Friday, June 12, 2020

Are You Glad You Didn't Hatch From An Egg? How we used retroviruses to become mammals

Are you glad you didn't hatch from an egg?  Here's a baby Echidna doing it.  An Echidna is ALMOST a mammal.

https://youtu.be/dHocViqKbbc

Well, you didn't hatch from an egg, and that has profound effects on our psychology!  we get to grow quite large inside our mothers and it's an intense 9 month relationship.  But we mammals don't take lightly to having alien creatures living inside us and feeding on our fluids.  What I mean by alien is that the fetus has its FATHER'S GENES!  The mother's white blood cells are constantly slurping through her body, slipping between tissue cells and searching for foreign invaders.  If they get to the fetus... TROUBLE! so...

how is it done?  VIRUSES!  yes that's right, The fetus uses viruses to build an impenetrable barrier against these white blood cells! As with everything in life, the evil is mixed in with the good.

here is an image of the baby placenta with its impenatrable barrier from
http://www.embryology.ch/anglais/fplacenta/fecond03.html




Somehow in the process of proto-mammals evolving to give birth to live young, they invented placentas with the help of scrappy random retroviruses they accumulated in their DNA 'junk drawers'.  The placenta is the organ responsible for integrating the fetus with the mother's tissues and keeping the mother's immune system from rejecting the fetus.  How do the retroviruses help?

Retroviruses attack mammals by fusing their membranes with mammal cell membranes, that is how they gain entry.  In the course of invasion, retrovirus DNA accumulates in their hosts and if it gets into egg cells.. it can survive generation after generation.  eventually many of the viral genes decay due to neutral evolution, but the genes for membrane fusion may still remain functional.

in fact by keeping old de-activated viruses around that can still express these fusion genes helps us to fight off new retroviruses by clogging our membrane receptors so they won't fuse with the new viruses!  and so mammals occasionally update their junk drawers of retrovirus fusion genes!

eventually proto-mammals figured out how to use them in their placentas.  One problem the placenta will face is maternal white blood cells trying to slip in between cells which is their function and explore the growing fetus.  If the white blood cells find the fetus, and sense the father's proteins, they will attack.  the father's proteins are foreign and don't belong in the mother.

Here is how the placenta uses the retroviruses to defend: the placental cells in a layer called the syncitiotrophoblast use the retroviral genes to fuse together into ONE HUGE CELL. This huge cell completely surrounds the fetus! This means there are NO spaces between cells for the mother's white blood cells to slip between and invade!

some references on this amazing syncytiotrophoblast.  so far i only have a suggestion from wikipedia that the function of forming ONE single membrane, is to block entry by white blood cells.  I'll keep looking.

https://www.sciencedirect.com/topics/neuroscience/syncytiotrophoblast

https://en.wikipedia.org/wiki/Syncytiotrophoblast

I'm not 100% sure this is the whole story on the usefulness of the retroviruses, it's very complicated in there and I thought there were more functions for the retroviral genes.. and I don't have a medical library at my disposal.  The placenta also produces hormones that help suppress the mother's immune response in other ways.  I'm still searching.


Another  fascinating thing is that different groups of mammals continue to use new retroviruses for these purposes.  the ones we use are different than the ones mice use.  each lineage caught its own retroviruses!


Is it safe to use viruses to build placentas?  well... placentas only stay in the body for 9 months, so maybe it's kinda safe!

Here is the full story about the retroviruses:

https://schaechter.asmblog.org/schaechter/2014/06/retroviruses-the-placenta-and-the-genomic-junk-drawer.html

Monday, May 18, 2020

Shorter Intro To My Complexity Lab Manual (still in preparation)

A brief outline of the complexity lab manual: 11 chapters

I was originally motivated to put together the Complexity Lab Manual in order to give people the tools they need to think about how evolutionary biology and even the origins of life from chemistry could possibly work.  I feel that the standard biology and chemistry education doesn't always point out the necessary insights, especially interconnections between far flung fields of studies. 

The Complexity Lab Manual is an interdisciplinary set of labs, videos, diagrams, games you play on paper, pointers into the literature etc.. that explore examples of how complex order is achieved by interactions of simple parts.  It spans biology, chemistry, geology, computer science, and mathematics.  The level of the labs runs from elementary school on up to open ended research.

There are many books that cover some of these ideas (with a lot of hand waving) but I feel very few show concrete enough examples in detail, and explain how to actually perform experiments so that the reader can get first hand experience in complex pattern formation and therefore come to their own conclusions.  Also many books and courses on complexity don't dive into the nitty gritty of the molecular nature of life and explore what chemistry is capable of.

The experience proceeds from the every day macroscopic down to microscopic cellular life, even deeper into chemistry, and to the very mathematics of the universe itself.  The chapters are:

(1) Natural history: explore the diversity of organisms and how detailed they are.

(2) Computer science: one way we know how to build complexity from simple parts. can we make a robot organism? not yet!

(3) How DO organisms build themselves? living cells keep replicating and arranging themselves into patterns.

(4) Watch single celled protozoa, what are they? Giant whorlwind dances of molecules.

(5) Explore the molecular world: trillions of sticky parts bumping into each other and responding to each other.

(8) Chemistry at rest: the dozen most common elements can form over 800 different minerals.

(6) Chemistry in motion: watch energy flow animate systems into  dynamic stable patterns.

(7) Chemistry is hard to do, so work out mathematical dynamical systems that show how repeating simple rules can lead to extreme complexity.

(9) Static mathematical systems, the roots of complexity ARE math.

(10) Watch complex programs evolve in computer operating systems.

(11) Now you have enough experience and imagination to begin your studies of chemistry of the origins of life!

Each chapter has labs, like collecting and keying out plants, learning to program in machine code, watching single celled protozoa, setting up convection cells in fluids, chemisty that create patterns like the Belousov Zhabotinsky reaction, programming cellular automata like John Horton Conway's Game of Life...



MORE EXTENDED DESCRIPTION WITH EXAMPLE LABS

Chapter 1 is natural history of macroscopic life, then once we experience the diversity and complexity of it, we ask: can we make robots that can mimic what an organism can do?

[6] learn to identify 100 different plant species, [4.5] study how honeybees perform over 270 different tasks and ultimately reproduce themselves,


So Chapter 2 moves to digital electronics and computer programming.  This gives concrete experience in the complexity we have so far been able to build out of many simple parts and give us an idea how hard the task is, because NO we cannot build such robots.  So we ask how does life do it? 

