Science Writing

On Science Writing

                                                                                                                                                                                                                                                          "Our species needs, and deserves, a citizenry with minds wide awake and a basic understanding of how the world works."

   -- Carl Sagan in The Demon-Haunted World

   To my mind, the greatest problem we face in our country and in the world is the lamentable lack of rationality and critical thinking in the population. It seems to me that, at least in democratic countries, this deficiency is the root of most social evils.

   For some years, as my contribution to the war on stupidism, I toiled in the trenches of academe, teaching science and mathematics to undergraduates. It was not the Sisyphean nature of that work that drove me to leave it; rather a confluence of factors related to growth and self-realization led me to the then unheard-of step of walking away from a tenured position. I'll tell more about my career in science and technology later on in this blog. For the moment, I'll just say that lately my interests have turned towards writing, in particular, writing about science for the general reader, both my own writing and the writing of others, the science writing genre in general.

   Science is the ultimate expression of the application of reason and critical thinking to our observations of nature. So the channels of informing the public on science-through print journalism, books, television, the Web-play a central role in encouraging reason in the public mind.

   Science is a major force shaping our culture. The progress of science depends on public support and so, to some degree, on public understanding. These are all reasons that point to the importance of science communication, including science writing for the general reader.

   Probably, for most of the "general public", exposure to science news is limited to the stories in daily newspapers, weekly newsmagazines, and television specials. While there are several newspaper science writers and editors whose work I admire-The New York Times weekly Science Times section being a gathering place for some of the best--, I am frequently appalled by some of the work I encounter in my local dailies. From time to time, I'll use this blog to hold up some of the worst examples to criticism.

   Moving up a level from this least-common-denominator of science journalism, we have books, called science popularizations, and magazines such as Scientific American and Discover, aimed at the intelligent, educated and scientifically curious lay reader. These readers, these books, and their authors, are my main areas of interest.

   I think a lot about the best ways of constructing metaphors and analogies. Good composition in expository writing, finding just the right order of presentation best to convey a proper understanding of the topic, is a craft that has always fascinated me, and one which I think I have practiced well on occasion. So, to the extent that I find time to read them and write about them, science popularizations in book form will be my main topic. I'll also be commenting on stuff I see in the science magazines and the daily press.
       

First post, new blog

This is my third time starting this blog, the previous two on two different blogging platforms, Radio Userland and Blogger, which both I found wanting for different reasons.  So now I start again with TypePad.  The first few posts will be edited versions of articles previously posted to one of those two previous blogs, a quick way for me to learn how to use this system.

Quantum Flapdoodle

Even Scientists Marvel at ‘Spooky’ Behavior Of Separated Objects.

That was the headline on Sharon Begley’s “Science Journal” column in the October 14, 2005, edition of the Wall Street Journal, which tries to report some of the recent experiments regarding quantum mechanical entanglement. It seems to me that this headline, indeed the entire column, is a prime example of what Murray Gell-Mann, in The Quark and the Jaguar, has called “flapdoodle” in discussing the features of quantum mechanics.

The column starts off poorly in emphasizing the barium borate crystals as producers of “special” photons. I think that Ms Begley chooses to mention crystals because of the mystical or magical connotation that it might evoke in the minds of some segments of the population. There is really nothing special about the crystal or the photons that emanate from it in the experiments. The key fact about the two photons is just that they were produced in a single atomic event and so are necessarily related by the fundamental conservation laws—in particular, conservation of momentum and angular momentum. They emanate from the same event and so their observable properties are correlated.

The column continues emphasizing spookiness and weirdness, as if these experiments manifest something supernatural that physics is at a loss to grapple with. The term “spooky action” or some variant of it appears in the column no less than eight more times after the headline, out of a total of 847 words in the entire column, and there is one occurrence each of “weird” and “crazy”. Unfortunately, the column characterizes the effect of the conservation laws as a “conspiracy loophole”, ignoring the fact that they are fundamental principles at the very foundation of all of physics.

