I thought I'd add an informational post as a response to Behe's new post criticizing the CNE theory of complexity. He writes:

The last step of the model is the “co-adaptation” of the two proteins, where other, complementary mutations occur in both proteins. Yet this implies that the protein complex must suffer deleterious mutations at least every other step, provoking the “co-adaptive” mutation to fix in the population. Wouldn’t these deleterious mutations be very unlikely to spread in the population?

We're actually talking here about slightly deleterious or neutral mutations and only in small populations. Still, my problem with CNE is actually that it downplays evolvability aspects. Regardless , here's a recent Nature publication 'Non-adaptive origins of interactome complexity' by Fernández A. and Lynch M. and the reaction of W. Ford Doolittle to that article are relevant to the whole CNE discussion.

This leads to the hypothesis that the accumulation of mildly deleterious mutations in populations of small size induces secondary selection for protein–protein interactions that stabilize key gene functions. By this means, the complex protein architectures and interactions essential to the genesis of phenotypic diversity may initially emerge by non-adaptive mechanisms.
here

To Professors Jerry Coyne and Richard Dawkins,

The concept of natural selection on the surface seems to be a rather simple concept to grasp and you both have explained the concept in your respective writings. I have a few question regarding your views about the nature of natural selection, questions that I feel are not explicitly answered or addressed in your various writings. I have four basic questions, each with their own subset of questions:

1) Is natural selection a prescriptive or descriptive term?
2) Is natural selection a mechanism?
3) Is natural selection a cause or a force?
4) Is natural selection a process or an outcome?
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Ethan Siegel has a few thing to say about nothing over at his blog. He assures people that there is a difference between the scientific definition of nothingness and philosophical (and logical IMO) definition of nothingness.

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The question of the likelihood or ‘inevitability’ of something human-like evolving seems to me a rather minor question of quantitative guesswork. I do have a fellow-feeling with Conway Morris over the general power of convergent evolution. I feel closer here to Conway Morris than I do to Gould’s ‘contingency’. But I am leagues away from anyone who draws theological conclusions from convergent evolution. Indeed, I am positively infuriated by the suggestion, as I am sure you are.
here

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The project to try and banish teleology by mechanistic-cum-empiricist interpretations of physical science looks like…well, still a project. People have been and still are trying and trying to explain it away and some even call it "science". Yet, no matter how hard people try, teleology is still “grinning residually up at us like the frog at the bottom of the beer mug”. Never mind the ironic fact that trying to explain away teleology is a teleological, goal-directed enterprise in itself.

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In 2000 Hanahan and Weinberg described the basic hallmarks of cancer (Hanahan and Weinberg, 2000). Briefly, these hallmarks are described as acquired capabilities.
1) Self-Sufficiency in Growth Signals
2) Insensitivity to Anti-growth Signals
3) Evading Cell Death
4) Limitless Replicative Potential
5) Sustained Angiogenesis
6) Tissue Invasion and Metastasis
This year that list was extended by them (Hanahan and Weinberg, 2011). They "summarize the essence of each hallmark" as described in 2000 and continue to address new developments and describing "two enabling characteristics crucial to the acquisition of the six hallmark capabilities, two new emerging hallmark capabilities, the constitution and signaling interactions of the tumor microenvironment crucial to cancer phenotypes, and we finally discuss the new frontier of therapeutic application of these concepts". The enabling characteristics include:
7) Unstable DNA (this links nicely to Heng et al.'s view that heterogeneity is a cause)
8 ) Promotes inflammation The acquired characteristics include:
9) Deregulated metabolism
10)Evading the immune system

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“We found that approximately half of individual differences … in intelligence can be explained by genetics and across a great variety of genes,” said Peter Visscher, co-author of a paper appearing in the Aug. 12 issue of the journal Molecular Psychiatry. “[And] this is likely to be an underestimate because we could only detect variation that is correlated with common DNA markers.”

here

I still have yet to read the book. However, Dr. Wilkins completely disappointed me with his review of this particular book. Not only did he fail to address the scientific examples, but he also made a rather bizarre statement (IMO):

Engineers do not accomplish defined functional goals. Instead they employ the results of prior experience on the presumption that what worked in the past will work now (and that includes the choice of goals themselves). No engineer has some cognitive “noetic ray” that allows them to see into the future; they are using the tested results of the past.

I would not really say that I agree with this as I think engineers probably do set/specify functional goals – although of course informed by experience and tested past results.

The goals of the goal-oriented model are defined by the designers or engineers with which they can analyze how to achieve the goal by means of the task to be performed. The impact analysis is when one or some of the tasks are affected in the future, for example when a Web application is developed and then some part of the web is changed, with the goal-oriented model I can know which tasks are affected, thus knowing if the goal can be achieved or not. Importantly, some of the tasks in the goal-oriented model are implemented, and some of them are not implemented at the beginning of the analysis.

A few outspoken scientists argue that it is wrong to believe in a supreme intelligence, but I don't think this is wrong in the usual sense of the word. In fact, a recent poll has shown that 36% of scientists believe in God, and about half are spiritual in some sense. How does a religious scientist accommodate both the questioning that is characteristic of scientific practice and a belief that there is a supreme intelligence behind it all?

I think there is a way for the questioning method of science to meet religious belief without generating the distressing anti-science clash that is newsworthy, yet ultimately destructive. It is clear that matter and energy interact according to a set of physical laws, and strong evidence indicates that the universe had a beginning we call the Big Bang. A religious scientist can comfortably believe that the universe and its laws were put in place by a creator. Science has nothing to say about this statement of faith because it cannot be submitted to experimental tests or observation.

If the emergence of cancer is a causal process and we want to know what causes cancer and we want to design something that causes cancer cells to die, I suppose a good way to start is to have a proper understanding of what a cause is in the first place. Again, what follows is an attempt to briefly lay out a few important Scholastic concepts with regard to causality as it will be relevant before ditching "random variation" and natural selection" as "explanations" or "reasons" or "causes" for the emergence of cancer. Again, I will mostly use the texts used previously for those interested in delving further into the topic.
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Before describing the process for the emergence of cancer using Aristotle’s four causes and hylemorhism, the basic metaphysical picture needs to be clear. Books can be and should be written about this topic. What follows is an attempt to briefly highlight a few important Scholastic concepts related to the accidental mode of being and kinds of change. I will mostly use the following texts for those interested in delving further into the topic.

Coffey P (1914). Ontology: or, The theory of being; an introduction to general metaphysics, Longmans, Green and co. (link)
Coffey P (1938). The Science of Logic: Conception, judgment and inference, P. Smith. (link)
Joyce GH (1916) Principles of logic, Longmans, Green and Co. (link)
Mercier DF (1916) A Manual of Modern Scholastic Philosophy, London, Kegan Paul, Trench, Trubner & Co., Ltd. (link)
Oderberg DS (2007) Real Essentialism, Routledge. (link)
Rickaby JJ (1916) General Metaphysics, London, Longmans. Green. And Co. (link)

Figure 1: Left to right: Albertus Magnus, Avincenna, Robert Grosseteste,William of Ockham, Duns Scotus and Thomas Aquinas. From http://medievalstudies.georgetown.edu/resources/cmp/

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