[8] learn the hierarchy from transistors to logic gates to processing units, to programmable computers, [9] write some computer programs using only a simple set of machine instructions, [61] watch a team of robot dogs play soccer


Chapter 3 explores developmental biology, in which we conclude life can do this because life is a property of its simplest components: cells.  Cells build us from the inside, by growing and reproducing.

[17] observe how plants are constructed out of cells under the microscope, [16] watch videos of animal development or maybe watch snails develop on glass of an aquarium


Chapter 4 watches living protozoa and does some simple chemical analysis to ask WHAT ARE THEY?  This moves us to the center of this lab. 

[22] watch single celled protists in pond water, [25] watch Oscillatoria grow from just water, air and glass in a jar, [26] do some paper chromatography to get hints at how many different parts these creatures are made out of, [27] look at electron microscope pictures to see how complex inside


Chapter 5 explores what is the molecular world?  Molecules come in a combinatorically bewildering variety of forms, they are in constant motion probing each other, are reactive... But how does this build dynamic complexity?  Then we peek at the bewildering complexity of the molecular biology of the living cell. How can simple chemistry give rise to this? The answers are energy flow and mathematics.

[] burn that dried Oscillatoria back into air, water and ash, [72] watch Brownian motion, a first hint at the discrete nature of matter, [73] try to make a lipid mono-layer on water to try to count the number of molecules, [29] count how many bricks there are in a large metropolitan city, [30] learn what Avogadro's number is and what it's implications are: more molecules in a cell than bricks in NYC, [27] study how clathrin coated pits are cooperative systems of molecules in a cell that can achieve global goals, [31] do some organic chemistry to watch how molecules can be sensitive to the conditions around them and to each other

(i'm not so experienced with the chemistry! I'd really like to find simple labs to hint at the discrete nature of chemistry, a way to suggest Einstein's and Perrin's work to measure Avogadro's number!)


But first, in Chapter 8 (I think it's best to put it here now), we first look at the complexity that chemistry can give us even before we move to dynamic systems, the complexity already inherent in the periodic chart of elements, the bewildering set of minerals on earth, phase transitions, snowflakes..

[70] explore how the periodic chart of elements is already a curious mix of complexity but not total chaos.  Why does simply adding one more proton at a time create qualitative changes?, [71] explore the world of minerals.  840 different minerals can form from just the dozen most common elements, [76] watch phase transitions in water and sulfur, [75] observe snowflakes and various forms of frost develop


Now we bring in energy flow.  Chapter 6 explores dissapative systems, macroscopic and chemical examples of how energy flow through fluids and chemical systems produces dynamic, creative and stable patterns.  But can the patterns achieve the complexity of life?  At this point the chemistry becomes hard to do, so we move to mathematical dynamical systems, where we can watch real complexity develop before our eyes.

[64.2] build the chaotic waterwheel, [33] build a thermo-acoustic engine or sterling engine, [34] watch Benard convection in a shallow fluid, [35] make the mercury beating heart oscillator, [42] watch 5 simple chemicals create dynamic spiral patterns in a petri dish: Belousov Zhabotinsky reaction, [44] watch chemistry and convection form a flame


Chapter 7 explores mathematical dynamical systems both discrete and continuous that show surprising examples of complex pattern formation by the iterations of simple sets of rules.

[48] play with John Horton Conway's game of life on a checker board, [48.5] program it on a computer and really have fun, [48.6] program Langton's ant on a computer and watch the simplest rule evolve a structure that takes 9000 steps! [53] explore the range of behaviors in 1 dimensional cellular automata, [58] learn how the Mandelbrot set (the most complicated mathematical object) is formed from simple geometrical rules


Finally to attempt to explore the ultimate roots of complexity Chapter 9 explores pattern formation in static mathematics: we watch how a small simple set of constraints can determine an interestingly complex but not infinitely chaotic array of structures.

[79] the definition of prime numbers is easy but leads to a non repeating pattern who's properties we've yet to fully comprehend
[87] combinatorics of finite graphs: how many ways can you put together Styrofoam balls with 1 toothpick, 2, 3... [80] now make the only 5 platonic solids, [81] review the surprising complexity in the classification of the finite simple groups


The two last chapters, Chapter 10 on evolutionary biology and Chapter 11 on Origins of Life studies, will be just hints.  We've laid the foundational tools, they can be another book!  Chapter 10 will explore systems like Tom Ray's Tierra and Hiroki Sayama's evoloops where we watch complex structures evolve.  I don't know what I want to put in chapter 11 yet.

[96] watch Tom Ray's Tierra evolve computer programs and ecosystems, [97] watch Sayama's evo loops evolve chaotically

Sunday, April 26, 2020

History Of Scientific Discovery In 500 Tweets (in progress)


1500
i have no clue when we decided rough scale of solar system. that the solar system is vast empty space

16th century Europeans decide to challenge and question the authoritative texts with their own observations

16th cent Europe: decide, contra Aristotle, the universe is orderly enough to find that order through painstaking observation and data collection

science begins as the assumption that processes in the sky, at all scales and in the past are the same as we can observe now on earth


assume the universe is governed by a set of universal rules which don't change over time and are the same in every lab, in earth and heavens

17th cent Europe invents regular cycles of experiment, methodical widespread publication of detailed reports of method, critical discussion


Magellan finally spans the globe of the earth

1540
Brahe trusting orderly universe, builds massive observatory and spends life recording details of the motions of seemingly chaotic mars

Kepler slaves away at Brahe's data and assuming sun at center of solar system finds 3 formulas of motion for every planet around the sun


Galileo, newton begin seeking mechanistic explanations of phenomena, from interacting isolatable parts, ultimately atoms



Galileo breaks with classical medieval un-analyzable holism: ballistic flight can be split into independent vertical and horizontal components

with this principle, G. cleverly used inclined plane and device to measure time to take data on time of descent, and discovered acceleration

the vertical component of ballistic flight accelerates towards the earth independently of the horizontal component, fixed velocity from launch

Galileo puts a linear number scale to temperature, allowing us to find analytical patterns in the relationship between temp pressure and volume

Galileo invents thermometer allowing us to find quantitative patterns between temperature, pressure and volume of gasses, heat and work


1600
Galileo puts new spyglass to the night sky and finds mountains on the moon.  it is a world with geology like earth

Galileo puts his spyglass to the night sky: there are more stars.  THOUSANDS more stars!

