The HP Way

"John Larkin" schreef in bericht news: snipped-for-privacy@4ax.com...

An old war-horse like "intelligent design" - even when lightly diguised as super-clever algorithms embedded in the DNA - isn't excatly intellectually exciting.

There are two problems with the idea. One is that you don't support your claim your DNA *must* have evolved a better evolutionary mechanism than random base-pair damage with any evidence about this mechanism. As far as I know, no biologist has found it necessary to postulate such a mechanism, so your proposition falls to Occam's Razor.

The other is that you don't seem to understand the complexity of the simulation software that would be required to predict the effects of non-random modification of the DNA on the performance of of the organism being modified. The protein-folding problem is already massively non-trivial and NP-hard, and the way the proteins define the structure of the organism is similarly obscure. Now work out how the modified organism will work in the real world, and you've got a set of simulation tools that will let you predict what you will achieve by intentionally changing one base-pair in your DNA.

Anybody who could riff on the idea would be able to see this ...

I've failed to win, in that I haven't your point, nor made you understand my point. I've also failed to stop digging.

Can I list a few points, and see what you agree on?

There are many ways for DNA change other than random base-pair damage. Some, like virus DNA swapping, are fairly accidental. But others of these ways are better, and evolved in higher-order organisms as better methods - sex is a pretty good example. In humans, random base-pair damage occurs much less than in, say, bacteria, as we have evolved better error correcting mechanisms and alternative and more productive sources of variation.

All these mechanisms are random. Evolution is a process of random changes and natural "survival of the fittest" selection.

Any non-random changes would imply guidance of some sort, which requires something/someone which can see the DNA, the effects changes might cause, and evaluate what DNA changes would provide useful effects on the organism as a whole. Humans have started dabbling with such things, with limited success in some areas, and some people (neither you nor I, I think) believe some sort of "intelligent designer" provides the guidance.

I have seen no reason to suppose that random evolution could not have produced the life we see around us. Further, I can see no way that DNA could in itself guide evolution in any way - there is simply no way for the DNA to view the organism as a whole or predict its future - it's not

You have regularly claimed that non-random evolution not only could exist, but should exist or even *must* exist. Yet you have not offered the slightest proof, or even the vaguest theory, as to how that might be the case.

mvh.,

David

In article , Bill Sloman wrote: [...]

God is a 14 year old boy playing Simuniverse and we are all just digital sprites in his PC.

The whole reason that quantum mechanics exists is because the game must fit into RAM. The memory needed to track the exact location of just one electron would be infinite were in not for the trick of making its location fuzzy.

A plausible hypothesis, but not a testable hypothesis. Not original either - Walter Jon Williams in his "Dread Empire's Fall" science fiction series, uses it as the basis of the state religion of the decaying dread empire - see ISBN 0-380-82021-8, amongst others.

Ian M. Banks uses a similar basis for the state religion in his science fiction book "The Algebraist" ISBN: 1841492299, which makes the idea soething of a cliche.

Not exciting? To discover how nature evolved a digital system capable of defining the structure of every living thing on earth? To analyze and ultimately modify a billion-year-developed computing language? A goodly number of Nobels have resulted from studying DNA so far, and it's just the beginning.

Well then, if understanding DNA, curing all disease, living practically forever, and inventing new organisms is dull, what *is* intellectually exciting?

John

Granting that you are an intelligent man, this is a deliberate and culpable perversion of what I wrote.

Understanding DNA - in the broader sense of understanding how the genome creates the phenome - is supremely intellectually exciting, and potentially profitable, though curing all disease and living practically forever probably aren't on the agenda for a few years yet.

What isn't exciting is looking for some kind of supernatural construct in the DNA - something clever enough to understand protein folding, how the folded proteins influence the development of body and behaviour, and how the developments of body and behaviour influence fitness in an evolving workl (give or take an asteroid impact or two).

Reduced to its logical constituents, this is just creationism, with an omniscient creator embedded in the nucleus of every human, more likely every mammalian cell. Polytheism on a grand scale - intellectually amusing. perhaps, but not to be taken seriously.

There's nothing supernatural about state machines.

