Tuesday, December 22, 2009

Funky Ho Down

Recently I copied this passage from Mae-Wan Ho's insane and wonderful The Rainbow and The Worm (the physics of organisms) into an email to a friend concerning the magic of muscles:

(after writing at length about the magic of an organisms eye, and the manner in which it collects data, and the rate at which that data is organized, processed, and refigured to usefulness, she writes...)  Another instructive example is muscle contraction.  About 40% of our body is made of skeletal muscle, i.e., muscle attached to bones, like those in our arms and legs and trunk.  Another 5 to 10% is smooth muscle such as those in the gut and body wall, and cardiac muscle in the heart.  Skeletal muscle consists of bundles of long, thin muscle fibres, which may be discerned under a magnifying glass.  These fibres are several centimetres in length, each of which is actually a giant cell formed by the fusion of many separate cells. A single muscle fibre, magnified a hundred times or more under the light microscope, can be seen to be made up of a bundle of 20 to 50 much smaller fibres, or myofibrils, each 1 to 2 micrometres, or one millionth of a metre in diameter.  A myofibril has regular, 2.5 micrometre repeating units called sarcomeres, along its length.  Adjacent myofibrils are aligned so that their sarcomeres are in register.  Under the much higher magnifications from the electronmicroscope-- thousands to tens of thousand times-- one will see extremely regular arrays of the periodic structures.  One will also see that each sarcomere consists of alternating thin and thick filaments, made up respectively of the two main muscle proteins, actin and myosin.  In three dimensions, there are actually six thin actin filaments surrounding each thick myosin filament, and the six actin-filiaments are attached to an end plate, the Z-disc.  Contraction occurs as the actin filaments surrounding the myosin filaments slide past each other by cyclical molecular tread milling between myosin 'head' groups and serial binding sites on the actin filament, forming and breaking cross-bridges between the filaments, in all three dimensions in the entire array.  (here she continues with a bunch of stuff about the uptake of ATP and it's conversion, ect. ect. very interesting, but not completely necessary to the mind blowing conclusion.)
(Continues...) In a typical muscle contraction, all the cells in the muscle-- billions of  them at the very least-- are executing the same molecular treadmilling in concert.  Simply waving our arms about is a veritable feat requiring a series of actions coordinated instantaneously over a scale of distances spanning nine orders of magnitude (!!!) from 10 E-9 metre (or a nanometre)  for intermolecular spacing between the actin and myosin heads, to about one metre for the length of our arm;  each action, furthermore, involving the coordinated splitting of 10 E19 individual molecules of ATP.  Now, then, imagine what has to happen when a top athlete runs a mile in under four minutes;  the same instantaneous coordination over macroscopic distances involving astronomical numbers of molecules, only more so, and sustained for a long period without break.  
(Cont..)  It is truly remarkable how our energy should be available to us at will, whenever and wherever we want it, in the amount we need.  Moreover, the energy is supplied at close to 100% efficiency.  This is true for muscle contraction, in which the chemical energy stored in ATP is converted into mechanical energy, as well as for all the major energy transduction processes, as for example, in the synthesis of ATP itself in the mitochondria where carbon compounds are oxidised into carbon dioxide and water in the process of repiration.  If that were not so, and energy transduction can only occur at the efficiency of a typical chemical reaction outside living organisms, which is 10 to 30% efficient at best, then we would literally burn out with all the heat generated.  
(Cont.)  To summarise, then: being alive is to be extremely sensitive to specific cues in the environment, to transduce and amplify minute signals into definite actions. Being alive is to achieve the long range coordination of astronomical numbers of submicroscopic, molecular reactions over macroscopic distances;  it is to be able to summon energy at will and to engage in extremely rapid and efficient energy transformation.
(Cont.) So, how is the sensitive, vibrant whole that is the organism, put together?  An organism that develops from the relatively featureless fertilised egg or seed to a complicated shapely creature that is nonetheless the same essential whole, until it dies?  
We have certainly not exhausted the wonders of being alive.

Oh no, we have not.

  The most important concepts in The Rainbow and the Worm, for me, have circled around the concept of life as a great big web, intimately associated with it's habitat, solar system, and sun; but built for comfort far above the thermodynamic equilibrium.  I'm crazy for these structures that catch falling electrons (a name of one of the chapters in RATW)  and crazy for the structures further down the chain that maintain the "quality" of the energy that the falling electrons give us, storing it as carbohydrates, or using that self same energy for enormously useful stuff.  Coupled with the history of the Earth's surface once it met cute with life: this oldest of materials (for example: you) has not only the usual fascinations assumed when one is speaking of life, but has terraformed the world to it's dictates:  and stolen from the way things ought to be: to sing a ballad in praise of "the will."  

