Thursday, June 19, 2008

Notes On the Species Problem From Futuyma

(Futuyma pg 448)

Early taxonomists (predarwin) held what Ernst Mayr has called a "typological" or "essentialist" notion of species. Individuals were members of a given species if they sufficiently conformed to that "type" or ideal, in certain characters that were "essential", fixed properties, a concept descended fom Plato's "ideas".

Nevertheless populations ARE variable. Quite often the variation among specimens falls into discrete groups, or clusters, as in the case of the raven versus crow. These clusters, for early taxonomists, were species. Each had certain "essential" defining properies, such as the ravens's pointed tail, that varied only slightly. But often gradations between such clusters DID exist. For instance , carrion crows whcih are entirely black, differ from hooded crows which have a gary back and belly, EXCEPT in certain parts of Europe, where some specimens ARE intermediate.

the existence of such cases has led some authors to conclude that species are arbitrary constructs of the human mind imposed on a a continuuum of variation. Darwin for one, took this position.

There coexisted, even in the eighteenth century, another criterion: common descent. Offspring of the same parents were the same species, EVEN if they differed considerably (from each other or the parents). [this is important, and leads to subtle points].. the striped and banded forms of the California king snake known to be born to the same mother, represent a genetic polymorphism, not different species.

By the early 20th cent.. Mayr, in his Systematics and the Origin of Species (1942) noted:

1) many, perhaps most, characteristics vary among the members of a single population of interbreeding individuals. Sometimes continuus quantitative variation; sometimes discrete like the king snake.

2) populations in different geographic locations usually differ in the mean of one or more characteristics. very often intermediate forms are found where such populations meet, providing evidence [?] that they interbreed.

3) what APPEARS at first to be a single, MORPHOLOGICALLY uniform species often proves to include two or more subpopulations that occupy the same area, but do not interbreed. these cryptic sibling species might be recognized on the basis of some form of reproductive barrier (different genetalia, different breeding seasons, etc..) for instance two treecreepers (birds) in central europe almost identical but for very different songs.

the abundance of variation within and between COMBINED with Darwin's view that all characters can keep evolving into more and more different characters led to the abandonment of the typological species concept. the biological species concept became more and more widely held. promulgated by the likes of Dobzhansky (1937) and Mayr (1942). Mayr defined it: "species are groups of actually or POTENTIALLY interbreeding poplations whcih are reproductively isolated from other such groups"

It has some drawbacks.

1) it only works in a particular slice of time. if you look at a branching lieage over time.. you can't test whether the population at time A could interbreed with the population at time B. these may be seperated into what are called chronospecies.

2) if a lineage forks, we do not know which fork... is it one lineage with a side lineage or is it 3 chronospecies...

3) of course it doesn't work for asexual populations

4) this is a definition in terms of populations, not individuals. chihuahuas don't (i don't think) mate with great danes, but in a population of dogs, chihuahuas can mate with dachshunds, which mate with i don't know my dogs! which mate with ... which mate with great danes. this last point opens up the whole can of worms! for instance Ring Species:
Ring Species: Unusual Demonstrations of Speciation
By Darren E. Irwin

[blending! till they meet at the begining again. so all it takes is .... extinction in the middle!]

5) the definition of reproductive isolation is "those which are naturaly [?] reproductively isolated from each other by their own behavior" which is WHAT? their behavior depends on the environment no? so as individuals migrate to different environments what might happen? anyway there are plenty of populations who DON'T mate in their usual habitat who CAN be induced to mate in artificial environments and who's offspring is fertile.

these last two lead us to an important fact. many seemingly fixed boundaries CAN leak occasionaly either through modification of behavior (by environment or by mutation) or through slow leakage through roundabout intermediates (like the chihuahua and great dane, or like ring species.

6) many populations are geographically isolated and will never manage to interbreed even though if we brought individals from them together they WOULD. hmm what to say? this is like (5)!!! BSC says they are both part of the same species. but frankly i think that stinks of essentialism! the fact is that species maybe is a property of the whole biome not just property of the organisms's essence! hence i say if we are not to be essentialists we call those two different species. the environment is part of what defines the species. and certainly with time the two populations might diverge reproductively anyway.

hell, the fact is that species might be nothing at all!

