Sunday, September 27, 2020

Important science books to go along with a 'humanities' list of "must read" books

In no particular order.  Have fun.

*Gregory Bateson, "Mind and Nature"
What processes does a mechanical system need to have to act like a mind? to evolve? are they the same?  concrete vocabulary to ask and answer.


*Alberts et. el. "Molecular Biology of the Cell"
You are a confederation of a TRILLION living amoeba, each amoeba is a dance of more nanotransformer robots than there are bricks in all of NYC


*Charles A. Sorrel and George F. Sandstrom, "Minerals of the World"
How does the chemistry of merely 2 dozen elements create the 1000s of wildly different minerals?  this is one book i learned chemistry from


*John Janovy, "Yellowlegs"
One biologist's journey to follow and enter the life of of a single migrating bird, or maybe it's a journey into his own mind as a biologist



*David Rindos, "Symbiosis and instability in Agriculture"
We were nomadic hunter gatherers for 100,000s of years and then in a flash, agriculture took us by surprise and spread like wildfire, how?

How did agriculture take over the human world so quickly? because it is unstable, always collapses, we disperse, and start it again

(this was a paper in a journal, or made into a book.  Never saw the book)


*Charles Darwin, "The Origin Of Species", 1st edition.
Darwin spent a life of exploring every nook and cranny of the living world and asked penetrating questions we are still trying to answer today


*Vernon Amadjian and Surindar Paracer?, "Symbiosis: An Introduction to Biological Associations"

Detailed examples of intimate connections between critters from deadly parasitic to mutually beneficial symbioses. do organisms have boundaries?

all the different stories of creatures living inside each other

worms that travel between snail and raccoon, fungi that


*Lynn Margulis and Karlene Schwartz, "Five Kingdoms: An Illustrated Guide to the Phyla of Life on Earth"

The 100 groups of critters on Earth that are more different from each other than plants are from animals, by lifecycle and molecular mechanics


*E. C. Pielou, "After the Ice Age: the return of life to glaciated north america"
Lush details of how our landscape and ecosystem grew back together as the Glaciers retreated over 10,000 years. Stability is not the norm



*Walter Tschinkel: "The Fire Ants"
30 years of experiments and measurements to tease apart and put back together the life stories of fire ant colonies. Step into the life of an alien species! We are no match for them!  


*Borror and White, "Peterson's Field Guide to Insects",
There may be a dozen kinds of mammals lurking 'round your back yard, but you can find at least 500 kinds of insects living there.


*Jack Harlan, "Crops and Man"
The complex ecology and evolution of weeds, humans and crops. how it all got started in multiple places in multiple ways.



*Holling Clancy Holling, "Pagoo"
Follow the story of a young hermit crab growing up in the sea. jam packed with lush illustrations of all kinds of sea critters and biology


*John C. Kricher and Gordon Morrison, "Field Guide to Eastern Forests",
Go out and see how your landscape is knit together by the myriad creatures, get to know some of them.  great details of ecological processes


*"Golden Guide to Pond Life",
Stick it in your back pocket and get to know what's happening at a pond near you.  from microscopic anamalcules to turtles and raccoons



*Donald Kroodsma, "The Singing Life of Birds"
Only 50 years ago we start LISTENING to birds.  they are singing elaborate creative patterns with rules.  we don't yet know what they are saying


*L. David Mech and Luigi Boitani, "Wolves: Behavior, Ecology, and Conservation"
Wolves are the most geographically and ecologically widespread mammals besides us.  they are also more civilized. we've hated them throughout history



*William Morton Wheeler, "The Fungus Growing Ants of North America"
How one ant sized mother eventually raises up a city of a million children the size of your living room. in south america, they are in charge.



*Paul Colinvaux, "Why Big Fierce Animals Are Rare",
2 dozen tales of how our world is knit together at the biological and chemical scale



*Lewis Thomas, "The Lives of a Cell",
These little biology essays got me started in highschool on lifelong expeditions of the biological world. They introduced me to the works of Harold J. Morowitz and Lynn Margulis.


Steven M. Stanley, "Earth System History"
The whole earth is similar to a self regulating organism with feedback loops between rock atmosphere and life.  It has an eventful history.  Learn how many processes and events have taken place.


