Month: September 2015

Looking for the logos of life VI: Gaian analysis

Williams, G. R. 1996. The Molecular Biology of Gaia. Columbia University Press. 210 pp.

This is a book I wish I had read when it was first published. Williams lays out so many interesting scientific problems so clearly that I would have expected that it would have considerable influence on subsequent research, somewhat as Schrodinger’s What is Life? the subject of the first post in this series. I was somewhat surprised that Google Scholar only finds a few citations of this book. Perhaps William’s scholarly papers have been more extensively cited.

William’s goal is to see why the famous Gaia hypothesis has attracted so much popular interest, while receiving little positive notice from practicing biologists. He wants to determine whether the hypothesis is actually useful, either as a metaphor or a verifiable model of the function of the biosphere. The central question is whether it can explain why the Earth has remained habitable throughout the several billion-year history of the biosphere. That it has is not in question: all evidence points to the occupation of Earth continuously by the descendants of the first living things, which originated 3.5 billion years ago. This strongly implies that the earth has not frozen or boiled and that life has not otherwise been poisoned or starved during that time. Some factor or factors has kept the conditions on at least some of the Earth within the ranges essential to living organisms of some kind. In fact the conditions have not become intolerable to land plants and metazoans at least for hundreds of millions of years. The concept of the continuity of descent, expressed beautifully by Loren Eisley’s image of each of us trailing a long chain of ghostly ancestors, stretching back to those first living things, is to me one of the most useful ways to imagine what evolution is all about. If there had ever been a break in that chain, you and I would simply not exist.

The Gaia hypothesis states that this stability is the result of homeostasis: the regulation by negative feedback (like a thermostat) of a living super organism, Gaia. In its strongest form, the hypothesis is that life on the planet, the biosphere, regulates itself just as a single organism, whether a single cell or a multicellular individual, does. This idea has an obvious appeal: just as networks of interacting macromolecules make up a cell, which is capable of regulating its internal environment, so do networks of interacting cells make up tissues, organs and whole organisms that are able to regulate their internal environment. At least some organisms, like ants and bees, live in self-regulating colonies. Why shouldn’t all the organisms on earth form a self-regulating system?

Williams answers that for biologists the problem is how such a self-regulated super organism could be put together in the first place. Natural selection can explain how self-replicating systems can evolve, because natural laws can discriminate among multiple variant copies that compete for limited resources. The Earth is not self-replicating. There are no variants among which nature can select. There is only one. This problem led Lynn Margulis to argue that Darwinian evolution was not really that important, and that symbiogenesis was the true explanation. Margulis’s great contribution was the discovery that certain cellular organelles, chloroplasts and mitochondria, were once free-living organisms. More broadly, she showed that evolutionary advances by the incorporation and integration of separate living parts were behind the origin of the eukaryotes and that similar processes continue to operate in the form of horizontal gene transfer. The trouble with claiming that symbiogenesis is a replacement for Darwinian natural selection is that it appears obvious that all such new combinations remain subject to survival of the fittest.

Would it be possible for a Gaia-like system to arise in part of the biosphere and then spread, supplanting the less effective parts? Only if it’s self-regulating effects were confined to where it first existed, as might work for something like the terrestrial nitrogen cycle. It seems less likely where the atmosphere and oceans are involved, since they carry the products all over the planet.

Williams also points out that there is more than one possible explanation for the continuous suitability of the Earth for living things. He lists four: luck, inertia, equilibrium, and homeostasis. He analyzes each possibility in turn, and shows how each may contribute to the persistence of habitable conditions. In the case of homeostasis, he distinguishes between negative feedbacks from purely physical and chemical forces involving the lithosphere, atmosphere and hydrosphere and ones that require the biosphere. It is possible that even if there were no life on Earth, the temperature would stay within habitable limits (basically the range where liquid water can exist) just because of feedback among the temperature and the release and sequestration of carbon from air, ocean and rocks.

