DNAunion

DNAunion: Thanks for the new info: I am adding it to my personal notes.

I have three comments. First, the subfunctionalization model as offered in the abstract you posted is apparently a relatively recent scenario, judging by the following.

DNAunion: Second, the abstract you presented uses the term subfunctionalization for duplicates differently than does the Science article I quoted from above.

DNAunion: However – and this is my third comment – “your” logic looks sound. That is, regardless whether it is a new model or what discrepancies in terminology exist, I would not argue against the notion that a typical enzyme performs one function very well and other functions to a lesser degree, and that one copy of a duplicated gene could diverge from the other to a point where its product performed one of the originally lesser-well-done jobs more efficiently and so would be tend to be retained by natural selection.

[ February 03, 2002: Message edited by: DNAunion ]</p>

theyeti

There is an article about this in a recent issue of Nature Reviews Genetics (dec. 2001 v. 2 no. 12 pp. 919-929) entitled Non-coding Genes and the Modern RNA World. But it talks about RNA encoding genes and does not mention introns unless I overlooked it. I don't know that the lariat structure of spliceosomal introns would be capable of having the regulatory role that these RNA genes have; I think the intron lariats are quickly degraded by RNAses, though I don't remember. Interestingly, I didn't see Mattick listed in the references of the Nature Reviews Genetics article. Here's a passage that I found neat:

theyeti

theyeti

DNAunion: thanks for those refs. I will download the Science article when I get a chance. As for the Patthy ref, is that a book? If so, do you know where it's available? I admire Patthy's work; he's got a good review on exon shuffling in <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=105709 89&dopt=Abstract" target="_blank">Gene</a>. You can get the fulltext somehow, but I don't remember how I got it.

theyeti

DNAunion

DNAunion: All of that is part of Behe's position. He does not deny (1) that the Earth is 4.55 billion years old, (2) evolution by natural processes, (3) common descent, or (4) that humans evolved from non-humans. His version just has some unknown assistance from time to time (okay, insert knee-jerk reactions here!). It is something like theistic evolution (which is widely accepted), except it isn’t like it (makes sense, huh).

And the type of design I favor would be indistinguishable from mainstream biological evolution. As opposed to a purely natural origin of life here on Earth, I favor an intelligent design of life as we know it - followed by seeding - by an ETI civilization of a completely different form of life (okay, insert pre-formulated ridicule here!).

So although I am not saying that any “design theory” has substantial evidence supporting it at this time, I don’t think it would be fair to imply that the our knowledge of evolution is inconsistent with all “design theories”.

DNAunion

DNAunion: Yes, it is a book. I personally got it from my membership in the "Library of Science" (a science book club featured in Scientific American). It might be available at Amazon.com (which actually has a good selection of science books: I bought the "The RNA World: Second Edition" from Amazon).

theyeti

I don't find the idea ridiculous, but it does have its problems. Namely the infinite regression problem (i.e. who designed the aliens?). If you're talking about front-loading, I think that carries with it a number of additional problems as well, and I'll try to post them after the Superbowl if I'm not too drunk. But general panspermia is quite viable IMO.

I don't necessarily think so either, but the DI type people apparently do. I don't think that Behe is that wacky, but he is closely associated with people who are. Intelligent Desing per se doesn't really bother me. It's when it's combined with an agressive "Darwin-hate" and an obvious ideological motive that I get irritated. I would like people like Behe better if he would disassociate himself with the DI and be more upfront about the extent of evolution that he accepts. In other words, I would like to see him rebuke Philip Johnson.

theyeti

lpetrich

I actually agree with that assessment. I have no objection with extraterrestrial-visitor design being advocated as a non-either-or alternative to natural selection of non-designed variations. It would be difficult to demonstrate that there was never any extraterrestrial meddling in any Earth lifeform's genes; the most one can reasonably expect is to be able to demonstrate that that is an unnecessary hypothesis.

Furthermore, if some features and adaptations were designed, their deficiencies and inelegant features could be a result of the finite capabilities and fallibility of their designers.

