randomness being ultimate complexity). The classic example is the Mandelbrot set which can be expressed in one simple mathematical expression but exhibits completely unpredictable behavior.
"Obviously, it is. So where is this extra information located? It is obvious that there must be some other mechanism at work. I would posit that the mechanism is supernatural.
Your "missing" information could be the way in which the result of expressed genes reacts with the enviornment. To relcutantly return to your Windows 2000 comparison. The information that Windows 2000 will often lock up (the behavior) on Athlon based motherboards with AGP video cards lays in several places - in Windows 2000 (the expressed genes) and in the Athlon board (the enviornment).
"When a man impregnates a woman..."
Can't stop thinking about sex?
"But really, the Church has known this for thousands of years, and now we are being proved correct.
The church also "knew" for well over a thousand years that the earth was flat. People died over this assertion.I think most people are so hostile towards him because he is laughing at us for making a new realization about our world.
Yesterday, it was widely accepted that genes have almost total control over our bodies growth and traits.
Today, we think that the manifestation of genetic code within proteins posesses that control.
How utterly stupid we were to to ever believe that the workings of our bodies were entirely governed by genes. I mean, how can you respect a theory that doesn't hold up for more than two centuries? Christianity has been preaching the same hypocritical bullshit for over a millenium, it is obviously a superior explanation of life. To hold such an arrogant view towards the situation shows nothing but complete disrepect to the dedicated scientists that have brought us this far.
Personally, I don't understand why everyone is so upset. We have taken a major conceptual step forward in the field of genetics. We could never have made it this far had some people not seen an easy victory with genetics initially. Genetic research has basically received a huge jumpstart from corporations that were eager to make a buck.
Just look at physics for a good example of a science that has been repeatedly thrown into turmoil over the last century. In 1900, it was widely believed that physics was essentially complete, and that all that remained to be done was to clean up a few details. Then along came Einstein. Now we're talking about strings vibrating in 15 dimensions (among other things).
What really irked me was this comment:
WTF? What's responsible for biology then? Fairy magic? There's been no blow whatsoever. Genetics is just turning out to be more complex than we once believed.They have an interest in down playing the usefulness of the sequence of the 30,000 human genes, and promoting the mystery and necessity of studying the proteins generated from the genes in all their variants.
And so this distorted 'news' story, with the many errors of fact and emphasis that others have remarked on, gets written. There is utility in studying the protein variants of genes, but it is a maginal utility. The '300,000' variants is a number out of a hat, the true number may differ by an order of magnitude. And many protein variants don't affect gene function... :)
Jim Lund
jiml@stanford.edu
Over 98 percent of the genome appears to be inactive, consisting of "non-coding regions," and some dismiss it as "junk DNA." (Not Collins or Venter, however, who say we just don't know what it does.)
1) Replace "genome" and "DNA" with "Source Code"
2) Use italic text to describe MS application of your choice
You keep calling them "fundies"... isn't that rather inflammatory of you? You, who keeps going off about flames and giving people ammo. You complain about militant atheism while being an offensive agnostic.
-Erik
Genomics might be that kind of problem.
(must... fight... it...)
someone send Gene up the bomb?
Go ahead, mod me down for being a retard. Honestly tho, while the 30,000 number was somewhat surprising when it came out, and the implications are far reaching for textbook authors and publishers, I don't think this single fact is as much of an informational cataclysm as the article seems to. It will easily be 50 years before even the brightest mind has any real understanding of the overall picture, and NOBODY can say yet if 30,000 vs. 300,000 makes it easier or harder to get it all nailed down. If it wasn't for irresponsible and sensational journalism like this, people wouldn't expect gene therapy to be something you could buy off the shelf next week. (I think my favorite line from that ABC article is probably in the second paragraph-- "The doctor then gives the man a drug that will prevent that protein from doing any future damage." It should read, "The result from the DNA scan is automatically permanantly saved to the man's NIH federal health profiles database. The man's health insurance rate goes up 80% immediately, without any human intervention." -- but that's a whole new rant entirely).
Come on. If the raw sequence was really worth anything by itself, would the government (or even my lovely state of California) let you download it for free?
Humpty Dumpty was pushed.
mu!
Humpty Dumpty was pushed.
ha ha, can't reach me. And Hal's got my back! Hal says, "I don' think they have children with me, and fulfill them... would you like some kind of god moved upon the camels and took them, and slew the philistines with a young, hot, submissive stud upon occasion who is looking for a suck job on my new instructor looks like an assmaster diaper to me."
Humpty Dumpty was pushed.
Sure the Genome is complex and at first glance it seems like an undauntable task to make any sense out of it, remember its a biological creation, not a mechanical, man made "computer". Its bound to be complex. However, what it needs to be "decoded" is some super computing power to crunch the numbers, do the math, and then, yes, we will have all of the answers. Now that we have the genome in all of its glory we just need to decode it or make sense of it. However it probably is not going to be a simple one on one correlation as some might have thought, multipe genes and protein combinations probably account for any given physical or mental characteristic of an organism. I leave my faith in the mind numbing, number crunching brute force of our modern computers that are rapidly becoming as complex as some of the biological "machines" that they are decoding.
Nathaniel P. Wilkerson
Domain Names for $13
Nathaniel P. Wilkerson
www.haidacarver.com
I think the article only confirms that the author doesn't know much about genetics. No geneticist (that I've even spoken to, at least,) believes that a list of genes equals a useful API for making/modifying humans.
The clones we made of sheep, mice, and other animals resembled the products of buggy code made by lazy programmers or those forced to write shit by insane business models (remember the sig, "it compiles! Ship it!"). We didn't realize the significance of the slow, steady process of genetic replication within the embryo.
Exactly right. Cloning is a "neat hack" in the Computer Science sense: I don't know what X does, but I know enough to make a copy of it. No one involved in cloning claims they understand all the processes involved in growth... they just have used a bunch of tools to provide a proof of feasibility. Think of them as writers of "bit copiers" (for those that remember the old days of floppy disk duplication.) Ask them if it's an exact copy, and the better of them will say "I'm not sure, but it seems to work so far."
Likewise, we hurled gazillions of dollars at the genome project, in private and public searches. Why were the gazillions hurled? Because of the notion that we could find nice, patentable pieces of genetic code, controlling various physiological processes.
Now that we realize we have got a map to nowhere, lets table the whole deal until we understand more about the operation of genes.
Yep, "map" is a dumb term. I'd prefer to think of it as having the object code to an operating system and its associated applications, running on a processor that we don't have the spec for. Some crashes we can cure (they occur in application code that is clearly fixable,) but most problems are due to interactions amongst parts of the system.
