Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Saturday, May 27, 2006

How not to apply evolution to culture

Here is a small piece in the Korea Herald, by Arne Jernelov on how evolution explains cultural excellence. It's all about sexual selection, you see - if you do something that is very hard and very costly, you are attracting mates, and this explains sports, painting, literature and science. It is only coincidental that the author is a scientist (an environmental biochemist). I bet he also plays sport competitively.

Friday, May 26, 2006

Microbial species 4: degrees of sex

When we attempt to apply to organisms that are not obligately sexual (that is, which don't have to have sex to reproduce) concepts that were specified to use with those that are, we have problems. The Recombination Model is one such attempt. Sure, some microbial species exchange genes. Others do it more frequently and more completely. There appears to be a continuum of gene exchange all the way from almost never to almost every time. So why should we expect that gene transfer will provide us with the sort of homogeneity of lineages and quasispecies that it does in obligate sexuals?

In part I believe this is because we always start from what we know. As I mentioned, the existence and ubiquity of asexual organisms has been resisted from a long time, and treated as exceptional rather than the rule, because biology began with large scale plants and animals, where the paradigm cases were encountered for the biospecies concept. As exceptional cases were encountered, these concepts were stretched, and modified, to serve the increasingly "deviant" cases, until now we realise that deviance is relative to the paradigm conceptions rather than a fact about the organisms. What should we say instead?

I believe we should treat this continuum idea more seriously and as the basis from which the metazoan and metaphyte conceptions are drawn out. And we should consider how the two factors of the Templeton conception - exchange and ecological niche - play differing roles according to the degree of sex a lineage has.

Before I deal with this in detail, let me note for the record that there can be, and must certainly often be, other reasons why the carpet is not smooth, but is patchy. Extinction can cause there to be patches in genome space. Some varieties die out. While this can be because of selection, often it will be due to plain old genetic drift, and contingency. A lineage of asexuals can stochastically drift due to random biases in the direction of mutation, for instance, while earlier forms can go extinct simply because of random drift or random termination of that clone. Moreover, if a genome evolves in a habitat that is sensitive to sudden changes in climate or even geological change that degrades it, then that genome and its neighbours will become extinct. Evolution doesn't explore the same coordinates in genome space all the time and everywhere. This is similar to the phylogenetic trends that occur through simple stochasticity, because clonal evolution is phylogeny.

So, back to the notion that sex is not an all-or-nothing affair, so to speak. If the continuum ranges from 0% gene exchange (total asexuality) to 50% gene exchange (total sexuality), then it follows that at the asexual end, exchange can have only limited to no effect on maintaining homogeneity, while at the sexual end, it can have a very great role in maintaining homogeneity. Likewise, at the asexual end, homogeneity not due to stochastic effects will be due largely to ecological selection (fitness peak tracking), while for sexuals this will not be so great a cause. I have given a schematic graph to illustrate this.

This will be why we find that gene exchange doesn't have a simple relationship to genomic homogeneity. It will depend on the rate and amount of genes shared across lineages case by case, as well as the degree to which the quasispecies is maintained by ecological interchangeability. Following on from my discussion about speciation earlier, and my 2001 paper on species concepts, where I employed this evolutionary aspect of the nature of sex to argue that being a species is an evolved trait, not a natural kind, we ought to expect that each species and group of species has its own unique evolutionary history and therefore properties, just as limbs and lungs and livers do. There will be a more general theoretical context of adaptive landscapes, genetic dynamics, and so on, but given that each evolutionary group has encountered different conditions, this means that each modality will be shared in a fairly limited way.

Moreover, this means that biospecies is not the most basal notion of species. In fact, biospecies, or reproductive conceptions of species in general, are derived modalities. The basal notion is quasispecies. All species are at least quasispecies; some are in addition reproductive cohesion or isolation conceptions. This means that some standard requirements for biospecies, such as reciprocal monophyly, do not need to apply to all species. But there is one rather interesting aspect to this approach that I find illuminating, although your mileage may vary: a simple quasispecies is cohered by more or less one adaptive peak (if it is cohered; stochastic clustering does not imply this), while a biospecies famously can be and often is adapted as a generalist or have polytypic traits for differing adaptive peaks.

What maintains a sexual species in this case will be, therefore, the combination of extrinsic selection, and internal or intrinsic cohesion, due to selection for reproductive compatibility with potential mates. I have a paper forthcoming in Biology and Philosophy which argues this in detail. Microbial species will tend to depend on adaptive peak cohesion inversely to the degree that they do share their genes and directly to what functional value of those genes they share have ecologically.

