Looking for the Logos of Life IV

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

Chapter 5: Origin of life

Pross gives a summary of research on this question that seems fairly reasonable, although he clearly doesn’t think much of historical approaches. I wonder whether he is not giving enough credit to geochemical analysis of rocks from the period before we find microfossils, that is to possible evidence of biogeochemistry back before the oldest fossil organisms. Also, he has not mentioned cosmochemistry – what was available in the part of the solar nebula that became the earth? None of that evidence in itself would answer the question, but he earlier talked about how historical studies could supply useful constraints on the free flow of speculative ahistorical studies of prebiotic chemistry.

He says sequence analysis fails on the origin problem because of horizontal gene transfer. If you start to see networks instead of trees, he claims that you can’t tell anything from the results. Is that so, or is that just a further challenge for clever analysts to overcome? After all, trees took a while to be generally useful. There still are lots of difficulties, but horizontal gene transfer isn’t just chaos. The process must have some logic, ultimately controlled by natural selection, like “normal” vertical gene transfer. I think he might be giving these approaches short shrift, because he has his own agenda.

He also assesses RNA world as unlikely, given the failure to create really complex self-catalyzing molecules in decades of lab studies. This despite his earlier claim that negative findings could not be used to rule out this very scenario. Well, if there was an RNA world, we haven’t been able to create a similar thing in vitro.

The other current scenario has a closed metabolic cycle evolving before self-replication kicked in. He calls such a cycle, “holistic autocatalysis.” So far, attempts to develop such systems by evolution in vitro have also not gone very far, according to Pross.

Biology’s Crisis of Identity

Pross asks three questions: what is life? How did it originate? And how would one make it? He says biology has reached a point, with the completion of the human DNA sequence project, that physics had reached in the late 19th century, prior to relativity, quantum mechanics and subatomic particles. How you can judge the state of mind of a body of scientists, I don’t know, but such an assessment feeds into his attempt to portray himself as breaking through confusion and complacency. To him, the problem is complexity. Is complexity a substance? Can there be a theory of complexity, as opposed to a complex theory?

Does all complexity go back to symmetry breaking, like quantum theory says, if I understand correctly? Life’s complexity clearly arises from the pure combinatorial possibilities of sets of fairly simple elements – four nucleotides, twenty amino acids, thousands of enzymes and similar numbers of intermediary products to create all those metabolic cycles. But they wouldn’t be of much use in a totally homogeneous environment. That’s the competitive exclusion principle. Life is complex because it exists in a large and complex environment, whose complexity is the result of irregularities in composition and past impacts, etc. leading to plate tectonics, and the uneven heating of a rotating almost sphere by the sun, leading to circulation of atmosphere and hydrosphere.

Pross says, “It is the organization of life, rather than the stuff of life, that makes life the unique phenomenon that it is.” Well, duh. He says “systems biology,” which tries to explain cells functions using mathematical ideas like “network topology, ” has not produced much in the way of insight. He also says that a holistic approach can be reductionism “dressed up.”

Another favorite of complexity mavens: non-equilibrium thermodynamics. Life, Pross says, can be said to be a dissipative structure, but what further insight comes from that? None, he thinks.

He then turns to John Conway’s Game of Life, the cellular automaton computer program, beloved of Gaia worshipers. These programs illustrate how simple deterministic games can generate complex patterns, but like the physical insights into complexity, there mathematical discoveries don’t seem to throw light on what Pross claims is the tough question about life: how does teleonomy arise within non-teleonomic worlds? I wonder if there is a fallacy in looking for the origin of “apparent purposiveness” when things apparent are clearly in the mind of the beholder. Can science find any sort of purposiveness at all? That’s a philosophic problem, as Socrates pointed out long ago. And as to “apparent purposiveness” is that anything at all? It’s not hard to explain how natural selection acts to give things apparent purposiveness: purposelessness is clearly maladaptive, it is not bothering to try. Is this his great insight?

