Discussion of fine-tuning at Journal of Theoretical Biology

_{Denyse O'Leary

June 19, 2020

Biology, Fine tuning, Intelligent Design}

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World hasn’t ended yet:

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.
Steiner Thorvaldsen and Ola Hössjer , “[article title]” at Journal of Theoretical Biology

The paper is open access.

From the paper: “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.”

It would be nice to have a civilized discussion of what fine-tuning means and implies in biology. Would incorporating an expectation of fine-tuning into biology hypotheses lead to quicker advances sooner? How will we test this—assuming that the village Darwin mob doesn’t storm the place, demanding that we shut down the discussion?

One issue is that nature is vast and we must make quicker progress than we are now doing if we are to address a number of problems. Can we frame fine-tuning hypotheses in such a way that we can acquire more knowledge faster via detection of expected patterns?

Comments

The organisms of TODAY are NOT the intelligently designed organisms! Disorders and diseases have come about thanks to genetic accidents, errors and mistakes. It's dumb to think that even if something was perfectly designed that it had to remain perfect.ET_{June 20, 2020
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EDTA @ 7
It implies optimization to a high degree of precision in at least one area or aspect, such that we can find it and realize its fine-tunedness. It does not imply that something is physically perfect. (We don’t even have a definition of that against which to judge anything.) So it does not have to be fine-tuned in every possible way.
I think we would all agree that it is currently beyond the capacity of human science and technology to design and build large multi-cellular organisms such as ourselves. If we were designed then it must have been by a more advanced extraterrestrial intelligence. We cannot know for certain how a more advanced intelligence might accomplish its designs so all we can do is look to human design and human designers generally. If they go to great lengths to optimize the performance of some parts of a design, they are unlikely to compromise those parts by sub-standard design elsewhere. A civil engineer who designs a bridge using the lightest, strongest, high-tensile materials available, is unlikely to specify the cheapest iron rivets he can find to hold the whole thing together. Yes, there are some impressive "parts" in living things which function extremely well. But there are other parts that look more like a kludge and, overall, living creatures like us are prone to a wide range of disorders and diseases that must call into question whether we are entitled to assume that we were designed at all.Seversky_{June 20, 2020
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In the following video Dr. Walter Bradley goes over the fine tuning of the fundamental universal constants, light, and biological life for each other.
Creation of the Cosmos - Dr. Walter Bradley - Walter Bradley - (35:49 minute mark) video https://youtu.be/T4_SQzM-1AY?t=2149
And here is an article from Dr. Bradley entitled, “Is There Scientific Evidence for the Existence of God? How the Recent Discoveries Support a Designed Universe”, in which Dr. Bradley also goes over the fine tuning of the fundamental universal constants, light, and biological life for each other.
Is There Scientific Evidence for the Existence of God? How the Recent Discoveries Support a Designed Universe - Dr. Walter L. Bradley Is There Scientific Evidence for the Existence of God? How the Recent Discoveries Support a Designed Universe - Dr. Walter L. Bradley Excerpt: Furthermore, the frequency distribution of electromagnetic radiation produced by the sun must be precisely tuned to the energies of the various chemical bonds on Earth. Excessively energetic photons of radiation (i.e., the ultraviolet radiation emitted from a blue giant star) destroy chemical bonds and destabilize organic molecules. Insufficiently energetic photons (e.g., infrared and longer wavelength radiation from a red dwarf star) would result in chemical reactions that are either too sluggish or would not occur at all. All life on Earth depends upon fine-tuned solar radiation, which requires, in turn, a very precise balancing of the electromagnetic and gravitational forces. As previously noted, the chemical bonding energy relies upon quantum mechanical calculations that include the electromagnetic force, the mass of the electron, the speed of light (c), and Planck's constant (h). Matching the radiation from the sun to the chemical bonding energy requires that the magnitude of six constants be selected to satisfy the following inequality, with the caveat that the two sides of the inequality are of the same order of magnitude, guaranteeing that the photons are sufficiently energetic, but not too energetic.{22},,, Substituting the values in Table 2 for h, c, G, me, mp, and e (with units adjusted as required) allows Equation 3 to be evaluated to give:,,, In what is either an amazing coincidence or careful design by an intelligent Creator, these constants have the very precise values relative to each other that are necessary to give a universe in which radiation from the sun is tuned to the necessary chemical reactions that are essential for life. This result is illustrated in Figure 3, where the intensity of radiation from the sun and the biological utility of radiation are shown as a function of the wavelength of radiation. The greatest intensity of radiation from the sun occurs at the place of greatest biological utility.,,, http://www.leaderu.com/offices/bradley/docs/scievidence.html
In the paper Dr. Bradley also lists four graphs. At the bottom of the four graphs he states:
