…complexes of just three or more different proteins are beyond the edge of evolution. They are lost in shape space.

In other words, you might get one protein waiting around with nothing to do. But if two proteins had to wait around with nothing to do until the third protein evolved, it wouldn't happen.

Now we may disagree with the arguments that Behe uses to get to this conclusion. But the conclusion itself looks pretty reasonable to me. Are there serious biologists who think that two useless proteins could just be waiting around until a third one evolves in order for the three of them to have a function? I doubt it.

The real issue, I think, comes in his next sentence:

And the great majority of proteins in the cell work in complexes of six or more. Far beyond that edge.

Though he doesn't state it, what he seems to be implying is that most of these complexes are in fact irreducibly complex. That they could not have come about gradually from simpler complexes involving less proteins. Now perhaps that's true. But perhaps it isn't. And that, it seems to me, is what is really at issue.

Evolution—the naturalistic kind—is dangerous. I’ve never seen that danger exposed so clearly as in Jesse Bering’s article today at Scientific American’s website, Polyamory chic, gay jealousy, and the evolution of a broken heart [caution: crude language]. He writes,

HT: Clare

There’s a strange whiff in the media air, a sort of polyamory chic in which liberally minded journalists, an aggregate mass of antireligious pundits and even scientists themselves have begun encouraging readers and viewers to use evolutionary theory to revisit and revise their sexual attitudes and, more importantly, their behaviors in ways that fit their animal libidos more happily.

… the basic logic is that, because human beings are not naturally monogamous but rather have been explicitly designed by natural selection to seek out ‘extra-pair copulatory partners’—having sex with someone other than your partner or spouse for the replicating sake of one’s mindless genes—then suppressing these deep mammalian instincts is futile and, worse, is an inevitable death knell for an otherwise honest and healthy relationship.

If you believe, as I do, that we live in a natural rather than a supernatural world, then there is no inherent, divinely inspired reason to be sexually exclusive to one’s partner. If you and your partner want to … [multiple suggested acts, omitted for reasons of decency] … then by all means do so (and take pictures). … Right is irrelevant. There is only what works and what doesn’t work, within context, in biologically adaptive terms….

Will naturalism's epicurean cadre ever cease their exploitation of evolution to further misguided behavioral norms?

Scientism is the ugly step-child of naturalism. Acceptance of scientism brings one a step closer to building a philosophical foundation needed for authoritarianism. The building process is fraught with logical slights of hand, subtle insertions of straw men and intellectual arrogance; all tools in the process of shaping young minds and a broader societal agenda.

HT: Clare, Paul and Joseph

Pernicious effects of scientism are detectable at the boundary of solid science and the philosophical ramifications of it. Emergence is a potential entry point. Physical phenomenon alluded to by emergence are clear. The concept is useful and necessary. Emergence offers a conceptual gateway to understanding even as its causal nuances and applicability offer opportunity for mischief. The linked article cites this quote of P.W. Anderson:

The ability to reduce everything to simple fundamental laws does not imply the ability to start from those laws and reconstruct the universe..The constructionist hypothesis breaks down when confronted with the twin difficulties of scale and complexity. At each level of complexity entirely new properties appear. Psychology is not applied biology, nor is biology applied chemistry. We can now see that the whole becomes not merely more, but very different from the sum of its parts.

Psychology is not applied biology but hazy understandings allow for weak speculative linkages and at times trouble. Also from the same link:

Emergence helps to explain why the fallacy of division is a fallacy. According to an emergent perspective, intelligence emerges from the connections between neurons, and from this perspective it is not necessary to propose a "soul" to account for the fact that brains can be intelligent, even though the individual neurons of which they are made are not.

Observe the entry point for mischief and scientism. The first sentence cites the fallacy of division. The following one advances the fallacy. That understanding brain function is advanced by a connections perspective is not disputed. But let the reader beware of the insufficiency of that perspective to demolish anything more than straw men. Human intelligence is not explained by vast numbers of neural connections. One could cite analogies between the mechanical connections in a machine and understanding the machine's function. But even that is only partially useful as laws of physics governing the interaction of machine parts are understood. Physical laws applicable to reasoning processes are not. Gapping is not even the issue. The unaided flight of jet engines and an association of a vast complex of neural connections with a capacity for human reason is.

The soul is a concept outside science. But direct implications stemming from it, like that of free will, touch on the boundary lines between empirically determinable and philosophically based beliefs. In fact a scientific explanation for free will may not even be possible. The very existence of free will can be evidence for the supernatural and a refutation of both naturalism and scientism.

C. S. Lewis on Mere Liberty and the Evils of Statism, Part 3 appears at the patheos site. Lewis gets to the heart of the pernicious application of scientism. It advances the cause of authoritarianism. If a virtue of science is a revelation of the truth of the natural world, the vice of scientism lies with its false linkage to that notion to concepts that are inherently political in nature. Reason is constricted by acceptable inferences of it. People of reason are defined by their acceptance of some philosophical pathways to the exclusion of other rational ones. Smug arrogance, rather than reasoned exchanges, become the currency by which scientism is propagated. The results are evident in a review of modern history. C.S. Lewis:

Under modern conditions any effective invitation to Hell will certainly appear in the guise of scientific planning — as Hitler's regime in fact did. Every tyrant must begin by claiming to have what his victims respect and to give what they want. The majority in most countries respect science and want to be planned. And, therefore, almost by definition, if any man or group wishes to enslave us it will of course describe itself as "scientific planned democracy". All the more reason to look very carefully at anything which bears that label.

