Naturalists Abroad: Three on the Amazon

Hemming, John. 2015. Naturalists in Paradise: Wallace, Bates and Spruce in the Amazon. Thames & Hudson. [I read the Kindle edition]

There was not a lot paradisiacal about the Amazon basin when three young, lower middle class Englishmen arrived there in the late 1840’s. It was a backwater of the Empire of Brazil, still recovering from a bloody civil war and not yet experiencing the rubber boom. Travel was difficult, often impossible, and living conditions ranged from merely hot and humid to nearly intolerable. No motorboats, no canned food, no bug repellents. Yet the three naturalists, the first from Great Britain to travel extensively and for many years in the Amazon region, could live cheaply and enjoyed the help of both Brazilian and foreign residents. They lived by the sale of the specimens they collected, something not commonly done today, at least by academic scientists, but then it was quite respectable. This was possible, in Henry Walter Bates and Alfred Russel Wallace’s case, because they had a reliable and energetic agent in London, Samuel Stevens, who marketed the exotic animals and plants they supplied to an eager and growing circle of collectors. Thomas Spruce enjoyed the support of George Bentham and William Hooker, director of Kew Gardens. They also accumulated personal collections of great value and volumes of notes, drawings, sketches, and accounts of the rivers, forests and the native peoples, of whose languages and cultures they learned much, to their great advantage, and ours. They relied on the skill of native boatmen and hunters, and procuring their services was a constant preoccupation for all three.

They generally worked alone, each going his own way and following different styles of exploration. Bates was mainly an entomologist and the most sedentary, working intensively in one area for months at a time. Wallace and Spruce ranged more widely, Wallace after birds and all other animals, as well as plants. He also accumulated extensive geological and ethnographic information. Spruce hunted new species of plants, including his favorites, mosses and liverworts. Wallace was accompanied at times by his brother, but Bates and Spruce were out of contact with their own countrymen for long periods.

The adventures described in this account are exciting, inspiring, and frequently hair-raising. The rivers and their falls and rapids were the greatest danger to the explorers and their precious collections, but the everyday toll of hunger and sickness on the men and of wet, mold and insects on their specimens probably did the most damage. Wallace’s brother died of yellow fever before he could return to England. All three had malaria, sometimes very severe, and in 1858 Spruce suffered an unexplained illness that left him crippled for life.

Catastrophe dogged Wallace: heading home in 1852, a shipboard fire destroyed almost all his personal specimens and records, except for the few he managed to grab as he abandoned ship. Still he went on to a successful voyage to the Malay Archipelago (modern Indonesia) during which he worked out the theory of natural selection, which he and Darwin jointly announced in 1858. In the second half of the 1850s, Spruce pushed far into the Andes, where he learned much about the hallucinogenic plants used by the natives, a topic later investigated by Richard Schultes and Wade Davis. He also made vital collections of Chinchona, the source of the antimalarial quinine, contributing to the establishment of plantations in India and the East Indies. He did this despite the hardships of the country, a civil war and his own prostration by that mysterious illness.

Hemming’s account is consistently lively and an excellent companion to reading the naturalists’ own work, like Bates’s wonderful Naturalist on the River Amazons. It has the advantage of weaving their travels together and providing the background of Brazilian history and the development of natural science in Great Britain. Hemming is an anthropologist, historian and geographer, whose own extensive travels in the region add much to the story.

The work accomplished by these three men in their time in the field was phenomenal: thousands of new species of animals and plants along with detailed descriptions of a country largely unknown to the learned world. They are deservedly members of the pantheon of the greatest naturalists in history.

A Natural Philosopher, Willy Nilly.

This post is a brief musing on parts of Brann, Eva. 2014. Un-Willing. An Inquiry into the Rise of Will’s Power and an Attempt to Undo it. Paul Dry Books. Philadelphia. 367pp. This is a fine book, like all of her writings. It is also worth listening to her discuss it on the podcast, Partially Examined Life. This attempt to summarize her rich argument, based on extensive reading and reflection, cannot do it justice, but it serves my own train of thought.

Not a lot of this was registering with me, possibly as a result of my reading it mainly in bed, just before I was going to sleep. Then I read, probably for the second or third time, chapter XI, section D, Self: Subject. Brann sets up a contrast between two pairs of terms, I/soul and self/subject. I/soul is the ancient pair: I, a being looking on a world by virtue of my soul, which apprehends physical things and immaterial things through faculties such as sensation or intellection. We can abstract or intuit the essential nature of the things that we encounter in this world, and whether it is at bottom purely material or ideal or undefinable, it is still one and the same for all souls. Moreover, souls can act in and upon this world and communicate with other souls.