Enough for now. I'll wrap up this series next post.

Microbial species 3: Quasispecies and ecology

The second main approach to a natural conception of microbial species (by which I mean, as opposed to operational, practical or conventional ones, collectively called "artificial" conceptions) is what I will call the Quasispecies Model. According to the concept developed by Manfred Eigen for viral species, a quasispecies ("as-if-species") is a cluster of genomes in a genome space of the dimensionality the number of loci. A quasipecies is in effect a cloud of genomes, with a "wild-type" coordinate (that is, genome) that may or may not actually have an extant or extinct instance.

A genetic cluster of the quasispecies kind is therefore not unlike James Mallet's Genotypic Cluster Concept (1995), although this is primarily an operational definition than a substantive underlying account of species. We still need to account for quasispecies existing in the first place. We have considered one possible mechanism - gene sharing by lateral transfer - and found it to be insufficient. Is there something else we might make use of?

There is one proposal by Alan Templeton (1989), devised for sexual organisms, which defines a species as a genetic cluster, as Mallet's does, but accounts for it either by genetic exchange, as in the recombination model, or ecological interchangeability. This latter notion is what we might call the "Fitness Peak Conception" of quasispecies.

Each coordinate in genome space, that is to say each genome, has a fitness value associated with it that is imposed by ecological factors. If the adaptive landscape is relatively smooth, which means that adjacent coordinates are correlated in their fitness values, we should expect in the absence of all other causes of clustering that the cloud of genomes will tend to centre upon the most adaptive genome. Of course, this is an abstraction and a gross simplification - genomes are not independent of each other, or from fitness values. Organisms create their ecological conditions to a degree, and how fit a genome is depends also upon what other genomes exist in a population (at least, in sexual organisms), but we can leave these complications to one side for the moment.

So one potential reason why quasispecies exist, why genomes cluster, is that they track local fitness peaks. Let's flesh this out, so to speak. Take a pathogen that is clonal. It needs to employ certain features of the host species in order to infect and exploit that host. Assuming these don't change - say they are recognition molecules on a cell surface - the quasispecies will cluster about those point in the genome space that are more effective than others with respect to the capacity to infect and exploit.

So now we have the two cohesion mechanisms proposed by Templeton - cohesion due to shared genes, and cohesion due to the need to exploit the environment better than competitors. Anything that can do well at the latter will tend to be better represented in the average population. Hence quasispecies.

But fitness peaks typically do not remain constant or decoupled from the populational structure, as I said. Does this mean that quasispecies are not real species because they are ephemeral? Of course not - all species are, over a suitably extended timescale, ephemeral. That is in the nature of evolution. What the fitness peak conception means is that a quasispecies will remain homogeneous so long as there is a more or less unitary fitness peak. If the peaks shift, there will be "speciation". Oh heck, let's stop the pretense that quasispecies aren't real species. There will be real speciation.

In the next blog, I will discuss a way to bring these two notions together, and to link quasispecies with biospecies (sexual species).

Eigen, Manfred (1993), "The origin of genetic information: viruses as models", Gene 135 (1-2):37–47.
——— (1993), "Viral quasispecies", Scientific American July 1993 (32-39).
Mallet, J (1995), "The species definition for the modern synthesis", Trends in Ecology and Evolution 10 (7):294-299.
Templeton, Alan R. (1989), "The meaning of species and speciation: A genetic perspective", in D Otte and JA Endler (eds.), Speciation and its consequences, Sunderland, MA: Sinauer, 3-27.

Thursday, May 25, 2006

Microbial species 2: recombination

The cluster of genomes of asexual organisms forms what is called a "phylotype" (Denniston 1974, a term coined by C. W. Cotterman in unpublished notes dated 1960; I like to track these things down). Phylotype is a taxon-neutral term, though, that is determined entirely by the arbitrary level of genetic identity chosen. For example, "species" in asexuals might be specified as being 98%+ similarity of genome, or it might be 99.9%+ (I have seen both in the literature). A phylotype of, say 67% or 80% might be used for other purposes (such as identifying a disease-causing group of microbes).

The phylotype concept, while useful in other respects, reinvents (or preinvents - 1960 predates the work of Sokal and Sneath) phenetics. A phenetic taxon was called the Operational Taxonomic Unit (OTU) and it used an arbitrary measure of similarity and difference: an 80% "phenon line" was the arbitrary measure for species based on phenotypic similarities. The problem was that the distances changes as you chose different principal components, and I warrant the same is true for phylotypes.