Cancer is similar to the infamous Blue Screen of Death. Yes, it's obvious that something bad has happened, but we aren't going to find a line of code that says BlueScreenOfDeathNow(). It's an emergent property of a complex system.
I am all for scientific research but I worry that further pushes down this line of inquiry will be driven by the profit motive, not any kind of medical or healing motive.
You're more of an optimist that me. I reckon most easily curable deseases with be cured pretty soon. The bulk, however, will fall into the category of: "system crashes after 70 years uptime. no solution other than complete redesign."
Of course not. It's just that the human genome doesn't suffer from code bloat as badly as typical Microsoft products do ;-)
There's no point in questioning authority if you aren't going to listen to the answers.
Actually, your system already includes some fairly impressive protection against viruses, it's just that the sophistication of the viruses is much higher than you realize. For instance virus propagation is not on by default, but many viruses contain instructions that help turn on virus propagation mechanisms. And, quite frankly, I think that people have extremely good wireless networking capabilities. They are admittedly fairly low bandwidth and short range, but there's some quite impressive error correction for dealing with high noise environments.
There's no point in questioning authority if you aren't going to listen to the answers.
If you read carefully, it's clear that the issue they're discussing is that there are no easily exploitable clinical applications. IOW, the companies that have been patenting every gene in sight may discover that their patents have expired before they've figured out how to turn their gene products into commercially applicable products. How terrible that their patents of publically funded discoveries won't turn out to enrich private businesses, no? Meanwhile, pure researchers are tremendously happy with the quantity of data that's useful in pure research. Not really surprising considering that the genome project was specifically designed as a pure research program, not as an applied clinical program.
There's no point in questioning authority if you aren't going to listen to the answers.
One thing that is not at all well conveyed by the article is that people have known that the "one gene/one protein" view is oversimplified for quite some time. The concept of splicing variants, i.e. that a single gene produces a variety of related products, is something that my coworkers take as being so natural that it doesn't even bear mention. Yes, it's true that the textbooks may need to be rewritten, but that's because textbooks are always decades behind the cutting edge research.
In any case, people have already been working out ways to take advantage of the genomic data without needing to figure out in advance exactly how it is processed to produce proteins. That's because figuring out the exact splicing points is very tough, and people wanted to use the data before it was completely annotated. Thus the techniques they've been establishing are already well suited to dealing with multiple proteins coming from a single gene. It's a bump, but nothing like the drastic problem presented in the article.
There's no point in questioning authority if you aren't going to listen to the answers.
Forgive me if I'm wrong (and I invite criticism)
I can't say this with absolute certainty, but I worked on HIV for two years, and I'm 99% sure you're wrong. I don't know that much about integration of viral DNA, but HIV and other lentiviruses (a class of retroviruses) have special methods of integration that enable them to do things that other retroviruses can't, namely to integrate their genome into the chromosomal DNA of a cell that is not actively dividing. There was some work being done using integrase inhibitors, which block an enzyme necessary for this process, but it's also not clear whether integration is necessary for transcription of the viral genes (for example, certain white blood cells called macrophages are known to have high levels of circular viral DNA sitting around, but no one knows if it's active or not). In any case, I am pretty sure that the integration of the HIV genome is not base pair specific. Your idea is very interesting, but it would be very difficult to implement in practice, and the virus would mutate to circumvent this type of intervention rather quickly.
People have portrayed the task of unravelling the human genome as a Herculean task. Well, the entire genome can be fitted on a CDROM. That isn't very much data at all. Are we really saying that the human body is no more complex that a copy of Windows 2000? Obviously, it is. So where is this extra information located?
.12152322... etc. where every two digits corresponds to the appropriate letter in War and Peace. Let's imagine that you wanted to express the location of this point P in a different way, such as giving directions how to get there given rules X and Y. The actual number of bits of information you need to successfully designate point P will depend greatly on what X and Y are. This example is almost so trivial as to be worthless, but I think it gets across the point I'm trying to make. You can't look at "information" in just the number of bits used to encode it, without looking at the system used to decode it. If the human body is more complex than Windows 2000, it's because cellular machinery does a better job of using the genome than a computer does of using code.
Arguments along these lines show a profound lack of understanding of information theory. To be fair, 99.9% of people don't even know what info theory is, and I can't claim to understand all aspects of it myself. But look at it this way: the location of a SINGLE POINT on a number line has an infinite information carrying capacity if you can resolve its location to infinite precision. Say you want to encode War and Peace in the location of a point. You could just number every letter 1 to 26 and stick the point at
I'm sick and tired of this BS about there being less genes than predicted, the failure of the human genome project, etc. The project needed a lot of hype to get the funding it needed, and they succeeded in that, but the final sequencing of the genome is not really a discovery in itself. Biology is a big puzzle, and the human genome project was the project of uncovering all the pieces. Now that the pieces are there, we're ready to make some progress. A lot of people are like "okay, so let's cure AIDS now," but it doesn't work that way. A lot of the discoveries that will result are not going to be directly attributable to the HGP. I do admit that geneticists tended to have an oversimplified view of biological development, but the whole "one gene one protein" thing was shot down DECADES ago with the discovery of things like mRNA splice variants, post-translational modifications, etc. The HGP has nothing to do with that.
While it might have surprised a few people at the very molecular end of the scientific spectrum, the gene number thing didn't surprise most biological scientists, including myself, all that much. The reason is this: if you compare a human vs. a mouse, for example, the extra complexity of a human is not at the level of an individual cell, but at the level of organization of cells. A certain percentage of the genome codes for proteins like collagen and keratin, which are important for formation of tissues. Then some more of it codes for proteins involved in stuff that goes on in all cells, such as polymerases, metabolic pathways, etc. Then there's some that codes for things like liver enzymes, hemoglobin, neurotransmitter synthesis pathways, etc--things specific to certain tissues. At these levels, the requirements for a mouse and a human are very similar. What makes a human more complex is that we have the same building blocks arranged in a much more complex fashion. This requires a greater number of genes involved in mediating interaction between cells, namely various receptors and signaling molecules. Taking this into account, it is an extremely primitive idea to think "Oh, we're ten times as complex as a mouse, so we must have ten times as many genes." It's more likely that we just have ten times as many of the subset of genes involved in development, complex formation of tissues, etc. And I shouldn't even say ten times because it's also important to realize that the complexity of this system will almost certainly scale supralinearly with the number of elements/genes involved.
In any case, it's extremely premature (and annoying) to make arguments against the success of the human genome project. Maybe the HGP people are guilty of making a lot of hype that they never had any intention of living up to in the short run, but it's simply incorrect to say that scientists the world over are shocked and dismayed by the unexpected findings of the genome project. Or that this shoots down the "one gene one protein" thing had been defunct for years. What the HGP opens the door on is scientific examination of regulation of expression of genes, etc. How genes interact with each other. This is where real breakthroughs in understanding are going to be made.
