Evolutionary biology

Denyse O’Leary writes about Barbara Forrest’s fact-free attack on Frank Beckwith, which recently appeared in Synthese. While Denyse focused more on Beckwith’s response to Forrest’s scholarly article diatribe, it might be worth taking a closer look not only at Forrest’s article, but the entire issue of Synthese in which it is found. First Forrest. In the abstract for her article with the breathtaking title “The non-epistemology of intelligent design: its implications for public policy”, Bar writes:

Intelligent design creationism (ID) is a religious belief requiring a supernatural creator’s interventions in the natural order. ID thus brings with it, as does supernatural theism by its nature, intractable epistemological difficulties.

Okay, so we’re only 2 sentences into the abstract and we can already see that Bar has no clue what ID is about. Read More ›

Dr. Cornelius Hunter recently posted on some findingsfrom the NCSE (the National Center for the Selling of Evolutioner, I mean, Science Education, on how many biology teachers are reluctant to teach evolution. Now, TV personality Bill Nye “The Science Guy” has given us his two cents worth on this controversy. In the interview he’s asked what he thinks about the reluctance of teachers regarding evolution. He says:

It’s horrible. Science is the key to our future, and if you don’t believe in science, then you’re holding everybody back. And it’s fine if you as an adult want to run around pretending or claiming that you don’t believe in evolution, but if we educate a generation of people who don’t believe in science, that’s a recipe for disaster. We talk about the Internet. That comes from science. Weather forecasting. That comes from science. The main idea in all of biology is evolution. To not teach it to our young people is wrong.

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Conventional, and fairly obvious, wisdom would suggest that the bear avoids being noticed by its prey by blending in with the landscape and moving through the snow on silent feet. Evolving that way should be easy enough – the colour gene drops out, and … We readily assume that the prey is on land, casting a wary eye around. Not necessarily. Some remarkable BBC footage suggests it may not be so simple: You can see it, no problem, but you must click the BBC link. – d. Here, you will hear the bear stomping and see it clearly visible above clear ice – as it would be to a seal approaching a blowhole. Presumably, the seal – apprised of an Read More ›

Cornell Geneticist John Sanford argued that Darwinism is wrong because the rate of genetic deterioration is so high that natural selection could not arrest it. If natural selection cannot arrest genetic deterioration, how then could it be the mechanism for evolutionary improvement? Sanford predicted through his research that human genome is deteriorating. This was a daring scientific prediction, and now Michael Lynch of the elite National Academy published on the topic for his inaugural paper. The NAS has now made the paper available to the public free of charge. Read it, and weep, literally: Rate, Molecular Spectrum, and Consequences of Human Mutation Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very Read More ›

This is a multi-part post in response to Merlin’s paper, “Evolutionary Chance Mutation: A Defense of the Modern Synthesis’ Consensus View”. See introduction and table of contents.

Merlin spends a large part of the paper trying to establish what does and does not constitute a directed mutation. Merlin, I think, fails in her attempt to properly differentiate Darwinian and Lamarckian mutations because she has not taken into account the main purpose of Darwinism as described in Part II of this essay. To recap, the entire point of Darwinism was to frame biology as to extricate itself from final causes. Therefore, any mode of genetic adaptation which fails to do so is non-Darwinian.

Explaining Away Apparent Purposefulness

Merlin, it seems, is somewhat aware of this, as she tries to explain away any apparent purposefulness within mutational mechanisms. She says,
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Caroline Crocker, of American Institute for Science and Technology Education (AITSE), writes me to comment,

Scientific Integrity and Dr. Hauser

Can being disorganized lead to scientific fame?

Harvard University scientist Marc Hauser became famous for his work in cognitive evolution. As a psychologist who investigates the neurological basis for morality and works with primates and people, you would think he would know better than to, at the least, keep inadequate records or, much worse, fabricate data. But, Dr. Hauser is on “academic leave” after a Harvard University faculty committee found him “solely responsible for eight counts of scientific misconduct”.

The history of the problems is long, starting in 1995, but the Harvard investigation was only initiated in 2007. Perhaps enough students had complained or maybe the comments from peers were becoming too embarrassing. Now Michael Ruse’s concern is that the field of evolutionary biology itself will suffer from bad publicity.