Since Descartes, the pair Self: Subject has emerged, as the inner life of the mind has become the focus, and what was in some way accepted as a mirror-like reflection of the outer world and even the reflection of the soul itself, open to philosophic examination as the inner landscape of our experience, becomes highly problematic. Descartes asks how a thinking substance can connect to an extended substance with which it has nothing in common. Kant analyzes how the subject makes an orderly world out of an influx of sensation. The modern consensus seems to be that in some way, my self creates a world out of whatever inputs it receives, not passively, but selectively. If this is true of the outer world, the other, it also applies to the inner: self-consciousness becomes a major topic of inquiry.

So my question is this: why does this shift in philosophical perspective seem to occur right at the time, and even coming from the same minds, as the great expansion of objective understanding of the world, in which it is confirmed that through mathematics and experimentation, we can establish laws that govern the appearances? Why, at the very time when we have a clearer, more rigorous grasp of the world we are in, when we can look at it in all its unfolding necessity, are we more doubtful than ever whether there is any truth? No wonder we have culture wars. On one side, we seem to have Baconian science saying, of course we can make our own world, but to do so we have to know the exact and rigorous rules that govern the materials we make it out of. On the other hand, we have philosophers and social scientists telling us that the rules themselves are of our own making.

Plainly this is at work in battles over issues like the definition of marriage. It seems my Catholic friends want to have both fixed nature (God made us man and woman for the fixed purpose of procreation) and a conserved culture (you ought not redefine an institution that has served society for a long time) on their side. The supporters of the expansive definition, that marriage is between any two persons who are of age and not already married to another, argue both that nature, when closely examined, has no such clearly demarcated binary gender, that cultural norms ought to reflect what most people’s views are today and that people ought to be allowed to make of their lives what they want. Thus we have conflicting definitions of liberty: 1. freedom from constraints other than what nature and the law impose, the one from God and the other through a fixed constitutional process, and 2. Justice Kennedy’s opening statement that our freedom is to make ourselves what we wish to become, a “constitutional right to define and express their identity,” like the rule of the abbey in Gargantua: do what you will, or rather, be what you will.

As Miss Brann explains very carefully in her book, this modern view is generally accompanied by a great emphasis on the idea of the will, in both its merely burdensome form (the individual’s need for will power to tame our own willfullness – a paradox) and also its truly pernicious form (under the name of the general will, impelling whole nations to atrocious acts). She recommends that we try to live in a way that sets the will in its place, as the process of formulating rational courses of action and putting them into effect, when circumstances demand that we act decisively. This is in part the view of the great Scholastic, Thomas Aquinas and other medieval thinkers. For the most part, however, she feels we can do without the will, substituting for it a kind of openness to experience accompanied by reflection and the pursuit of a quietly well-ordered existence.

In my excursions into natural philosophy (the old name for biology) I am decidedly in line with the ancients and Bacon, in the sense that I am sure I am discovering, and not inventing the natural world. I gaze upon an ever-changing nature that nevertheless follows fixed laws, which don’t change when I change my ideas. I can get it wrong, but there is truth out there to be discovered. On the other hand, I feel very much that my choice of object of study and the exact questions that I try to answer, are of my own making, though certainly influenced by my society. But even here, the direction of my activity is also influenced by the ancient view, as summed up in Aristotle’s Nicomachean Ethics, that the life of contemplation is the best. In that sense, I do not see myself as doing what I will, but as doing what is good.

Looking for the Logos of Life V: Some most unusual paradoxes

Wagner, Andreas. 2009. Paradoxical Life: meaning, matter and the power of human choice. Yale University Press.

[Note: This is a lengthy post. If you did not like the earlier Looking for the Logos of Life, I recommend skipping it]

This book is described as an account for the general reader of a large and complex question of the paradoxical tensions in biology and the way human life has created our world.

At the start, Wagner describes what goes on in a developing embryo as involving communication, which he says implies meaning. So molecules, he says convey meaning. T of human awareness, logos and what goes on in the developing embryo. He is quite bold in proclaiming that all matter conveys meaning and all meaning is material, yet the two are distinct. This seems to be very similar to Spinoza’s different modes of a single substance. Is he aware that he is answering by fiat a question that has been with us since Heraclitus? Is he just tossing out paradoxes for the sake of getting attention?

