Tuesday, July 31, 2018

finally i can post my science salon pictures

ok here are the photos of my first science salon last month. (thanks to John Boyd for taking cool photos)

I started the evening by asking if life on Earth was an unusual accident or whether this universe easily spawns complexities like us.  And either way the answer goes... profound implications!

I used some of my complexity web page as an outline:


Lots of good questions and discussion!

Some people were very interested in the examples of complexity from simple mathematical rules and games described at the end of that page.

Then I talked about some of the research of the chemistry at alkaline hydrothermal vents and how they are possible places where life might have gotten some of its tricks.


This is exciting because two years ago spacecraft Cassini dove through the plumes of Saturn's moon Enceladus and found dissolved silicate minerals and molecular Hydrogen (H2), hints that there might be hydrothermal vents at the bottom of the ocean under the ice of Enceladus.

Then we grew chemical gardens ('Magic rocks') because these mimic some of the processes in these hydrothermal vents.  Everybody helped out.


I didn't know how well that part would work, especially I wanted to watch them grow under the microscope. Everything worked.  Of course I was too pre-occupied to take pics of them under the microscope through my cameraphone!  alas.  We had a Blast.

We will do science salon every other sunday 6:30pm at Iconica Social Club in Northampton MA (coffee, pressed juices, amazing pastries, often live music). next one is 12Aug2018, though Iconica is on vacation that week.  We'll figure it out.


testing: tiny wasp

i caught her with my phonecamera and lense fast enough!  reminds me of a wasp i used to work with that layed her eggs inside the eggs of caterpillars.  we were doing this because the wasp larvae hatch inside the caterpillars and then eat the caterpillars from the inside while the caterpillars ate grass leaves that were or weren't infected with a fungus that lived inside them...  long story.  at any rate this kind of horror to egofocused critters like us was one of the reasons that Charles Darwin decided there couldn't be a benevolent god...

at least blogger works again.

more to come

Sunday, February 25, 2018

Sketch Of My Harlem Library/Bedford Limestone Story

i was living in harlem new york a few years ago, and we were out on the fire escape and i noticed that the stones in the building had cool fossils in them. limestone with lots of crinoid/blastoid things.


i just happened to have a pocket field guide to fossils, so i looked them up and got them down to the pennnsylvanian. then i had chanced to find an old stratigraphy text book, so i tried to see if i could find where this kind of rock might be found in the U.S. lo and behold the book mentioned the stratum of pennsylvanian limestone called the Bedford limestone in Indiana.

the next day i went to the internet to look up this bedford limestone and found a website for a quarry in it!


on the site was listed some famous buildings that were made from the stone in the quarry. one was called the Harlem Library from the '20s or someting. so i did more research and found out that our apartment building had actually been the Harlem Library back then!

[pic of harlem library here]

this was immensely satisfying! i rarely get to do such fun detective work with biology and geology! i felt like sherlock holmes!


33. Greater Bethel A.M.E. Church
32 West 123rd Street, southeast corner of Malcolm X Boulevard and W. 123rd Street - Designated New York City Historic Landmark
One of the oldest black churches in New York, the Greater Bethel A.M.E. was founded in Lower Manhattan in 1819 and moved into the Harlem Library building in the early twentieth century. Edgar K. Bourne, architect of this limestone and brick building constructed from 1891-1892, was also a member of the library's board of trustees. The church moved into the structure on West 123rd Street when the Harlem Library was moved to 9-11 West 124th Street after being added to the New York Public Library System in 1901.

Friday, January 5, 2018

I Need To Give This Lecture About Whether Life Spontaneously Arises From Chemistry In The Universe

Here it is in a half filled in sketch from this morning.  I might try to present some of it at a Nerd Night (20 minute talk and slides.  not sure how much I can get into 20 minutes)

I will need to find or create some cool animated videos and put together some images...

