Tuesday, June 26, 2007

on evo devo and Sean Carroll's new book:

Sean Carroll has a great book, fun to read on this topic. highly recommend it:

Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom. Sean B. Carroll.

it's about all those homeobox genetic networks that guide metazoan development, and the surprise is that ALL metazoan phylla have similar networks, so it all evolved before all the earliest fossils we have for these boogers.

my summary:

A) we are actually learning in the past 20 years how
cells repeatedly transform themselves into two non
identical daughter cells, and then further communicate
with each other to increase the differentiation
between themselves and eventually build a creature!

B) surprise: only 25,000 genes in large verebrates.
seems too simple to create a whole critter, especially
complex mammals. wait... we've found that many genes
involved in development have a whole slew of switches
behind them that can get turned on and off depending
where in the developing embryo these genes' cells are.
there's the complexity we are looking for. we missed
the existence of the switches with the old style
drosophila genetics.

C) surprise: fish birds bats slugs bugs starfish worms
jellyfish are built with the SAME kinds of networks of
developmental genes and switches. for instance the
gene that turns on when eyes develop, are involved in
humans, octopi and jellyfish, even though these three
have vastly different eyes and we thought that they
came up with those eyes independantly.

D) this means that the creative bit that happened to
make metazoan bodies happened in some unknown common
ancestor to ALL metazoans before the cambrian
explosion. the plot thickens! the next common
ancestor going back that we all have is single celled
critters called Choanoflagellates. do THEY have these
genes and switches and what do THEY do with them?

E) the nature of the switches is such that we may have
discovered interesting mechanisms for evolution of
different body plans. it may be EASY with the flick
of one switch to turn a crab into a lobster or a
millipede into a grasshopper. (sort of) the current
dogma is that evolution happens gradually. for some
reason biologists have been resisting the possibility
of evolution by jumps (smells of creationism...) but
we are gathering evidence that evolution might also
occur by some high acceleration moves!

F) the genes have cool names like sonic hedgehog and

here's another review:

The New Just So Stories: PAULA M. MABEE

so in WHAT KIND OF CRITTER did this stuff evolve? is there some of it in the protistan ancestors to metazoans? i'd love to do a survey of the protistan phyla and see what's known about their behavior/cell physiology what would encourage/enable these critters to coordinate and become metazoan? for instance i found a paper that was easy to find on the web about similar genes in single celled choanoflagelates. there must be tons more.

i love singled celled critters. i should get my microscope out of storage and watch 'em again. i use to love watching stentor.

protistan ancestors:

Science 18 July 2003:
Vol. 301. no. 5631, pp. 361 - 363
DOI: 10.1126/science.1083853

Evolution of Key Cell Signaling and Adhesion Protein Families Predates Animal Origins
Nicole King, Christopher T. Hittinger, Sean B. Carroll*

The evolution of animals from a unicellular ancestor involved many innovations. Choanoflagellates, unicellular and colonial protozoa closely related to Metazoa, provide a potential window into early animal evolution. We have found that choanoflagellates express representatives of a surprising number of cell signaling and adhesion protein families that have not previously been isolated from nonmetazoans, including cadherins, C-type lectins, several tyrosine kinases, and tyrosine kinase signaling pathway components. Choanoflagellates have a complex and dynamic tyrosine phosphoprotein profile, and cell proliferation is selectively affected by tyrosine kinase inhibitors. The expression in choanoflagellates of proteins involved in cell interactions in Metazoa demonstrates that these proteins evolved before the origin of animals and were later co-opted for development.


related to this is a discussion i was having about evolution of eye development some time ago:



my posts are blackskimmer

Thursday, June 21, 2007

initial cosmic rebellion against flesh

warning: another sketch:

now of course from very early in human experience we have that Homo sapiens had thrust upon them this immense 20billion tangled neuron labyrinth of consciousness of his life of his experience and it sent them reeling! they got a tad lost in its immense depths and detours and richness and coupled with their growing horror at DEATH of such a wonderful thing as human experience, REBELLED against their fleshy muddy Earthy iterations of trial and error of lives in time nature. (that is to say, Earth creates the miriad creatues amazin creations by a process of trial and error with children's lives. parents overproduce an abundance of DIFFERENT kids and the ecosystem weeds 'em out. amazingly crafted dragonflies, cauliflowers, people are ALSO just food!) THERE'S the cosmic rebellion for you

so of course WAY before science we've been disconnected from this Earth, Cosmos. but the flipside is that we rebelled from the fact that Earth creates with ACCIDENT! Variation amongst children is due to accidental mutation, and accidental rearrangement of genes. the makeup of ecosystems is due partially to accidental extinctions of whole populations due to the vaguaries of weather volcanoes and meteorites...

