I haven't written anything here in many months. In some ways not much has happened in the world, in other ways a lot. The problems of unsustainable economic and ecological systems increasingly occupy my mind. In the face of a corrupt oligarchical political system, the only way to prevent mass revolt by the starving masses is to increase total growth. As long as most people have an acceptable minimum income (whatever that level is), they seem willing to tolerate gross total inequality of distribution. "Growth" is presented as a panacea, and every piece of evidence of it is taken up by mainstream media as a positive message.

The problem is, as a biologist I see unrestrained growth as an evil. Our bodies grow when we are young, but once we reach maturity, continuing growth of any subunit of the body basically means cancer, which is ultimately fatal. The entire body can't grow indefinitely, for one thing we aren't built that way, for another we would obviously reach physical limits. For example, several hundred million years ago, the concentration of oxygen in the atmosphere was substantially greater than it is currently (it's now about 21%). One consequence was that insects could be larger. As a group, insects lack a dedicated circulatory system, so the only way the interiours of their bodies can get oxygen is by diffusion (ok there are systems of air ducts in at least some insects, but not an active circulatory network). If their bodies get too large, the cells in the center can't get enough oxygen to support their energy needs, which limits potential growth. If the overall oxygen pressure of the air is higher, then enough oxygen can diffuse to support larger bodies. There are fossils of things like dragonflies with wing spans of feet versus inches. In the case of humans, we have all kinds of physical limits that are not usually considered by economists. We can't live in air of 10% oxygen, I'm not sure where the lower limit is but it must be somewhere between 10 and the current 21% I imagine. We can't tolerate extreme heat and humidity, if we can't sweat then we die of internal overheating. We need a regular daily dose of pure water or salt concentrations and pH become unbalanced which is fatal (probably to our brains first).

Economists tend to assume human technologies can overcome all such physical limits. Indeed this may be the case at least enough to support some people, but not all. Technological solutions have to work not just for a few, but for all 7+ billion of us, else we end up with dystopias as described by many science fiction writers and movies.

The point is that economic growth requires energy consumption. For now that mostly means fossil fuels, with the result of increasing greenhouse gases. If we keep this up too long, we'll end up like Venus (atmosphere mostly carbon dioxide and water, super high pressure and temperature that of molten lead). I imagine a handful of elite could survive this underground, but imagine bunkers for 7 billion - not likely.

Even if we manage to wean ourselves from fossil fuels, energy consumption still means heat, as there is no beating the second law of thermodynamics (when it comes to energy, you can't win, and you can't even tie). If the heat can't escape the earth, then temperature rises. Things like melting the permafrost and releasing trapped methane, could cause a Venus-like future even if we were fully "green" in terms of energy production.

No one can predict the future. Extremists like Guy Macpherson aver that it is already too late and the earth will become void of all large plants and animals inevitably in the next century if not decades. I agree this could happen, although from what I read of climate science, even given very alarming evidence of accelerating ice cap melting etc, it still doesn't seem a foregone conclusion. But even if not, it's a likely outcome, in centuries if not sooner. What rational species would continue on the same path given this information? None of course, which just goes to show that mankind is not as rational as it tends to claim it is. From the basic theory of evolution, I presume that all species have a drive to grow and expand in numbers, and that any limits are imposed only by the external environment not by any evolvable behavior. That bodes poorly for mankind. The tragedy is that the same evolutionary forces have given us minds that are capable of imagining such a future. If only those minds were strong enough to allow us to modify our actions to contradict the deeper biological drive to expand, grow, reproduce. But I fear not, ever or anytime soon at least. The question is whether we can survive as a species until we mature sufficiently to attain such mastery over basic evolutionary impulses.

