Book Review — The Universe Speaks in Numbers

Let’s say that back in the day, as a budding grad student in chemistry you had to take quantum mechanics to see where those atomic orbitals came from.   Say further, that as the years passed you knew enough to read News and Views in Nature and Perspectives in Science concerning physics as they appeared. So you’ve heard various terms like J/Psi, Virasoro algebra, Yang Mills gauge symmetry, Twisters, gluons, the Standard Model, instantons, string theory, the Atiyah Singer theorem etc. etc.  But you have no coherent framework in which to place them.

Then “The Universe Speaks in Numbers” by Graham Farmelo is the book for you.  It will provide a clear and chronological narrative of fundamental physics up to the present.  That isn’t the main point of the book, which is an argument about the role of beauty and mathematics in physics, something quite contentious presently.  Farmelo writes well and has a PhD in particle physics (1977) giving him a ringside seat for the twists and turns of  the physics he describes.  People disagree with his thesis (http://www.math.columbia.edu/~woit/wordpress/?p=11012) , but nowhere have I seen anyone infer that any of Farmelo’s treatment of the physics described in the book is incorrect.

40 years ago, something called the Standard Model of Particle physics was developed.  Physicists don’t like it because it seems like a kludge with 19 arbitrary fixed parameters.  But it works, and no experiment and no accelerator of any size has found anything inconsistent with it.  Even the recent discovery of the Higgs, was just part of the model.

You won’t find much of the debate about what physics should go from here in the book.  Farmelo says just study more math.  Others strongly disagree — Google Peter Woit, Sabine Hossenfelder.

The phenomena String theory predicts would require an accelerator the size of the Milky Way or larger to produce particles energetic enough to probe it.  So it’s theory divorced from any experiment possible today, and some claim that String Theory has become another form of theology.

It’s sad to see this.  The smartest people I know are physicists.  Contrast the life sciences, where experiments are easily done, and new data to explain arrives weekly.

 

 

Bye bye stoichiometry

Until recently, developments in physics basically followed earlier work by mathematicians Think relativity following Riemannian geometry by 40 years.  However in the past few decades, physicists have developed mathematical concepts before the mathematicians — think mirror symmetry which came out of string theory — https://en.wikipedia.org/wiki/Mirror_symmetry_(string_theory). You may skip the following paragraph, but here is what it meant to mathematics — from a description of a 400+ page book by Amherst College’s own David A. Cox

Mirror symmetry began when theoretical physicists made some astonishing predictions about rational curves on quintic hypersurfaces in four-dimensional projective space. Understanding the mathematics behind these predictions has been a substantial challenge. This book is the first completely comprehensive monograph on mirror symmetry, covering the original observations by the physicists through the most recent progress made to date. Subjects discussed include toric varieties, Hodge theory, Kahler geometry, moduli of stable maps, Calabi-Yau manifolds, quantum cohomology, Gromov-Witten invariants, and the mirror theorem. This title features: numerous examples worked out in detail; an appendix on mathematical physics; an exposition of the algebraic theory of Gromov-Witten invariants and quantum cohomology; and, a proof of the mirror theorem for the quintic threefold.

Similarly, advances in cellular biology have come from chemistry.  Think DNA and protein structure, enzyme analysis.  However, cell biology is now beginning to return the favor and instruct chemistry by giving it new objects to study. Think phase transitions in the cell, liquid liquid phase separation, liquid droplets, and many other names (the field is in flux) as chemists begin to explore them.  Unlike most chemical objects, they are big, or they wouldn’t have been visible microscopically, so they contain many, many more molecules than chemists are used to dealing with.

These objects do not have any sort of definite stiochiometry and are made of RNA and the proteins which bind them (and sometimes DNA).  They go by any number of names (processing bodies, stress granules, nuclear speckles, Cajal bodies, Promyelocytic leukemia bodies, germline P granules.  Recent work has shown that DNA may be compacted similarly using the linker histone [ PNAS vol.  115 pp.11964 – 11969 ’18 ]

The objects are defined essentially by looking at them.  By golly they look like liquid drops, and they fuse and separate just like drops of water.  Once this is done they are analyzed chemically to see what’s in them.  I don’t think theory can predict them now, and they were never predicted a priori as far as I know.

