Month: March 2015

Looking for the Logos of Life II

Pross, Addy. 2012. What is Life? How chemistry becomes biology. Oxford University Press. 200 pp.

I found this an interesting and generally readable book, but I think it promises more than it delivers. My reflections on it are rather lengthy, so I’ll begin with:

Prologue and Chapter 1

Pross’s question is, “What is Life?” His book is offered as an advance over Schrodinger’s 1944 essay, What is Life? He will use “Systems Chemistry” to state a new law on the “emergence, existence and nature,” of living things. He claims to have found an overlooked form of stability in nature. According to Pross, “Darwinism is just the biological manifestation of a broader physical-chemical description of natural forces.” This will allow him to put forward a “generalized theory of evolution.”

Like Schrodinger, he starts with the laws of thermodynamics – heat transfer, entropy, etc. He sees his task as like Schrodinger’s: to account for the stability of a living cell, despite its being far from thermodynamic equilibrium. He also wants to explain how the first one could arise. He says the goal of that understanding is to be able to synthesize a living organism from scratch. I wonder whether in his “generalized theory of evolution” there is a deliberate echo of general relativity? Does this point to scientific hubris or is it an attempt to pump us a thesis is that is really not all that revolutionary?

The discussion begins by identifying certain “strange” characteristics of life that he thinks are problematic: life’s organized complexity, its purposeful and dynamic character, diversity, far-from thermodynamic equilibrium state and chirality (the “handedness” of amino acids)

Like almost every discussion of the origin of living cells, his begins by emphasizing the cell’s complex structure. I think he confounds small size with intricacy of design, which is ok, if you want to compare a cell to a refrigerator, but it seems odd to claim that an eye is a less intricate design than the ribosomes in the cells the eye is composed of. He tries to define complexity in terms of organization. Does that make sense? He uses the shape of a boulder to define complexity one way – what would it take to describe it precisely, I guess he means. He introduces the idea of information at this point. He claims that as far as the definition of a boulder, the exact shape is arbitrary, implying that the information describing a living cell is less so, but is this only because he ignores the internal composition of the boulder, how it acquired its particular shape and the relation between composition and shape, etc? He points out that even tiny changes in DNA can alter a cell, but this is potentially true of boulders as well, if we alter the makeup or distribution of components. Also, both cells and boulders can vary in exact makeup over quite wide ranges.

He says organized complexity and the second law of thermodynamics are inherently opposed. Cells need energy to maintain their ordered state. Does this really mean complexity is opposed to the second law? I find that physical scientists and some biologists make a very big deal out of what seems to me to be an artifact of looking at their experimental subjects in isolation. The opposition only arises if you ignore part of the system – the biosphere as a whole. Pross admits that this is the reason for the apparent contradiction.

Now he sets up another straw man: Darwinian theory only deals with biological systems, so it can’t account for the origin of the first, self-replicator, the protobiont. Darwin’s theory is biological and does not try to account for the origin of life, but does that mean a Darwinian theory can’t? Darwin himself says that natural selection is the result of natural laws, including presumably, those of chemistry and physics. In fact, apart from these, what are biological laws? Geometric growth is in a sense purely mathematical, but arguably so is a lot of physics and chemistry. Genetic variation and struggle for existence, even natural selection, are expressible in mathematical language. His question, “how did a system capable of evolving come about in the first place?” seems wrongly expressed, possibly because evolving is not the fundamental thing. Darwin’s is a theory of the origin of species. Is evolution a capacity or a faculty of living things? It seems more like the overall pattern that emerges. The word evolution has that troubling sense of preordination or unfolding.

He brings up chance and talks about how unlikely a cell is to form spontaneously. I guess you have to rule that out at some point. He refers to the “first microscopic complexity” coming into being, which seems to ignore that things are “complex” at the microscopic level in many ways other than being living things. He does not begin his argument by saying self-replication is the fundamental defining character of life, which I think unnecessarily draws out his discussion.

