Tag Archives: science

Rama’s ape

12.3-11.7 million years ago

Ramapithecus (Rama’s ape) is no more. Another Hindu god has taken over the franchise; Ramapithecus is now subsumed under Sivapithecus, an earlier discovery, and is no longer a valid taxon name.

The story is interesting from a history-of-science point of view. Ramapithecus used to be presented as the very first ape on the human line, postdating the split between humans and great apes, maybe even a biped. This was given in textbooks not so long ago as established fact. Then geneticists (Sarich and Wilson) came along, and declared that the genetic divergence between chimps and humans is so low that the split had to be way later than Ramapithecus. There was a lot of fuss over this. Paleoanthropologists didn’t like geneticists telling them their job. Eventually, though, the paleoanthropologists found some new fossils. These showed in particular that the line of Ramapithecus‘s jaw was not arch-shaped, like a human’s, but more U-shaped, like a non-human ape’s. So after thinking it over a while, paleoanthropologists decided that Ramapithecus (now part of Sivapithecus) looked more like an orangutan relative: likely ancestor of a great radiation of orangutan kin that left just one surviving species in the present.

rama jaw

There are plenty of examples of experts in different fields coming up with different answers. For example, paleontologists didn’t like physicists telling them why dinosaurs went extinct. And we’ll see other examples in days to come: geneticists, physical anthropologists, and archeologists arguing over modern human origins. And very recently geneticists coming in on the side of old-fashioned historical linguists, and against recent generations of archeologists, in the matter of Indo-European origins.

It would be nice if there were a simple rule of thumb to decide who’s right in these cases. Maybe experts know what they’re talking about (except that experts were telling us recently that low fat diets were the key to losing weight and eggs would kill us with cholesterol*). Or maybe harder science experts know better than softer science experts (except that physicists like Kelvin were telling geologists that the Sun couldn’t possibly have produced enough energy to support life on Earth for hundreds of millions of years – then along came Einstein and E=mc2). So the best we can do maybe is realize people, scientists included, are prone to overconfidence and group think – and not just those other people, either, but you and me.

* Memories of the fallout from 1990s nutrition expert wisdom

  • Snackwells cookies
  • Jelly beans prominently labelled “No fat.”
  • A fellow grad student laughing about an older relative who said bread and pasta can make you fat, and confidently declaring “Fat makes you fat.”
  • Me in Brazil talking with my landlord, who was planning to lose weight by sticking with sausage, and cutting starch. I told him modern science had shown this was precisely the wrong approach. He politely (Brazilians can be pretty good-natured) disagreed, stuck with his plans, and lost weight.

 

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Evolution and broken symmetries

8.33-7.88 billion years ago.

No big news in the universe today. Some evolutionary thoughts: Species evolve. Do planets? stars? galaxies?

Charles Darwin didn’t use the word “evolution” often. But he did write a lot about “descent with modification,” which is pretty much what biologists mean by evolution. For example, the usual definition of genetic evolution is “change in gene frequency,” i.e. descent with (genetic) modification.

However, people sometimes talk about evolution that doesn’t involve descent with modification, in contexts that have nothing much to do with biological evolution – cosmic evolution or stellar evolution in the history of the universe, for example, or mineral evolution in the history of the earth. Another Victorian writer, the sociologist and philosopher Herbert Spencer, offered a definition of evolution that might cover these cases.

Evolution is an integration of matter and concomitant dissipation of motion; during which the matter passes from an indefinite, incoherent homogeneity to a definite, coherent heterogeneity.

It’s easy to make fun of this definition. It’s the sort of abstract word pile that style manuals tell you to avoid, and that gives sociology a bad name. For that matter, it’s easy to make fun of Herbert Spencer. He may be some of the inspiration for the character of Mr. Casaubon, the dried up, impotent pedant in George Eliot’s “Middlemarch.” (Spencer probably turned down a chance to marry George Eliot = Mary Ann Evans. You should be careful about offending a writer.) But it may be that Spencer was groping toward the important modern concepts of symmetry and symmetry breaking.

