A Map to Nowhere? 191
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."
Re:And... (Score:1)
Re:Object complexity != design complexity. (Score:2)
And in the case of some guys, really really small.
Re:So where does the information come from? (Score:2)
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.
Re:How does Dawkins feel about this? (Score:1)
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?
History repeats itself? (Score:2)
Re:Map to NOWHERE? (Score:2)
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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Re:Map to NOWHERE? (Score:3)
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."
Re:So where does the information come from? (Score:1)
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).
Re:Towel throwin' time. (Score:2)
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.
Re:So where does the information come from? (Score:3)
In the service packs!
How many sequences so far ? (Score:2)
Re:So where does the information come from? (Score:1)
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?
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This is a Spectator editorial; not science (Score:1)
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 [spectator.org] includes articles that make even moderate conservatives queasy such as More Money in Politics, Now! [spectator.org] 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 [spectator.org].
Ben
Or, the simple answer is... (Score:1)
My personal Buddha is laughing (Score:1)
My personal Buddha is laughing.
Re:Optimism was based on over-simplistic model (Score:2)
Surfing the net and other cliches...
Re:So where does the information come from? (Score:2)
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 [bu.edu].
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?"
OT: That FPGA experiment. (Score:1)
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]).
These results are wonderful - we're modular. (Score:2)
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.
Re:Not so fast (Score:2)
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.
Object complexity != design complexity. (Score:5)
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.
All hope is not lost (Score:2)
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.
AIDS genes known for 14 years (Score:2)
We know so little about biochemistry, really.
mammals are more complicated (Score:2)
Re:Map to NOWHERE? (Score:2)
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.
Re:Map to NOWHERE? (Score:2)
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.
Re:Object complexity != design complexity. (Score:1)
In fact, since the preservation of information does impose an evolutionary burden you'd expect it to tend towards a minimal data requirement.
The more data that is required for a functioning organism, the more that various replication costs and error correction become expensive. The encoding may be large, for redundancy and the like, but the information stored in that encoding should tend towards the smallest it can be (but no smaller).
American Spectator? (Score:1)
How sure are they that they've found them all? (Score:2)
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
Re:The gene / protein disparity. (Score:1)
Re:So where does the information come from? (Score:1)
Re:Map to NOWHERE? (Score:1)
One Gene One Protein? (Score:1)
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.
Re:One Gene One Protein? (Score:1)
In response to exotics plants etc....Yes, it is very possible to engineer plants or bacteria or yeast to produce drugs for us much more easily and cheaply enabling them to be more available to a wider audience. You only have to look at the sub-Saharan countries and their AIDS epidemic to see one possible benefit of cheaper drugs.
Nova on PBS (Score:1)
Re:Map to No where? I don't think so... (Score:1)
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
<P>
LL
Re:So where does the information come from? (Score:1)
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.
The big Deal? (Score:1)
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.
Re:Not so fast (Score:1)
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...)
genes and behavior (Score:1)
Protein Map (Score:1)
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.
Re:So where does the information come from? (Score:2)
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 %-)
The article is right (Score:2)
Re:two words: data compression (Score:2)
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...
Re:So where does the information come from? (Score:2)
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
Re:BULLSHIT (Score:1)
The rest of your comment seems sound enough, but there is no way scientists can know what a mouse's perception [dictionary.com] 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!
Self-Negating Criticism? (Score:1)
Re:So where does the information come from? (Score:1)
Ah yes, a true troll would NEVER claim to be troll. Well done moderators!
Take your foot out of your mouth. (Score:1)
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.
The gene / protein disparity. (Score:5)
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.
-cRe:Map to NOWHERE? (Score:1)
Re:I'd have to disagree (Score:1)
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.
Re:Object complexity != design complexity. (Score:1)
Re:So where does the information come from? (Score:1)
Think about you're C compiler ..... (Score:2)
Re:So where does the information come from? (Score:2)
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.
What about the insulin gene (Score:2)
Highly Factored Data (Score:2)
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."
Optimism was based on over-simplistic model (Score:5)
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!