Talking about the apparent purposiveness of living organisms, he uses the word “teleonomy,” a coinage designed to avoid the supposed meanings of “teleology.” Pross says our interactions with the non-living vs the living world have a different quality, because of living things’ teleonomic character. He says we don’t use teleonomic explanations in the non-living realm, but then why is he always saying systems seek a lower energy state? Is the conservation of energy teleonomic? We can think of machines as having needs and of animals as machines. Teleonomy is a function of our way of seeing the world, not a measurable property of things: you can certainly think of a rock as wanting to fall or electricity wanting to discharge itself, and contra Pross, you can get some guidance from the laws of physics about the likely behavior of animals as well as trying to read their intentions in postures and expressions or consulting your own likely responses (putting yourself in their shoes). He sets it up as a stark duality, but is it? He then lumps under teleonomy things as diverse as chemotaxis and human voluntary behavior. He also identifies function with teleonomy.

In his long discussion, Pross never mentions the telos of teleonomy: self replication. Pross’s rhetorical withholding continues. It gets murkier when he does bring it up, because he says, while we can have a lot of goals as a human, we need to look at simple organisms to get at the real one. So is our purposiveness different from that of living things generally? He refers to it as a powerful replicating drive. What does “drive” mean? He claims teleonomy is as “real” as gravity. But gravity is in some way fundamental, as the physicists say, or at least an aspect of something more fundamental still, while teleonomy seems a by-product of self-replication. Teleonomy cannot, can it, be unified with the other forces of physics. He says gravity is quantifiable and teleonomy is not but that it doesn’t make teleonomy less real. He claims we stake our lives on the teleonomic principle when we drive our cars. What does he mean? Is it the design of the car or my ability to drive it to where I want to go and avoid hitting obstacles or going over cliffs?

Part of the problem is he starts talking about a teleonomic principle, not just teleonomy. Where did the principle come from? Teleonomy seems like an analogy to our own purposiveness, but what laws govern it? Is there any real similarity? Is the analogy in any way useful to reasoning accurately about living things?

Pross says, “Metaphysically…gravity and teleonomy are mental constructs that assist us in organizing the world around us [does he mean sense data?] So is he an anti-realist in the school of Hume and logical positivism or a Realist of the idealist school like Kant? Then again, the Scholastic ideas of gravity and teleology are organizing principles. Is teleonomy like the Scholastic gravity, going to be swept away by a better concept? At one point, he says “all inferred patterns are conceptual and are found nowhere else than in our minds.” How closely can he stick to this principle, and in that case, what is his book going to explain, patterns in our minds?

I think simply admitting that self-replication is a property of living systems, and not the goal, would obviate the need for teleonomy. If there is a need to talk about “purpose” to avoid prolixity when describing biological structures and behaviors that are aspects of self-replication, we should just use the term and not invent new words because we fear someone will accuse us of teleological thinking. I wonder if these constant verbal contortions are because we are still fighting battles with those who identify the ultimate cause with a Creator whose plans are often crudely anthropomorphic, like his appearance.

In the section of life’s great variety, Pross says, “non-living diversity is arbitrary.” That hardly seems true of geology or the atmosphere. Perhaps he means it is easier to see the relatedness of living organisms: classification of plants and animals by non-literate people is often very close to the scientific classification. He repeats the false characterization of species as, “each perfectly adapted to function and survive in its particular ecological niche.” So, he’s not an ecologist or evolutionary biologist, but even popular books like those by Steven Jay Gould warn against that sort of talk.

He claims further that there is an inescapable contradiction between the principle of natural selection and the principle of divergence [of character]. Again, this is not a bad point to bring up, but if it really were a contradiction, then something would be seriously wrong with our theories on the origin of species, and this is not the case. There is nothing preventing diverse things from being selected. If the conditions of life were always and everywhere identical, then selection would prevent divergence. The problem goes away once you include the idea that organisms exist in varying environments. He seems to confuse debates over mechanisms of speciation with debates over these two principles.