A simple example: imagine you’re holding a bicycle exactly upright. The bicycle is pretty much bilaterally (mirror image) symmetrical. (OK, not really, the gears are on the right side, so it’s not a perfect mirror image. But just pretend …) Now let go of the bike. It will fall to one side or the other. The symmetry is broken, and you need one extra “bit” of information to tell you which side the bicycle is on.

Symmetry breaking is a fundamental concept in physics. In the very early history of the universe, the four forces of nature — gravitational, strong, weak, and electromagnetic – were united, but then as the universe cooled, one by one, these forces broke the symmetry and turned into separate forces. More symmetry breaking generated elementary particles, and nuclei, and atoms. When atoms first formed, they were distributed symmetrically through the universe as a diffuse gas. But gravitation pulled atoms and other particles together into clumps, leaving other parts of space emptier, and the spatial symmetry was broken (a “translational” symmetry in this case).

Symmetry breaking will keep showing up throughout the history of the universe. Consider sexual reproduction. A simple early form of sex involved two equal sized gametes (sex cells) joining to produce a new organism. Some species still do it this way. But more commonly the symmetry is broken – some organs or organisms produce little gametes that move around easily (sperm or pollen), others produce big gametes that don’t move around so easily (eggs or ovules). We call the first sort of organs or organisms male and the second sort female. Sex in most multi-cellular organisms is a broken symmetry. This broken symmetry will go on to have a dramatic consequences for human social evolution. It entails, for example, that patrilineages can expand their size much more rapidly than matrilineages.

Or consider the rise of political stratification, the move from small-scale societies where “every man is a chief” to large-scale societies of chiefs and commoners, rulers and ruled. Another broken symmetry. It may be more or less an accident (good or bad luck, Game of Thrones style) who ends up being king, but it’s not an accident that somebody is, past a certain social scale.

We don’t attach much moral significance to broken symmetries where the physical world is concerned. You’re being way too sensitive if you feel sorry for the poor weak nuclear force that missed its chance to be the strong nuclear force, or for the dwarf galaxies that got cruelly tossed around and cannibalized by the Milky Way. Broken symmetries in social life – males and females, kings and commoners – are another matter …

The curve of binding energy

More stardust

Looking at the abundance of different elements in the universe, we get the following:

element abundances

Note that the vertical scale is logarithmic, so there is vastly more hydrogen and helium in the universe than any other element. As noted in the last post, all the elements except hydrogen and helium were formed after the Big Bang, spewed out by supernovas and the collisions of neutron stars. In general, heavy elements are less abundant because it takes more steps to produce heavy elements than light ones. But the curve is not smooth. The lightest elements after hydrogen and helium (lithium, beryllium, boron) are relatively rare, because they get used up in the nucleosynthesis of heavier elements. And there is a saw tooth pattern in the chart, because nucleosynthesis favors atoms with even numbers of protons. So we get lots of oxygen, magnesium, silicon, and iron, the main constituents of our planet. Lots of carbon too. Finally, iron (Fe) is more than 1000 times more abundant than might be expected based on a smooth curve. Iron nuclei are especially stable because binding energy, the energy that would be required to take the nucleus apart into its constituent protons and neutrons, reaches a maximum with iron. Here’s the famous curve of curve of binding energy (nucleons are protons and neutrons):

curve of binding energy

An implication of this curve is that if you can split a really heavy nucleus, of Uranium-235 say, into smaller nuclei (but still heavier than iron), you will release energy equal to the vertical difference between U-235 and its lighter fission products (not shown) on the vertical scale. This is lots of energy, way more than you get from breaking or forming molecular bonds in ordinary chemical reactions. And if you can fuse two light nuclei, of hydrogen say, into a larger nucleus, you can get even more energy. When we split uranium, we are recovering some of the energy that a star put into synthesizing elements heavier than iron, before or as it went supernova. When we fuse hydrogen, we are extracting energy from the Big Bang that no star got around to releasing.

