Goodbye to the blind watchmaker — take I

The Michelson and Morley experiment destroyed the ether paradigm in 1887, but its replacement didn’t occur until Einstein’s special relativity in 1905.  One can disagree with a paradigm without being required to come up with something to replace it. Unfortunately, we tend to think in dichotomies, so disagreeing with the blind watchmaker hypothesis for life itself tends to place you in the life was created by some sort of conscious entity.  “Hypotheses non fingo”  (Latin for “I feign no hypotheses”) which is what  Newton famously said  when discussing action at a distance which his theory of gravity entailed (which he thought was pretty crazy).

Here are  summaries of four previous posts (with links) showing why I have problems accepting the blind watchmaker hypothesis.  These are not arguments from faith which nowhere appears, but deduction from experimental facts about the structures and processes which make life possible. Be warned.  This is hard core chemistry, biochemistry and molecular biology.

First the 20,000 or so proteins which make us up, a nearly vanishing fraction of the possible proteins.  For how vanishing see — https://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/.  Just start with 20 amino acids, 400 dipeptides, 8000 tripeptides.  Make one molecule of each and see how long a protein you wind up with making all possibilities along the way.  The answer will surprise you.

Next the improbability of a protein having a single shape (or a few shapes) for some chemical arguments about this — see https://luysii.wordpress.com/2010/08/04/why-should-a-protein-have-just-one-shape-or-any-shape-for-that-matter/

After that — have a look at https://luysii.wordpress.com/2010/10/24/the-essential-strangeness-of-the-proteins-that-make-us-up/.

The following quote is from an old book on LISP programming (Let’s Talk LISP) by Laurent Siklossy.“Remember, if you don’t understand it right away, don’t worry. You never learn anything, you only get used to it.”   Basically I think biochemists got used to thinking of proteins have ‘a’ shape or a few shapes because that’s what they found when they studied them.

If you think of amino acids as letters, then proteins are paragraphs of them, but to have biochemical utility they must have ‘meaning’ e.g. a constant shape.

Obviously the ones making us do have shapes, but how common is this in the large universe of possible proteins.  Here is an experiment which might show us (or not)– https://luysii.wordpress.com/2010/08/08/a-chemical-gedanken-experiment/.

From a philosophical point of view, the experiment is quite specific.  From a practical point of view quite possible to start, but impossible to carry to completion.

Well this is a lot of reading to do (assuming anyone does it) and I’ll stop now (although there is more to come).

Why do this at all?  Because I’ve been around long enough to see authoritative statements (by very authoritative figures) crash and burn.  Most of them I didn’t believe at the time — here are a few

l. The club of Rome’s predictions

2. The population bomb of Ehrlich

3. Junk DNA

4. We are 98% Chimpanzee because our proteins are that similar.

5. Gunther Stent, very distinguished molecular biologist, writing that we were close to the end of our understanding of genetic biology.  This in 1969.

The links elaborate several reasons why I find the Blind Watchmaker hypothesis difficult to accept.  There is more to come.

“Hypotheses non fingo”

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Book recommendation

“It’s complicated”.  No this isn’t about the movie with Meryl Streep but the response I got from several Harvard PhD physicists five years ago at Graduate Alumni Day in April 2014.  A month earlier the BICEP2 experiment claimed to have seen B-mode polarization in the cosmic background radiation, which would have been observational proof of cosmic inflation.  Nobel prize material for sure.  Unfortunately the signal turned out to be from dust in our galaxy, the milky way

You can read all about it in “Losing the Nobel Prize” by Brian Keating, who developed the instrumentation for BICEP2.  I recommend the book for several reasons.  The main reason is the discussion of cosmology and its various theories starting with Galileo (p. 28) getting up to  the B-Modes that BICEPs thought it saw by p. 138.  The discussion is incredibly clear, with discussions (to name a few) of how Galileo knew Ptolemy was wrong (the way the moons of Jupiter moved around it in time), refracting vs.reflecting telescopes, Hubble and cepheid variables, Vera Rubin and why she didn’t get a Nobel — she died too soon, how polaroid glasses work, and why bouncing of water is enough to polarize unpolarized light.  Want more? Fred Hoyle and steady state cosmology, the problems with the big bang (smoothness problem, horizon problem, flatness problem) solved by Alan Guth and inflation, false vacuum, and finally what B-modes actually are.

If you’ve a typical reader of blogs scientific but not a pro in physics, astronomy, cosmology, you’ve probably heard all these terms. Keating explains them clearly.

Even better, he writes well and is funny.  Here is the opening paragraph of the book.