In the section on life’s far-from-equilibrium state, he seems to be setting up a straw man to knock over later. Yes, non-equilibrium thermodynamics is exceptional, but it is not confined to living things. The lithosphere, hydrosphere and atmosphere are not in equilibrium, so why should it be surprising that processes occurred at some point that led to small parts of these moving further from equilibrium? As long as there is sunshine and radioactive decay, there’s the possibility of a system being supplied with enough energy to move it far from equilibrium. By far the trickiest part is to get the autocatalytic process going in an environment where it can be safe from degradation long enough to become robust enough to deal with the challenges of a changing environment and to diversify so as to occupy more places. But with no competition from already-existing organisms and billions of years…

I suspect the mystery of chirality (as he calls it) will prove to be another straw man. A phenomenon to be explained, yes, but not really that much of a mystery, at least not in the sense of requiring new principles to account for it.

His claim that we fully understand and can explain the characteristics of water or other inorganic substances, while we can’t understand living things also seems problematic. Do we really know all there is to be known about water? Again, he seems to be trying to hype up the level of mystery, instead of just saying that it’s a really complex problem. This would make his supposedly new principle seem more marvelous, I suppose. His promise is that he will reveal the hitherto hidden essence of life. TO BE CONTINUED.

Amphibious reflections

I have been carrying out a study of wood frogs Rana (Lithobates) sylvatica for a couple of years now on the campus where I work. We’re trapping frogs as they move toward the small vernal pond where they breed, to see how far away from the breeding site they overwinter. Wood frogs are explosive breeders, doing all their mating and egg-laying in a few days in late winter, after the pond thaws. The other night, after checking the traps and releasing the captured frog into the water, we stood on the N side of the pond and listened as the occasional calls began, gradually building up to a full chorus. I reflected that these frogs must have been coming to this pond for thousands of years to put their eggs in this collective womb, where their embryos can grow safely. Late winter after late winter, they have rasped out their certainty that another spring will arrive. The next morning sitting and contemplating, another thought occurred to me.

How is a college like a frog pond? Female frogs bring eggs to put in pond; parents bring students to college. Males come to inseminate eggs. Faculty plant the seeds of learning in the students.

Eggs are not simply passive matter, as Aristotle thought: they contain half the genome and are in many ways already non-genetically programmed to develop along certain lines. Rarely, eggs may develop apomicticly, not accepting any of the genes of the male. Students come already full of opinions, beliefs and predispositions that reflect their culture, social environment and upbringing. Some may refuse to absorb anything new.

Some frog eggs may already be badly damaged goods, burdened with issues that may stunt development and prevent successful growth and metamorphosis. New students can be the same.

Male frogs are intensely competitive, trying to inseminate as many eggs with their own seed as possible. Some faculty want to create exact copies of themselves; whole departments and program can become like this. Luckily, unlike frog eggs, students can undergo multiple fertilizations. The faculty, like the frogs, are driven by eros. As Socrates’ friend Diotima says in Plato’s Symposium, love is the desire to beget immortal beauty, wisdom and human excellence in the soul of another, as it was once conceived in the teacher’s own soul. Like male frogs, faculty love to engage in noisy display at times.

The male frog does not fill the egg up with stuff and shape it into what it is going to become. The male brings another part of the heritage of the frog population, new material that complements and completes what is already there. Good teachers sow ideas and let them complement, complete or rarely overwrite what is already in the student, sometimes supporting, sometimes challenging their beliefs and opinions.

The pond is the womb of the frog embryos, before and after they hatch. It must provide all the nutrition beyond what is in the egg itself, if the tadpole is to metamorphose into a froglet. A good pond contains a rich stock of nutrients and an active ecological community. A good college is an environment for learning. Students are not force-fed predetermined packages of nutrition, but instead forage for themselves in a place that holds a great store of thought from the past, especially recorded works of words and symbols. Unlike tadpoles, the students must learn to read these recorded thoughts and feelings for themselves.

A pond may be polluted, undergo eutrophication from excess nutrients, be invaded by predators or parasites, drained or have its water supply diverted, be filled in with sediment or disrupted by careless small boys or scientists. Like the pond, the college may allow the problems of the outside world to overwhelm it, become over-enriched with amusements, fall prey to ambitious or self-aggrandizing leaders, have its critical resources drained away or diverted, be destroyed to build something else or muddied up in the name of assessment or accountability by people who don’t realize the delicacy and vulnerability of what takes place.  As when ruling a great nation or cooking a small fish, a college must be handled very carefully, and those to whom a college is entrusted have tremendous responsibility.

