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Sorting through DNA
An Anonymous Coward sent in this note: "There's an interesting article at Forbes.com discussing the issues scientists are finding in analyzing and sorting the DNA info now that it's been sequenced. It seems that the functional and useless DNA is all mixed up together. I like this line: "If you want an analogy, think Microsoft Windows: a big kluge of code containing long stretches of old subroutines and dormant bugs and all sorts of other stuff left over from past generations. It shouldn't work, but usually it does.""
I hope you're just trolling, because it's difficult to imagine how someone could refer to the foundation of all future genetic work as "[nothing] truly useful". Why not just say Darwin's theory wasn't "truly useful" either? After all, it didn't solve any human problems either, at least not directly. If the scientific revolution of the past century has taught us anything, it should have taught us that understanding and knowledge of reality is *always* useful, even if there isn't an immediate application.
And besides that, useful (functional) applications of the genome knowledge *have* already appeared. Aside from the obvious (genetic therapies, recents insights into Alzheimer's, and on and on), the anthropological knowledge revealed by what's in the genome is giving a fascinating window into the history of human evolution. Consider: we've found that two people of different "races" commonly have less genetic differentiation than two people of the same "race". Given the history of prejudice, racism, genocide, and other horrors that one population of men has inflicted on another in our history for no better reason than the color of their hair or the shape of their nose, the genome is giving us an education in ourselves that we've desperately needed for centuries. If that isn't "useful" knowledge, then I don't know what is.
That was bad wording on my part. Yes this is fundamental and much much needed information. My main point is the misinformation that seems to be plaguing the mass media seems to say things that are misleading or not even true. With headlines like "DNA As Buggy Code" where they equate a working delicate and so far not well understood strand of DNA to a bloated buggy untested piece of windows code. And you might disagree, but this is just a really small step in the great scheme of things to come. I don't think it should be blown out of proportion. People are going to start thinking mad scientists are out there changing around genetic code willy nilly without any forethought and thats not whats happening.
We don't have a buggy piece of windows code here. We have an elegant masterpiece of genetic material that our only real knowledge of so far consists of an overhead map of which we only the rudiments of knowledge. We've still got a long way to go. And while I agree completely that "understanding and knowledge of reality is *always* useful, even if there isn't an immediate application," I also think that we as scientists and people need to step back a moment and see that our crowning achievement with DNA will only come once we've had sufficient time to study and understand it more. And this is what the human genome project is going to allow.
These "functional applications" from the genome have been, at most, informed but lucky stabs in the dark. And generally, cures for genetic diseases have come more out of the study of cells and living processes than anything. We understand that familial Alzheimer's *may* have something to do with chromosome 19. But biologically we *know* that we can reduce the likely hood or increase the longevity of brain function by reducing the breakdown of acetylcholine in the brain. The current genetic therapies are either extremely slow tedious and nonpermanent or are extremely dangerous as producing a proper vector for gene replacement in living cells is still much in its infancy and we still don't know enough about how it works to really do this well.
And besides this specific article having the few bad analogies, its no different then any of the other news pieces on this same thing. These "anachronistic sequences" that it speaks of are actually our past and there is a lot of good that can come from that information. "It shouldn't work, but usually it does," is one of the most arrogant statements I've heard on the subject. Having so little knowledge of how it works how can we say that it shouldn't work.
This article just left a bad taste in my mouth and wasn't nearly as useful as some of the others that I've read recently. I'd give it a C- if I had read marking pin available.
If something is a mess (buggy code), then there has obviously been random processes at work (i.e. random features, random bugfixes, etc...). Evolution is an example of a random process (it is not entirely random, but there certainly are random elements within it). On the other hand, if something is elegantly carefully crafted, that would mean someone intelligent (i.e. God) would have designed it.
So, if you believe that humans are a product of genetic evolution (which is more or less the only scientific theory at the moment), and you believe that evolution is somewhat random, it would be very hard to explain why the genetic code should not be a mess.
There are examples within programming, that potentially could teach us a lot about how the genetic code works. First let's look at the experiments of genetic programming. Genetic programming is a method of evolving programs by letting programs combine and mutate, where combinations of programs are allowed to "mate" depending on their "fitness" and some randomness. The resulting programs, as you can imagine are not exactly elegant masterpieces, but usually horrendous stupidities, that does things in an awkward roundabout way that just happens to produce the right result (or something that is right most of the time). But sometimes it works, although I haven't heard of many practical uses for the technique.
Genetic algorithms is a similar idea, but is usually applied to optimization problems. As opposed to genetic programming, genetic algorithms actually have been used succesfully for several real-world applications. The idea is the same as that behind genetic programming, but here we use evolution to tune some parameters to find the "best" function. There is no guarantee that the resulting functions after say 10 000 generations is especially good, but with good tuning of the genetic parameters the technique has been found to be useful for some specific problems.
The human immune system does from what I understand look very much like the result one would expect from a genetic algorithm. There are lots of individual parameters that must be fine-tuned, and they interact in non-trivial ways. The resulting mess works, but one could hardly call it elegantly designed, as it is a result of evolutionary processes, not divine design. This very much speaks in favour of genetic algorithms as a model of evolution as it occurs in nature.
When we look at the genetic code, we must (if we believe in the theory of evolution) believe that what we are looking at is the result of billions of years of evolution. While we may not totally understand the process of evolution, we believe that it's results would be mostly like the results of genetic programming or genetic algorithms. Of course, nature might be better at it than we are, or perhaps nature is flawed. Only research can answer basic questions like these.
Conclusion: It is not arrogant to say that the genetic code is a mess. We don't even have to look at it, it is after all what we expect. It is possible that further examination might find that, in fact, the genetic code is well-designed and understandable. I highly doubt that, but we can never rule that possibility out (not even after 1000's of years study, as it can be hard to understand someone elses design, in a very alien programming language).
This doesn't really surprise me, and here's why.
When I took a History of Science course in university, we eventually got to Darwin, and here's how he described evolution. But first of all, I hope you guys know what the Red-Green Show is. If you don't, hopefully you'll still get the idea.
People tend to think of the human body to be like something built by Bob Vila. When there is a percieved need (a new table for the house, for example), it is done from scratch, it is something crafted, measured, and precicely built from an expert resevoir of knowledge. This is not the case. It is much more like Red-Green, where the Handyman has a percieved need, and instead he looks around in his room full of junk and figures out what he can duct-tape together to make a passable subsitute.
So it surprises me little that the DNA is such a mess, we're just duct taping together all the useful junk in our geneitc code.
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