Biology is Chemistry

The answer, he says, lies in systems chemistry. What defines it is that it deals with simple chemical systems that have life-like properties of self-replication. After dismissing all the previous attempts involving RNA or metabolic cycles, what is he offering that is different? He starts by justifying all over again the utility of simple systems, with the argument that since we think life started from simple stuff it will be informative to experiment with simple systems. This, however, is unproved: what if comets bombarded the proto-earth with really complex stuff, like Buckyballs and other cosmic macromolecules? Also, this comes after he says that we have no idea what sort of simple stuff life came from. I wonder if he’s headed for another case like those he dismisses.

He claims that systems chemistry is like looking at the Wright brother’s flyer to understand flight, as opposed to a 747. That is, if we can strip down to the simplest possible replicating system, we can get somewhere. But he just said that’s not possible because we don’t have any idea what the earliest living organisms were like. As if we did not know anything about airplanes prior to say, WWII, and we’re trying to imagine the ones from1903, could we do it? He seems to be saying both yes and no.

So here comes his “bombshell,” Darwin applies to replicating chemical systems, thus removing the distinction between chemistry and biology. Fine. But if this is really a momentous original discovery, a lot of folks must not have been thinking very clearly. Anyhow, we know Darwinian theory can apply to designing electrical circuits, why not replicating molecules? But can you actually use that to account for life on earth, more than just in principle? Now he brings in competitive exclusion, and we are off to the races. How well can you demonstrate this principle in a purely chemical system? He says replicating RNA molecules competing for different substrates, evolved to optimize their use of two different substrates, thus precisely mimicking the evolution of Darwin’s finches. Well, precisely is putting it a bit strongly. He claims totally without conclusive evidence that the finches are only doing what molecules were doing five billion years ago. He says that somehow replicating molecules transformed into living cells. I agree, but this is no profound insight, just an attempt to dress up a few clever experiments as a major breakthrough. And maybe the fact that a chemist can learn something from paying attention to ecology and evolution.

The earlier chemists, whose work he seems to dismiss, we’re studying the same things as he is, and he still has no idea what molecules to study. It seems exactly like non-equilibrium thermodynamics or systems biology or Game of life: some clever demonstrations, but no meaningful answers. On pages 132-134, he cites experiments that laboriously mimic the process that was already obvious, that evolving systems become more complex over time, but actually the experiment only shows that two interacting molecular species replicate more efficiently than a single species. Cross catalysis, in this case, speeds things up. So is all life one giant cross catalytic system? Of course it is. Herclitus’s ONE:EVERYTHING::EVERYTHING:ONE holds. Yes, it is chemical; life is an interacting system of macromolecules in an aqueous medium, but it is more. For one, it is largely cellular. Why? Can Pross explain that transition from chemistry to biology with more than a somehow?

Pross wants to add complexification into the sequence replication, mutation, selection, evolution. He puts it after mutation, but that makes no sense, and in his experiment it was the experimenter who in effect introduced it. Even the bare sequence is not right. Evolution doesn’t belong. It is not inevitable, it only happens if the frequencies of the interacting elements change, and that requires an outside physical/chemical/biological cause, a selective force. The system only evolves because of some constraint. Complexification is not a force, no more than evolution; it is the outcome of selection operating under varying conditions. It isn’t a cause. Evolution is change. Complexity is variability, they are not causes, they are results. True, it seems as if complexity is somehow auto catalytic, generating more and more complexity, but there is no law that says that has to be. Diversity does not necessarily result in stability or increasing diversity. Those outside constraints ultimately set the limits. Pross knows a little ecology and evolution, but not enough.

Pross says chemistry and biology are connected by a complexity continuum. What does that mean? Just that he’s repeating his claim in a different way? Wouldn’t discontinuity be more complex? His holistic claims seem more like good old reductionism dressed up. Is his bridge between the two more than just analogical? Physically, of course, it is the same stuff, but until you can actually make molecules evolve into living cells, what have you added to our understanding?