This page describes many of the topics with pictures and videos


what is life?  I'm gonna take you through some history of different conceptions of what is life to the brink of thinking that life is way too unusual and complex and must be designed (God or at least Cosmological Anthropic Principle)... to an alternative view that we can't conclude this... and then to new developments that give us hope that we can find a more general scientific quest for many kinds of life in many kinds of universes

Some 10s of thousands of years ago (look at cave paintings and burials?) we awoke to this incredibly intense complex inner experience.  the experience of our minds blew our minds!

this lead us to believe that creative mind was infused in the cosmos was the very foundation to the cosmos (Gods)

Lucretius, though, reports an alternative view: atomistic hypothesis for molecular biology of the developing chick in the egg, Wildly spot on hypothesis, but no experimental science to back it up.  THAT took about 1400 years to get started.

so there always seemed like a continuum of life forms from slime on up to animals except soul is added to make men (maybe some pets)  (i should see though, what aristotle thought of all this, he LIKED biology, and observed well), This sentiment existed even among scientists even up to the 17th century

finally once science got going in the west, Redi dispells that animals spontaneously form from slime. by keeping flies off of rotting meat with gauze he showed that no maggots spontaneously formed. Life and Slime are diff phenomenon.

but then leeuvenhoek confuses the issue.  why his discovery so muddy (150 years to clear up) and gailelos telescope so clear!  well... the biology of pond water WAS way muddier than the paltry few orbs in th solar system.  also apparently it turns out that it is VERY hard to make a good microscope, leeuvenhoek was something of a genius craftsman and wouldn't share how he made his lenses!  so for a hundred and fifty years it again looked like life existed in smaller and simpler versions all the way down to the tiniest specks (living or nonliving) we could see in microscopes, and hard it was to determine what we were seeing.

but by the mid 19th century,  3 things:
1) pasteur, leiden, schwann, koch: even Leevenhoeks animalcules, (microscopes were better by here), they ARE distinct from slime and they ONLY come from each other, no spontaneous generation.  in fact, ALL life comes in the form of cells giving birth to one another.  life, cells, NEVER spontaneously form from slime!

2) the science of chemistry begins to clarify

3) darwin: all life is a continuous lineage of grandmother to grandmother from the ur cell to us.


1905: trio of Boltzman, plank to einstein, perrin, xray diffraction nails that matter does IN FACT come in discrete parts!  atoms and molecules!  we can start looking for a mechanical basis for life.

avogadros number: most of you learned it and your chemistry teachers probably didn't spend the time to drive home its profound implications for human intellectual history.  what a criminal act!  The fact that there are TRILLIONS of interacting parts available to make life as subtle and creative as it is, is a profound discovery.

it's not that atoms are so tiny, it's that WE ARE HUMOUNGUS. we are societies of a trillion of those microscopic single celled amoebas (and thinking? experience? is it therefore the conversation that ensues when billions of them have conversations in our brains?  we STILL don't know what human thinking IS),

And each of these living amoeba is a whorlwind of more interacting molecular nanorobots than there are bricks in all of new york city!

what does this insight give us?

by the 20th century, chemistry is mature, we start discovering the heteropolymers: proteins, DNA, the network of 100s of discrete reactions that is biochemistry of life, and we begin thinking that we can ferret out the abiotic origins of life from bare chemistry. It seemed like an achievable goal.

[what is the history during all this of 'elan vital'?  that life could not POSSIBLY have a mechanistic explanation?]



By the 1960s we see that it's not so simple:

[give a picture of Life as a basically a network of 800 different interlocking chemical reactions between 100 different small molecules.  make a wall size animation]

by itself chem looks like this: [make an animation of the dozens of chem reactions in a flame or at least doszens of chem reactions that makes broad patterns in the BZ reaction, a little complex, but not terribly organized, not 100s of different parts!]

life makes it's network of reactions FAR MORE intricate with its set of 1000 different enzymes/proteins/nanorobots that select the specific reactions out of the possible chemical chaos.

but how does this cast of 1000 nanorobots come about?

show a wall size animation of the core: set of 100 nanorobots (proteins and RNA) that can reproduce themeselves and the whole show.  self replicating life.

there is a HUGE GAP between the bare chemistry we know of in the lab and this..  we don't know how to breach!