If all goes well, in a few weeks or months the tadpoles reabsorb their childish tails, put forth their limbs and venture out onto the land to face the challenges of adult life well prepared. Likewise students, if they are well nourished, will leave behind the juvenile stage and enter into the vigor of young adulthood. Unlike frogs, it may be possible for them to return periodically throughout life to the pond to refresh and renew themselves.

Colonial lives

Hoyt, Eric.1996. The Earth Dwellers: Adventures in the Land of the Ants. New York. Simon and Schuster. 319pp.

Excellent book about ants at La Selva, the Organization for Tropical Studies’ field station in Costa Rica, both because it describes several species of very different ants from an ant’s eye view and for the endearing descriptions of two great myrmecologists, Bill Brown and E.O. Wilson, at work together in the field. Wilson is known to almost everyone, but Brown was also one of the greatest entomologists of the last century. Their contrasting personalities make them like characters from a movie about the adventures of two mismatched buddies. I was amused and edified by Hoyt’s description of their field techniques and sometimes reckless determination in the search for the miracle ant, Thaumatomyrmex. Brown’s views on taxonomic and systematic work, described here, are worth considering, and it is also worthwhile to look up his and Wilson’s published papers. Hoyt includes interesting biographical accounts of both men and quite a lot of readable information on the biology and evolution of ants and ants’ social behavior.

Wilson, E.O. and Jose M. Gomez Duran. 2010. Kingdom of Ants. Jose Celestino Mutis and the Dawn of Natural History in the New World. Baltimore. Johns Hopkins University Press. 96 pp.

Jose Celestino Mutis spent over forty years as a physician, botanist, linguist and priest in what is now Colombia (when he arrived from Spain in 1761, it was the New Kingdom of Granada). He began studying ants at the suggestion of Linnaeus, whose system he used in his work on plants. His detailed reports on ants are apparently lost, but this little book contains long quotes from his journals, which give accounts of his studies several species, including leaf cutter and army ants. Every aspiring naturalist should study these notes to appreciate Mutis’s clarity, perseverance and, above all, skepticism and honesty. This is best shown in the passages where he explains how he realized that the big-headed “soldier” ants were not the males, but instead, when he finally was able to observe copulation, males turned out to be the small winged individuals, who he originally took for young females, not fully grown. He expresses his gratitude to God for enabling him to correct his error and make such a wonderful discovery. In another entry, he reproaches himself for letting the press of his experiments on smelting metals in the mines cause him to forget to follow up on a potentially valuable observation. Another day, he forgets to record part of what he saw, and so with reservation, he allows himself to write it down the next day. He constantly refers to the need to check his conjectures with more observations and to try to reconfirm what others report to him. He often asks the local farmers for their views, but he never accepts them without the evidence of his own eyes. When he tries to estimate the number of army ants in a colony, he uses several independent methods of arriving at the number. As Wilson and Duran point out, about all you could wish of him is a naturalist is that he had included sketches of his ants to help modern myrmecologists identify them. They wonder why he did not do for ants what he did for plants: fit them into Linneaus’ system and have illustrations prepared. Despite owning a huge library, he was evidently not aware of Maria Sibylla Merian’s work on insects in Surinam or any published works on ants. He was quite on his own, with no prior experience and no expert to guide him when he began his work at age twenty-eight. Linnaeus had named only a handful of ants, all in one genus and with very sketchy descriptions. Although Mutis’s descriptions show him to be clear sighted, he does not attempt any sort of systematic classification of the species he encounters, based for example, on the number of petiole segments or the presence of a sting in the workers. This job was left to later workers. His greatest contributions were to the study of ants’ social behavior. He was without doubt one of the finest scientists of the 18th century. Perhaps only von Humboldt equals him as an observer. On the 200th anniversary of his death, the Colombian myrmecologist, Fernando Fernández and E.O. Wilson, named a new ant species, Pheidole mutisi (Fernández, F.; Wilson, E. O. 2008. José Celestino Mutis, the ants, and Pheidole mutisi sp. nov. Revista Colombiana de Entomología 34:203-208). 

