Wistar Day

Koprowski and I, the only biologists present, were confronted by a rather weird discussion between four mathematicians – Eden, Schutzenberger, Weisskopf, and Ulam – on mathematical doubts concerning the Darwinian theory of evolution. At the end of several hours of heated debate, the biological contingent proposed that a symposium be arranged to consider the points of dispute more systematically, and with a more powerful array of biologists who could function adequately in the universe of discourse inhabited by mathematicians.

– Martin Kaplan

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Design by Evolution

Evolution is Nature’s design process. The natural world is full of wonderful examples of its successes, from engineering design feats such as powered flight, to the design of complex optical systems such as the mammalian eye, to the merely stunningly beautiful designs of orchids or birds of paradise. With increasing computational power, we are now able to simulate this process with greater fidelity, combining complex simulations with high-performance evolutionary algorithms to tackle problems that used to be impractical.

Design by Evolution: Advances in Evolutionary Design

I was like great! A book that will finally tell me how Evolution designs such magnificent designs. But there’s that “problem” word again. Is Evolution faced with design problems that it then solves? And I wonder if, over time, Evolution has learned how to make better designs, advances in evolutionary design. Some folks certainly seem to think so.

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Biology as viewed through 19th Century Lenses

Most modern readers have difficulty appreciating the resilience of spiritual or metaphysical overtones to 19th Century scientific thought, alternatively referred to as “vitalism” & “teleology”. At this point, a quick historical digression is in order.

What exactly is life?”! Traditional education systems were well-grounded in the classics, and many 19th Century naturalists could relate to an ancient Greek philosopher named Aristotle who was convinced no real boundary existed between “living” and “non-living”. According to Aristotle, non-living matter could give rise to living things because our universe possesses some vital life force or soul, “anima”, which could “animate” non-living matter. In Aristotle’s view: the universe, as a whole, had its own soul. In modern terms the universe could be considered as some giant fractal and we are all but elements therein. Even today, various mystical traditions hold similar ideas.

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What did Lamarck and Darwin really say?

Historically and conceptually, modern Genetics and modern Evolutionary Theory are closely intertwined. Mendel and Darwin both published their masterpieces in the mid-1800s and both were promptly misunderstood and discounted for half a century. Both theories required several more “kicks at the can” before final acceptance. Put simply: the Theory of Evolution itself evolved in response to an emerging understanding of Genetics.

Some quick questions:

Question: Name the scientist that first suggested “the effects of use and disuse” were passed from one generation to the next?

Answer: Charles Darwin and NOT Jean-Baptiste Lamarck who actually had a somewhat different theory.

Question: Name the scientist who first to employed the term evolve/evolution while also suggesting human beings had “evolved” from apes?

Answer: That would be Jean-Baptiste Lamarck. (Lamarck in fact invented the word “evolution”, a word which never appeared in Darwin’s Book “Origin of the Species”). Continue reading

Impractical Naturalism of Dan Graur vs. the NIH

I’ll be making a presentation at AM-NAT 2016, and Dan Graur will be the poster boy of impractical naturalism. Below are some things I collected from his websites, some of which I view as highly anti-science. The aim of my presentation isn’t to settle the question of God or no God or ultimate questions of whether godless naturalism is the best description of reality. The goal is to suggest there are some unspoken naturalistic creeds that often take priority over experiments and observations. In a manner of speaking, there are some interpretations of naturalism that actually go against dispassionate examination of how the natural world actually operates.
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Miracles of Evolution

From time to time, when I am not actively engaged in “dishonest quote-mining” of materialists and evolutionists, I take time to actually read their writings. Today I was reading John Maynard Smith.

I now want to take a great leap forward in time, and suppose that not only has a modern protein-synthesizing machinery evolved, but that specific enzymes exist catalysing specific reactions, and that the organism has a cell membrane which prevents the products of catalysis from diffusing away.

– p. 115

This isn’t a great leap forward in time, it’s just a great leap. Poof! A cell membrane! I love how that just magically appeared. Let’s assume a fully functional cell membrane.

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Tetrapod Evolution and the Evolution of Consciousness

It is here proposed that the evolution of life was destined to produce self consciousness out of physical matter just as surely as self-consciousness is destined to be produced by the build up of matter from the human zygote.