One solution to the Problem of Homogeneity for asexuals is what I will call the Recombination Species Concept. Proposed by Dykhuizen and Green in 1991, it basically the Biological Species Concept for lineages that occasionally share genes or gene fragments through lateral transfer.

There are several mechanisms by which lateral transfer of DNA can occur among "prokaryotes". One is DNA fragment reuptake, in which DNA from a cell that has lysed (its membrane or wall has disintegrated, releasing the cell contents into the medium) is taken up by another cell, and rather than being digested it becomes active. There are variations on this. Entire chromosomal rings, called plasmids can be taken up this way. Or a cell can "bleb", forming vesicles or compartments of lipids, containing DNA (including plasmids), which then attach to the receiving cell, opening up to the interior.

I mentioned prokaryotes before. This refers broadly to a paraphyletic group of organisms that are basically not-eukaryotes. Nowadays we refer instead to several groups: Bacteria, Archaea (which is sometimes decomposed into several other groups), and Eukaryota. One thing the not-Eukaryotes have in common, though, is a lack of a nuclear membrane, allowing the transfer of genetic material between genomes.

So the Recombination model of microbial species is based on the claim that the greater the genetic distance between strains, the less likely it is that the genes will be functional and useful in the receiving strain, and this is what serves to maintain the homogeneity of bacterial and other microbial species. One of the claims is in fact that the differences in genetic structure, and in some cases differences in restriction enzymes, that break DNA sequences, will make a nonsense of the DNA fragment or insert it in a nonfunctional location in the target genome.

These compatibility issues act like sex does to maintain the overall "location" in genome space of the population. Those strains that deviate too far from the mode will be unable to take up the functionally useful lateral genes, and so will be more susceptible to extinction through genetic load.

So the Recombination model is a mix of Maynard Smith's theory of sex, and Mayr's notion of biological species. The only problem is that it isn't consistently true. A beautiful explanation is spoiled by ugly facts. Recombination via lateral transfer appears to be rather more profligate than first appeared (Beiko, et al. 2005), and there are some "species" of bacteria, such as the Lyme Disease-causing spirochete Borrelia burgdorferi, that appear not to share genes much, if at all (as Dykhuizen himself observes, Dykhuizen and Baranton 2001). So if in those cases clustering occurs, it is not due to lateral transfer, but some other processes.

I failed to mention a process that is directly analogous to sex in bacteria - conjugation. This is a case where part of the genetic component, usually plasmids, which are secondary small chromosomes (B), or the main nucleoid (A), can be inserted into another cell via processes called pili, which are part of the Type IV secretory system used for other purposes and which is homologous to flagella. The typical mode of conjugation is that one mating type (often called the "male") is activated by pheromones from another mating type ("female") to attach the pilus to the recipent, and insert the genetic material.

Now this is "almost-sex", because there is no genetic reassortment, but other processes will tend to shuffle genes into the nucleoid, as well as utilising the taken-up plasmids. But again, while the mating types seem to act as cohesive mechanisms, conjugation can be profilgate across large, even vast, phylogenetic distances (and hence genetic distances). It has been observed between bacteria and yeast, bacteria and plants, and there has even been a case in which it was observed between bacteria (E. coli) and mammalian (hamster) cells (Waters 2001).

So while it may be that recombination of lineages through partial genetic transfer operates as a reason for some phylotypes, it does not account for all, and is therefore not a sine qua non of specieshood, or homogeneity, among microbes.

Next, we'll consider ecological accounts, as well as drift, migration and geographical isolation.

Beiko, Robert G., Timothy J. Harlow, and Mark A. Ragan (2005), "Highways of gene sharing in prokaryotes", Proceedings of the National Academy of Sciences, USA 102 (40):14332-14337.

Denniston, Carter (1974), "An extension of the probability approach to genetic relationships: One locus", Theoretical Population Biology 6 (1):58-75.

Dykhuizen, D. E., and G. Baranton (2001), "The implications of a low rate of horizontal transfer in Borrelia", Trends in Microbiology 9 (7):344-350.

Dykhuizen, D. E., and L. Green (1991), "Recombination in Escherichia coli and the definition of biological species", Journal of Bacteriology 173 (22):7257-7268.

Waters, V. L. (2001), "Conjugation between bacterial and mammalian cells", Nature Genetics
29 (4):375-376.

Wednesday, May 24, 2006

On microbial species

OK, this is one of a series of posts in which I will play with ideas that might become a paper.

The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).

