[Paleopsych] genetics as an intelligent system
Val Geist
kendulf at shaw.ca
Tue Nov 30 17:46:54 UTC 2004
Dear Howard,
I am about to head for the airpot. However, on the "genetics as intelligence etc.": treat retrovituses a classical parasites, but parasites of chromosomes. Much will fall painlessly into place! Cheers, Val Geist
----- Original Message -----
From: HowlBloom at aol.com
To: paleopsych at paleopsych.org
Cc: dranees at compuserve.com
Sent: Friday, November 26, 2004 8:18 PM
Subject: Re: [Paleopsych] genetics as an intelligent system
Instead of "metagenetics", can I offer an alternative term--geneteams. How do gene teams work together to learn to learn? Which brings us to some other questions whose answers I've been trying to pin down.
When did the full suite of modern atoms--the 92 natural elements--become complete? Did the full panoply of modern atoms arrive after the collapse of the first meg-stars, stars that swelled, ignited, then died off very quickly? That first period of star death would have been a mere two million years after the big bang.
Or did the complete suite of modern atoms have to wait six or seven billion years until several generations of smaller, longer-living stars had collapsed?
More important, when did the first carbon-based MOLECULES appear in this cosmos? We know many of the details and the timeline of nucleogenesis--of the genesis of subatomic particles.
But the term "moleculogenesis" doesn't yet exist. Nor does the concentrated study of this topic. At least I've been able to find nothing about it on NASA's absolutely terrific resource, its Astrophysics Data System --http://adsabs.harvard.edu/default_service.html.
Another question. At what point does learning and memory first appear in the evolution of the cosmos? Is an atom of iron a summation of a big slice of the history of the cosmos? Has it survived one catastrophe after another, thus demonstrating its adaptive hardiness? In other words, is there memory, learning, and projection of future possibilities at the inanimate level?
Then the big question. How long did it take after the genesis of the first simple carbon-based molecules before those molecules learned how to condense information from the past and aim toward an imperialist goal--to take over as much inanimate stuff as possible and turn it into biomass?
Competition first appeared as atoms--brand new things in 380,000 abb-- discovered gravity. Greed first appeared when clumps of matter competed to become galaxies, stars, planets, and moons.
But there was something new about the greed of massive teams of atoms arranged in twists that could replicate. There was something new about the hunger of the dna-and-cell based teamwork that generates the incredible variations that contribute to the spread of biomass.
Paul's words suggest that restlessness and boredom have been a key part of this learning system. I've been calling this a restless cosmos, a driven cosmos, an obsessive compulsive cosmos for a very long time. But Paul is suggesting that we make computer-based learning machines restless too. That we make them try out new possibilities just for the hell of it, just to evade the pain of boredom, the pain of staying precisely the same, the pain of ennui. Paul is on the brink of suggesting that we make computational programs hunger for pop culture, for music and games that test and expand the silicon brain in new ways.
Paul is suggesting that genes may be as restless and boredom-prone as Baudelaire, who painted ennui as the ultimate pain. He's suggesting that on the sly, when they're not working, genes play around and dance in leisure time. Or at least that's what Paul's ideas inspire in me.
I know that leisure, entertainment, pop culture, art, and play are not useless. I've known it since I began my 20 years of fieldwork in these fields--poetry, art, magazine publishing, and finally popular music. Paul seems to be whispering to me that these cultural expressions may be a stochastic search for new possibilities. And his words suggest to me that genes play games too. They play the sort of musical games--establishment of a theme, then variation on it--that Greg's mechanisms make possible.
Paul, my apologies if I've bent your words, but they're extraordinarily evocative.
Can you share the Einstein-Bear connection you were pondering?
Meanwhile, here comes some relevant material from Instant Evolution. Howard
How does biomass invent new body-combinations, new phenotypes? That's what Greg and Eshel's papers make us question. Perhaps the process isn't Darwin's gradualism. Perhaps its Stephen Jay Gould and Niles Eldridge's saltation, their big jumps all at once, their punctuated equilibrium. Perhaps it's my "instant evolution".
But when I wrote about instant evolution (http://howardbloom.net/instant_evolution.htm), I never looked at the underlying genetic mechanism. I simply tried to demonstrate that geneteams work much faster at invention than we think.
Meanwhile, Eshel has called for a new view of evolution, one that's "orthoganal to Darwinism". He's called for an approach that doesn't follow the standard lines of argument but steps way outside the boundaries of evolutionary theory as we know it today.