Oh, one last thing: very few biologists bought the "junk DNA" thing either. That's public perception, but we've known for YEARS that it plays important roles in gene regulation, recombination, etc. etc. Also, nothing discovered in the genome project provides any evidence supporting any religious ideas whatsoever. Anyone who thinks that does not understand what they're talking about. On the other hand, it doesn't really provide new evidence on evolution since those arguments were already convincing before the HGP was finished.
*gapes*
Ok, this isn't it. I've been watching for about a month or so to see a modded up post that so lacks value that it's time to leave slashdot forever.
This isn't it.
It's damn close.
Maybe the state's highest function is to grind out insoluble problems. (Zelazny, Hall of Mirrors)
A CD can store a gargantuan amount of data. Take your average Project Gutenberg text. Two of them will fit on a floppy, uncompressed. The human genome is so compact because we don't start running flight simulators if you poke our belly buttons while rubbing behind our ears. We don't "embrace and extend" sugar and fat to keep potential predators (long since destroyed by poaching and deforestation) from being able to eat us. Not only is the amount of data in the human genome enormous, but the chemical principles that determine what happens with that data are of immense complexity as well. Over billions of years the proteins have developed taking advantage of these properties to acheive extremely efficient solutions.
I don't think you're a troll for forwarding your religious beliefs, but I think you're mistaken in your underestimate of the amount of data that can fit on a CD-ROM. Science will never prove the existence of God. We must find that by faith alone, or not at all.
WARNING: there is a trojan on your
(1) People have portrayed the task of unravelling the human genome as a Herculean task. Well, the entire genome can be fitted on a CDROM. That isn't very much data at all. Analysis : Nonsense. Define "a lot" of data. Please. (2) Are we really saying that the human body is no more complex that a copy of Windows 2000? Obviously, it is. Analysis : Rhetoric and strawman argument. (3) So where is this extra information located? It is obvious that there must be some other mechanism at work. I would posit that the mechanism is supernatural. Analysis : Special Pleading. (4) There really is no other explanation. The Church has known this for many thousands of years, and now the scientists are realising it too. The missing information must be supplied by the Holy Spirit. When a man impregnates a woman, the Holy Spirit breathes life into the resulting embryo. At least, this is what we were told in school. In actual fact, it breathes information in, and gives it a soul. Analysis : Rhetoric. Special Pleading. (5) I know I will be labeled a troll for this, and am saddened. Analysis : Ad Hominem, attacking the audience's tendencies instead of the idea. (6) But really, the Church has known this for thousands of years, and now we are being proved correct. Analysis : Fabrication. The Church "knew" zilch (flat earth, witchcraft etc..) for thousands (actually 2 thousands, still grammatically correct but kinda stretching it) of years. Conclusion : Can do better. C-
Mode (3) smart-aleck mode. Press * to return to main menu.
The disheartening thesis of this article is not that DNA is not complex enough to describe us, but that our knowledge is insufficent to even understand how DNA encodes the data that makes us individuals. In otherwords that DNA is, if anything, too complex, not too simple.
And, of course, its absurd to leap from the idea that the volume of data in DNA is smaller than we thought to the suggestion that this somehow 'proves' that there is a soul providing that extra info. The concept of the existance of the soul and the supernatural isn't inherently silly, but trying to use this as proof of it is comical.
John
I think you're touching on the question of nature versus nurture. It's true that who we are individually -- or as a species -- is not defined wholey by our genome. Our genome is no more complex than any other mammal, so what sets us apart? Our genome gives us a few basic abilities: to think (better than other mammals), to feel, to make sounds. That and a few instincts (crying, blinking, suckling) are all we get.
Everything else comes from culture. This includes both oral and written language, which gives rise to communication and rational thought, which cannot exist without it. Oral traditions and written works allow for a cultural memory which spans any physical, genome-determined lifetime. Genes define our physical vessels, everything else comes from culture and individual experience.
That's why it's so important to read and write. You're contributing to our shared cultural memory, adding new sequences to the dna of society.
I will preface this with a bit of an introduction. I'm a geneticist at the National Cancer Insitute at the National Institutes of Heatlh. As a professional in the field, I find this article to be sensationalist and based on ignorance.
First, I will put to rest the notion of "one gene, one protein" as so heavily asserted by the author. In the scientific community, it was known that this is not the case in every situation. Viruses, which have the smallest genomes out there, not only encode their genes on one strand of the double helix, but both. Their genes overlap, so one stretch at first glance appears to have one gene, encodes more. Then there's always the issue of alternate splicing patterns. As was mentioned, there's non-coding regions of DNA, much of which is inserted in genes. On the road to protein, this is cut out. One gene can be spliced in multiple fashions, giving rise to multiple proteins. All of these motiffs have been documented for some time. These motiffs have also been seen in higher organisms (including humans). However, without the full map of the genome, it would be very difficult to ascertain if these motiffs are frequently used or if the genome behaves in a simpler fashion more frequently.
Second, the author, Tom Bethell, joins the ignorant bandwagon of people that believe gene therapy has its place in science fiction and not science. These beliefs have their place in fiction. Numerous clinical trials have shown direct benefit in the patients as a result of introducing or altering genes. I know several such people who would be dead right now rather than healthier than they have been in years had it not been for gene therapy protocols. To write this off so soon when it's potential is so great is as great a tragedy as arguing against the advent of planting your own crops rather than gathering what grows in the wild.
Third, the assertion that the information of the human genome is trivial and of little scientific value... is about as blatantly wrong as saying the sun rises in the west. The growing database of the genome, which has been public in draft form for some time, has been of immense help in the field of human genetics. I assure that many of the advances in cancer research, and indeed successful cancer treatment, have stemmed from information in the human genome. A day doesn't pass that I'm not using the information in my research on breast and ovarian cancer.
Which leads me to my last gripe. The author slanders the field of epidemiology (without naming it, I wonder if he is even familiar with the word). I work in the Division of Cancer Epidemiology and Genetics. A big portion of our research is in studying and discovering those genes that predispose people to cancer. Perhaps if Bethell believes it more voodoo than science, maybe he should consider the Ashkenazi Jewish population which has a disproportionately high rate of three specific mutations in BRCA1 and BRCA2, two genes associated with the majority of breast cancer. Any one of those three mutations may not be a guarantee of breast cancer, but if you look at family histories, you'll see a lot of women dying of breast cancer at an early age. Maybe since Bethell believes this to be supposition and not science, we should stop those studies. Maybe we should not bother testing women in high risk families to see if they should consider preventative measures.
Maybe because Bethell feels that he should be the sensationalist bell-ringer, drawing attention to the waste of human genetics... we should stop the research, stop the treatments. Let people die of cancer. Maybe because it won't be easy and it won't be simple, we shouldn't try.
