Books here, books there.

Oh, what a pang of homesickness I got when I went to check out ecology books at the SMC library and found out I could only have them for two weeks at a time! I miss you my old pal the Ivory Tower of yesteryear, with your term-long loans and virtually no penalties for flakiness. On the other hand, with you I spent four years fucking around, finally learning nothing more than that no matter what grand policy any government may enact in the hopes of making people be nice to each other, it never will work. Which I guess is a pretty good lesson to have learned by 22.

The real challenge for today will be studying for my bio exam thursday. Because even though I can read and enjoy and understand, like whatever evo-devo morphometrics levels of selection complex system wave action vertical zonation math science gobbeldygook, I’m still like “duh, what’s an energy activation barrier?” Those damn little molecules are just so TINY and I don’t understand where their capacity to do work comes from! Like, when ATP is converted into ADP all of a sudden I’m able to go on with my day? And not that I’m questioning the truth of this, but feedback inhibitor proteins and the production of certain psychoactive hormones in my pituitary makes the difference between me sitting in a chair crying all day and me getting up at five a.m. three days a week to bike 13 miles to school and back and LIKING IT? (Actually, what makes all the difference there is the coffee, though I’m trying hard to lay off that one).

Even a protist–all of whose chemical pathways has been or can be understood down to the last disulphide bridge in the rarest pathological quaternary structure protein–is in the final summation an unpredictable, spontaneous, dynamic, alive creature, whose existence is inexplicable and without logic. We can read the length of its entire DNA, we can map its cytoskeleton and track the motion of its motor proteins. We know about feedback inhibition of all sorts and we know that recognition and communication between them depends on nothing more than the shapes of their glycoproteins. And we know that these pathways and these structures are in their essence constant for every form of life on planet Earth, with only slight modifications and additions, yet there I am standing at the register at pinkberry, spending $10 I don’t have on soft serve with fruit for myself and Kelly, and there is no explanation for why. I understand that all life is, is the increasingly complex obedience to chemical signals. These chemical signals are math, they make sense, they are easy to model, and even to link to one another in a web, but somewhere down the column of figures there is a break, the system is no longer computable, the reasons are lost, the strings are cut and we start maybe wondering if this God person isn’t such a ridiculous idea after all.

I know I’m not going to get an A in my class by getting hung up on mystical questions, but for some reason I can’t get myself to understand molecules without them.

Shaping my research

To begin with, I want to know everything about how these species interact with each other and their environments. I want to know their ecology. I want to know where they interact, where they do not interact, and I want to be able to come up with an explanation of why.

Relative heights in the intertidal zone: At sites where both species are found, do they coexist or do they have distinct territories? If they are always separate, is the lateral zonation a result of one being more tolerant of the stresses inherent to the high intertidal zone, or of one being more able to compete with other predators for resources in the lower zone? What if they coexist on certain types of rocks and not on others? In certain types of surf exposure? What do you think is going on where only one or the other species is found?

While I’m at it, I can also see what kind of variation there is across environments: In the sizes of each species, and in their relative average sizes both where they do and do not interact. Also across latitudes, surf magnitudes, sizes of rocks, height in intertidal zone, &c &c &c.

I’ll devote a long weekend of field collecting at each of three sites, probably La Jolla, Monterey, and Bodega. How much should I trust what the Marine Invertebrate handbook tells me about the ranges of these animals? Bodega is actually outside the range of one. Should I pick two sites in addition to the sites where I know the ranges overlap to see what is going on with each species at the extreme of its range?

My study advisor told me that I am asking all the right questions, which makes me very happy, but then he told me that I need to take a year of statistics, a year of calculus, a year of physics, a year and a half of chemistry, and some upper-division biology classes before I can start getting in to grad school, which makes me very sad, but I just need to remind myself that life is mostly backbreaking toil. However, dropping my Physical Oceanography course would free up a lot of time for band practice, which I have currently been having trouble fitting in between hours of bike riding, studying biology and physical oceanography, preparing my independent study, and exhausting myself in the garden. Nah. I can do it.

Species chosen

I have chosen to study the marine snails Acanthina punctulata and A. spirata for my independent study.

A. punctulata  inhabits the high intertidal zone on rocky shores exposed to moderate but not strong surf, from Monterey Bay to Punta Santo Tomas (Baja California), is a drilling carnivore, and bears a very strong resemblance to A. spirata.

A. spirata inhabits the high to middle intertidal zone on protected rocks and pilings from Tomales Bay (Marin Co.) to Camalu (Baja California), and is also a drilling carnivore.

A. punctulata and A. spirata were long united under the name A. spirata and many studies supposedly done on one were probably actually performed upon the other or perhaps both.  Where their ranges overlap, they are said to have distinct distributions and are easily distinguishable one from the other.

Could this be an example of sympatric speciation in action?

Sympatric speciation has always been a mind-bender for me: how can gene flow become sufficiently restricted among members of a single population so as to allow genetic drift to the extent that an entirely new species will evolve?  As someone supposedly interested in ecology, I can acknowledge that this question verges into territory claimed already by the Anthropic Principle.  It doesn’t matter how it happened, because obviously it did… now how can we keep all marine ecosystems from collapsing before my kids are born?  But I just can’t shake the feeling that it would be so cool to understand sympatric speciation.  Almost even cooler than preventing widespread ecological catastrophe.  Is that wrong of me?  It doesn’t matter whether or not I’m callous… I can only study what interests me, and I’m hooked on sympatric speciation.

So, where do I go now?  Assuming it is possible for me to reverse-derive the parameters of growth according to the Rice (1998) model for the bio-geometry of mollusc shells, those equations aren’t going to include what else is at work making the two Acanthina species really different, like breeding or feeding or their preferred milieu.  Some of these characters I will be able to ascribe in the field, and they may be different depending on lattitude.  Is that phenotypic plasticity, or genotype variance exhibiting also the expected norm of reaction for a variety of environments?  Maybe I’m understanding this wrong, but Lewontin (2006) seems to have come up with an analysis of variance that can parce out these variety of causes.  He calls it an analysis of causes, and I don’t understand the math at all.

The problem is that I only have a superficial understanding of  norm of reaction, epistasis and the analysis of causes, all of which are going to play a very important role in figuring out this phenotypic plasticity/sympatric speciation thing.  So, back to the books… but which books?

Response to Rice, 1998

Rice (1998) made a model of molluscan shell growth whose parameters can be altered to create the shape of any gastropod species fossil or extant. Even better, his parameters are based on biological realities, as determined by all sorts of research teams all over the place, such as which cells where are producing cell tissue, where, and at what rates. The result is a tool that allows us to model an hypothesis for what developmental parameters must be changed in order to derive one shell form from a seemingly very different ancestral form. (Question: do we know or only hypothesize the ancestor-descendant relationship?)

I think that’s cool.

My favorite quote: “In a sense, this model describes the “natural logic” (cf. “natural history”) of shells. Natural logic here refers to the relationships that must hold between different developmental and physiological processes and between these and phenotype. when combined with natural history (the actual attributes of the animal and its environment), this describes the opportunities and constraints that evolution has to work with.”

What I really want to know: Can equations for the morphospaces of actual animals be reverse-derived from measurements taken in the field? And then if we can derive the equations of two closely-related species, will the parameter variations between them paired with what we know of their natural history illuminate a mechanism for their sympatric radiation?