Futuyma (pg 452) says it would be absurd to call every geographicaly isolated pocket of frogs a different species. this is similar to the problem with dandelions. who at some point in the past were sexual, but now have given it up and have split into thousands of pockets of nonbreeding slightly different populations. of course frogs occasionaly travel (by flood maybe) and these dandelions OCCASIONALY have sex...


Baum and Shaw's genealogical species concept adds to this idea of leaks. (p452)

one thing we gotta mention now is that organisms are mosaics. genetically we are mosaics of thousands of discrete (almost, everything has messy exceptions) genes each in pairs, one from each parent. for each gene position on the chormosomes, in the population there might be many versions, in fact since we are diploid, even an individual organism can have two versions of a gene, one from each parent. these versions are called alleles. the gene is called a locus.

(of course it's very messy, not only can genes get mutations so that one of an offspring's allele can differ from its parent, you can have all kinds of mutations. for instance a gene can get duplicated! now where a parent has one gene called A332, the offspring has two of them from one parent and one from the other. in time this gets passed down and one of the copies can get a mutation and now some members of the population can have A332 and A332...)

the point is, that two subpopulations can be similar for SOME genes and different for OTHERS! each gene can evolve INDEPENDANTLY to varying extents.

so, genealogical species concept: after a population splits in two, each half has a mix of these different alleles for each gene. now whether alleles make it to the next generation is a chancy event, or it might be selected for. so eventually for gene 12444 a member of pop A might have alleles similar to pop B, while for gene 24432 a member of pop A will have alleles similar to pop A. so which genes do we look at to tell whether these two populations are distinct species or not?

this by the way is the case for ALL human populations. can't tell if there are distinct races for ALL genes. we all split up TOO recently, and still too much MIXING.

the genealogical species concept is we wait till the populations keep going until enough alleles get lost through randomly not breeding into the next generation so that pop A has only alleles in common with it for ALL (or MOST?) genes and pop B has alleles in common with it.

more problems with BSC:
1) narrow hybrid zones. there are cases where what looks like different species meet at a border and for a narrow zone at that border you find hybrids. there is evidence of pairs like this existing for some time, yet remaining distinct. some kind of mechanism is allowing SOME hybridization to take place, but the hybrids are not as fit as the parent species and the zone of hybridization doesn't spread through the seperate populations. this does NOT mean that individual genes, cant travel from one population to the other! the overall mix in the hybrid might be rather unfit, but single genes from populoation A might still eventually spread throughout population B. LEAKS!

2) this can even happen with two populations sharing the same teritory. just that hybrids are VERY RARE.

the question is what mechanism maintains this!

plants however work different than animals. and in fact the BSC may not be as useful for plants as animals. for instance there are many plant groups that rampantly hybridize all over the place like Quercus (oaks) and even worse: Crataegus (hawthorns)

so here is the point since different genes can have different propensity to spread from one population to another... some genes might affect something minor like color. some genes might affect something major like adaption to new niches. and some genes might affect MATING BEHAVIOR.

and now we have to talk about reproductive isolation.

what are the things that can cause this:

1) geographical isolation

2) behavioral difference: what time of day to mate, on which plant to mate, which way to dance, which color plumage you like, what kind of song you learn...

3) anatomical diff: maybe your penis is shaped the wrong way..

4) biochemical mechanisms that block the viability of sperm or pollen

5) difference in genetics (chromosomes ) that make the zygote unable to form

6) differnece in genes that make development botch up somehwere down the road

7) differences in genetics that make the offspring unable to perform mieosis and thus make viable eggs or sperm and thus GRANDCHILDREN are impossible.

biology is fun, no?

each of these mechanisms CAN be the product of a single mutation so potentially this can happen in one generation. for instance in plants, it is common that an offspring gets the wrong number of chromosomes (double or 2/3 etc..) and can only therefore mate with another offspring with the same mutation.

What's the upshot? the dicotomy is: are species a property of the whole history of the whole population structure or is species a property of some innate properties of individual organisms?

the Eldredge and Gould claim that a large part of the fossil record consists of: for layer after layer fossils of a certain type wander around a mean of morphology for a coupla million years and then switch to a nother mean quickly (in geological time) and then stay wandering around the new mean. (punctuated equilibrium) or the type splits into a FEW distinct types which each then wander around their distinct means...

there are two poles and probably everything inbetween:

1) individuals reproduce to randomly varying offspring and the set of individuals wander higgledy piggledy all over the space of all possible varieties. but since each niche has finite carrying capacity there is arbitrary extinction. therefore after awhile gaps appear between lineages. i don't know how much natural selection is needed for this to happen.