Galileo puts his spyglass to the milky way, it's actually stars, many more stars.  MILLIONS of more stars

watching Venus over the years, Galileo finds phases like the moon but both full and crescent phase near the sun so Venus revolves around the sun


Galileo's telescope observations and Brahe's measurements show that all the planets orbit in ellipses around the sun, not the earth.

by watching Jupiter day after day in his telescope, Galileo finds 4 moons revolving round a disk. it's another world with moons like earth

Galileo finds that his telescope magnifies the planets to disks, but never magnifies the stars to disks, they must be very far away



Galileo infinity paradox: associate 1,4,9,16.. with 1,2,3,4.. shows subset of integers is just as numerous as larger containing set




1620
with Von Helmont, we discovered gasses as a weighable component to chemical reactions.  this allowed us to account for reactions completely


1660
Boyle breaks with classical 4 unisolatable elements.  It's not a chaos of infinite variety of combinations but it's more than 4 elements.

Boyle: substances aren't continuous mixtures of 4 unisolatable 'principles', there are a discrete number of elements which can be isolated.

studying pressure, volume, temperature relationships in gasses allowed us to eventually equate temperature with motion of molecules

chemistry, astronomy, and mathematics begin to show that the universe is interestingly messy, but not a total inseparable chaos.

Leeuwenhoek crafts remarkably powerful lenses and sees microscopic creatures never seen before.  takes science 150 years to take seriously

animals and plants come only from eggs that come from other animals and plants, they do not form higgledy piggledy from rotting schmutz.

life on earth today does not spontaneously form from the principles of physics, but is a hereditary affair, only coming from other life

when did scientists start questioning fanciful faunas, seeking confirmation of bizarre claims?  Even as stranger creatures were discovered?

by Lineaus' time, 10,000 species of plants had been discovered, described and sorted out

at some point, 100,000 life forms were classified.  What effect did this number have on our view of life? by Darwin's time, how many?

and then a million?  and even today, we don't know if there are on the order of a million or 100million, nor what a species even is!



When did we notice that warm air rises? i guess round boyle's time we knew heat reduced density increased buoyancy?


Roemer, records the motions of Jupiter's moons, notices a delay the further Earth is from Jupiter, and calculates a finite speed for light. it's FAST

Roemer, finding apparent orbits of Jupiter's moons delayed when Earth is further from Jupiter, calculates finite speed for light. 186,000 miles/s


1680
the difference in temperature between a hot fire and cold water propels a steam engine into spontaneous motion

hot cylinder expands, causing cold water valve to open, contracting cylinder, closing valve, cylinder heats again... neg feedback causes cycles

measuring gasses allowed us to discover central reaction of life: flesh burns to breath: CO2, H2O, powering movement and releasing heat

Then plants use sunlight to combine breath molecules back into burnable plant substance releasing Oxygen for burning again

Newton synthesizes Kepler's formulas for planets with Galileo's acceleration of falling objects and finds universal law of gravational motion

Newton found the way to see that the motions of the heavens could be explained with the same rules as ballistic motions here on earth


1760 ?
Redox reactions between different metals can propel charges along a wire.  This is an electric current from a battery.



1780
life: continuous cycles of sunlight fusing CO2 and H2O to CH and O2 then burning CH in O2 back to CO2 and H2O, releasing heat back to night

life: continuous cycles of sunlight fusing breath into plantflesh then animals burning flesh back to breath realeasing heat back to night

so in steam engines as in life, flow from high potential energy to low (hot to cold, sun to night) causes cycles and pattern formation


Cavendish measures minute gravitational force between 2 10lb spheres & comparing that to the force between 1 sphere and earth, weighs the earth

weighing Earth allows us to find density: 5g/cc it's not hollow or superdense! bedrock has density ~2 so deeper layers must be denser, iron?



1800
geology begins by watching processes today of volcanism, erosion, deposition, and extrapolating these backwards in time. yields LONG timeline

Geologists begin mapping rock layers, building up a sequence of events, endless cycles of rock building and erosion?



1820
electric current carrying wires can induce each other to move, build a motor!


interference patterns between beams of light show that light travels in waves.  SOMETHING is oscillating.



by 1820s there are hints of integral proportions in chemical reactions hinting in an atomic theory but there is also still too much chaos.

by 1820s there are 49 known elements, with many curious properties and no systematic classification in sight

by 1820s there are 2000 known compounds

when do we decide that we find no new substances that are NOT made of elements we already know?

we find 2 chemicals with same composition but different properties. are properties due to ARRANGEMENT of atoms? chemicals have structure?


first hint of molecular biology, Mulder finds consistant similar high molecular weight formulas for various proteins.  1000s of atoms each

Babbage and lovelace envision a mechanical device that can be programmed to execute step by step any sequence of symbolic/arithmetic operations

detecting shift in star's apparent position as earth orbits the sun shows their distance (parallax). 10,000 times the distance to planets

look at finger with each eye, it shifts. look at star when earth moves around sun.  it shifts a LOT less.  we calculate it's REALLY far away


1840
Joule measures that a specific amount of motion produces a specific amount of heat by friction, and hypothesizes heat is motion of atoms.

Clausius' kinetic model: gas molecules rebounding from chamber walls accounts for measured relationship between pressure, and temperature

volumes of gasses react chemicaly in small integer proportions: 1:1, 1:2, 2:3 ... as if combining molecule by molecule


many diseases are found to be caused by microscopic organisms (germs) which can be identified and grown in the lab.

Spallanzani, Virchow, Pasteur: not only do all animals and plants come from eggcells, ALL cells, even bacteria, come only from other cells

All life on Earth comes as assemblages of amoeba like cells or in fact single amoebas.  cells only come from other cells, never spontaneously formed

every living creature, even a single celled amoeba comes only from parents, we've never observed one to form from nonliving elements

All life on Earth is a continuous lineage of amoeba giving birth to each other generation to generation slowly varying, 3.6billion years


organic chemists slowly begin making sense of their results by imagining their chemicals as specific 3 dimensional arrangements of atoms



DARWIN

geology: 1000s of rock layers can be identified in succession based on different fossils appearing and dissapearing never repeating: deep time

major feature of design in nature: constraints.  no six legged mammals.  creatures appear in fossil record based on previous designs

major feature of variation in nature: similar species are found geographically close to each other

as we catalogue more life we realize that adaptations like the eye are not fixed and perfect but exist on a continuum of variation and fitness

there are no fixed perfectly adapted designs in nature but seemingly endless random experimentation with varying degrees of fitness

Darwin/Malthus: organisms give birth to way more offspring than there is room for, only some can survive.

each generation, different new heritable traits appear, if environment keeps selecting for some kinds over others, populations will change

Since traits don't have to be perfectly adapted to function, the game of life can experiment with them through random variation and selection

the layers of rock strata suggest there were millions of generations of creatures through history

the sheer number of variations of creatures discovered by the 19th century was enough to put the idea of special creation in question.

if a new heritable trait helps its bearer to compete in the maltusian game, over generations, the prevelance of that trait will increase in a population, populations will change



Lichen: two kinds of organisms: fungus and algae, join as one organism, propagate as combined unit, can outcompete either separate organism


1860
mendeleyevs periodic chart of elements shows we've found the complete set of 92 which are responsible for all variety of matter on earth

99% of all materials, colors, textures, lifeforms, is accounted for by simply rearrangements of only 2 dozen different chemical elements

by simple geometric rearrangement of the atoms CHNO nature gives us extreme creativity: air, water, fire, wood, oil, colors, smells, life...