The great failing of the column is in missing the opportunity to broach the issue of alternative interpretations of quantum mechanics. The idea that entanglement phenomena imply instantaneous action at a distance follows from the conventional Copenhagen interpretation, in which the solution of the governing equations is interpreted as giving the probabilities for finding the system in each of its possible states, and which was widely accepted for many decades. But the Copenhagen interpretation in itself is weird, in the way it leaves the state of the system undefined until measurements are made, and in the way the act of measurement mysteriously “collapses” the wave function.

For the past twenty years or so, many leading physicists have adhered to modified versions of the Copenhagen interpretation, which look carefully at how predictions of macroscopic observations are to be computed by properly averaging over the unobserved parameters. These interpretations talk about “consistent decoherent coarse grained histories” of the system. The big names associated with them include Murray Gell-Mann, Stephen Hawking, James Hartle, Roland Omnès. These interpretations are partly reminiscent of the “parallel universes” interpretation of Hugh Everett. You can find a good starting point for learning about these issues at http://en.wikipedia.org/wiki/Interpretations_of_quantum_mechanics

Last spring I heard Roger Penrose speak at Cody’s Books in Berkeley, at a book signing for his The Road to Reality. On that occasion I heard Sir Roger state unequivocally “quantum mechanics doesn’t make sense”. Indeed, in the book there are several references to problems with QM and Sir Roger’s feeling that it needs to be changed, albeit in subtle ways since it is undeniably an enormously successful theory.

Last month I attended a two-hour lecture by Murray Gell-Mann in Santa Clara, on the subject of complex adaptive systems. On questioning on the issue of Penrose’s discomfort, Murray insisted that QM is correct, consistent, makes perfect sense, and there is nothing weird about it—once you accept that it only predicts probabilities and is subject to the limitations of the Heisenberg uncertainty principle. He expands on these points a bit in The Quark and the Jaguar, and you can find further emphasis of these points in some of his writings posted on the Santa Fe Institute website, www.santafe.edu.

I might write a little more in future posts comparing the Penrose and Gell-Mann points of view. But not right away, because my main interests in science reading and writing these days are outside the flow of issues in fundamental physics, but running more towards the subjects of complex systems, evolution, and theoretical biology. More on these readings soon.
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Brian Greene's double headed entropic arrow of time

As mentioned in my previous post, I do not buy Greene’s argument, in Chapter 6, for the double-headedness of the entropic arrow of time. This argument bothered me much. I’ve spent a lot of time worrying about it, have decided that it really is not correct.  Moreover, this argument, on which he spends many words on several pages, is really not needed for the essential results of the chapter, namely, that the universe must have been in a state of minimum possible entropy at its beginning,  that the high degree of order of this system, in spite of its  homogeneity (which in itself implies disorder), can be ascribed to the effect of gravitation, and that all the order in subsystems that we have observed (such as the formation of galaxies and planets or the origin of life) derives from this original gravitationally determined order.

Therefore, it seems to me that this is an example of science writing that falls short.

Greene’s main example to illustrate the double-headedness of the statistical entropic arrow of time has you sitting in a bar on a very slow Friday night, being served a glass of water with some ice at 10:00 PM.  There’s not much action, so you sit there watching the ice melt.   Greene claims that, at 10:30 PM, when you notice the partially melted ice cubes in your glass, correct application of mathematics leads you to conclude that it is most likely, most probable, that half-an-hour earlier, at 10:00 PM, there was even less ice in the glass than now, contrary to your own memory, which has the concurrence of your neighbor on the next stool, and is further supported by the evidence of the tape in the video surveillance device. He admits that this is hard to accept, that it seems absurd, contrary to all experience, but he insists that it is, nevertheless, mathematically correct.  

Here are a few reasons why I feel that this entire part of the discussion is just not right.