Among the delights of this "oldest of materials," life, there is the oldest of questions, like, why is life improbable.  Or, rather, why doesn't life just self assemble, in the laboratory, without much trouble.  Turns out the selfsame high energy that I was describing in the above paragraph, stored in very large amounts in covalent bonds as electronic bond energies, make frankenstein smoothies a bit difficult:  equilibrium states simply, by definition, don't fluctuate much of anything into a high energy life form like you.  You're special. Even in the morning before you've had your coffee.

This is such a revelation to me.  

And it doesn't just go for organisms: since very, very large, complex systems, also contain high energy flows, and material cycles, which form interdependent reflective relationships: witness the jet stream effect on flows, and temperature of air masses, and the weather they create.  Witness the probable impact of CO2 on ocean streams cycling from the tropics to the poles:  change.... what kind of change, who knows, but any change means serious changes in the weather of places that are rather culturally unready for sudden lattitudinal changes in their "normal" weather.  The material of our world: quantity of greenhouse gases in the atmosphere, cause a change in gross flows of material and energy gradients, which as boring as that sounds, is the difference between zero Celsius and zero Fahrenheit. 

The entirety of The Rainbow and the Worm is a sort of elaborate metaphor, carefully built by a physicist,  and constructed amongst a dozen fields, to show how the seemingly material qualia of physical organisms, are in reality constructed of highly organized energy, and complex structures that result (and proffer) such organization.  

Among the subroutines of the metaphor are discussions of a number of fascinating topics:  for example:  The Benard-Rayleigh convection cells.  These are the convective movements that make the honeycomb holes in your shallow pan of rice, before you give it it's final stir.  Unless your some kind of bachelor slob, who microwaves his way through life, you have undoubtably seen these honeycomb patterns in a pan.  While it's fascinating to know they have a name, I'm sure, why do I mention them?  Well... they represent a sort of H20 molecular roller coaster for individual molecules:  each cell comprised of something like 10 E23 water molecules, cycling around and around.  So, picture this:  a giant playground where happily squealing kids (I walk through one such lovely place with a more or less public sidewalk going through it, when I stroll over to my friends' Mike and Luane's place.  The other day I was sort of time machined by the squealing of a few of the girls: so high pitched and random: never changes, never will... thank God.  Dennis Lehane has a kind of extended ode to such behavior as part of the healing and grieving process by his father in the incredible Mystic River... it made me really admire Lehane's grasp of real fatherhood, and love.)  Let me try this again... picture this: a giant playground where happily squealing kids are running around American style (not doing martial arts, for crying out loud) about as organized as you can well imagine.  All the sudden, the sun rises a bit higher, things heat up a bit and every single kid grabs another kids hand in in strict formation pinwheels like some Cirque de Soleil skit.  The teachers are delighted until they realize... there's no stopping it, as long as the sunshine flows, the kids pirouette....   those annoying little shits have become dancing zombies (what'll we tell the parents?)

This is more or less what happens to the water molecules; it's strange, extremely strange, since below a certain temperature, the water molecules dart about like any fluid must, when not frozen: randomly moving about, without a lick of organized movement.  But the moment the Benard-Rayleigh convection cells form (at just below boiling temp): suddenly a molecule moves in a relatively tight formation (though huge for the molecule, given that there's 10 E23 of them per cell...)   As long as the heat remains (energy flow) a "structure" of cycling molecules is maintained across the shallow pool of heated water.  

Throughout the rest of the book Ho makes arguments for energy to create other, perhaps not similar, but you might say, similar enough, emergent structures.  Other cycles, energetic, chemical and material, are evidenced for scrutiny of the physics at play within living things.

In a previous post about falling electrons (I've been rereading this incredible book for almost four months) I mentioned the rattling around that a unit of energy has to do, through the structure of the biosphere.  This rattling around, amounts to the obstacle course that ecosystems put up, which in effect is what allows life to rob entropy blind.  So while things wind down, anyone who knows me, knows that I (something of a lifeform) don't wind down in the least.  