According to Williams, if you try to assess this possibility, the difficulty is that today the rates of almost all steps in this process, except volcanism, are under catalysis by organisms. We don’t know what an abiotic planet would be like. As of the time he wrote this book, not enough was known about the global chemical cycles at the molecular level to settle the question how much life matters. He gives an example of what was known about the molecular biology of nitrogen to show how complex the regulation of these cycles is likely to be. Nutrients move among four pools: inorganic forms in the lithosphere, hydrosphere and atmosphere; nutrients in forms available for uptake by organisms in the same three spheres and the biosphere itself as accumulated by organisms; nutrients incorporated into living cells and tissues; and bio products, from the cellulose of wood in trees to dead plants and animals to dissolved organic compounds to fossil fuels. All these are connected by flows and many of those flows (mobilization, assimilation, regeneration, sequestration and excretion) are controlled by living organisms, via enzyme-catalyzed, energy-requiring reactions.

I like this book because Williams thinks about Earth and ecology very much as I do. I learned from my professors at Cornell in the early 1970s about five processes of ecology: population dynamics, natural selection, energy flow, nutrient cycling and cultural evolution. These are closely interrelated ways of looking at the overall phenomenon of life on earth, or as I like to define ecology, the structure and function of the biosphere. Is the function of the biosphere to regulate the habitability of the planet, or does the planet have the property of remaining a stable habitat for life without life being involved? You can’t really answer that question with only one habitable planet and one biosphere to study.

I will add that I tried to read another account of the same problem of why the Gaia hypothesis had been largely criticized by biologists while being so well received by non-biologists: The Gaia Hypothesis: Science on a Pagan Planet by Michael Ruse (University of Chicago Press, 2013) I did not find it helpful, being mostly a historical narrative, with a focus on a wide variety of –isms, such as Platonism, Mechanism, Organicism, Hylozoism (the belief that all matter possesses life) and Paganism. I have never been much interested in –isms or cultural explanations for why people accept of don’t accept given ideas. Williams gives us a scientific way of thinking about the problem.

Assessment and the seeds of learning

“Though I do not believe that a plant will spring up where no seed has been, I have great faith in a seed. Convince me that you have a seed there, and I am prepared to expect wonders.” – Thoreau

I have taught for forty years at a state institution that started out as a small state college in 1971 and has become, as of 2015, a university, at least in name. For about the past five years, the main thrust of my institution’s curriculum development efforts have been geared towards developing detailed lists of “Essential Learning Outcomes.” These are objectives that are supposed to be evaluated on a three step ordinal scale of “aware, competent, or skilled.” Faculty are being told to develop ELOs for their academic programs and individual courses and to align their assessments to their ELO rubrics (or maybe it’s their assessment rubrics to their ELOs). The goal is to demonstrate that students are learning very specific skills and “competencies” as a direct result of what happened in the classroom, during or immediately after the “activity” took place. This is no way to assess real learning, which is something beyond the reach of techniques based in so-called “learning research.”

The current drive to assess “learning outcomes” is equivalent to demanding that teachers produce fully developed knowledge in the minds of their students immediately. It it like demanding that a gardener show you a fully developed garden of plants, with flowers and fruit, in a day, or at most a few months. Such a garden can only be a hot house full of exotic plants in pots or a heavily tended garden, using every artificial help available. Hothouses and artificial landscapes have no organic connection to the environment in which they are growing. Once the heat, water and fertilizer are are cut off, the plants die.

This botanical metaphor is quite revealing. Just as there are subjects that can be learned quickly and retained if the mind is well prepared (the minds of children are extremely retentive and often not overly cluttered), sometimes the effect of seeding is immediate, and plants take root and begin to grow. More often in teaching, the best that happens is that a few weeds of false opinion are rooted out or at least identified, preparing the mind to receive something true. Teachers of science know that this weeding is essential: students do not understand and retain correct ideas if they continue to harbor false ones that interfere. Most seeds do not germinate right away. Indeed, they often wait years to develop. The teacher must have what Thoreau called “faith in a seed.” In some future circumstance of the student’s life, the environment of the mind may be right for this idea, and then it will develop. Most of the important things we learn in our lives have to develop like natural vegetation, through a process of succession in which different ideas only grow under the circumstances that are suited to them. Because natural communities have a “seed bank,” of dormant seed accumulated over many years, as well as a constant influx of seeds from outside, as one plant dies, another will immediately occupy the spot where it grew. Often many new plants will spring up and compete for the space until one takes over, or a plant that has been waiting, as it were, in the shadow of the current dominant one, will quickly grow up to fill its place.