But surely this should not be the main concern! Dr. Ruse makes the point that Dr. Hauser may have been under pressure to attract grant money, graduate students, and postdoctoral students–and this is mostly accomplished through publication. The pressure may have been exacerbated by the fact that Dr. Hauser holds a prestigious position at a leading university. In other words, Dr. Hauser may have succumbed to political, financial or even ideological temptation to forgo scientific integrity–thereby publishing at least three unsubstantiated scientific papers, possibly misleading numerous other scientists, and wasting countless tax dollars.

What is the answer? Raising the profile of scientific integrity in our nation. We need, as Kate Shaw said, to “encourage responsible science, experimental replication, and an even more thorough review process.”

Many will know Crocker as the scientist who got the boot from George Mason University for questioning the Prophet Darwin. I understand she will be posting here after she finalizes her book.

That said, here’s The Edge on Marc Hauser:

Along with Irv Devore, he teaches the Evolution of Human Behavior class, a Core Course at Harvard with 500 undergraduate students. The interdisciplinary course, “Science B29” (nickname: “The Sex Course”), has been running for 30 years, was started by Devore and Robert Trivers, and is the second most popular course on campus, behind “Econ 10”. Section teachers over the years comprise a who’s who of leading thinkers and include people such as John Tooby and Leda Cosmides, and Sarah B. Hrdy. In 1997-98, he sponsored a trial run of “Edge University” in which the students in Science B29 received Edge mailing as part of required reading in the course. Read More ›

Casey Luskin, Program Officer in Public Policy and Legal Affairs for the Discovery Institute, has recently published an article entitled ZEAL FOR DARWIN’S HOUSE CONSUMES THEM:HOW SUPPORTERS OF EVOLUTION ENCOURAGE VIOLATIONS OF THE ESTABLISHMENT CLAUSE in the Liberty University Law Review. Luskin continues to be a favorite target of the anti-ID crowd over at The Panda’s Thumb, and this article is no exception. The task of misrepresenting Luskin fell to attorney Timothy Sandefur, who frequently contributes to the Panda’s Thumb blog site.

Luskin clearly lays out the intent of the article in the very first paragraph and writes:

The common stereotype in the controversy over teaching evolution holds that it is the opponents of evolution who are constantly trying to “sneak religious dogma back into science education.”1 While perhaps in some
instances this caricature is not entirely undeserved,2 the mainstream media and legal community pay scant attention to incidents where proponents of Darwinian evolution transgress the boundary between church and state erected by the Establishment Clause. By documenting ways that evolution advocates encourage violations of the Establishment Clause—in some instances, explicitly advocating state endorsement of pro-evolution religious viewpoints in the science classroom—this Article will show the impropriety of the common “Inherit the Wind stereotype.”3

Apparently this clear of a statement isn’t good enough for Sandefur who sniffs:

It will come as no surprise to anyone that Luskin’s argument is flimsy, his evidence illusory, his readings of the case law distorted, and the overall effect essentially a fun-house mirror version of First Amendment law.

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Bioethicist Gregory Kaebnick, Ph.D., has an interesting take on the recently announced synthetic cell created by a team of researchers led by J. Craig Venter at the J. Craig Venter Instititute (JVCI). In a recent article in The Scientist entitled Is the “Synthetic Cell” about Life?, Kaebnick writes:

…the technical accomplishment is not quite what the JCVI press release claimed. It’s hard to see this as a synthetic species, or a synthetic organism, or a synthetic cell; it’s a synthetic genome of Mycoplasma mycoides, which is familiar enough. David Baltimore was closer to the truth when he told the New York Times that the researchers had not created life so much as mimicked it. It might be still more accurate to say that the researchers mimicked one part and borrowed the rest.

The explanation from the Venter camp is that the genome took over the cell, and since the genome is synthetic, therefore the cell is synthetic. But this assumes a strictly top-down control structure that some biologists now question. Why not say instead that the genome and the cell managed to work out their differences and collaborate, or even that the cell adopted the genome (and its identity)? Do we know enough to say which metaphor is most accurate?