Interestingly, for folks bored silly by all this biology talk, there are implications from these very questions at the bleeding edge of studies done on energy creation, storage, (fuels) and policy.  In other words: the rising costs of energy, and the seemingly endless questions surrounding where we might get the electrons we need without begging alchemists for suggestions.  How much energy is in the worlds biomass?  A very interesting question, indeed, discussed by one of my favorite professors at MIT, whom I have been watching the lectures of for the last year, and who influenced my views on energy enormously.  He received an enormous grant from the recently unveiled partitioning of the DOE's stimulus money.  I wrote a blog entry on it a few weeks ago, given that I am considering investing in his commercialization of electrolysis.  His lab developed a special catalyst to split dirty water, at lower temperature, and atmospheric pressure, than the state of the art electrolysis machines.  Read: cheaper hydrogen.  This gentleman, Dr. Dan Nocera, has an arresting way of looking at energy, around the world.  And after you hear his views on how our Earth's population is going to consume energy, you will realize how implicitly uncompassionate  even our most pedestrian views about global policies are: we depend heavily on the poverty of others, so as not to have to share in a common endeavor.  I'd love to hear some of my less thoughtful friends ponder these things, for the solutions are hardly available through even the best of thoughtful lifestyles.  Solutions like building one nuclear power plant A DAY, for the next forty years, to have even a fraction of the energy we will need.  Nuclear power is a dead end, globally.  But you won't hear that frequently.  I mention all this, because Dr. Nocera is one of the more admired surveyors of estimation of global biomass energy.  His numbers speak to how much energy is in our total global biomass (whether burned, or turned into biofuels, total energy.  Here's a link to his incredible talk on MIT World: you should watch him.  Be advised however, he's a Doctor, Jim, not a course of Paxil.  You might have trouble sleeping should you listen very carefully.  If you give a ^&$% about human beings.  You do... you really do.

So, lest you think I've gotten off the topic.... I HAVE NOT.  I promise.  For Ho, in The Rainbow and The Worm has a few things to say about storage in the biosphere:

(don't worry about these numbers too much. they're real, and interesting, but not at the heart of why I am sharing this excerpt....)

Ho writes:  Unlike chemical species, however, energy cannot be tagged, for example, with a radioactive label, and its fate followed through the system; so the residence time for energy cannot be measured directly.  However, as the flow of energy into the biosphere is always accompanied by the flow of materials, especially CO2, into the system , the mean residence time for energy can be taken as the mean residence time for carbon in the system.   (Cont.) The size of the various carbon pools on the surface of the earth has been estimated, giving the toal biomass (both living and dead) on land and in the sea ats 2.9 X 10 E18 gm and 10.03 X 10 E18 gm, respectively.  The values for carbon flow, i.e., the total fixed by photosynthesis per year, on land and in the ocean, are respectively, 0.073 plus or minus 0.018 X10 E18 gm and 0.43 plus or minus 0.3 10 E18 gm.  Putting these values into the Flow of Species  formula :

Flow of species = Total amount of the species in the system/ Mean residence time

gives residence times of 40 years (on land) and 21.8 years (in the ocean) repectively. (!!!!)  

(briefly... I ask you to ponder that for a moment.  That's how long it takes carbon to "cycle."  And this material cycling of forty years duration, and 21 years duration for land and sea, is presented to stand in as a material shadow, for energy, material and energy flows being siblings of equivalent scale and relevance.  How lucky I am that such simple stuff can make me so very, very happy. Now for a little more funky "Ho down"....)

An interesting question arises here: what is the significance of the long residence time  of the energy that comes to the biosphere in photons from the sun?  The energy of the photon meanders through innumerable cycles and epicycle of metabolism such that it is released and stored in small packets ready for immediate utilisation or in medium term depots such as gradients and fields to longer term deposits in the form of glycogen and fat, and even longer term depots in the form of fossil fuels.  The efficiency (and perhaps stability) of metabolism is associated with this drawn-out web of coupled energy transfer, storage and utilisation within the highly differentiated space-time structure of the organism and, in the case of ecological systems, the ecological communities of organisms.  Metabolic and structural complexity prolongs the energy residence or storage time, perhaps by an equal occupation of all storage times (or all storge space times), affording the organism an efficient and stable living.  

So, not only are the falling electrons of the biosphere captured in high energy bonds, which then give and degrade and change through the "innumerable" cycles, and "space"/"time" of the biosphere, but the entirety of this extremely complex pinball machine, serves possibly to stabilize, and smooth out both the mega structure of the biosphere and the individuated structures of the organism, one being something of a fractal of the other.  See what I mean, Ho is a poet of energetics and our physical realm.