DNAunion

DNAunion: I don't want to sidetrack this thread (though it looks like I unintentionally have already). I will make one last post on this here.

I believe there is a possible resolution to the infinite regress problem, but it is speculative.

First of all, I truly believe that within the next 100 years we humans will have designed and created robotic life. We have already designed robots that design other robots - based on the laws of physics and the goal of mobility alone: no details or plans provided. These same robots then physically constructed their own designs (with humans having to play only one role at the end) and the resulting robots functioned. In addition, humans have designed and created hardware that evolves (I have notes on an experiment involving the evolution of FPGAs: field programmable gate arrays). And as a general point, look at how far personal computers have come since the IBM PC was introduced in 1980: it had no floppy drive or hard drive, and had a CPU slower than a snail, a monochrome monitor capable of displaying text only, the user could interact with it only through a command-line prompt (no GUIs with icons or mouse support), had only 64K of memory, had a single-user single-tasking operating systems, etc. Shoot, going back to 100 years ago, an electronic computer of any type was “science fiction”. But look where we are now! All the while, our understanding of what the very fundamentals of being alive are have increased, as have our attempts – and desires - to create life. If the current trend in technology continues, I fail to see how we could not have created robotic life by the year 2100.

You might say, "Okay DNAunion, let us say we agree .... what's your point?"

Let me now move to science fiction to make my point. We fast forward through time to the year 3100: one thousand years after robotic life arose. Being superior to humans in every respect (physically stronger, physically faster, physically more accurate, able to retain more information, able to access more information, able to access information faster, able to communicate faster, able to process information faster, able to evolve in the much more efficient Lamarckian "inheritance of acquired traits" fashion, being fully mature at the time of birth, potentially capable of immortality, etc.), robots took over the world in a "Terminator II" scenario. Way before 3100, humans were things of the past: useless bits of information consuming precious memory locations. So we were wiped out of the robots memories to make room for more-meaningful information (such as pi to one billion decimal places: every robot needs to know that).

But after 1,000 years - in 3100 - robots have pretty much finished empirical science. There's basically little else to do, and so a strange new type of thinking arises: "philosophy". Robots start pondering things such as "Where did we come from?". All robots admit that they are extremely complex, even the simplest imaginable autonomous robot - and that poses a problem.

Some robots are stumped and so say that a great magical robot in the sky must have created them. But they are ridiculed. It is pointed out that every operation that occurs in a robot is explained completely by the known laws of nature. There is no magic in the computation of pi to a billion decimal places, nor in the retrieving of an instruction from memory, nor in the addition of two values in an ALU, etc. So since purely natural processes account for every operation that occurs in extant computers, there is no valid reason for assuming a magical robot was needed in the past.

That argument convinces some robots, but not entirely. They point out that how something operates now does not explain how it arose (in fact, the other robots - from above - cannot come up with a convincing explanation for the origin of robots by purely natural processes alone). So the robots reject great magical robots but do not hold to completely natural processes as being capable of producing the first computer from scratch. Perhaps a nonmagical intelligent agent constructed the first robot, and from there on, everything evolved according to standard purely natural processes. But the only intelligent agents known are robots, so where could that designing robot have come? What created the creator? Something must have created that robot, and that creator must have been a robot too (since that is the only form of intelligence capable of creation), and so on, and so on, etc. An infinite regress. So this idea is also discarded by most.

But some holdouts consider what happens if a different form of intelligence is introduced into the hypothesis. Perhaps it wasn't a robot that created the first robot, but a completely different form of intelligent life. That way, it would not have the same level and/or same kind of complexity as robots and so may not have faced the same hurdles in arising by purely natural means alone. Maybe, but then how did that intelligent agent - whatever it was - come to be? Well, since it could have a different level of complexity and would not have to be built upon silicon circuitry, perhaps - unlike robots - it was simple enough to have arisen by purely natural processes. And if not, now that the idea of one form of life being designed and created by a completely different form of life has been introduced, then these contemplating robots can carry on this thought process back just one more, or maybe two or three more, steps into the past, each time relying on a form of life that is based on simpler constructs until one is reached that is simple enough to have arisen by purely natural means. So, for example, one simple form of life arose by purely natural processes, evolved to a level of intelligence capable of designing and creating another form of life, which then eventually designed and created robots: all without invoking magic. It is a climb up a 2- or 3-step complexity ladder.