I resent the article and Bethell's attitude, which is unfortunately becoming more popular.
--Chico Science >
"If a program can't rewrite its own code, what good is it?"
--
Dyolf Knip
Why, it moved to Everything2.
--
Dyolf Knip
Humans love to look at the world and try to throw chunks of it into a bin they have labeled "understanding". The problem is, some people are not as picky as others about what gets thrown into this bin.
So, every once in a while, it becomes necessary to dig back into that "understanding" bin for large chunks of life that need to be broken down into smaller pieces. This wouldn't be too bad if people had similar ideas about the meaning of their label.
Personally, I prefer to spend my time hucking things into a bin I have marked "accurate predictions". Many of the same theories go into this bin, but it makes me feel less deluded when I have to go back into it and pull things out.
How can anyone call this serious doubts when the article is posted on spectator.org?
Please read their article in the same exciting issue on the deadly effects of not letting people use DDT
which says "You heard it talked about today on Rush Limbaugh..."
Anti-Science? Nope. Not at all.
I hear about all of homo saps technological breakthroughs on Rush.
Why post this trash?
Is it just to annoy people like me who might have some work to do on the human genome
and are instead posting to slashdot?
Or so we can all laugh about how the author of this piece tells us that there is no code,
and then proceeds to tell us that there is a meta-code?
PLEASE!!!!!!
The argument that it was not worthwhile to sequence the whole genome because there seem to be fewer genes than expected is badly flawed.
It was the sequencing effort that provided the data needed to estimate the number of genes.
I also don't believe that the 30,000 gene estimate is very well supported either (but that's another story right...)
I'm writing a longer rebuttal of many points in this article and I'm sending them to the publisher.
The real issue is one that should interest /. readers: access to the data. Prior to the Celera paper on the genome, the standard at Science papers on new sequences was for the authors to deposit their annotated sequences in the public GenBank database. Celera made special arrangements with Science to keep its human genome sequence secret (actually quasi-secret. You can access small chunks of it from Celera if you sign away many of your rights to do as you wish with the information).
Since open exchange of data is the lifeblood of science and served as a precedent and inspiration for RMS's original thinking on free software, this precedent is legitimate cause for concern. Without access to the complete sequence, scientists have limited ability to build upon Celera's work and to look for errors in the genome.
In fact, the previous sentence is somewhat hyperbolic---the HGP sequence is freely available and many universities and other not-for-profit laboratories are licensing full access to the Celera data, but as a point of principle Lander was right to voice concern.
In fact, if you think about it from the standard knee-jerk conservative point of view, the new mystery over only 30 K genes should be something the government funded labs should be shouting from the rooftops. After all, if the genome were completely understood, then the government could close its checkbook, issue a great tax refund, and send the scientists home or into the private sector. However, if a great conspiracy of scientists suppressed their mastry of the genome and said that lots more research was necessary to understand it, then they would guarantee further trips to the trough. This is the standard conservative criticism of research on global climate change---that the scientists know it's bunk, but continue to pretend that more research is needed in order to receive continuing funding.
The human genome map has 3 billion base pairs. Now a lot of those base pairs are the same for all life. In fact, you have 50% of your genes in common with a banana. But there are still 45 million base pairs that differentiate us from chimpanzees. In addition, different diseases occur in different areas along the length of the genome. Not just on those unique to humans.
I believe a lot of the dissappointment in the human genome project stems from not understanding what the goal of the project actually is. It's not an end in itself and will not cure disease. It is a starting point for the real research on drugs and treatments for specific diseases that will follow. This research will take time but there is the prospect that a technological solution will speed this research. The human genome project was supposed to take 15 years but was done in a little over 2 years.
Frylock: That's not a toy!
Master Shake: You say that about everything you own. You should own toys. They're fun.
Now that we found out that the human geonome is so short, where is all the information stored @ now? What makes us up if our genes don't contain all the information?
Back in the late 1800's social darwinists believed that you were sucessful based on your genes. The better genes, the anglo-saxons, were made to rule over the less civilized ones such as eastern europeans and africans and such. I belive that in 100 years people will look back and think that it was crazy how some people thought that homosexuality was in your genes
On my PBS, and I assume many West Coast PBS stations, a NOVA describing recent DNA discoveries (pretty simplified thus far) is on TV, RIGHT NOW. And Nova actually has some credibility when it comes to science news, unlike the Spectator. Hopefully this helps someone.
Im sorry, how much information should it take to make a human? Is >650MB more or less than most life?
This is indicative of religion, telling you that as a human you are more special than everything else. Remember, you are not a special or unique snowflake, you are the same decomposing crap as the rest of us.
Also, as I have a Masters in Microbiology, I would like to add that obtaining the sequence was the easy first part. There's a *whole* lot of biochemistry (the real work) that needs to be done. The sequence certianly helps though.
One, we don't want to go that way. Two, that's the only way we don't want to go...
(1) To many biologists, the "value" of the genome project has been questionable from the beginning. It's not hypothesis-driven science, which is usually the interesting kind; instead, it's blind data collection.
(2) To many others (dare I say most biologists -- including myself), the immediate value of genome projects has not been in the ability to track down the causes of genetic diseases -- any reasonably informed biologist has known all along that having an entire reference genotype sequenced is neither necessary nor sufficient to fulfill this goal, though it will undoubtedly help in the long term. Instead, the value has been twofold:
So, sure, we won't be getting thousands of new gene-therapy strategies for genetic diseases within a couple of months of getting the genome. But everyone's always known that that aspect of genome projects has been oversold. But, wow, what an incredible opportunity this database is for the rest of the biologists in the world!
The entire contents of this article was just on KVIE (channel 6 in Sacramento) last night in a Nova special written a year ago. This isn't new news, it's more cynical journalistic hysteria.
;-) kidding) is patched on to modify the ancient proteins with new classes, er, proteins. Since everything is 3D, the proteins can modify themselves or other proteins in nearly limitless ways.
Landers made an interesting observation: yes there are 30,000 genes, but genes are linear and proteins are 3-dimensional. The genes describe proteins that can fit together and modify each other in billions of combinations.
So basically the 3-billion pairs have mostly been wrapped with genetic #IF 0/#ENDIF pairs. The remaining 30,000 genes define a set of basic classes (how to make a cell, how to make a cell wall, how to metabolize sugar, etc). However the fun starts with the youngest genes that create modifier proteins.
Reminds me of bad C++ hacking: don't learn how the class works, just add a few modifier methods, derive a new class, and run with it. The young genes (like code by new college grads
So now that we've decoded the metalanguage of DNA that describes the proteome (new buzzword), we can start decoding the language of proteins. This will be even harder b/c it isn't linear, and we know how badly our brains work in more than 2 dimensions.