Greg's synthesis of work on genes looks like it fits with instant evolution and with the megateams that geneteams make when they work together en masse. Some geneteams work in megateams to learn and to create. Some get inventive and superbrainy via the complex parallel processing that hooks trillions of computational engines, trillions of genomes, together in Eshel's bacterial colonies.
Some gene-and-cell-teams seem to get restless, they seem to ache for self-reinvention in Greg's multicellular organisms.
That ache is held in check rigorously. Then one day things change, and that ache shows what it was trying to be in private, when it was still restrained. How many of these aches for reinvention are memories of old strategies, old body types, that worked in previous circumstances? How many body-shifts are totally new? We can see the radically new wherever we look in the fossil record.
Well, not so radically new. The difference between a tyranosaurus rex and an anolis lizard skittering across a sidewalk in Florida is not that great. The difference between a crab and a fish is huge. But that difference seems to have appeared very quickly in the fossil record. It unfolded during the quick creative burst of the Cambrian era roughly 550 million years ago. (I could be wrong. There may have been an earlier split among the first primitive multicellular ancestors roughly 1.2 billion years ago.) But one way or the other, the change that tossed crustaceans down one path and proto-reptiles down another was swift,and the variations since then on the theme of crustacean and quadruped has been much smaller than we tend to think.
Here's more on instant evolution from my four-year-old paper on the subject. What new meaning does the material I gathered take on in the light of what Eshel and Greg have put forth? Howard
from http://howardbloom.net/instant_evolution.htm
INSTANT EVOLUTION
The Influence of the City on Human Genes
A Speculative Case
by Howard Bloom
Geneticist Neil Howell, of the University of Texas’ Galveston-based Medical Branch, contends that one form of human DNA—that contained in the mitochondria—sometimes makes adaptive shifts in a mere one or two generations. [11] The research with which he hopes to prove this is still in its infant stage. But Howell’s suspicion that genes can be swift gains credibility from the rate of phenotypic change among insects and fish.
Here’s an illustrative passage on the subject from my upcoming book, Global Brain: the Evolution of Mass Mind from the Big Bang to the 21st Century (John Wiley & Sons, August 2000):
If a passel of nearly identical animals is cooped up on a common turf, it frequently splinters into opposing groups which scramble determinedly down different evolutionary paths. E. O. Wilson, who brought attention to this phenomenon forty years ago, called it character displacement. [12] The battle over food and lebensraum compels each coterie to find a separate slot in the environment from which to chisel out its needs. [13] For example a small number of lookalike cichlid fish found their way to Lake Nyasa [14] in Eastern Africa roughly 12,400 years ago. It didn't take long for the finny explorers to overpopulate the place. As food became harder to find, squabbles and serious fights probably pushed the cichlids to square off in spatting cliques. The further the groups grew apart, the more different they became. [15] The details of this process are somewhat speculative, but the result is indisputable. The cichlids rapidly went from a single species of fish to hundreds, [16] each equipped with a crowbar to pry open opportunities others had missed. Some evolved mouths wide enough to swallow armored snails. Others generated thick lips to yank worms from rocks. One diabolical coven acquired teeth like spears, then skewered its rivals' eyeballs and swallowed them like cocktail onions. In the geologic blink of twelve thousand years, what had begun as a small group of carbon copies became 200 separate species--a carnival of diversity. [17]
Not only did twelve thousand years suffice to change the genes which gave these fish their body shape and bio-weaponry, that micro-sliver of an eon also provided ample time to rewrite the inborn script of fish psychology. Each new cichlid species was born chromosomally equipped with the hunting or scavenging instincts essential for its new specialty.