But many microbial species either do not share genes to reproduce, or they can but do not need to. So, the question is sometimes raised whether microbes (of this kind) form species at all, or if there is some replacement term or concept for microbial taxonomy.

Historically, it took a long time to even accept that there were asexual organisms. Darwin discussed hermaphroditic species, but they still had mating types or genders; it was just that a single individual had both kinds. It was long recognised that some plants could propagate vegetatively. But the notion that there were obligately asexual organisms was doubted, for instance, by Fisher as late as 1958 (in the second edition of the Genetical Theory of Natural Selection). George Gaylord Simpson, the famous joint architect of the synthesis and paleontologist, simply denied that asexuals formed species. Call them something else, he said.

But bacteriologists, mycologists, and virologists all continued to name and describe species, even though they could not really make use of the Biological Species Concept of Dobzhansky and Mayr. They relied on their staining properties, the colony shape, the microscopic morphology of the cells, and of course the ecological conditions under which they lived. There was lacking, though, a clear definition of what a species could be for these organisms.

Part of the problem is this: if a species were obligately clonal, then each mutation would make a new clonal lineage:

and we would expect to find not clusters but a carpet of strains more or less evenly distributed. How can we account for this? I will call this the Problem of Homogeneity: why are asexual lineages ever found as groups at all? Why are they homogeneous over time, and stable enough to be called "species"?

I will follow this up in the next post, but I want to get your feedback first.

Monday, May 22, 2006

What, if anything, is a rabbit?

Darren Naish [via Pharyngula] has a lovely article about the morphology and taxonomic and phylogenetic relationships of Lagomorpha, rabbits and hares. In the course of the piece, Naish quotes one Albert Wood, from 1957, whose paper with the title of this post starts out
The title of this paper is slightly modified from that of an article I encountered some years ago, which appeared to be approaching the problem of the relationships of the Lagomorpha, or rabbits and their relatives, from the most basic point of view. This paper, entitled “Gibt es Leporiden?”, seemed to be questioning the very existence of such animals. Investigation showed, however, that the question involved was not whether members of the family Leporidae existed, but whether rabbit-hare hybrids did. Since then, I have met no one who questions the existence of rabbits and hares, and I have been reluctantly forced to accept them.
They don't write papers like that any more. I, too, question the reality of rabbits. Just because.

Sunday, May 21, 2006

Islamist paradise: selling children

The Times is reporting that 20 young boys were bought from an Islamist leader, Gud Khan, in Pakistan, who runs a "pure Islamic environment" at a centre initially funded by al-Qaeda, by Osama bin Laden directly. The sale was made to a Christian missionary who was freeing them and returning them to their parents, from whom they had been kidnapped. Khan apparently knows that the children will be used for sexual and illegal activities, and doesn't care, because they are Christian. The proceeds are used to support his Islamic paradise, free from the corruption and degradation of the West. Oh irony!

The obvious inference to draw here is correct but insufficient. Islamism is not based on some morally pure foundation. It is political, pure and simple. Sure, this is true, but a much better inference is that religion makes for a very bad foundation for morality. Not only Islamists, but Christians, Jews, Hindus and every other religious movement, privileges believers over unbelievers morally. It's OK to kill abortionists or gays, to disenfranchise Jews or Arabs, and so on, because They Aren't The Same As Us.

And Christians in the US and here (Australia, in case you forgot) will often criticise those who think that all human beings deserve the same rights and privileges in society as "humanists". In fact, humanism has become the all-purpose bogey among religious circles. Of course it is - it undercuts the basic moral intuition of all religions: that rights are given based on conformity to their, and only their, standards of behaviour.

I am proud to be a humanist. I think that Jews, Muslims, Hindus, Catholics, Scientologists and even those evil atheists (spelled athiest by fundamentalists) have exactly the same rights as any other person. That means they can run for office, vote as they wish, take any course of action even if it contravenes the "deeply held moral standards" of some religious majority so long as it is not illegal, and live wherever they like. This is a measure of civilisation. The covert prejudices and bigotry of religion need to be opposed openly by a civilised state.

To my religious friends, who are not at all like this, most of the time, I can only say that your morality is civilised in spite of, not because of, your religious traditions. It was but an eye blink since your own traditions, if they are enlightened now, were treating those who differed as subhuman. Christians, Muslims, Jews, it doesn't matter. The underlying social function of religion is to exclude, not include. Thus it ever has been.

Humanism is not a religion. It is a general principle - that human life is equally valid no matter the social status, ethnicity, religious belief, or sexual orientation of the individual. Somebody should found a country on these principles...