Is the first gene or the first enzyme buried somewhere in our cells, still doing a job, albeit not necessarily what it did billions of years ago? Or did it go the way of the protobiont and so many other species that are now extinct? If we could reverse engineer a simple bacterium into an even more minimal creature, would we be replicating our now vanished ancestors, or just making test tube freaks that never could have competed in the biosphere? Pross says the bacteria have remained simple, but how does he know? Is the bacterial component of the biosphere becoming ever more complex, just in a different way, than the higher plants and animals?

Assume he’s right, and some bit of RNA started the whole thing. Did it manage to do this in some primordial soup competing with uncounted numbers of other molecules, or was it in some incredibly sheltered, simplified environment, like those laboratory test tubes? One thing you don’t have to worry about is sufficient numbers to let mutation and selection act on. Enough might be produced in seconds, if you hit on the right mix. Even if it was much less rapid, as Pross notes, there was certainly plenty of time back then.

Natural selection is kinetic selection

Are competing organisms much like competing molecules? That’s a very loose analogy. Organisms don’t just compete for substrate. He claims we have to explain biology in the language of chemistry, but he uses all language very loosely. He really makes an unwarranted jump in equating chemical kinetics with biological reproduction. If you say that one species winning out over another is just chemical kinetics, I think you will get demurrals from most biologists. He’s back to hiding crude reductionism under his holistic claims. What he says about chemical systems being more amenable to mathematical analysis is just wrong, too (p. 139-140).

Fitness equals dynamic kinetic stability

He’s already in trouble by claiming fitness is a population phenomenon, not an individual one. Even chemically, I’d say that’s dubious, although there may be a population aspect. He is shoehorning a biological idea into a much simpler chemical concept. He claims you can focus on the population aspect, evidently without considering the individuals. But that is just wrong. The only real aspect of fitness is which individuals are the parents of future generations. Who is going to have descendants? Perhaps highly predictable with molecules that replicate. Not so easy with organisms. Even in general it isn’t easy. Who would have picked out the ancestors of angiosperms and placental mammals in the Jurassic? Connecting fitness to stability seems hugely wrong. On the level of the persistence of simple forms, maybe. Lots of genes seem not to have changed all that much.

His attempt to explain fitness landscapes and to make an analogy to a flock of birds seeking higher peaks is not particularly helpful, and didn’t that come from Richard Levin’s work in ecology? Actually the Eigen-Schuster Quasispecies concept is a neat mathematical formulation, but it is not clear what it applies to. Maybe viruses, maybe the origins of DNA RNA transcription/translation! maybe sex (see Wikipedia on quasispecies model) Certainly nothing like all evolving species. This is another analogy that seems to break down on close inspection. He’s trying to bridge the gap by forcing these analogies to do more than they are suited to do. After all, the real unification would mean that you can reduce equations of population genetics to chemical equations, doesn’t it?

He ends up not making a clear connection to the quasispecies concept and goes on to talk about his dynamic kinetic stability, which he admits can’t be measured absolutely, just like fitness, which also depends on the environment in which it is measured. Given how vague DKS seems, it does share the character of “fitness,” in as much as both can be what you want them to be. He suggests (p. 146-147) two measures: abundance and persistence, that are like part of Wilson’s definition of ecological success.

Incidentally, why does he not discuss the Eigen-Schuster hypercycle idea, which seems like a real theory of evolution of simple replicating molecules into linked pathways?

He now says that the cause of evolution is the drive toward greater DKS. But isn’t the cause self copying, with imperfections in a variable, limited environment? It’s differential reproduction, not any drive to achieve stability in any sense of stability I understand. A driving force towards something that he admits can’t be quantified and a mechanism that is a process of becoming a mechanism that is made up of more diversely interacting components (complexification) Seems pretty incoherent to me. He can’t put this into an equation, can he?

