What he said

I’m politically pretty moderate, with some very strong opinions on specific issues that cross party lines.
The current administration is in favor of:

  • spending a lot of money we don’t have
  • reducing civil liberties in ways, like secret trials, that this country was started in order to avoid
  • moving beyond legitimate self-defense to miltary adventurism
  • protecting the oil industry instead of getting cost-effective energy technology that frees us from middle east dependence and smog
  • pursuing a foreign policy that emphasises weapons of destruction at the expense of weapons of salvation

I’m pretty worried about the consequences of these policies. They could make this country and the world a lot worse for a long time.
(The Economist article might cost money to read; it’s Jeffrey Sachs on proven-effective ways of reducing poverty and suffering around the world. If you want the article, I’m pretty sure I can email it in a way you can read it for free, so ask.)

The Origin of Animal Body

The Origin of Animal Body Plans by Wallace Arthur

This is a test of the BookPost feature written by Paul Bauch. BookPost is a web service that lets you post book reviews while browsing the book on Amazon. Bookpost uses a JavaScript bookmarklet that calls an ASP script that uses the Amazon API to pull in the book’s title, author, and URL; and the Blogger API to automatically post to your weblog.
Unfortunately, the Amazon API does not seem to cover reviews; I would love to be able to cross-post reviews to Amazon and the weblog!
This book looks nontrivial but fascinating. Into the to-read queue it goes. So many books, so little time.