“Each year, on December tenth, thousands of worshippers convene in Scandinavia to commemorate the passing of an arms dealer known as the merchant of death.  The eschatological ritual features all the rites and incantations befitting a pharaoh’s funeral.  Haunting dirges play as the worshippers, bedecked in mandatory regalia, mourn the merchant.  He is eerily present; his visage looms over the congregants as they feast on exotic game, surrounded by fresh-cut flowers imported from the merchant’s mausoleum.  The event culminates with the presentation of gilded, graven images bearing his likeness.”

Anything dealing with the creation of the universe has theological overtones, and we can regard the book as a history of various scientific creation myths, the difference being that they are abandoned when evidence is found which contradicts them.  Georges’ Lemaitre, a catholic priest and relativist puts in more than an appearance (p. 56) as he predicted what is probably the first big bang theory — the primeval atom with its subsequent expansion.

The book isn’t all science, and the author whose Jewish father abandoned them was raised by a catholic step-father describes being an altar boy for a time.   Then there are adventure stories of journeys to the south pole for the BICEP experiment.

There’s a lot more in the book, which is definitely worth a read.

Finally a few personal notes.  The man who brought BICEP2 down to earth David Spergel appears.  He’s a good guy.  At my 50th reunion there my wife and I  were standing in our reunion suits outside our hotel across route 1 waiting for a bus to take us across.  Some guy (Spergel) sees us an offers a ride to campus. On the ride over I asked what he did, and he says astronomy and physics.  So I asked how come the universe is said to be homogenous when all we see is clumpy galaxies and stars — you asked the right guy saith Spergel, and he launches into an explanation (which I’ve forgotten).  I mention that Jim Hartle is a class member.  “He’s very smart” saith David.  Later I tell Hartle the same story.  “He’s very smart” saith Jim.

Another good person is Meryl Streep.  A cousin is in movies both acting in the past and now directing and knows her.  Her father was a great admirer, so Meryl took the trouble to hike over to New Jersey and say hello.  She didn’t have to do that.  Unfortunately in the movie mentioned first, Meryl had to play a porn star with her aged scrawny body (probably Harvey Weinstein put her up to it).  I couldn’t stand it and walked out at that point.

A creation myth

Sigmund Freud may have been wrong about penis envy, but most lower forms of scientific life (chemists, biologists) do have physics envy — myself included.  Most graduate chemists have taken a quantum mechanics course, if only to see where atomic and molecular orbitals come from.  Anyone doing physical chemistry has likely studied statistical mechanics. I was fortunate enough to audit one such course given by E. Bright Wilson (of Pauling and Wilson).

Although we no longer study physics per se, most of us read books about physics.  Two excellent such books have come out in the past year.  One is “What is Real?” — https://www.basicbooks.com/titles/adam-becker/what-is-real/9780465096053/, the other is “Lost in Math” by Sabine Hossenfelder whose blog on physics is always worth reading, both for herself and the heavies who comment on what she writes — http://backreaction.blogspot.com

Both books deserve a long discursive review here. But that’s for another time.  Briefly, Hossenfelder thinks that physics for the past 30 years has become so fascinated with elegant mathematical descriptions of nature, that theories are judged by their mathematical elegance and beauty, rather than agreement with experiment.  She acknowledges that the experiments are both difficult and expensive, and notes that it took a century for one such prediction (gravitational waves) to be confirmed.

The mathematics of physics can certainly be seductive, and even a lowly chemist such as myself has been bowled over by it.  Here is how it hit me

Budding chemists start out by learning that electrons like to be in filled shells. The first shell has 2 elements, the next 2 + 6 elements etc. etc. It allows the neophyte to make some sense of the periodic table (as long as they deal with low atomic numbers — why the 4s electrons are of lower energy than the 3d electons still seems quite ad hoc to me). Later on we were told that this is because of quantum numbers n, l, m and s. Then we learn that atomic orbitals have shapes, in some wierd way determined by the quantum numbers, etc. etc.

Recursion relations are no stranger to the differential equations course, where you learn to (tediously) find them for a polynomial series solution for the differential equation at hand. I never really understood them, but I could use them (like far too much math that I took back in college).

So it wasn’t a shock when the QM instructor back in 1961 got to them in the course of solving the Schrodinger equation for the hydrogen atom (with it’s radially symmetric potential). First the equation had to be expressed in spherical coordinates (r, theta and phi) which made the Laplacian look rather fierce. Then the equation was split into 3 variables, each involving one of r, theta or phi. The easiest to solve was the one involving phi which involved only a complex exponential. But periodic nature of the solution made the magnetic quantum number fall out. Pretty good, but nothing earthshaking.