Starting to figure this all out was part of a scientific revolution that made physics in 1950 look very different from physics in 1900. The new physics resolved a paradox in the study of prehistory. Geologists were pretty confident, based on rates of sedimentation, that the Earth had supported complex life for hundreds of millions of years. But physicists couldn’t see how the sun could have kept shining for so long. The geologists were right about deep time; it took new physics to understand that the sun got its energy from fusing hydrogen to helium (via some intermediate steps).

As the scientific revolution in atomic physics was picking up steam, it was natural to assume that it would be followed by a revolution in technology. After all, earlier scientific revolutions in the understanding of masses and gases, atoms and molecules, and electrons and electromagnetism, had been followed by momentous innovations in technology: the steam engine, artificial fertilizers, electrification, radio, to name just a few. But in some ways, the Atomic Age hasn’t lived up to early expectations. The atom bomb brought an earlier end to the Second World War, but didn’t change winners and losers. The bomb was never used again in war, and it’s a matter for debate how much the atom bomb and the hydrogen bomb changed the course of the Cold War. Nuclear energy now generates a modest 11% of the world’s electricity (although this number had better go up in the future if we’re serious about curbing carbon dioxide emissions). And a lot of ambitious early proposals for harnessing the atom never got anywhere. Project Plowshare envisioned using nuclear explosions for enormous civil engineering projects, digging new caves, canals, and harbors. Even more audacious was Project Orion, which developed plans for a rocket propelled by nuclear explosions. Some versions of Orion could have carried scores of people and enormous payloads throughout the solar system. Freeman Dyson, a physicist who worked on the project, said “Our motto was ‘Mars by 1965, Saturn by 1970.’”

On the purely technical side these plans were feasible. There were concerns about fallout, but the problems were not insurmountable. Nevertheless both Plowshare and Orion were cancelled. Dyson said “… this is the first time in modern history that a major expansion of human technology has been suppressed for political reasons.” The history of the Atomic Age  and its missed opportunities is a refutation of pure technological determinism. How or even whether a new technology is exploited depends on social institutions, politics, and cultural values.

We are MacApes, O’Monkeys, and Ben-Reptiles

1764-1777

A couple years back, Jonathan Marx and Jerry Coyne had an online spat on the question “Are humans apes?” (Marx says noCoyne says yes; see also John Hawks, who says no.) I offer my own solution below, after talking about Linnaeus (1707-1778) and biological categorization.

There’s a branch of cultural anthropology that studies “folk biology,” also known as “ethnobiology,” which is (among other things) about how different groups classify living things. Folk biological categories don’t vary randomly across cultures; there are some general principles at work. A quick summary: the basic level of categorization is roughly the genus. American folk genera include oakcrow, and fox (although a lot of Americans today are really bad at folk biology, maybe using that part of the brain for Pokemon.) Many peoples, and most hunter-gatherers, only take categorization down to the genus level. Others (especially horticulturalists) take it down to the species level, often with two part names (red oak, silver fox). Going toward more inclusive groups, genera are lumped together in larger, intermediate-sized, non-overlapping categories (palmhawk), which belong in turn to the more inclusive level of “life forms”: (bird, snake, fish, tree, grass/herb).

From an anthropological perspective, Linnaeus’s famous scheme of classification is an elaboration of these universal principles, with more species and more taxonomic levels (the famous Kingdom, Phylum, Class, Order, Family, Genus, Species).

A version of Linnaeus’s scheme served evolutionary biologist well for centuries. But starting in the later twentieth century, many biologists turned to another approach that was claimed to be a better fit for evolutionary principles: According to cladists, the classification of living things should be based on clades: groups containing all and only the descendants of an ancestor. This requires overturning or revising many familiar categories. For example, monkeys are not a clade, since Old World monkeys are more closely related to apes (including humans) than to New World monkeys. Reptiles are not a clade, since crocodiles are more closely related to birds than to lizards and snakes. Fish are not a clade, since lungfish are more closely related to amphibians and reptiles than to most other fish.

