Biology

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Table of Contents

• 1. Personal Background
• 2. History
• 3. Introductory Texts
• 4. By Topic
  • 4.1. Biochemistry -- protein folding
  • 4.2. Biochemistry -- metabolic pathways
  • 4.3. Cell
  • 4.4. By classification
  • 4.5. By location
  • 4.6. Natural History
• 5. References

1. Personal Background

My earliest recollections of nature were the woodland and pond behind our house in Kentucky. We would tramp through the woods, chase rabbits, built forts, and climb trees.

Then my family moved to Washington (uphill and inland a couple of miles from Puget Sound). Portions of a hilly farm had been bulldozed to make way for suburban houses. There were still horses, cows, and chickens nearby. There was second-growth forest behind the house, and a bit of old-growth forest along the road. There were grouse in the thickets, raccoons everywhere, and an occasional coyote. Climbing to the top of a massive cedar, we could see a broad sweep of Puget Sound.

Where the bulldozers had run, the soil eroded immediately into gullies so deep you could get lost a few feet from the house, and there were mud flats where you could sink to your waist. The parents along the street put in a great deal of work to stabilize the banks, pickaxe the hardpan, sift rocks, fill in gullies, fertilize, water, and tend to fresh lawns, flower gardens, and store-bought trees. Volunteer alder, elderberry, and blackberries took over where no one paid attention.

When tent caterpillars came, we sprayed. The portions were very approximate, we wore no protective gear, and we often sprayed upwind. Who knows how thoroughly we poisoned ourselves and our land? By the end of the 1960's we were reading Carson's Silent Spring. We quite spraying and cut-and-burned the infestations instead.

In the spirit of 1970's-back-to-nature, the family decided to chop up part of the back yard to make a vegetable garden. The soil was hardpan just below the surface, but after many tillings and some pick work we managed to get the garden going. (Also in the spirit of back-to-nature, my girlfriend (now wife) and I spent time living off the land on Orcas Island. Fish, clams, mussels, limpet stew, sea urchins, boiled nettles, etc.)

I completed a degree in cellular and molecular biology (equivalent these days of combined "biology" and "biochemistry"). My wife and I then moved to the Tricities, where I ran the Biomedical Information Center and she completed her nursing degree. We spent time out in the desert environment with cactus, scorpions, and rattlesnakes, and marveled at the springtime flowering.

In time my parents moved. My wife and I bought the place and continued to coax life back into the land. We did mulch, compost, power tilling, double-dug, no-till, more plantings, bird feeders, etc. My wife watches over it all with careful attention to each living creature, plant or animal.

There is now plant life everywhere. The soil is alive. Frogs sing in spring. Songbirds get the cherries, while we collect the plums and apples. We contest with the squirrels for walnuts and filberts. Hummingbirds winter over. Hawks and eagles visit. As global warming changes our local climate, we are shifting from formal lawns to native groundcover. And we have just added a flock of chickens (with protection from hawks of course).

2. History

We have been biology-aware since long before we were humans. Modern man (Homo sapiens sapiens) has been hunter, food-gatherer, herder, farmer, and observer of nature since prehistoric times. We are still learning. In many ways, biology is still in the "natural history" phase of scientific maturity.

My choices for key turning points in our understanding are:

• Renaissance artists: Anatomy

  This effort made clear there were mechanical devices involved. There were joints and stresses and tubes and pumps. We continue to learn that it is an incredibly complex mechanism, but the anatomy movement is what replaced myth with observation.

• Linnaeus: Classification system

  Life-on-Earth is prodigiously varied and complex. The classification scheme gave a way to keep track of the specimens. We've since learned that evolution and DNA are the reasons these groupings work, but the classification scheme got us asking the right questions.

• Darwin: Theory of evolution

  The idea had been around for a long time. Darwin put detailed observations together with the hypothesis and made it a theory. We have learned that the details aren't as tidy as he reported, but he did put it in play.