In arguing for the idea that life has undergone complexification he points to the fragility of self replicating molecules in the lab. I don’t see that that self-evidently applies to the first replicators in nature. Maybe we are all descended from a horrendously tough little replicator that just happened along out of the seemingly infinite possibilities. Maybe there are theoretical limits set by the problem of mutation in a small set of elements, something seemingly discussed by Eigen and Schuster. Small sets are inherently unstable, so it’s hard to conserve the replication when the replicates are too unlike the original. If a sequence is going to assume the role of a template, or even just determine catalytic properties, it can’t vary too much. Isn’t that just a trivial result, though? It sounds more profound if you introduce the term information into the discussion, but is that really necessary? Jacob Klein always denied that what geneticists talked about was information. I’ll stop at this point, because I think I have about reached my limit in thinking about where life comes from. Pross has made an interesting attempt to  define a new agenda for research in this area. I don’t think he’s got anything really significant, though. Perhaps if we can ever find another biosphere to examine, we will see just how narrow or how loose the constraints are.

Thoreau’s Maine Woods

Thoreau, Henry David. The Maine Woods. I listened to the excellent Librivox recording by “Expatriate.”

This is the posthumously published account of three trips Thoreau took between 1846 and 1857 to the vicinity of Mount Katahdin, all by canoe or bateau, on two of which he employed native guides. The land he saw was thinly settled, but it had already been greatly changed by cutting of the white pine and the construction of numerous dams to facilitate floating the large logs down to the sawmills. They frequently visited or slept at vacant lumber camps. The descriptions match very closely the reconstructed one I visited years ago near London, Ontario.

Thoreau was of course, an unmatched observer of nature, whose journals are still a valuable resource for modern ecologists seeking to understand the New England landscape as it existed in the first half of the nineteenth century. He gives many detailed descriptions of the landscape, from the forbidding slopes of Mount Katahdin to the falls and rapids of the Penobscot River. He gives the scientific names of the plants he saw, most of which were familiar to me, like jack pine, Pinus banksiana, and Lilium canadense. He mentions many birds, including the shelduck, which I take to mean the common merganser, Mergus merganser, the cat owl (probably the great horned owl) and bald eagles along the rivers. He has some excellent descriptions of the geology of the routes, such as Mount Kineo, in Moosehead Lake, whose flint-like rhyolite was sought by the natives for toolmaking. His accounts of the difficulties of walking along the rocky, timber strewn banks of the streams and through the boggy ground at the divide between the major drainages evoke memories of similar hikes. The photo by KD Swan, river driving in 1937 in  Kaniksu National Forest, from the US Forest Service Northern Region, gives an idea of the challenge.

Thoreau the transcendentalist’s belief in the spirit lodged in every person is evident in his narrative of these trips. Some of the best descriptive passages are of the the solitary hunters and the timber scouts, who spent months in the wilderness, searching out the uncut stands and the routes for bringing logs to the mills, or the ones engaged in piling up hay and other stores in the camps, to feed men and beasts over the winter of timber cutting. His descriptions of camping out, under simple cotton tents, next to roaring fires, cowering under veils and blankets from mosquitoes and black flies, fishing, hunting and skinning moose and dressing the huge, heavy hides are vivid. Best are his accounts of his native Penobscot guides, particularly Joe Polis, who accompanied him on the third trip to the St. John’s and Penobscot. His interest in Native American language and woodcraft is evident in his careful accounts of Joe and his ways. He gives a detailed and nuanced description of this man, who had travelled to Washington D.C. To pay his respects to Daniel Webster and who had led the pro-education faction of his village against the Catholic priest, who wanted to tear down their “liberty pole” and shut the school. This struggle included a simulated attack on the priest and his party, as they tried to lay hands on the pole, by a gang of painted, naked young men. Despite his tendency to keep his communication minimal and to refuse to answer a question more than once, Joe was a superb teller of tales. He was also a superb handler of his canoe, shooting dangerous falls and rapids, handling the heavily laden craft on stormy lakes and portaging over rough trails. Thoreau tells how Joe taught him the techniques of paddling, which sounded very similar to what I practiced when I earned canoeing merit badge. Joe Polis knew the properties of most plants, could make numerous varieties of tea from them, and yet he was not as familiar as Thoreau with the arrowheads and other flint tools that Thoreau found and showed to him. Overall, Thoreau’s portrait is of a man successfully bridging two cultures.