Our external vantage point allows us to see the process whereby an individual human matures from the point of conception  We are in a position to witness all the stages in the life of individual humans. Activities such as birth, death, growth and decay go on all around us. Conversely on the grand scale of things, taking life as a whole, we are in the middle of evolving life and so we don’t have an overall, clear picture of the process.

In this video Sean B. Carroll states that:
…living things are occupying a planet whose surface is always changing. Hurricanes, earthquakes, volcanoes, tectonic movement, ice ages, climate changes whether local or global, all of these keep changing the environments that species are in, they are running to keep up and most of the time they fail. So we have to think about earth’s history to understand life’s history. We have to understand what’s going on at any particular place to appreciate what’s going on with any particular species.

The same could be said for the cells in your body. Their environment is always changing and most of them do not survive as you change from embryo to adult. From an individual cell’s point of view there may not seem to be any direction.Some live some die, some change slowly, others change dramatically. But from the higher perspective of the whole body there certainly is direction.

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Wright, Fisher, and the Weasel

Richard Dawkins’s computer simulation algorithm explores how long it takes a 28-letter-long phrase to evolve to become the phrase “Methinks it is like a weasel”. The Weasel program has a single example of the phrase which produces a number of offspring, with each letter subject to mutation, where there are 27 possible letters, the 26 letters A-Z and a space. The offspring that is closest to that target replaces the single parent. The purpose of the program is to show that creationist orators who argue that evolutionary biology explains adaptations by “chance” are misleading their audiences. Pure random mutation without any selection would lead to a random sequence of 28-letter phrases. There are 27^{28} possible 28-letter phrases, so it should take about 10^{40} different phrases before we found the target. That is without arranging that the phrase that replaces the parent is the one closest to the target. Once that highly nonrandom condition is imposed, the number of generations to success drops dramatically, from 10^{40} to mere thousands.

Although Dawkins’s Weasel algorithm is a dramatic success at making clear the difference between pure “chance” and selection, it differs from standard evolutionary models. It has only one haploid adult in each generation, and since the offspring that is most fit is always chosen, the strength of selection is in effect infinite. How does this compare to the standard Wright-Fisher model of theoretical population genetics? Continue reading

Hopelessly frustrated – most likely confused regarding latest on Xenoturbella

I would be grateful if somebody could help me out here as Bioinformatics is not my strong card.

Regarding the recent Nature publication

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

I query the authors’ explanation; to wit…

The sister group relationship between Nephrozoa and

Xenacoelomorpha supported by our phylogenomic analyses implies that the last common ancestor of bilaterians was probably a benthic, ciliated acoelomate worm with a single opening into an epithelial gut, and that excretory organs, coelomic cavities, and nerve cords evolved after xenacoelomorphs separated from the stem lineage of Nephrozoa.

 

My problem arises with their placement of Ctenophora on their own phylogenetic tree as the “more primitive out-group” (for lack of better words on the spur of a rushed moment).  Myself, I always considered Ctenophora as bilateral – in this case more primitively bilateral which IMHO should root the bilateran tree… which of course begs more than one question upon rereading their analysis.

Forget Ctenophores – what about Cnidarians!?  Some taxonomists argue that Cnidarians are descendents of ancient bilateral coelomates and not the other way around. Biologists have known since the 1920s that Cnideria had a directive axis which gave them right and left-hand sides.  Volker Schmidt goes on to argue that non-radially organized hydrozoan larvae have an anterior concentration of sensory and ganglionic nerve elements, suggesting that a fundamental genetic toolkit for the establishment of bilateral and polarized anatomies was already present before the Cnidaria-Bilateria divergence.  Volker Schmidt goes so far as to suggest that diploblastic status of adult Cniderians is derived and that true mesoderm can be even be detected during Cniderian embryogenesis.  OK – I concede that last argument is particularly contentious… but you get my drift.

I am partial to the notion the UrBilateran that subsequently gave rise to “Protostomes” & Deuterostomes and was itself coelomate with possessed a dorsal nerve chord.  Any subsequent acoelomy and pseudocoelomy was derived… ditto ventral nerve chords.  But hey…  now I am being really contentious!