No chemist in their right mind would have made them to study.  For one thing they contain tens to hundreds of different molecules.  Imagine trying to get a grant to see what would happen if you threw that many different RNAs and proteins together in varying concentrations.  Physicists have worked for years on phase transitions (but usually with a single molecule — think water).  So have chemists — think crystallization.

Proteins move in and out of these bodies in seconds.  Proteins found in them do have low complexity of amino acids (mostly made of only a few of the 20), and unlike enzymes, their sequences are intrinsically disordered, so forget the key and lock and induced fit concepts for enzymes.

Are they a new form of matter?  Is there any limit to how big they can be?  Are the pathologic precipitates of neurologic disease (neurofibrillary tangles, senile plaques, Lewy bodies) similar.  There certainly are plenty of distinct proteins in the senile plaque, but they don’t look like liquid droplets.

It’s a fascinating field to study.  Although made of organic molecules, there seems to be little for the organic chemist to say, since the interactions aren’t covalent.  Time for physical chemists and polymer chemists to step up to the plate.

Two Christmas Presents

Two Christmas presents for you.  Yes Christmas presents.  I refuse to be culturally castrated by the professionally aggrieved.

The first is a link to a great scientific website — https://www.quantamagazine.org. It’s primarily about math and physics, with some biology thrown in. Imagine the News and Views section of Nature or the Perspectives section of Science on steroids.

Quanta is an editorially independent division of the Simons Foundation. And what is that you enquire? It is the answer to “If you’re so smart, why ain’t you rich”. Jim Simons is both much smarter and much richer than you and I. You can read more about him in a book I’m about to review on the blog — “The Physics of Wall Street”

Simons was a very accomplished mathematician winning prizes with a friend James Ax in the 60’s and 70’s — not quite the Fields Medal but up there. The Simons Chern 3 form is part of string theory. The two founded Renaissance Technologies in the late 80’s a stock fund using mathematical techniques to beat the market. And beat it they did, averaging 40% a year (after fees which were hefty). Even in the most recent market blowout in 2008 they were up 80% for the year. The firm employs about 200 people, mostly mathematicians and physicists. It was described by an MIT math prof as ‘the best mathematics and physics department in the world”.

At any rate after becoming a multibillionaire, Simons established his foundation, of which Quanta is a small part. It’s very good, with some heavies writing for it — such as Ingrid Daubechies full prof of math at Princeton who did a good deal of the early work on wavelets.

I haven’t read it all but the math is incredible, mostly about the latest and greatest new results and why it is important placing it in context. Physics isn’t forgotten, and the lead article concerns the philosophy of science and how it’s a’changin’ a la string theory, which is light years away from an experimental test of any of it.

Your second Christmas present is a Joke

The pope visited Colorado 22 years ago. A little known fact about him is that he loved to drive. Although Colorado is famed for the Rockies, the eastern half is high plains, so flat that you can see Pike’s peak from 100 miles away across the plains. At any rate the pope was being driven by his chauffeur from Colorado Springs to Denver on the Interstate, when the pope asked if he could drive. “Only if we go out on the plains where no one will see you” said the chauffeur.

So they switched when they got about 30 miles out in the middle of nowhere with the pope driving and the chauffeur in the back seat both behind tinted opaque windows. The pope started driving, really enjoying it, going faster and faster. He got up to 85 when a state trooper pulled them over.

Where’s the fire saith the trooper. He blanched when the driver’s window came down and he saw who was driving, and called headquarters. Arrest him came the answer. The trooper said I’m not sure, this guy is very big. I don’t care how big he is, arrest him. Are you sure. Yes.

I dunno boss, this guy is so big he’s got the pope driving for him.

Merry Christmas and Happy New Year to all