The visible portion of the electromagnetic spectrum (~1 micron) is the most intense radiation from the sun (Figure 3.1); has the greatest biological utility (Figure 3.2); and passes through atmosphere of Earth (Figure 3.3) and water (Figure 3.4) with almost no absorption. It is uniquely this same wavelength of radiation that is idea to foster the chemistry of life. This is either a truly amazing series of coincidences or else the result of careful design.,,, It is remarkable that both the Earth's atmosphere and water have "optical windows" that allow visible light (just the radiation necessary for life) to pass through with very little absorption, whereas shorter wavelength (destructive ultraviolet radiation) and longer wavelength (infrared) radiation are both highly absorbed, as seen in Figure 3.{23} - ibid
And as the following video states at the 4:00 minute mark,,,
4:00 minute mark,,, “These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe’s entire range of electromagnetic emissions.” Privileged Planet (Chapter 9 of 12) https://www.youtube.com/watch?v=quhucmOAdss
And in the following article entitled 'The "just right" relationship of the light spectrum and photosynthesis', the author points out that for photosynthesis to occur, 'light must be of the right color. Light of the wrong color won't do the trick'. ,,, and the article further goes on to state “There was only one chance in 10^25 of the Sun's providing just the right kind of light necessary for us,,,”
The " just right " relationship of the light spectrum and photosynthesis Excerpt: The American astronomer George Greenstein discusses this in The Symbiotic Universe, p 96: Chlorophyll is the molecule that accomplishes photosynthesis... The mechanism of photosynthesis is initiated by the absorption of sunlight by a chlorophyll molecule. But in order for this to occur, the light must be of the right color. Light of the wrong color won't do the trick.,,, The harmony between stellar and molecular physics that Greenstein refers to is a harmony too extraordinary ever to be explained by chance. There was only one chance in 10^25 of the Sun's providing just the right kind of light necessary for us and that there should be molecules in our world that are capable of using that light. This perfect harmony is unquestionably proof of Intelligent Design. http://reasonandscience.catsboard.com/t1545-origin-and-evolution-of-photosynthesis
Moreover, the efficiency of photosynthesis trounces any machine man has ever built in terms of efficiency. The following study found that ‘Certain biological systems living in low light environments have unique protein structures for photosynthesis that use quantum dynamics to convert 100% of absorbed light into electrical charge,,,’
Unlocking nature's quantum engineering for efficient solar energy - January 7, 2013 Excerpt: Certain biological systems living in low light environments have unique protein structures for photosynthesis that use quantum dynamics to convert 100% of absorbed light into electrical charge,,, These biological systems can direct a quantum process, in this case energy transport, in astoundingly subtle and controlled ways – showing remarkable resistance to the aggressive, random background noise of biology and extreme environments. http://phys.org/news/2013-01-nature-quantum-efficient-solar-energy.html
Whereas, on the other hand, the very best solar panels ever tested in a lab (i.e., not the ones actually available for sale and installation on your house) are only able to convert about 34% of the light that hits them into electricity.,
What's quantum physics got to do with biology? - June 2012 Excerpt: certain bacteria can capture 95% of the light that hits them and turn it into useful energy. Solar panels also convert light from the Sun into energy—but they aren't nearly as good at it. The very best solar panels ever tested in a lab (i.e., not the ones actually available for sale and installation on your house) were able to convert about 34% of the light that hit them into electricity.,, Why can't we use the Sun's energy as effectively as bacteria can? The secret may be that the bacteria are using quantum physics to transmit energy. - per boingboing
Furthermore, and as the following recent 2019 article stated, “It’s now known that some form of positional information makes genes variously switch on and off throughout the embryo, giving cells distinct identities based on their location.,,, that cells extract as much useful information from their complex surroundings as is theoretically possible.,,, when researchers have been able to appropriately determine what cells are doing, many have been surprised to see clear indications of optimization.,,,”
The Math That Tells Cells What They Are - March 13, 2019 Excerpt: It’s now known that some form of positional information makes genes variously switch on and off throughout the embryo, giving cells distinct identities based on their location.,,, That mounting evidence is leading some biologists to a bold hypothesis: that where information is concerned, cells might often find solutions to life’s challenges that are not just good but optimal — that cells extract as much useful information from their complex surroundings as is theoretically possible.,,, when researchers have been able to appropriately determine what cells are doing, many have been surprised to see clear indications of optimization.,,, “I don’t think optimization is an aesthetic or philosophical idea. It’s a very concrete idea,” Bialek said.,,, https://www.quantamagazine.org/the-math-that-tells-cells-what-they-are-20190313/
"Optimal" is not just some word that they are carelessly tossing around. When they describe a biological system as being in a 'optimal' state, they mean exactly what they are saying. As the following article states, "In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants."