 Capitalism has a number of dangerous inherent flaws. It has no way to deal with externalities, leading to unstoppable depletion of natural resources and accumulation of waste (including things like carbon dioxide and even heat). It has no intrinsic mechanism for determining a "fair" division of surplus wealth (i.e. profits) between workers, management and owners, leading to incessant and often violent negotations over wealth sharing. It tends to create monopolies which are at odds with the basic concept of a free market. The actual way in which it functions is highly dependent on the societal and legal framework in which it operates. It probably isn't even possible at all without strong central governments, whereas it rejects the idea of external regulation and claims to be autonomously sufficient. These are not problems that can be resolved by "tweaking" the pure economics of capitalism, they are inherrent. Clearly only a modified form of regulated capitalism has any chance to function effectively in the long term (if that). This is basically the system that came out of world war II, and it worked fairly well until several things happened that may perhaps be linked. First and foremost, right wing ultraconservatives established a long term explicit plan to roll back as much as possible of the New Deal and post-war evolution, including things like high marginal tax rates, estate taxes, capital gains taxes, Social Security, minimum wages, and so on. This is clearly a case of pure class warfare. It is obviously not sustainable in the long term, as an impoverished population can't afford to purchase the products, thus reducing demand and ultimately making the capitalist system itself dysfunctional. Second, there is the component of pure costs of production, which must be presumed to have risen significantly with the end of cheap US oil in the mid 1970s. I remember myself when gasoline was less than 30 cents at the pump, and each penny increase was a newsworth. Nowadays prices in the US are at least 3-4 times that, and are even higher in Europe. Whether as a source material for chemical industry (as in plastics) or as a source of energy, a several fold increase in price must reduce profits if the price index does not rise equivalently. To me it is highly suspicious that the beginning of the triumph of the right wing neocon agenda began shortly after the mid-1970s. It could be coincidental, but could also be that the increase in oil prices and lack of control of those prices translated into greater energy put into subverting our political process. Further support for this idea comes from the relatively recent recovery of the US economy (in terms of GDP if not wages), also coincident with the use of new technologies to increase national oil production thereby reducing dependence on middle -eastern oil (reducing but not eliminating).

Story coming out of New Jersey, due to problems with budget negotiations many state services are shut down over this Fourth of July weekend. That includes various state parks and beaches. OK, except that the governor (C.C.) apparently took his family to one of those parks and there were various pix posted on the internet of them sunning on an otherwise empty expanse of sand. The sheer arrogance seems beyond belief, except that it's only too believable. We know well that some people lack all empathy, however we prefer that such people not be elected to manage our affairs. In this case, the governor is probably a lame duck, after a seriously failed presidential run plus being spurned by the administration. He may simply be thumbing his metaphoric nose at everyone. But he is still running the state, in theory. And yet, he probably does feel a sense of empowerment, given that America has been giving positive signals to politicians to behave with increasing meanness and haughtiness. In addition to the message that poor people and minorities should not share equal opportunity or even basic civil rights, this is being extended to practically everyone who is not wealthy. How self-avowed populists can reconcile such behavior with the basic idea of populism is difficult to understand. But clearly the republican party, for all its supposed patriotism, has actually little interest in understanding or functioning under the true values by which the US was founded. The founders espoused the values of the Enlightenment, which have nothing to do with the actions (as opposed to the rhetoric) of the conservatives these days.

There is a lot of media attention these days to a supposed crisis in the replication of scientific studies. However, I don't agree that there is such a replication "crisis". Biological experimentation involves a very high degree of complexity, with many variables that are extremely difficult to control. For example, even the same inbred mouse strains, or tissue culture cell lines, can actually be quite divergent between different laboratories. It is very difficult for one lab to assess the number of statistical degrees of freedom in its own work. Thus it is to be expected that some, many even many, results which are reported reliably on experiments performed in good conscience, will fail to replicate among labs. That is part of the cost of doing truly novel research. Just based on an anecdotal sense of the kinds of work being described as "non-replicable", much of it is either in the social sciences, where controlling variables is even harder, or in clinical trials on human cohorts where again it is challenging to control for environmental factors. In contrast, in my own field of human medical genetics, results tend to be highly replicable, as we are usually looking at the effects of severe high penetrance mutations. Different mutations in the same gene typically generate very similar, though not identical phenotypes even in very different populations. A quick survey of the Human Gene Mutation Database corroborates this observation.

That said, it is true that scientists are under way too much pressure to generate positive results, especially for very expensive programs like clinical trials or large scale population genetic studies. Moreover, the hypercompetitive state of grant funding these days encourages hype and excessive optimism over sober analysis. This is not the fault of the NIH, this is the result of decades of government underfunding of science measured as a proportion of national GDP.

