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Friday, 15 May 2015

The blind mariner?

Heads or Tails: The Problem of Evolving Animal Body Plans

Even when the signaling pathway is stripped to its simplest, it still involves a cue to cause a signal to be sent and received. The cue is of no use unless it triggers a signal that can be received and cause downstream effects. That is what is necessary to begin to establish a difference in cell fates, and that requires a minimum of three molecules all to be present in order to work. It would take a very long time to assemble such a pathway, but would the result be of any selective advantage? Not unless there were more pathways involved that caused movement in the direction of some resource, or assigned a special function to particular cells that benefitted the whole.
These signaling pathways pre-date the animals that use them now. Based on genomic analyses, these signaling molecules have been around well before the first bilaterian animals ever existed. They are expressed in organisms that lack these body axes completely. Even more surprising, many of the molecules used to make complex structures such as muscles, eyes, and brains also predate their use for those purposes.
What were these signaling molecules used for before there was a left and right, a top and bottom, a head and tail? How did they come to be at all, and why did they persist until they could be co-opted for the establishment of body axes? It has been suggested that they were used to establish body sections in the earliest multicellular animals, but that only pushes the question back a step. Where did that use come from? How did the signaling pathways start?
With these questions, I conclude the series I began to address the white space in evolutionary thinking -- how to account for the evolution of C. elegans. First there is the problem of getting a cell, then of getting aeukaryotic cell, then of getting a multicellular animal, and now of getting one with a head and a tail and multiple cell types. Saying C. elegans didn't have to solve the problem all at once is merely to suggest that the problems are easier if taken one step at a time. They are not.

Thursday, 14 May 2015

Why Darwinism's quest for a free lunch re:information is doomed.

Probabilistic Programming and Conservation of Information

Argument by asertion and insult?

Contradictions, Irony, and Appeals to Authority Permeate The Language of Science and Faith


On Darwinism's sexual issues.

Sex, the Queen of Problems in Evolutionary Biology

The origin of sexually reproducing organisms from asexually reproducing ancestors is a profound mystery which has baffled many an evolutionary biologist. The origin and subsequent maintenance of sex and recombination is a phenomenon not easily explained by Darwinian evolution. Indeed, there are several substantive, well-known reasons why the origin of sex presents a serious problem for conventional evolutionary explanations. Graham Bell described the dilemma in his book, The Masterpiece of Nature: The Evolution of Genetics and Sexuality:
Sex is the queen of problems in evolutionary biology. Perhaps no other natural phenomenon has aroused so much interest; certainly none has sowed as much confusion. The insights of Darwin and Mendel, which have illuminated so many mysteries, have so far failed to shed more than a dim and wavering light on the central mystery of sexuality, emphasizing its obscurity by its very isolation.
What Are The Problems?
There are several reasons why the origin of sex presents a problem. For starters, there is the waste of resources in producing males. Assuming a sexually-reproducing female gives birth to an equal number of male and female offspring, only half of the progeny will be able to go on to have more offspring (in contrast to the asexually reproducing species, all the offspring of which can subsequently reproduce). Thus, it is to be expected that the asexual female will proliferate, on average, at twice the rate of the sexual species. Given the disadvantage thereby confronting the sexually-reproducing species, one would expect them to be quickly outcompeted by the asexual species. Moreover, it must be borne in mind that, in contrast to the asexual species, the females of the sexually-reproducing species perpetuate only half of their successful genotype. To transition, therefore, from a state of asexuality to sexual reproduction is, in effect, to gamble with 50% of one's successful genotype. Given that the whole purpose of natural selection is the preservation of those organisms which pass on their successful genes, this strikes at the heart of evolutionary rationale.
These dilemmas are nothing new. In his book, Evolution: The Triumph of an Idea, Carl Zimmer acknowledges these problems:
Sex is not only unnecessary, but it ought to be a recipe for evolutionary disaster. For one thing, it is an inefficient way to reproduce...And sex carries other costs as well...By all rights, any group of animals that evolves sexual reproduction should be promptly outcompeted by nonsexual ones. And yet sex reigns... Why is sex a success, despite all its disadvantages?"
The problems extend even deeper than this. For there is, of course, the additional conundrum related to the fact that gametes (i.e. sex cells) undergo a fundamentally different type of cell division (i.e. meiosis rather than mitosis). Meiosis entails the copying of only half of the chromosomal material. In similar fashion to mitosis (which occurs in somatic cells), each chromosome is duplicated to yield two chromatids. In contrast to mitosis, however, the homologous chromosomes are also associated. So, at the start of meiosis, each visible 'chromosome' possesses four chromatids. At the first division, these homologous chromosomes are separated such that each daughter nucleus has exactly half the chromosome number. At this stage, each is present as two copies (chromatids). These chromatids are hence separated at the second division such that each new nucleus only has a single copy. In order for sexual reproduction to work, it is essential that the process of meiosis evolve to halve the chromosome number. And this ability must also only occur in the gametes and not in the somatic cells. This difficulty is accentuated by the multitude of novel elements which are found in meiosis, rendering it unlikely to be explicable in terms of single mutational steps.
And then there is the added problem of male and female complementarity -- a seemingly remarkable incidence of co-evolution.
Attempted Solutions
On the same day last week, two articles were published in the popular science media offering two different (but completely contradicting) accounts of the evolutionary origin of sexual reproduction.
One of these articles bears the headline, "Sex evolved to prevent parasite infections, say scientists". The article opens by acknowledging the problems which I outlined above:
Sexual reproduction that involves two partners is far less efficient than self-fertilization -- at least, from the perspective of evolution. So why did creatures like humans ever start having sex with each other? According to a new study, we did it to fight parasites. We spoke with the researchers to discover what this says about sex.
The article goes on to explain,
Biologists at the University of Indiana found some of the most convincing evidence yet that the evolutionary driver of sexual reproduction is a need to avoid death by parasites. The basic logic is that, if an organism reproduces asexually, then the genetic variation of its species as a whole will slowly grind to a halt, and it becomes increasingly likely that a parasite that can kill one member of the species can wreak havoc on the entire population. (For proof of that, just look at bananas.)