Another paradox is self versus other, especially in associations, from the cells making up a body to rival nations on the same planet. In the same paragraph, he refers to cells as, “unthinking lumps of protoplasm.” How does that fit with his matter and meaning paradox? Meaning must not imply thought, then.

He is going to maintain, he says, that self and other are inseparable. He also maintains various other paradoxes, which, he says give humans power. Is this an echo of New Organon? He says self vs other has no place in mathematics. Is that true?

He ends the introduction by quoting Lao Tzu. Where is this going?

“The elementary particles of communication are signs, which convey meaning.” Signs may be icons or symbols.

He makes cell surface molecules the exemplar of all he is talking about, but then he overreaches immediately, by saying the receptor molecule “recognizes” the signal molecule. Recognize from cogito, I think, yet he said earlier such communication doesn’t involve thought. He even says the molecules “recognize” the meaning in some molecules but not others.

In his perspective, as he calls it, my TV remote and my TV are conversing.

Does the probabilistic character of human conversation (we don’t invariably understand the other person) really find a useful model in the probablistic character of cell surface protein interactions with molecules in the cellular environment?

He claims that the alternative to his conversation idea is the doctrine of cause and effect, and he says if you can’t see it his way, it is because you are too indoctrinated to the cause and effect perspective. He invokes quantum mechanics to justify his claim that we can no longer assume that cause and effect is the correct perspective, but all his examples are from systems too big to involve quantum effects (note that they are called quantum effects, not quantum messages or quantum meanings). He actually calls his view “logocentric” Why then, I wonder, has he said nothing about mathematics? That would be the bridge between cause and effect and his idea of communication.

His conversational idea makes very little sense to me, if I think of something like weather. Does the sun send messages to earth? Do the oceans and atmosphere get each other’s meanings? The signaling metaphor makes some sense when talking about cells that interact with each other in an organism, or the nerve cells that interact with the environment. In both cases, we can talk about signal transduction, etc. At the actual level of what’s changing, though, we can describe these processes in the language of chemistry, which is that of cause and effect.

The other puzzle is how it helps to understand developmental processes or ecological interactions, which we have a pretty good handle on the basic principles, using a phenomenon like language, and the memory, etc. language relies on. We have no good grasp of basic principles in that case, and only study the higher level appearances. To me he’s trying to use levels of understanding in reverse. I see meaning as an emergent property of complex systems in social animals with highly developed memory and learning, as in Greenspan and Shanker’s The First Idea. I think he’s pushing it down onto levels where it doesn’t belong.

His treatment of altruism in the chapter on self and other illustrates the folly of using value laden words like selfish and altruistic to talk about genetic alleles. It’s another example of trying to apply a concept appropriate to explanation at one level to a much more basic level of phenomena. To his credit, he points out that since genes change over time, even as they retain the same basic function, it is not exactly right to talk about them as isolated entities perpetuating themselves through generations.

The discussion of parasitism in the same chapter concludes that all organisms are parasites. This conflates parasitism with competition, failing to see that one relation is +/- while the other is -/-. He also seems to misunderstand the prisoners’ dilemma.

There is a chapter on parts and wholes, which does not discuss emergent properties. This is strange, because emergent properties like meaning and communication, etc. are used all the time as metaphors for what goes on at lower levels – cells communicating, etc. is this just a consequence of avoiding explanations that are “too technical?” Wagner seems to prefer explanations that work at every level, so for example, his parts and wholes chapter covers everything from subatomic particles to societies. The forest or the trees? According to him it just depends what question you ask or how you choose to look at it. I suspect a strong touch of postmodernism in his outlook: His everything is a conversation” sounds suspiciously like, “everything is a text.”