After some bitter disputes. cladists seems to have won the battle among scientists. But cladism has made less headway among non-scientists. In Naming Nature: The Clash Between Instinct and Science, Carol Yoon argues that cladistics is just too much at variance with the way the human mind understands biological categories. Most people are never going to take to cladistics any more than they’re going to take to twelve-tone music, or Loglan. So different answers to the question “Are humans apes?” reflect disagreement about how far we can or should bring folk categories in line with the austere logic of cladism. Apes, including humans, are a clade. Apes, not including humans, are not (since chimpanzees are more closely related – but not really more similar – to humans than to gorillas).

I suggest a compromise. Folk categories like ape, monkey, reptile, and fish, defined by shared ancestral traits, are useful, even if they aren’t clades, defined by shared derived traits. But the concept of a clade is also important one for biologists. So maybe when we want to talk about the clades associated with folk categories, why don’t we use a prefix – the Scottish Mac, Irish O’, or Hebrew/Arabic ben/bin. (Any of these will serve.) So human beings are not apes, monkeys, reptiles, or fish. But we are MacApes, O’Monkeys, Ben Reptiles, and/or Bin Fish.

(For other We Are posts see We Are Upside Down Bugs and We are Stardust.)

Steam engine time

1714-1730

The steam engine was a child of seventeenth century science; the Scientific Revolution gave birth to the Industrial Revolution. That’s not at all the conventional story, but David Wooton’s recent book The Invention of Science: A New History of the Scientific Revolution makes the case.

According to the conventional story, the steam engine resulted from the work of generations of inspired tinkerers, ingenious craftsmen with no particular scientific training and no great scientific knowledge. Indeed, according to one historian, “Science owes more to the stream engines than the steam engine owes to science.” (After all, the steam engine did inspire Carnot’s thermodynamic theory.)

But Wooton traces a path from scientific theory to practical application, beginning with the seventeenth century science of vacuum, air and steam pressure. The pioneering scientists here were not just theorists. They built (or at least designed) a number of devices for making use of differences in gas pressures, including an air gun (Boyle), a steam pressure pump (della Porta), and a vacuum-powered piston (von Guericke). Huygens took up the last idea, using an explosion to empty air from a cylinder, through a valve, and then using the partial vacuum to move a piston. This in turn was taken up by Denis Papin, a French Protestant medical doctor and mathematician, who worked as an assistant to Huygens, and then to Boyle. Papin combined scientific knowledge and engineering experience to design several steam engines. None of these was very practical – sadly Papin ended his life in failure and poverty. But the first of them was very similar to the first commercially viable steam engine, produced by Newcomen in 1712 – so similar that many historians have been convinced that Newcomen must have been familiar with Papin’s design.

Up to recently there’s been no convincing account of how Newcomen could have learned of Papin. But now Wooton has discovered the likeliest link, a book by Papin with the unpromising title A Continuation of the New Digester of Bones. The book has been neglected by historians, not surprisingly, but sold well in its own day. It gives plans for a pressure cooker (hence the title). But it also contains detailed descriptions both of vacuum powered piston, and of the use of steam condensation to produce a vacuum: just what Newcomen needed to put together to build his first engine. Wooton writes:

Newcomen’s steam engine is a bit like a locked-room plot in a detective story. Here is a dead body in a locked room: How did the murderer get in and out, and what did he use as a weapon? … We cannot exclude the possibility that Newcomen went to London and met Papin in 1687 … But we do not need to imagine such a meeting. With a copy of the Continuation in his hands, Newcomen would have known almost everything that Papin knew about how to harness atmospheric pressure to build an engine. … From this unintended encounter, I believe, the steam engine was born.

He concludes:

Historians have long debated the extent to which science contributed to the Industrial Revolution. The answer is: far more than they have been prepared to acknowledge. Papin had worked with two of the greatest scientists of the day, Huygens and Boyle. He was a Fellow of the Royal Society and a professor of mathematics. … Newcomen picked up … where Papin began. In doing so he inherited some of the most advanced theories and some of the most sophisticated technology produced in the seventeenth century. … First came the science, then came the technology.

The last of the magicians

1676-1694

If I have seen further than others, it is by standing upon the shoulders of giants.