Sexual reproduction, then, serves as a way to keep introducing genetic variety, a process that has to constantly be repeated in order to continue staving off attacks the latest and deadliest parasites. This is known as the "Red Queen Hypothesis", taking its name from a line in Lewis Carroll's Through the Looking Glass in which, "It takes all the running you can do, to keep in the same place."

And thus, it is argued that the apparent disadvantages of sex, outlined above, are compensated by the advantage which comes from the immense genetic flexibility which arises from the shuffling of genes through the process of recombination and fertilisation. This entails that the population is in a better position to enable it to adapt more readily to environmental hazards such as parasites. This would thereby give the sexually-reproducing species a significant advantage, while rendering the asexual species more susceptible to extinction.
But here's the thing: the fact of this obvious advantage does NOT explain how sexual reproduction arose in the first place. Indeed, such immense genetic flexibility is of benefit only to future generations, and not to the present population. But natural selection, being devoid of foresight, is not able to retain biological phenomena for their potential future utility. The problems which I outlined above are potent short-term disadvantages which should have mitigated against sexual reproduction evolving in the first place! Moreover, sexual reproduction is a phenomenon of such complexity sufficient to render it extremely unlikely to evolve by mutation on a frequent enough basis that we might expect it to become fixed by virtue of a few organisms somehow surviving these obvious disadvantages.
Moreover, the efficacy of the Red Queen Hypothesis has been increasingly challenged of late. As noted in one BBC article in 2004, "for this theory to work, there have to be an awful lot of parasites about, and they have to have very dramatic effects."
As John Maynard Smith stated in chapter 12 of his book, The Theory of Evolution,
We are therefore driven to the conclusion that the early stages in the evolution of the sexual process took place under the influence of selective forces quite different from those which are responsible for the maintenance and spread of sexual processes once they were erected.
The second article, published on Science Daily, bore the heading, "Sex Is Not About Promoting Genetic Variation, Researchers Argue". This article acknowledges the problem with the hypothesis in the previous article, and reports,
Heng and fellow researcher Root Gorelick, Ph.D., associate professor at Carleton University in Canada, propose that although diversity may result from a combination of genes, the primary function of sex is not about promoting diversity. Rather, it's about keeping the genome context -- an organism's complete collection of genes arranged by chromosome composition and topology -- as unchanged as possible, thereby maintaining a species' identity. This surprising analysis has been published as a cover article in a recent issue of the journal Evolution.

