The 'Fathomless Elegance' of Biological Systems

I have just started reading 'Darwin Devolves: The New Science About DNA That Challenges Evolution' by Lehigh University biochemist Michael Behe. It's an impressive read!

He argues that with the continuing advance of modern biological technology, the evidence that unguided evolution can account for all the diversity of living things is unravelling.

A major theme of this book, a a fascinating approach to rebutting  Neo-Darwinism is that “Darwinian evolution proceeds mainly by damaging or breaking genes, which counter-intuitively, sometimes helps survival". In other words, the mechanism is powerfully devolutionary. It promotes the rapid loss of genetic information.

Laboratory experiments, field research, and theoretical studies all forcefully indicate that, as a result, random mutation and natural selection make evolution self-limiting.

To quote Behe:  'Darwin’s mechanism works chiefly by squandering genetic information for short-term gain” (37-38).

Here's a couple of interesting quotes about the book: "Michael Behe, professor of biochemistry at Lehigh University, has been keeping committed Darwinists awake nights for years. His 1996 book Darwin’s Black Box: The Biochemical Challenge to Evolution asked a long-ignored question: If Darwin’s theory explains everything so well, why hasn’t anyone shown how it works at the minutest level, biochemistry? If it doesn’t work there, it doesn’t work anywhere. ¶ Now Behe has released a new book, based on new science, showing once again that it doesn’t work there. Darwin Devolves: The New Science About DNA That Challenges Evolution is going to cause a lot more sleepless nights."TOM GILSON,  

"Behe’s latest masterpiece takes the evidence marshaled in defense of the unbounded power of blind evolution and deftly brings it to the opposite conclusion: evolution is self-limiting by design. Time for the Behe-bashers to retire." DOUGLAS AXE, DIRECTOR OF BIOLOGIC INSTITUTE AND AUTHOR OF UNDENIABLE
 (Douglas Axe is one very impressive scientist himself who has done some amazing research). 

Below are a few quotes from Behe, both from the book and from some followup correspondence: 
“What can the theory account for? If it can’t explain even color patterns, how much has it been exaggerated? Quite a bit, it turns out. To see the problem more clearly, let’s first think about studies of human nutrition. For decades the public was told to avoid foods with a lot of cholesterol. Recently, however, a government panel changed its mind, saying there’s no evidence that’s harmful. Here’s the problem for grand claims about evolution. Science can’t tell if cholesterol is bad for modern humans, who can be studied in great detail. Yet if that’s too hard, then how can science claim to know what affected plants and animals in the distant past? Ones that can’t be studied in real time like people? Ones that encountered myriad environmental influences over millions of years? That’s easy to answer: Science can’t and doesn’t know” ...

“Gratuitous affirmations of a dominant theory can mesmerize the unwary. They lull people into assuming that objectively difficult problems don’t really matter. That they’ve been solved already. Or will be solved soon. Or are unimportant. Or something. They actively distract readers from noticing an idea’s shortcomings. “Of course,” students are effectively prompted, “everyone knows what happened here—right? You’d be blind not to see it—right?” But the complacency isn’t the fruit of data or experiments. It comes from the powerful social force of everyone in the group nodding back, “Of course!” ― Michael J. Behe, Darwin Devolves: The New Science About DNA That Challenges Evolution

"It must take Darwinian tunnel vision to cite a paper that emphasizes how a complex ancestor gave rise to simpler yeast species by losing abilities over time as support for arguing that Darwinian evolution can build complexity. "
From <https://evolutionnews.org/2019/03/response-to-my-lehigh-colleagues-part-2/> 

A basic difference between the views of Greg Lang and Amber Rice and my own concerns the nature of the molecular foundation of life. They object that I consider many biochemical systems to be actual machines. They quote a line from Darwin Devolves stating that protein systems are “literal machines — molecular trucks, pumps, scanners, and more.”

They write disapprovingly that the book claims “rod cells are fiber optic cables … The planthopper’s hind legs are a ‘large, in your face, interacting gear system.’”
They do concede that I didn’t make up those claims about the machine-like nature of the systems out of whole cloth: “Most of the analogies in Darwin Devolves are not Behe’s creation — he has done well to scour press coverage and the scientific literature for relatable metaphors; and he is generous with their use.” Nonetheless, they say, “reality remains: proteins are not machines, a flagellum is not an outboard motor.”
On this point they are simply wrong. “Molecular machine” is no metaphor; it is an accurate description.

Unless Lang and Rice are arguing obliquely for some sort of vitalism — where the matter of life is somehow different from nonliving matter — then of course proteins and systems such as the bacterial flagellum are machinery. What else could they be? Although they aren’t made of metal or plastic like our everyday tools, protein systems consist of atoms of carbon, oxygen, nitrogen, and so on — the same kinds of atoms as are found in inorganic matter, nothing special.
A dictionary definition of “machine” is “an assembly of interconnected components arranged to transmit or modify force in order to perform useful work.” Take a look for yourself here at the gears of the planthopper, here at the fiber-optic cells of the retina, and here at the bacterial flagellum. Do you think they fit that dictionary definition?
Just like arms, legs, and jaws at the macro-level of life, all of which are organized to perform tasks and work by mechanical forces, so too the molecular foundation of life.
Biologists routinely use the phrase “molecular machine” (just do a search of PubMed or Google Scholar), and have done so for a long time. For example, consider from 1997, “The ATP Synthase — a Splendid Molecular Machine” and from 1999, “The 26S Proteasome: A Molecular Machine Designed for Controlled Proteolysis.”