Recursion relations made their appearance with the solution of the radial and the theta equations. So it was plug and chug time with series solutions and recursion relations so things wouldn’t blow up (or as Dr. Gouterman, the instructor, put it: the electron has to be somewhere, so the wavefunction must be zero at infinity). MEGO (My Eyes Glazed Over) until all of a sudden there were the main quantum number (n) and the azimuthal quantum number (l) coming directly out of the recursion relations.

When I first realized what was going on, it really hit me. I can still see the room and the people in it (just as people can remember exactly where they were and what they were doing when they heard about 9/11 or (for the oldsters among you) when Kennedy was shot — I was cutting a physiology class in med school). The realization that what I had considered mathematical diddle, in some way was giving us the quantum numbers and the periodic table, and the shape of orbitals, was a glimpse of incredible and unseen power. For me it was like seeing the face of God.

But what interested me the most about “Lost in Math” was Hossenfelder’s discussion of the different physical laws appearing at different physical scales (e.g. effective laws), emergent properties and reductionism (pp. 44 –> ).  Although things at larger scales (atoms) can be understood in terms of the physics of smaller scales (protons, neutrons, electrons), the details of elementary particle interactions (quarks, gluons, leptons etc.) don’t matter much to the chemist.  The orbits of planets don’t depend on planetary structure, etc. etc.  She notes that reduction of events at one scale to those at a smaller one is not an optional philosophical position to hold, it’s just the way nature is as revealed by experiment.  She notes that you could ‘in principle, derive the theory for large scales from the theory for small scales’ (although I’ve never seen it done) and then she moves on

But the different structures and different laws at different scales is what has always fascinated me about the world in which we exist.  Do we have a model for a world structured this way?

Of course we do.  It’s the computer.

 

Neurologists have always been interested in computers, and computer people have always been interested in the brain — von Neumann wrote “The Computer and the Brain” shortly before his death in 1958.

Back in med school in the 60s people were just figuring out how neurons talked to each other where they met at the synapse.  It was with a certain degree of excitement that we found that information appeared to flow just one way across the synapse (from the PREsynaptic neuron to the POST synaptic neuron).  E.g. just like the vacuum tubes of the earliest computers.  Current (and information) could flow just one way.

The microprocessors based on transistors that a normal person could play with came out in the 70s.  I was naturally interested, as having taken QM I thought I could understand how transistors work.  I knew about energy gaps in atomic spectra, but how in the world a crystal with zillions of atoms and electrons floating around could produce one seemed like a mystery to me, and still does.  It’s an example of ’emergence’ about which more later.

But forgetting all that, it’s fairly easy to see how electrons could flow from a semiconductor with an abundance of them (due to doping) to a semiconductor with a deficit — and have a hard time flowing back.  Again a one way valve, just like our concept of the synapses.

Now of course, we know information can flow the other way in the synapse from POST synaptic to PREsynaptic neuron, some of the main carriers of which are the endogenous marihuana-like substances in your brain — anandamide etc. etc.  — the endocannabinoids.

In 1968 my wife learned how to do assembly language coding with punch cards ones and zeros, the whole bit.  Why?  Because I was scheduled for two years of active duty as an Army doc, a time in which we had half a million men in Vietnam.  She was preparing to be a widow with 2 infants, as the Army sent me a form asking for my preferences in assignment, a form so out of date, that it offered the option of taking my family with me to Vietnam if I’d extend my tour over there to 4 years.  So I sat around drinking Scotch and reading Faulkner waiting to go in.

So when computers became something the general populace could have, I tried to build a mental one using and or and not logical gates and 1s and 0s for high and low voltages. Since I could see how to build the three using transistors (reductionism), I just went one plane higher.  Note, although the gates can be easily reduced to transistors, and transistors to p and n type semiconductors, there is nothing in the laws of semiconductor physics that implies putting them together to form logic gates.  So the higher plane of logic gates is essentially an act of creation.  They do not necessarily arise from transistors.

What I was really interested in was hooking the gates together to form an ALU (arithmetic and logic unit).  I eventually did it, but doing so showed me the necessity of other components of the chip (the clock and in particular the microcode which lies below assembly language instructions).

The next level up, is what my wife was doing — sending assembly language instructions of 1’s and 0’s to the computer, and watching how gates were opened and shut, registers filled and emptied, transforming the 1’s and 0’s in the process.  Again note that there is nothing necessary in the way the gates are hooked together to make them do anything.  The program is at yet another higher level.

Above that are the higher level programs, Basic, C and on up.  Above that hooking computers together to form networks and then the internet with TCP/IP  etc.

While they all can be reduced, there is nothing inherent in the things that they are reduced to which implies their existence.  Their existence was essentially created by humanity’s collective mind.