The Maine Woods joins books by Ruben Gold Thwaites, Mark Twain, Richard Bissel, and, continents away, Eric Newby, on my short but growing list of great river narratives. I’m about to post on a fine account of three British naturalists, Bates, Wallace and Spruce on the Amazon.

Along the Ohio

Ruben Gold Thwaites. Afloat on the Ohio: An Historical Pilgrimage of a Thousand Miles in a Skiff, from Redstone to Cairo.

If this book were made into a film, its musical score should be Antonin Dvorak’s New World Symphony. The varied settings and historical reflections match up well with its varied musical themes. This narrative is similar to his Historic Waterways, but this is a longer trip, with his friend the doctor and his wife and 10 year old son together the whole time. It is historic in that much of the text concerns events that occurred in the previous two and a half centuries. The Ohio Valley is also where the battle to expand the colonies and later the United States beyond the Eastern seaboard took place: the accounts he gives of the conquest and settlement of the region sent me to Wikipedia to learn about the beaver wars, the Northwest War and other conflicts that my school history classes and U.S. stamp collection only left me with a few names like Fallen Timbers and General Braddock. The voyage takes Thwaites and his companions past the sites of Native American towns, forts, trading posts, ambushes, battles and settlements. George Washington spent much time before the Revolutionary War in the Ohio country, both as a military officer and as a surveyor, marking out lands both for his own speculations and for others. The struggles of the colonists from Virginia and Pennsylvania to drive out first the French and then the British from the Ohio had effects on the larger global struggles of these two nations. These were among the bloodiest conflicts in our history, although the later wars with the plains Indians have garnered more attention, along with those in the Hudson Valley and central New York, thanks to James Fenimore Cooper

The other part of the story is of the valley as it appeared in the late nineteenth century: The country they passed through was much more heavily settled and industrialized than the rural regions of Wisconsin described in Historic Waterways. Beginning at Redstone on the Monongahela, the banks were lined with coal tipples, oil and gas wells, mills and factories as well as river towns large and small, and farms that range from prosperous to squalid. There is more river traffic, including a steady procession of steamboats making waves that threaten to swamp their skiff or flood their tent on the bank. These are not bucolic streams but busy waterways in what was, in 1897, the industrial heart of America. The resources of the country were being rapidly converted into goods to be floated up or downriver or loaded onto railcars, which were already displacing the steamboats. Everywhere the waste from mills, mines and wells was being dumped on the banks or poured into the river itself. Thousands of Eastern Europeans were coming to the factories to earn a fortune that they could take back to the homeland, according to Thwaites’s informants, and already there were complaints about the downward pressure on Americans’ wages.

Below Cincinnati and Louisville, though, the river flowed through less developed country, and the rural poverty on both sides made it hard to find the supplies they needed for daily sustenance. Still, there were many well-kept farms and moderately prosperous towns. There was also a stark reminder that this was during the successful counter-reconstruction period, when the hopes of freed slaves were being overturned by southern whites. Thwaites reports, without comment, an exchange between a group of blacks working on an island on the Kentucky side and a black man on the Ohio shore. Their taunts are silenced when the Ohio man points out that at least he has not been put to work doing gang labor on an island that he can’t leave.

As in Historic Waterways, there is rich detail about the river, the weather, the people they meet along the way. The rivermen especially, have that independence of mind, along with a penchant for repartee, that is found in Mark Twain’s Life on the Mississippi or Richard Bissel’s wonderful A Stretch on the River. There is less of natural history, although his wife avidly botanized at every opportunity and he describes the wildflowers they find. So much of the country had been emptied of wildlife a hundred years of uncontrolled exploitation, and the air and water so polluted by slag, mine tailings, coal smoke and oil that fish and birds were becoming scarcer all the time. A more recent account of the devastating changes wrought upon the fish of the Ohio River (and the Great Lakes) by development, channelization and drainage can be found (if you can locate a copy) in the introduction to The Fishes of Ohio by Milton Bernhard Trautman. Ohio State University Press, 1957.