*Frank Shu, "The Physical Universe: an Introduction to Astronomy"

Read about, do the physics of the grand drama between gravity and the 2nd law of thermodynamics which creates all the structures of our universe

Calculate how much energy the pulsar looses to glow of the crab nebula, then how far back in time it began in an explosion. yes one was recorded there 1000 years ago!


or a simpler text like:
Michael A. Seeds, "Horizons: Exploring the Universe"

or

James Binney "Astrophysics: a very short introduction"


*John Janovy, "On Becoming a Biologist"
Biology is a unique science half way between chemistry and geology, @ the human scale, ready to teach us if we listen to the critters.


*Gerald Holton and Stephen Brush, "Introduction to the Concepts and Theories in Phyiscs"

Why trust science?  each theory takes a 100 years of exacting observation, brutally honest constructive criticism, back and forth before being woven into a stable edifice

Learn how hard, how long, with what back and forth confusion to wrest basic facts of science: heat is the motion of atoms that make up matter


Jim Baggott, "Perfect Symmetry: The Accidental Discovery of Buckmisterfullerene"

Chemists dreamed about soccer ball shaped carbon compounds but Astronomers making actual observations found them.  How laboratory practices and personal interactions work in science.


*Philip Davis and Reuben Hersh, "The Mathematical Experience"
History and exercizes of the mathematician's art. details. what IS mathematics? whimsical creation of the human mind or bedrock of reality?


*Guy Alexander, "Silica and Me"
Thin. easy read. how does a scientist make sense of puzzling experiments? beautiful details. learn some chemistry. geology is silica.



*Duncan C. Blanchard, "From Raindrops to Volcanoes"
A delightful romp through observation and experiment.  how to collect microscopic water drops in sea spray? have a baby spider build you a net...

one scientists experimental journey to understand rain. how to collect microscopic water drops in sea spray? have a baby spider build you a net...


*Richard Feynman, "The Meaning of it All",
*Richard Feynman, "The Pleasure of Finding Things Out",

Science as a way of life of exploration, being able to live without certainty, striving for brutal honesty, is it valuble for human society?


*Richard feynman: six easy pieces
Master physicist introduces you to his craft.  what is matter, energy? gravity?  one experiment that describes the alien quantum world.




*Wilson: 4 colors suffice: how the map problem was solved
Math is weird: 5 color theorem takes only 9 pages to go over 5 cases, you can learn it! but 4 color theorem takes a computer to go over 1400 cases!



*rebecca stott: darwin and the barnacle
Get inside the very human world of Charles Darwin as he spends 20 years to hone his craft as a naturalist before daring to explain his world shattering theory of Evolution.



*Almost Any Freshman Biology Textbook,

*Garrett Hardin, "Biology: Its Principles and Implications" 2nd edition


I can't remember if any of Ilya Prigogne's books are well written or accessible enough to be on this list or whether I pieced together an understanding of his ideas from him and Morowitz.

I can't remember in which book I learned of Morowitz's characterization of life as a cyclic phenomenon running on energy flow.  Or his cycling theorem that states that energy flowing through a finite system induces chemical cycles.

Sunday, September 20, 2020

Correct Protein Function Depends On Sequence and RATE Of Folding. Genes Code For BOTH!

New work hints at a reason why the genetic code is redundant!  Needs to code not only for sequence of aminos but also the RATE at which the sequence gets translated to get the right shape and right function.  Clever!  Explainer:

Reading genes with 4 possible bases 3 at a time can lead to 4x4x4 possible words, translated to 64 possible amino acids to build proteins. Yet biology uses only 20!  Presently most aminos are represented by 2 to 6 possible base combos.  Redundant!  or is it? 1/n

Protein function is dependent on shape.  We knew shape is dependent on amino acid sequence specified in genes.  But it's not like computer code, it's also physics, so shape is also dependent on RATE of building a protein.  Cells need to regulate THAT.  wait for it... 2/n

The redundancy in the genetic code allows for this.  For each amino, different codons that code for it can have a different tRNA molecule translate the code to amino.  Different versions of tRNA for each amino are made in varying amounts.  3/n

Needing a tRNA of low abundance will slow down the protein building process. By coding for a rare tRNA or abundant one the genes can also code for the RATE of translation (=building) of the protein and therefore its correct finally folded shape. 4/4

