At Mind Matters News: Life is so wonderfully finely tuned that it’s frightening

_{Denyse O'Leary

September 20, 2021

Fine tuning, Intelligent Design, Irreducible Complexity}

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A mathematician who uses statistical methods to model the fine tuning of molecular machines and systems in cells reflects…

Ola Hössjer: It turns out that [only] a very small fraction of amino acids sequences give us a functioning protein. That is the first definition of fine tuning. It’s complex. It is unlikely to happen by chance, to get a functioning protein. The second part: We should have an independent specification. In this case, the specification is that the protein works. For that reason, a protein is an example of a fine tuned structure in biology.
Then we could get up to the next hierarchical level and look at complexes of proteins, like molecular machines. The ribosome that manufactures proteins in the cell is itself a molecular machine that consists of many proteins that have to be arranged in a certain structure in order to work.
Another example is mitochondria in the cell plasma. These are the power stations of the cell that generate ATP. This is also an example of a molecular machine where all parts have to be structured in a certain way. One could say — we talked about this during the first episode — a specific case or a special case of fine tuning are irreducibly complex systems: It consists of many small parts, and all parts must function in order for the whole system to work.
Robert J. Marks: So if you remove one of the parts in the process you’re talking about, the whole thing breaks down. Let me give you a guess as an example, on the macroscopic level. Our lungs, for example, have a bunch of individual cells, and one of these cells has no idea what the other cells are doing but they all work together to allow us to breathe and put oxygen in our blood and other things. Would that be a big example of what you’re talking about?
Ola Hössjer: Yes. And another, you could view the whole cell as a cellular city. It has a network of roads, or factories and power stations.
Robert J. Marks: These are things which display irreducible complexity. You take away one piece, the whole thing falls apart. News, “Life is so wonderfully finely tuned that it’s frightening” at Mind Matters News

Takehome:
Every single cell is like a city that cannot function without a complex network of services that must all work together to maintain life.

You may also wish to read:

Ours is a finely tuned — and No Free Lunch — universe. Mathematician Ola Hössjer and biostatistician Daniel Andrés Díaz-Pachón explain to Walter Bradley Center director Robert J. Marks why nature works so seamlessly. A “life-permitting interval” makes it all possible — but is that really an accident?

and

Fine-tuning? How Bayesian statistics could help break a deadlock Bayesian statistics are used, for example, in spam filter technology, identifying probable spam by examining vast masses of previous messages. The frequentist approach assesses the probability of future events but the Bayesian approach assesses the probability of events that have already occurred.