Throughout, Thwaites makes reference to the early narratives of travel in the Ohio Valley, which he himself played a major role in editing and publishing. I think I may want to read some of those myself.

Northern traveller: Ruben Gold Thwaites

Thwaites, Reuben Gold, 1853-1913 Historic Waterways—Six Hundred Miles of Canoeing Down the Rock, Fox, and Wisconsin Rivers. Chicago A. C. Mcclurg and Company. 1888 [I listened to the Librivox recording]

In 1888 Ruben Gold Thwaites, with his wife Jessie Turvill Thwaites and a physician friend, canoed three rivers in Wisconsin and Illinois. This book is an account of those trips. He describes the people, landscape and history of the areas they passed through, their encounters with farmers, townspeople and river people. Before much of the land adjacent to these rivers was drained for farming, there were long stretches of heavily-wooded bottom land, and the streams were shallow during dry spells, with confusing mazes of channels and islands. He describes encounters with barbed wire fences and with mill dams and mill races that would horrify most modern canoeists. Today, such things would be walled off or posted by the managers of our recreational rivers to prevent people from hurting themselves. Yet he and his wife, after cautious scouting to be sure, took them head-on, fending off with paddles and ducking under the strands of wire or the roofs of culverts. The closest I can come to a comparable account is in Snowshoeing Through Sewers: Adventures in New York City, New Jersey, and Philadelphia 1994 by Michael Aaron Rockland where he and a friend do something similarly crazy in Trenton NJ.

Gold Thwaites was a good naturalist, well acquainted with the plants and birds along the river, so I find it easy to picture the riverscapes he describes. The extensive marshes and winding channels at that time were still full of emergent plants, ducks, pickerel and sturgeon. He describes a humming swarm of mayflies headed upstream in the twilight, like a reverse river over their heads. His descriptions of the homes and the quasi-inns where they spent the nights are at turns amusing and appalling. Rural poverty was as pervasive or more so then than it is today. Many towns that had once thrived were bypassed by the railroads and were dying, their factories shut or burned and their dams and bridges crumbling in the late 1880’s.

I glanced at his other river voyage book Afloat on the Ohio: An Historical Pilgrimage of a Thousand Miles in a Skiff, from Redstone to Cairo on Project Gutenberg http://www.gutenberg.org/files/29306/29306-h/29306-h.htm There is a fascinating account of their side trip up to Big Bone Lick, the salt springs famous for the vast quantity of prehistoric animal bone, especially mammoth, found by the early settlers, some of which ended up in museum collections. He also describes the poor health of the inhabitants of that swampy bottomland, because of endemic malaria. I’d like to read the rest on my Kindle or listen to it on Librvox, if that recording is as well read and produced as this one.

His profession was as a historical archivist: He was a prolific editor of early American historical documents, including the Wisconsin Historical Collections (volumes xi-xix, 1888-1911); The Jesuit Relations (73 volumes, 1896–1901); Early Western Travels, 1748-1846 (32 volumes, 1904–1907); Original Journals of Lewis and Clark (7 volumes, 1905); and similar works. Much of this was accomplished with support from the state of Wisconsin, which he worked hard to obtain, when his attempts to obtain private donations fell far short. I doubt that the current governor and state legislators are willing to fund such efforts. Links to his work can be found at http://en.wikipedia.org/wiki/Reuben_Gold_Thwaites  An appreciation of his life and work by Frederick Jackson Turner can be found at https://archive.org/details/reubengoldthwait00tu

Looking for the Logos of Life III

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

Chapter 2 The Quest for a Theory of Life

Pross discusses previous attempts to develop what he calls a theory of life, beginning with Aristotle. The only aspect of Aristotle’s views that he describes, though, is telos. He also characterizes Copernicus, Bacon, Descartes, Galileo and Newton as banishing telos from the universe, instead of only from their philosophical explanations of motion. [It is worth noting that he retrospectively applies the name “science” to what they and others were doing.] Pross quotes Jacques Monod as saying that a purposeless cosmos is the most important discovery of the past 200,000 years. Besides being completely unverifiable and hence clearly unscientific, the supposed discovery doesn’t even seem that obviously useful. I guess you could say it frees us to do destructive experiments on animals, but our current regulations suggest that we don’t think that. Pross says it propels us into a new conceptual reality. What does he mean by that? Pross also adds that Schrodinger, in his What Is Life, said that the explanation of living things would involve as yet unknown laws of physics.