I the human mind, if it remains active and receptive, old ideas are gradually replaced as the short-lived ones fade and are replaced by those that live longer. These may be new, but more often, I believe the best ones were first encountered earlier in life and have lain dormant, like seeds in the seed bank, or have been waiting in the shadow for us to reject an idea that up to then had been dominant. Gradually, one develops a set of ideas that have stood the test of time and the challenges of surviving in a complex world. If the good ideas are there at the time when circumstances become right for them, they will grow and flourish. All the teacher can do for the minds of his young students is to try to plant ieas of lasting potential value and have faith that they will eventually grow.

I am extremely grateful that I had the benefit of a home and school environment that made me reasonably competent as a reader, a fair master of math up through algebra and geometry, with a little bit of Latin and French, before I went to college. Furthermore, these were taught me in a way that did not kill my enjoyment of learning.

I attended Saint John’s College in Annapolis, Maryland and Santa Fe, New Mexico, as an undergraduate. The core of the all-required curriculum was the seminar, a twice weekly evening class, where for two hours or more around 15-20 students and two tutors discussed a sequence of great books, from Homer and Dante to Darwin and Freud. Discussions began with a question from one of the tutors and then went, slowly or sometimes explosively, around and through the text, following the argument where it led, occasionally being set back on course by the tutors. Some tutors were more active in pushing the question; others preferred to sit back and see what we would come up with. The outcome of a Saint John’s seminar was that, as the etymology of “seminar” implies, seeds would have been planted in the minds of the participants.

Outside of class, we students often wondered what it was we were learning. It was very hard to summarize what any seminar was “about,” and impossible to state in a few words what had been concluded from the reading and discussion. Attrition at Saint John’s was quite high, and a frequent reason was the sense that we were “not getting anywhere.” Math tutorial and laboratories, another major component of the curriculum were subject to similar criticism, as we worked our way through texts like Euclid’s Elements, Newton’s Principia and Maxwell’s Experimental Researches on Electricity. I stayed with the Program to the end and went on to a successful graduate career at Cornell in ecology. I have never regretted my Saint John’s education and still view it as the best undergraduate program in the country.

I did learn a lot of things while at Saint John’s: The rudiments of Greek and some important ideas about geometry and arithmetic, the nature of mathematical proof, etc. I could recollect some of the specific content of the many books I read. But what was really valuable was that the experience made me confident in my ability to understand texts, to dissect arguments and to hold my own in discussion. This preparation of the ground enabled me to breeze through most of what I was required to learn in graduate school and to pass my qualifying exams without difficulty. Even there, though, it was the seeds that were sown, especially while reading many key papers in ecology assigned by my professors, that were most valuable. These came to fruition over my years as a college teacher. There were quite a few subjects, animal physiology for example, which I took and passed with A’s, from which I can recall almost nothing, yet I still have the notebooks and final exams to prove I once knew them very well. I passed the graduate reading exam in German (a particularly dreaded “assessment”) without much sweat. Having, however, no necessity or leisure to read anything in German, I forgot most of it in a matter of months. Short term memory stuffing is easy; long term requires a lot more application, at least for me (and many of my students).

Many of the great books from Saint John’s and benchmark papers from my Cornell years are still part of the courses I teach, both in the Environmental Studies Program and in General Studies. I still lead discussion-based classes. Over the years, I have received some, but not much, support for this approach from colleagues and administrators.

I hear from many of my former students who have gone on to successful careers. Often I am surprised by the places they have ended up. Rarely is the memory I have of how well they did a predictor of how brilliantly they have succeeded. Many an ugly duckling has proved to be a swan. Of course, the love of a subject, if it is a real passion, often grows into a brilliant career, but it is not necessarily the case that those students would have come off well in assessments of their learning at the time. Quite a few were low B and even C students in many of their courses.

Colleges and universities and those that fund them have to learn to deal with the fact that short term assessment is not a good predictor of future success. Changes made in teaching methods and curriculum will not show up until long after the students have gone on. It is far more important to look carefully to the quality of the seed being planted. This can only be done if you have a faculty who are willing to think long and hard about what things are important to include in the curriculum and who are not forced to waste their time developing short term assessments, rubrics and other specious projects that only value pretty but ephemeral flowers.