Comments

Don't forget about "quantum criticality", where certain proteins have a characteristic that only 1 in 10^50 random molecules would have.EDTA_{September 21, 2021
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BA77
If Evolutionary Biologists had any integrity whatsoever, they would never, ever, admit to anyone that they made a living as Evolutionary Biologists.
Or else they would be calling for a significant reform of that field of study. Looking for Bob O'H to comment. And Seversky also.Silver Asiatic_{September 21, 2021
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As well, (as if that was not astonishing enough), the Ribosomes of the cell are also found to be very similar to a CPU in an electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 Excerpt: An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
Moreover, the construction of protein making machines, (ribosomes), in eukaryotic cells is an extremely complex process that requires more than 200 helper proteins to get the job done.
Armed Forces in the Cell Keep DNA Healthy - September 8, 2015 Excerpt: According to Prof. Hurt, the production of ribosomes is an extremely complex process that follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be "trimmed" at specific points during the manufacturing process, and the superfluous pieces are discarded. "Because these processes are irreversible, a special check is needed," explains Ed Hurt. - per evolution news
Question, how in blue blazes did the first ribosome ever get get constructed if there were no ribosomes around to construct the scores of 'helper proteins' needed to construct the first ribosome? As George Church of Harvard himself asked of the ribosome, "how did that thing come to be?"
LIFE: WHAT A CONCEPT! Excerpt: The ribosome,,,, it's the most complicated thing that is present in all organisms.,,, you find that almost the only thing that's in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that's what I would focus on; how did the ribosome come to be" - George Church http://www.edge.org/documents/life/church_index.html
And as Robert Shapiro stated, "I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously"
Leading Biologists Marvel at the "Irreducible Complexity" of the Ribosome, but Prefer Evolution-of-the-Gaps - Feb, 2008 Excerpt: CHURCH: But that’s what we need to do — otherwise they’ll call it irreducible complexity. If you say you can’t get below a ribosome, we’re in trouble, right? We have to find a ribosome that can do its trick with less than 53 proteins. VENTER: In the RNA world, you didn’t need ribosomes. CHURCH: But we need to construct that. Nobody has constructed a ribosome that works well without proteins. VENTER: Yes. SHAPIRO: I can only suggest that a ribosome forming spontaneously has about the same probability as an eye forming spontaneously.,,, - per evolution news
As to mitochondria, i.e. ATP production
Your Motor/Generators Are 100% Efficient – October 2011? Excerpt: ATP synthase astounds again. The molecular machine that generates almost all the ATP (molecular “energy pellets”) for all life was examined by Japanese scientists for its thermodynamic efficiency. By applying and measuring load on the top part that synthesizes ATP, they were able to determine that one cannot do better at getting work out of a motor,,, The article was edited by noted Harvard expert on the bacterial flagellum, Howard Berg. http://crev.info/content/111014-your_motor_generators Thermodynamic efficiency and mechanochemical coupling of F1-ATPase - 2011? Excerpt: F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,,?Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase. http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1 See also: Davies et al., “Macromolecular organization of ATP synthase and complex I in whole mitochondria,” Proceedings of the National Academy of Sciences and: Tamás Beke-Somfai, Per Lincoln, and Bengt Nordén, “Double-lock ratchet mechanism revealing the role of [alpha]SER-344 in F0F1 ATP synthase,” Proceedings of the National Academy of Sciences Molecular Machines - ATP Synthase: The power plant of the cell https://www.youtube.com/watch?v=XI8m6o0gXDY Shaking up cell biology - October 20, 2014 Excerpt: a team of scientists,,, has imaged mitochondria for the first time oscillating in a live animal,,, “The movements could last from tens of seconds to minutes, which was far longer and frequently at a faster tempo than observed previously in cell culture,” said Roberto Weigert, Ph.D.,,, The mitochondria also appear to synchronize their movements not only in an individual cell but, quite unexpectedly, into a linked network of oscillators vibrating throughout the tissue. “You look through the microscope, and it almost looks like a synchronized dance,” said Weigert. “The synchronization, to borrow an old cliché, tells us that we need to differentiate the forest from the trees — and vice versa — when studying mitochondria. It may be that the forest holds the key to understanding how mitochondria function in human health and disease.”,,, “We saw things in live animals that you don’t see in cell culture. The reasons, in this case, very well may be that the mitochondria continue to receive an influx of signals from the blood vessels, the nervous system, and their surrounding environment. The entire system can’t be reassembled (i)n cell culture.”,,, http://www.nih.gov/news/health/oct2014/nidcr-20.htm Powering the Cell: Mitochondria - video http://www.youtube.com/watch?v=RrS2uROUjK4
Of further note,
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/
For Darwinists to adamantly and stubbornly claim, in the face of all contrary evidence, that this unparalleled level of optimal 'fine-tuning' came about by mindless processes is to insult the intelligence of every human being on the face of earth. If Evolutionary Biologists had any integrity whatsoever, they would never, ever, admit to anyone that they made a living as Evolutionary Biologists. Garbage Truck driver is, by a long shot, a far more noble occupation than Evolutionary biologist is. (My apologies to any Garbage Truck drivers that I may have insulted by comparing you to Evolutionary Biologists).bornagain77_{September 21, 2021