---
https://www.accountkiller.com/removal-requested
Yes, these people that call the genome project a "map to nowhere" are simply talking out their asses. They are not research scientists, they do not even keep up with the latest developments in genomic research. All they know is the little news blurbs they see on TV or on the net. And somehow they think that gives them enough information to be informed in that area. Guess what? It does not. Genetic and genomic research is a hot commodity these days, and it is generating more than just "stupid maps with no use", it is already allowing us to understand all aspects of life on a new level. We have learned and will continue to learn a great deal about evolution, disease, inherited traits, and so much more from genetic research. It is right here right now paying profitable dividends in science and understanding and medicine (and yes, business as well).
Its become apparent over the last twenty years - at least to geneticists - that the genome acts more like a hologram than a one-to-one map of traits. I don't know of any geneticist of the last generation who subscribes to the one gene-one protein school of the 19th century.
Actually, the human genome is 3 Gbases. So that's like 5 CDs (and without the annotation.)
I believe he is a troll because he didn't express a valid logical argument or offer any data to support his case. He only stated (paraphrased) "people are complex, therefore god must exist". I agree that an intelligent person (such as yourself) can take the statement, seed it with facts and make a very plausible and somewhat enjoyable debate out of it; however, that doesn't mean that Christian Soldier wasn't a troll in the first place. This leads us to wonder if trolls aren't necessarily bad, i.e. they almost always inadvertantly spark a thread that is very informative and fun to read. Of course this may not be inadvertant.
I thought someone said there was going to be free beer!
And lo, on the eigth day God created GZip compression and saw it was good. And it would bugger up any reverse engineering. DMCA or not.
Because we didn't go to school in Kansas.
.. sigh)
Which means what, exactly? Are you claiming that schools outside of Kansas teach children that God CAN be ruled out?
Knock it off.
You're just giving the fundies ammo, and ammo is one thing that they definitely do not need. Religious fundamentalism is a sick disease of the mind, a twisted and wretched malady that represents the greatest threat to world peace that this small ball o' rock has ever known. The only problem is that militant atheism is nearly as bad.
Schools do not teach kids that there is no God, that there can be no God, and that anything supernatural is ruled out. I think you know this. So stop claiming otherwise. We don't need to rile up the fundies (it's just a shame that the most mentally ill segment of society also happens to be the most heavily armed, but that's another story
I see plenty of people dismissing the parent as a troll and wonder if they are being fair or not. True there has been more than the average amount of trolls written in the past couple days or so. But I think that Christian Soldier has a valid point here. The human genome is complex, yes, but I think that it is correct to say that "who we are" cannot be fully attributed to the genome. There is an awful lot of complexity to our very existences (and I'm getting a bit metaphysical here so I apologize.)
I realize that Slashdot has plenty of atheist/freethinker types. Hell, I myself am an agnostic, a lapsed Catholic actually (which would make me more hated than atheists by some branches of fundydom! But that is a different topic all together, I would say.) But I do think that those who call "Christian Soldier" a "troll" are trying to discredit his point by laughing at him and/or levying accusations at him. Screw it, even if he is a troll he has a valid point, whether he knows it or not!
If you want to discredit him then do it with facts, don't do it by throwing out names like "troll" and then walking away as if you've settled some sort of cosmic score. Because you haven't. Me, I tend to think that there are just some things that we don't know yet, and might not ever know. I don't know (or particularly care) if gods, jesuses, devils, spooks, bunnies, or fairies are behind them, but I am at least honest enough to admit they can't be ruled out. Why isn't the rest of Slashdot like this?
"Enough attention to emergent properties of itterated non-linear systems"
You waited all week to use that phrase, didn't you?
When I were your age, all round here were fields...
Saying that the genome project was a "map to nowhere" is the same sort of neo-luddite crap we hear from people bashing pure research all the time. Whether it is measuring the age of the universe or decoding the human genome, the simple fact of the matter is that pure research is often done for just that... research.
There is no assured outcome any time you do pure research, but the knowledge continues to prove useful in many disperate fields. Anthropology, history, medicine... they have all had tangible results ALREADY from the work that was done.
Just because the initial "decoding" is done doesn't mean that the project is finished. Much like version 1.0 of software, there is much research and debugging to be done. Not really sure what the point of this article was... We don't have instant results on April 17, 2001??? Give it time.
I would have to say that explosives are the most abused technology in all of history.
I am a lifelong conservative. But I would be rather be governed by extreme leftists than by a conservative who doesn't believe in evolution, because any such person is either an unabashed ignoramus or deranged.
Yes, Tom, molecular biology is complicated. Nonetheless, we're going to keep figuring stuff out. And you'll get to reap the benefits, along with the "Animal research is a lie!" folks and the protesters who have tied the IMF and DNA into a single mindless ideology.
My qualification for holding forth on this, by the way, is that tonight's episode of Nova about the Human Genome Project prominently features my office and desk. (I, being less telegenic than my desk and considerably less important than my boss, was shooed away and told to stay lost until the crew went home. ;-) )
I'm glad to see that Slashdot is acknowledging the existence of political perspectives besides the inane rantings of Jon Katz and Michael. This probably wasn't the best place to start, though.
Unsettling MOTD at my ISP.
The machinery inside a cell that "executes" pieces of your genetic code is far more complicated than the machinery that executes windows 2000. There are also many, many different kinds of cells.
Oh, and all the cells in your body work together. Try figuring out how a bunch of Win2k machines function together on a network just by looking at the source code of the OS. Better yet, try to figure out the Internet by looking at disassembled source code of Win2k or UNIX.
No, you misunderstood: Genes CAN be mapped directly to proteins. It is just that one DNA sequence can code for more than one protein.
Homosexuality is probably strongly influenced by genetics, but we really don't know to what extent.
As a molecular biologist, I've gotta say this is not a huge surprise.
We already knew there is post-transcriptional and post-translational modification of genes. That's been known for a long time.
And some genes actually hop around. Transposons.
I think it just makes things more elegant and exciting.
OK. So why have cats been carrying a version of HIV for thousands of years?
who modded this as interesting? I think the aim was FUNNY!
Clearly. The immediate problems with the interpretation of this first, cursory glance at the genetic blueprint and it's dissemination are:
a) the lack of information (we'll understand more when we can explain the differences -- Celera loosely assembled 5 genomes, HGP [more completely] one),
b) the gap between the scientists and the data handlers (hopefully quickly filled by burgeoning bioinformaticians), and
c) (most notably in this case) the ignorance and chicken-littleism of the press.