Acquiring Genomes: A Theory of the Origins of Species

Acquiring Genomes: A Theory of the Origins of Species contains some fascinating biology surrounded by a muddled argument in a poorly organized book.
Authors Lynn Margulis and Dorion Sagan are advocates of a theory that compound cell structures evolved by means of symbiogenesis — symbiosis which becomes permament.
The best-known example of symbiosis is lichen, in which a fungus lives together with an alga or cyanobacterium; the organisms propogate together in a joint life cycle. The book includes many other wonderful examples of symbiosis. A species of green slug never eats; it holds photosynthetic algae in its tissues, and it crawls along the shore in search of sunshine. A species of glow-in-the-dark squid has a organ which houses light-emitting bacteria. Some weevils contain bacteria that help them metabolize; others have bacteria that help them reproduce. Cows digest grass using microbial symbionts in the rumen; humans take B-vitamins from gut-dwelling bacteria.
The associations take numerous forms; a trade of motility for photosynethsis; nutrition for protection; one creature’ waste becomes
another’s food. The authors argue that the posession of different set of symbionts can leads to reproductive isolation and speciation. Much more than that, the authors argue that all species are the results of symbiosis that became permanent and inextricable. The bacteria that fix nitrogen for pea plants are no longer able to live independently. The biochemistry of the symbionts become intertwined; the symbionts together produce hemoglobin molecules to move oxygen away from the bacteria; the heme is manufactured by the bacteria, while the globin is produced by the plant.
The final symbiotic step is a fused organism. The authors contend that algae and plants developed photosynthesis by ingesting photosynthetic bacteria and failing to digest them. Based on research by several scientists, the authors believe that a cell structure called the karyomastigont, including the nucleus and its connector to a “tail’ that enables the cell to move, was once a free-living spirochete which became enmeshed in another bacterium that was good at metabolizing the prevalent resource (sulfur?), but could not move well by itself. The bacteria merged their genomes, as bacteria are wont to do, and henceforth reproduced together.
At least at the cellular level, the symbiogenesis argument is fascinating and plausible for the origins of the first species. Species are conventionally defined as creatures that can interbreed. But bacteria of various sorts, whose cells lack nuclei, can and do regularly exchange genetic material. Their types change fluidly. Therefore, bacteria don’t have species. According to the theory of symbiogenesis, eukaryotes, organisms whose cells have nuclei, were formed by the symbiosis of formerly independent bacteria. Eukaryotes, including fungi, protoctists, plants and animals are all composite creatures. Margulis and Sagan propose a new definition of species: creatures that have same sets of symbiotic genes.
According to Margulis and Sagan, therefore, the graph of evolution is not a tree with ever-diverging branches; it is a network with branches that often merge.
The symbiogenesis theory is a logical proposed solution to the puzzle of how nature can evolve living systems with multiple components. If you look at software as another kind of information-based system; it seems only reasonable that composition would turn out to be an effective means of creating larger, more complex units. None of the artificial life experiments that I know of have achieved this so far (although the Margulis/Sagan theory suggests a way to test this, by creating artificial metabolisms that can evolve codependency).
While Margulis and Sagan make a plausible argument that symbiogenesis is a plausible mechanism for evolution, they fail to persuade that it is the primary mechanism for all of evolution.
The authors contrast evolution by symbiogenesis with a “neodarwinist” view that evolution proceeds in gradual steps by means of random mutation. They observe that in ordinary life, mutations are almost always bad, and therefore cannot be a source for evolutionary change.
But this argument against change by means of gradual mutation is a straw man compared to contemporary theory. First of all, mutation may not be the prime source of fruitful genetic variation. The math behind genetic algorithms shows that where sexual reproduction or other genetic recombination is used in reproduction, these recombinations generate more variation and often more fruitful variation than random mutation. This may also be true in nature. Reproductive recombination may be a fruitful source of natural variation that is more important than mutation.
Second, evolutionary biologists including Stephen Jay Gould have moved away from the notion of slow, gradual change, toward a theory of “punctuated equilibrium”, positing faster change driven by times of stress. The theory of stress-driven change also helps combat the argument about the uniformly deleterious effect of mutation. In a stable circumstance, most changes to the status quo are going to be bad. In a sulfurous atmosphere, bugs that breathe sulfur and are poisoned by oxygen live well; a sport that preferred oxygen to sulfur would soon die. But if the atmospheric balance changed to include more oxygen, an oxygen-breathing mutant would be at an advantage.
Margulis and Sagan bring up the old canard that gradual change can’t create a complex structure such as a wing. However, Shapes of Time, a book about about the role of the development process in evolution, explains elegantly how substantial changes in form can be produced by small modifications in the algorithms coding an organism’s development. Margulis and Sagan don’t have any explanation for how symbiogenesis could possibly explain the evolution of four-legged creatures from fish, or humans from chimps; developmental theorists have plausible explanations for these transformations.
The symbiogenesis argument is seems strongest in dealing with single-celled organisms, where the fusion of genomes is not hard to imagine, and harder to explain in dealing with more complex life forms. The most dramatic argument from the symbiogenesis camp is that the larval stage found in many species is actually an example of symbiogensis. At some point, frogs, sea urchins, and butterflies aquired the genomes of larva-like animals. It would take a lot more explanation to make the case for this — if different creatures acquired a larval form by means of symbiosis, why would larval form always be at beginning of life cycle; why doesn’t a butterfly molt and become a caterpillar? If the animal contains two seperate genomes, what developmental process would govern the switchover from the first genome to the second. I will certainly look for other evidence and arguments to prove or disprove this one. Readers who are familiar with this topic, please let me knowif this argument has been discredited or if any more evidence has been generated to support it.
The summary of the book’s argument here is more linear and direct than the book itself. Chapters 9 through 12 focus on the area of the authors’ scientific expertise — examples of bacteria, protoctists, and fungi in symbiotic relationships, and proposed mechanisms for the role of symbiosis in evolution. These chapters are the strongest and most interesting in the book. The rest of book contains vehement yet fitful arguments about various tangentially related topics
The authors have some seemingly legitimate complaints with the structure of biological research. The authors believe that symbionts are a primary biological unit of study; yet scientists who study plants and animals are organizationally distant from those who study fungi and bacteria, making it difficult to study symbiosis. Moreover, the study of small, slimy, obscure creatures generates less prestige and money than the study of animals, plants and microbes that relate directly to people; slowing progress in the field of symbiosis and rendering it less attractive to students.
The book has a section on the Gaia hypothesis — the argument that the earth itself is a living being. The connection to the book’s main thesis is not made clearly, and the section is rather incoherent. The authors have a written a whole book on the subject, which may be worth reading; or there may be some other treatment worth reading (recommendations welcome, as usual).
The book includes a section attacking the commonplace metaphors of evolutionary biology, such competition, cooperation, and selfish genes. But the authors don’t seem to use metaphors any less than the people they attack — they have a particular fondness for metaphors of corporate mergers and acquisitions, and human intimate relationships. The use of metaphor in science has its advantages and limitations; but this book doesn’t add anything intelligent to that discussion.
In general, the authors are aggressively dismissive of other approaches to evolutionary biology. In a typically combative moment, the authors argue that “the language of evolutionary change is neither mathematics nor computer-generated morphology. Certainly it is not statistics.” The authors clearly have a hammer in hand, and see a world full of nails. In posession of a strong and original idea, the authors lack the perspective to see their own idea as part of a larger synthesis incorporating other ideas.
In summary, I enjoyed the book because of the strange and wonderful stories of symbiosis and the description of the symbiogenesis theory. But the book as a whole is not coherent or well-argued. Read it only if you’re interested in the topic strongly enough to get through a muddled book. And don’t buy retail.

Clicks and Mortar

Execution happens at ebb tide, when the hype waves have receded offshore. I was looking for The Self-Made Tapestry and found that Barnes and Noble Online now lets you search inventory of its local stores, enables you to reserve the book online for pick-up at the store, and even tells you in what section of the store it can be found. I wish that the local bookstores had this capability, but they don’t yet.
The last feature is particularly helpful for those who prefer books that aren’t clearly in one subject area. Is The Computational Beauty of Nature in Biology, Math, or Computer Science? Is The Printing Press as an Agent of Change in History, Sociology, or someplace else? Much time has been spent wandering bookstore aisles in search of books without an obvious category; this is one reason that I buy a lot of books online (of course, they could always reshelve sections on Social History of Technology and Computational Biology…).
By the way, they didn’t have Self-Made Tapestry, so I bought Acquiring Genomes instead, which is on the Lynn Margulis theory that cell organelles used to be free-swimming critters.