1880
Newtons laws of motion for 2 planetary bodies yield simple complete solutions. add a 3rd body? took 200 years to solve: unpredictable chaos


a new kind of phenomenon that is not accounted for by Maxwell's grand synthesis of light, electricity and magnetism: radioactive decay of Uranium

by Darwin's time, Kelvin calculated the time for Earth to cool was ~10s of millions years.  Geologists/Paleontologists thot 100s million

radioactive decay was discovered to be source of heat in the earth that could account for the extreme age of that geological layers suggest

By Darwin's time physicists could not explain how the sun shone for the 100s of millions of years the geologists thot life existed on Earth



1900
Eddington realizes that nuclear fusion could account for the billion years of sunshine that fossil record of life requires

combining steady rate of radioactive decay with % of decay products in rock allows us to find absolute ages for strata: to billions of years

The earth's surface has been worn down, melted, recycled and recycled.  It is not likely we can find the first earth rocks ever formed!



Devries rediscovers mendelian genetics: traits r products of many discrete packets of heredity which r not lost by blending and can vary by mutation

source of new random variations, and mechanism of inheritence without loss due to blending was found in mendelian genetics of discrete genes

darwin problem: traits can't be selected for over many generations if they blend into each other. answer: they are inherited as distinct packets



WEIRDNESS IN MATH
arrange pennies in rectangles: 2x2, 2x3, 3x3, 2x5... 4, 6, 8, 9, 10... what numbers are left? 2, 3, 5, 7, 11... these are prime numbers

Euclid shows a proof that even though the primes get more and more spread out, the sequence is unending

becuase primes cannot be factored we can show there is never a repeating pattern in the sequence of prime numbers

there is an algorithm to tell whether the next number is prime, hence we have an algorithm that gives an unending sequence of novel patterns

there is a fraction between any 2 fractions, infinitely dense. so r there MORE fractions than integers? Cantor shows how to count them: NO!

Pythagoreans found simple proof that square root of 2, a number between 1 and 2, cannot be a fraction, what sort of number is it?

draw a square with sides of 1. draw the diagonal.  draw a square who's sides are that, it's area is 2. The diagonal cannot be a fraction

but it's strings of small fractional ratio length that sound nice together, so call such a nonfractional length, irrational

long division is an algorithm of discrete steps which gives the sequence of decimal digits of any fraction.  The pattern always repeats

There is an algorithm to give the sequence of decimal digits of square root of two. since it is not a fraction, its sequence can't repeat

square root of 2 is not a fraction, so the deterministic algorithm giving its sequence of decimal digits cannot repeat, infinite creativity

as the diagonal of a square of side 1 cannot be expressed as a fraction, neither can the circumference of a circle of diameter 1: pi.

****
DATE THESE.  WHEN R THEY SIGNIFICANT?

Cantor discovers a bigger infinity than the amount of integers: since decimal expansions of non fractions never repeat, they cannot be counted

nonrepeatability of decimal expansion of nonfractions implies a list of them CANNOT be put in correspondence with integers, a new infinity



Einstein and Perrine nail AVOGADRO'S NUMBER
it's pretty likely to get 7 heads out of 10 coin flips, but nearly impossible to get 700,000 heads out of a million coin flips

dust motes jiggle in water because sometimes an excess of atoms strike it on one side, as with coin flips, this helps us count how many atoms!

Einstein: dust motes jiggle in water because a FINITE # of atomic collisions on each side give unequal statistical fluctuations: gives # of atoms

Einstein: if water were infinitely divisible (no atoms) collisions of water particles with a dustmote would cancel out exactly: it wouldn't move

Einstein and Perrin by 1920s finaly NAIL the reality that stuff is made of finite number of discrete atoms by COUNTING their collisions

Einstein and Perrin finally nail atomic nature of stuff: the palm of your hand is made of 600,000,000,000,000,000,000,000 atoms! atoms r small!

We can count the number of atoms in your hand: 600,000,000,000,000,000,000,000!  atoms are SMALL!  life is made of MANY MANY parts



1920
QUANTUM
the number of atoms in a glass of water IS the 2nd quantum fact, the fact that mass/energy comes in discrete packets

the # of atoms in a glass of water is the 3rd quantum fact: it explains how FAR REMOVED we are from quantum facts because we are SO big

quantum particles show interference patterns with each other showing they are spread out like waves, no well defined position or momentum

quantum waves, light, cannot be made infinitely dim, it comes in discrete packets, like particles: photons

4th Quantum fact: at the quantum level: individual particles and processes are inherently unpredictable, free random number generator!

Quantum mechanics deals in probabilities, yet it is the most quantitatively accurate piece of physics we have


Rutherford shoots alpha particles at gold foil, almost all go thru, minute amount recoil back surprisingly.  atoms are mostly empty space

The basic properties of solids is explained by quantum mechanical properties of pauli exclusion principle and heisenberg uncertainty! (this says nothing! explain it)




between QM, 3body chaos, radiogenic mutations... there are sources of random input for a creative universe.



heat a thin layer of fluid from below, cool on top, the heat flow drives the layer to stable dynamic pattern of hexagonal convection cells

heating bottom of container of fluid warmer than top, and fluid executes stable hexagonal pattern of cyclic motion, like a steam engine

2nd law thermodynamics: hot and cold eventually mix to disordered lukewarm, but meanwhile a small region between hot and cold becomes ordered



at some point we catalogue a million species and 1/4 of them are beetles.  W T F?  so we can ask, how so many?  at same time y not billion?

why does much of life fall into discrete species at all?  why not a continuously varying population of organisms?



The oldest solid rocks in the solar system, meteorites, have been radiodated to 4.6billion years (so? what's this mean?)


GALACTIC ECOSYSTEM
henrietta Leavitt finds a class of variable stars who's period is related to their brightness. find the distance to one, and map the cosmos

shapley uses leavitts cepheid tape measure to map out globular clusters showing we are 25,000 light years from center of our galaxy

Hubble uses the new palomar telescope to show andromeda fuzzypatch has individual stars, cephieds, it's 2million ly away, it's another milkyway!