Greene’s argument is based solely on counting the number microscopic states in which there is no ice in relation to the number of states in which there is the original full serving of ice cubes.  His conclusion depends on the assumption that all these states are equally probable, and since there are vastly more states with no ice than states with full ice, the probability for no ice dominates.  This equal probability assumption has no justification in classical statistical mechanics.  The equal probability assumption yields important and correct results for isolated systems that are in thermodynamic equilibrium.  Indeed, a standard exercise in statistical mechanics  is to show that the Gibbs formula for the entropy in terms of the probabilities of the microstates is maximized when the probabilities are equal. Your glass of ice water sitting on the bar, absorbing heat from its environment as its ice is melting, is most definitely not an isolated system in thermodynamic equilibrium.   It’s worth adding that some physicists, notably Einstein,  have never been comfortable with the assumption of equal probabilities, even for systems in equilibrium.

Greene uses the terms “probability” and “likelihood” in a way that does not agree with their usual usages in math and physics. An essential feature of probability in normal usage is that the probability that you ascribe to an assertion must depend on the amount of information you have about the experiment. That is, the notion of conditional probability is essential.  The fact that we see some ice in the glass at 10:30 is important in estimating probabilities about the history of the experiment.  The hypothesis that there was no ice in the glass at 10:00 entails that we must be observing an enormously improbable statistical fluctuation now at 10:30, while the hypothesis that there was a full ice cube in the glass at 10:00 entails that we are observing exactly the expected amount of ice at 10:30.  From this we can conclude that the probability that there was more ice in the glass at 10:00 is much greater than the probability that there was no ice in the glass at that time.  I think this can be formalized algebraically by what is called Bayes’ Theorem.

Besides time-reversal invariance, there is another fundamental symmetry principle that Greene does not mention and which seems to me to conflict with his argument, namely, invariance under time translation or time displacement. That is, the laws of physics don’t depend on what instant of time you call t=0. So it seems to me that if statistical entropy increases both towards the future and towards the past from any specified instant of time, then statistical entropy, whatever it is, violates time translation invariance, and so must be without physical meaning.

Another criticism that I have of Greene’s chapter 6 is that he does not give a clue to  how gravitation defines order, or the negative of entropy.  

It is interesting to compare Greene’s Chapter 6 with an entirely analogous Chapter 15,  in Murray Gell-Mann’s excellent book, The Quark and the Jaguar,  first published in 1994.  This chapter, called “Time’s Arrows, Forward and Backward Time”,  treats several arrows of time, including an entropic arrow, and none of them are double-headed.  Gell-Mann also treats several features of the entropy concept that Greene ignores, in particular, the role of information and ignorance in the entropy budget.  The fact that Greene’s barroom scene is being recorded on a video tape actually compensates for some of  the increase of the room’s entropy associated with the melting of the ice.  It is only after that tape is erased that the full entropy increase potential in the melting of the ice is realized.  

Gell-Mann essentially attributes the entropic arrow of time to the very high  degree of order in the initial condition of the universe, again due to the gravitation of the large mass of the primordial soup, (Greene’s final conclusion) but again without a clear indication of how one would compute the (negative) entropy caused by gravitation in that state.

I will probably do another post entirely on The Quark and the Jaguar.

"The Fabric of the Cosmos" by Brian Greene

Everyone is interested in cosmology, right? Well, I’d like to think, anyway, that most people consider the cosmic questions from time to time. How did this all begin and why are things like this, anyway?

Every culture, even every primitive tribe has had its cosmology, its story of The Origin. Then, all the tribe must learn the story by rote. Okay, so God said “Let there be light”, then created the world and all its stuff in the next six days. Makes sense, glad I asked, story over, and now we have to turn to practical stuff, like sharpening our spears for the next mastodon hunt.

No, you don’t need to ask who it was that put God in charge, or to consider possible alternatives. Turtles all the way down? Forget about it.

