Wolfram, in his book "a new kind of science" (poorly written, full of himself, but FASCINATING DATA) shows how scores of different kinds of the complex cellular automata (one example here) can simulate each other, and in a sense, ANY cellular automata (or mathematical system, or machine) which is reasonably complex enough can do ANYTHING that we consider interesting. This leads me to the following kinds of questions:
is the kind of biological life we have (and brains and behavior and minds and experiences) a consequence of the particular kind of chemistry this universe gives us, or would ANY remotely interesting chemistry be able to produce critters like us? Wolfram's results HINT at a yes for the latter possibility.
This is interesting because we can extend it to the following dilemma:
There is a concept called the cosmological anthropic principle. (look it up) In it SOME physicists say that if the physical constants to the universe as we understand them now, where just .00000001% different, suns would not form, atoms would not be created in them, and no chemistry even would result, let alone life. These people and some christians too, use this argument to say that the universe was fine tuned to create us, and that means either a god who loves us created it, or the universe itself is some kind of god who loves us.
Their argument is faulty however! Yes, we can tell that if the universe where .0000001% different our kind of chemistry and suns and planets and life wouldn't exist, BUT we are NO WHERE near capable as physicists and mathematicians to predict what ELSE might happen. (We had quantum chemistry for 60 years or so and never even figured out Bucky Balls from scratch!) Things on space and time scales that we couldn't imagine might become interesting instead, and this might be interesting enough in the sense of Wolfram's results, to create systems that could create TOTALLY different critters, who can nevertheless become richly interesting, come to explore and 'know' the universe and be 'worthy of a god's love'.
So where does that leave us?
If in a 1000 more years of math and science we COULD show that this universe is the only kind that can produce interesting beings, well, that would be interesting. can't imagine how we could do that, but there are some mathematical results that might point the way.
the other result? say we can map out ALL possible physicses.. (ok, maybe 10,000 years from now...) and show that 99% of them end up with something interesting (this is like exploring the phase space of the parameters of a dynamical system...) THAT would be interesting too.
Thursday, August 28, 2008
Tuesday, August 12, 2008
Loricifera, Cycliophora, Micrognathia: New Phyla Get Me Wondering About Twisty Metazoan Evolution
pic of loriciferan and life cycle
pic of cycliophora and life cycle
pic of micrognathia and phylogeny
after reading this article i woke this morning thinking about where these critters fit so i reviewed all these phyla...
loriciferans, cycliophorans, and micrognathozoa. So i review the phyla: priapulid, kinorhynch, loricifera, nematode, sipuncula, bryozoa, phoronida, brachiopoda, gastrotrich, rotifer, acanthocephala, entoproct, cycliophora, gnathostomulid...
in my invertebrate biology text. What chaos of lifestyles and phylogeny.
well actually the phylogeny is confused! we do not know when the phyla differentiated from each other, nor how long it took? 70million years int the precambrian? 10million years right at the beginning? faster?
a lot is going on. many levels of organizition are evolving in parallel with and against each other:
ecology
organismal anatomy
genes
genetic networks.
In each clade one can find instances of radical switches in ecology, which select for radical difference in morphology. lineages can go back and forth between these ecological strategies multiple times. see the chart of switches between planktotropy and lecithotrophy in annelid larvae quoted on page 491 of Valentine, from:
Rouse, G. W. 2000. "the epitome of hand waving? Larval feeeding and hypotheses of metazoan phylogeny". Evol. Dev. 2: 222-233
so it is hard to infer phylogeny from looking at aparent homologies in the anatomy/behavior.
the next level of messiness is in the genetics. the genes and the regulatory circuits guiding development can evolve independantly. the same gene can be coopted again and again for a different developmental task. and we know that genetics can be subject to recombination, so that whole level doesn't form a clean phylogenetic tree...
Sean Carroll on Evo Devo
I'm struck by what a rich fragrant MESS evolutionary biology is.
check out a nice summary in
James W. Valentine, "on the origins of phyla"
chapter 3 discussing the fragrant chaos of developmental genetic regulatory networks. the book has chaps describing the phyla, the molecular phylogenies, the fossil record and speculations about there mysterious evolution at the end.
one day i will get to read it.
pic of cycliophora and life cycle
pic of micrognathia and phylogeny
from:
"An Introduction to Loricifera, Cycliophora, and Micrognathozoa" by Reinhardt Møbjerg Kristensen
get a look at that cycliophora life cycle. what insanity! where's the individual? these are whole new phyla, on the level of mollusks or segmented worms or arthropods, discovered within the past few decades."An Introduction to Loricifera, Cycliophora, and Micrognathozoa" by Reinhardt Møbjerg Kristensen
after reading this article i woke this morning thinking about where these critters fit so i reviewed all these phyla...