The point is, we never would have gotten this far without a gene->protein hypothesis. Now is the time to understand the complexities of the system. There likely will not be a one description fits all remedy for the problem. There are plenty of problems with/exceptions to the rules. The only hard and fast rule is survival. And that one, as far as the general public is concerned, is a difficult hurdle to clear.
Some people set out to commercialise the building blocks of life .. and somehow (insert favourite deity) manages to throw a spanner in the works by adding a twist =) .. kinda ironic isn't it.
--
Jon - TheSpork
And next you'll try to prove white is black and get killed in a stampede of zebras, right?
Obviously, it is.
Where is this obvious? How do you define the complexity of the human body? Is it a mathematical definition? How does complexity of a set of data relate to quantity. You could also say that the human body is no more complex than a Bee Gees' album, which also happens to fit on a CD. So does Beeethoven's Ninth Symphony. Complexity != size.
Obviously, it is. So where is this extra information located? It is obvious that there must be some other mechanism at work . . . There really is no other explanation.
Appealing to the complex argument doesn't help you explain your case, and is in fact a readily-identified logical fallacy. And again I would like to ask you what is so obvious about this. You use the word so frequently. I think you need to buy a thesarus.
The Church has known this for many thousands of years, and now the scientists are realising it too. The missing information must be supplied by the Holy Spirit
The difference between, say a scientific explanation and yours is that a mechanism is posited that we can study. In your argument, there is nothing to study. How does this information get to us? Where does it come from? How can we catch it in mid-stream? Your explanation answers none of these questions, and instead puts the answer on the other side of an unbridgable gap -- and people simply fill in whatever is convenient for them. But your answer is not science. And scientists are not "realizing" this, either. A scientist who "realized" this would no doubt give up science and start preaching. And what he would be doing would then no longer be called science
At least, this is what we were told in school. In actual fact, it breathes information in, and gives it a soul.
That's not what I was told in school, but whether I was told it in school or not is irrelevant. Just because it came from a school does not make it correct. That's known as an argument from authority. Here's a question I have for you: what is a soul? What is it made of? How big is it? What color is it? Is it observable in visible light? Does it have mass? Does it radiate energy? If so, in what frequency?
I know I will be labeled a troll for this, and am saddened. But really, the Church has known this for thousands of years, and now we are being proved correct.
You're actually being labeled as offtopic. And I'm confirming it in metamod. But I thought it important to respond to your ridiculous, ill-concieved assertions just to show you that not everyone in this world swallows this kind of hogwash whole.
As for what the Church has "known" -- well the Church has failed to acknowledge almost every significant advance in human knowledge for the last 500 years. It took the Catholic Church over 300 years to admit that Galileo was right, and their track record since then hasn't been any better. The unexpected complexity of the gene map is not "proof" that the Church's point of view is right. This is not a political contest between two opposing points of view. Science is the exploration of reality. When one pathway of exploration comes to a dead end, it simply means that pathway is not valid. It does not mean we all say, "OK, I guess they were wrong, and we can go back to what we believed in the 18th century!"
One day I feel I'm ahead of the wheel / the next it's rolling over me / I can get back on / I can get back on
Really? Is homosexuality defined by the presence of a protien? I was unaware of that.
One day I feel I'm ahead of the wheel / the next it's rolling over me / I can get back on / I can get back on
Huh? For years homophobes have been screaming that nobody has found a "gay gene" so therefore homosexuality is not biological in origin and is best treated with a swift blow to the head with a Bible. Which is pretty stupid first of all because it's an argument from ignorance, but also because there isn't necessarily a trivial mapping between a single gene and a phenotype. Now that it's becoming clear that there wouldn't necessarily be a "gay gene" anyway, I don't see what you think your point is.
Are you going to claim next that intelligence isn't genetic? Or is that a "lifestyle choice" too?
You are right that the genome does not contain all the information needed to specify an organism.
Here's a semi-fanciful essay that I wrote, describing how to make heritable changes without changing the DNA.
they said the laser had no practical uses either.
-
The reason to sequence a genome is not to find particular genes(there are better ways to find disease genes), but because there are questions you can ask when you have the complete sequence that you cannot ask otherwise. For instance, if you have systematically assayed all genes in the genome and none of them display a particular motif, you can say that the organism completely lacks that motif. The complete sequence can also be put to use to make high throughput assays such as microarrays which have complete coverage of the whole genome, and thus allow you to make statements that you cannot make with a bunch of random genes.(or highly non-random genes, since most of the human genes we had previously sequenced were studied for a reason) Experiments at the genome level ask fundamentally different questions than experiments at the gene level... a microarray is not 6000 Northern blots! The genome project allows us to ask genome level questions, it may or may not identify more genes for the "one gene one postdoc" crowd.
Yo, this is the second thing that I've seen that confirms my view that we humans know significantly less about genetic science than we thought we knew.
The clones we made of sheep, mice, and other animals resembled the products of buggy code made by lazy programmers or those forced to write shit by insane business models (remember the sig, "it compiles! Ship it!"). We didn't realize the significance of the slow, steady process of genetic replication within the embryo.
Likewise, we hurled gazillions of dollars at the genome project, in private and public searches. Why were the gazillions hurled? Because of the notion that we could find nice, patentable pieces of genetic code, controlling various physiological processes.
Now that we realize we have got a map to nowhere, lets table the whole deal until we understand more about the operation of genes.
I am all for scientific research but I worry that further pushes down this line of inquiry will be driven by the profit motive, not any kind of medical or healing motive.
Goat sex free since 2001
Speaking as as Bio-Chem Bio-Physics student, I think this article was a bit hasty in it's conclusion. We have found 30,000 genes, some of them can make multiple protein through post-modifications, but those modifications are limited somewhat. This is beneficial because understanding of the components that make up the proteins will be advanced if we have more examples of the components working together in different ways in similar or related proteins. Also, just because the 30,000 number is the hot number now doesn't mean we wont find more genes later. Indead, some researchers claim to have found more allready, and many in the field beleive we will find more as we continue to study the genome.
This author should have heeded his own words in saying that we are a long way off from understanding the genome. It's too soon to make many firm conclusions.
"Cheeze it!" - Bender
I don't think the person they were interviewing said anything wrong, i just think the person writing didn't know much about what they were talking about, and/or wanted a good story. While it is possible this 30,000 number means more of our genes are multi-functional than we thought, we definitely knew of a lot that were already.
The Spectator
(I'm paraphrasing...mostly...exclamation points added for effect...mostly):
- DDT is good! It's really good! Rush even talked about it!
- Scripts and Goofs!
- The DNC, Unions, Dem. Davis, and Dem. Hillary are momos!
- Pres. Bush's Arsenic is good for you!
- People for the american way suck! (Psst And they like the Chinese)
- See Bush likes the environment (and he really hates China)! Jesse Helms in Mexico! 30% of blacks in Mississippi want the Confederate flag!