2) the logic of development, physiology, ecology act as feedback loops which encourage mutations of only certain types to persist and rejects other mutations, until a combination of mutations creep in that throws the system into a new set of feedback loops keeping the system around a new norm (which would give punctuated equilibrium) This would correspond to typological species concept.

Sunday, June 1, 2008

On Discovering The Chemical Origins Of Life: Dissecting Nanofilm Fossils Of Chemical Reactions!

At some stage in Geochemistry chemical reactions acccumulate heredity! Somehow the catalaysts have to couple their existence to their product! So if there is a catalyst that produces some organic compound that HELPS BRING MORE OF THAT CATALYST TO THE REACTION SITE then that catalyzed reaction will explode!

In a sense it's not a matter of the improbability of life but the fact that since the ULTIMATE product, life, is so much better at capturing the most common form of energy flow around, sunlight, then those reactions that moved TOWARDS life would have outcompeted the millions of other possibilities! Is this RIGHT? It's teleological after all? Is the origin of life simply an optimization problem solved by simulated annealing?

So for the origin of life we got to search for the reactions where metal ions will catalyze a reaction that produces a product that helps bring that ion into the reaction arena, or that uses up a reactant that keeps that ion from coming into the reaction arena. Or teams of reactions that help each other out...

Are there any FOSSILS of this era left? hmm... either embedded in current biochemistry, OR in the rocks.

So all sorts of geochemistry was happening. We have to search the rocks that are left from 4.5billion years ago to 3.6billion years ago and analyse each one for HOW IT FORMED. We have to find the ones of sedimentary origin and reconstruct the chemical reactions and their environment that produced them. We might be talking ULTRAMINUTE geochemical fossils! What could POSSIBLY be their chances of having survived to the present???? What we are looking for is the result of some of these geochemical reactions that gets buried beyond reach before the new round of reactions got to the results to rework them!

Could it all be possible; (A) that enough of these has survived? (B) that we can FIND them, they might be widely scattered thin films smaller than bacteria! (C) reconstruct what happened!

Well, science has become a 400 year tradition of ULTRAMASTER CRAFTSPEOPLE with very sophisticated instruments! We'd have to dissect ancient strata atom by atom, perhaps! We'd have to do a LOT of simulations! We'd have to explore ALL MANNER of combinations of crazy reactions between organic compounds and minerals in all kinds of conditions! It'd be a LOT of work. Is it Worth it?

Knowing how life is a natural consequence of the chemistry we can see, play with today? that the universe is so stable that it worked 4billion years ago with the same laws as it works today? That we ARE PART OF this universe and in reconstructing the creation that happened 4billion years ago, we have hope of BECOMING PART OF THE NEXT 4 BILLION YEARS OF THIS CREATIVE UNIVERSE STORY?

God! in order to accomplish that promise, we'd have to become wise. Or clever. Well, either way it means, if we want to survive that long, learn to explore new niches and cooperate! That means GET OFF THIS PLANET!

To explore new niches means colonize other places outside this Earth and get away from each other for awhile, then cooperate with each other's colonies. That's the way it always is!

I imagined this scenario in high school: If humanity is to survive, we have to get off this planet, get into a historic cycle of hopping from planet to planet, where each time we get to a new planet, our technology is basically lost, start from scratch, but we retain history of our social arrangements and as technology keeps resetting, our social wisdom steadily grows over 10s of thousands of years... hmm... not bad.

Just as some clever reaction cycles ultimately covered every niche on this 16million square miles of Earth, life can eventually cover the universe?

more on Homo sapiens learning to master the universe:

The Social Insects Created The Amazing Tropical Forests Of This Earth, How Can We Match Their Feat?

Some sunday morning musings on cooperation vs competition in evolution and human history:

The popular idea has always been that it's a jungle out there, red in tooth and claw, survival of the fittest and all that. And of course Humans have always heaped glory upon their warriors for entering that fray!

But the fact of the matter is that the more time you spend cometing with your neighbors the LESS time you are spending RAISING KIDS. RAISING KIDS is what evolution is about, not competing. So there are two strategies that life has come up with for spending less time competing so it can raise kids:

1) divide up the environment by exploring niche space and diversifying. if i stick to hunting rabbits and you stick to collecting nuts, we don't have to compete!

