Maddening to Forget Your Origami

One of my Aha! moments in studying sub-cellular biology came when I learned that proteins, which are carefully-sequenced amino acids, rapidly fold into shapes more or less spontaneously. “More or less” because other factors are involved, among them the presence of water, salts, temperature, and so-called chaperons that help with the folding. The chaperones are yet other proteins; they also participate in the unfolding of proteins. What with such external factors present, a protein intended to be useful in cellular life because it has a certain (if sometimes very complex) shape, proteins may unfold or fail to fold properly. Then troubles begin. The same protein that delivers a service may turn toxic when still, or again, a strand.

Yesterday I mentioned a Wall Street Journal story on Mad-Cow disease—but I didn’t read it. Brigitte, who never passes a scientific story without close scrutiny, and recognizing a subject I ought to read about, flagged it for me. I read it this morning and discovered that origami-challenged proteins are at the core not only of Mad-Cow disease but also Alzheimer’s, Parkinson’s and Lou Gehrig’s disease—and Type II diabetes, for that matter. I am showing a strand (bad) and a fold (good) of the same chain of protein from Wikipedia (link).

Brigitte also tracks my own constantly folding ideas of the cosmic. Thus for motivation she annotated the WSJ illustration, similar to the one that I’m showing, with the words: “Bohm’s Universe?” This reference is to David Bohm, the physicist, who suggested that the visible cosmos is a tiny, unfolded part of the Great Universe, which is deeply implicated. Hence ours is a fallen world, the GU is the real one. As above, so below. In each case unfolding leads to madness.

Is Ether Back?

A May 19, 2011 story in Science Daily (here) carries this headline: Dark Energy is Driving Universe Apart: NASA’s Galaxy Evolution Explorer Finds Dark Energy Repulsive. Most of the text is quoted directly from NASA’s own site here, a press release also dated 5/19/2011.

Fascinating story. We’re approaching a major redefinition of reality. Herewith some background I’ve extracted from Wikipedia. The notion of dark matter surfaced in 1934 and is attributed to the Swiss astronomer Fritz Zwicky. His calculations suggested that the Coma galaxy cluster had to have considerably more mass than its luminosity indicated. He referred to the invisible mass, necessary for the rotational behavior of the cluster, to be due to “dark matter.” Dark energy got its name in 1998 from the American cosmologist Michael S. Turner. He took his phrasing from Zwicky to give a name to something. That “something” was an even more invisible mass necessary in the cosmos, but present outside of galaxies. This “something” was what caused the observed expansion of the universe; it was some kind of force. Ironically, the theoretical root of this concept dates to 1917 when Einstein introduced a fudge factor into his gravitational field equations; he called it the cosmological constant. Einstein’s equations suggested that gravity would ultimately cause the universe to collapse. A steady-state universe was then the orthodox view; the cosmos was neither growing nor expanding; for this reason Einstein chose a constant that would counteract the gravitational pull suggested by his equations just to the right extent to keep the cosmos in a steady state. When Edwin Hubble’s later observations suggested an expanding universe, Einstein is said to have labeled his constant his biggest blunder; and removed it. Prematurely, it seems. The constant is now back, as dark energy.

Indeed there is, based on calculations of the expansion (now said to be accelerating) and the anomalies observed in galactic rotation (that cannot be explained by gravity working on the visible bodies), far more of it than anything else. Contemplate the picture (from Wikipedia here but downloaded from NASA) of the constitution of the cosmos. Virtually all of the cosmos is dark energy and dark matter, leaving a mere 4 percent for matter; of that 4 percent only 0.4 percent are stars, and the matter of planets is too small to note.

To this I might add that both dark energy and dark matter are based on inferences, not on direct observations, one of cosmic expansion the other of anomalous galactic rotation. I will not be surprised if, in the fullness of time, the two will be found to be the same. It’s all dark energy. And that, folks is the cosmos.

* * *

Now Brigitte (my unfailing muse) pointed me to that story in Science Daily yesterday because of an earlier discussions about David Bohm (see this post). It turns out that Bohm’s own formulation of Quantum Theory in 1993—but already articulated in various forms in 1980 and before—offers a grand theory of the cosmos entirely in consonance with what we are seeing today. Bohm suggests that reality consists of two orders. One he calls the Implicate (enfolded) and the other the Explicate (unfolded) Order. He pictures the first as an “immense ocean of cosmic energy.” A sudden wave pulse within that ocean could create our universe, the Explicate Order, in extent tiny relative to that ocean. “This pulse,” Bohm continues, “would explode outward and break up into smaller ripples that spread yet further outward to constitute our ‘expanding universe’.” These words are from Bohm’s Wholeness and the Implicate Order (1980), p. 192. The scientific presentation of these ideas is in his 1993 The Undivided Universe.