In future posts I would like to discuss a little more closely some of the things I have learned from Ho, and from another book, Oliver Morton's Eating the Sun, about photosynthesis.  The mechanisms life has at it's employ operate in a manner quite unlike the tools we utilize to accomplish the tasks we sometimes imagine as similar to the mandates of "living things."  The truth about the engines of the biosphere is far weirder, and more wondrous than our fleshed out metaphors could attempt to mimic.


Ande said...
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Ande said...

I love how you interlink our species with life. Nature is well-heeled when allowed to run free. You touched our current problem (how on earth are billions of people going to be fed within our societies conformities?). No, there is too much weight on the ecosystems (developing nations are developing. shit!).

Everyone wants to live. Cells want more and more. As you pointed out; welfare depends on other people’s poverty. Capitalism made people think that the many can win. But capitalism developed in a world where recourses where almost limitless. We boldly went to sea to find more. So, we’re stuck it seems, in rich countries, used to the taste and juice life. Many people I know have an attitude of “boundlessness”. OK, so sources are running out, let’s find some more. How are we going to find it when every grain of dust is reserved? As you pointed out, there seems to be a grave in front of us. Is there a way to solve the emergent recourses crises without ragnarök? I don’t think so (needs are one thing, wants another). Oppression has proven to be a favorable option to the painful process of diverging from the blueprint.

Andy Coffey said...

Hey Ande,

Thanks (you frequently seem to be the first to read me , and more or less always comment. I need to try harder to show you the same loyalty.)

First of all: what's "ragnarok?" You and Jenny were speaking of it in one of Jenny's poems the other day, and I wanted to ask, but felt it was important to speak of my feelings instead of making inquiry in a comment. This, however, is my blog, so I'm curious: what's ragnarok?

Yes! capitalism was developed in a world where resources were regarded as existing independently from any notion of scarcity, save a possible price. It is our particular curse today that even a willingness to pay a price comes with the constant reminder, like Marley's chains, that we have thought only of our selves, and our victims are becoming better and better at expressing themselves. Just as you and I are becoming better at sharing with one another. This is a disaster for the folks who were hoping to sweep consequences of our lifestyles under the carpet for another lifetime. Fifty years from now, the cost of living may very well be a shorter life. And like most of the drunks, and sick folks on the American scene I know, who wouldn't even dream of asking for medical attention (my favorite quote, from a friend, "I can't get swine flue: I'm unhealthy. Swine flu kills the healthy. I'm safe." Such thinking will help many Americans come to terms with the new shape of the world in the future. They will not understand, but rather rationalize bizarre self conceptions.

Harlequin said...

so, this post brought me back to my exercise physiology days .... and also to some wonderful stuff I read years ago about autopoeisis... biology can be as close to metaphysics as, well, metaphysics...

I also enjoyed your comments on the book.... and am looking forward to hearing more of your ruminations, interrogations and reflections

Andy Coffey said...


I had no idea you had "exercise physiology days." What were they? Did you study it as a discipline? Did it have something to do with your current work with autism, and "health." I'm intrigued.

Also, rather than looking it up, I'd love to hear your thoughts about autopoeisis. I love seeing you here, but feel very sad at not having seen your blog (and a wonderful, wonderful space, it is.) So, see you in about six minutes at your blog. Thanks for saying hi, and showing me just what I needed to do (now!)

Ande said...


Thanks for your interest. Well, most Swedes knows this tale, and its exciting.

Ragnarök is the fall of the Viking Gods, told by an ancient prophecy, written down in the early middle ages on Island by Snorri Sturlasson “Gylfaginning” (about the Swedish king Gylfi who meets the Aesir Gods). Island was deadlocked in a civil war at the time between traditionalists (wanting to preserve the Asa or Aesir Gods) and christians.

The whole point of Ragnarök is that it hasn't happened yet. Yggdrasil is an ash tree where Gods, men and beasts live:

I know an Ash standing | called Yggdrasill,
A high tree sprinkled | with snow-white clay;
Thence come the dews | in the dale that fall--
It stands ever green | above Urdr's Well.

The prophecy speaks of a time in the future when Yggdrasil begins to die:

Ash Yggdrasill | suffers anguish,
More than men know of
The stag bites above; | on the side it rotteth,
And Nídhöggr gnaws from below.
More serpents lie | under Yggdrasill's stock
Than every unwise ape can think:
Góinn and Móinn | (they're Grafvitnir's sons),
Grábakr and Grafvölludr;
Ófnir and Sváfnir | I think shall aye
Tear the trunk's twigs.
This leads to a resources crises which provokes great turmoil:

Brothers shall strive | and slaughter each other;
Own sisters' children | shall sin together;
Ill days among men, | many a whoredom:
An axe-age, a sword-age, | shields shall be cloven;
A wind-age, a wolf-age, | ere the world totters.