we rebelled from the fact that we were an accident, in fact so insecure had we become from our intense consciousness of the fragility and contingency of a human life, of human history (the flood myths) that we infantily DEMANDED that the universe in the form of a FATHER had planned us. not as a MOTHER! mothers' relationships with their kids are too ambivelent, too risky! but fathers! they run no risk in fathering a kid! and when agriculture finally came around, fathers welcomed the idea of having lots of kids around to work the farm while mother's risked DEATH for it.

hmm... delve into this mother father accident think more carefully. recall my idea, that as hunter gatherers children are valuble but risky, and valuble in much smaller numbers than we experience today. so that probably mothers had much control over contraception, and aborting kids if she didn't feel she had enough resources. whether a kid survived WAS CONTINGENT... then with agriculture, if men could wrest enough land from each other, enough cattle from each other, they could afford plenty of kids, even plenty of kids were an asset, and they demanded kids, and mothers lost control. kids became inevitable.

now i'm mostly thinking of Greek, near eastern myth finally feeding into judaism and christianity. is the broader range of myths different? in all agricultural societies men win, become gods. the universe becomes male. the Cosmic story leads up to mankind.

at least in campbell's view all the myths seem to point to some stronger reality BEHIND this Earthy reality. and does that reality always inevitably create mankind in it's image?

so which myths have mankind as the PURPOSE of the cosmos? which ones carry this male fear of paternity, so the story that the kid is inevitable?

anyway by christianity child of classical greece and judaism, the universe is... we are not OF this Earth certainly, and maybe even not of this universe, we are breathed into the cracked rotting female shells of Earthclay by a male space alien god. a god alien to Earth, a God alien to the risky female practice of birth, a god alien to the trial and error creating properties of time. a VERY insecure God. a God born of our insecurity of knowing our contingency.

so eventually we develop the myth that we are children of a space alien father who does not risk death in childbirth, and therefore loves us 100%. who created us as pure spirit beings, who will bring us back to him, creates a rigid system of behavioral rules, that if we follow, it will all work out, bannishes birth/death and it's all very COZY.

somewhere in here we got to explore how this father came to reside in the heavens, in the planets. was it just that he was fleeing from the obviously birthing mother? what did i say the planets represented to us?

what about the Earthy Egyptian horus osiris isis thing. what do you say about them? hmm... i don't know that i know them. i don't know that any of us knows them yet. let me see... certainly they had a very visceral connection to their very special river, Nile. who fed them and created their world? well, on his own the nile is a tad chaotic, their world required some further organising principle in the form of human group effort to build dikes after the flood and save up the seeds to plant the next year...this group effort is tricky for humans, and innevitably leads to male leaders, fighting and conquering, and finally some kind of mutual standoff, with careful rules to hold it together.

it is human politics that ultimately becomes the stronger experience the more day to day matter at hand than the experience of the fertility and rottingness of Earth. so while you got osiris/isis birthing themselves into life each year, you've got ever present horus/chaos threatening the system and thus the need for ... what's the Egyptian image for how it all balances? eventually Re takes over in consciousness, no?

but what about the sense of a stronger reality of spirits behind this osiris/isis rebirthing thing?

ah.. now maybe we get into the jaynesian thing. definitely in Ancient Egypt there was a strong sense of the presence of the dead ancestors. is osiris the MIND of fertility? everything that happens is propelled by MIND, just like the way my hand moves, mind moves it. unless it's a reflex.. pharoah becomes horus after death?