Could something be going on in the levels of the world seen in physics.  Here’s what Nobel laureate Robert Laughlin (he of the fractional quantum Hall effect) has to say about it — http://www.pnas.org/content/97/1/28.  Note that this was written before people began taking quantum computers seriously.

“However, it is obvious glancing through this list that the Theory of Everything is not even remotely a theory of every thing (2). We know this equation is correct because it has been solved accurately for small numbers of particles (isolated atoms and small molecules) and found to agree in minute detail with experiment (3–5). However, it cannot be solved accurately when the number of particles exceeds about 10. No computer existing, or that will ever exist, can break this barrier because it is a catastrophe of dimension. If the amount of computer memory required to represent the quantum wavefunction of one particle is Nthen the amount required to represent the wavefunction of k particles is N^k. It is possible to perform approximate calculations for larger systems, and it is through such calculations that we have learned why atoms have the size they do, why chemical bonds have the length and strength they do, why solid matter has the elastic properties it does, why some things are transparent while others reflect or absorb light (6). With a little more experimental input for guidance it is even possible to predict atomic conformations of small molecules, simple chemical reaction rates, structural phase transitions, ferromagnetism, and sometimes even superconducting transition temperatures (7). But the schemes for approximating are not first-principles deductions but are rather art keyed to experiment, and thus tend to be the least reliable precisely when reliability is most needed, i.e., when experimental information is scarce, the physical behavior has no precedent, and the key questions have not yet been identified. There are many notorious failures of alleged ab initio computation methods, including the phase diagram of liquid ³He and the entire phenomenonology of high-temperature superconductors (8–10). Predicting protein functionality or the behavior of the human brain from these equations is patently absurd. So the triumph of the reductionism of the Greeks is a pyrrhic victory: We have succeeded in reducing all of ordinary physical behavior to a simple, correct Theory of Everything only to discover that it has revealed exactly nothing about many things of great importance.”

So reductionism doesn’t explain the laws we have at various levels.  They are regularities to be sure, and they describe what is happening, but a description is NOT an explanation, in the same way that Newton’s gravitational law predicts zillions of observations about the real world.     But even  Newton famously said Hypotheses non fingo (Latin for “I feign no hypotheses”) when discussing the action at a distance which his theory of gravity entailed. Actually he thought the idea was crazy. “That Gravity should be innate, inherent and essential to Matter, so that one body may act upon another at a distance thro’ a Vacuum, without the Mediation of any thing else, by and through which their Action and Force may be conveyed from one to another, is to me so great an Absurdity that I believe no Man who has in philosophical Matters a competent Faculty of thinking can ever fall into it”

So are the various physical laws things that are imposed from without, by God only knows what?  The computer with its various levels of phenomena certainly was consciously constructed.

Is what I’ve just written a creation myth or is there something to it?

Catching God’s dice being thrown

Einstein famously said “Quantum theory yields much, but it hardly brings us close to the Old One’s secrets. I, in any case, am convinced He does not play dice with the universe.”  Astronomers have caught the dice being thrown (at least as far as the origin of life is concerned).

This post will contain a lot more background than most, as I expect some readers won’t have much scientific background.  The technically inclined can read the article on which this is based — http://www.pnas.org/content/115/28/7166

To cut to the chase — astronomers have found water, a simple sugar, and a compound containing carbon, hydrogen, oxygen and nitrogen around newly forming stars and planets.  You need no more than these 4 atoms to build the bases making up the DNA of our genes, all our sugars and carbohydrates, and 18 of the 20 amino acids that make up our proteins. Throw in sulfur and you have all 20 amino acids.  Add phosphorus and you have DNA and its cousin RNA (neither has been found around newly forming stars so far).

These are the ingredients of life itself. Here’s a quote from the article — “What I can definitively say is that the ingredients needed to make biogenic molecules like DNA and RNA are found around every forming protostar. They are there at an early stage, incorporating into bodies at least as large as comets, which we know are the building blocks of terrestrial planets. Whether these molecules survive or are delivered at the late stage of planet formation, that’s the part of it we don’t know very well.”

So each newly formed star and planetary system is a throw of God’s/Nature’s/Soulless physics’ dice for the creation of life.

As of 1 July 2018, there are 3,797 confirmed planets around 2,841 stars, with 632 having more than one (Wikipedia).  And that’s just in the stars close enough to us to study.  Our galaxy, the milky way, contains 400,000,000,000.

Current estimates have some 100,000,000,000 galaxies in the universe.  https://www.space.com/25303-how-many-galaxies-are-in-the-universe.html.  That’s a lot tosses for life to arise.

