Alex Rosenberg in his new book "The Atheist's Guide to Reality: Enjoying Life without Illusions", in his article for the New York Times and in the article "The Disenchanted Naturalist’s Guide to Reality" writes to defend scientism and naturalism. There are of course different varieties of naturalism, for example neo-Aristotelian naturalism, Scholastic naturalism, methodological naturalism etc. So too for scientism. The way Alex Rosenberg describes his naturalism and scientism seems to imply a sort of Empirical Scientism and Empirical Naturalism whereby all knowledge is limited to the empirical sciences.

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"What distinguishes systems biology from earlier traditions is the tendency to define importance less in operational terms (e.g., necessary or sufficient to produce a behavior) than in terms of relevance to the goals of a system. In making this leap, systems biology inextricably binds itself to teleology (Lander, 2004). Indeed, without the presupposition of goals or purposes, the very notion of “system” itself is hollow."

-Arthur D Lander, "Morpheus Unbound: Reimagining the Morphogen Gradient",

A recent discovery highlights the importance of viewing living things as purposeful and goal-oriented systems. Here, scientists at the Fred Hutchinson Cancer Research Center discover that breast cancer cells are in sophisticated communication with a whole array of physiological processes within the body from wound repair to immune response to metabolic homeostasis and the blood clotting cascade – all from the very earliest stages. We can detect these communications in the plasma proteome as nascent cancer cells seek strategies and suitable recruits to assist metastasis.

It's sort of like studying terrorists by listening to their communications chatter as they try to recruit and plan their attack, as opposed to studying them by watching them blow up a disco.

In this comment at the DI blog, Casey seems bewildered by the fact that researchers can spot selection at work without knowing the exact function of the new gene:

To illustrate why I used the word “magic,” we often see that papers (which Nick would probably claim show the “origin of new genetic information”) invoke natural selection, but then:
DO NOT EVEN KNOW THE FUNCTION OF THE GENE, AND THUS HAVE NO IDEA WHAT FUNCTION WAS BEING SELECTED FOR

…

(For example, the following papers invoke natural selection to explain the origin of a gene whose function was at-the-time unknown, meaning they did not even know what function was being selected

…

Forgive me Nick, but I have trouble accepting claims of natural selection when evolutionary biologists:
(a) don’t even know the function that is being selected,

Casey meet Kimura

It is often claimed that quantum mechanics or quantum phenomena disprove the principle of causality or at least cast doubt on whether it is a logically defensible axiom. Examples of quantum phenomena include radioactive decay, the Stern-Gerlach experiment, the double-slit experiments etc. Examples of people using quantum phenomena in such a type of an argument can be found here, here, here, here, and here etc. Olegt thinks the Stern-Gerlach experiment is an example whereby "classical logic is simply not equipped to deal with phenomena of this sort". That may be true, I don't know what olegt exactly means when he talks about “classical logic”. I just disagree that the principle of causality needs to be abandoned when it comes to quantum physics.

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People often say this or that is not "science" or that  "science" has proven this or "science" can or can't do that. Are they all talking about the same thing? Perhaps not.

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It's fun reading the gnus and the creationists attack Darrel Falk. Kind of reminds me of this.

My nostalgic streak continues

If Eoandromeda appeared after the cnidarians, the authors argue, bilateral symmetry would have to have evolved twice — once for the cnidarians and again for the bilateral organisms that came after Eoandromeda. Far simpler is the idea that Eoandromeda evolved first (see 'Simplest solution'). "This model of animal relationships calls for the least number of origins of bilateral symmetry," says Bengtson.

here

It'd hardly be worth noting, if not for the fact that the only 9/11 "truther" I've seen pop up on either side of the creationism/evolution blogosphere is Bilbo, formerly of the pro-ID Telic Thoughts blog. Bilbo defended his regular postings about how 9/11 must've been an elaborate plot by whoever, writing:

here

I don't think that 9/11 truthiness resembles anything, whether it be ID or "Darwinism". Yes, ID creationist Bilbo was (and still is) a toofer (and we've debated on this issue). However, there are toofers on all sides of this debate, such as philosopher James Fetzer, co-editor of the ID critique published in Synthese recently.

Over at the DI blog we read this about a recent PLOS paper

This is a further indication, of course, that non-coding regions of the genome, previously dubbed "junk DNA," are functional.

here

I don't see how finding high levels of conservation for non-protein coding sequence around some, but not all, wing development genes means that all non-coding regions are functional (particularly around the key gene Wingless and Ecdysone Receptor).

It's doubtful this heroic effort has shed any light on evolution. Nor is likely that similar efforts will do so any time soon

That's a strange thing to say considering that, among other things, they identified an expansion of the family of alcohol dehydrogenase genes (via duplication):

Among the genes identified, we discovered five tandemly arranged genes similar to Alcohol dehydrogenase (Adh), which potentially represent an expansion in the Lepidoptera. Comparative studies of sequence, expression and function of these genes are necessary to shed light onto their evolutionary history and ecological importance.

Like many of my generation, I became an interventionist in Bosnia. Sickened by carnage, and by the lies and ignorance of Western politicians who prolonged the carnage, I understood that caution — or more accurately hypocrisy masquerading as prudence — can be as criminal as recklessness.

A war with very specific reasons and equally specific crimes committed overwhelmingly by Serbian forces was dressed up as a millennial conflict beset by Balkan fog and moral equivalency in order for craven Western leaders to justify an inaction that killed.
here

A very interesting philosophical paper on these issues by a danish philosopher. Discusses one of the many physical conditions I find interesting, the closeness of the "Hoyle state" to the 4He+8Be threshold. If this closeness would not exist, there would not be enough carbon and oxygen.

Since its origin in the early 1970s the anthropic principle has exerted a major influence on ideas of theoretical cosmology. Although it is today as controversial as ever, its impact is beyond discussion. This paper examines some of the early formulations of anthropic ideas, including those of Russian cosmologists G. Idlis and A. Zelmanov. These early formulations are at best vague anticipations of the anthropic principle, which as a research tool for cosmological theory was first proposed by B. Carter in 1973. The paper offers an account of how Carter came to the idea of the anthropic principle and how he originally formulated it.

here