What is interesting is that philosopher and ID critic Robert Pennock offered an analogy very similar to the second to explain the (d)evolution of the flagellum. A marine chronometer depends upon springs and balances in order to keep time accurately at sea. Suppose it lost one or more springs. It wouldn't be any good for keeping time at sea, but it could still function very well as a clock on land. Thus, he suggested, the flagellum also may have devolved from a more complex system in a similar manner.

I don't think Pennock offered any suggestions as to the identity of the more complex system from which the flagellum evolved. However, and no doubt inadvertently, he did hit upon the conceptual problem of the evolution of the flagellum. It is easier to imagine a marine chronometer losing a balance spring and still functioning as a land clock, than it is to imagine a land clock accidentally acquiring all the right springs in the right place and functioning as a marine chronometer.

Which is why the Pallen/Matzke paper may not have succeeded in dismissing "the need for any great conceptual leaps in creating a model of flagellar evolution." Conceptually, it might be far easier to imagine a flagellum losing a few parts and functioning as a secretion system, than imagining a secretion system gaining just the right parts in the right places and functioning as a flagellum.

But science isn't just about imagining scenarios. It's about trying to test them. Could we test the flagellum to T3SS scenario? For example, could we place the appropriate flagellar bacteria in an environment that selects for secretion and see what happens?

Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints

The authors are Douglas D. Axe, Brendan W. Dixon and Philip Lu. It is published in PLoS ONE. The abstract:

The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions—relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure–function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure–function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector proteins by evolving successive lines from a single starting gene. These homologues show sequence and structure divergence resembling those of natural homologues in many respects, suggesting that the system may be sufficiently life-like for informative comparison to biology.

There was also this:

However, the models purporting to explain structural radiation generally use simplistic representations of selectable function. As Zeldovich et al. point out, many evolutionary models lack any causal connection at all between sequence and function [8]. But even when causal models are used, they tend to be simplistic. Hirst has discussed the various aspects of structural soundness (e.g., folding stability or speed) that are singled out as proxies for selectable function [9]. Recognizing the distinction between structural soundness and functional utility, he required lattice structures to form a pocket (analogous to an active-site cleft) in order to be deemed functional [9]. This was certainly a step in the right direction, but the underlying problem remains: While these properties are all necessary for the function of real proteins, they are not sufficient. If they were, one good structure would suffice, whereas in reality we see not only a great variety of structures but also a strong connection between this variety and the great variety of specific functions they perform.

Oversimplification of function tends to obscure this fundamental connection. As an example, consider the recent lattice study of Zeldovich et al., which ties a genome's fitness to the lowest stability of its encoded proteins [8]. Their model enables a population carrying the gene for a single lattice structure to diversify to the point where evolved structures span the entire space of possibilities. But it achieves this not only by using stability as a proxy for function, but also by dispensing with the notion of a stability threshold—a minimal stability, below which structures are deemed non-functional [8]. In the end, structure space is freely explored here because it is entropically favorable for it to be explored, making structural variety an entropic artifact rather than a functional necessity. Because one good structure really does suffice in such a world, it seems unlike the real world, where “the great functional capacity and importance of proteins largely stems from the remarkable ability of these polymers to adopt distinct 3-dimensional structures” [3].

Can a new model be framed so as to capture this fundamental aspect of biology? A key step in this direction may be to base it on real function rather than a definitional substitute for function. Because real functions involve both specificity and real constraints, this would guarantee a level of functional realism that is not otherwise easily achieved. This principle is demonstrated by artificial-life simulations, like Avida [10], where computational tasks must be performed in order to gain a selective advantage. But because these tasks are performed by instructions rather than structures, Avida does not readily lend itself to protein studies.

Credit: bigfoto.com
http://www.bigfoto.com/

If you consider all the talking points in ID–irreducible complexity, privileged planet, cosmological fine-tuning–some of which I find useless (irreducible complexity) and some of which I find interesting (the apparent sensitivity of life to the values of constants) no one observation from the world of science or mathematics has ever struck me as a more powerful apologetic than Feynman's and Wigner's point.

The world is not only governed by orderly laws, but those laws are expressible in simple enough terms that we can make sense out of them and use them to make astonishingly accurate predictions. As Feynman suggested, if I read him correctly, science can never explain why this is so. It is, in fact, unreasonable that this happens.

Faith in man-made global warming had never been more widespread, with liberal academics and media subjecting to ridicule any who dared question the "settled science."

Ridicule. That's a favored tool. Practically speaking how is it working out? We'll find out in November.

How the tables have turned in a short time. On May 20, Oxford Union, the prestigious 187-year-old English debating society, formally considered the question of whether it was more important to focus on growing the economy or solving global warming.

Very good. Global warming bills are among many options about how to best allocate our resources to meet multiple problem threats. They need to be considered on a comparative basis and not in isolation. The private sector in the USA is moving in the direction of cleaner energy sources without the policing of big brother.

"We think we need public policy that's based in facts, rather than facts that are based on a public agenda," Colorado State University professor Scott Denning said.

Don't be dictated to by special interest groups if this is truly just about science.