CURRENT Origins of Life RESEARCH almost wants to find the excact route to how this particular version of earthlife formed. NASA wants to 'follow the water' and find DNA and amino acids.

BUT THIS IS THE WRONG way to go about it!!  They will miss all the good stuff!

If we were to find a single sequence of events that reproduces how life on earth formed step by step from nonliving chemicals... and even if we found the same kind of life on other planets... but NO OTHER ALTERNATE KINDS of life, where would that leave us?  We'd have to conclude that life is a very rare contingent phenomenon, a chance draw of luck out of the zillions of possibilities in the universe.

without any variations on a theme for life in this univrse, we would basically not be able to call studying life a science at all. there'd be no generalizations we could make.

we might even conclude that the universe is uniquely designed to exactly produce this kind of life, after all, if we were to alter  ANY of the physical constants of physics by the mere thousandth or milionth of a percent, stars wouldn't even form, or atoms beyond Helium wouldn't form, no planets, no chemsitry, no life.

This line of thinking goes along the name of Cosmological Anthropic Principle.  It could even lead to conclude that the universe was designed by a God.  well... why NOT?  the more we study physics and the universe, the more we find some VERY STRANGE things.  and we don't even understand what 95% of the observable universe is made out of (we call that portion dark matter and dark energy)

Instead of looking for just one path to just one kind of life, lets try to place life in a broader range of possible chemical systems that can become complex.

silverchloride swarms  these are silver chloride particles in suspension in solution of sulphuric acid and hydrogen peroxide which under UV alternately repell and attract each other producing weird patterns

Belouzov Zhabotinsky reaction: here we start with 5 simple chemicals and watch it unfold and it unfolds into a swirl of dozens of chemicals and reactions and all the while from homogenous begining develops long range spiral patterns

CIMA: a similar kind of reaction produces all sorts of patterns, even self reproducing blobs that swarm around the petri dish

and there are differential equations that can mimic CIMA and produce those curious self reproducing blobs. 

there is even a generalized version of conway life (see below...), Larger than Life, that ALSO produces those self reproducing moving blobs.... VERY curious

and even the multichambered 'chemical gardens' that grow at alkali deep sea vents that i will describe later...

conway life (some of these are spelled out on this page with pictures)
langton's ant (ditto)
langton's, Sayama's, Byl's self replicating loops
Tom Ray's evolving reproducing computer programs...

Each of these is a kind of miniature universe with its own simple laws of phyics that we can follow step by step, and in each, curious complex patterns can form from simple sets of rules, simple starting conditions...

So now after exploring this breadth of complexity, there are two more ideas that lead us to find an alternative to this narrow bind of the Cosmological Anthropic Principle or Intelligent Design..

1) wolfram's book A New Kind Of Science (i know, an insufferable book by an insufferable ass so full of himself that he ignores all research outside of his own and even gets many things WRONG because of that, and his outlook is rather odd... BUT...  he has spent hundreds of hours watching patterns form in these simple systems...

remember, we thought of Conway's life and Langton's ant as little miniature alternative universes with their own chemistries and each produces some interesting 'critters'.  What wolfram shows is that there are DOZENS of classes of these discrete dynamical systems.  and in each class there is a certain range of systems that are computationaly universal, that is...even conway life, we can build a giant pattern that works like a computer out of all those blinkers and glider guns that form in it and with that computer... we can simulate ANY of the
other alternate kinds of dynamical systems... What Wolfram shows is that for each style of math system, there are a range of them that can simulate any other kind.

2)  In "The Theory Of Everything", Laughlin and Pines explain that we do NOT know how to predict the macroscopic patterns that we see in the universe just from an understanding of the microphysics (laws of physics and quantum mechanics)...