anyway there are these "ba"s and "ka"s. definitely animating principles. so do you recall if ancient Egytptians felt ALIENATED from Earth? on the practical realm they certainly respected him (really Earth was a HE for Egypt? hmmm, well for the Maya, quetzelcoatl -venus - fertility is also a HE. hmmm...) and the Nile, and certainly made no attempts at a concerted massacre of croccodile and hippopotomous... did they feel that their time on Earth was temporary and their proper place was... well, DID they imagine another realm? or merely another TIME, or even, another QUALITY of time?

so could we figure out in these myth views that this realm behind Earthy living dying reality is not another PHYSICAL PLACE but an alternate way of seeing... or is this a very modern notion? didn't you propose that uroboric and apocalyptic were two alternate ways of experiencing time? that post bicameral was a third way of experiencing time... was another form of alienation? you are forgeting all the meditational, mystical ecstatic states... states of experience yes, but AFTER the experience does the practitioner accept it as an alternate experience or does he demand that he's experienced a different OBJECT?

my this is wandering about lazily.
i wish i had my library.

Saturday, June 16, 2007

important science experiences for kids

) the experience of going outside with a field guide and looking at their favorite kind of plants/animals and figuring out which kinds there are, seeing how many kinds there are, seeing the detail of them. learn to make distinctions by naming the similar but different organisms.

) how to measure length of everyday things and how to use arithmetic to think about miles, feet, meters, area...

) experience helping an adult take apart, repair, rebuild, maintain the family car! There are so many math and science concepts and skills learned in this concrete way. plus you learn not to just be a helpless consumer of technological tyrrany

) and thus what all that 1/2, 3/8 inch and 14mm is all about!

) stories of the lives of some famous scientists and mathematicians. when they lived.

) the experience of working on an easily stated math puzzle and WANTING to see how it comes out. learning that many easily stated math puzzles have not yet been solved after 300 years of intense work!

) maintain a fishtank. collect pond critters themselves from their favorite spot and watch em in the fishtank. how long can you keep it going before it goes bad and stuff dies off. you can even try maintaining a complete ecosystem and see how long it works with no fishfood!

) look at the pond muck, fishtank muck/algae under a microscope and see there are WORLDS in there. and that there are TINY critters. Absolute requirement is to understand how HOW tiny they are. 20 microns, 1/50th of a millimeter, 1/400th of an inch etc...

) draw, sketch plants, animals, stuff from microscope, mechanisms, buildings, as a way to communicate ideas. as a way to commune with detail.

) play with a chemistry set

) learn to identify some minerals, learn distinctions between color, lustre, hardness, fracture, that the minerals are chemicals.

) grow a garden.

) grow plants for a long while, propagate them.

how's that for a start?
i guess in part this list expresses my own childhood experience. I would be interested to see what others think.

Years Woven Into Wood

Don't people love things anymore?
a marble
toy truck
frying pan
an acorn?
The texture and grain of solid wood lovingly polished?

To polish wood takes time
supple emery cloth
sensitivity to the give and take of wood.

The grain of wood is years back into time.

One time,
when i cut pine boards into shelves
and the pine i was cutting had such a fine grain,
must'a been that each piece of wood
(i counted it)
took a hundred years to grow.

I was cutting them for a cheap clothing shop
surely the shop would go under within a decade
and all would be scrapped!

This pine wood was once a house
that generations of pine buds had built.
Took 'em over a hundred years
of summer light
fall winds
winter sleep
and spring upgushing of sap.

Skin after skin of treebud
fibers shed each fall
woven into wood.

the heart it can get holes in it, but you cant live if you can't die

god's vagina

western civ is alienated from god's vagina. a pity.

so vagina's beckon us back from our mind's tortuous journeys inside our skullvault labyrinths to come back to flesh to come back to the source of Earth creativity.

vaginas lubricate the passage to the dangerous act of creation of procreation to create the future of ourselves to take part in this 3.6billion year long journey of grandmothers all the way back to the first spark caught on the first muddy oxidation reduction reaction vagina in warm shallow seas or in dark violent seavents, no matter, flesh/mud and sparks been creating a long time.

takes a moist place to pull us away from the excell spreadsheet and come back to this Earthjourney of creating beating hearts that can go on flexibly beating time after time after time one BILLION times who has the mind spirit to keep up that rhythm that long to carry us?

god's vagina is the long harrowing history of birth of humanity painful out of the eden womb to a complex world to learn to wend the labyrinth of choices ahead of us to match this infinity yearning mind to the finite bucket of mud we all have to share.