Over the past 90 years or so, cosmology has become a scientific discipline, part of physics and astronomy. All that we’ve learned in terrestrial labs about the nature of space, time, energy, and the structure of matter applies to what we see in the sky. Physics lets us put together credible, consistent models for the evolution of stars, galaxies, and the expanding universe itself. We have a good story for the synthesis, through astrophysical processes, of the known chemical elements from an initial soup of pure energy. Conversely, because conditions in the very young universe were extreme, with temperatures and densities far beyond what can be achieved in earthly labs, observations of the cosmos yield clues for remaining questions at the very frontiers of ultramicroscopic physics. Cosmology, the study of the biggest know thing, the universe itself, is intimately connected with the study of elementary particles, the smallest known things.

It is a great challenge to write a book to lead the cosmically curious lay reader through the web of observations, theories, and speculations that make up modern physical cosmology. Brian Greene’s The Fabric of the Cosmos is an impressive response to the challenge. It received many laudatory reviews when it appeared last year, without much criticism. In this entry I report a little about my experience with the book and my feelings about it.

As well as challenging the author, any such book poses a challenge also to the interested reader. This isn’t Eden any more, Toto; to achieve enlightenment, we have to try to understand a lot of fundamental physics. We have to be willing to commit some time and effort to it. But still, no matter how curious, as lay readers, we are not able to devote our lives to mastering the subject. We do have other spears to sharpen.

I have a considerable background, a formal education in physics and mathematics, acquired in an era preceding the development of many of the crucial results discussed in this book. So, while very well prepared in fundamentals, my prior knowledge of both cosmology and elementary particles were a couple of decades out of date. After having put considerable effort into reading the book, I’m not totally satisfied with it and wonder how illuminating it might be to readers with much less formal education in math and physics than I have had. I can imagine a typical, intelligent, scientifically aware lay reader, who would be naturally attracted to the subject, but who, on finishing the book, might feel bewildered about what he has read, his head spinning with a sea of terms--entropy, inflation, entanglement, Higgs ocean, strings, branes, super symmetry, broken symmetry, flatness, Calabi-Yau manifolds—but without a satisfying understanding of the logical relationships and mutual implications among them.

I recall that when I read Greene’s The Elegant Universe a few years ago, I was not always happy with his choices of metaphor in presenting quantum ideas. Similarly, with this book, I find some of the metaphors less than congenial, and I think sometimes not well explained. As an example, I’ll look at his metaphor for the all-important hypothesized Higgs field, important both to the fundamental theory of elementary particles, and to explaining inflation, the great new idea of what actually banged in the Big Bang origin of the universe.

Greene’s basic metaphor for a chaotic field in the fantastically hot early universe has a poor, tortured frog frantically hopping on an extremely hot metal bowl, too hot to stand on, while trying to get to his lunch, a pile of worms at the bottom center of the bowl. For the Higgs field, this picture is modified by adding a bump or tower with a plateau at the center of the bowl, with the worms resting on the top.

The important distinguishing characteristic of a Higgs field is that the minimum energy does not occur when the field value is zero, but the significance of this is lost without some discussion of the meaning and use of the field value. If it is not a representation of energy, then what is it.? The meaning of the Higgs field value certainly wasn’t clear to me at the time that he first introduces the metaphor. It has become a little clearer on reading another popularization of the same subject, namely, The Inflationary Universe, by Alan Guth, the actual discoverer of the inflationary theory. I haven’t yet read the Guth book entirely through, but on reading the corresponding sections on Higgs and inflation, which feature diagrams very similar to those in Greene;s book, it seems to make more sense to me than Greene’s presentation, and without having to torture a frog, or harm any other animals in any way.

For one thing, Greene offers the (I think) misleading statement that the frog’s distance from the worms represents the field’s value and the height of the bowl represents the energy. Actually, these diagrams are graphs of the field’s energy density as a function of the field value as independent variable, and in this picture, the field value is a pair of real values, perhaps a complex variable. The magnitude of this complex variable is the radial coordinate in a cylindrical polar coordinate system, so the frog’s distance from the vertical axis of the bowl. (Actually I learn from the Guth book that there must be 24 different Higgs field values).