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A friend directed me to this fun little article from the Jewish World Review. I’m not a regular reader of JWR, so missed this wonderful little piece from Paul Greenberg, in which he recalls the Sokal Hoax of 1996. For those not familiar with it, the Sokal Hoax was an article written by Professor Alan Sokal, a professor of Physics at New York University and submitted to a not too widely followed academic journal called Social Text as part of a series on Science wars. The article was entitled Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity,( Social Text, Spring/Summer 1996), and was, according to Greenberg, Read More ›

In the latest issue of Nature, a definitive role for pseudogenes is established. In the last sentence of the Abstract the authors conclude: These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs. Haven’t read the full article* (no time at present), but there’s a related link at PhysOrg.com that gives an overview. Yes, “junk” DNA now “communicates” with itself. A new “language”, an RNA language, is discovered. Another 30,000 pieces of functional information (over and above proteins) are part of cell architecture. And even more for Darwinists to explain per RM+NS. And the old standard explanation, of gene duplication and pseudogenes ‘evolving’ new function, takes Read More ›

Pagels and others (like Nei) have argued that the majority of biological features could not have emerged from Darwinian means. If they are right, it stands to reason that if evolution is true, it has to be mostly non-Darwinian. At UD we have explored various non-Darwinian theories of evolution by scientists like Jukes, King, Kimura, Nei, Morgan, Bateson, Davison, and others. There are more names such as : Portmann, Troll, Heikertinger, Goldshmidt, Bertalanffy. Martin also lists Friedrich Nietzsche and Marx as non-Darwinians. Here is the website: http://cadra.wordpress.com/

Formation of “irreducibly complex systems” via purported scaffolding has been an ongoing debate amongst evolution and intelligent design theorists. Now a natural scaffolding has been discovered – and it may itself be part of another “irreducibly complex system”.

Sharma et al., discovered that natural fat works as a biological scaffold for “cells to grow and mature”. Then fascinatingly, “when the cells have matured into the desired tissue, they secrete another substance that breaks down and destroys the scaffold.”

Could the formation of this natural biological scaffold AND its subsequent removal form an irreducibly complex system? E.g. is such scaffolding essential or necessary to achieve a minimum growth rate? Could the secretion removing the scaffolding also be essential to trim function rather than being “bloated”? I expect this fat scaffolding/removal system will be found to be another irreducibly complex system which very efficiently reuses its materials.

See: Body fat may help us heal Read More ›

recent molecular data supports the theory of mutation-driven evolution rather than neo-Darwinism.

Masotoshi Nei
Member National Academy of Sciences
Selectionism and Neutralism

Not only is the notion of Darwinism challenged by ID proponents and creationists, but it is also challenged by non-Darwinian theories of evolution. The competing schools of thought are the Mutationists and the Neutralists. Dawkins describes some of the history of the Mutationists versus the Darwinists:

It is hard to comprehend now but, in the early years of this [20th] century when the phenomenon of mutation was first named, it was not regarded as a necessary part of Darwinian theory but an alternative theory of evolution!

Richard Dawkins
Blindwatchmaker

Darwinism so dominates evolutionary thinking that most presume evolution must proceed under the influence of selection. Not so. In fact the absence of selection is also a mechanism of evolution! In the words of yet another member of the National Academy of Sciences:

many genomic features could not have emerged without a near-complete disengagement of the power of natural selection

Michael Lynch
The Origins of Genome Architecture, intro

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Today’s Fox News website had this little story, entitled Climate Scientists Plan to Hit Back at Skeptics. In the article, Stanford University climate researcher Paul R. Ehrlich had this to say about global warming skeptics:

“Most of our colleagues don’t seem to grasp that we’re not in a gentlepersons’ debate, we’re in a street fight against well-funded, merciless enemies who play by entirely different rules,” Paul R. Ehrlich, a Stanford University researcher, said in one of the e-mails.

Its worth noting Ehrlich’s use of the phrase “merciless enemies”. In other words, challenge the preferred dogma, and you’re not just ignorant – you’re an enemy, and thus, by extension, deserving of any and all ad hominem attacks hurled your way. One can almost hear “let me assure you, we haf vays to make you accept the dogma!” Read More ›

This is the first of probably three posts on applied Intelligent Design. This is not an extensive list of applications of ID concepts, but I thought that giving people examples of how ID can be not only interesting and informative but actually useful in solving both biological and engineering problems.
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