Suppose that some day life is found on one such planet.  Does this invalidate Genesis, the Koran?  Assume that they are the word of God somehow transmitted to man.  If the knowledge we have about astronomy (above), biology etc. etc. were imparted to Jesus, Mohammed, Abraham, Moses — it never would have been believed.  The creator had to start with something plausible.

 

 

Chemistry and Biochemistry can’t answer the important questions but without them we are lost

The last two posts — one concerning the histone code and cerebral embryogenesis https://luysii.wordpress.com/2018/06/07/omar-khayyam-and-the-embryology-of-the-cerebral-cortex/ and the other concerning PVT1 enhancers promoters and cancer https://luysii.wordpress.com/2018/06/04/marshall-mcluhan-rides-again/ — would be impossible without chemical and biochemical knowledge and technology, but the results they produce and the answers they seek and lie totally outside both disciplines.

In fact they belong outside the physical realm in the space of logic, ideas, function — e.g. in the other half of the Cartesian dichotomy — the realm of ideas and spirit.  Certainly the biological issues are instantiated physically in molecules, just as computer memory used to be instantiated in magnetic cores, rather than transistors.

Back when I was starting out as a grad student in Chemistry in the early 60s, people were actually discovering the genetic code, poly U coded for phenylalanine etc. etc.  Our view was that all we had to do was determine the structure of things and understanding would follow.  The first xray structures of proteins (myoglobin) and Anfinsen’s result on ribonuclease showing that it could fold into its final compact form all by itself reinforced this. It also led us to think that all proteins had ‘a’ structure.

This led to people thinking that the only difference between us and a chimpanzee were a few amino acid differences in our proteins (remember the slogan that we were 98% chimpanzee).

So without chemistry and biochemistry we’d be lost, but the days of crude reductionism of the 60s and 70s are gone forever.  Here’s another example of chemical and biochemical impotence from an earlier post.

The limits of chemical reductionism

“Everything in chemistry turns blue or explodes”, so sayeth a philosophy major roommate years ago.  Chemists are used to being crapped on, because it starts so early and never lets up.  However, knowing a lot of organic chemistry and molecular biology allows you to see very clearly one answer to a serious philosophical question — when and where does scientific reductionism fail?

Early on, physicists said that quantum mechanics explains all of chemistry.  Well it does explain why atoms have orbitals, and it does give a few hints as to the nature of the chemical bond between simple atoms, but no one can solve the equations exactly for systems of chemical interest.  Approximate the solution, yes, but this his hardly a pure reduction of chemistry to physics.  So we’ve failed to reduce chemistry to physics because the equations of quantum mechanics are so hard to solve, but this is hardly a failure of reductionism.

The last post “The death of the synonymous codon – II” puts you exactly at the nidus of the failure of chemical reductionism to bag the biggest prey of all, an understanding of the living cell and with it of life itself.  We know the chemistry of nucleotides, Watson-Crick base pairing, and enzyme kinetics quite well.  We understand why less transfer RNA for a particular codon would mean slower protein synthesis.  Chemists understand what a protein conformation is, although we can’t predict it 100% of the time from the amino acid sequence.  So we do understand exactly why the same amino acid sequence using different codons would result in slower synthesis of gamma actin than beta actin, and why the slower synthesis would allow a more leisurely exploration of conformational space allowing gamma actin to find a conformation which would be modified by linking it to another protein (ubiquitin) leading to its destruction.  Not bad.  Not bad at all.

Now ask yourself, why the cell would want to have less gamma actin around than beta actin.  There is no conceivable explanation for this in terms of chemistry.  A better understanding of protein structure won’t give it to you.  Certainly, beta and gamma actin differ slightly in amino acid sequence (4/375) so their structure won’t be exactly the same.  Studying this till the cows come home won’t answer the question, as it’s on an entirely different level than chemistry.

Cellular and organismal molecular biology is full of questions like that, but gamma and beta actin are the closest chemists have come to explaining the disparity in the abundance of two closely related proteins on a purely chemical basis.

So there you have it.  Physicality has gone as far as it can go in explaining the mechanism of the effect, but has nothing to say whatsoever about why the effect is present.  It’s the Cartesian dualism between physicality and the realm of ideas, and you’ve just seen the junction between the two live and in color, happening right now in just about every cell inside you.  So the effect is not some trivial toy model someone made up.

Whether philosophers have the intellectual cojones to master all this chemistry and molecular biology is unclear.  Probably no one has tried (please correct me if I’m wrong).  They are certainly capable of mounting intellectual effort — they write book after book about Godel’s proof and the mathematical logic behind it. My guess is that they are attracted to such things because logic and math are so definitive, general and nonparticular.