The Aesir Gods are largely untouched by this until giants, the wolf and the giant serpent join forces together with the trickster-traitor Loki (or Loke) and Hel's riders in an assault on Valhalla:
High blows Heimdallr, | the horn is aloft;
Odin communes | with Mimir's head;
Trembles Yggdrasill's | towering Ash;
The old tree wails | when the Ettin is loosed.
What of the Æsir? | What of the Elf-folk?
All Jötunheim echoes, | the Æsir are at council;
The dwarves are groaning | before their stone doors,
Wise in rock-walls; | wit ye yet, or what?
(Hrymr is the enemy, my comment)
Hrymr sails from the east, | the sea floods onward;
The monstrous Beast | twists in mighty wrath;
The Snake beats the waves, | the Eagle is screaming;
The gold-neb tears corpses, | Naglfar is loosed.
From the east sails the keel; | come now Múspell's folk
Over the sea-waves, | and Loki steereth;
There are the warlocks | all with the Wolf,--
With them is the brother | of Býleistr faring.
Surtr fares from southward | with switch-eating flame;
On his sword shimmers | the sun of the war-gods;
The rocks are falling, | and fiends are reeling,
Heroes tread Hel-way, | heaven is cloven.
(the All-father Odin is slayed by the Wolf, my comments)
Then to the Goddess | a second grief cometh,
When Odin fares | to fight with the Wolf,
And Beli's slayer, | the bright god, with Surtr;
There must fall | Frigg's beloved.
Odin's son goeth | to strife with the Wolf,--
Vídarr, speeding | to meet the slaughter-beast;
The sword in his hand | to the heart he thrusteth
Of the fiend's offspring; avenged is his Father.
(Thor is slayed by the giant Serpent, my comment)
Now goeth Hlödyn's | glorious son
Not in flight from the Serpent, | of fear unheeding;
All the earth's offspring | must empty the homesteads,
When furiously smiteth | Midgard's defender.
The sun shall be darkened, | earth sinks in the sea,--
Glide from the heaven | the glittering stars;
Smoke-reek rages | and reddening fire:
The high heat licks | against heaven itself.
Vígrídr hight the field | where in fight shall meet
    Surtr and the cherished gods;
An hundred leagues | it has on each side:
    Unto them that field is fated."

The Gods win the battle, but the world is burned. It continues:

Ande said...

“In that time the earth shall emerge out of the sea, and shall then be green and fair; then shall the fruits of it be brought forth unsown. Vídarr and Váli shall be living, inasmuch as neither sea nor the fire of Surtr shall have harmed them; and they shall dwell at Ida-Plain, where Ásgard was before. And then the sons of Thor, Módi and Magni, shall come there, and they shall have Mjöllnir there. After that Baldr shall come thither, and Hödr, from Hel; then all shall sit down together and hold speech. with one another, and call to mind their secret wisdom, and speak of those happenings which have been before: of the Midgard Serpent and of Fenris-Wolf. Then they shall find in the grass those golden chess-pieces which the Æsir had had; thus is it said:”
In the deities' shrines | shall dwell Vídarr and Váli,
When the Fire of Surtr is slackened;
Módi and Magni | shall have Mjöllnir
At the ceasing of Thor's strife.
It ends with the Swedish king being cast back into the mortal world;

“Thereupon Gangleri heard great noises on every side of him; and then, when he had looked about him more, lo, he stood out of doors on a level plain, and saw no hall there and no castle. Then he went his way forth and came home into his kingdom, and told those tidings which he had seen and heard; and after him each man told these tales to the other.”

Well, excuse me of the length of this Andy. Merry Christmas by the way.

Andy Coffey said...

Jesus Ande,

I had read some of this in Bullfinch's Mythology (I don't know the Swedish version... Bullfinch' is basically the Western Bible on Mythologies around the world. When I first read it, I found Loki very fun indeed. A friend of mine's cat is named for Loki!)

What a generous and lovely post... and what a wonderfully violent end to our crazy world... with the serpent and wolf and the God's all having at it. I just read this to my father, who enjoyed it while making me an espesso, which I am now savoring, as I thank you many times over.
And wish you and yours a fine Christmas as well.
May your family be close, and your wife smiling.

Andy Coffey said...
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