Further, I think that the pile of worms is a red herring, i.e., a distraction. The frog is not really trying to get to the worms when they are atop the central plateau, but rather, like all systems, he is seeking his minimum energy configuration, which occurs at some distance from the central axis in the case of the Higgs field. Greene uses the worms to cause the frog to hang out a bit on the central peak when he happens to land there by chance in his jumping, after the bowl has cooled a bit. Guth doesn’t need the worms, because he has a little dimple in the energy function at the center of the bowl, invokes supercooling to have the system get trapped there, and invokes quantum mechanical tunnelling to have the system eventually roll down to its minimum energy at a non-zero vacuum expectation value for the the Higgs field, causing the brief but violent exponental inflation of the universe in the process.

Another big problem that I have with The Fabric of the Cosmos is a discussion in Chapter 6, “Chance and the Arrow”, which gives attention to the question of the direction of time-- what, in physics, distinguishes the future from the past? It is not the deterministic laws of simple systems and fields—e.g., Newton’s laws of motion, Maxwell’s equations of the electromagnetic field, the Schroedinger equation in quantum mechanics-- which are all invariant under time reversal. It is only the laws based on statistical approaches to physics that define an arrow of time, in particular, the Second Law of Thermodynamics, which says that the total entropy, or disorder, of the universe only increases in time.

For some reason that I do not yet understand, in Chapter 6, Greene spends a lot of words and a lot of effort arguing for what he admits is a seemingly absurd proposition, namely, that, from any point in time, statistical entropy must increase not only towards the future but also towards the past. In other words, the entropic arrow of time is double-headed. His prime example has you sitting in a bar on a slow Friday night, watching the ice melting in your glass of ice water. At 10:00 PM the bartender served you this glass of water, with a large ice cube. At 10:30, the cube is partially melted, smaller than when you were served it. Now, his proposition is that, based on considerations of probability and mathematics, sitting there staring at your glass at 10:30 you must conclude that the overwhelming odds support the assertion that half-an-hour earlier the ice cube must have been even smaller than now, not larger, notwithstanding your memory, the concurrence of your eqally bored neighbor on the next stool, and the evidence of the tape in the video surveillance device, which all support the opinion that the ice cube was even larger at 10:00 PM than it is now at 10:30.

First, I’m not quite sure why Greene hews to this proposition, except that it seems to have something to do with need to invoke gravitation as the source of the very highly ordered state, a state of lowest possible entropy, which, according to the 2^nd Law, the universe must have had at its origin. Gravitation somehow contributes high order, or negative entropy, because of its potential for forming clumps from the high-entropy uniform distribution of energy in the beginning.

Second, I really have not been able to buy the argument for the double-headed entropic arrow of time (which omits any actual demonstration,or even a rough sketch, of the mathematics he is arguing about). It seems to me that it omits a number of considerations that should be relevant, such as the notions of conditional probability, Bayesian probability, and the relations between entropy, information, and ignorance. I’d like to see at least a sketch of the way one would apply the methods of statistical physics to calculate the probabilities in support of Greene’s assertion. I’ve been struggling with using these methods to sketch a contra argument to this assertion.

I’ll post more on this subject later.

It is pretty interesting to compare Greene’s Chapter 6 with an entirely analogous Chapter 15 in Murray Gell-Mann’s book, The Quark and the Jaguar. Which I may also get to soon in this blog.

Experience, intent, and some old works

A passion for learning new things and for going off on new sorts of adventures is a salient feature of my character and a driving force in all that I have done or attempted. I have always been changing my major, even into graduate school, and continuing into real life.

