Sunday, June 22, 2014

Larva and metamorphosis (Part 1)

One of the positions that Margulis generated a lot of controversy by supporting (though not necessarily stating that she thought it was true) is Donald Williamson's proposal for the evolution of metamorphosis in crustaceans and insects. He suggests that the larva and adult stages of many metamorphic animals descended from unrelated common ancestors that hybridized to create the species with metamorphic life cycles that we are familiar with today. Upon publication, Williamson's positions were met with immediate widespread scorn from most of the academic community.

I don't know much about crustaceans, and I don't know whether Williamson has suggested that the same might be true of, say, amphibians, but I doubt that he has. In the case of frogs and salamanders, it's pretty abundantly clear that the standard Darwinist account of natural selection on a single lineage adequately explains the evolutionary process. The metamorphosis really isn't that drastic. Internal organs of the juvenile stages map directly to homologous organs of the adult. Neotenous individuals that never undergo pubescence without metamorphosis can mate with ordinary adults. We can find fish that exhibit similar life cycles and we know of environmental factors that would selectively favor the adaptations exhibited by amphibians. The changes from juvenile stage to adult stage, while they happen quickly, are gradual. A tadpole can become a frog in day, but it doesn't discard it's tadpole shell and pop out a frog. It simply goes through a growth spurt in which most growth occurs in a particular set of limbs. Many fish undergo similarly drastic changes as they age. Some fish change gender. Other fish, for example flounder, have a body morphology that changes from a vertical orientation to a horizontal one. A huge percentage of chordates exhibit some morphological changes other than uniform changes in size in response to hormonal changes as they age. In this clade, it is very common for the most drastic of these changes to occur around the time that the animal becomes a reproductively viable adult.

In short, we really don't need any special explanation of how metamorphosis evolved in amphibians. Some fish developed a tendency to become increasingly suited to life on land instead of aquatic life as they aged. In many ways, the origin of amphibians is a lot simpler than the origin of reptiles or mammals. Some biologists even speculate that multiple lineages evolved independently and went extinct.

Contrast all of these things to the insects that undergo complete metamorphosis. The first drastic difference we observe amphibians and Pterygota, the subclass of insects in which metamorphosis occurs, is that in some members of Prerygota, the juvenile form bares practically no resemblance to the adult. We call these drastically different creatures larva. Fascinatingly, in every case where the distinction is sufficiently drastic for as to call the juvenile form larva, there is another intermediate form in which the insects changes drastically from the larva int the adult. During this phase, it is typically extremely passive. Many pupa perform no normal biological functions like eating or reproducing or, in most cases, even responding to its environment. This phase more closely resembles regression to an egg than it does to any life phase seen in animals. (It remains extremely metabolically active during this time, making hibernation a poor analogy.)

A second observation that follows closely on the first is that the adult morphology predates the metamorphic life-cycle whereas, in amphibians, it was the juvenile state that had a precedent. In terms of phenotype, many insect larva aren't arthropods. They frequently lack joints. They also tend to have extremely thin exoskeletons that exhibit no mineralization, even though practically all adult insects have much thicker, mineralized exoskeletons as do the adults of most close relatives of insects. The oldest surviving order of insects, Archaeognatha, undergoes no metamorphosis; and has the adult phenotype just described. The oldest members of Pterygota subclass of insects, such as dragonflies and cockroaches, species that have remained largely unchanged morphologically for as long as the fossil record has contained examples of Pterygota, likewise have no larval form. The physiological changes that occur in these species as they age are frequently described as "incomplete metamorphosis" but the changes are not particularly drastic. Nymph/naiad and adult tend both have joints and thick exoskeletons. They share adaptation such as the complex jaw structure common throughout insect species. Some share an environment and food source with the adult. They change gradually into the adult form through a succession of molts. (Larva of species undergoing more thorough metamorphoses molt, but their successive instars do not bare increasing similarity to the adult.) In the case of the orders of insects undergoing "incomplete metamorphosis", like in the case of the amphibians, the young tend to resemble recent common ancestors much more thoroughly than the adult does. The resemblance of Archaeognatha to dragonfly naiads is stronger than its resemblance to dragonfly adults. All have the morphological characteristics of insects and arthropods that I've just described, but dragonfly naiads like all (? -- all that I know of --) insect nymphs and naiads are flightless.

The final observation for this post is that the drastic superficial differences between larva and adults in species undergoing complete metamorphosis accompany underlying structural differences. I already pointed out that larva tend to lack some defining characteristics of arthropods, exoskeletons and joints. It should therefore not be surprising that they also frequently lack defining characteristics of insects such as bodies separated into three regions or having six legs. These two observations are not rigid. Beetle grubs have a more adult exoskeleton than other insect larva, especially in the head. Grubs, in general, have features corresponding much more closely to adult insects than do the other insect larva.

