Re biological Rube Goldberg: I disagree vehemently. The more I learn of DNA, RNA, proteins, signalling, etc., the more impressed I am. Biologic systems have an incredibly sophisticated coding system that enables a lot of redundancy (coding distance) when it is needed, yet it also allows for a limited amount of change so evolution can take place. Remember, these biologic systems are really _small_, and they are operating at 300K. Ask your friends in the computer chip industry in a few years how complex their lives become when flip-flops go flap-flub-flux-flax-... For example, the process of mere _copying_ of DNA operates very close to the thermodynamic limit -- i.e., it would be very difficult to design _any_ system for copying DNA that produced less waste heat than our own DNA copying. DNA copying is operating so close to the limit that it copies "2 steps forward; one step back" -- i.e., it is very close to being a _reversible_ chemical reaction. Only at the very end of the copying, when the DNA end has to be tied off, does the system invest 10kT or so per bit to irreversibly finish the job. If our DNA copying were any less thermodynamically efficient, and we continued to copy at the same rate, our dividing cells would fry themselves like a fried egg. --- Most evolutionary biologists will tell you that _none_ of the DNA is truly "junk". The proof: if it weren't important, it would relatively quickly disappear after a few generations. Several biologists have proposed that complex organisms have lots of DNA as a form of "diagonalization": all of its siblings with less DNA didn't survive. This is akin to comparing the power of Turing Machines with more or less tape: those with "more" tape can simulate _all_ Turing Machines with "less" tape and do something different. For example, some of our DNA encodes experiences with viruses, some of which may be long extinct or at least dormant. Yet if that virus suddenly shows up, there are at least some fraction of humans that will survive. I think that the plague killed a majority of the population of some parts of Europe, but there was enough of a genetic reservoir of techniques to deal with this disease, that it didn't completely wipe out the human population. So whichever humans remained, their DNA (which remembered enough techniques to survive), was passed down & inherited by modern day Europeans. Plants (which typically don't move) seem to require more DNA than animals (which do move). One can speculate that plants have to sit there and take every insult, while animals can avoid the insult by moving and even emigrating when necessary. Viruses & other small pathogens make up for their lack of DNA storage by being able to evolve quickly. Another way of looking at this is that for these creatures, the genetic memory is stored in their entire _colony_/species, rather than in every individual. Once again, there is a very sophisticated redundancy mechanism to "remember" important advances in the collective genome. ---- Re "junk" coding in software: Every software engineer is aware of the "commented out" portions of code that they don't bother compiling, or at least don't bother running. This commented out code usually pertains to different versions of hardware, different operating systems, different (human) languages, etc. I.e., exactly the same sorts of things that "commented out" portions of DNA would concern themselves with. For example, some animal species can regenerate limbs, while humans cannot. Yet it is likely that much of the "code" for regenerating limbs continues to exist in humans, but was "commented out" at some point -- probably because it never got properly debugged before the specials was "released". Another example: some organisms can go into fully suspended animation -- e.g., to make it through a 50-100 year drought. I would guess that a significant amount of the DNA required to do this feat still exists within humans, but since it hasn't been used for hundreds of millions of years, it isn't likely to work very well just now. We do know that humans _almost_ have the same capacity to go into cold hibernation as some of their mammal cousins: the proof is that some small fraction of people who inadvertently get frozen will wake up and fully recover. The fact that not every human can do this simply requires a bit more debugging before this "feature" can be advertised in the next "release". The good news is that even if only 1 in 1,000 people can survive this, there will still be a handful of people left to carry on the human race after a global cold snap. At 11:45 AM 9/6/2012, Dave Dyer wrote:
The whole biochemistry of life is the most complex Rube Goldberg system in the known universe. Anything that doesn't break the machine completely is just carried along in the next generation of the design, and every eon or so a closet full of "junk" gets opened and a new use is found for the stuff.
One of the main mechanism in evolution is accidentally duplicating a bunch of stuff, which creates spare copies that are not really need. These spares are free to become nonfunctional, and then to acquire new functions, given geologic time.