What comes after

I woke this morning from a very interesting and (for me) atypical dream. Most dreams are of a private nature and publishing them nothing but an exercise in vanity, but this is perhaps one of those rare exceptions.

In the dream I was in the afterlife. No idea how I got there, that was irrelevant. It was not clearly depicted, but there many of "us", again not very clearly visualized. I seemed to be seated (?) at a console like a microfilm or microfiche machine, and images went speeding by as when one fast forwards through that type of film. The images were in color.

An authority, again not visualized, more like a voice (perhaps I was drawing on Tolkien's short story Leaf by Niggle), was explaining how things worked. Essentially all possible information was available, in other words everything that had ever happened (on earth? in the entire universe?), but it was up to each of us to focus our minds to narrow in on any information of interest to us. As a preliminary exercise, the voice suggested we solve a simple math puzzle, the answer to which was a number. I don't recall the number, but as I focused on it, the images I was seeing slowed, came into focus, and eventually settled on the correct number. As that was happening, I was also seeing images of children. The voice, now close to me, noted that before I arrived here (wherever here was), I had asked to see my grandchildren. They were among the children whose images had gone by, thus I had come near, but not perfectly, at obtaining my desired information. As it happens, earlier in the day (the real day, not the dream) I was leafing through Steichen's classic photoessay, Family of Man; perhaps the images of children in my dream were stimulated by that real-life activity. I am not aware of feeling strongly about grandchildren (none so far), perhaps it's more important to me than I realized.

Anyway, the voice continued that I had wanted to know something else, namely whether quantum mechanics and general relativity could ever be reconciled as a coherent theory of everything in physics. This is indeed something I've love to have solved by physicists (not me of course), and have often joked that that would be my first question on arriving in Heaven (or the other place, hopefully they both know!) The voice said that the answer was that the two theories could not be reconciled. I asked whether that meant both were incomplete approximations of a true mathematically consistent theory, which the voice confirmed.

Then I woke up. If only I had slept a few more moments, I might have had the answer to all physics! Probably not though, probably I woke up because that was as far as I could go. But I awoke with a sense of perfect peace, because the universe was about not struggle, but about knowledge and correct understanding, from which action and consequence flow naturally. This now seems rather buddhist to me, though most of the time I tend much more to activity, spontaneity and trial and error, versus deep thought. My wife must be changing me, or else I am changing myself in response to her wisdom.

Theories

What is a theory? At first this seems like a rather unnecessary question. However, it is not. Unfortunately "theory" is a word that exists equally in the realm of common discourse and in the realm of professional science, and it does not automatically mean the same thing in both contexts. This has been commented on abundantly in discussions of of evolution "theory", such that the common imprecise use of the word is often conflated with the technical use in attempts to discredit the concept of natural selection. The archetypal misuse of the word typically appears as "such-and-such (e.g. evolution, or the Big Bang) is "only" a theory). There may not be a definitive set of meanings for the word "theory", and I am certainly not an etymologist. From here on I write idiosyncratically, that is according to my own best understanding of the word.

In my understanding, the word "theory" as used in common speech is more or less equivalent to the word "idea". Thus one could say, I have a theory as to why men have more body hair than women, or, I have a theory as to why the store across from the gas station closed last month, or even, I have a theory that the moon is made of cheese. In this sense, essentially any statement of explanation can be called a theory. One would not normally say, I have a theory that this food is too salty, since that is simply a restatement of an observation. One might say however, I have a theory that this food is too salty because the cook put in too much salt, although such a statement appears rather self-evident. Thus even in common usage the word theory carries an implication of some kind of explanation going beyond a pure observation.