As mentioned in my previous post, I did a substantial stint at college teaching. Before and after that duty, my career has wound its course through several areas of science and technology: experimental elementary particle physics, experimental cosmic ray physics, theoretical astrophysics, pure mathematics, mathematical modeling of ecosystems, computational fluid dynamics, systems engineering and software development for supercomputer applications and scientific visualization, software development for mechanical design and manufacturing automation, developing software geometry and physics engines for immersive 3D games, 3D graphics API development, and several engineering functions in three startup companies, of which one was Web-based. In each of these areas I have done at least some interesting work, interesting to me, anyway, and in a few cases, work that I think was very good, important, or leading-edge.

A common thread running through this occupational odyssey is the enjoyment that I've derived from the writing part of the job, whatever it was--research papers, engineering reports, white papers, trade journal articles, proposals, training materials, etc. Nice feedback on the quality of my writing from editors, clients, and coworkers has sustained this enjoyment.

I even have some credentials as author of the sort of science popularizations that I'm making the focus of this blog. One fun project was an article on supercomputers for Scientific American, which won the cover graphic honor for that issue. I won't show its details, quite out of date. (In the 23 years since it appeared, the standard of supercomputer performance, as measured in peak megaflops, has increased by about a factor of a million).

The success of that article led Scientific American to invite me, five years later, to contribute a very short piece on scientific visualization to dress up a special advertising section on scientific workstations. This was a great exercise in brevity. The illegible graphic shows the first of its two pages.

The point of this post is to give some background for my interest in science writing and my motivation for starting this blog. I intend to try to do some more science essays for the general reader of my own, both on subjects in which I have special experience and on others that I'm still learning, while examining works of some of today's respected practitioners of the craft for inspiration. It seems to me that a blog is an excellent medium in which to pursue this endeavor, scary as it might be to expose myself to whatever public I might attract here.

On Science Writing

"Our species needs, and deserves, a citizenry with minds wide awake and a basic understanding of how the world works."

-- Carl Sagan in The Demon-Haunted World

To my mind, the greatest problem we face in our country and in the world is the lamentable lack of rationality and critical thinking in the population. It seems to me that, at least in democratic countries, this deficiency is the root of most social evils.

For some years, as my contribution to the war on stupidism, I toiled in the trenches of academe, teaching science and mathematics to undergraduates. It was not the Sisyphean nature of that work that drove me to leave it; rather a confluence of factors related to growth and self-realization led me to the then unheard-of step of walking away from a tenured position. I’ll tell more about my career in science and technology later on in this blog. For the moment, I’ll just say that lately my interests have turned towards writing, in particular, writing about science for the general reader, both my own writing and the writing of others, the science writing genre in general.

Science is the ultimate expression of the application of reason and critical thinking to our observations of nature. So the channels of informing the public on science—through print journalism, books, television, the Web—play a central role in encouraging reason in the public mind.

Science is a major force shaping our culture. The progress of science depends on public support and so, to some degree, on public understanding. These are all reasons that point to the importance of science communication, including science writing for the general reader.

Probably, for most of the “general public”, exposure to science news is limited to the stories in daily newspapers, weekly newsmagazines, and television specials. While there are several newspaper science writers and editors whose work I admire—The New York Times weekly Science Times section being a gathering place for some of the best--, I am frequently appalled by some of the work I encounter in my local dailies. From time to time, I’ll use this blog to hold up some of the worst examples to criticism.

Moving up a level from this least-common-denominator of science journalism, we have books, called science popularizations, and magazines such as Scientific American and Discover, aimed at the intelligent, educated and scientifically curious lay reader. These readers, these books, and their authors, are my main areas of interest.

I think a lot about the best ways of constructing metaphors and analogies. Good composition in expository writing, finding just the right order of presentation best to convey a proper understanding of the topic, is a craft that has always fascinated me, and one which I think I have practiced well on occasion. So, to the extent that I find time to read them and write about them, science popularizations in book form will be my main topic. I'll also be commenting on stuff I see in the science magazines and the daily press.