"A code within the genetic code: codon usage regulates co-translational protein folding"

https://biosignaling.biomedcentral.com/articles/10.1186/s12964-020-00642-6

Tuesday, September 15, 2020

Or Should I flesh out this story? the Deep Story behind the recent hype on possible life on Venus

 
somehow we have to get across the very buzzy HUMAN DRAMA of ... so the venus announcement is that they used these impressive peices of machinery to listen to radio waves traveling through atmosphere of venus and we CAN determine that it's diff shaped molecules DANCING!

and..the HISTORY we gotta get across that science is a LOONG HAUL story, not the latest fashion buzz, not the quick salvation from aliens.  it took 150 years of really hard work, confusing work, to understand that stuff is made of dancing molecules, hell, Boltzman died for it

so the sense of mastery, the precision craftwork it takes to work with these radio detectors and have CONFIDENCE we've detected a particular molecule dancing in the atmosphere of what looks like a DOT in the sky!

we have to keep talking about how science is this grand slow collective endeavour of 1000s of people carefully taking apart and putting together an understanding of results from many different realms to get them to fit together into a stronger and more wideranging world view

our job is to explore the philosophical implications of the question "what is life".  We don't know what life is! we don't know how life fits in with the rest of physics and chemistry!  is it totally alien?  is it a phenomenon on a continuum of complexity possible? etc...

we have to portray how amazing it would be  if we even ONLY found, say, something like the reverse krebs cycle happening on venus and nothing else.  putting life in the continuum of levels of complexity of chems instead of it being a miracle invented by alien space dude, god.

Writing Chemistry Poetry is hard! should I keep trying?

from whence new locks of flaxen hair?
how do deep gashes heal?
Are there weavers in her scalp?
factories made of steel?

i marvel that a crawling babe
from its mother's womb can come
grown only by the food she eats
how is this transformation done?

we've looked within by microscope
and still it's mystery
till by centuries of dirty labor
we learned whats chemistry

we watched microscopic urchin egg
split to two then four then eight...
till more and more form embryo
the cells move 'round and differentiate

it is the way with all living beings
from cells do other cells become
and we've found single cells in ponds
behave like miniature animals

what are these living sacklike beings?
more cells inside em ad finitum?
no! we discovered molecules
that run round and round and exite em.

two hundred years of fruitful confusion
in laboratories of fire and glass
we learned to weigh the very air
completing accounts for chem reactions

lucretius imagined molecules
that made everything we know
it took till 1922
that by measuring we could show

jiggling in the palm of your hand
the number of atoms boggles the mind
six hundred thousand billion billion
of 92 different kinds

each living amoeba single cell
contains a swirling multitude
of molecules who's number exceeds
all the bricks in new york city

these molecules are more than bricks
they jiggle and swirl all around
sensing each other upon collision
making decisions of what to do

springloaded mechanisms guided by equations
join each to each or disband
building structures quite complex
and dynamic patterns profound

thru networks of these logical decisions
protein molecules in your cells
engage in elaborate computations
coordinate behavior of a complex being

....
a poem on molecules?

Molecular Zine I wrote on a folded piece of paper once

 Sometimes the world seems so solid.  but then it rains on a cold spring morning and you go out for a jog anyway and you notice your breath exhale as mist and you wonder am I water too?

and you wonder so hard you do some chemistry and find your breath does condense into water on a cold window pane and further.. if you breath into a solution of slaked lime your breath can precipitate out as limestone... some of your breath can turn into rock?

and the plants, the tall firm trunks of wood, all made of breath, can be burnt back into breath like you can when you are finnished.  