Then there’s the swarm of bird-biting London mosquitoes which moved into the tunnels of the Underground in roughly 1900 when the city’s half-built subway system was still occupied primarily by construction crews. Once below the sidewalk, the mosquitoes switched from feeding on feathered fliers to gorging on such delicacies as rats, straphangers, and maintenance workers. By the summer of 1998, the subterranean swarms had changed their genes so thoroughly that they could no longer mate with their distant relatives who lived above the pavement of the street. The pesky Tunnel bugs had taken their genome and gone off on their own, forming an entirely new species. [18] In reporting the story, Agence France Presse interviewed Roz Kidman Cox, the editor of BBC Wildlife Magazine, the publication responsible for initially breaking the news to a mass audience. Said Kidman Cox, "The scientists we talked to say the differences between the above and below ground forms are as great as if the species had been separated for thousands of years, not just a century.” [19] A mere one hundred years for a major shift in genes is not the painful crawl invoked by champions of Pleistocene fixation. Instead it is the quick-paced hop that Huxley called saltation. [20]
Yet another insect can change its genome twice that fast. It’s the soapberry bug, which has renovated its chromosomes to fit new needs at a pace that’s dizzying…taking not 100 years but a mere 50. From roughly 1900 to 1980 landscapers and city planners in Florida and in Louisiana produced a bonanza for any insect enterprising enough to go after it. The landscape designers imported new breeds of ornamental trees in an effort to help their clients outdo the neighbors or to spruce up a town’s streets. Florida’s sprucer-uppers chose the Golden Raintree (Koelreuteria elegans), which packaged its seeds in a slender pod whose walls were paper-thin. Louisiana’s outdoor decorators went for Koelreuteria paniculata and Cardiospermum halicacabum, whose seeds were stashed in packets with far thicker casings. Soapberry bugs moved in to mine the new arboreal territories. Each developed genes for a proboscis appropriately sized to seize the opportunities. In Florida where the Raintree pods were easily pierced, the proboscises of soapberry bugs were short. This made for easy sipping, thus saving on resources and on energy. In Louisiana, where seeds of the new eye-pleasing trees were protected by thick rind, soapberry bugs developed a proboscis of a rather different kind—long, slender drilling cylinders which made the sipping rougher but could bore through sidewalls of a kind far tougher.
Was this really a genetic alteration, or had soapberry bugs whose proboscises were already short or long simply moved long distances, each to the appropriate destination. Genetic testing showed that the specialized bugs had not come from far away, but had evolved from local insects whose proboscises had previously been adapted to harvest the bounty only of the local trees. By checking the dates at which the new greenery had ben brought in, researchers could pinpoint the time it had taken to tweak genes for proboscis length. That span turned out to be a breathlessly brief half a century. [21] So a flick of reproductive time can remake genomes in fast-breeding bugs, but what about in larger beings?
In the 1970s, Thomas and Amy Schoener [22] deliberately stranded Anolis sagrei lizards from Staniel Cay on numerous smaller islands in the Bahamas, each with a different sort of foliage. Lizards on islands with stumpy plants adorned with small leaves can operate more efficiently with short hind legs. Lizards on islands whose plants are larger and more luxuriant do better if they have the long legs perches on large leaves and large plant trunks allow, since long legs also increase escape speed when running from the local lizard eaters. Washington University biologist Jonathan B. Losos predicted that over time natural selection would prune the lizards’ genes to equip the scattered creatures with the limbs which best fit their needs. But how much time would genetic pruning take? Return trips to the islands revealed it hadn’t taken much time at all. The lizards on each island were soon measurably different. Some managed to diverge genetically from their parent strain in the twitch of a single decade. That’s the equivalent of ten generations—200 years—in human time.
Yet according to University of Washington evolutionary ecologist John N. Thompson, even this genetic sprint is painfully slow. Says Thompson, "dozens" of genetic transmutations have been known to take place in a matter of mere decades. [23] Thompson backs up his claims with rather startling facts:
· “Gene‑for‑gene coevolution in wild flax and flax rust in Australia has produced large changes in allele frequencies within and among populations over just the past decade alone
· “The frequency of clones in Potamopyrgus antipodarum snails within a single lake in New Zealand has changed within the past decade through time‑lagged selection imposed by a major trematode parasite.
· “The introduction of myxoma virus into Australia as a biological control agent against rabbits resulted in rapid evolution toward decreased virulence within only a few years.” [24]
Thompson explains that one cause of swift genetic change is the sort of race in which one species has to keep pace with its enemies and ecological partners. And lizard expert Jonathan Losos adds that, “ If colonizing populations are displaced into an environment that is often very different from that of their source, they are particularly likely to diverge evolutionarily. ” What’s more, writes Losos, the greater the difference in habitat, “the greater the magnitude of differentiation.”
In a message dated 11/25/2004 10:56:31 AM Eastern Standard Time, paul.werbos at verizon.net writes:
Having spent all of about 5 minutes of real thinking about the
questions Greg raises... enough thoughts pop into the mind that
I doubt I have time to type them all.