"If sex was merely for increasing genetic diversity, it would not have evolved in the first place," said Heng. This is because asexual reproduction -- in which only one parent is needed to procreate -- leads to higher rates of genetic diversity than sex.

The article goes on to ask,
In fact, two billion years ago in Earth's biosphere, life relied exclusively on asexual reproduction, and every organism was capable of bearing young without costly competition to mate. With asexual species' faster and more efficient mode of reproduction, the origin and maintenance of sex -- not exactly the fittest means of reproduction -- puzzles scientists, who for decades have been asking, Why has sex evolved and survived?
And what solution are we offered this time, you might be wondering?
According to Heng, the hidden advantage sex has over asexual reproduction is that it constrains macroevolution -- evolution at the genome level -- to allow a species' identity to survive. In other words, it prevents "Species A" from morphing into "Species B." Meanwhile, it also allows for microevolution -- evolution at the gene level -- to allow members of the species to adapt to the environment.
That's right. Sex evolved in order to limit evolvability. Apart from the fact that this still doesn't provide anything like the type of causal explanation which we require (nor does it really resolve any of the problems I outlined previously), the thesis that sex evolved in order to prevent macroevolution renders even more implausible the grander claims of evolution that all extant species are the product of descent-with-modification as a result of random variation acted upon by selection.
Sex continues to reign as the ultimate conundrum, the queen of problems, in evolutionary biology. Accounting for its origin in terms of evolutionary rationale is inevitably doomed to failure. As David Tyler recently remarked, "Time and time again, Darwinists fill the gaps in knowledge with their theoretical models, but sooner or later, the next generation of scholars will realise that Darwinists have constructed a virtual world that does not match the real world revealed by research."

Tuesday, 12 May 2015

Thomas Nagel's walkabout on stage?

Thomas Nagel's Evolutionary Critique, on London Theatrical Stage?

It seems so from what I read about the new Tom Stoppard play The Hard Problem, now at London's National Theatre, which dramatizes a familiar clash of ideas in the person of a God-believing psychology undergrad student, Hilary, and her Dawkins-like academic supervisor, Spike, who's also her lover. Thomas Nagel was evidently an influence on Stoppard, particular Nagel's presentation of the challenge posed by consciousness to evolutionary materialism.
Listen to evolutionary biologist Armand Leroi, a friend of Stoppard, discussing the play in a public lecture -- just a half hour and very entertaining, especially the part with the audience experiment drawing on game theory and the fate of the male passengers on the Titanic.
The "hard problem" refers to the difficulty, given materialist premises, of accounting for how meat in the form of the brain can give rise to mind. For Hilary, consciousness is the dilemma on which purely materialist science unravels. Leroi professes not to know on which side of the debate Stoppard comes down, whether in denying the Darwinian model (as Nagel does), or with Dawkins in affirming it.
The hostility of some of the reviews Stoppard has received would suggest that the reviewers sense Stoppard is more sympathetic to Nagel, and that such sympathy is not allowedThe Guardian gnashes its teeth: "Often taxed with being too intellectual as a playwright, he is here not intellectually stringent enough."
New Scientist similarly laments: "What was irritating about The Hard Problem was the weight it gave to the hard problem" and "there is more than a whiff of anti-science here, since it argues that we will never be able to explain the conscious experience."
The play doesn't directly mention intelligent design -- for whose theorists the atheist philosopher Nagel has expressed admiration, earning him denunciations across academia. But Stoppard's protagonist Hilary says at one point that she's working on a paper whose equations cast doubt on aspects of human evolution and specifically whether the conventional account allows sufficient time for it. By the end, she has announced that she is making plans to continue her research and studies at New York University -- where, the audience may or may not realize, Nagel himself teaches. That is sly on Stoppard's part. Nagel is not cited by name, but he is in the program notes.
I'm unaware of plans to mount the play in Seattle, so I don't anticipate getting to see it anytime soon. However it sounds like a thoughtful and critical consideration of evolutionary themes.
Well, it's easier for a famous playwright like Stoppard to go off the reservation on these issues, for the same reason it's easier for a distinguished philosopher like Nagel. You reach a certain pinnacle of achievement in your field, and you no longer have to worry about sniping colleagues or tottering status.
It's a nice thing about being venerable. You can say what you want.

Monday, 11 May 2015

Falsehood in defense of truth?

Darwin-Defending Historians Debate Whether It's Justified for Cosmos "to Lie" for the Sake of Science