Re:So where does the information come from? (Score:2)
That would explain a lot of things.
BULLSHIT (Score:5)
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.
In other news, 1903 (Score:2)
"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.
two words: data compression (Score:2)
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.
Look at the mess in computational chemistry (Score:3)
Genomics might be that kind of problem.
Map to No where? I don't think so... (Score:2)
Nathaniel P. Wilkerson
Domain Names for $13
Re:Towel throwin' time. (Score:5)
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."
Re:Map to NOWHERE? (Score:2)
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.
We've known this for some time (Score:5)
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.
this is a stupid argument (Score:2)
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.
Re:So where does the information come from? (Score:2)
*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.
Re:So where does the information come from? (Score:2)
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.
Re:So where does the information come from? (Score:2)
Re:Overreacting (Score:2)
"If a program can't rewrite its own code, what good is it?"
--
Re:Where is everything then? (Score:2)
Why, it moved to Everything2 [everything2.com].
--
Re:I love this .. (Score:2)
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.
Re:two words: data compression (Score:2)
That said, I have a few comments on your analysis. For the most part, I agree. But you left out the problem that every coding sequence must have an in frame start, and an in frame stop codon. Thus, while it's POSSIBLE you could have ABCDEF, ACDEF, ABDEF, ABC, AEF, it's more likely only one or two would actually contain an in frame stop codon. It's also theoretically possible to have all in order permutations of ABCDEF: ie. BCDEF, BDEF, BCD, BCDE, CDEF, CDF, etc, but again, two codons are required to exist in the same frame, and this makes the possibility of high numbers of proteins from a single strand very unlikely. It's more likely that 2 or 3 proteins can be coded from any single strand of DNA.
Serious Doubts? (Score:2)
Please read their article [spectator.org]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!!!!!!
Nova on recent DNA discoveries, west coast, NOW (Score:2)
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.
genetic OOP, metalanguage, it's in the proteins (Score:2)
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.
---
Re:Map to NOWHERE? (Score:2)
Not so fast (Score:3)
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?
Map to NOWHERE? (Score:5)
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.
Absolute nonsense (Score:2)
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.
Overreacting (Score:2)
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.
Re:One Gene One Protein? (Score:2)
*IANADoctor
Re:Towel throwin' time. (Score:3)
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.
I love this .. (Score:2)
--
The human genome was not sequenced to find genes. (Score:2)
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.
Towel throwin' time. (Score:2)
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.
Know your Source:Top Ten Stories on the Spectator (Score:3)
The Spectator [spectator.org]
(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 [spectator.org]
(Mr. Shows "Scams and Flams" comes to mind)
Scripts and Goofs! [spectator.org]
Buildings Romance [spectator.org]
Poisoner-in-Chief Is Saving Lives [spectator.org]
Creepy People for the American Way [spectator.org]
The Greening of George W. Bush [spectator.org]
(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 [spectator.org]
Map to Nowhere [spectator.org]
Clinton's Pay the Price [spectator.org]
No New News (Score:2)
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.
Actually, the genetic map could tell all for AIDS. (Score:3)
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.
Re:So where does the information come from? (Score:2)
--Blair
"Occam is sporting a goat."
Re:..."Whispered the Washington Post"... (Score:2)
Never. I was dead serious. Genomics is a simple syllogism. Gene sequences A acts in time sequence B and environment C to produce Protein D. And all higher-order set combinatorics of sequences and environments and proteins. Listing the genome was just a start. What follows will simply require some real computing power.
The Spectator had no business pretending that the Washington Post can whisper, and it had no business spreading FUD about the ability of genomics to succeed in determining the detailed mechanisms of genetics.
--Blair
Re:So where does the information come from? (Score:2)
Certainly not a fragile, bulbous, smelly one like this.
--Blair
"Or wouldn't you rather be a pig?"
Re:So where does the information come from? (Score:5)
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.
not necessarily (Score:2)
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.
--
So where does the information come from? (Score:3)
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.
And... (Score:2)
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.
Looking for the good news? (Score:3)
"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.