Hubble finds that distant galaxies have reddened doppler shifts, they are fleeing from us, the more distant, the faster they are fleeing

using redshift as a distance marker we find galaxies more than 5 billion light years distant. they must be older than our solar system

we find white dwarfs (suns that have used up their fuel) less massive than our sun, must have grown slower than our sun thus must be older!

With parallax we find distance to sun is 96 million miles, therefore it is huge: 800,000 miles wide.  dwarfs the mass of all the planets

stellar spectra show stars are 98% hydrogen and helium, since they dwarf the planets, universe is mostly Hydrogen, earth elements rare

spectra show that oldest stars are even scarcer in earth elements and we can show earth elements are produced inside stars by nuclear fusion

The universe begins with hydrogen and 25% Helium, the oldest stars have this composition.  all other elements are cooked in massive stars

Physics tells us that stars more than 8 times solar mass have enough pressure to start fusing helium to carbon nitrogen and oxygen and beyond

massive stars create all the elements and then explode causing new stars to form more enriched in these elements generation after generation

so we have ferretted out the ecology of stars enriching universe in all the elements of chemistry and giving birth to each other and planets

we can count over 100 billion galaxies each with 100 billion stars most with planets and 10^50 atoms so universe is over 10^70 parts.  why?




CELL BIOLOGY
a new level of organic chem: instead of combinations of merely C H N O, each protein is unique arrangement of 20 diff amino acids, 100s long

new level of chemistry: instead of a few atoms connecting to make a molecule, 100s of molecules (amino acids) connect to make a protein


if proteins are monster molecules, ribonucleic acids are monstermonsters: seem to be chains of MILLIONS of small molecules

we finally nail that the mysterious ferments of the 19th century and the enzymes that coordinate each step of metabolism are proteins

krebs sees dozen metabolic reactions are in fact arranged in everturning cycle that transforms pyruvate one chemical bond at a time into CO2

life is cycles of discrete steps: one molecular configuration of atoms transforming into another, each step guided by its own protein robot

a new picture of life: dozens of connected molecular transformations arranged in tangled loops whereby teams of molecules build each other

life too is a digital process. transformations of plant to animal to breath to plant occur as step by step atomic rearrangements of molecules

as fluids are swarms of billion billion slippery parts, so LIFE is dancefloor of billion billion discrete transformations of atomic arrangements

inventing the electron microscope helped us discover that living 'protoplasm' is in fact full of millions of incredibly intricate structures




goedel: arithmetic and logic are complex enough to produce mathematical statements that can neither be proved nor disproved.  

CYBERNETICS
Turing invents mathematical model that can encode any algorithm, execute it step by step, even modify itself. leads to programmable computer

Turing proves that we CANNOT prove whether a particular step by step algorithm which loops back on itself, will ever end or not



1940
digital computer can execute millions of computations in reasonable amount of time, leading to discovering new kinds of mathematics

digital computers get us thinking about complex processes in terms of repetition of different discrete operations. new way to look at universe

with fast digital computers we discover simple mathematical systems that could spawn complexity simply by iterating simple rules over and over

digital computer allows us to amplify certain styles of thinking, eventually can beat any chess player

computer programming leads us to attempt inventing an artifically intelligent machine that can be as intelligent as humans or more

at the same, trying to simulate thinking with computers, gives some concrete hints at how enourmously complex thinking is.

invention of transistor proplells us into era where computational power doubles every 2 years, so in 60 years a billion times more powerful

inventing digital computers has indeed acted like a thought amplifier and allowed us to solve scientific puzzles impossible with pen and paper

Burks/Von Neumann: a mathematical description of a complex machine that can reproduce itself out of simple building blocks


theory of superconductivity understanding how motions of positive charges in cold matter make electrons pair up into virtual particles...



Turing begins to formulate a mathematical theory of how a uniform brew of 3 chemicals can interact to create patterns as in embryogenesis

Miller and Urey zap a simple mixture of CO2, N2, H2O with electric sparks and get dozens of kinds of biochemical molecules


Franklin, Watson, and Crick solve the 3 dimensional structure of the DNA molecule showing that it can encode information AND replicate


animals move by muscles which are arrangements of millions of proteins each acting as a hinge that contracts by a single chemical reaction

basis of animal motion: myosin proteins are nanomolecular machines each with a hinge that can grab and contract by a single chemical reaction


Sanger: 10 year laboratory analysis: first to determine the complete arrangement of the 54 amino acids strung together to make a protein

exact 3 dimensional structure of a protein (myoglobin) solved by x-ray diffraction. on our way to complete understanding of protein mechanisms





1960
we transform swords into plowshares and learn to turn german war rockets into spacecraft that can rise through the sky and reach the moon

using newtons laws of gravitation we can calculate how fast to fling a rocket so it doesn't fall back down to earth, but travels to the moon

Mariner 2 spacecraft reaches venus and peers beneath the clouds: 90x earth atmospheric pressure, sulfuric acid and 800degrees. no paradise!

Mariner 2 Spacecraft reaches venus and looks around, we transform a dot in the sky into a world


Leaky decides why not, lets observe apes. sends women to chimpanzees, gorillas, orangutangs. find complex social arrangements, tool use

we begin looking at other animals, apes, octopi, elephants, whales, crows... find tool use, complex social life, culture, problem solving



CONTINENTAL DRIFT/PLATE TECTONICS

science works by exploring every possible thing with wildly different tools and approaches and find that it all interlocks

Columbus' first voyage into the unknown most certainly doomed to take more months than he had supplies, lucks out and discovers new continent

using the stars on a spherical sky as guide, we begin to map coastlines onto a globe, the coasts of europe/africa fit north/south america!

we find rock formations and fossils on both sides of the atlantic that match each other.

we sound the entire floor of the Atlantic ocean and map its valleys and mountains, we find a ridge in the middle that matches both coastlines

this ridge is hot with fresh magma rising and cooling to basalt, forming new ocean floor

core samples all along the ocean floor, the bedrock is all basalt

the continental crust however is mostly granite with basalt inclusions and folded metamorphosized sediments it has a much more complex history

core samples along ocean floor have deeper and deeper layers of sediment on top as you get closer to the coasts, closer to the coasts is older?

when we discovered radioactive decay, we learned how to tell the age of REALLY OLD rocks. yup, the ocean bedrock is older towards the coasts.

but ocean bedrock is, over all, young, only a few hundred million years old, continents much older, some rock billions years old.