• Hooke: Cell theory

  The microscope led to a major breakthrough in understanding: All life is made of cells. We've since learned a lot about internal structure, and we've yet to understand how that structure arises from physical forces, but the basic idea of cells was revolutionary.

• Pasteur: Microbe theory of disease

  The microscope also let us see what had been making us sick: Little one-celled animals. We've since learned that there are also viruses and prions, but the breakthrough was discovering that little critters can have big effects. Again, there is a very common sense understanding of what's happening once you can see it directly.

• Mendel: Genes

  He didn't know why it worked, and his results are statistically too-perfect, but he did get us onto the path of understanding inheritance. We've since learned about DNA, but that is just the mechanics.

• Lorenz, Tinbergen, von Frisch: Ethology (biology of behavior)

  This goes right back to hunter/observer. The difference is that instead of just noticing behaviors, you experiment to tease apart their constituent parts. I'm convinced this was pivotal in raising the notion of "emergent behavior", which has become the unifying concept of all complex systems (biological or not).

• Watson, Crick: DNA

  This bridges the gap from quantum chemistry to observed phenotypes. We've since learned that actual gene expression is mediated by local environment, but understanding DNA gives us hope of understanding biology at the chemical level.

• Carson: Humans-can-impact-ecology

  Obviously, people have observed the impact of human behavior on the environment for millenia. Also, ecological studies of food chains, energy transfer, nitrogen cycles, etc. were being done prior to Silent Spring. But I am convinced the book is what inspired an explosion in awareness (and funding) for such studies.

  It also brought the complexity of the biosphere into the popular debate. Environmentalists were no longer just "bird watchers" and "tree huggers", but scientists with facts-and-data to show that this pollutant or that housing project would have specific results. It was up to the body politic to weigh the tradeoffs.

3. Introductory Texts

I happen to have Campbell (campbell93) on my shelves. I presume there are more recent editions, and there may be better treatments. However, this one is solid and usable as-is.

At the introductory level, you are absorbing some chemistry, a bit of history, and a lot of hints about things that are in fact extremely complex. At best you expect a text to setup your wetware neural nets so that the real details will fit in smoothly, should you happen to go further.

Here is the problem:

Start with first principles, with Big Bang and quantum field theory and quantum chemistry. We can't solve the problems analytically, and at the size of biochemicals, we can't solve them numerically.

So we take a leap of faith to the next level of structure: DNA/RNA/protein folding. We can barely get the sequencing down, and even then we can't do protein folding. Even if we could, we couldn't even begin to solve for the full chemical processes inside a cell. At best we can look with electron microscopes, and do nuclide tagging, and ferret out some of the intra-cellular mechanisms. We can work out how it generally works, but can't simulate a specific cell.

Another leap of faith: Multi-cellular organs and organisms. Interactions at cell walls, receptors, embryology, chemical gradients, organs, physiology, etc. You have to think in terms of control systems and feedback loops. Chemistry is just the (very complex) mechanism for doing control systems. Just when you have barely worked this out for simple cases, you run up against neural systems. You spend decades teasing apart neurons, and testing the effects of external stimulation on specific sections of the brain, but can't simulate much less compute a specific human brain.

[At this point the behavioral sciences diverge. AI researchers use what we know of the brain as inspiration to build artificial thinking mechanisms, without reference to chemistry. Biologists build simulations of as much of the brain as we understand, and use that to help pose questions to be answered by testing real brains. Either way, we are a long way away from a rigorous science based on first principles.]

Another leap of faith: Ethology and Psychology. We assume the brain works somehow, and that the results manifest as observable behaviors. But the behaviors are so complex (or their relationship to stimuli so non-trivial) that we must hypothesize entire internal mental models as mediating layers. We trust that as neuro-science gets better, we'll understand these models in terms of neural connections and receptor sites. But we can't wait for that. We push ahead.