However, in significant distinction from common usage, a theory to a professional scientist is not simply any such statement of causal explanation. A professional astronomer would not be likely to theorize that the moon is made of cheese to explain why its surface looks holey, or that stars are caused by small holes in a dark globe that surrounds the earth outside of which is a universal source of light. Nor would most marine scientists theorize that the tides are caused by the gods blowing on the ocean with their breath. To a scientist, a theory is indeed a statement or more often a set of statements. However, these statements must have certain properties: First and foremost, they must possess explanatory power for a set of direct experimental observations. Thus, the observation of tides on our world's oceans can be explained by assuming that the moon exerts a gravitational force on earth, to which the water in the oceans responds in a measurable way. Moreover, by various mathematical operations one can deduce a specific number for the likely mass of the moon, which together with its measured size, can be used to calculate a density which is much greater than that of cheese. Such calculations were performed long before astronauts actually walked on the moon, observing at first hand that it was indeed made of rocks and minerals as predicted. The more observations that are explained, the stronger the theory. Thus the theory of gravity explains not just the tides, but the orbits of planets and their elliptical paths, as well as many other astronomical measurements.

This example also points to the second major component of scientific theories, namely that they posses predictive power. The theory of gravity, together with specific measurements made in laboratories on earth, allows one to make predictions about the behavior of other systems (such as the oceans and the moon) for which such direct measurements (such as weighing the moon) cannot be made. Moreover, these predictions must involve some fairly specific obligations, namely observations of a system made under circumstances different than those used to develop the theory. These can involve either an experimental perturbation of the system (admittedly hard to do with the moon and oceans), or observation of the system with a new technology or under some new conditions. This in fact could be done for tides, given that the moon's distance from the earth is demonstrably changing due to the extremely slow decay in its orbit. Presumably such changes in the moon's orbit will eventually lead to measurable differences in oceanic tides, which could be measured if one waited long enough. Alternatively, if there were a way to measure the properties of tides many millions of years ago, when the moon was at a different distance from the earth than it is today, this would also constitute a type of historical prediction. In fact, the observation of the changing number of days in the year, documenting the loss of energy from the earth/moon system and the concomitant decay of the moon's orbit, as determined by counting rings in ancient fossil trees, it itself a major successful prediction of gravity theory that Newton probably would have greatly appreciated though he might not have ever thought of it.

In a very important sense, scientific theories therefore are actually simplifications. If one has a large set of observations, such as the height of sea level at various times of the day and year at various seashore locations, a theory of tides must somehow reduce these observations to a simpler set of statements. If one has a large set of observations of the luminosities and distances and speeds of various astronomical objects (starts, galaxies, quasars, and so forth), a theory of the origin of the universe must account for these quantitatively, and in principle make predictions of the future of the universe that could be tested over time.

In fact, there is a word in scientific usage which to my mind is more in keeping with the common usage of the word theory, and that is "hypothesis". To me as a scientist, a hypothesis (an hypothesis?) is a statement that may explain one or a small set of observations, but without having necessarily put large amounts of effort into testing any predictions of the hypothesis, or even being sure whether it can make predictions. The distinction is subtle, but very important. The theory of evolution by variation and natural selection entails a set of multiple statements, all very sophisticated, potentially explaining a multitude of observations about the diversity of life on earth, the physical appearance and behaviors of all plant and animal life, the basic biochemical basis of life, the extreme similiarities of DNa sequences in the genomes of organisms, and so forth. Thus it constitutes a scientific theory. On the other hand, statements such as "men have more body hair than women because they have more muscle mass and sweat more" or "men have more body hair because women happened to like the look so such men had more children" are hypotheses, as they are at least at first glance efforts to explain a very limited set of observations, and in fact may not yield any testable predictions.

From this perspective, it is quite unusual for scientists to express major disagreements about the status of current theories. That is simply because almost by definition theories do a good job of explaining the available observations. To the extent that a current theory fails to explain important results (such as the equivalent speed of light in various geometric configurations in the Michelson-Morley interferometry experiment) in fact argues that the theory is incorrect or at least invalid for some particular circumstances. Eventually, in the face of many discordant observations, theories are at last updated, replaced or simply nullified. This last is rare however, since the theory arose to explain many previously made observations. More often in science, theories are shown to be oversimplifications, valid only under certain circumstances. The Newtonian theory of gravity, mass and motion is just as valid today as when Newton theorized it. However, it is an approximation that become increasingly inaccurate at higher speeds (approaching light speed) and for very high mass objects (such as stars), circumstances for which Newton had no observations to confound his equations. The theory of relativity is in that sense an update, or complexification of the older theory, with more sophisticated mathematics and usable under a much wider array of circumstances. As long as one is just looking at the planets far from the sun however, Newton's equations of motion remain useful.