Chemistry and molecular biology aren’t general this way.  We study a very arbitrary collection of molecules, which must simply be learned and dealt with. Amino acids are of one chirality. The alpha helix turns one way and not the other.  Our bodies use 20 particular amino acids not any of the zillions of possible amino acids chemists can make.  This sort of thing may turn off the philosophical mind which has a taste for the abstract and general (at least my roommates majoring in it were this way).

If you’re interested in how far reductionism can take us  have a look at http://wavefunction.fieldofscience.com/2011/04/dirac-bernstein-weinberg-and.html

Were my two philosopher roommates still alive, they might come up with something like “That’s how it works in practice, but how does it work in theory? “

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Relativity becomes less comprehensible

“To get Hawking radiation we have to give up on the idea that spacetime always had 3 space dimensions and one time dimension to get a quantum theory of the big bang.”  I’ve been studying relativity for some years now in the hopes of saying something intelligent to the author (Jim Hartle), if we’re both lucky enough to make it to our 60th college reunion in 2 years.  Hartle majored in physics under John Wheeler who essentially revived relativity from obscurity during the years when quantum mechanics was all the rage. Jim worked with Hawking for years, spoke at his funeral and wrote this in an appreciation of Hawking’s work [ Proc.Natl. Acad. Sci. vol. 115 pp. 5309 – 5310 ’18 ].

I find the above incomprehensible.  Could anyone out there enlighten me?  Just write a comment.  I’m not going to bother Hartle

Addendum 25 May

From a retired math professor friend —

”

I’ve never studied this stuff, but here is one way to get more actual dimensions without increasing the number of apparent dimensions:

Start with a 1-dimensional line, R^1 and now consider a 2-dimensional cylinder S^1 x R^1.  (S^1 is the circle, of course.)  If the radius of the circle is small, then the cylinder looks like a narrow tube.  Make the radius even smaller–lsay, ess than the radius of an atomic nucleus.  Then the actual 2-dimensional cylinder appears to be a 1-dimensional line.

The next step is to rethink S^1 as a line interval with ends identified (but not actually glued together.  Then S^1 x R^1 looks like a long ribbon with its two edges identified.  If the width of the ribbon–the length of the line interval–is less, say, than the radius of an atom, the actual 2-dimensional “ribbon with edges identified” appears to be just a 1-dimensional line.

Okay, now we can carry all these notions to R^2.  Take S^1 X R^2, and treat S^1 as a line interval with ends identified.  Then S^1 x R^2 looks like a (3-dimensional) stack of planes with the top plane identified, point by point, with the bottom plane.  (This is the analog of the ribbon.)  If the length of the line interval is less, say, than the radius of an atom, then the actual 3-dimensional s! x R^2 appears to be a 2-dimensional plane.

That’s it.  In general, the actual n+1-dimensional S^1 x R^n appears to be just n-space R^n when the radius of S^1 is sufficiently small.

All this can be done with a sphere S^2, S^3, … of any dimension, so that the actual k+n-dimensional manifold S^k x R^n appears to be just the n-space R^n when the radius of S^k is sufficiently small.  Moreover, if M^k is any compact manifold whose physical size is sufficiently small, then the actual k+n-dimensional manifold M^k x R^n appears to be just the n-plane R^n.

That’s one way to get “hidden” dimensions, I think. “

The bias of the unbiased

A hilarious paper from Stanford shows the bias of the unbiased [ Proc. Natl. Acad. Sci. vol. 115 pp. E3635 – E3644 ’18 ].  No one wants to be considered biased or to use stereotypes, but this paper indicts all of us.  They use a technique called word embedding to look at a large body of printed material (Wikipedia, Google news articles etc. etc.) over the past 100 years, to look for word associations  -e.g. male trustworthy female submissive and the like. In word embedding models, each word in a given language is associated with a high dimensional vector (not clear to me how the dimensions are chosen) and the metric between the words is measured.  A metric is simply a mathematical device that takes two objects and associates a number with them.  The distance between cities is a good example.

 

The vector for France is close to vectors for Austria and Italy.  The difference between London and England (obtained by subtracting them) is parallel to the difference between to the difference between Paris and France.  This allows embeddings to capture analogy relationships such as London is to England as Paris is to France.

So word embeddings were used as a way to study gender and ethnic stereotypes in the 20th and 21st centuries in the USA.  Not only that but they plotted how the biases changed over time.

So in your mind the metric between bias == bad, stereotype == worse is clear

So just as women’s occupations have changed so have the descriptors of women.  Back in the day women, if they worked out of the home at all, were teachers or nurses.  A descendent of Jonathan Edwards was a grade school teacher in the town of my small rural high school.

