"Origins of Religious Disbelief"

This is a few months old, but I just came across it.

"The origins of religious disbelief "
Ara Norenzayan and Will M. Gervais
Trends in Cognitive Sciences January 2013, Vol. 17, No. 1
http://dx.doi.org/10.1016/j.tics.2012.11.006

Check out a podcast by Gervais, a University of Kentucky prof, on the origins of religious disbelief here, and read the review paper on the subject here.

"Intelligent Design not a true science"

As I recently mentioned, the Alligator's archives are screwed up and a great many links are broken from publications that I or Gator Freethought have gotten in the newspaper. As a result, I'm reposting as many of these as I have the time and ability to, just to preserve and provide an electronic copy of the documents. Below is the first thing I ever submitted to a newspaper in my life, and it got in. After that, I guess it got a little addictive.

Intelligent Design not a true science
by nsfl
http://www.alligator.org/pt2/050826column2.php
published 8/26/2005

In response to Eric Wang's well-written, but somewhat shortsighted column, he cries foul that, "...there is not a marketplace of competing ideas in our public schools today, but only a monopoly of evolutionary theory." Today is the result of 2000+ years of competing ideas. Aristotle and Plato argued that nature, especially living things, showed "final causes" in their apparent design. Today, ID activists claim the same—that nature shows “the evidence of design”. Empedocles, among others, argued that change could occur in organisms to allow adaptation, giving the appearance of design. Darwin argued 150 years ago the same.

The crux of the issue is whether or not a force or "Designer" moves us towards a presumed goal, teleologically. The error in Wang's thinking is that science has, or can, reject or accept this philosophical notion. How? It can, and does, subject the premise of change and adaptation, both of which are natural phenomena, to its method of inquiry. Science is by definition methodological naturalism, and as such posits, tests, and questions only physical and natural phenomena. Science is limited in scope (and "on purpose") to questions of natural philosophy, not whether or not a "Designer" had it all in mind, or whether or not this "Designer" exists. It ignores the question because science is constrained to natural explanation of natural phenomena.

So now the question remains—can science empirically detect God’s fingerprints? Is it possible, without arguing from incredulity, to know scientifically, rather than “by faith” if “designed”? What is the a priori, natural evidence of supernatural creation/design? How does one distinguish ignorance of natural phenomena from knowledge of supernatural phenomena? Is it possible to scientifically argue for Design without arguing from incredulity? For hundreds of years, gaps in knowledge were filled with “God did it”. Now they are being filled with “Designer did it”. Has science proven either one philosophically wrong, or simply shown us that the mechanism by which posited Designers work is inextricable from the natural universe, and that the this universe and its natural laws is all that science can and will comment upon?

So in short, science describes a natural process, known as "descent with modification". If we want to teach science, we teach natural mechanisms and processes, without invoking supernatural causes. If we want to teach anything else, Wang and others had better realize we may no longer honestly call it “science”, but must admit we have moved into metaphysics, philosophy, or theology. Is there a “monopoly” of thought, or is science the one way of rationally, and objectively, viewing our natural universe? Why did the Kansas board consider redefining science itself into one of these latter three? Is it the job of our state, or of families, to lay the foundation for those?

If I get a new link for the Alligator's archive of this, I'll update it.

New NAS Report on Astrobiology & Abiogenesis

**Update: Carl Zimmer remarks on this in the NYT
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A new National Academies of Sciences publication, The Limits of Organic Life in Planetary Systems, can be read for free in HTML at the site, or downloaded as a .pdf after login. The executive summary may be downloaded here as a .pdf (and the entire book here as a .pdf (1.1MB), if you're too lazy to login and do it yourself). I'm reposting some earlier material on abiogenesis, evolution and the origin of the genetic code below, with updated links that were previously broken.

Repost:

I have compiled a very useful list of papers (continually revised), covering abiogenesis, the evolution of genetic information, the origin of the genetic code, and human evolution. I will list some of those papers below.

For more on the evolution of information in the genome:

1. Natural selection as the process of accumulating genetic information in adaptive evolution, M. Kimura, Genetic Research Cambridge, 2 (1961) 127-140
2. Rate of Information Acquisition by a Species subjected to Natural Selection, D.J.C. MacKay, open-source @ http://arxiv.org/, (1999)
3. Evolution of biological information, T.D. Schneider, Nucleic Acids Research, (2000), 2794-2799
4. The fitness value of information, C.T. Bergstrom and M. Lachmann, open-source @ http://arxiv.org/, (2006)
5. Review of W. Dembski’s No Free Lunch, J. Shallit, BioSystems, 66 (2002) 93-99
6. The Evolution and Understanding of Hierarchical Complexity in Biology from an Algebraic Perspective, C.L. Nehaniv and J.L. Rhodes, Artificial Life, 6 (2000) 45–67
7. On the Increase in Complexity in Evolution I, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 63 (1976) 375-384
8. On the Increase in Complexity in Evolution II: The Relativity of Complexity and the Principle of Minimum Increase, P.T. Saunders and M.W. Ho, Journal of Theoretical Biology, 90 (1981) 515-530

In addition to these papers, I wanted to highlight six other recent reviews that give a great overview of the present scientific thinking towards the origin of the genetic code:

