Behe on IC (Introduction)
by David Turell 
, Sunday, December 24, 2023, 16:54 (125 days ago)
In his words:
https://www.discovery.org/f/45693/
"Here analogies to mousetraps break down somewhat, because the parts of a molecular system have to automatically find each other in the cell. They can’t be arranged by an intelligent agent, as a mousetrap is. To find each other in the cell, interacting parts have to have their surfaces shaped so that they are very closely matched to each other, such as pictured in Figure 19.2. Originally, however, the individually-acting components would not have had complementary surfaces. So all of the interacting surfaces of all of the components would first have to be adjusted before they could function together. And only then would the new function of the composite system appear. Thus, I emphasize strongly, the problem of irreducibility remains, even if individual proteins homologous to system components separately and originally had their own functions.
***
"In Darwin’s Black Box I argued that the blood clotting cascade is an example of an irreducibly complex system. (Behe 1996, 74-97) As seen just by eye, clotting seems like a simple process. A small cut or scrape will bleed for a while and then slow down and stop as the visible blood congeals. However, studies over the past fifty years have shown that the visible simplicity is undergirded by a system of remarkable complexity. (Halkier 1992) In all there are over a score of separate protein parts involved in the vertebrate clotting
system. The concerted action of the components results in formation of a weblike structure at the site of the cut, which traps red blood cells and stops bleeding. Most of the components of the clotting cascade are involved not in the structure of the clot itself, but in the control of the timing and placement of the clot. After all, it would not do to have clots forming at inappropriate times nand places. A clot that formed in the wrong place, such as in the heart or brain, could lead to a heart attack or stroke. Yet a clot that formed even in the right place, but too slowly, would do little good.
***
"This is not at all what Darwinists expected. As Bruce Alberts wrote earlier in the article “The Cell as a Collection of Protein Machines”: We have always underestimated cells. Undoubtedly we still do today. But at least we nare no longer as naive as we were when I was a graduate student in the 1960s. Then most of us viewed cells as containing a giant set of second-order reactions....But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that
nearly every major process in a cell is carried out by assemblies of 10 or more protein
molecules. And, as it carries out its biological functions, each of these protein
assemblies interacts with several other large complexes of proteins. Indeed, the entire
cell can be viewed as a factory that contains an elaborate network of interlocking
assembly lines, each of which is composed of a set of large protein machines. (Alberts
1998)
"The important point here for a theory of intelligent design is that molecular machines are not confined to the few examples I discussed in Darwin’s Black nBox. Rather, most proteins are found as components of complicated molecular machines. Thus design might extend to a large fraction of the features of the cell, and perhaps beyond that into higher levels of biology. Progress in twentieth-century science has led us to the design hypothesis. I expect progress in the twenty-first century to confirm and extend it."
Comment: Behe sees IC everywhere down to the complex reactions in a single cell. So, do I.
"consider the words of the philosopher Michael Ruse:
For example, Behe is a real scientist, but this case for the impossibility of a small-step
natural origin of biological complexity has been trampled upon contemptuously by the scientists working in the field. They think his grasp of the pertinent science is weak and
his knowledge of the literature curiously (although conveniently) outdated. For example, far from the evolution of clotting being a mystery, the past three decades of work by Russell Doolittle and others has thrown significant light on the ways in which clotting came into being. More than this, it can be shown that the clotting mechanism does not have to be a one-step phenomenon with everything already in place and functioning. One step in the cascade involves fibrinogen, required for clotting, and another, plaminogen [sic], required for clearing clots away. (Ruse 1998)"
Behe on IC: a new Neo-Darwinism is required
by David Turell , Friday, December 29, 2023, 17:06 (120 days ago) @ David Turell
A new paper recognizes the need:
https://evolutionnews.org/2023/12/5-story-of-2023-peer-reviewed-paper-finds-neo-darwini...
"A peer-reviewed paper published towards the end of last year in the Elsevier journal Progress in Biophysics and Molecular Biology has a provocative title: “Neo-Darwinism Must Mutate to Survive.” The paper’s abstract opens with points that few would dispute:
"Darwinian evolution is a nineteenth century descriptive concept that itself has evolved. Selection by survival of the fittest was a captivating idea. Microevolution was biologically and empirically verified by discovery of mutations.
"However, there then comes a major “but”:
"There has been limited progress to the modern synthesis. The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution.
***
"...just what is the basis for saying this? It’s calculations showing that the likelihood of microevolutionary processes adding up to macroevolutionary changes is highly improbable:
"Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10^50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms.
" “We are critical, as previously explained, of the position that macroevolution is sufficiently explained by the processes useful for microevolution — in particular that mutations and survival of the fittest are adequate to the task,” and argue that “Microevolution does not explain speciation — only smaller changes.” (my bold)
***
"...clearly they share a critical perspective on neo-Darwinism that is very similar to that of the intelligent design community. Consider this striking passage:
"Survival of the fittest is adequate to select for such changes (gains) which occur within one genome primarily by single fixed mutations (and perhaps sometimes by horizontal gene transfer). Macroevolution, however, requires major changes necessitating multiple changes that logically most frequently occur in multiple genomes. Therefore, the concept survival of the fittest is inadequate to conserve individual changes in multiple genomes where the individual changes generate no increased fitness. … Thus, survival of the fittest is illogical when proposed as adequate for selecting the origination of all complex, major, new body-types and metabolic functions because the multiple changes in multiple genomes that are required have intermediate stages without advantage; selection would not reasonably occur, and disadvantage or death would logically prevail. (my bold)
***
"It is our perspective that the burden is too great for survival of the fittest to select evolutionary changes that accomplish all evolutionary novelty. Thus, evolution lacks a sufficient mechanism for multifactorial selections because a process that looks forward, is nonrandom, deterministic, or occurs by an unknown biological process, is required. The position of mainstream biologists regarding this aspect of evolution is that nature is always non-purposeful and, therefore, the proposed selection (process, force, tendency), could not possibly be natural (scientific). However, our perspective is that this is a supposition of necessity rather than an established principle. Logic demands that it be open to investigation. This first requires an openness to ideas and science must be open to new ideas.
***
"They use a case study of the origin of the Krebs cycle — a metabolic pathway involving 12 enzymes that is necessary for life. They believe that this is a useful test for evolution. They assume that the genome is “ripe” to produce each enzyme where a minimal number of mutations is needed for a gene to suddenly become functional. They therefore choose an incredibly generous value of 0.00001 as the probability that a given enzyme can be created by a single mutation.
"They calculate the likelihood of producing all 12 enzymes needed to produce a selectable function as 10^51. They note this is below 10^50, a probability that was called “negligible” by Émile Borel, the French mathematician, who stated “this process of evolution involves certain properties of living matter that prevent us from asserting that the process was accomplished in accordance with the laws of chance.”
***
"In the end, producing a complex feature like the Krebs cycle is just too improbable because “Selection based on survival of the fittest, for anything beyond single mutational changes in a genome, is insufficient scientifically and biologically.” They conclude, “there is something besides mutations and survival of the fittest needed to explain evolution.'” (my bold)
Comment: As Behe noted about reactions in cells being IC, the Krebs cycle is obviously IC md is in all cells that are active. This negates dhw's expanded assumptions about the meaning of IC's required associations. The complex cellular reactions and organs must all be considered as stand alone, just like the mousetrap doing its function with no outside help.