I do not know what I may appear to the world, but to myself I seem to have been only like a boy playing on the seashore, and diverting myself in now and then finding a smoother pebble or a prettier shell than ordinary, whilst the great ocean of truth lay all undiscovered before me.

These familiar quotations from Newton are sometimes presented as expressions of his humility (a quality not otherwise much in evidence). In fact, though, it became clear in the course of the twentieth century that they are really an expression of Newton being not just a great scientist – the greatest ever – but also a great kook. Here’s a less familiar quotation from Newton about the intellectual origins of heliocentrism

It was the opinion of not a few, in the earliest ages of philosophy … that under the fixed stars the planets were carried about the sun; that the earth, as one of the planets, described an annual course about the sun, while by a diurnal motion it was in time revolved about its own axis. … This was the philosophy taught of old by Philolaus, Aristarchus of Samos, Plato, … and of that wise king of the Romans, Numa Pompilius, who, as a symbol of the figure of the world, erected a round temple … and ordained perpetual fire to be kept in the middle of it.

The Egyptians were early observers of the heavens; and from them, probably, this philosophy was spread abroad among other nations … It was their way to deliver their mysteries, that is, their philosophy of things above the common way of thinking, under the veil of religious rites and hieroglyphic symbols.

The Renaissance was committed to recovering the ancient past. This led not only to the recovery of ancient art, literature and science, but also to the recovery of a whole body of ancient magic and pseudoscience. For example, many Renaissance thinkers, and Newton, were fascinated by the mystical writings of Hermes Trismegistus (Thrice Great Hermes, hence “hermeticism”), an alleged Egyptian sage. By Newton’s time it had already been demonstrated that these writings were “pseudepigraphia,” a nice scholarly term for “fakes”; Hermes Trismegistus never existed. Nevertheless, Newton was convinced that there was an esoteric tradition preserved by the ancient Egyptians, passed on to Moses, Pythagoras, and Plato, and hidden away in the Bible. Read the Bible or stories of Pythagoras closely enough and you could recover the inverse square law of gravitation. Newton spent huge amounts of time throughout his life trying to recover further scientific secrets from the Bible.

John Maynard Keynes, who got hold of some of Newton’s papers wrote

In the eighteenth century and since, Newton came to be thought of as the first and greatest of the modern age of scientists, a rationalist, one who taught us to think on the lines of cold and untinctured reason.

I do not see him in this light. I do not think that any one who has pored over the contents of that box which he packed up when he finally left Cambridge in 1696 and which, though partly dispersed, have come down to us, can see him like that. Newton was not the first of the age of reason. He was the last of the magicians, the last of the Babylonians and Sumerians, the last great mind which looked out on the visible and intellectual world with the same eyes as those who began to build our intellectual inheritance rather less than 10,000 years ago.

After Newton, it became clear that modern science had surpassed anything achieved by the ancient world, and natural science and the humanities went their separate ways. Reverence for the secret wisdom of the ancients would survive in the novels of Dan Brown and in the weird Masonic pyramid on the back of the US one dollar bill.dollar-bill-eye

Copernicus versus the scientific method

1532-1558

I have to confess that for a long time I didn’t really “get” Copernicus. That is to say, while I knew that Copernicus is right and Ptolemy is wrong, I wasn’t clear on just why Copernicus had a better scientific theory, partly because I didn’t bother understanding Ptolemy. So here’s a brief summary of the two. (Howard Margolis’s book helped me out.) There’s a larger point here: what makes Copernicus’s theory better doesn’t quite fit with a lot of pronouncements about “the Scientific Method.”

First, a diagram that illustrates Ptolemy’s model.

ptolemy

To account for the motion of the planets, Ptolemy needed to assume that the five planets (not counting the sun and moon) have both cycles (the big circles) and epicycles (the little circles). If you’re going to put Earth at the center of the system, then you have to have epicycles to account for the motions of the planets, like the retrograde motions where planets seem to go backwards.