These two lines of thought lead us to the following reasoning:  Yes it is true as the Anthropic principle people say... that if we shift even one of the laws of physics in the slightest we won't get suns, atoms, planets, chemistry and earthlife.  BUT by laughlin and pines' reasoning we can't predict WHAT WE WOULD GET INSTEAD, maybe something just as interesting?
Well... by Wolfram's examples with alternate mathematical systems... it seems possible that a significant proportion out of an uncountably infinite number of variations on physics are at least rich enough to be able to simulate any other.  Even if as in Wolfram's example of a simple cellular automata taking a huge amount of space and time to run a simulation of another one, an alternate universe might develop lifelike patterns on scales unimaginably huge or slow that can simulate our physics, but for creatures in that physics, they wouldn't know it was a totally different scale than life in our universe... after all... WE are HUGE AND SLOW compared to the basic molecular level of interactions that simulates US.

blows anthropic principle out of water

my goal then is to show that in the phase space of all possible physicses, lifelike complexity is not a rare contingent phenomenon, it's a basic mathematical property of any number of kinds of physicses.  no need for physics to be carefully designed!

that's a 10,000 year project, what of near future?


where willl we find this chemsitry?

describe the amazing adventure: in 1970 we sent the voyager II space craft on an immense 10 year journey... and we found so many different worlds... each with its own version of geochemsitry, each similar and different than Earth.  hints of an ocean under the frozen surface of Jupiter's moon europa. Sulfur volcanos on Io.  We sent more crafts... Cassini to Saturn, New Horizons to Pluto, Dawn to the Asteroids Vesta and Ceres...  More hints of internal oceans, more geochemistries.

Cassini flew through ERUPTING GUYSERS coming out of Saturn's moon enceladus.  It DOES have an internal ocean, and not only that, Cassini tasted the vapors coming out of those plumes: It detected silicate, carbonate minerals in the water.  and after much careful analysis: molecular hydrogen: H2.  what does THAT mean?

at same time we discovered deep sea vents.  and even alkaline deep sea vents... waht are they? Martin and Russel where inspired when Russel's son, discoverd one day in a fit of anger that his magic rock garden crystals (the ones you buy at the store and grow in a solution in a jar) were HOLLOW.  Russel noticed that these were slightly similar to the silicate chimneys that grow at the deep sea vents.

Chemistry is actually capable of alot: deep sea water seeps into cracks in the ocean floor and flows deep into the hot mantle of the earth were there are minerals called olivines.  down there, olivines are not in equilibrium with water, so chemical reactions occur, heat is produced, and alkali solutions are produced along with molecular H2.  this is the serpentinization reaction (the olivine is converted into the mineral serpentine).

these solutions rise back to the surface rock at the ocean floor.  this time it is the alkali solution and the H2 that is not at equilibrium with the slightly acid and CO2 rich ocean waters (especially so in conditions before photosynthesis evolved to produce oxygen in the atmosphere).  reduced iron and sulfides also issue forth and when all this meets the cold ocean waters... they build frothy chemical gardens.  these are silicate structures that are full of millions of microscopic chambers, alkaline rich on the inside, acid on the outside, H2 on the inside, and H+ on the outside.  with catalytic iron and nickel sulfides embedded in the walls. 

These structures curiously, closely mimic how living cells today are built, and in fact, these structrures have the potential to engage in reaction cycles that build up organic molecules out of the CO2 and H2 in some ways similar to how the molecular biology of life does.  Active research is being done on this now.

and we have hints that this is now happening deep in the other oceans across the solar system!

And this is just ONE example being explored.

lets not discount the non ocean planets: Io with its crazy sulfur volcanoes, Venus with it's high temperature and pressure acid atmosphere that however has some regions which, again, are oxidized and some reduced... 