In the chapter on risk, after an interesting discussion of diminished DNA repair in aging bacterial colonies, he says, “a cell most likely does not benefit from shutting down DNA repair. Most likely it will die. In contrast, the entire colony benefits immensely when one (my italics) cell survives and becomes the seed of new life.” Wait: it seems he doesn’t understand risk. True, the cells are unlikely to survive even if they stop DNA repair, but that slim chance has to be compared to the chance of surviving in a colony that does not stop DNA repair, and hence has fewer mutations. Also, one mutant cell that starts a new colony, certainly does benefit in a Darwinian sense. The rest of the colony may or may not benefit, depending whether cells without the beneficial mutation can 1. mate with the mutants, 2. exchange genes directly with them or 3. use the enzymes produced by the mutants or the enzymatic breakdown products to increase their own chances of survival. There is no noble self-sacrifice necessary. The whole business only works out if the mathematics of probability end up in its favor. How to model a colony that ends up being a group of competing clones? He has a note (24) later, that tries to explain the benefits being shared by the colony, but I don’t find it helpful, unlike the notes on varying mutation rates. Actually, a lot of what he talks about are not what you usually think of as mutations. The enzymes involved seem also to remove blocks to expression of existing genes, thus allowing use of different food sources.

Later on in talking about long term patterns in evolution, he uses words like “learned” and “acquired” with respect to adaptation. He also has cattle egrets originating in the New World, which I think is incorrect.

His chapter on creation/destruction, including apoptosis, is quite interesting. I wonder if apoptosis is a case of parental manipulation of offspring, more than of altruism. In this respect, an organism is much more of a population process than a social insect colony, where often only one can actually make copies. It’s also different from mere herds or aggregated populations. Would it be in any way possible to have an organism if cells competed with each other in proliferating? Obviously not.

Is natural selection “impossible without death?” It would simply require that populations be free to grow exponentially. Wagner doesn’t seem to see differential reproduction of phenotype as the key to natural selection. He also says, “natural selection alone does not create the world of living things.” Pross might object to that notion (see earlier posts Looking for the Logos of Life II-IV).

When he discusses organisms’ ecological niches, which he calls “lifestyles,” he says they amount to a tangible expression of a hypothesis about the world. This is another example of applying emergent properties to a lower level. What useful insight does it provide?

In the chapter on choice, chance, and necessity there’s a discussion of deterministic chaos, in which he asserts that unpredictability and indeterminism are the same thing. This is because he sees no practical difference between them, since sufficiently accurate knowledge of the input values is not possible in a physical system. He denies the reality of infinitesimals, as in calculus, calling it a mental construct. He says that no finite mind can overcome those limits. I guess that’s right, but isn’t nature (or god, which is the same thing) an infinite mind, and don’t I mean by in principle what is possible by nature? Am I just taking Einstein’s(?) position that “God does not play dice with the universe?”

I don’t like Wagner’s way of describing life as making predictions. Organisms don’t predict the future, and except in very few cases, they don’t deliberate about possible courses of action. In his effort to bring mind and meaning down to the molecular level, he’s doing violence to the language of explanation. It may be true that the same mechanisms exist in complex, multicellular organisms with elaborate nervous systems as in a bacterium, but that does not mean that all we are doing is what a bacterium does in response to varying concentrations of food in its environment. For instance, multicellular organisms with complex nervous systems have memory, something he does not talk about a lot. The automatic unfolding of the life cycle of a mosquito depends on certain other things happening around it – rain, food for the larva, vertebrate animals, etc. – but that is not in my view a prediction, except in a very figurative sense. And certainly not in the way that an astronomer, using mathematics, predicts the motion of the stars. One way of seeing that is to think how much we do rely on gut reaction, common sense, instinct, whatever in dealing with everyday life. As Socrates says, most people just act at random, much like the bacterium. So much more important, therefore, to distinguish the few times when action is based on memory, reason or principle. He trivializes this by saying only the individual can decide whether bacteria choose, because it’s just a matter of point of view, not of truth. By calling the set of characteristics that define the ecological niche of a tick, “convictions, assumptions or beliefs about the world,” he is trivializing in a vain and pernicious way the difficult human choices those words refer to. Is he suggesting we can live our lives the way ticks and bacteria do? Of course organisms’ bodies have features that can be explained by natural law. That’s what Darwin says he means by “natural selection.” Wagner is saying nothing more than Darwin said; he just has more experimentally verified examples to back it up. But I do not think Darwin would say that this means organisms themselves are making “predictions.” What do I understand more clearly by saying different genotypes make different “predictions?” He goes further and seems to claim that philosophical disputes are somehow equivalent to these “predictions.” He seems to want his paradoxes to stand, not to be resolved by shifting point of view to another level or way of looking at the problem, but instead to serve as evidence of the world’s fundamental unintelligibility.

