Fine tuning specifics: applied to biological systems (Introduction)

by David Turell , Wednesday, October 07, 2020, 20:45 (1508 days ago) @ David Turell

A new paper analyzing fine tuning as seen in biology:

https://www.sciencedirect.com/science/article/pii/S0022519320302071

"Abstract
Fine-tuning has received much attention in physics, and it states that the fundamental constants of physics are finely tuned to precise values for a rich chemistry and life permittance. It has not yet been applied in a broad manner to molecular biology. However, in this paper we argue that biological systems present fine-tuning at different levels, e.g. functional proteins, complex biochemical machines in living cells, and cellular networks. This paper describes molecular fine-tuning, how it can be used in biology, and how it challenges conventional Darwinian thinking. We also discuss the statistical methods underpinning fine-tuning and present a framework for such analysis.

"Fine-tuning and design are related entities. Fine-tuning is a bottom-up method, while design is more like a top-down approach. Hence, we focus on the topic of fine-tuning in the present paper and address the following questions: Is it possible to recognize fine-tuning in biological systems at the levels of functional proteins, protein groups and cellular networks? Can fine-tuning in molecular biology be formulated using state of the art statistical methods, or are the arguments just “in the eyes of the beholder”?

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"The odds against our universe developing were “enormous” – and yet here we are, a point that equates with religious implications,

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"Behe exemplified systems, like the flagellum bacteria use to swim and the blood-clotting cascade, that he called irreducibly complex, configured as a remarkable teamwork of several (often dozen or more) interacting proteins. Is it possible on an incremental model that such a system could evolve for something that does not yet exist? Many biological systems do not appear to have a functional viable predecessor from which they could have evolved stepwise, and the occurrence in one leap by chance is extremely small. To rephrase the first man on the moon: “That's no small steps of proteins, no giant leap for biology.”

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"Though proteins tolerate a range of possible amino acids at some positions in the sequence, a random process producing amino-acid chains of this length would stumble onto a functional protein only about one in every 1050 to 1074 attempts due to genetic variation. This empirical result is quite analog to the inference from fine-tuned physics.

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"Recently Kozulic and Leisola (2015) made careful analyses of these results, and concluded that even with very conservative conditions, the probability of finding ATP binding activity that would function in a cell, would be less than 1 in 10.

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"...even if the natural laws work against the development of these “irreducible complexities”, they still exist. The strong synergy within the protein complex makes it irreducible to an incremental process. They are rather to be acknowledged as fine-tuned initial conditions of the constituting protein sequences. These structures are biological examples of nano-engineering that surpass anything human engineers have created. Such systems pose a serious challenge to a Darwinian account of evolution, since irreducibly complex systems have no direct series of selectable intermediates, and in addition, as we saw in Section 4.1, each module (protein) is of low probability by itself.

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"As the complexity of an interacting system increases, the likelihood of such an indirect route drops quickly. Hence, Darwinian explanations of irreducibly complex systems are improbable. Ultimately, this is a question that must be studied both experimentally and by computer simulations. Behe’s concept of irreducible complexity has not been falsified by computer models biochemical or cellular system, “only a variety of wishful speculations”

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"Protein complexes perform their biological functions in a cooperative manner through their participation in many biological processes and networks, from the nucleus to the cell membrane. Cellular networks are also known to contain feedback loops and cycles.

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"A major conclusion of our work is that fine-tuning is a clear feature of biological systems. Indeed, fine-tuning is even more extreme in biological systems than in inorganic systems. It is detectable within the realm of scientific methodology. Biology is inherently more complicated than the large-scale universe and so fine-tuning is even more a feature."

Comment: No question fine tuning is seen in living biology. This paper has lots of mathematics as they try to look for statistical systems to clarify the issue. Much more work is needed is their answer. They widely quote the ID folks as a reasonable basis for this view.