More deeply still, internal organs in insect larva frequently lack mappings to homologous organs in the adult.

Finally, there is no accepted explanation for how insect metamorphosis evolved. In amphibians, we have a compelling explanation of the process by which fish acquired the ability to survive no land. Obviously, we don't know all of the details, and we probably never will, but when we look at what we do know, we aren't left with the feeling that much more explanation is required. We understood what happened well enough that, given the ability to accelerate time, we can be pretty confident that we could choose some fish with the appropriate characteristics and subject them to the appropriate environmental factors to produce amphibians.

For insects undergoing metamorphosis, we have no such story. The evolutionary history of insects is not an easy thing to study* because it, in general, does not have anything close to the amount of published and collated research as exists for the evolutionary history of chordates. Particular facets of their evolution of insects such as their divergence from other arthropods, the process of metamorphosis, how they adapted to land, and how they developed flight are not well understood.

Margulis and Williamson were certainly correct in asserting that one of these facets of insect evolution, metamorphosis, requires additional explanation. They may or may not be correct in their belief that some of these things will require a significant reappraisal of some of our core beliefs about how evolution works. Margulis was certainly correct in her insistence that understanding the origin of Eukaryota required a significant revision of understanding. Almost everything she proposed related to endosymbiosis has been vindicated by genetic studies in the last 30 years.

The reaction that Williamson has received is the reaction that has plagued the history of thought and science throughout recorded history. In particular, we often see entrenched academic communities reject the assertion that there current understanding is incomplete, when in fact, everyone's understanding of everything is always incomplete. Williamson has picked a very specific example of something for which our current understanding is grossly incomplete and proposed a radical explanation, one that has no accepted precedent in the study of animals, though hybridization is known to regularly occur in plants.

None of these observations say anything about the particular merits and demerits of Williamson's proposal. I plan to discuss the subject some in the future.

(Full disclosure: Margulis has a lot of unconventional ideas. I strongly agree with about half of them such as the relative importance of genes vs. cellular structure, the relative impact of human vs. microbes on the environment, the computational intractability of reality, and her general stance that it is productive and accurate to view human creation of machines as an extension of biology. As I expressed in my last post, I strongly disagree with her views on meiosis. That is her only opinion in (non-medical) biology with which I strongly disagree. I am also not an AIDS denier. I find the medical community's perspective more credible than Margulis' on that subject. If the symptoms of HIV/AIDS really were just a manifestation of syphilis, it is hard to imagine that no one would have found a way to treat it. There are known ways to treat syphilis into remission. I haven't scoured the literature to try to find out if anyone's ever tested syphilis treatments on AIDS patients. However, it is almost inconceivable that no one has ever been diagnosed with both diseases and treated for the one that is treatable. If such treatments consistently caused the disappearance of AIDS symptoms, someone would probably have noticed and begun testing syphilis treatments on more people with AIDS. I am also not a 911 truther. However, I don't know enough about the subject to have an informed opinion on it, largely because I don't really care. As far as I'm concerned, it's simply a matter of whether to assign primary blame to one party or the other for one particular incident in the increasing conflict between Western elites and traditional Middle Eastern peasants that has been escalating for the past thirty years. For my own part, I think there's enough blame to go around that assigning 4,000 extra deaths to one side or the other doesn't noticeably add to the crimes of either side.)

*I use the word study to mean "read what other people have researched." I use the term research to mean either "investigate through painstakingly detailed observation" or "perform experiments." In general, you can accumulate information much more quickly and assimilate information from a much broader range of sources by studying than you can by performing research. Professional scientists tend to make their living, at least early on, by doing research because that is the part that actually requires work. I am of the opinion that studying results in the formation of more accurate ideas than research does because there is a great wealth of inadequately analyzed research in existence. Generally speaking, great scientists before the twentieth century tend to do their own research, but the most influential scientists of the past hundred years have tended to study other people's research instead. (Notable examples of people in the second category include: Einstein, Heisenberg, Wheeler, Feynman, Hawking, and Margulis. My list is obviously colored by the fact that I have tended to be more interested in physics than other hard sciences (and by the fact that I dislike typing non-ASCII characters).

Sunday, June 15, 2014

Microcosmos: meiosis and parthanogenesis

Microcosmos is an excellent book and its author was a fascinating woman.

In keeping with the name of this blog, I will try to have my first post about any given book focus on the parts that I disagree with. Microcosmos is so full of unorthodox perspective that any disagreement I could have with it, will necessarily be more orthodox than the perspectives in the book. Hence, I will have to revisit some of the topics in order to express how strongly I am persuaded by Margulis's insights.

The only major points in the book that I find highly dubious have to do with its assertions relating to meiosis. Margulis believes that eukaryotic sexual reproduction is maladaptive, and that meiosis is valuable because it provides increased stability by serving as an elaborate biochemical roll call. She disagrees with the belief that it serves to increase diversity.