loriciferans, cycliophorans, and micrognathozoa. So i review the phyla: priapulid, kinorhynch, loricifera, nematode, sipuncula, bryozoa, phoronida, brachiopoda, gastrotrich, rotifer, acanthocephala, entoproct, cycliophora, gnathostomulid...
in my invertebrate biology text. What chaos of lifestyles and phylogeny.
well actually the phylogeny is confused! we do not know when the phyla differentiated from each other, nor how long it took? 70million years int the precambrian? 10million years right at the beginning? faster?
a lot is going on. many levels of organizition are evolving in parallel with and against each other:
ecology
organismal anatomy
genes
genetic networks.
In each clade one can find instances of radical switches in ecology, which select for radical difference in morphology. lineages can go back and forth between these ecological strategies multiple times. see the chart of switches between planktotropy and lecithotrophy in annelid larvae quoted on page 491 of Valentine, from:
Rouse, G. W. 2000. "the epitome of hand waving? Larval feeeding and hypotheses of metazoan phylogeny". Evol. Dev. 2: 222-233
so it is hard to infer phylogeny from looking at aparent homologies in the anatomy/behavior.
Sean Carroll on Evo Devo
I'm struck by what a rich fragrant MESS evolutionary biology is.
check out a nice summary in
James W. Valentine, "on the origins of phyla"
chapter 3 discussing the fragrant chaos of developmental genetic regulatory networks. the book has chaps describing the phyla, the molecular phylogenies, the fossil record and speculations about there mysterious evolution at the end.
one day i will get to read it.
Is the Evolution of Complex Eyes an Unlikely Contingent Event or the Inevitable Consequence of The Axioms Of Physics?
I was thinking about the evolution of eyes and such and whether they are odd contingent results of evolution on Earth or whether they are EASY for chemistry and biology to come up with...
It's a current question in evolutionary theory, for instance:
If you play the tape over again of evolution wold you get COMPLETELY different weird critters and morphologies as S. J. Gould posited in his Wonderful Life,
or would evolution converge on many similar structures, as Simon Conway Morris posits in his "Life's Solution: Inevitable Humans in a Lonely Universe"
Here we find out that the two are having something of a feud, and Conway Morris is a theist, besides.
more ideas on this dilemma: Lewin's book "Complexity: Life At The Edge Of Chaos"
Take eyes. are they unexpectedly difficult things to evolve or are they nearly inevitable consequences of the way biology, chemistry and light interacts? or to take it to the extreme: as Conway Morris posits, is human intelligence ALSO an inevitable consequence of the laws of phyics?
Odd thoughts and the gut response is: of course not! but then i started thinking of the classification of finite simple groups.
You set up a simple set of axioms for what constitutes a mathematical group. then you go exploring the space of all possible groups by messing around, kind of like how evolution explores morphospace, except that we can possibly be more mathematially thorough! In fact can we find ALL the possible kinds of groups? is the morphospace infinitely complex, dirt simple or somewhere in between?
The surprise came a few decades ago when it appeared that we COULD map out all the possible kinds of groups (actually we found all the finite simple groups, kind of like the prime factors of groups)! And what we found was that there was moderate complexity: 18 different classes, plus... some chaos: 26 different sporadic groups that did not fall into any of classes.
The sporadic groups are odd, HUGE and complex. the largest has: 808,017,424,794,512,875,886,459,904,961,710,757,005,754,368,000,000,000 elements!
How on earth did the simple definition of a group imply this interesting space of structures with just a LITTLE bit of chaos?
Description here (describes axioms for group, some examples you can work out, and pointers to the mathematical results):
finite simple groups
So i'm wondering... if you look at physics, chemistry and the basics of cell bio as the axioms for life, is the possible morphospace a huge infinte chaos, where anything is possible, or is it more manageable with just a little bit of chaos? And thus, maybe there is not a chaos of sensory organs possible, but a finite bunch of them with eyes, being one of the classes? Of course the corresponding classification of possible structures must be WAY HUGER than the classification of finite simple groups. And we also have to model how the historical process of evolution constrained by the specific conditions of a planet (which are in turn modified by the evolution of the organisms...) explores that morphospace!
Another process that might whittle down the regions of morphospace possible for evolution, is that only a very small fraction of it might be attractive orbits to the evolutionary dynamical system
Say, as Stuart Kaufmann finds in his random boolean networks
So, maybe eyes are not so surprising after all.