He talks about life’s endless creativity in terms of the diversity of species, molecules and functions. The result is a vast array of interactions. Wagner says this creativity is based on the same principles as human creativity. But then he goes off on function, claiming that we can’t talk about the function of the features of organisms. He cites the bee’s barbed stinger as having no function, when there is a perfectly obvious explanation, given that workers are expendable: the potential attacker cannot stop the sting by brushing off the bee. He claims that dead bees and also cancers are the price we pay for not being locked into a world of intelligent design. The price, according to Wagner of being free of predestination is to give up knowledge of the future ( but cf long-term cosmological certainties, even if surrounded by longer term cosmological doubts). In my view all we know for sure about life is that self-replication has led to all the complexity we see. No other purpose seems necessary, but without that, what sense does any of it make? None of it seems to provide an answer to the basic philosophical question, “what is good for…?”

I think he confuses the shortcuts we use to describe our scientific findings with the science itself. Chicks that cower from shadows do not interpret the shadow as a hawk. Parasitic plants do not think that the chemical impinging on their root tips come from a tree. That’s applying concepts appropriate to one level of organization to a level where they make no sense, even if they occasionally allow succinct expression of our beliefs about what is going on. These organisms and the others he cites, except possibly in a few highly debatable cases, do not form explanations, predictions, interpretations. It seems to me his claim is in opposition to his notion that thought such as we have is embodied in material configurations, because in the case of these so-called explanations, where is the embodied form? I think if he tries to say it is in the molecules involved in the events – the retina of the chick, or its muscles, the flagellar “motor” of the bacterium or its cell surface proteins, he’s going to quickly run into a contradiction. My actions are not their own explanation, prediction, interpretation, etc. Those reside in an entirely different place from the physical embodiment of the action itself. Somehow I think he’s making the explanation into the thing explained, the conversation into its own subject, the prediction into the thing predicted or vice versa. That’s certainly a way to create paradoxes, but they don’t seem to be of the enlightening sort.

I also don’t see how describing conceptual advances in science as making choices is really adding anything. His examples actually show that after those breakthroughs, apparent contradictions could be resolved. It’s not like heliocentricity, gravitation, electromagnetism, or relativity are still one among possible choices. The discoveries did not expand choices; they eliminated many alternatives. The only example I can think of is Euclidean vs Lobachevskian geometry. In a way, you can choose either, but that’s how mathematics is. That’s not natural science. If there are choices in natural science it is either because there are different applications where one is more convenient than the other or because one or both are wrong in at least some respects. Things can be useful without being entirely correct. Carnot had his heat engine backwards, but he still developed useful ideas. You can still use Ptolemy to make fairly decent astronomical predictions.

When you see a correct mathematical proof, if you are open to truth, you don’t feel like you are making a choice to see it. You just see it. I imagine that’s how scientists feel about their work. You don’t choose a truth, you discover it, or at least you think you have.

He even invokes Heraclitus at the end, which annoys me even more because he only talks about change and strife and not about logos. He goes on about Godel’s proof and Turing’s halting problem, as if somehow this proved that his so-called paradoxes in biology are unresolvable. Again, he’s taking truths about much different things and willy-nilly applying them to other areas. It is not obvious that questions about life run up against the limits of quantum theory or mathematical decidability. There are limits, set by things like deterministic chaos, maybe, but that is not the same. And do those limit our understanding, or just our ability to forecast?

He paraphrases one article on philosophy of science that claims to refute the notion that scientific theories get closer to truth over time. I expect that there may be a valid point there, but it also seems absurd to deny that we have a better understanding of the origin of species than we did before 1859, so what is it getting at? Of course the more light we shed, the more we can see the darkness around us, but that’s not the same as his lost in the hall of mirrors analogy (p.178).

The Godel’s incompleteness theorem does show that we can’t know everything, which he points out, but I don’t see how it follows that truth is not important anymore. Mathematicians are still concerned with true and false as are scientists. Same with Turing and the computability or halting problem, but they still wanted to know what those Enigma messages really said. The logos is probably beyond our ultimate comprehension, but we don’t know enough yet to take the position that Wagner does. This is just post-modernist conceit.