Thanks to Wilson and Duran for making this gem available to naturalists.

Rau, Phil and Nellie Rau. 1918. Wasp Studies Afield. Princeton, NJ. Princeton University Press. 372 pp. [Dover Books reprint]

This is a fascinating early twentieth century work on solitary and social wasps. The Raus carried out their studies in the midwestern U.S. Their research covered hunting wasps with a wide range of prey. The wasps included both soil and wood nesting species in diverse habitats; one even dug in the clay infield of a baseball diamond. The Raus made detailed behavioural observations on many species and did experiments on paper wasp homing ability. They mention the drop off in aggression by paper wasps as winter approaches, all the brood matures and the workers die off and are replaced by overwintering queens. That’s just one example of many behaviors that I have noticed but not really thought about until they described it. Another good read for anyone who aspires to study insects in the field.

Looking for the Logos of Life I

Schrodinger, Erwin. 1967. What Is Life? The Physical Aspect of the Living Cell and Mind and Matter. Cambridge. Cambridge University Press. 178pp.

I wanted to put up this brief post before I launch into some much longer ones on books that purport to extend Schrodinger’s ideas and the tremendous biological discoveries that followed in the ensuing decades. I got started on this when I read another book, Eva Brann’s The Logos of Heraclitus [2011. Paul Dry Books. 160 pp], about which more later.

This is the first of a genre: physicists and chemists look at life. Schrodinger, in these lectures, delivered in Ireland in 1943, introduces the idea that life exists far from the thermodynamic equilibrium that physics sees most systems as tending towards. He is also the source of an idea I first heard when I was a graduate student, that organisms feed on “negative entropy.” The essay is worth reading for the quality of his reasoning and clear exposition, even though his predictions about the nature of the material carrier of heredity turned out not to be quite right.

Just one interesting thought: he points out that whatever molecule the hereditary material consists of carries out its functions in a way different from most of the enzymes in a cell. While most reactions in the cell rely on basically random interactions between molecules, in that you can only predict the general rate of reaction and not whether a specific molecule will react, there’s just one copy of a given gene in each cell. It has to be essentially certain that it will participate when needed in its particular role. Nevertheless, the basic processes of translation and transcription do involve many enzymes, along with the building blocks of nucleic acids and proteins, in what must be the usual sort of collectively predictable, individually unpredictable, dance. DNA is after all, a template, a fixed model against which to construct a product. Keeping that template stable and making sure it is copied correctly is the job of a whole complex set of enzymes in the cell. As Schrodinger points out, a big molecule like DNA can have the stability of a crystal, being held together by essentially the same forces.

V.G. Dethier, entomologist

Dethier, Vincent G.  1992. Crickets and Katydids, Concerts and Solos. Cambridge MA. Harvard Univ. Press. 140 pp.

A wonderful little book, recounting his summer as a field assistant to G.W. Pierce, who studied the acoustics of insect songs. Also gives keys to both the orthopterans discussed and their sounds as well as a bibliography. Lovely pen and ink illustrations by Abigail Rorer .

The chapter entitled The Shield Bearers (p. 100) begins as follows: “The stereotypical entomologist is an odd character, long of nose, short of vision, adorned with Ben Franklin spectacles, and given to dashing madly o’er the lea, with net and beard streaming in tandem in the breeze of his pursuit.” The chapter epigraph is a quote from John Phillips’s “Cyder.”  which advises catching wasps that swarm on ripe apples by hanging up vials of “Moyle,” a kind of cider made from Moyle apples, “Mum,” a type of beer, or “Treacle’s viscous juice,” that is , blackstrap molasses. Just about the formula we still use today for moth bait.

Vince Dethier (1915-1993) is a writer every aspiring entomologist ought to read, especially his To Know A Fly [1962. Holden-Day. 119 pp] or for the serious student, The Hungry Fly [1976. Cambridge MA. Harvard Univ. Press. 512 pp. His writing is humorous, lucid and just fun.

Image: male macropterous form of Russel’s bush cricket – Flickr