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Moreover, (to the surprise of researchers operating under Darwinian presuppositions), proteins are found to be “analogous to the way wine glasses tremble”,,, "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave,",,, "Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don't get any sustained sound."
Symphony of Life, Revealed: New Imaging Technique Captures Vibrations of Proteins, Tiny Motions Critical to Human Life - Jan. 16, 2014 Excerpt: To observe the protein vibrations, Markelz' team relied on an interesting characteristic of proteins: The fact that they vibrate at the same frequency as the light they absorb. This is analogous to the way wine glasses tremble and shatter when a singer hits exactly the right note. Markelz explained: Wine glasses vibrate because they are absorbing the energy of sound waves, and the shape of a glass determines what pitches of sound it can absorb. Similarly, proteins with different structures will absorb and vibrate in response to light of different frequencies. So, to study vibrations in lysozyme, Markelz and her colleagues exposed a sample to light of different frequencies and polarizations, and measured the types of light the protein absorbed. This technique, , allowed the team to identify which sections of the protein vibrated under normal biological conditions. The researchers were also able to see that the vibrations endured over time, challenging existing assumptions. "If you tap on a bell, it rings for some time, and with a sound that is specific to the bell. This is how the proteins behave," Markelz said. "Many scientists have previously thought a protein is more like a wet sponge than a bell: If you tap on a wet sponge, you don't get any sustained sound." http://www.sciencedaily.com/releases/2014/01/140116084838.htm
Moreover, not only are proteins 'finely-tuned' to receive photons, proteins, (and DNA), are also found to emit specific frequencies of 'bio-photon emissions'
The Real Bioinformatics Revolution - Proteins and Nucleic Acids 'Singing' to One Another? - 2007 Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see' and ‘hear' each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1 000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions. ,,, The same results were obtained when regulatory DNA sequences were analysed. http://www.i-sis.org.uk/TheRealBioinformaticsRevolution.php Cellular Communication through Light - 2009 Excerpt: Information transfer is a life principle. On a cellular level we generally assume that molecules are carriers of information, yet there is evidence for non-molecular information transfer due to endogenous coherent light. This light is ultra-weak, is emitted by many organisms, including humans and is conventionally described as biophoton emission. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005086
As to ribosomes,
The Ribosome: Perfectionist Protein-maker Trashes Errors - 2009 Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm Inferring efficiency of translation initiation and elongation from ribosome profiling - 2020 Abstract Excerpt: Our method distinguishes between the elongation rate intrinsic to the ribosome’s stepping cycle and the actual elongation rate that takes into account ribosome interference. This distinction allows us to quantify the extent of ribosomal collisions along the transcript and identify individual codons where ribosomal collisions are likely. When examining ribosome profiling in yeast, we observe that translation initiation and elongation are close to their optima and traffic is minimized at the beginning of the transcript to favour ribosome recruitment. https://academic.oup.com/nar/article/48/17/9478/5895331 Honors to Researchers Who Probed Atomic Structure of Ribosomes - Robert F. Service - 2009 Excerpt: "The ribosome’s dance, however, is more like a grand ballet, with dozens of ribosomal proteins and subunits pirouetting with every step while other key biomolecules leap in, carrying other dancers needed to complete the act.” https://www.science.org/doi/full/10.1126/science.326_346 Ribosomes Optimized for Speed, Flexibility - August 2, 2017 Excerpt: The DNA translation machines in the cell show unexpected complexity, forcing molecular biologists to revise what they thought they knew about ribosomes. In particular, they appear optimized for speed of self-duplication and modularized for flexibility.,,, if you think of “orchestrated function” again, the sheet music won’t do any good if the stage isn’t already set up and the players aren’t in their seats.,,, The “orchestrated function of hundreds of proteins” has time limits. The conductor is pounding his foot and tapping his baton on the podium, rushing the orchestra to get in place. Imagine how much harder if each player, instrument, chair, and music stand has to make a copy of itself first for a show across town!,,, https://evolutionnews.org/2017/08/ribosomes-optimized-for-speed-flexibility/ Endoplasmic Reticulum: Scientists Image 'Parking Garage' Helix Structure in Protein-Making Factory - July 2013 Excerpt: The endoplasmic reticulum (ER) is the protein-making factory within cells consisting of tightly stacked sheets of membrane studded with the molecules (ribosome machines) that make proteins. In a study published July 18th by Cell Press in the journal Cell, researchers have refined a new microscopy imaging method to visualize exactly how the ER sheets are stacked, revealing that the 3D structure of the sheets resembles a parking garage with helical ramps connecting the different levels. This structure allows for the dense packing of ER sheets, maximizing the amount of space available for protein synthesis within the small confines of a cell.?"The geometry of the ER is so complex that its details have never been fully described, even now, 60 years after its discovery," says study author Mark Terasaki of the University of Connecticut Health Center. "Our findings are likely to lead to new insights into the functioning of this important organelle.",,,? , this "parking garage" structure optimizes the dense packing of ER sheets and thus maximizes the number of protein-synthesizing molecules called ribosomes within the restricted space of a cell. When a cell needs to secrete more proteins, it can reduce the distances between sheets to pack even more membrane into the same space. Think of it as a parking garage that can add more levels as it gets full.,,, http://www.sciencedaily.com/releases/2013/07/130718130617.htm