Many species exhibit parthenogenesis. Some reptiles are entirely parthenogenic. They survive. They exhibit phenotypic diversity within the species. Sex is not biologically necessary even for Eukaryota. Hurrah!

Cnemidophorus neomexicanus is entirely parthenogenic. There are no males in the entire species and the species doesn't mate. It's more numerous than its close relatives, indicating that parthenogenesis can clearly be adaptive if it can be pulled off. It's close relatives mate normally.

The same is true of other species that reproduce parthenogenicly. Their close relatives very seldom do.

Parthenogenesis has clearly evolved independently on many different occasions. It is extremely unlikely that all of those occasions occurred in the past ten million years. Rather it has been happening for as long as their have been animals. Yet these species almost never go on to form clades. Some clades, like rotifers, have many species that exhibit both male-female mating and parthenogenesis. But there is no existing clade of more than five species that is entirely parthenogenic.

The available evidence strongly indicates that parthenogenesis evolves frequently and easily in some classes of animals. However, the species that develop it rarely issue new lineages that survive past the million years or so of environmental consistency that typically constitutes a given species's time in the sun. As the world changes, these species remain the same. Hence, they go extinct. Their mating relatives much more successful issue progeny adapted to the evolving world.

In the case of Cnemidophorus neomexicanus, we know with certainty that the species didn't somehow evolve into its sexually reproducing near relatives. Its two closest relatives can hybridize to create new female, always female, Cnemidophorus neomexicanus. (I.e. this is a hybrid species of two sexually reproducing species.)

Let's pick another species.

Komodo dragons can reproduce parthanogenically, but all offspring so produced are male (which can then mate with the female Komodo dragons to produce female or male Komodo dragons).

Clearly, they aren't leveraging parthanogenesis as much of a survival strategy. There are plenty of males on the Galapagos, and we have no reason to believe that males randomly die out while the females survive. Instead we see that under reptilian reproduction, parthenogenesis is an easy adaptation. Komodo dragons exhibit this trait simply because they can. It doesn't help them survive. It hasn't helped them colonize new territory (they are naturally confined to a very small area). It's simply something they do because Komodo dragons can hatch with a haploid chromosome count, and then develop diploidy as they mature which means that whenever a female can lay unfertilized eggs, the males of that batch can survive. (Komodo dragons do not have X and Y chromosomes to determine gender like humans do. They have ZW chromosomes. Males are ZZ; females are ZW. Only the males survive birth in parthenogenic reproduction because WW is not viable, and they they start out haploid.)

Other animals that display parthenogenesis display it because it has been similarly easy for them to evolve it, not because it is a winning strategy. It might be winning in the short term for some species, but these species that develop extreme dependence on this strategy as a means of reproduction rarely speciate into new lineages, and typically fail to survive the environmental shifts that cause new species to emerge among the mating animals.

If it was easy and adaptive, it would be ubiquitous. We have strong evidence that parthenogenesis is an easy adaptation for many species. We know that it is not ubiquitous. Far more species reproduce sexually. Therefore, we have very strong reason to conclude that sexual reproduction, not parthenogenesis, is adaptive, at least in the long term.

Hermaphrodism among animals and plants would lead us to the same conclusion. Many hermaphroditic species have adaptations that prevent them from mating with themselves, again indicating that sexual reproduction is adaptive for Eukaryota. Hermaphrodism is a very easy mutation. A huge proportion of plants and animals have some hermaphroditic mutants in the species. It's likely that all do. Yet very few species are predominantly hermaphroditic. The clades that are, e.g. many groups of plants as well as some animals like snails and slugs, have also developed traits to prevent autosexual reproduction. Again, this gives us strong evidence to believe that the genetic exchanges from mating produce variety that helps species adapt to changes in their environment and evolve accordingly. Autosexual reproduction is obviously less expensive in the short term, therefore it is in some sense adaptive. It's pretty obvious that animals that can clone themselves without going to the trouble of finding a mate can reproduce to fill their evolutionary niche a lot more easily than their less fully endowed relatives. However, such species rapidly go extinct once their niche goes away and they leave no daughter species after them.

Margulis may be right about a lot of things. I strongly believe she is. However, the biological evidence (not just the entrenched consensus of academia) is overwhelmingly against her in her claim that sexual reproduction is a maladaptive vestige of early Eukaryotic evolution that will vanish when faced with the superior reproductive methods of Eukaryotic species that can clone themselves. Locally, when the ability to essentially clone oneself develops in an individual that is very well-suited to a particular niche, yes, that individual and its clones will go on to out compete their relatives and fill the niche. However, brief survey of Eukaryotic life will quickly tell you that those species will not survive to produce daughter species; whereas the mating organism occupying other parts of the world and its other ecological niches much more frequently will.