THE ROLLING OCEAN CRUST MAGNETIC TAPE RECORDER:

why not measure the magnetic orientation of rocks? it orients to the magnetic field of the earth when the rocks form from molten magma

in young bedrock, the magnetic field is oriented towards the poles, in older bedrock, not so, either the poles move or the bedrock moved!

map the magnetic fields across the ocean floor! on either side of the ridge, parallel matching stripes, flipping north, south, north, south...

the north and south poles were reversing orientation every few million years?

look at the magnetic orientations of older and older bedrock on continents, they all point to stationary poles if we MOVE the continents!

well? lets go and WATCH the continents, ARE they moving apart?  HELLS YEAH, umm... by half an inch per year.  this takes radio, or radar or satelites

but 1/2 inch a year is enough if you multiply it by the radiodates of the oldest ocean crust, BINGO, you get the distance between the coasts!

can entire continents REALLY move? how many MORE INTERLOCKING measurements do you want before you are convinced?  this is how science works

half inch out of 3000 miles is like 1 part in 100 million.  to get these measurements to match we are measuring THAT accurately.  SCIENCE!


so, like soup in a pot, the entire earth is gyrating round and round in a series of interlinked convection cells, continents floating on top

theory of plate tectonics interweaves all the disparate phenomena of geology: continents, oceans, volcanos, earthquakes, mountain building...






uniform background noise of microwaves discovered that matches correct wavelengths of theoretical prediction of aging glow of hot big bang



Ribosome: an ensemble of ~160 nanomolecular robots (proteins) that can manufacture any nanomolecular robot from the blueprints in the DNA

each biochemical process and cell structure is produced by a different nanorobot that ribosomes build from distinct sequences of DNA code

ribosomes can translate robust codes stored in DNA using only 4 molecular 'letters' into different connected sequences of amino acids that fold up into nanomolecular robots

We break the code that ribosomes use to translate from letters of DNA to a connected sequence of amino acids that can fold up into distinct nanomolecular robots

ribosome translates each of the 64 different sequences of 4 kinds of nucleotides on a strand of DNA into one of 20 amino acids in a protein

ribosome reads DNA sequence 3 beads at a time to build up sequence of amino acids on a protein.  each sequence gives a protein unique behavior


jacob and monod find 6-molecular-component negative feedback loops that regulate production of healthy concentrations of components in cells

excess nutrient binds signal protein which binds  DNA switch blocking gene so ribosome can't get the code to make enzyme that makes nutrient




1970
freeze fracture technique and scanning electron microscope give us images of spatial complexity in cells built by actual molecular assemblies


CAN WE PREDICT EVENTUAL BEHAVIORS OF ALL SIMPLE PHYSICAL SYSTEMS? SIMPLE MATH SHOWS NO!

in ____ Newton calculated all possible orbits of 2 mututally gravitating bodies: totally predictable. but add a 3rd? unsolved problem

in 1900 Poincare showed that the NEXT simplest physical system, the eventual behavior of 3 gravitationally attracting planets is unpredictable

in 1970 Lorenz found same unpredictability and complexity in system of 3 differential equations describing convecting fluid system

in 19__ May found same chaos and complexity in simplest chaotic arithmetic system: multiply fraction by 1 minus itself, times 4, repeat.

repeating the simple rule: multiply fraction by 1 minus itself then multiply by 3.5 yields simple behavior, but multiplying by 3.6, chaos!

mathematical descriptions of some simple physical systems show that very similar initial conditions can diverge wildly in eventual behavior

mathematical descriptions of some simple physical systems show that very similar systems can show wildly different patterns of behavior

some systems are stable, predictable, and stable to minor perturbations, while other systems are impossible to predict after minor changes

[this is a hard one to describe]


pick a number, if even, divide by 2, else times by 3 and add 1, repeat: 5 16 8 4 2 1 4... does every starting value end 4 2 1? no one knows

try 27: 82 41 124 62 31 94 47 142 71 214 107 322 161 484 242 121 364 182 91 274 137 412 206 103 310 155 466 233 700 350 175 526 ... hmmm...

simple geometric rule followed by mechanical checkers leads to complex pattern formation. can simplicity of chemistry lead to complexity of life?




1971 Mariner 9 reaches mars, closeup photos of mars geology: lifeless, dry, but had massive flows of water in the past!


much evolutionary change in fossil record is not uniformly gradual but long episodes of stasis punctuated by shorter bursts of change. why?



Gierer and Meinhardt figure out how Turing mechanism creates striped patterns out of initial homogenous chemical system

Zhabotinsky convince chemists that far from equilibrium chemical reaction can oscillate and produce patterns from initial homogenous state

Zhabotinsky convinces chemists that not all chemical reactions settle to equilibrium.  Some may oscillate back and forth and make patterns

Prigogene et al characterize the dissipative system, when energy flows through a fluid system, patterns and robust cycles spontaneously arise

even simplest combustion reaction CH4 + O2 results in complex network of reaction cycles between dozens of reactants in dynamic convecting flame



we find the molecular sensors, switches, paddles and feedback mechanism that bacteria use to swim towards food and away from harm

negative feedback mechanism gets bacteria to dissolved food: concentration increasing? spin paddles, swim ahead, else reverse 'em and tumble



we land the viking crafts on mars.  amazing detailed images of sunsets, frost, dustdevils...

we fly first spacecraft to jupiter and saturn and find the moons all have different geological history, volcanos, ice covered oceans...

flying to jupiter and its moons we discover that tidal heating can produce active geology even in small moons, IO has active volcanos

pattern of cracks and gravitational anomalies and magnetic field suggests that jupiter's moon Europa has a subsurface ocean!


after traveling to venus, mars, jupiter and saturn, there is no obvious signs of macroscopic life in the solar system, we are alone



1980
classification of finite simple groups: first mathematical proof that takes 10,000 pages, 100s of mathematicians, what kind of proof is it?


we begin to find high temperature superconductors, we don't understand them, nor do we know if room temperature superconductors exist


we find the first simple chemical system that produces stripes from a homogenous starting state, just as Turing predicted


fossil bacteria within 200million years of the period of late heavy bombardment of meteorites.  life did not need billions of years to start


langton simplifies VonNeuman's self reproducing math machine to a loop of 96 cells with only 100 rules

simple machine on square tiling: if tile white turn right, if black turn left, flip the color, move forward, repeat. builds pattern 9,977 long


even as far out as neptune, voyager 2 spacecraft finds complex moon: Triton with geology and nitrogen geysers




1986
Tom Ray surprises everyone with an operating system of simple computer programs that reproduce, evolve and form complex ecosystems

Pearson finds parameters of Gray Scott reaction diffusion differential equations that yield reproducing spots

Pearson finds ferrocyanide iodate sulphite system in uv evolves into blobs that move around and reproduce, mimicing gray scott equations



Schoomaker and Levy discover comet that then slams into jupiter, driving home importance of impacts in recent earth history


Mayor and Queloz craft the precision necessary to discover first planet revolving around another star, soon we find 1000s of solar systems

Galileo spacecraft at Jupiter finds complex dynamics of surface ice cracking, melting, refreezing on moon Europa.  complex dynamic ocean beneath?

sayama modifies langton's loop so that they can interact, die, give birth and evolve




2000
[alkali vents]

Cassini/Huygans spacecrafts find methane/ethane hydrological cycle on Titan and possible ethene redox cycle, surface lakes on another body!