Loving Stentor: Science vs. the New Age on Love

A small conversation about loving living creatures from a discussion forum:

New Age perspective:
"frequency of Love comparison to cells:

..I am currently channeling information from my spirit about cells..it says that love is designed to bring cells to life...Love as a frequency is trust, honesty and compassion...cells carry this frequency for they all have a knowing side that connects them to an openness to their own flow..honesty is the state when the cell realizes its purpose and function...."


So, I said:

Learning to communicate about these things...

You said>I am currently channeling information from my spirit about cells

Ok, but i have been actually looking at and playing with cells in ponds and in plants etc.. for quite some time, so lets see if our observations have anything in common...

>..it says that love is designed to bring cells to life...

MY love? if i love a dead cell, or a blob of mud, it will come to life? what do you mean? no doubt something basic about human love is a property shared by all living creatures. what do you mean?

Anyway, i do love Stentors in a way, have you seen them in pondwater? the blue ones are really cool. They are about the size of a period. shaped like a curvy icecreamcone. very thoughtful little creatures. they hold onto a duckweed root and beat their hairs to swirl the water into their mouths and suck in food. then all of a sudden they get bored and let go, change into a blobby shape and swim off... graceful, too. they are cells. i can tell you details about em. they swim differently than Rotifers, which are made up of many cells, but are smaller than they are. they swim differently than Euglena because they have thousands of swimming whips, while Euglena has only one... i can tell you the way my girlfriends smile looks, the color of her eyes. the point is that to love either of these the first step is to get to KNOW them in DETAIL. and not make up any stories about who they are, cause then you are bound to hurt their feelings...

That is MY science, to respect others enough to get to know them in detail, to replace the stories i make up about them in my head with detailed knowledge about who they are, so that i can respond to them and help them grow. If i want to find out what's upsetting Stentor or my girlfriend, I do NOT read a book about it, i do not CHANNEL information about it. I listen to her. I watch her. I ask questions. I ask other people to help me, to watch her and i compare what i see with what they see to make sure I'm not kidding myself, to make sure my perceptions aren't warped by anger, lust, selfishness...

So tell me what you know about these cells that hopefully you love more than cars and nuclear bombs and ignorance.

p.s. you might want to look at M. Scott Pecks's book 'the road less traveled', he loves people for a living and has a reasonable definition of it.

nickster said:
As is clear from the above poster, there is a connection. To dedicate yourself to science, you have to learn to love the physical world. We are raised to love ideals, nations, religions, etc... these are imaginary ideals! But love of the air, the water, microbes in the soil, minerals dissolved in the sea... that is something you can only learn through endless, dedicated study.

How I miss that feeling!

The previous poster hit the nail on the head. Love arises from first-hand, experiential knowledge. Not from reading what other people tell you, or making up what you would like to believe about things. I thought I was the only one who felt that way! I thought I was an off-the-scale nerd for feeling that way!

and i said:

off the scale nerds unite!

how else does so much basic science get done if it weren't for off the scale nerds thinking that chemicals and mud and bugs and worms and number patterns wern't really cool?

isn't it scary how many people every day are into all those bullshit imaginary ideals? and they totally ignore bugs and rocks and rivers and hills... and in this country a growing hoard are getting ready for the imaginary ideal of the RAPTURE where they will nuke away all the bugs rocks flowers eyebrows...

how do we get more people to be off-the-scale-nerds??

nickster:I don't' know... Why don't people love *this* world? Why do they need to make up religious mumbo-jumbo to get themselves inspired about existing? Why make up "heaven" to inspire you? What is wrong with the world we have right here? You could spend your entire life studying a gram of soil, and still never come close to understanding it completely. There is so much here!

why is the beating heart love?

the heart's blood is our vulnerability which is our ability to open the love door. love is hard work is commitment to life, so is a heart, committed to beat for us every blub blub, every minute, every day, every year, for life, till we are ready.