As women moved into the wider workforce from them the descriptors of them changed.  The following is a pair of direct quotes from the article.”

“More importantly, these correlations are very similar over the decades, suggesting that the relationship between embedding bias score and “reality,” as measured by occupation participation, is consistent over time” ….”This consistency makes the interpretation of embedding bias more reliable; i.e., a given bias score corresponds to approximately the same percentage of the workforce in that occupation being women, regardless of the embedding decade.”

English translation:  As women’s percentage of workers in a given occupation changed the ‘bias score’ changed with it.

So what the authors describe and worse, define, as bias and stereotyping is actually an accurate perception of reality.  We’re all guilty.

The authors are following Humpty Dumpty in Alice in Wonderland  — ““When I use a word,” Humpty Dumpty said, in rather a scornful tone, “it means just what I choose it to mean—neither more nor less.” “The question is,” said Alice, “whether you can make words mean so many different things.” “The question is,” said Humpty Dumpty, “which is to be master—that’s all.”

I find the paper hilarious and an example of the bias of the supposedly unbiased.

Consensus isn’t what it used to be.

Technology marches on.  The influence of all 2^20 = 1,048,576 variants of 5 nucleotides on either side of two consensus sequences for transcription factor binding were (1) synthesized (2) had their dissociation constants (Kd’s) measured.  The consensus sequences were for two yeast transcription factors (Pho4 and Cbf1).  [ Proc.  Natl. Acad. Sci. vol. 115 pp. E3692 – E3702 ’18 ] .  The technique is called BET-seq (Binding Energy Topography by sequencing).

What do you think they found?

A ‘large fraction’ of the flanking mutations changed overall binding energies by as much as consensus site mutations.  The numbers aren’t huge (only 2.6 kiloCalories/mole).  However at 298 Kelvin 25 Centigrade 77 Fahrenheit (where RT = .6) every 1.36 kiloCalories/mole is worth a factor of 10 in the equilibrium constant.  So binding can vary by 100 fold even in this range.

The work may explain some ChIP data in which some strips of DNA are occupied despite the lack of a consensus site, with other regions containing consensus sites remaining unoccupied.  The authors make the interesting point that submaximal binding sites might be preferred to maximal ones because they’d be easier for the cell to control (notice the anthropomorphism of endowing the cell with consciousness, or natural selection with consciousness).  It is very easy to slide into teleological thinking in these matters.  Whether or not you like it is a matter of philosophical and/or theological taste.

Pity the poor computational chemist, trying to figure out binding energy to such accuracy with huge molecules like a transcriptional factors and long segments of DNA.

It is also interesting to think what “Molar” means with these monsters.  How much does a mole of hemoglobin weigh?  64 kiloGrams more or less.  It simply can’t be put into 1000 milliliters of water (which weighs 1 kiloGram).  A liter of water contains 1000/18 moles (55.6) moles of water.  So solubilizing 1 molecule of hemoglobin would certainly use more than 55 molecules of water.  Reality must intrude, but we blithely talk about concentration this way.  Does anyone out there know what the maximum achievable concentration of hemoglobin actually is?

The death of the pure percept — otoacoustic division

Rooming with 2 philosophy majors warps the mind even if it was 60 years ago.  Conundrums raised back then still hang around.  It was the heyday of Bertrand Russell before he became a crank.  One idea being bandied about back then was the ‘pure percept’ — a sensation produced by the periphery  before the brain got to mucking about with it.   My memory about the concept was a bit foggy so who better to ask than two philosophers I knew.

The first was my nephew, a Rhodes in philosophy, now an attorney with a Yale degree.  I got this back when I asked —

I would be delighted to be able to tell you that my two bachelors’ degrees in philosophy — from the leading faculties on either side of the Atlantic — leave me more than prepared to answer your question. Unfortunately, it would appear I wasn’t that diligent. I focused on moral and political philosophy, and although the idea of a “pure precept” rings a bell, I can’t claim to have a concrete grasp on what that phrase means, much less a commanding one.

 Just shows what a Yale degree does to the mind.