In trying to argue that material and meaning are just different sides of the same coin, bringing meaning down to the molecular level, I think he confuses the logos with our everyday notions of meaning. He does finally bring in the logos, in a suggestion that we try a “logocentric” perspective as a basis for a worldview (is this an echo of Husserl?) But the notion he suggests as a basis is “meaning.” I don’t recall that as one of the possible definitions of logos, although it makes some sense. Still I doubt that “meaning” in Wagner’s book aligns well with “logos.” His thinker, taking a certain point of view, seems to be saying, “listen to me,” not “listen to the logos.” He’s got the paradoxical part partly right, and he’s right about strife, but I think he has the logos wrong. Only a little bit: he is clear that you can’t simply choose to ignore gravity. That’s apparent in his concluding sections, The solitude of true choice and The choice to choose.

His whole approach seems to lean to much towards making man the measure of things or possibly to blur the distinction between man and the things around him. I think he’s trying to have it too many ways at once.

Palearctic excursion to the Iron Age

Robb, Graham. 2014. The Discovery of Middle Earth: Mapping the Lost World of the Celts. W. W. Norton & Company. 416 pp.

Graham Robb first conceived of the ancient Celtic map of the world and had an inkling of the mysterious Mediolanum in a cottage on the upper Thames. The first line on that map was the ancient Via Heraklea from Sagres at the southwest tip of Spain to the Matrona Pass in the Alps a thousand miles away. This line is that of the angle of the midsummer sunrises and midwinter sunset of two millennia ago. What he discovered, as it gradually unfolded, turned out to be a grid of places, extending over that whole region and beyond, even to the distant corners of the British Isles, which was the world of the Celts, the diverse cultural and linguistic grouping of peoples that dominated the region before the Roman conquest. Robb depicts them as a scientifically and mathematically advanced society, who, without GPS or Google, nevertheless had a network of map locations, sacred and military, connected by roads and tracks, or simply by the bearings of sunrise and sunset, which among other things, would have facilitated long distance travel. Messages could be relayed by shouts from carefully chosen points or by signal fires, much faster than horses could travel, as noted by Caesar in his Gallic Wars.

Celtic culture lasted from possibly the late Bronze Age until the extinction of the Druids around 600AD. An Iron Age society that was literate, to judge by surviving writing tools and inscriptions, but who left few written records of their religion, culture, etc. Much of what we can learn suggests strong influence from the astronomy and geography of the Greeks. Most of what we know is second hand from the Greeks and Romans, with some possible corroboration from ruins, coins and other artifacts.

Robb is a geographer/historian, author of books on Paris and provincial France. Place names are key evidence for his inquiry into Celtic prehistory. Often the places themselves are undistinguished hillocks, valleys, low ridge tops, few producing any significant signs of habitation or artifacts. What they represent are not forts or settlements, which follow the dictates of the natural environment, but nodes in a cartographic net laid over the land, following the dictates of the heavens, particularly the polestar and the sun. He shows how the Greeks’ knowledge of geography was carried over by the Celts, tied into the great sacred centers of Hellas, like Delphi. This seems to have worked well even in the dense and nearly trackless forests that covered much of the region (now reduced to small, heavily managed remnants) and that contained many of the sacred places of the Celtic culture.

Of the Druids, he says their twenty year course of study taught the size and shape of the earth and the universe, the motion of the heavens and stars and the will of the gods. Using Pythagorean geometry, they could map the lines of the meridian, equinoxes and solstices onto their lands, basing the system on the great center at Mediolanum Bituriges (Chateaumelliant) and the Gallic capital at Alesia, the place they made their last stand against Julius Caesar. Robb ties the Druids’ cosmology and geography to the politics and military strategy followed by the Gauls, which eventually proved to be their weakness in the face of the ruthlessly pragmatic Romans.

Rome ended up pursuing the remnants of the Druids to the farthest ends of the British Isles, and the firm establishment of Christianity seems to have snuffed out this remarkable culture, at least its Greek-influenced scientific understanding of the cosmos. Robb ends with an exploration of the traces that remain in the Roman and “Royal” roads and ancient sites in England, Scotland and Ireland. He ties this to historical events, like the revolt of Queen Boudica. He offers his own anecdotes of searching for the traces of the lost world among the shopping centers, parking lots and housing developments of modern England. Human history has left deep marks on the surface of the Earth, not all of which are easily seen and touched, but which are accessible to those who know geometry and astronomy.

This book is full of ancient and modern geographic detail and full of historical speculations as well as documented accounts of wars in Gaul and Britain and journeys undertaken by intrepid Celtic tribes to distant parts of the world. There is a strong sense of might have been, had the conquering Romans not been so efficient at crushing the resistance they encountered from these astronomer-warrior-priests.

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.