Cassini dives through Saturn's moon Enceladus' geysers and finds evidence of contact with minerals and even alkali hydrothermal vent chemistry

New Horizons reaches Pluto after 10 years operates flawlessly and discovers ice mountains, convecting nitrogen sea and methane and complex organic snow

New Horizons reaches Pluto after 10 years flight and discovers that Pluto is not a frozen dead ball but a geologically active planet

Dawn spacecraft with its new ion propulsion drive becomes first spacecraft to orbit one body then pick up and orbit another

Dawn spacecraft discovers Asteroid Ceres has subsurace salty slush ocean which resurfaces in recent timescale


observing asteroid belt, it has been mixed, early in solar system history, the planets have been playing pinball, chaos.

we discover a new realm of solar system: Kuiper belt beyond neptune full of new mini planets, pluto foremost among them

after 40 years of refining to accuracy of 1 part in 10^20, LIGO detects its first gravitational wave, a totally new realm of astronomy opens




FIND WHERE THESE GO

1st quantum fact: the vapor of an element in an electric discharge tube radiates light in only discrete wavelengths, not a continuous spectrum

each element is discovered to have unique spectral fingerprint thru a prism. These are found in our sun, so the sun's made of earth elements



>pre 1900


kepler? observes a comet and shows that it is not atmospheric! it is further away than the moon

Halley calculates positions of his comet, predicts it will return with an orbit of 75 years, like a very far planet.

kepler? observes a new star appearing in the sky.  and then it fades.  what does THAT mean?


finding some meteorites after they fell and analysing them, we realize they correspond to no terrestrial rocks, they are from outerspace


>1900


pick a number, even?, divide by 2, odd? times by 3 and add 1, repeat: 5, 16, 8, 4, 2, 1, 4... does every starting value end 4, 2, 1? no one knows

by 1950s? we realize we are finding a plethora of subatomic particles and there is no rhyme or reason






>1960
von Fritch discovers that honeybees can communicate distance, and direction of flower patches to nestmates using symbolic dances

after viking or something:
we realize that some of our meteorites have bubbles with same makeup as mars atmosphere, they came from mars!

__ builds a bag around a 300foot tropical tree and gasses it with insecticide. collects 500 new species of beetle.  what does this mean?


we realize we STILL don't know how many species there are on earth by order of magnitude.  10million? 100million?


we build unified quantum theory of electromagnetism with strong and weak nuclear forces. but we can't find a quantum theory of gravity



Anderson, Laughlin and Pines point out that we cannot predict macroscopic behavior from microscopic laws (quantum)

after we discover a new macroscopic law we can explain it using quantum mechanics but we can't predict new macroscopic laws from quantum alone

we realize that social insects form complex cooperative societies with no leaders.  we begin to ferret out the interactions that make them work

Seely observes mechanism by which 100 honeybees explore and mutually decide on a single nesting site to move into to with 98% success rate.

we watch 1/4 inch termites with no blueprints build 10 foot tall complex nests, the global structure comes from simple local interactions

different groups of dinosaurs are more different than each other than one group is from birds, dinosaurs have feathers, birds ARE dinosaurs



our immune system explores antigen morphospace by constantly inventing new matching antibodies by genetic recombination without sex

immune system explores how to recognize new foriegn antigens by generating novelty in antibodies by recombining components of antibody genes

immune system imagines new antibodies by miniature evolution: recombination of genes for variation and then selection of those that bind invaders



we find forms of cancer in dogs and tazmanian devils that can jump from host to host and be essentially immortal, a new kind of parasite!

biologists have been cultivating a line of human cancer cells from one patient that is immortal in the laboratory, a new species of creature

there are microscopic layers of alga/lichen ecosystems living 1mm deep inside antarctic rock surviving 6 month nights 60mph winds 60below 0

get the numbers!

we begin finding living bacterial communities 2 miles deep in bedrock, in >100degree high pressure ocean vents, hyper salt or acid, EVERYWHERE

as wildly different as fungi, animals, algae and bacteria are... they are ALL biochemically the same.  life happened on earth ONCE.

there are bacteria that can derive their energy and food solely from mineral chemistry, no need of sunlight

all plants, animals, fungi use basically two kinds of metabolism, yet there are DOZENS of different bacterial metabolisms

but the core molecular machinery that all life uses to construct itself from chemistry is the same, we have only ONE example of life on earth

entire thriving ecosystems miles under the sea at volcanic vents living off of mineral chemistry and no sunlight, a different world!


alvarez finds evidence for large meteorite impact during the cretaceous tertiary mass extinction, when dinosaurs went extinct. a cause?



studying birds during spring singing season we learn that brains are still growing new neurons and wiring new connections at adulthood

brains are wired very stochastically during development.  how do we come out at all the same? how do 10,000 genes produce myriad behavior?

[you made a start on counting algorithms in honeybee, 260 of them, how many do you suppose there are in human?]


while the interior of silicon crystals, like most metals, has simple cubic stacking of atoms, the surface has complex 7x7x3 patterns of atoms


records finally show that the concentration of the greenhouse gas, CO2 is steadily rising for 20 years, slowly warming the earth


naked mole rats!  burrowing rodents found in africa to have similar hive lifestyle as honeybees, with a fertile mother and infertile workers


1980-1998
observations of neutrino oscillations is one of the few outstanding puzzles in the standard model of particle physics


Cichlid fish in a few african lakes represent over a 1000 species that may have evolved within the past 10 to 100 thousand years. fast!