It's a current question in evolutionary theory, for instance:
If you play the tape over again of evolution wold you get COMPLETELY different weird critters and morphologies as S. J. Gould posited in his Wonderful Life,
or would evolution converge on many similar structures, as Simon Conway Morris posits in his "Life's Solution: Inevitable Humans in a Lonely Universe"
Here we find out that the two are having something of a feud, and Conway Morris is a theist, besides.
more ideas on this dilemma: Lewin's book "Complexity: Life At The Edge Of Chaos"
Take eyes. are they unexpectedly difficult things to evolve or are they nearly inevitable consequences of the way biology, chemistry and light interacts? or to take it to the extreme: as Conway Morris posits, is human intelligence ALSO an inevitable consequence of the laws of phyics?
Odd thoughts and the gut response is: of course not! but then i started thinking of the classification of finite simple groups.
You set up a simple set of axioms for what constitutes a mathematical group. then you go exploring the space of all possible groups by messing around, kind of like how evolution explores morphospace, except that we can possibly be more mathematially thorough! In fact can we find ALL the possible kinds of groups? is the morphospace infinitely complex, dirt simple or somewhere in between?
The surprise came a few decades ago when it appeared that we COULD map out all the possible kinds of groups (actually we found all the finite simple groups, kind of like the prime factors of groups)! And what we found was that there was moderate complexity: 18 different classes, plus... some chaos: 26 different sporadic groups that did not fall into any of classes.
The sporadic groups are odd, HUGE and complex. the largest has: 808,017,424,794,512,875,886,459,904,961,710,757,005,754,368,000,000,000 elements!
How on earth did the simple definition of a group imply this interesting space of structures with just a LITTLE bit of chaos?
Description here (describes axioms for group, some examples you can work out, and pointers to the mathematical results):
finite simple groups
So i'm wondering... if you look at physics, chemistry and the basics of cell bio as the axioms for life, is the possible morphospace a huge infinte chaos, where anything is possible, or is it more manageable with just a little bit of chaos? And thus, maybe there is not a chaos of sensory organs possible, but a finite bunch of them with eyes, being one of the classes? Of course the corresponding classification of possible structures must be WAY HUGER than the classification of finite simple groups. And we also have to model how the historical process of evolution constrained by the specific conditions of a planet (which are in turn modified by the evolution of the organisms...) explores that morphospace!
Another process that might whittle down the regions of morphospace possible for evolution, is that only a very small fraction of it might be attractive orbits to the evolutionary dynamical system
Say, as Stuart Kaufmann finds in his random boolean networks
So, maybe eyes are not so surprising after all.
Stuart Kaufmann's Random Boolean Networks
take N nodes that can be on or off. hook 'em together into a network with various logical gates coming into each one with an average of k inputs from the others. look at the ensemble of all such possible systems.
let each cycle synchronously, the nodes turning each other on and off. there ought to be 2^N possible states to such a system. Kaufmann found that when K is around 2 most of the systems end up falling into one of a MERE sqrt(N) possible attractive cycles! the systems do not explore anywhere NEAR the 2^N possible states.
let each cycle synchronously, the nodes turning each other on and off. there ought to be 2^N possible states to such a system. Kaufmann found that when K is around 2 most of the systems end up falling into one of a MERE sqrt(N) possible attractive cycles! the systems do not explore anywhere NEAR the 2^N possible states.
Monday, August 11, 2008
Sketch Of How Women Drive The Story In The Bible
women in tora
core of stories in the first five books and beyond with very consistent language, style. look at Bloom's "book of J" and Freidman's "hidden book of the bible"
nothing voodoo here, just literary analysis.
In these stories we find the men shirking duty and women taking active role.
1) adam and eve lounging around the garden, eve gets the whole story rolling by choosing MORE.
(not sure if this one goes along, but i just thougt of it: twice abraham goes down to some kingdom, egypt, the other one i don't remember, fears the king will kill him for sarah, so she lies for him says she aint married to him and becomes king's consort. SURE IT DOES, she saves his ass!)
2) isaac favors the son that god does not, a son who apparently does not have the right AMBITIONS for the ongoing story, so his wife takes things in hand instructs yaakov what to do and how to trick the father, isaac for the birthright.
3) are the 12 tribes important to the story? it's yaakov's 4 wives jockying for best position that ends up producing these 12 kids.