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A few related notes, As to proteins,
Water Is 'Designer Fluid' That Helps Proteins Change Shape - 2008 Excerpt: "When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life." http://www.sciencedaily.com/releases/2008/08/080806113314.htm Water's quantum weirdness makes life possible - October 2011 Excerpt: WATER'S life-giving properties exist on a knife-edge. It turns out that life as we know it relies on a fortuitous, but incredibly delicate, balance of quantum forces.,,, They found that the hydrogen-oxygen bonds were slightly longer than the deuterium-oxygen ones, which is what you would expect if quantum uncertainty was affecting water’s structure. “No one has ever really measured that before,” says Benmore. We are used to the idea that the cosmos’s physical constants are fine-tuned for life. Now it seems water’s quantum forces can be added to this “just right” list. http://www.newscientist.com/article/mg21228354.900-waters-quantum-weirdness-makes-life-possible.html Copying enzyme design to make industrial catalysts - 2020 Excerpt: Enzymes are a vital class of proteins that are catalysts. That is, they speed up chemical reactions without being consumed in the process. Without enzymes, many reactions essential for life would be far too slow for life to exist. For example, a reaction “absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years in water. But an enzyme (orotidine 5?-monophosphate decarboxylase) makes this reaction go 1018 times faster,1 so it takes less than 3 milliseconds in the cell.2 Another enzyme (inositol phosphatase) speeds up a reaction vital in cell signalling and regulation by 1021 times. With the enzyme, the reaction takes 10 milliseconds; without the enzyme, it would take a trillion years. This is almost a hundred times the,, age of the universe (about 15 billion years)!3 https://creation.com/copying-enzyme-design "I Have Seen the Light!" Vision and Light-Induced Molecular Changes Excerpt: Excerpt: “Thus, when 11-cis-retinal absorbs a photon in the visible range of the spectrum, free rotation about the bond between carbon atom 11 and carbon atom 12 can occur and the all-trans-retinal can form. This isomerization occurs in a few picoseconds (10-12 s) or less.” – Rachel Casiday and Regina Frey, Department of Chemistry, Washington University http://www.chemistry.wustl.edu/~edudev/LabTutorials/Vision/Vision.html 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,,,, 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
in the following 2015 paper entitled, “Quantum criticality in a wide range of important biomolecules” it was found that “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” and the researchers further commented that “finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
Quantum criticality in a wide range of important biomolecules – Mar. 6, 2015 Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say. That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.” The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one (biomolecule) that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,, “what exactly is the advantage that criticality confers?” https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552
And this follow up 2018 article stated that “There is no obvious evolutionary reason why a protein should evolve toward a quantum-critical state, and there is no chance at all that the state could occur randomly.,,,”
Quantum Critical Proteins – Stuart Lindsay – Professor of Physics and Chemistry at Arizona State University – 2018 Excerpt: The difficulty with this proposal lies in its improbability. Only an infinitesimal density of random states exists near the critical point.,, Gábor Vattay et al. recently examined a number of proteins and conducting and insulating polymers.14 The distribution for the insulators and conductors were as expected, but the functional proteins all fell on the quantum-critical distribution. Such a result cannot be a consequence of chance.,,, WHAT OF quantum criticality? Vattay et al. carried out electronic structure calculations for the very large protein used in our work. They found that the distribution of energy-level spacings fell on exactly the quantum-critical distribution, implying that this protein is also quantum critical. There is no obvious evolutionary reason why a protein should evolve toward a quantum-critical state, and there is no chance at all that the state could occur randomly.,,, http://inference-review.com/article/quantum-critical-proteins Gábor Vattay et al., “Quantum Criticality at the Origin of Life,” Journal of Physics: Conference Series 626 (2015); Gábor Vattay, Stuart Kauffman, and Samuli Niiranen, “Quantum Biology on the Edge of Quantum Chaos,” PLOS One 9, no. 3 (2014)
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I still think the idea of sexual reproduction evolving is a very simple and practical objection that has no answer as well.zweston_{September 21, 2021
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Michael Denton keeps adding to the list for biological fine-tuning. He points out the factors on earth that have to be in place for life to exist - so that the environment is adaptive. It's a huge list. Even just thinking about one element: water. That substance has so many necessary features built in that are necessary for life - so the planet has to be fine-tuned to contain the right amounts of water at the right temperatures, easily accessible.Silver Asiatic_{September 21, 2021
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It would be useful to have a list of all the fine tuning example in a a list like an archive for easy accessibility. Maybe one already exists.jerry_{September 21, 2021
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