Pross thinks, along with Monod, that teleonomy requires an explanation. Isn’t teleonomy only supposed to be apparent purposiveness? So what is the problem? If we assume organisms lack real purpose and simply obey the laws of chemistry and physics, then there is nothing to explain except our perception of purpose. That may be a problem, the problem of consciousness. Is he going to solve that with his chemistry?

In his section on definitions of life, he carefully distinguishes individual living things, which cannot evolve, from populations, which can evolve, but he then talks about a population of mules, possibly not seeing that there can be no such thing.

He does seem to be on track in suggesting that most attempts to define life fail. The examples given either make mistakes like saying life is self-sustaining without qualification, instead of pointing to reliance on energy inputs, for instance, or only list some characteristics of life as known to us, or seem just ridiculous, like Freeman Dyson’s information definition.

Chapter 3 Understanding “Understanding”

Pross links understanding to induction, citing Bacon. He says all scientific explanations are inductive, being based solely on pattern recognition. True, patterns in some sense must match, but induction is a reasoning process, so it should describe not the explanation but the way it was derived. In that case, it seems clear that deduction plays as great a role as induction in our understanding. In talking about mathematics’ role in explanations, he goes from pattern recognition to pattern formulation, without noting that he’s moving between induction and deduction.

In discussing the problem of where the underlying patterns come from, that is, what is the reality behind them, he denies we can know that scientifically, and he quotes Wittgenstein to that effect. This would seem to put him into the linguistic positivists’ camp, but I doubt he’s that clear about questions like realism vs. anti-realism, although so far, his statements seem consistent with anti-realism. He does however seem to qualify himself at one point by saying that patterns are to some degree subjective. He also distinguishes quantitative, qualitative and statistical patterns. Then we get a dose of pragmatism to the effect that adequate understanding is whatever works. Then, in another twist, he says that the patterns we recognize are only reflections of the underlying reality of nature. Once again, it is not clear whether he’s an anti-realist, as he seemed to say earlier, or some sort of Kantian realist. Could he even be a Platonist? Images of reality?

The reductionism vs holism section doesn’t add anything. The problem is that he’s leaving out any discussion of the environment of life. If you frame the problem as what environment and what inputs do I have to supply to create a self-replicating molecular system that can undergo natural selection, you have a pretty good reductionist program for developing an understanding of life. If by life, you mean the biosphere, then you still have a long way to go, and it becomes necessary to use more complex terminology than what you would use to describe life in a simple experimental system.

Chapter 4 Stability and Instability

Pross agrees with my idea of auto catalysis: if something is auto catalytic the rate of formation increases as there is more of it around: dn/dt = rn provided you maintain steady inputs of reactants, while in a normal chemical reaction with a catalyst dn/dt = r, where n is the concentration of product and r is the rate of conversion of reactants to products. He expresses the idea in terms of the time required to produce a given amount of product, if you have a given amount of catalyst. For the Spiegelman RNA autocatalysis, you should get a logistic growth pattern, because the rate will be constrained by both the RNA and the protein enzyme acting catalytically. This seems like it ought to apply to PCR, for example.