Another leap of faith: Ecology. Organisms interact with one another and with a complex non-life water/mineral/chemical context. It is hopeless to try to model this at the level of quantum chemistry, or even with simulations of organs. We have to treat organisms as whole units, and model their interactions with a sparse set of attributes. Even so, the problem is prodigiously complex for a pond or an ocean reef or a watershed. For one thing, where do you draw the lines? It is all connected, and those connections have serious impact on local conditions. Further, in studying the behavior of at least some creatures in the mix, we suspect purposeful, will-ful actions.

Another leap of faith: Consciousness. When it was a garden slug, or even an octopus, we could get away with thinking just about models and stimuli/response mechanisms. But under a microscope, a human neural net looks a lot like those, and we *know* the person is conscious. Was the octopus? Was the slug? Where in the scale of increasing neural complexity does consciousness kick in? Why can't we see it under the microscope?

In summary, biology is complex. An introductory text can only show a few postcards from the journey. A good text will choose postcards which make later journeys understandable.

4. By Topic

[I've read so many over the years, it is daunting to go back and find citations. I'll fill these in as time permits.]

4.1. Biochemistry -- protein folding

See chemistry.

4.2. Biochemistry -- metabolic pathways

Intro texts cover the basics. A more advanced text provides the reaction rates, energies, etc. [Need to find a good current text.]

4.3. Cell

The cell is the basic unit of all known life. It was amazing enough to discover it at all, and to later visualize its internals via electron microscopes. But the real payoff is to trace the structure and behavior back to specific molecules and their reactions. Thus the study of cells is largely a study in biochemistry. See cooper97

4.4. By classification

As far as I can tell, every chunk of the classification tree, at every level, has one or more texts. You are looking for a treatment that is exciting to read yet covers anatomy, physiology, diseases, behavior, population dynamics, and interaction with environment.

For microorganisms we have brock2000. Each species can be a career in itself, sometimes for odd reasons. Thus, some fossil shell-forming creatures are associated with oil-brearing formations and thus have had extensive research.

For multicellular organisms, Agricultural plants and animals are also well covered. You can get material at the level of a farmer's or pet owner's handbook, an ag extension agent's pamphlet, or a veterinarian's reference texts. See Sustainable_living, section on traditional farming. Species used for laboratory experiments (fruit flies, rats, pigs, rabbits, and chimps) have even more detailed texts and compendia, with every aspect of anatomy, physiology, disease, etc. covered. In fact, these species are usually better understood than humans. Humans are well covered by medical texts.

Beyond that, you are often looking for a researcher who made a life's study of some critter, and just happens to also be a good story teller. E. O. Wilson's books on the social insects comes to mind.

4.5. By location

An ocean, a pond, a stream, a watershed, a forest, a jungle, etc. May cover a single example, or may survey many examples around the world. [Find citation for "Jungles"]

4.6. Natural History

Biology is so vast, that we cannot investigate it all in the laboratory or even in field experiments. Sometimes all we can do is go out and take notes on what we find. This is natural history.

Field Guides help you recognize a specimen in the wild. Usually the clues are visual "field marks" ("has white tuft on top and black throat patch"). For birds, learning the sounds is important. For mammals, learning tracks is important.

Hunting and food-gathering books cover behavior and environmental context. Sustainable_living, section on hunting and food gathering. These were historically (and prehistorically) observations from those who spent a great deal of time in the area and knew the creatures from observation. These days this insight is augmented by field experiments (radio tagging, scat analysis, etc.).

5. References

brock2000

Michael T. Madigan, John M. Martinko, Jack Parker. "Brock: Biology of Microorganisms", 9th ed. Prentice Hall, 2000. ISBN 0-13-081922-0.

campbell93

Neil A. Campbell. "Biology",3rd ed. Benjamin/Cummings, 1993. ISBN 0-8053-1880-1.

cooper97

Geoffrey M. Cooper. "The Cell: A Molecular Approach". ASM Press, 1997. ISBN 0-87893-119-8.