In Wholeness Bohm introduces this subject saying:

What is implied by this proposal is that what we call empty space contains an immense background of energy, and that matter as we know it is a small, ‘quantized’ wavelike excitation on top of this background, rather like a tiny ripple on a vast sea.… In this connection it may be said that space, which has so much energy, is full rather than empty. The two opposing notions of space as empty and space as full have indeed continually alternated with each other in the development of philosophical and physical ideas. Thus, in Ancient Greece, the School of Parmenides and Zeno held that space is a plenum [fullness]. This view was opposed by Democritus, who was perhaps the first seriously to propose a world view that conceived of space as emptiness (i.e., the void), in which material particles (e.g., atoms) are free to move. Modern science has generally favored this latter atomistic view, and yet, during the nineteenth century, the former view was also seriously entertained, through the hypothesis of an ether that fills all space. Matter, thought of as consisting of special recurrent stable and separable forms in the ether (such as ripples or vortices), would be transmitted through this plenum as if the latter were empty. [p. 191]

Well, it seems to me that ether is back once more, but differently named. New names are necessary because reputation is so vital in science, and while it is now fashionable to be darkly energetic, it will not do to be ethereal.

Words, words, words. To see our great universe as a minor bubble deep in an ocean of eternity, a bubble broken up and carried by the ocean’s immense energy towards re-absorption in the whole (read expanding universe), is humbling but has a promising flavor. Indeed, NASA seems to agree. It suggests that as Dark Energy has its way with the universe, time will come when we will no longer see the stars out there. Eventually even our own galaxy will begin to spread apart.

Fitting Equations

All that is clear about the quantum theory is that it contains an algorithm for computing the probabilities of experimental results. But it gives no physical account of individual quantum processes. Indeed, without the measuring instruments in which the predicted results appear, the equations of the quantum theory would be just pure mathematics that would have no physical meaning at all. And thus quantum theory merely gives us (generally statistical) knowledge of how our instruments will function. And from this we can make inferences that contribute to our knowledge, for example, of how to carry out various technical processes….

It follows from this that quantum mechanics can say little or nothing about reality itself. In philosophical terminology, it does not give what can be called an ontology for a quantum system. Ontology is concerned primarily with that which is and only secondarily with how we obtain our knowledge about this. [David Bohm and B.J. Hiley, The Undivided Universe, Routlege, 1993, p. 1-2]

David Bohm (1917-1992) was a quantum physicist. He wrote the definitive Quantum Theory (1951) that Einstein read and of which that sage said that it helped him, finally, to understand the theory. The book remains the central text in the field. The book from which I quote was Bohm’s last work, published posthumously, produced in collaboration with Hiley, a younger mathematician. It is subtitled An ontological interpretation of quantum theory. The book introduces an intuitively accessible (thus “physical”) version of quantum events in which new equations still produce the correct results but beneath them is another conceptualization of what really happens. Bohm approaches the perplexing particle-wave duality issue, for instance, by hypothesizing “that the electron is a particle with well-defined position and momentum that is, however, profoundly affected by a wave that always accompanies it. Far from being hidden, this particle is generally what is most directly manifested in observation.”

I bought this book soon after it appeared. I chanced across it, if that’s the word, while browsing in a bookstore near daughter Monique’s then new apartment; it fell into my hands. I read it, despite its forbidding difficulties (not written for the layman). It opened up huge vistas about the nature of science for me, and particularly the state of science in our times. The content of this book is quantum physics, but its thematic is the profound difference between knowing how we know (epistemology) and knowing what we know (ontology). So long as science is satisfied with fitting equations to observations—without a genuinely physical conceptualization of what actually is or happens behind the observations, science enters a stage of stagnation and of symbolical wizardry without genuine meaning. Bohm quotes a telling statement of fellow physicist, Murray Gell-Mann: “Quantum mechanics, that mysterious, confusing discipline, which none of us really understands but which we know how to use.”

My elated reaction to these revelations from a genuine insider then (and that’s now twenty years ago) was: “I knew something was wrong—but now I know why.” In a way, nothing derails as surely as huge success. And mathematical modeling of phenomena—without genuinely, intuitively, understanding them—has been exactly that. But in that process, in a way—having gained the power to predict and therefore to control—the deeper urge that actually feeds real science, the search for truth, is lost. I would, of course, extend this view backward to relativity (space-time?) and upward to astrophysics (singularity?).

Until I encountered this volume, I only knew of Bohm as one of the physicists—and no doubt often confused him with Niels Bohr, the Danish physicist, who forms the other polarity of quantum theory. Bohr was its high priest, its pope, and a dogmatic preacher of know-nothingism. He is quoted as saying: “There is no quantum world. There is only an abstract physical description. It is wrong to think that the task of physics is to find out how nature is. Physics concerns what we can say about nature...” [Emphasis in the original.]

Bohm own view of the problems related to relativity as well as quantum theory was that the answer lay beyond both; both were approximations that frayed at the edges. His own theory of an undivided universe, however well expressed in equations and however accurately matching observations, has not exactly caught on since 1993. But it’s early days yet. In a vast and contentious social process like science, where orthodoxy is very helpful in rising professionally, it takes a long time before paradigms fall.