John

No, but a state machine that could use "sophisticated meta-mechanisms that themselves drive evolution more efficiently than random base-pair mutation" would have tobe prescient, and that *is* supernatural.

Incidentally, mutations in human and other primates aren't primarily driven by mutations in individual base pairs, but by the random insertion of specifc relatively short segments - mostly Alu segments.

There's nothing very clever about it - the insertions are still much more likely to kill the cariier than to do them any good - but it does seem likely to be producing a higher (if still very low) proportion of viable new proteins than does changing individual base pairs.

levels

Sorry, that makes no sense to me. A Pentium isn't conscious, but it can do some pretty spiffy things, like run thousands of optimal, adaptive control loops simultaneously, or simulate structures, or (if anybody supported it) test subroutines and drivers in protected mode before installing thaem.

That's my point: whenever higher-level DNA constructs are suggested as being likely, or even possible, everybody screams that the suggestions are religious and unscientific. The only mechanisms that should be discounted as impossible are those that violate fundamental physical law. But complex algorithms violate no rules of nature,and we know that simple algorithms can generate complex algorithms, so the bootstrap is there.

Random mutation is a religious cult, a closed-minded belief system.

And if you're prescient, what makes it impossible for your DNA to be prescient, too? Other than your prejudice, of course. It's just a bunch of chemicals, but you're just a bunch of chemicals too.

"However, evidence has been emerging that lurking within junk DNA are armies of transposons (mobile genetic elements) that play an indispensable role in ?natural genetic engineering? the genome. They make up nearly half of the human genome, and serve as ?recombination hotspots? for cutting and splicing, and hence reshuffling the genome. They are also a source of ready to use motifs for gene expression, as well as new protein-coding sequences."

Yup, that's the sort of stuff I mean. It's not much more than hinted at, at our current level of understanding. DNA is a hell of a state machine.

Then why wouldn't we evolve "mutation" mechanisms - gene activations and substitutions, for example - that tended to not kill the carrier? They would be more like structural experiments than shotgun blasts. Would that be supernatural?

John

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intellectually

Sure it can, but it is no better than the data it is working on, and there isn't any mechanism for getting useful data back into the DNA for the algorithms to crunch.This is basic systems egineering,

Without the information to crunch, the spiffiest algoritm is still Baron Munchausen pulling himself out of the bog by pulling at his bootstraps.

Scarcely. Give them evidence and biologists react as fast as any other scientist - which is to say, cautiously. Check out the history of prions and of jumping genes sometime if you want to see how orthodoxy gets turned over.

Well if I - or anybody else - were prescient, we'd be in a wholly different ball game. Parapsychologists have been looking for evidence of prescience for a long time now, and the answer - so far - is a big fat zero.

Yes. It would. The genome has no way of knowing what a gene does, so it has no idea what it might be substituting or activating.

All the transposons do is muck up genes by breaking them up in relatively large chunks, often at the boundaries defined by introns and exons, so the random products of this random process look more like working genes than the variants produced by single point polymorphisms. It is still a process that produces millions of duds for every (usually minor) improvement, but evolution can be relied on to get rid of the duds, so who cares - not our intelligent designer, obviously.

Right. Things could have started that way. And bacteria are a lot more numerous and "expendable" than, say, mammals, so bacteria can do fine with random mutation as the source of variation.

Doesn't DNA itself evolve? And why wouldn't it evolve better mechanisms of evolution itself? Your last sentence is equivalent to declaring that you don't believe in evolution. Well, I do.

You accept that the creatures defined by their DNA evolve; what's so hard to accept about the idea the functionality of DNA is *itself* subject to evolution?

It's the most complex thing on the planet. If I survive a virus attack, my immune system learns, usually for life, to recognize that virus and immediately attack it. That becomes encoded into my immune system's cells somewhere. Why not pass that along to my sperm cells, so my kids can take advantage of it? If that mechanism is even possible, it would be very strongly selected for; and it's certainly not impossible.

Why did the 1918 flu die out?

They will remain philosophical until someone does serious research to find examples. Meanwhile, they are heretical, hence hard to fund.

The theory is called "evolution." And yes, it's still vague.

I'm not a biologist. But I do believe in evolution, and evolution selects the mechanisms that work best.

