Wednesday, November 23, 2011

Too much or too little?

Ecology seems to me like a hodge-podge of different ideas. A result of this (or a manifestation or a cause?) is that we teach and learn ecology as a hodge-podge. The single overarching theme is levels of organization, typically as individuals, populations, communities, ecosystems, landscapes, and global issues, with a generous dose of climate, geology, and geography at the beginning. Applications, statistics, experimental design, and primary literature are scattered throughout.

Quick perusal of two evolution textbooks (Ridley, and Freeman & Herron) showed me that they do not have chapters on "The Physical Environment" or "Biomes" or "The Earth's Climate System." The evolution textbooks instead focus on the math and biology that is universal.

What if a book laid out ecology completely independently of natural history and environment? Would the books look the same? Do we need context? If we lead with context (e.g., a pond, a forest, a grassland) what do we gain, what do we lose?

Why do we lead with the physical environment? Perhaps because we have been ecologists for at least the past 2 my, and we know a lot?

What if we learned B = aM^z and dX/dt = aX - bX^2 before we learned that trees dominate the eastern US, and deep water bodies are dark?

This same question plagues the niche vs. neutral ecology. Evolutionary biologists learned long ago that it is both, in different measure. Ecologists and humans generally are plagued with the notion that niche matters. It makes it hard for us to think outside the box.

US Government as Central Dogma of Molecular Biology

Spoiler Alert: There is nothing new here. However, writing it helps to form the thoughts in my own head ....

Complex adaptive systems
A colleague of mine -- a very successful molecular biologist -- recently gave a Sigma Xi Researcher of the Year presentation. In it, he made the relative specific analogy relating the central dogma of biology to the operation of the U.S. federal government. It blew my mind. It was is SO cool to me, because I take seriously those "far fetched" analogies between different complex adaptive systems. I realize that others have made these analogies before, but they are cool to me, because I rarely hear them.

Social institutions, such as governments, are complex adaptive systems under selective pressures. Each governing institution acquires mutations which maybe retained or discarded. Each governing institution competes with other governing institutions for limiting resources. Different institutions exhibit different levels of survival and growth and spread. These institutions tend to be passed on from generation to generation because humans have written records, and also simply and more importantly, humans remember what they did yesterday and twenty years ago, and change is both intellectually challenging, and financially restricted.

Governments exhibit
-- phenotypic variation,
-- heritable phenotypic variation, insofar as governments persist and self-replicate,
-- fitness differences among variants.

As a consequence of these phenomena (1), governments tend to evolve. As you know, evolution does not always optimize performance. Rather, they undergo probabilistic responses to selective pressures,. It is possible for these responses to result in objects which are poorly suited for future conditions. Evolution is always backward-looking.

Social Darwinism? No, not in the original sense.

The above smacks a bit of "Social Darwinism." However, the earlier incarnation of that phenomenon was used as an excuse for greed and imperialism (2). In the past 50 years, however, strong evidence has accrued that cooperation can easily evolve and is an evolutionary stable state (3). All successful societies or nations rely heavily on within-group cooperation. It seems further that cooperation among nation-states provides increased fitness as well. This seems like a no-brainer, given that nation-states are themselves composed of interacting groups that cooperate as well as compete.

One of the primary requirements of the evolution of cooperation is that fitness of individuals within groups is increased through the cooperation. This central criterion is often easily met.

Another important criterion for the emergence and maintenance of cooperation is repeated interactions among the same agents so that "learning" can occur. Repeated interactions is the key difference between the standard Prisoner's dilemma game, where cooperation is not advantageous vs. games in which cooperation is advantageous. [I put "learning" in quotes, because it need not be learning in the usual sense of a cognitive process by an individual, but rather can be an adaptation to respond to cues given by cheaters that they are cheating. "Cheating" is defined as the receipt of benefits of cooperation without incurring the costs of cooperation and reciprocity.]

The ease with which cooperation can arise, and become a stable equilibrium does not exclude the possibility that cheating cannot also arise. However, under easily met conditions, if a "mutation" does give rise to cheating, it can be eliminated, or kept at low levels, depending on the conditions.

References cited

1. Endler, J. Natural Selection in the Wild. Princeton monographs.
2. Wikipedia, 2011,
3.  Nowak, 8 December 2006, Science; Nowak et al. 26 August 2010. Nature.

Wednesday, November 9, 2011

Oops. Another poorly implemented assignment

For a graduate class I asked grad students to prepare for a Monday class by reading a text book chapter and writing down two research ideas complete with a very short literature based rationale. In class on Monday they began collaborating, and for Wednesday's class they wrote 2-3 page preproposals. In class on Wednesday, they reviewed each others' preproposals. I had given them more guidance (see Week 12 in the linked document), but this was the gist of it.

The preproposals were horrible. Although the grammar was fine, and some of the ideas might have been adequate, but the ideas were not well-supported by the weekly readings nor based on deep thinking about the material I had assigned. I think some of their ideas came from their own research projects, but they did not construct convincing arguments as to why anyone would invite a full proposal.

I need to break down the assignment into smaller, more explicit pieces. For example:
"From the material that you have read for this week,
1. What are the important topics in this area of this sub-discipline of ecology?
2. Of the important topics that you identified (for this week, within this area of this sub-discipline), which topics have a sufficient literature upon which you can build, that is, to build a convincing case that your new idea will also be important? [Cool ideas are cool, but they have to be based upon evidence, and evidence is presented in the literature. Mere cool ideas don't get published or funded. A well-reasoned cool idea gets both published and funded.]
3. How do you convince a reader that (a) this area of ecology is important and interesting, and (b) our research idea(s) is likely to bear fruit (i.e., become an important contribution)?"

I had students work in fairly large groups 3-5, and I think it is hard for each member to contribute in a substantial way to the writing. I think the groups should be 1-3 students in size. I will have to pick a size for next week. Perhaps individuals....

When I asked for feedback, students expressed the concern that, while they enjoyed it, they would have gotten more out of lecture. I think that is because they are used to being lectured to by bright, engaged faculty (my colleagues), often on topics not well covered in the reading. In contrast, I am letting Peter Morin lecture (through his text book), and I want the students to grapple -- get sweaty -- with the reading. That is why I assigned both exploratory and formal writing exercise, in order to enable them to dig into it. They did a poor job of it, because I did not give them enough guidance.

I think that they each need to do their own next week, and bag the group work. We will use class time for that. Maybe I will make pairs (but not 3's) optional....

Sunday, November 6, 2011

Pathogen-mediated promiscuity

If the spread of (human) sexually transmitted diseases requires humans to have sex, wouldn't selection favor pathogens which increase our promiscuity? Very interesting...someone smart must have already thought of this and figured out the some level...maybe there is something to add?

Can joy be modelled with a SIR disease model?

I guess the better question is how, and whether it would make sense or lead to interesting hypotheses. I just like the idea of modelling the spread of something wonderful using a model of something we think of as bad. :-)