An earlier work of Bohm’s, first published in 1980, titled Wholeness and the Implicate Order, provides a more accessible approach to his thought. Alas, I found that book long after I’d broken several teeth on his scientific summation.

Three Follow-Up Notes

   
Empedocles

My post on “diamond bodies” could have mentioned the legendary Empedocles, a pre-Socratic Greek (around about 490-430 BC) who, in the Graeco-Roman-Western line of civilization was the first to concern himself with the origin of elements (or the first of whom something survives). It is from him that we have the core elements—fire, air, water, and earth—and theories of how these fundamentals generate all else. The western world embraced this classification.

If we permit ourselves patronizing chuckles in looking back at this sort of thought, we shall be viewed as very naïve and backward when we arrive in heaven. This was serious thought, on Empedocles’ part as well as on the part of those who found merit in it later. These words were technical concepts (or so we would call them today); they referred to certain fundamental qualities that fire, air, water, and earth brought to mind—rather than the actual phenomenon of oxidation, gas mixtures, H₂O, or a mixture of minerals and organics. Great thinkers are never stupid; but those who dismiss them inevitably are.

In the early, creative stages of civilization the sage-scientist-poet-mystic is one complete personality; in late stages comes specialization. Newton engaged in biblical commentary, indeed spent much of his time on it. Einstein, the latecomer, only permitted himself some few expressions of not-quite-mathematical wonder. Empedocles was a wizard, you might, say—and expressed himself in verse. Here are the first lines of his poem, one of two we know of, called Hymns of Purification. We have this fragment thanks to Diogenes Laertios who wrote about Greek philosophers in the third century of our era. I've rendered this fragment in my own words to heighten its effect a little. The translation is referenced below. The lines produce the aura of its author:

To friends who live near mighty, tawny Acragas,
To those who love good deeds in the proud citadel
Crowning its noble height—my greetings to you send.
Amongst you I wander, an immortal I am,
Death have I conquered, am honored by all, adorned
With holy diadems; blooming garlands cover me.
No matter what illustrious towns I visit,
Men and women merge their praises and follow
In my steps by thousands thirsting for deliverance.
Some ask for prophecies, some beg for remedies
Against a swarm, a pest of all kinds of disease.

In the above I don’t rely on my “learning,” which is conspicuous mostly by absence, but on the Dictionary of Philosophy and Religion, edited by William L. Reese, Humanities Press, 1980. The original of the edited fragment courtesy of Wikipedia here.

Dark Matter

In waxing eloquent on elements two posts back and above, I failed altogether to mention the latest fly in the ointment, namely dark matter. Dark matter is a latecomer too, like Einstein. It was first postulated the other day, as it were, in 1934, two years before I came screaming into the world one stormy night in July. With such a theory already in the air, I had reason to be displeased!

Here is my understanding of the (dark) matter in a thimble. Dark matter—you cannot see or weigh it; it is transparent and seems to have no mass—is stipulated to exist for a reason. And the reason is? The reason is that the rotation of stars on the outer fringe of galaxies takes place at a slower, a much too stately, pace than it ought to based on the laws of gravitation as propounded by the above mentioned Newton. This gravitational anomaly forces the conclusion that there is much, much more matter in the cosmos than we can actually detect. The issue really is the gravitational anomaly as such. Dark matter is the hypothesized cause.  One possible alternative explanation of this anomaly is that gravitation diminishes in force over very great distances. Now we have a description of gravitation, not really an explanation of it. We have yet to detect particles that are exchanged (gravitons, as it were). Our explanation is that mass distorts space—a theory at least as marvelous as dark matter itself. If we understood gravitation better, the anomaly might disappear. Since that problem—gravitation—is thought to be settled by space-time equations, it is, as it were, no longer on the table, hence we reach for dark matter.

I detect the seeds of a quite different explanation in the work of David Bohm (1917-1992), particularly in his book, The Undivided Universe: An ontological interpretation of quantum theory. He wrote it with B.J. Hiley. Bohm’s very novel theory is that our universe is a tiny part of a greater cosmos that has been unfolded (explicated) from a greater whole, the implicate (enfolded) cosmos. Thus what we call the universe is a minute little bubble of expansion within a vastly more compressed surround. The seed notion here (it’s mine, not one that Bohm proposed) is that gravitational anomalies may be due to the presence of the greater whole as a container—and that this influence is detectable only in very large segments of space, not in the local, e.g., the solar system.

Undivided Universe is very tough reading. It took me years to get used to its premise—and never mind the thick bristling of equations. A more accessible book is Bohm’s Wholeness and the Implicate Order, Routledge, 1996.

Inspired on Tuesday by Monday

This third note to tip my hat to a fellow blogger and reader of Ghulf Genes who styles himself Montag, which happens to mean Monday in German. His blog is here. Montag made some comments yesterday elsewhere. He mentioned both Empedocles and dark matter—and these annotations made me reflect this morning and thus led to the above.

Books mentioned at Amazon:

The Undivided Universe: An ontological interpretation of quantum theory.
Wholeness and the Implicate Order.