John

Again I ask, have you the slightest hint of any evidence to the contrary? As Bill said in another post, scientists will react when the see evidence. It had better be dramatic evidence before it will sway the mainstream, but I'd be happy to hear of anything you can come up with.

DNA evolved - the evidence that it has changed over time can be seen in the occasional organism that uses a different base molecule, even though most have settled on the standard four letters. Mechanisms for copying and changing the DNA have also evolved. But the idea of evolution - changes through random mutations and selections - is in a different category altogether. The concept exists independently of life, and can be applied to many other things. It is not something that developed or evolved from or with DNA. What you are suggesting is some mechanism beyond evolution. I'll grant that just because neither I nor any biologist can think of any plausible mechanism, it does not mean that it could not happen. But there is no need, no reason, and no evidence for such a concept. To a scientist, there is therefore no reason to pursue the idea further.

Here's a suggestion for you to think about. Suppose there *were* some way for DNA to discover flaws in its surrounding organism, the deduce changes that could improve on these flaws, and make these changes to itself. That would be very much more resource-intensive than the "normal" DNA work of providing protein patterns, duplicating cells, and the like. You would require some very specialised cells to do this work (having it in every cell's nucleus would be grossly inefficient), with much more activity than other cells, and with all sorts of feedback mechanisms for monitoring the organism as a whole. Call it naive faith in science, but I think if such a system existed, someone would have noticed.

If, however, you dispel the requirement that this is all directly involving and controlled by the DNA, then the answer is obvious. It's called sex. Animals actively choose mates based (partly) on a desire to produce offspring that are better than the current generation.

We know a great deal about DNA, actually. There is a lot more still to learn, especially in biology in general, but a lot of the fundamentals about DNA are understood.

It is possible - but not for you. Certainly your immune system learns, but that information is not passed along in sperm cells (it's your immune system that learns, not the sperm cells). It's a very different matter for women - there are all sorts of mechanisms for passing information on to their children in addition to inherited nucleic DNA. There is DNA and other bits and pieces in the egg cell outside the nucleus, and the kid spends nine months swapping blood with the mother. After that, they get a lot of antibodies (and therefore inherit some of the learned wisdom about diseases) through their mother's milk.

In other words, what you are suggesting is not only possible (although from the mother, not the father), but occurs all the time. It is, however, not at the DNA level - there is a great deal more to defining an organism than just its DNA.

I don't know exactly - there are many things that influence the comings and goings of epidemics. But if you have some idea why the question is relevant here, then let me know.

People do "heretical" research all the time. It generally requires a higher standard of evidence to get mainstream scientists to pay attention, but if your theory is worth pursuing, someone will look into it sooner or later. Meanwhile, I am still waiting to hear any hint of evidence or research - even if it is not serious.

It sure doesn't look planned.

I'm sure that there are creatures around somewhere who would look like gods to us, if we ever came in contact. I'm equally sure that the gods that regular religions pray to don't exist - they are the "spanish prisoners" in the oldest con-trick in the world.

There does seem to be some kind of deformity in the human brain that makes us excessively willing to believe in gods - I've certainly got it

- but the hard evidence doesn't exist.

Check out Daniel Dennett's ''Breaking the Spell: Religion as a Natural Phenomenon" - I've not read it, but the reviews suggest that it covers the ground pretty thoroughly.

We have viable samples of the 1918 virus. It was very contageous in

Lots of such experimants can be imagined, if you let yourself. Not many are being done.

John

That's the only point of view we know anything about

Dan Dennett has done the honework on this, and I've yet to read the book. The discussions I've seen have been mre interested in the human tendency see patterns of planned behaviour in random coincidences. It is obviously better to entertain 100 cockanamy conspiracy theories than to miss one real conspiracy, so we have a built in tendency to detect moving spirits that don't really exist.

Most of the documented "miracles" that I've heard of come down to spontaneous remissions, which occasionally also happen in people who haven't asked for divine intervention.

Do you have any examples of miracles expicable only in terms of divine intervention?

I'm currently reading it, at about page 103. It's got a slow start, so far, but seems to finally be moving towards his goals.

Jon

"The lethality of that virus was actually very low"

In what sense? It was unusual in that it killed the strong, rather than the weak.

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