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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."
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.
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.
--
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."
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.
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'
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.
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
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
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.
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.
My theory is that the Kansas board of education cracked Slashdot's slashcode.
;)
That would explain a lot of things.
--Lawrence Lessig for Congress!
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.
"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.
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
Genomics might be that kind of problem.
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."
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.
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.
"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!!!!!!
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.
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.
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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).
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?
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.
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.
Good point! One thing I think you left out is the identification of genes that responsible for those gradual neurological problems like Hodgkins (sp?) or even tweak the immune system a little for all the crazy stuff thats floating around. If we didn't have to rely on exotic plants for medicine and animals for insulin drugs would be so cheap and peace and love and blah blah blah...you get my point.
*IANADoctor
BOSTON SUCKS!
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.
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Jon - TheSpork
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
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."
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.
If there is a supernatural genetic force, then there's no need for a nucleic genetic force.
--Blair
"Occam is sporting a goat."
Flamebait?
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
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?"
[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.
"...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.
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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.
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.