Organic chemists have also long used the term, albeit for much more modest assemblages than are found in life, even if they did win the 2016 Nobel prize in Chemistry. As the Royal Swedish Academy of Sciences announced then: The Nobel Prize in Chemistry 2016 is awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa for their design and production of molecular machines. They have developed molecules with controllable movements, which can perform a task when energy is added.
Lang and Rice do not argue that proteins are not machines.

Rather, they simply declare “proteins are proteins, and not machines,” list a few things some proteins do, and assume that makes it obvious they can’t be machines: “Proteins are promiscuous. They moonlight, by chance interacting with other cellular components to effect phenotype outside their traditionally ascribed roles.” 

Well, now. So can a nut or bolt be “promiscuous” by, say, holding together various kinds of machines? Can a mousetrap “moonlight” as a tie clip?

What exactly is it about those features they list that contradicts the dictionary definition of a machine? Or contradicts the evidence of your own eyes when viewing the images of protein machinery linked above? — Nothing at all.
Hand-Waving at Irreducible Complexity, Lang and Rice use their misunderstanding of molecular machinery as a basis for attacking irreducible complexity: “By acknowledging the reality that proteins are proteins, and not machines, we immediately recognize the shortcomings of irreducible complexity.” How so?

They quote my definition of IC as “a single system composed of several well matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.” 

They then object that:The concept of irreducible complexity is flawed for two reasons. First, it considers a system only in its current state and assumes that complex interdependency has always existed. Second, irreducible complexity does not consider that proteins perform multiple functions and, therefore, evolutionary paths that seem unlikely when considering only one function may be realized through a series of stepwise improvements on another function.

They are wrong on both counts. There is nothing in the definition of IC that requires their conclusions. Irreducible complexity does focus on the current state of a system, but it does not assume that “complex interdependency has always existed.” Rather, it strongly implies (although does not absolutely rule) that the complex interdependency did not arise by Darwinian processes — that it required intelligent input to produce. IC also does not require that proteins do not perform multiple functions. In fact, in 1996 in Darwin’s Black Box, I pointed out several that do, and showed why that does not help at all in explaining IC.  

After all, I used to believe that a Darwinian process did indeed build the wonders of life; I had no particular animus against it. Yet I believed it on the say-so of my instructors and the authority of science, not on hard evidence. When I read a book criticizing Darwin’s theory from an agnostic viewpoint it startled me, and I then began a literature search for real evidence that random mutation and natural selection could really do what was claimed for them. I came up completely empty.

In the over thirty years since then, I’ve only become more convinced of the inadequacy of Darwinism, and more persuaded of the need for intelligent design at ever-deeper levels of biology, as detailed in my books.Clearly Greg and Amber honestly disagree. How to explain that? To help answer, let’s first consider a different scientific discipline — physics.

The history of physics offers powerful lessons that widespread agreement on even the most basic ideas in a field is no guarantee that there is sufficient evidence to support the theory, or indeed that there is any evidence for it at all. Just ask James Clerk Maxwell, who wrote the article “Æther” in 1878 for the ninth edition of the Encyclopedia Britannica: 

Whatever difficulties we may have in forming a consistent idea of the constitution of the æther, there can be no doubt that the interplanetary and interstellar spaces are not empty, but are occupied by a material substance or body, which is certainly the largest, and probably the most uniform body of which we have any knowledge. [Emphasis added.]

Maxwell, one of the greatest physicists of all time, calculated the density — to three significant figures — of the æther, a substance that doesn’t exist. If that doesn’t make the case for the peril of over-reliance on theory — and the need for profound scientific humility — nothing will. From <https://evolutionnews.org/2019/03/a-response-to-my-lehigh-colleagues-part-3/> 

Even in their own review, at best the authors argue that they see no obstacle to Darwinian processes producing functional complex systems; they surely don’t demonstrate that it can.

And of all the relevant literature in books and journals, the two papers they pointed to as examples of the power of Darwin’s mechanism are quite modest indeed.

When my first book, Darwin’s Black Box, was published in 1996 it elicited comments by bona fide evolutionary biologists such as: “there are presently no detailed Darwinian accounts of the evolution of any biochemical system, only a variety of wishful speculations,” and “There is no doubt that the pathways described by Behe are dauntingly complex, and their evolution will be hard to unravel…. We may forever be unable to envisage the first proto-pathways.” It’s hard to reconcile such statements with an assertion that the data are “more than sufficient.”

As quoted earlier, Lang and Rice write: “Scientists — by nature or by training — are skeptics. Even the most time honored theories are reevaluated as new data come to light.” That claim wouldn’t survive even a short trip through the history of science, which is of course replete with people (that’s another name for scientists) fighting tooth and nail to defend their ideas. Few scientists are as emotionless as Mr. Spock, and to maintain otherwise is little more than group-flattery. More to the point, scientists do not have a corner on the market for skepticism. In all walks of life that trait has its uses. A banker evaluating a loan, a voter listening to a politician’s speech, a teacher wondering whether the dog really did eat this student’s homework, a judge considering whether a defendant is indeed remorseful, an historian evaluating the direction of her academic field — pretty much everyone is skeptical when they smell a rat. And “pretty much everyone” is another way to say “the public.”

For what it’s worth, my advice on this matter for Lang, Rice, and others with similar views is to respect the opinions of the public, even if one disagrees with them and thinks them ill-founded, because, when it comes to the grand claims for Darwin’s theory, many folks think they smell a rat and are prudently exercising their skepticism.

Indeed, instead of blaming the public, they should consider the possibility that perhaps the evidence for the vast scope of Darwin’s theory really isn’t as strong as biologists over the years have been telling each other.   see https://evolutionnews.org/2019/03/a-response-to-my-lehigh-colleagues-part-3/

The world only makes sense if we see it as the product of a great, purposeful, highly intelligent designing Mind.

tbc ...