1. "Selection, history and chemistry: the three faces of the genetic code.", Trends in Biochemical Sciences, Volume 24, Issue 6, 1 June 1999, Pages 241-247 (full-text .pdf)
   
2. "Genetic code: Lucky chance or fundamental law of nature?", Physics of Life Reviews, Volume 1, Issue 3, Dec 2004, Pages 202-229 (full-text .pdf) [low-quality pub, but expansive overview of the subject]
   
3. "Stepwise Evolution of Nonliving to Living Chemical Systems.", Origins of Life and Evolution of the Biosphere, Volume 34, Issue 4, Aug 2004, Pages 371–389 (full-text .pdf)
4. "The Origin of Cellular Life.", Bioessays, Volume 22, Issue 12, Dec 2004, Pages 1160-1170 (full-text .pdf)
5. "The Origin of the Genetic Code: Theories and Their Relationships, A Review.", Biosystems, Volume 80, Issue 2, May 2005, Pages 175-184 (full-text .pdf)
6. "The Origin and Evolution of the Genetic Code: Statistical and Experimental Investigations.", Robin D. Knight, Ph.D. Dissertation, June 2001.
   

And three more about evolution and complexity:

1. Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons, Human Mutation, 28(2):99-130, Oct 2006, Download PDF
2. The origin of new genes: Glimpses from the young and old, Nature Reviews Genetics, 4(11): 865-875 Nov 2003, Download PDF
3. Evolution of biological complexity, PNAS, 97(9):4463-4468, April 2000, Download PDF

No one pretends that all questions are sufficiently answered within the complex topics surrounding abiogenesis and the evolution of life. But to pretend that there are no answers is to engage in self-deception.
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Technorati tags: Abiogenesis, Intelligent Design, Evolution, Creationism

The Science of Climate Change

So I finally got around to watching An Inconvenient Truth -- rented it from the UF Library West, in fact.

While I had already heard many of the climate change skeptics' arguments, and I was already aware of the consensus position, one particular thing jumped out at me from the film: the study cited by Gore, performed by Naomi Oreskes, which purportedly summarizes the scientific consensus on the issue by finding 0 out of 928 papers disagreeing with the consensus position. Here is a long excerpt of the article in Science:

The scientific consensus is clearly expressed in the reports of the Intergovernmental Panel on Climate Change (IPCC). Created in 1988 by the World Meteorological Organization and the United Nations Environmental Programme, IPCC's purpose is to evaluate the state of climate science as a basis for informed policy action, primarily on the basis of peer-reviewed and published scientific literature (3). In its most recent assessment, IPCC states unequivocally that the consensus of scientific opinion is that Earth's climate is being affected by human activities: "Human activities ... are modifying the concentration of atmospheric constituents ... that absorb or scatter radiant energy. ... [M]ost of the observed warming over the last 50 years is likely to have been due to the increase in greenhouse gas concentrations" [p. 21 in (4)].

IPCC is not alone in its conclusions. In recent years, all major scientific bodies in the United States whose members' expertise bears directly on the matter have issued similar statements. For example, the National Academy of Sciences report, Climate Change Science: An Analysis of Some Key Questions, begins: "Greenhouse gases are accumulating in Earth's atmosphere as a result of human activities, causing surface air temperatures and subsurface ocean temperatures to rise" [p. 1 in (5)]. The report explicitly asks whether the IPCC assessment is a fair summary of professional scientific thinking, and answers yes: "The IPCC's conclusion that most of the observed warming of the last 50 years is likely to have been due to the increase in greenhouse gas concentrations accurately reflects the current thinking of the scientific community on this issue" [p. 3 in (5)].

Others agree. The American Meteorological Society (6), the American Geophysical Union (7), and the American Association for the Advancement of Science (AAAS) all have issued statements in recent years concluding that the evidence for human modification of climate is compelling (8).

The drafting of such reports and statements involves many opportunities for comment, criticism, and revision, and it is not likely that they would diverge greatly from the opinions of the societies' members. Nevertheless, they might downplay legitimate dissenting opinions. That hypothesis was tested by analyzing 928 abstracts, published in refereed scientific journals between 1993 and 2003, and listed in the ISI database with the keywords "climate change" (9).

The 928 papers were divided into six categories: explicit endorsement of the consensus position, evaluation of impacts, mitigation proposals, methods, paleoclimate analysis, and rejection of the consensus position. Of all the papers, 75% fell into the first three categories, either explicitly or implicitly accepting the consensus view; 25% dealt with methods or paleoclimate, taking no position on current anthropogenic climate change. Remarkably, none of the papers disagreed with the consensus position.

Admittedly, authors evaluating impacts, developing methods, or studying paleoclimatic change might believe that current climate change is natural. However, none of these papers argued that point.

This analysis shows that scientists publishing in the peer-reviewed literature agree with IPCC, the National Academy of Sciences, and the public statements of their professional societies. Politicians, economists, journalists, and others may have the impression of confusion, disagreement, or discord among climate scientists, but that impression is incorrect.

To be fair, Richard Lindzen followed this study up with an op-ed criticizing the methodology, but so far as I know, there is no counterargument that relies upon an examination of the literature like hers. Lindzen pointed out there are only 905 abstracts available (not 928), and that the consensus position is only explicitly endorsed in 13 of these abstracts.

Pretty stark, eh?

Also see New Scientist, Real Climate, and the science page at Al Gore's site.