And Titon: another moon (of Saturn) with an ocean underneath a frozen ice surface, but... it's so cold that its atmosphere is not boiled off, and its atmosphere?  Nitrogen like ours but with copious amounts of methane and ethane which because it is so far from the sun and cold, can ... condense into methane rain!  Titan has methane and ammonia rain and rivers and lakes and clouds... running its 'hydrological' cycle on top of the frozen ice 'rocks' which itself is over an ocean which sits on a warm mantle of silicate rock...  are there water guysers there too mixing chemistries with the methane hydrocycle?  more exploration...

In Titan's atmosphere... there may be a kind of metabolic cycle with solar radiation converting ethane to high energy bonded ethene, which rains to the clouded surface where chemcial reactions with it relese energy and turn it back to ethane.  all the while solar radiation and cosmic rays are cooking the nitrogen and methane into complex goops of organic molecules which slowly snow down to the surface...  These also occur on Pluto and Triton (moon of Neptune)...

There is SUCH A VARIETY OF 'GEOCHEMISTRIES' out there.  we need to stretch our minds, who knows what we might find.

are a couple dozen planets and moons not enough for you?  for the past 20 years we've been discovering OTHER SOLAR SYSTEMS around other stars.  seems almost EVERY star has planets, planets in even more different arrangements than what we have... the possibilities are truly endless.

will we get to explore these too?  current technology would take hundreds of years to get conventional space craft to them... but we keep inventing new shit, we keep discovering new shit.  400 years ago we dind't even know the moving dots in the sky were suns and planets.  It was only a 100 years ago that we began dreaming that we could actually fly to them.  20 years ago, we din't even think we could SEE those exoplanets so bleeedin far away...


so along with the range of chemical systems we are begining to explore, this planetary exploration will hopefully push us into broadening the range of chemical systems we start studying and the synergy between our chemistry exploration and the pattern formation in all those mathematical dynamical systems...

hopefully we can not only bridge the gap between bare chemnistry [show the flame chemistry video] and this tight surprising clusterfuck of interlocking bewildering complexity at the core of earthlife [show the video of the core molec bio of DNA to Ribosomes to Proteins to DNA], we will also be able to find enough alternate examples like it to show that it is not an unexplainable singularity, but a basic consequence of mathematics itself, a creative process we can explore and take part in.  To be gods ourselves.


Tuesday, August 8, 2017

It IS Cyperus Esculentus, the Nut Sedge

so the other day i found a slightly different sedge, and looking carefully at the flowerspikes i decided it was a different species, and today i dug it up and found tubers:

here is Cyperus strigosus, which i see all over the place in moderately damp situatio s.  you can see it in the foreground, very full and spikey.  Behind it is a taller looser yellower sedge.

here is a closer comparison, C. strigosus on the right

even closer, notice strigosus on the right has long thin green keeled flower scales while the plant on the left has more smaller stubby browner scales

so, today i went back and dug up one of the flimsier sedges and found tubers. that's a tuber growing off of one of the roots beneath the sedge. It's Cyperus esculentus, nut sedge.  the tubers are supposed to be edible.  if i find a bigger mature patch maybe i will try.  probly gotta boil or roast them?

I will try posting my pics and drawings of 18 sedge species later.

Sunday, July 30, 2017

reviewing sedges and rushes

worked on 13 species/speimens this week

here's a a little seed from... Eleocharis.. engelmanni?

i'll go back out to the field to get better shots
what else in my phone?
Scirpus atrovirens

these six lived in a small wet patch.  Ok, so know i know that the big red bunches are actually insect galls on the Juncus acuminatus.  which i also found samples of by my house

Saturday, July 22, 2017

Critters On The Porch!

first we have an ant with a heart shaped butt: genus Cramatogaster
shiny little ant.  you can see the porch railing reflecting on her.

next a dusky Lasius ant.  this ant was VERY fast.  very hard to get a shot.
these ants are about a quater of an inch long..  Lasius you will find making a bunch of tiny volcano entrances to their nest along sidewalks and in other open places

next we have zebra jumping spider.  I should have tried to gt infront of it and get a good mug shot.
ok thats enough for today.