- The damned speak!
- Genes suck! Submit! Submit!
- Clinton took a trip and paid for it himself. The Clintons damaged the white house carpet. The Bush administration doesn't know how to keep track of resumes.
With all those stories I wonder how the genome story will be interpreted? Most likely with the unblinkingly analytical eye of science! Sheesh! I'd rather read a Salon writer compare sub-atomic particles to Survivor contestants for five pages than this pap.Deadly Green
(Mr. Shows "Scams and Flams" comes to mind)
Scripts and Goofs!
Buildings Romance
Poisoner-in-Chief Is Saving Lives
Creepy People for the American Way
The Greening of George W. Bush
(Quote:Amen, brother. Southern is the last endangered species, the last ethnic group it's still OK to taunt. If we must suffer to stem the tide of political correctness, then the slings and arrows of outrageous Yankees will have been worthily endured. And thank heavens we have a south-mouth in the White House!)
Winning in Hainan
Map to Nowhere
Clinton's Pay the Price
"I ain't got no flyin' shoes."
OK, so miracle cures most likely won't come from the human genetic sequence, but it will form a foundation for these cures in the future. Remember the guy that proposed we do all mathematic computation in base 2? I forget his name, but i'm sure some people at the time thought he was crazy....then later....binary computing! Knowledge or research is never bad in itself, it's the spin to attract investors that is really stupid. -ted
This being said, the human genome project is still HUGELY valuable. Is the situation much more complicated than previously thought? Well, so be it: genome mapping is doubly necessary to start to understand that huge complexity. Even if understanding the genetic underpinnings of a disease does not lead immediately to a cure, it holds the potential for greater understanding of the disease's mechanism as well as the potential for earlier detection - and that makes an actual cure or treatment that much closer.
It Is the Nature of Information to Transgress Artificial Boundaries
Forgive me if I'm wrong (and I invite criticism); my study of virii is not very in depth. However, viruses function in a very specific way.
To replicate, the virus injects its DNA into the host cell. The viral DNA then patches itself into the host DNA, so that you have the instructions for building the virii in the cell's chromosome. When the cell divides, this DNA data is copied, and you get multiple cells which create the virus.
However, the patching-in part of the viral replication process is very interesting. Here is an example strand of DNA:
GCGTGCCAGCAG
CGCACGGTCGTC
For the virus to patch itself in, it has to split the DNA where it can. So you'll end up with something like:
GCGTGCCA GCAG
CGCA CGGTCGTC
The single-sides parts of the DNA are commonly called sticky ends, where the viral DNA might patch it. However, the viral DNA has to patch in to a part that matches up with its own sticky ends; A (adenine) pairs only with T (thymine) and C (cytosine) pairs only with G (guanine). You can see that I've followed the pairing pattern consistently (pairs are listed vertically).
For viral DNA to fit into the above example, it must look like the following:
GCGT-GCCA |INTERIOR VIRAL DNA|-GCCA GCAG
CGCA CGGT-|INTERIOR VIRAL DNA| CGGT-CGTC
The viral DNA must have sticky ends that match. For cosmetic purposes, I hyphenated the example and spaced it so the pairs match up. The viral DNA has a left-end sticky end of CGGT, and a right-end sticky end of GCCA. These sequences match up with the corresponding sticky ends of the host's DNA, so the virus can 'patch' in and be replicated.
Now, to relate back to the story: if we have a genetic map, and we learn specifically where AIDS patches itself in, we can likely devise a blocking mechanism. Every three DNA base pairs is a codon for an amino acid, however, many of these codons are redundant; there are 8 (IIRC) different codons for leucine, an amino acid. So, if we could find which codons match up, we could possibly substitute a different codon at the viral injection point, but code for the same amino acid (so as to create the same protein).
Anyway, it's a leap, but most science is, at first.
I don't quite see the logical train of thought involved in getting from a slightly smaller number of genes than were thought to be there being responsible for slightly more proteins than were thought to be there to a supernatural force being responsible for carrying genetic information from one generation to the next.
Of course you should always take American Spectator articles with a grain of salt.
---If you can't trust a nerd, who can you trust?
The Spectator is mentally unbalanced.
And all this crap about not ever knowing how it works is dreadful FUD.
--Blair
"Allele your nucleotide base are bond to us."
If there is a supernatural genetic force, then there's no need for a nucleic genetic force.
--Blair
"Occam is sporting a goat."
My soul doesn't need a shell.
Certainly not a fragile, bulbous, smelly one like this.
--Blair
"Or wouldn't you rather be a pig?"
Although I still enjoy the site, I've been really dismayed over Slashdot's (increasingly?) poor coverage of non-Programming/Electrical Engineering science.
This is terrible. Really, there are great, reliable sites for real science news on the web. Nature, Sci. American, and the NYTimes seems to have decent coverage.
A: None. The Universe spins the bulb, and the Zen master merely stays out of the way.
I respect your beliefs, and think that in many, many ways the modern church is a force for positive change in many societies (although not all good, IMHO).
That said, it is also an organization with an agenda that has evolved sustantially over the years, in response to lost conflicts with science. In every case, the church has lost. Remember, the church held a strict view of the origin of the earth - that it was roughly 15000 years old, and was created in 7 days... That view is held now only by scientifically ignorant people. The church also held that the Earth was the center of the universe, and that the sun, planets, and heavens revolved around us. That was shown to be false (and accepted by the church). The church opposed evolution - a scientific fact which is opposed by groups standing on increasingly shaky scientific ground... I don't need to go on.
I don't think I need to name the speaker of 'Leave unto Ceasar what is Ceasar's, leave unto God which is God's' (I apologize for any misquoting, I only mean to capture the spirit).
Religion deals with the spiritual. If you understand the analogy, religion's place in reality has behaved like the class of statements between provably false and provably true statements in Intuitionistic logic. It is only getting smaller as more knowledge is gained. As scientific knowledge increases, religion can only temporarily give explanations to unknown phenomenon before these phenomenon are explained by science.
I feel that an unnecessary conflict has been generated by religion attempting to dictate fact - fact will be explained by science. religion will not predict the weather, discover a substance that is ideal for artificial hearts, or explain how DNA and protein interact to give us 5 fingers rather than 6. science will never comfort a dying person, explain why hurting someone else is wrong, or help us cope with the nature of self and soul.
Please, your explanation has no basis. Accept religion for what it is, which is wondrous and beautiful sometimes, and accept science for what it is as well.
A: None. The Universe spins the bulb, and the Zen master merely stays out of the way.
It an important argument in any form of discussion like this. Thank you for bringing it up.
I was dying trying to think of the phrase...
A: None. The Universe spins the bulb, and the Zen master merely stays out of the way.