So I asked a classmate, now an emeritus prof. of philosophy and got this back

This pp nonsense was concocted because Empiricists [Es]–inc. Russell, in his more empiricistic moods–believed that the existence of pp was a necessary condition for empirical knowledge. /Why? –>
1. From Plato to Descartes, philosophers often held that genuine Knowledge [K] requires beliefs that are “indubitable” [=beyond any possible doubt]; that is, a belief counts as K only if it [or at least its ultimate source] is beyond doubt. If there were no such indubitable source for belief, skepticism would win: no genuine K, because no beliefs are beyond doubt. “Pure percepts” were supposed to provide the indubitable source for empirical K.
2. Empirical K must originate in sensory data [=percepts] that can’t be wrong, because they simply copy external reality w/o any cognitive “shopping” [as in Photoshop]. In order to avoid any possible ‘error’, percepts must be pure in that they involve no interpretation [= error-prone cognitive manipulation].
{Those Es who contend  that all K derives from our senses tend to ignore mathematical and other allegedly a priori K, which does not “copy” the sensible world.} In sum, pp are sensory data prior to [=unmediated by] any cognitive processing.

So it seems as though the concept is no longer taken seriously.

I’ve written about this before — as it applies to the retina — https://luysii.wordpress.com/2013/02/11/retinal-physiology-and-the-demise-of-the-pure-percept/

This time it involves the ear and eye movements.  Time for some anatomy.  Behind the eardrum are 3 tiny little bones (malleus, incus and stapes — the latter looking just like a stirrup with the foot plate pressed against an opening in the bone to communicate movement of the eardrum produced by sound waves to the delicate mechanisms of the inner ear).  There is a a tiny muscle just 1 millimeter long called the stapedius which stabilizes the stapes making it vibrate less protecting the inner ear against loud sounds.  There is another muscle called the tensor tympani which tenses the eardrum meaning that external sounds vibrate it less.  It protects us against loud sounds.

An article in PNAS (vol. 115 pp. 1309 – E1318 ’18) shows that just moving your eyes to a target causes the eardrum to oscillate.  Even more interesting, the eardrum movements occur 10 milliSeconds before you move your eye.  The oscillations last throughout the eye movement and will into subsequent periods of steady fixation.

It is well recognized in addition to the brain receiving nerve input from the inner ear, it sends nerves to the inner ear to control it.  So ‘the brain’ is controlling the sense organs proving input to it.  Of course the whole question of control in a situation with feedback is up in the air — see https://luysii.wordpress.com/2011/11/20/life-may-not-be-like-a-well-but-control-of-events-in-the-cell-is-like-a-box-spring-mattress/

As soon as feedback (or simultaneous influence) enters the picture it becomes like the three body problem in physics, where 3 objects influence each other’s motion at the same time by the gravitational force. As John Gribbin (former science writer at Natureand now prolific author) said in his book ‘Deep Simplicity’, “It’s important to appreciate, though, that the lack of solutions to the three-body problem is not caused by our human deficiencies as mathematicians; it is built into the laws of mathematics.” As John Gribbin (former science writer at Natureand now prolific author) said in his book ‘Deep Simplicity’, “It’s important to appreciate, though, that the lack of solutions to the three-body problem is not caused by our human deficiencies as mathematicians; it is built into the laws of mathematics.” The physics problem is actually much easier than the brain because we know the exact strength and form of the gravitational force. We aren’t even close to this for a single synapse.

Life at 250 Atmospheres pressure 1.8 tons/square inch

Tube worms (actually a form of mollusc) live on the depths of the ocean floor where there is almost no light, and very little oxygen. Just as plants use light energy to remove electrons from water to form oxygen and fix carbon, passing the stolen electrons back to oxygen taxing it though intermediary metabolism, symbiotic bacteria living in the worms remove electrons from hydrogen sulfide (H2S) formed by the hydrothermal vents on the seafloor. . How did the tube worms get this far down? By riding decaying wood down there. [Proc. Natl. Acad. Sci. vol. 114 pp. E3652 – E3658 ’17 ] This is the wooden-steps hypothesis [Distel DL, et al. (2000) Nature 403:725–726] which states that the large chemosynthetic mussels (ship worms) found at deep-sea hydrothermal vents descend from much smaller species associated with sunken wood and other organic deposits, and that the endosymbionts of these progenitors made use of hydrogen sulfide from biogenic sources (e.g., decaying wood) rather than from vent fluids.

At 2500 meters down the water pressure is 3750 pounds per square inch. One can only imagine the changes required in the amino acid sequences of their proteins required so they aren’t denatured or aggregated by such pressure.

The idea that life on planetary moons with subsurface oceans (Ganymede, Europa, Titan, Enceladus) could exist is no longer as fantastic as it initially seemed.

If it be found the implications for our conception of our place in the natural world are enormous.

Why wasn’t this mentioned in Genesis or any known creation myth? Assume for the moment that there actually is a creator who made itself known to our ancestors. If it tried to give Abraham, Gautama Budda, Mohammed et. etc. knowledge of these things, it wouldn’t have been believed. Planets? Planets with moons? Please. A few miracles here and there would be all that would be needed.