and if you wonder so hard at such transformations that you math the hell out of them like Einstein and Perrin did and decide that breath is a billion billion molecules who's collisions can be cleverly counted

and you patiently count and count and yes... 623,000,000,000,000,000,000,000 of them in the palm of your hand and you look deeper and deeper and you watch yourself when you were an

egg

in your mother's womb and watch that tiny amoeba suckle at her womb and grow so lush it splits into two amoebas and then 4 and 8 and 16 and 32 and 64 and 128 and 256 and 512 and 1024 and 2048 and everyday it's

growing, 4096... 262164...524188... 1048576... 2 million, 4 million amoebas bustling and hustling and building and learning to dance eyeballs and heartbeat and muscles and lungs

and 268435456... 536870912 and a billion and 2 billion and 4 billion and a vast nation of amoebas connecting and conversing and inventing and talking up a whole brainful of thoughts and desires to look inside themselves asking what is this amoeba

life?  with its hustling and bustling of 623,000,000,000,000,000 molecules each amoeba is and how does it live?  more molecular robots than there are bricks in all of New York City

in motion and jiggling and wiggling and dancing with each other,  calculating... and calculations come together to make comparisons, and counting and differentiating and deciding and sifting and sorting through

random jiggling quantum fluctuations of the universe to create nano transformer robots a society of them a clever squaredance of one hundred different dances with a

thousand robot dancers in each one and they all swirl together so that out of the crowd of jostling robots they can recreate any dance and spilling this tale out from scratch with pen and paper surely

got hopelessly lost in a bustling confederation of a trillion squaredances of a hundred thousand billion dancers each and it takes more than 12 small pages to comprehend life.

Sunday, August 23, 2020

Ode to My Bic 4 Colored Pen and Engineering Analysis

So, I started using the bic four color pen for editing computer programs, back in high school.  For GROKKING them as i put it.  To get the gist of the whole thing.  Did i get it for that purpose or did i have bic pens before that?  I can't remember .  I might have used one color for variables, another for loops another for hmm.. i don't remember the scheme.  But it helped make the order, the pattern in a long stream of computer program statements come alive, when looked at in one gestalt.

After this experience, I always had a BiC 4 color with me, and used it for taking notes in lectures: green for questions, red for statements i disagreed with, black for copying statements of the lectures and blue for my own ideas.  i liked this scheme and kept it up for a long time, in taking notes on books or taking notes in books.  I use this scheme to this day.

What else can i say about it? It is a cheerful white and sky blue and kind of fat and stubby like a cigar or a bear.  it is smooth and fits in the hand in a nice way.  not sharp and angled like some other pens or not too thin like smooth round ones.  it give me something to play with, clicking the colors.

once a long time ago i had a TWELVE color pen from the American Museum of Natural History gift shop.  that one was really fat, and i remember writing with it, the choice of all those colors...  cheating i suppose, the color of the writing should come from the tone.  It was from Italy.

though in boston i became fond of writing with brown ink, so earthy.  i messed with brown and pine green and purple.  why not color my world, my productions as do flowers, insects and birds?


The pen is in two plastic parts the lower blue barrel unscrews and you can see the four ink cartridges, softer clear plastic, thin and tipped with a copper point holding a smaller ball.  or maybe  it is brass.  It appears to be in two segments, the one that fits in the plastic cartridge and the other that holds the ball.  the ball appears under my hand lens to be steel colored.  the cartridge is  about 10cm long and one mm inside diameter, 2 mm outside diameter the plastic being about a .5mm thick.  the brass tip is 1cm long and fits inside the plastic cartridge, the second portion of the brass tip is about a mm long and wide.  the part of the ball that protrudes is only about .5mm wide and .3mm sticking out.  i suppose the entire ball inside the brass tip is slightly bigger.

the soft plastic cartridges must be fit back into the upper barrel with a satisfying push, "ka-chunk".  Later in this essay we discover why that satisfying "ka-chunk" happens.

the next part is the upper barrel containing many parts.  it is white with a black inner part at the bottom which has the four holes or inner barrels that the soft plastic cartridges fit into.  the black part has outer screw ridges that the lower hollow blue barrel screws onto.  the outer white part has a clip that you can clip it onto your pocket or notebook with and a curious whimsical french ball at the top.  fun to hold onto with your teeth.

Inside all this are the 4 plastic triggers black, red, green, blue.  Their outer and upper portions appear through, stick out through four windows in the upper barrel.  Each has an outer tooth that makes it easy to press down to engage that color ink's cartridge and push its tip out the lower barrel for writing.  they are placed against four springs, so that when you push one down it resists. Also so that when you are done with that color and release it, the spring pushes it and the ink cartridge back up into the barrel. they are cleverly shaped to act in concert in the following way:

Each has a little tooth on the lower inside portion.  these face each other from the four directions of the square symmetry of the pen.  Each also has an upper tooth on the inside.  when you push one trigger down against the spring, the upper tooth is pushed below the lower teeth of the remaining three triggers and these catch the upper tooth and hold the engaged trigger down beneath them against the pressure of the spring.  this pushes the ink cartridge of the desired color out the bottom of the lower barrel.  the triggers have enough play in their movement and the springs supply pressure to work against so that in pushing the single trigger down it can push past the lower teeth but then remain locked below them once they snap back into place.