Here’s something to note about this diagram: some of the cycles and epicycles vary independently, while others are exactly tied to the motions of the sun. For Mercury and Venus, the epicycles vary independently, taking different periods of time (88 days, 225 days) to complete a circuit. Their cycles, by contrast, take exactly one Earth year to complete a circuit. Furthermore, the deferent, the point at center of each epicycle, is always exactly in line with the sun. For Mars, Jupiter and Saturn on the other hand, the cycles vary independently (1.88, 11.86, and 29.46 years to make a complete circuit). But the epicycles take exactly one Earth year to complete a circuit. Furthermore, in each case the line from deferent to planet is exactly parallel to the line from Earth to Sun. Note that it’s hard to see any reason why the epicycle for Jupiter, say, couldn’t take 3.14 years to complete a circuit. But instead somehow, mysteriously, it’s connected with the sun’s motion around the earth.

(A large fraction of diagrams on the web purporting to illustrate Ptolemaic astronomy get this crucial point wrong! They show higgledy-piggledy non-parallel deferent/planet lines, pointing any which way. This makes it impossible to understand why Copernicus had a better theory. So I’m not the only person not to get Ptolemy.)

Copernicus’s model, by contrast, doesn’t just replace five circles (the cycles for Mercury and Venus, and the epicycles for Mars, Jupiter and Saturn) with one (for the Earth going around the Sun). It also automatically explains why the five superfluous cycles show an otherwise unexplained synchronic parallelism.

copernic

People who read Copernicus 1543 book carefully (not many at first) could see he had a real explanation for something that’s just a mysterious coincidence in Ptolemy. But contrary to what you may have heard, and what students get taught, about the Scientific Method, Copernicus did not formulate a hypothesis and then collect data to test his hypothesis, and show that it made the right predictions. Ptolemy and Copernicus make the same predictions about where the planets will appear in the sky. (Both are slightly off because they assume circular rather than elliptical orbits.) Eventually other scientists would gather data in support of Copernicus – Galileo’s observation of the phases of Venus was the real clincher – but the explanatory economy of his theory was a very strong reason for believing in it even before that.

Fortunately, there is a modern theory of how induction works – Solomonoff induction – that can explain why Copernicanism is a better theory. According Ray Solomonoff, induction has two parts. First there is Bayes’ Rule. Bayes’ Rule is an application of probability theory that tells you how you should revise probability estimates in the face of new evidence. Eliezer Yudkowsky gives one of the best introductions around to a counter-intuitive approach that has become enormously influential in recent years. (It’s fun to read too).

But Bayes’ Rule is only part of the story. The rule assumes that you have already assigned some prior probabilities to events before you look at the evidence. And where do scientists get their prior probabilities? Yudkowsky gives one answer: “There’s a small cluttered antique shop in a back alley of San Francisco’s Chinatown. Don’t ask about the bronze rat,” i.e. “Don’t ask.” Solomonoff offers a different answer. He argues that we can use the theory of algorithmic complexity, as developed by Kolmogorov, to assign prior probabilities. Roughly, if your theory were turned into a computer program, how long would the program be? The longer the program, the lower the prior probability. (Probabilities fall off exponentially with length of program, and are weighted to sum to one.) Suppose I give you a sequence of numbers corresponding to the first 1000 decimal digits of π. A computer program to calculate the first 1000 digits of π is going to be a lot shorter than just a list of the first 1000 digits, so the theory that I generated the list by calculating π is astronomically more likely than the theory that I generated the list at random. This is a formalization of Occam’s Rule, that simple explanations with fewer working parts are better.

So collecting evidence in support of a theory is part of good induction. But proposing more economical theories, accounting for more data with fewer working parts, is another part. Sometimes a new theory is so much better than the alternatives that we can assign it a much higher likelihood even before we collect more evidence. With Copernicus, explaining some striking coincidences which were otherwise unexplained, this was the first act in the modern Scientific Revolution.

This isn’t just a matter of historical interest. Physicists now, as they close in (hopefully) on a final theory of fundamental physics find themselves in a similar situation to Copernicus. Our best looking theory – some version of string theory – provides immense explanatory economy (or so we’re told), but just now is difficult or impossible to test. Here’s an article on the conundrums this poses for philosophy of science and the “scientific method.”