4) judah gets tamar as wife for his first son. the son is not enough for her wild powers of life and dies. the second son, onan, is supposed to take his place, shirks his duty on the ground and is killed for it. judah fears for his third son's life and sends tamar away for awhile. she's tired of waiting, so she takes matters in her own hand, tricks judah into siring kids off her himself.
the importance of these kids? they lead to David to moshiach by way of Boaz, see Ruth.
5) lot flees sodom with his two daughters. as far as the DAUGHTERS know, huddled in the cave having seen their whole world destroyed, they are IT, so they trick him into having kids. One kid is.. MOAB. significance? see Ruth.
6)Moses tries to shirk his calling 5 times before grudgingly accepting. then on the way back to egypt he tries to shirk again, asking god to kill him rather than make him a prophet ( a VERY tough calling, common for prophets to wish death instead) but his wife zipora says "oh know you don't you have a duty to me your wife, to your son to enter into the covenant of jews, to your people! she saves him with a ritual circumsision.
7) finally, Ruth: Naomi is Boaz' relative, she and her two sons and husband move to MOAB, where her sons die and leave no kids. one of their wives is Ruth who loves Naomi and the jews, the STORY so much, she asks to come back to israel with her. there, Boaz is the nearest relative and his responsibility is to give Ruth kids, but he isn't interested. Naomi and Ruth seduce him into it. Ruth is of MOAB, lot's daughters' decendants.
she has a kid. this joins two ancient antagonistic people into the line that will lead though david to the moshiach bringer of world peace.
Just What is the story that this extended J tradition is trying to teach? something about preservation of this grand story by acts of women? must read Bloom again for some clues.
Side note on christianity. everybody wants to enter this grand jewish STORY, so the christians try to adopted themselves into it FORCEFULLY. Mary takes god into her, but it's not in David's line, only her husband is, so where from Jesus? odd. the new testament certainly does NOT continue in this 'book of J' literary tradition! It's way too abstract!
core of stories in the first five books and beyond with very consistent language, style. look at Bloom's "book of J" and Freidman's "hidden book of the bible"
nothing voodoo here, just literary analysis.
In these stories we find the men shirking duty and women taking active role.
1) adam and eve lounging around the garden, eve gets the whole story rolling by choosing MORE.
(not sure if this one goes along, but i just thougt of it: twice abraham goes down to some kingdom, egypt, the other one i don't remember, fears the king will kill him for sarah, so she lies for him says she aint married to him and becomes king's consort. SURE IT DOES, she saves his ass!)
2) isaac favors the son that god does not, a son who apparently does not have the right AMBITIONS for the ongoing story, so his wife takes things in hand instructs yaakov what to do and how to trick the father, isaac for the birthright.
3) are the 12 tribes important to the story? it's yaakov's 4 wives jockying for best position that ends up producing these 12 kids.
4) judah gets tamar as wife for his first son. the son is not enough for her wild powers of life and dies. the second son, onan, is supposed to take his place, shirks his duty on the ground and is killed for it. judah fears for his third son's life and sends tamar away for awhile. she's tired of waiting, so she takes matters in her own hand, tricks judah into siring kids off her himself.
the importance of these kids? they lead to David to moshiach by way of Boaz, see Ruth.
5) lot flees sodom with his two daughters. as far as the DAUGHTERS know, huddled in the cave having seen their whole world destroyed, they are IT, so they trick him into having kids. One kid is.. MOAB. significance? see Ruth.
6)Moses tries to shirk his calling 5 times before grudgingly accepting. then on the way back to egypt he tries to shirk again, asking god to kill him rather than make him a prophet ( a VERY tough calling, common for prophets to wish death instead) but his wife zipora says "oh know you don't you have a duty to me your wife, to your son to enter into the covenant of jews, to your people! she saves him with a ritual circumsision.
7) finally, Ruth: Naomi is Boaz' relative, she and her two sons and husband move to MOAB, where her sons die and leave no kids. one of their wives is Ruth who loves Naomi and the jews, the STORY so much, she asks to come back to israel with her. there, Boaz is the nearest relative and his responsibility is to give Ruth kids, but he isn't interested. Naomi and Ruth seduce him into it. Ruth is of MOAB, lot's daughters' decendants.
she has a kid. this joins two ancient antagonistic people into the line that will lead though david to the moshiach bringer of world peace.
Just What is the story that this extended J tradition is trying to teach? something about preservation of this grand story by acts of women? must read Bloom again for some clues.
Side note on christianity. everybody wants to enter this grand jewish STORY, so the christians try to adopted themselves into it FORCEFULLY. Mary takes god into her, but it's not in David's line, only her husband is, so where from Jesus? odd. the new testament certainly does NOT continue in this 'book of J' literary tradition! It's way too abstract!
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