The next bit of cleverness about the design is that when you push down the trigger of the next desired color while the last trigger is already locked below, pushing the NEW trigger's lower tooth out of the locked pattern makes enough space to release the previous trigger locked below and that trigger's spring pushes it back up to the normal position while the new trigger can then take its place being locked by the next three triggers.  

One wonders what kind of earlier mechanism this evolved from or did someone at bic come up with it out of pure genius!

The triggers can be pulled completely out of the barrel through the windows, though this takes some work and almost NEVER happens during normal use.  The springs can be pop out with them.  The mechanism still works after i've taken one out!  nice design.  though not as well once i pop out the spring, do the springs push against each other laterally?  Two triggers and two springs don't work at all.  woops!  i tried taking the last trigger out and without all the others to hold it back, its spring popped it across the room.  I've lost it.

with everything apart i notice that there is nothing in the upper barrel to catch the ink cartridges.  do they insert into the springs?  let me see:  the black segment of the upper barrel is about 2cm long. it has 4 cylindrical holes into which the cartridges fit.  i wonder if the springs fit into these holes too.  I wonder if so, whether i can insert them back into them.  I cannot tell by looking at another assembled pen.  let me try to fit a spring and cartridge back into the emptied pen.  

When the triggers are taken out of the pen, one can see two more features below the bottom inner tooth.  a third tooth 5mm below that, and a small pin sticking out the bottom.  this pin must fit into the hollow of the spring to hold it in place, as the springs must have a tendency to move laterally when under pressure and movement. 

So i've gotten one spring back in.  and the blue trigger sitting above it.  the pin in the trigger keeps the top of the spring from wondering.  i've fit a cartridge up the hole in the bottom of the upper barrel. It fits INTO the spring and can catch in the bottom coils of the spring.  i should describe the spring.  it is coiled tightly at the top and the bottom and loosely in the middle.  there are 5 coils tightly adjacent to each other on one end and 4 coils the same way on the other end.  now that i have the springs out i don't know which end is the one that engages the cartridge and which the trigger, i'll have to take another pen apart to see.  there is then 3 cm of loosely coiled spring, about 10 coils of it. It should be noted that the cartridge has 4 very subtly protruding fins at the end that engages the spring.  it can insert into the hollow of the spring but will catch slightly.  i suppose it catches more strongly when the spring is inside it's small barrel inside the larger upper barrel.

When you push up on the cartridge inserted into the spring, if only one assembly is in place, and if it catches at the bottom of the spring, it will cause the spring to bow out.  obviously the 3 other springs in place prevent this and pehaps THAT behavor effects the pressured spring in a subtle way to make it catch against the cartridge more strongly.  let me investigate by putting the whole thing back together.

But one more question: does the lower portion of the spring insert into one of the four inner barrels of the upper barrel?  Dammit, i just lost a second spring.  An engineer i am not!  No, they do NOT insert.  With two springs and triggers in place adjacent to each other, not opposite in the barrel i will investigate the mechanism, inserting the cartridges.  The cartridges don't seem to catch as they do in the fully functioning pen, they slip right up inside the springs!  hmm...  AHH... i'm not pushing hard enough!  the cartridges don't catch into the springs, you push them THROUGH the springs entirely and they catch onto the lower protruding pin of the trigger which is inserted into the spring!  That pin is 4mm long and the bottom last mm is a slightly enlarged ball which fits snugly into the inside of the cartridge engaging it!