William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … Scientists have identified and mathematically anatomized an array of cases where optimization has left its fastidious mark, among them the superb efficiency with which bacterial cells will close in on a food source; the precision response in a fruit fly embryo to contouring molecules that help distinguish tail from head; and the way a shark can find its prey by measuring micro-fluxes of electricity in the water a tremulous millionth of a volt strong — which, as Douglas Fields observed in Scientific American, is like detecting an electrical field generated by a standard AA battery “with one pole dipped in the Long Island Sound and the other pole in waters of Jacksonville, Fla.” In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html
Moreover, as the following article states, “There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.”,,, Moreover, the "amazing and surprising" outcome of the study is applicable to any living organism or biochemical network of any size.,,,”
Math sheds light on how living cells 'think' - May 2, 2018 Excerpt: "Proteins form unfathomably complex networks of chemical reactions that allow cells to communicate and to 'think' --,,, "We could never hope to measure the full complexity of cellular networks -- the networks are simply too large and interconnected and their component proteins are too variable. "But mathematics provides a tool that allows us to explore how these networks might be constructed in order to perform as they do.,,, Dr Araujo's work has focused on the widely observed function called perfect adaptation -- the ability of a network to reset itself after it has been exposed to a new stimulus. "An example of perfect adaptation is our sense of smell," she said. "When exposed to an odour we will smell it initially but after a while it seems to us that the odour has disappeared, even though the chemical, the stimulus, is still present. "Our sense of smell has exhibited perfect adaptation. This process allows it to remain sensitive to further changes in our environment so that we can detect both very faint and very strong odours. "This kind of adaptation is essentially what takes place inside living cells all the time. Cells are exposed to signals -- hormones, growth factors, and other chemicals -- and their proteins will tend to react and respond initially, but then settle down to pre-stimulus levels of activity even though the stimulus is still there. "I studied all the possible ways a network can be constructed and found that to be capable of this perfect adaptation in a robust way, a network has to satisfy an extremely rigid set of mathematical principles. There are a surprisingly limited number of ways a network could be constructed to perform perfect adaptation.,,, Professor Lance Liotta, said the "amazing and surprising" outcome of Dr Araujo's study is applicable to any living organism or biochemical network of any size.,,, https://www.sciencedaily.com/releases/2018/05/180502094636.htm
Thus, in regards to physics, (and to quote Princeton Physics Professor William Bialek), life is "More Perfect Than We Imagined"
Psalm 139:14 I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.
bornagain77_{June 20, 2020
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>Fine-tuning implies a design that is optimized to a high degree of precision. It implies optimization to a high degree of precision in at least one area or aspect, such that we can find it and realize its fine-tunedness. It does not imply that something is physically perfect. (We don't even have a definition of that against which to judge anything.) So it does not have to be fine-tuned in every possible way. All our diseases and so on just mean that we are not perfect, when measured against what we want life to be like.EDTA_{June 19, 2020
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Intelligent Design is NOT anti-evolution. Blind watchmaker evolution is only good at producing disorders and diseases.ET_{June 19, 2020
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Fine-tuning implies a design that is optimized to a high degree of precision. Evolution implies reaching a level of function that may be far from perfect but is just good enough to provide a competitive advantage in the struggle for survival. Bearing in mind all the disorders and diseases to which the human organism is prone, which approach offers a better contextual understanding for what we observe?Seversky_{June 19, 2020
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"..civilized discussion of what fine-tuning means and implies in biology." Sure. I would think the medical industry could benefit from those implications. We have seen the approach born from a vestigial organ point of view. Appendix issue? Cut it out. Gallbladder issue? Cut it out. Parathyroid issue? Cut it out. Thyroid issue? Nuke it (or cut it out). Seems most research goes toward a solution that basically comes down to cut it out or we have a pill for that. If your issue is something like a drought or flood mitigation is fine. The goal is to eliminate a symptom. If you're fixing a car mitigation can make things worse. Knowing how the car is supposed to work leads to restoring the optimal function. One approach addresses symptoms, the other uses the symptoms to address function. I wonder if research looking for the optimal liver or optimal cardio system would be fruitful? If bodies were designed with a specific purpose, organs would have some optimal function or state. Instead of cutting an organ with issues out, perhaps finding out a way to restore it to it's optimal form or function?David P_{June 19, 2020
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Please, let’s keep in mind that the “fine tuning” is a necessary but insufficient condition for OOL. Hopefully we’re all in complete agreement on this. Any objection?jawa_{June 19, 2020
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You can demand anything you want. No one has to listen to your demands, though. :cool:ET_{June 19, 2020
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We can demand the discussion be shut down?Seversky_{June 19, 2020
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