In consequence, scientists place much more weigh and respect on theories than hypotheses. Thus, although as critics of evolution are quick to note, biologists disagree on many aspects of evolution theory, in fact there is no serious disagreement among professional biologists on the theory itself, meaning its major statements as beautifully summarized by Ernst Mayr in his many essays, or by Douglas Futuyma in his classic textbook. We may disagree on whether new species always arise in geographic isolation or only sometimes, or how often. We may disagree on whether a particular bone's structure proves that birds are descendants of dinosaurs (generally thought to be true) or whether the diminutive fossils of Flores island in Indonesia result from a truly different species of human or from normal genetic variation within the species Homo sapiens (not universally agreed as yet). But such arguments do not imply any doubt of evolutionary mechanisms per se. Evolution by natural selection is a scientific theory like any other, and could indeed be "proved" wrong or more likely shown to be oversimplified. At this time professional biologists would be hard put to imagine what kinds of data would disprove the theory. However, short of accepting the verbatim validity of the Hebrew Old Testament (why just the OT, and not the Vedas or other religious texts is not addressed by critics), there are no generally accepted biological observations inconsistent with evolution theory. Even the recent and fairly sophisticated argument that the current theory of life arising as an RNA molecule is impossible since RNA cannot be made from small organic molecules in the laboratory, has recently been invalidated by some wonderful biochemistry demonstrating the organic synthesis of RNA-like precursors from simpler molecules.

The nature of information, and the definition of simple versus complex, is surprisingly tricky. Scientific definitions, while in a very general way similar to common usage of these words, differ in full technical detail, so that one's intuition must be trusted with extreme caution. For example, those gorgeous fractal patterns one can see everywhere nowadays, are generated by very simple mathematical formulas. Similarly, a pretty simple mathematical algorithm, when run for a long time, generates the value of pi to as many decimal places as one could want. Pi is an irrational, and moreover a transcendental number, which never repeats and has no obvious internal "pattern", yet can be generated by a simple calculation. A truly random series of numbers has no internal pattern, and by definition therefore cannot be generated by any simpler formula or calculation, it can only be described by writing the number itself to as many digits as there are. But for a given large number, with no obvious internal pattern, it's very hard to be sure that it cannot in fact be generated by a simple algorithm (i.e. set of calculations). If I understand correctly, it can be proved that it is impossible to prove that there is no possible algorithm to generate a given output. So, short of actually finding a simple algorithm to generate a number (like pi), it's hard to know that a given number is truly truly random - maybe someone smart enough will figure out the algorithm in the future.

So much for pure math. The human genome has approximately 1.5 billion "unique" bits of information (i.e. GATCs), which can be thought of for some purposes as a code or "number" containing data, but it's very hard to known how much actual information is contained. By comparing our genome to those of other animals, some estimates are that only about 1% of our unique DNA sequence is highly conserved, though other estimates are much higher - it depends to some extent on which other animals are used for the comparison. At this point in time we don't know the answer.

So much for the genome in the abstract. There's no question regarding the tremendous complexity of the human brain in terms of the absolute number of neurons (cells) and synapses (links). But it's very unclear how much genomic complexity is required to create the structural complexity. Maybe the underlying algorithm is very simple, and is simply repeated a large number of times, like fractals, only with lots of feedback from the environment so that no two human brains end up working the same way. I like to keep in mind that many types of plants are biochemically much more "complex" than we are, in that they can carry out many more types of chemical reactions and have more different types of small molecules (like glucose, ATP, acetyl-CoA, etc) than we do. It is somewhat animal-o-centric to hold that complex 3-dimension bodies with lots of different tissue types are "more complex" than complex biochemical networks. Plants might feel that they are actually more advanced, and better adapted than we are too. If the amount of oxygen in the atmosphere dropped from 21% to say 15%, I imagine most living animals, or at least mammals, would quickly go extinct, whereas many plants could probably adapt quite well. Superior adaptation to a specific environment does not necessarily equate with overall success under environmental change. Let's see who's left standing 100-200 years from now, after the global average temperature goes up 5 degrees C. I predict there will be a lot fewer humans, but probably about the same number of cats!