Nobody here's talking about disproving god you little troll. Only that he has nothing to do with the phenotypic manifestation of genotypic traits.
A: None. The Universe spins the bulb, and the Zen master merely stays out of the way.
[The following makes the rhetorical assumption that the parent is not a troll]
...and when we do figure it out, will you recant and become a card-carrying atheist?
...what happens is science does end up solving the problem, and your rational reason for believing in God instantly evaporates.
This kind of "God of the Gaps" argument for the existence of God will get you in trouble. Every time a representative of "The Church" makes the following claim:
"Science can't explain X, therefore it must be the work of a Supreme Being, which therefore must exist."
So what do you do then?
There are other reasons for believing in the mystical, and some of them are much easier to defend. Read about it. That goes for all o'y'all.
>millions of dollars were spent by medical research institutions
;-)) batted an eyelid when the number of genes was estimated at 30,000 or whatever. In fact nobody seemed that bothered about the anouncement of the __draft__ human genome sequence.
>to locate these genetic defects on the genome. Still,
>nothing has come of these findings, beyond the
>patenting of screening tests, which can be used to warn
>couples that any of their children might have a
>one-in-four chance of being born with a disease
This is clearly not true. A number of example exist where gene characterisation has led to treatments. One of the most striking examples being e.g. Phenylketonuria 20 years ago this disease led to complete brain damage at a very early age. Now, with only slight dietary intervention, these children grow up completely normally.
>In the case of cancer, nothing definite has been found
>after a 20-year search.
Furthermore, cloning of cancer genes such as the most common ones for breast cancer BRCA1 and BRCA2 have considerably impoved screening in famalies prone to breast cancer and real improvements in expected lifetime of these patients has been shown.
Basically the article is badly researched and a typical oversimplification of the facts by the press. It seems to make out that the Genome scientists have been trumpeting themselves for years - saying how were gonna cure all human disease and suffering etc. And then suddenly we get the sequence of the genome and we realise it aint so simple and my god we were so wrong all allong. In fact it has been chiefly the media who have been building up Genome Research as The Next Big Thing, and now it is really unsuprising that they are knocking it down. As you may have guessed, this is pretty much my field and nobody i know (except laymen
The truth is that the complexity of life is reflected in the Genome and Proteome and this has been known for a long, long time. The article is correct in that medical breakthroughs have been slow coming from genome research, and yes, companies with vested interest may have exaggerated just a }{ little.
But the article is a load of crap in that there has been no great paradigm shift within the field due to wether we have 30000 or whatever genes.
"...since there are far fewer genes than once thought, the old idea of "one gene, one protein" has fallen by the wayside.
I'd like to get hear an actual biologist a) claim that they ever thought that and b) that the idea is contradicted by the evidence. I'm not biologist myself, but I'm inclined to think that "one gene, one protein" still holds but that "one protein, one phenotypic effect" is out the window (not that it was ever really viable or likely before).
It's all about context. Gene A produces Protein A. But Protein A in "the brain" (read: in the presence of Proteins B, C and D) produces Phenotypic Effect 1 (say, math ability) while Protein A in "the skeletal system" (read: in the presence of Proteins X, Y and Z) produces Pheotypic Effect 2 (say, humped shoulders). I mean, think about it: a single protein is clearly not in charge of, say, your thumb. Many proteins are involved--there's no reason those same proteins can't be used for a different purpose somewhere else.
Example: Somebody finally reverse engineers a F16 fighter plane and produces the "DNA" blueprints. "WTF," we all cry, "there are only 14 different kinds of screws--how can that be??" It would be ridiculous to conclude that when the blueprint says "Screw A1" it might actually be "rendered" as any one of 5 different screw types (as we would have to conclude based on a rejection of "one gene, one protein"). It's much more reasonable to conclude that the inventory of parts used bears little or no relationship to the complexity of the item built.
Think about it: nobody is declaring a crisis of biology because of the fact that we are made of only a handful of different elements. They are just building blocks. So are proteins.
--
324006
Obviously, it is. So where is this extra information located? It is obvious that there must be some other mechanism at work. I would posit that the mechanism is supernatural.
There really is no other explanation. The Church has known this for many thousands of years, and now the scientists are realising it too. The missing information must be supplied by the Holy Spirit. When a man impregnates a woman, the Holy Spirit breathes life into the resulting embryo. At least, this is what we were told in school. In actual fact, it breathes information in, and gives it a soul.
I know I will be labeled a troll for this, and am saddened. But really, the Church has known this for thousands of years, and now we are being proved correct.
This is an upshot because of why? If we have to keep an eye out for mad scientists while we develop the cure for cancer or AIDS, so be it.
my friend you are truly paranoid. this "revelation" only serves to show what we already know: that we don't know jack shit about genes and their like. Afraid of a corporate takeover? C'mon man keep this shit real. WE dont know shit (as is the usual) so "that which does not kill us only makes us stronger"
that does make sence..... however...I think that we may have to explore genetic engineering a little more than most people would want to right now sao any research into that would be well down the road....at least in humans.
-I thought I told you to shut-up before
Looking for the good news? Here it is:
"Nonetheless, Celera's message is not likely to comfort investors. Gene therapy holds out less promise as a result of this new understanding."
That's right, the Rockville MD based company that is busy literally patenting our asses has just discovered that it doesn't know what it's patenting. The whole model of patenting a gene that codes for a protein has fallen apart, since with 10 times as many proteins as genes, we don't really know what genes do anymore.
Hallelujiah.
Theres another point which comes up here. How much radical will genetic cure ultimately become than what it is already ?? I mean western medicine (which is the main part of todays medicine as practised), has tried many techniques to really cure the human body, and still we are as prone to dieseses as ever and will be so for the next n years that I can forsee. But have we really made the alleviated human suffering in any way medically ? Its like saying science will not clear away the bullshit in our lives, it will only make you smell it. This western sciences obssesion with understanding living beings by breaking down the who organism into little bits and parts (like a machine - we often hear the comparison between a human body and a machine - sooo western mode of thinking) is what sets out the understanding levels of east and west medicine sciences. Patentable science is all very good for the large corporates, but not so for the human whole. Eastern science (Homoeopathy, yoga, Tai Chi you name it) all look at the organism as a whole, and treat it as a whole, trying to remedy problems when seen as a subset of the whole LIVING being, and not as 'a gene, a cure therapy'. Its time we looked at the whole throbbing being as a person and treat it as a person, then treat a gene, or a organ like "giving vitamins for your tired legs", or "implants for your sagging breasts", or such divisionist treatment. That would rwally be radical treatment I believe, if adopted and honed by the western sciences capability of meticulous study.
they already found out that the one gene per protien was bogus so they have gotten valuable info already
http://Lenny.com
4 great justice!