First -- one of the reasons why the establishment may find it difficult to
fully
address the questions is that they are very limited in this case in the degree
of mathematical abstraction they use. It's a kind of qualitative limitation
in how mathematical thinking is used...
The neuroscience establishment (which I know much better) has been struggling
with similar limitations... maybe a bit harder and a bit more successfully
so far...
------
It is interesting to ask: now that we have learned a lot about intelligent
systems in GENERAL..
and now that some of us have a reasonable first-order idea of how this maps
into the brain..
what about the genetic system?
Forgive me for using a new term which sounds a bit pretentious --
"metagenetics."
The prefix "meta" has been badly misused lately, but in this case -- what
else would
be a good single word to refer to the idea of a genetic system which
"learns to learn"?
^^^
Part of Greg's message is that we need to understand metagenetics in order
to make
any sense at all of 97 percent of the human genome. That's a big step, a
good one,
and an important one. That idea has existed in some form for a long time,
but to
give it a snazzy new one-word version and focus more attention on it is
still a good step.
But is there more going on here?
A natural way to interpret "metagenetics"... is to think of ... a kind of
second-order system which is
still designed to perform the same basic functions people think about in
genetic algorithms
or evolutionary computing: maximizing some kind of fitness function U(w) as
a function of a set
of weights or parameters w. (Parameters could be anything from body
characteristics
to behavioral response characteristics .. to anything...) A sophisticated
way to explore the space
of possible .. genotypes. Back in 1999
(at a plenary talk at CEC99, the IEEE Conference on Evolutionary
Computing), I challenged
people to send me proposals to address a more interesting computational task:
to design systems which LEARN to do stochastic search to maximize U(w,X),
where w is as before,
and X is a set of observed variables available to enhance performance. I
have reiterated this in many
talks and tutorials... I call this task "Brain-Like Stochastic search."
It's very important in
engineering, for example; if we use evolutionary search to find the best
possible chip design
for some task.... it would be good to represent DIFFERENT chip design tasks
by a vector X,
and then use a system which learns to do better on chip design task in general.
For now, it's enough of a challenge to treat X as "exogenous," but someday
one could advance to
dynamic X...
Now: one COULD follow up on Greg's questions by asking whether we can model
the genetic system
as one which implements "Brain-Like Stochastic Search" with dynamic X. We
may ask: to what
extent does this richer functional interpretation become essential to
understanding the basics
of what we really see with the genome?
Now -- a certain degree of "stockpiling" can be important even in that
limited context.
But another question occurs to me today: would it make any sense to go even
further,
and evaluate the possibility of a still higher level of intelligence in the
genetic system?
I wonder.
In brains, evolutionary computing is certainly far from enough, in any form.
(And I suppose I know a few key things about Edelman's work that Edelman
doesn't....)
In a word -- TIME. Optimizing results INTO THE FUTURE, with anticipation or
foresight
(both explicit and implicit), is absolutely central to how brains work.
Could there be anything like THAT in the genetic system? I wonder...
Various types of memory are essential in brains. There are many levels of
stockpiling in brains.
Could any of THAT be transferrable to the genetic case?
I wonder.
This morning I was thinking more about Einstein than about Greg... but I
suppose such thoughts would be
off-topic on this list. Oh, well.
Best of luck,
Paul
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Howard Bloom
Author of The Lucifer Principle: A Scientific Expedition Into the Forces of History and Global Brain: The Evolution of Mass Mind From The Big Bang to the 21st Century
Visiting Scholar-Graduate Psychology Department, New York University; Core Faculty Member, The Graduate Institute
www.howardbloom.net
www.bigbangtango.net
Founder: International Paleopsychology Project; founding board member: Epic of Evolution Society; founding board member, The Darwin Project; founder: The Big Bang Tango Media Lab; member: New York Academy of Sciences, American Association for the Advancement of Science, American Psychological Society, Academy of Political Science, Human Behavior and Evolution Society, International Society for Human Ethology; advisory board member: Youthactivism.org; executive editor -- New Paradigm book series.
For information on The International Paleopsychology Project, see: www.paleopsych.org
for two chapters from
The Lucifer Principle: A Scientific Expedition Into the Forces of History, see www.howardbloom.net/lucifer
For information on Global Brain: The Evolution of Mass Mind from the Big Bang to the 21st Century, see www.howardbloom.net
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