Saturday, October 6, 2018

Once I Explored Are There Crabs Evolving To live Entirely On Land?

if you are interested in evolution of land crabs first find a book on invertibrate zoology with LOTS of examples and lots of pictures and descriptions of the physiology and behavior of all these critters. here is one:

Animals Without Backbones (Hardcover)
by Ralph Buchsbaum, Mildred Buchsbaum, John Pearse, Vicki Pearse

http://www.amazon.com/gp/product/0226078736/002-9871747-0573642?v=glance&n=283155


realize that there are over 100 different families of arthropods(insects, spiders, scorpions, sowbugs, millipedes, crabs, shrimp, krill, copepods...) each with it's own lifestyle!

there are loads of different crabs:

some climb trees and crack open coconuts:

birgus latro

http://www.arkive.org/species/GES/invertebrates_terrestrial_and_freshwater/Birgus_latro/

This species is a type of land hermit crab with a spectacular appearance and intriguing biology. It is probably the largest terrestrial arthropod in the world and is able to grow to relatively gigantic proportions. Unlike most other hermit crabs, only the juveniles of this species find and use gastropod shells for protection as they develop. Adults have abandoned the shell-carrying habit, and instead have hardened shells over the abdomen. This protects the crab, reduces water loss and does not restrict its growth, allowing it to reach up to a metre in size. This huge crustacean is well adapted to life on land with long strong legs. It also has large muscular claws which are used for punching holes in coconuts and scooping out the flesh. This is a unique behaviour amongst crabs and explains why this species is called the coconut crab. The claws are in fact so powerful they can lift objects such as vegetation or rocks weighing up to 28 kg. Its stalked eyes are red, and this crab�s body colour varies between islands from purplish-blue to orange-red. Studies show that males are considerably larger than females.

here is a video of coconut crab cracking open a coconut!

http://www.arkive.org/species/GES/invertebrates_terrestrial_and_freshwater/Birgus_latro/Birgus_latro_00.html?movietype=rpMed





and look at these guys! < blackskimmer > 03/03 12:36:25


they keep water in their shells, which they collect from dewdrops rain puddles etc... to keep their efficient gills moist and breath in the AIR. they however goto sea to realease eggs. the larvae develop in the sea:


The Caribbean Terrestrial Hermit Crab Coenobita Clypeatus (herbst, 1791)

http://www.fmrpets.com/promotions.ivnu


here is another family of terrestrial crabs:

pics:
http://www.geocities.com/ericdemuylder/gecathum.htm

http://www.geocities.com/ericdemuylder/index.htm



the level of detail, and kinds of details you want, to ask can these buggers evolve to be truly land critters:
Osmoregulation in the terrestrial Christmas Island red crab Gecarcoidea natalis (Brachyura: Gecarcinidae): modulation of branchial chloride uptake from the urine

H. H. Taylor1,* and P. Greenaway2

http://jeb.biologists.org/cgi/content/full/205/20/3251



can crabs escape ENTIRELY from the sea? look: here are freshwater crabs that breed OUT of the ocean, and are on their way to breeding entirely on land:

REPRODUCTION IN THE FRESH-WATER CRAB CANDIDIOPOTAMON RATHBUNAE (BRACHYURA: POTAMIDAE) IN TAIWAN
Hung-Chang Liu,a and Chia-Wei Lia
http://0-www.bioone.org.library.lib.asu.edu/bioone/?request=get-document&issn=0278-0372&volume=020&issue=01&page=0089

note:

"The reproduction of fresh-water crabs differs from that of marine crabs. Eggs of fresh-water crabs are large and yolky, and hatch directly into young crabs rather than free-swimming larvae. The hatched crabs are brooded by their mother under her abdomen for several days before they are released (Ng, 1988). In some cases (e.g., Metopaulias depressus Rathbun), highly developed larvae emerge from the eggs and complete their development in fresh water (Diesel and Schuh, 1993)."



these babies are on their way to hatching fully terrestrial young without any water needed at all! kind of like what mammals and some toads do.




crabs can spend their ENTIRE lives in trees: many aquatic critters live in water filled tree holes, or water filled bowls of the plants called bromeliads:

more mother crabs caring for young in bromeliads:

http://bromeliadbiota.ifas.ufl.edu/crbrom4.htm

Crustacea in Bromeliad Phytotelmata

Wolfgang Janetzky
Carl von Ossietzky Universit�t Oldenburg,
ICBM - AG Aquatische �kologie,
D-26111 Oldenburg, Germany

http://bromeliadbiota.ifas.ufl.edu/crbrom.htm




crabs dropping in shells to adjust pH water: < blackskimmer > 03/03 12:44:26


The East Usambara tree-hole crab (Brachyura: Potamoidea: Potamonautidae) - a striking example of crustacean adaptation in closed canopy forest, Tanzania
J. Bayliss
Abstract

An undescribed species of freshwater crab with a remarkable life history was studied over 2 years in areas of natural forest in the East Usambara Mountains, north-east Tanzania. It was found occupying the water-filled boles (tree holes) of several tree species at altitudes between 150 and 900 m asl, a single tree species Myrianthus holstii accounted for 26% of all trees identified as such. There was no apparent association with other freshwater bodies. The 'tree-hole crab' is largely nocturnal but will also forage by day during periods of heavy rainfall, leaving its tree hole in search of leaf-litter molluscs. Once located it carries pieces of the snail shell back to the tree hole and releases these into the water filled bole which is typically acidic. This releases calcium ions (Ca2+) into solution from the snail shell resulting in a more neutral solution (mean pH = 6.6, standard deviation (s) = 0.46, n = 25). This act provides a source of dissolved calcium for the development of exoskeletons following ecdysis. Significant differences were found between depth (P = 0.01) and height (P = 0.05) of occupied and unoccupied water-filled tree holes. This is the first record of a crab exhibiting such behaviour in East Africa.


http://www.blackwell-synergy.com/doi/abs/10.1046/j.0141-6707.2001.00333.x




wow, you really love crabs < uknoit >

i love all bursting with inventiveness biology < blackskimmer >

the point is before talking about evolution, gather up LOTS of examples. that's why Darwin went on a 3 year long voyage and then waited 25 years to publish his conclusions.

p.s. i had only VAGUE notions that these critters existed before i just hunted them down for the original poster. i had NO idea that there was a crab that CRACKED open coconuts!


Tuesday, July 31, 2018

Science Salon: Origins Of Life In The Universe: Lecture With Experiments! Photos Too

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:

https://blackskimmer.blogspot.com/2007/07/before-decending-into-question-of-wher.html

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.

http://nick-lane.net/wp-content/uploads/2017/01/Sojo-et-al-Astrobiology-review-The-origin-of-life-in-alkaline-hydrothermal-vents.pdf


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.

https://physicstoday.scitation.org/doi/full/10.1063/PT.3.3108


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.

http://www.iconicasocialclub.com/

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.


http://www.fossilmuseum.net/Fossil-Pictures/Blastoids/Crinoid13/BC05A.jpg


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!

http://quarriesandbeyond.org/articles_and_books/stone_quarries_bedford.html

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!

more


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.