Friday, June 15, 2007

thoughts on evolution/creation battle

realize that the gap in our knowlege between what chemistry can do and what the simplest bacteria can do is IMMENSE. this gaping chasm only openned up 50 years ago.

how do you get from this:
Chemistry of the Elements, Second Edition (Paperback)
by A. Earnshaw, Norman Greenwood

to this:
a day in the life of a cell

some adamant atheists say "of course life came about through some (mumbly mumbly) chemistry" and really havent thought it through. they just don't want their ignorant religious neighbors bringing in their LORD.

some scientists say the same thing, but really what with specialization these days i don't think theyve thought it through.

without going through this:

complexity lab manual

kind of training (which i think (sadly) most who graduate with a B.S. or even Phd rarely get) i realy don't see how anyone could even have a descent intuitive feeling that chemistry CAN make life. it's all wishful thinking.

so it's no wonder that such irreducible complexity arguments are floating around. i'm not talking about specific arguments about flagela, yeah i know how those can evolve. i'm talking about how the HELL did we get cells capable of evolving them in the first place. it's all a little mindnumbing.

the next important aspect is: Intelligent design is a PERFECTLY reasonable hypthesis. the only trouble is that we don't have anywhere near a decent exploration of what we mean by: what is an intelligent system?

we DON'T know how the human mind works, we DON'T know how neurons MAKE/BE it. we don't even know how a single celled protozoan wends it's way creatively through its environment, how the innards of the cell, the dynamic cytoskeleton, the 100s of chemical feedback loops coordinate to make A COHERENT ENTITY.

we don't know how to ask: is honeybee hive an entity? is an evolving ecosystem an entity. is Earth an entity? i.e. are the growing interactions between organisms over time cohesive enough to call it that.

we don't have a general theory of HOW intelligences in general might create. therefore we can't say "well, does this look like the work of AN intelligence?"

we've got vague mumblings about, well why would an intelligence create a 20foot vagus nerve running all the way up then back down the neck of a girraffe... the creationists rant: well, who knows the mind of god, maybe there is a purpose?

who knows? we don't have a general theory of intelligences.

i will grant that such a creator is probably NOT like a grey bearded old man in the sky.

it does not help, certainly, that most religious folk make no effort at an experimental or synthetic exploration of what their beloved intelligence IS like.

some do, they are called mystics, and i suppose ultimately some come to a conclusion that such an intelligence they contact is nothing more than the grandness of the universe...

so frankly i think that most of the problem is that really this discussion in popular media is basically at the level of the National Enquirer, or a mobfight at a baseball game. truly i think the particular ideas, not thougth out, evolution vs creation are just arbitrary banners being held by waring classes in america. the war is really about something ENTIRELY different! what does the average person care about these complex issues of chemistry, complex systems and artificall intelligence?

i'd like to find out what that war is REALLY about. my suspicion is that it is:

one class wants to continue this glorious (?) european enlightenment cultural/economic experiment

the other class, who came here wanting to get AWAY from eruopean civilization who created the wasteland of the wild wild west, now knows it's destined to work at wallmart and 7/11.

if anyone has any ideas, i'd be very intersted in hearing.

Saturday, June 2, 2007

warm stones and silent walks

Once when I worked at the botanical garden in the Bronx, I was giving a forest tour. They always gave me the hard cases so i had this group of deaf kids. We had a great time! I just pointed at everything, we touched everything, we found cool stuff like the fluff that flies out of princess paulonia pods and incredibly intricate wood carvings by carpenter ants, so smooth.

At one point the kids are acting really quiet and mysterious but the teachers/parents don't know why, and then one of the kids passes me a big pebble, it was very warm, aparently it was warmed in the sun. Anyway they had been passing it back and forth so amazed by its wormth.

Another time I was giving a tour in the woods and these are usually pretty rambunctios kids, 3rd 4th grade etc.. and i decided to try a silent walk for like 5 or 10 minutes. I told them be quiet and LISTEN and then after 10 minutes we'll talk about what we heard. I wasn't so hopefull about this game!

Well it worked pretty good but the surprising thing was that when the 10 minutes were up and I wanted to ask them what they heard, they were so into it that they wanted to do another 10 minutes of silence!

Lots of surprises like that.