So the cartridges are always INSIDE the springs and THIS keeps the springs from bowing out laterally when under pressure.  NICE.  More detail:  From the third pen i pulled a trigger spring assembly out the top before pulling the cartridge out of it from below and the whole trigger - spring - cartridge assembly came out Its window at the top.  now i see that the lower 4mm pin of the trigger fits ENTIRELY into the cartridge WHILE the spring is around the cartridge at the top.  when the BALL at the bottom of this pin fits into the cartridge it widens it a tad.  That's what makes the ink cartridge fit into the upper assembly with its satisfying "ka-chunk"!  Furthermore this extra width now is too wide for the spring to fall back down below it and thus helps coordinate the actions of the spring a little, i think, though i don't think there is any room vertically for the spring to slip once this is all together.  NICE DESIGN.  The cartridges must fit into the springs to ensure the smooth action of the concerted effort of the triggers mutually catching and releasing each other.  Indeed, before, when i wasn't sure this mechanism was working with only three triggers in place it might have been that i had removed one of the cartridges.  with three entire assemblies in place: trigger, spring, cartridge, the mechanisms works splendidly.  

I now notice that the design of the walls of the upper barrel also help hold the upper tooth in place against the lower teeth of the other  triggers.  In fact, the mechanism works with only TWO complete assemblies in place either adjacent OR opposite.  Very nice.  It Almost works with ONLY ONE assembly.  On further investigation of only two assemblies working together, i realize that what keeps a trigger in the looked down position is that the OUTER upper tooth which also functions to make the trigger easier to push with your finger is the part that actually catches with ridges in the BARREL  It is NOT the concerted action of the other three triggers' lower teeth that hold it in place!   Even with only one assembly in place, the barrel and spring will guide it to push slightly towards the CENTER of the barrel and then the outer tooth catches against these ridges, locking it into place.  The only trouble is that with only ONE assembly the trigger bends TOO far into the barrel and comes out of its TRACKS on the inner surface of the barrel and cannot then be pushed back up.  It is the job of at least one other trigger to keep this from happening pushing the locked trigger outward with its lower tooth, so that it remains in its tracks!

The complexity of discovering how this design works has been fascinating!  The details of the design mind boggling.  Is the design recent enough to be able to interview some of the people involved and trace the roots of it?  Surely some of the details of this mechanism where found in previous machines?  Or at least the ideas... did they all come full blown from the brow of Zeus, or did the designers chance upon them by recalling UNCONSCIOUSLY previous elements of design they had seen?

I still cannot discern a function for the third lowest tooth.  for sure it helps keep the spring from pushing UP past the trigger but i don't see why the tooth needs to be so big.  only by shaving one off a little bit at a time might i discern it's full function.  it also might function to help keep the trigger from pushing down and getting jammed into one of the 4 inner barrels that the cartridge inserts into.

Finally I have completed the reconstruction of a complete pen out of the parts of two of them.  it works fine.  a very robust construction!  


It is a pity that it is difficult to purchase replacement ink cartridges!  usually i run out of blue and black MUCH more quickly than red and green.  but the stores usually carry packs of all four color cartridges.  that's wasteful.  Sometimes one can find a pack of two black or two blue cartridges.  most often one can't find them at all.  sometimes you do find them but then to one's disappointment that they have dried out!  Probably because there is not such a quick turn around in these items and they've been sitting in the store for years!

the white upper barrel also has in relief the logo BiC surrounded by an oval like an ancient egyptian hieroglyphic cartouche, and also an image of a little man.  he has a big round dot for a head like the round ball atop the pen.  his legs are made of three separate sections each giving an effect reminiscent of the Michelen man.  He appears to be brandishing a pen behind him which is nearly as large as himself or perhaps reminiscent of a bayonet.

Some comments on how they write.  they write smoothly and easily. the ink flows well and i almost always use the medium point variety which makes a satisfying engagement with the paper while writing.  BiC also sells a fine point which comes in an ORANGE lower barrel, but that point is too sharp for me and doesn't make as bold a line and also does not make as SMOOTH an engagement with the paper as i'd like.

On the inks themselves.  the black ink is satisfyingly dense.  The blue is darker than sky blue, a tad purple, on some batches or when i don't press hard enough it runs a tad light to my taste, i'd prefer if it were denser.  Hmm... on this pen, the green is satisfyingly bright and deep enough, usually i find it too thin for my taste.   The red, too, is a cheerful strawberry red, but is too light for my taste, i'd like the red to be bolder, deeper, more striking.  The inks always flow well.  I rarely have to mess around with the ball of the cartridge to get them to flow better.


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