Such a robot would be onto something. In the science fiction story being told - which has the first part built upon valid extrapolation of current technology into the future - it would indeed be the fact that robotic life was designed and created by a form of life completely unlike itself: we humans.

Of course this is pure speculation, but I don't know of any evidence or scientific knowledge that can actually fully reject the notion that life as we know it (let's say carbon-based, cellular life) could not have been designed and created by a completely different form of life (which could have started off extremely simple and then evolved intelligence) on another planet that then intentionally seeded that life here on Earth.

Okay, I am done hijacking the thread.

But the way, my free time was just for the weekend. I probably won't post much here again for some time (I'll likely be spending any free time I have for the internet debate at ARN).

theyeti

Wow, that was some Superbowl. Fortunately, I didn't do any drinking. I'm going to start another thread about what I see as the problems with front loading, and I hope you'll stick around long enough to give me some feedback.

As for this issue, well, I guess that's one way to avoid the regress problem, but it is a bit odd. First of all, the fact that something must be evolving naturally should make us suspect that we can too. Unless there's massive evidence that we cannot; such "evidence" difficult to get because it takes an exhaustive search through all possiblities. Of course, that's the nature of the debate -- I don't think there is such evidence, but IDers would disagree. At the very least though, the "we evolved naturally" hypothesis should be the default unless the other has strong evidence favoring it (parsimony and all that jazz). Another problem I have is with considering our "designer" to be less complex than ourselves. I doubt that something could be much less complex and yet still have the level (or higher) of intelligence that we have.

But the robots should have access to evidence that we were around to create them. Some fossils, ancient cities, or some sort of trace that would be detectable. If we had evidence that there are/were aliens either here or elsewhere with the wherewithall to create life, then the ETI interference hypothesis would be perfectly legit. Until then, as you say, it's just speculation. But it also requires additional assumptions to explain why we don't have evidence of the aliens (of course, that evidence might pop up at any minute). And when you have to make a lot of additional assumptions, you start to piss off Ockham and he goes for his razor.

theyeti

Kevin Dorner

I don't like the "seeding" hypothesis as it's not only speculative, but as it can't be tested, the aliens might as well be gods for all the explaining it does.

The other problem is: it's completely unnecessary. If there were a place for abiogenesis to have occurred, the early earth circa three billion years ago was the place for it. Earth had (and still has in most cases)

• Sufficient atmosphere to prevent the oceans from boiling away, to hold heat in, and to capture water vapor allowing rainfall.
• A reducing atmosphere, as the oxygen component has been accumulated due to plant activity and would not have been present then. Fragile, newly formed and unprotected organic molecules are shredded in oxidizing environments.
• A range of temperatures that allowed liquid water of much of its surface, an ideal (some would say required) medium for life to form in.
• Plenty of water, over most of the earth's surface.
• Tides, which regularly carried water onto the land and deposited it into tidal pools, a possible origin of life.
• Active crust causing hydrothermal vents in the oceans, another possible source of life.
• Close enough to its star for warmth, but not enough to be tidally locked (as the moon is; one side always faces earth.)
• Sun is a stable main-sequence star, not too large or small.

Now, I am certainly not arguing that the earth was designed this way, but rather that life exists on earth because it was perfect for the formation of it, and does not exist on millions of worlds that are not perfect. To argue otherwise is again to invoke the unnatural.

I could entertain (but not accept) a seeding hypothesis if and only if there was something about this planet that was not conducive to abiogenesis. Maybe we were seeded by aliens, but they had to form somewhere, or their seeders did.... abiogenesis had to happen at some time and place, and it could not have been much more conducive than the earth three billion years ago, so the seeders are unecessary.

[ February 03, 2002: Message edited by: Kevin Dorner ]</p>