2) cooperating! I'm very fond of the social insects, and the reason why the ants rule the tropics is because they cooperate! I know that Honeybees for instance have AMAZINGLY low infant mortality in their hives, compare that to the mass of insects that lay 100s of eggs to have maybe 1 survive to adulthood! Ants take care of the place, they recycle all the materials, they spread out the trees and keep species diversity high, in fact there are over 8,000 different species of ants, they keep their OWN diversity high! And with the trees spread out so far, it takes the social stingless bees to pollinate them, making trips miles long just to pollinate a single species of tree when it blooms.

then i got to wondering about the chemical origins of life, and our next 4billion years of history ahead of us co-creating the universe. I thought up a scenario where we could possibly find ancient chemical fossils of the origins of life and learn how it happens, maybe learn to do it ourselves. But it would take a LOT of work. Do we have the TIME to accomplish the task? Can we avoid a really DIRTY world war III? How can we slowly mature and explore the potentials of Homo sapiens?

How does cooperation or niche exploration vs competition relate to our current dilema? Well, Homo sapiens IS the cooperating critter PAR EXCELENCE! that's why we are coming to rule the whole planet just as the ants rule the tropics! unfortunately whereas the ants probably took 10s of millions of years to learn the art of ecosystem governance, We tried to accomplish the feat a TAD too quickly: 100,000 years maybe? 10,000 years? We are not doing so well at it! While the ants and bees have built up amzingly diverse tropical forest over the past 10s of millions of years, we are taking them down in a mere coupla thousand!

Some ants even form supercolonies! (But so far I know of NO examples of TWO DIFFERENT species of ants COOPERATING! That's odd. There certainly are plenty of symbioses out there between other species. I even recall that there are two different species of Rock Hyraxes that nest together and raise each other's kids! (odd story, needs to be looked into!) )

Though we liberals are resisting this Global economy kicking and screaming, perhaps ultimately (after ironing things out and surely along the way MANY disenfrachised will suffer) it will provide a mechanism for cooperation between major ideological groups of us now currently fighting?

I don't know.

The other option is niche diversifcation. The Earth is pretty full, we are all crammed up against each other, there is no room to experiment with new languages, new cultures, new forms of government...No room to start out from scratch! The last such experiments where in australia and north america, and those have pretty much played out! We NEED MORE ROOM! Think of what a VAST PLAYGROUND this earth was for those tiny simple ants to explore! But we humans are VAST creatures. First of all we are BIG. Second of all we tend to coagulate into colonies of 100s of millions, covering an ENTIRE CONTINENT, that's INSANELY BIG, few species of ants come close to matching that! But mostly OUR MINDS are vast. An individual can imagine whole ecosystems in there! We can imagine mastering the cosmos itself. We need a larger arena to grow up in!

Well, there is a lot of real estate out there in the cosmos! Science is nice, technology is nice, but what we need is some WISDOM in how to be human beings! We need more TIME AND ROOM to do experiments in human civilization!

In high school i imagined the following scenario: If we were to send a ship of colonists out to colonize another planet, think of what they are starting from: scratch! Perhaps like ants sending their mated queens into the wind hither and thither, 100s of colonist ships spreading randomly out there exploring. maybe a few find some habitable planets in a coupla hundred years, and when they land? i tried to imagine what it would take to reproduce our massive network of industrial/technological abilities that we take for granted!

forgedaboutit! they are gonna be struggling to grow crops, build shelter, have kids and survive! What i hope is that we can set up a new cycle: reset our technological level to almost zero every coupla hundred years as we hop to the next planet, but retain the knowlege, the history of our sociology, psychology, educational and governing methods. By resetting the technology each time we will allow the experimenting in social interactions to go on slowly. And continuing to spread out the human experiment, will give us some space from each other, a chance to get our bearings and then have new rounds of economic and cultural interactions on vaster scales!

I think we can slowly explore the human potential! And that potential is VAST. Just as some some tiny colonies of simple bacteria, each a ten thousandth of an inch wide, 4billion years ago have come to spread across the 16million square miles of Earth and RESHAPE it, I can fully imagine us becoming gods, learning to master the foundations of the cosmos and reacreating new universes!