Another thing about the RNA replication reaction is that it is template replication, so it actually yields copies with a highly specific structure – meaning that analogies to information become possible. Is that what all the talk about “information” in biology is, a physical analogy? How would the idea of a physical analogy apply to a computer or a brain? It seems as if information theory is a mathematical formulation applicable to understanding a variety of things, some of which (cells, telephone signals, computers) we think of as physical and others (language) that seem not to be. I would say that what goes on with cells is physical and the information is only metaphorical. A computer seems more problematic, especially since what it does can be represented as a Turing machine, and even though it isn’t a machine but a mathematical hypothesis its relation to meaningful information seems very immediate. Since information theory involves representations in mathematical symbols of concepts that are not physical, why invoke physical analogies? In all the physical systems covered by information theory, is there a point at which a mind is needed to interpret the meaning of the information? That seems to have been the original motivation in fields like cryptography, communications, etc. but in cybernetic systems there may be times when the information is used only by the machine. Still, someone has to eventually determine whether the machine is doing what it is supposed to, at least until we find ourselves in the Matrix, etc. Stephen Hawking apparently worries that this is where Artificial Intelligence is leading us. A biosphere is like that. It doesn’t need to be meaningful to us to be a biosphere.

What about crystal growth? Clonal growth?

What sense does it make to talk about kinetic dynamic stability or about the “efficiency” of maintaining a large population (p. 74) by rapid replication? I would think that in a way, autocatalysis is very unstable, because it tends to exhaust resources so quickly. He talks about Cyanobacteria being around for billions of years. Is persistence of a clade with little obvious development or change the meaning of stability? Success, might be a better term. To me, the Heraclitean flux is the only really persistent feature of the biosphere. Moreover, it looks as if the pace of change is accelerating: metazoans only in the last billion years, a full terrestrial biosphere only in the last 300 million years, hot blooded life only in the last hundred million, and cultural evolution only in the last six million? Is this all the result of auto catalysis? Is dn/dt = rn, where n is “information?”

It seems as if “stability” is not a very good word to encompass the persistence of biological entities through time, given the tremendous range of life histories found among living things. The mathematical complexities are very great (cf. Cole, L.C. The population consequences of life history phenomena. Quarterly Review of Biology Vol. 29, No. 2, Jun. 1954, pp. 103-137) and there are many dimensions to the whole problem of what is it that persists: genes, phenotype, species, clades? What about the stability of Redfield ratios? If true, it is an indication of an extremely widespread pattern. He claims the more stable replaces the less stable. Doesn’t that imply that species should last longer and longer in the fossils record? What is the actual pattern? TO BE CONTINUED

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.

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

For the Love of Leps

bflyLeach, William. Butterfly People. An American Encounter With the Beauty of the World. Pantheon. New York. 388 pp. 2013.

This book, beautifully illustrated, is a history of the discovery and documentation of the butterfly fauna of the United States and of the entomologists, amateur and professional, who fed the public fascination with butterflies in the 19th century – Samuel Scudder, William Henry Edwards, Herman Strecker, Augustus Grote, W. J. Holland, and many others. The author has many reflections on the importance of both Darwin and Romanticism (especially German) on the interpretation of the biology and meaning of butterflies. There is also a lot on the collectors, scientific and commercial, who travelled throughout North America and the rest of the world to satisfy the demand for specimens, often at considerable risk and always with much hardship. Butterflies and moths were much more than a scientific concern: there was a great deal of commerce in specimens, as many, if not most, young men of middle class aspirations had a Lepidoptera collection, even if few collected themselves. It is strange to think in our day of fancy cars, world travel and electronic devices, how much one’s status might have been tied up in various collections, whether, insects, stamps, shells or books.

Leach mentions George Santayana’s The Sense of Beauty several times as a perspective on the 19th-century’s fascination with natural form and color. As well as commercial specimens, large format books with color plates were an important part of the butterfly business. He talks about the illustrators and the changing technology of color reproduction.

The Academy of Natural Sciences of Philadelphia was one of the repositories of collections, including the very early and important Titian Peale collection, which was to have formed the basis of a never-completed series of books by that second-generation Philadelphia artist. The American Entomological Society, founded 1859, played a role as well. The society’s book collection, still housed at the Ewell Sale Stewart Library of the Academy, includes many of the most attractive 19th-century publications.

This is a fine account of what natural history meant to Americans in the first century and a half of the nation and of the friendships and rivalries among these early naturalists.