Wednesday, February 28, 2024

A Biochemist's Promissory Note About Explaining Minds Sounds Very Lame

 The site www.realclearscience.com calls itself the "Real Clear Science" site, but what it often gives us is not real clear science, but articles that are clearly ideology and propaganda pieces.  Occasionally the propaganda includes PR pieces written to serve the vested interests of the pesticide industry. On January 6 the site had an article written to defend the pesticide industry and to attack whistleblowers who point out the hazards of pesticides. On the same day the site had a link to an article in the Irish Times entitled "Will science be able to explain consciousness?" with the title subtitle "There is every reason to believe that consciousness will eventually yield to scientific analysis just as the general nature of life yielded."  The article is by emeritus biochemistry professor William Reville.  The article is a very lame promissory note.

Reville starts out by claiming that "science now understands the basic molecular basis of life" and then stretches this into the claim that science understands the "general nature of life." He attempts to use this triumphal boast as a kind of springboard to suggest that solutions to the mystery of mind will be forthcoming. It's kind of like someone saying, "I was able to finish the one-kilometer race, so you can bet that I will be able to finish the marathon race." 

But the claim that science understands "the general nature of life" is untrue. Scientists do not understand any such thing. In particular:

  • Scientists lack any credible explanation of how cells in the human body are able to reproduce. Cells are fantastically organized units so complex they have been compared to factories. Scientists can describe various phases in cell reproduction, but do not understand how cell reproduction is able to occur. The reproduction of every eukaryotic cell is a marvel as hard to explain as a jet aircraft splitting up to become two working jet aircraft. One of the main reasons why scientists cannot explain how cells reproduce is that the DNA in the nucleus of cells does not contain any instructions for how to build a cell. Neither DNA nor its genes even specify how to make any of the organelles that are the main building components of cells. DNA merely specifies low-level chemical information such as which amino acids make up a protein.  So we cannot at all explain the reproduction of cells by imagining that a cell reads from DNA some blueprint on how to make a cell. 
  • Scientists lack any credible explanation for the origin of any type of protein molecule. Living things require very many different types of protein molecules. In the human body there are more than 20,000 different types of protein molecules, each a different type of complex invention. Most types of protein molecules require hundreds of well-arranged amino acid parts, and that altogether requires thousands of very well-arranged atoms in an average protein molecule. How did so many types of protein molecules so organized originate? Scientists do not understand how this occurred. You do not have any credible explanation if you merely refer us to Darwin or natural selection or evolution. The problem is that the functional thresholds of functional protein molecules are very high, ruling out a Darwinian explanation for their origin.  Darwin knew nothing about the complexity of protein molecules, and certainly did not explain their origin. For a good explanation of why Darwinism fails to explain the origin of protein molecules, read computer scientist David Gelernter's widely discussed book review entitled "Giving Up Darwin."  I may note that in that  book review, Gelernter misstated the average amino acid length of a protein molecule, listing it as merely 250. For the type of cells humans have (eukaryotic cells), the average length of a protein molecule is about 472 amino acids, meaning the probability of evolution producing a successful protein molecule (estimated by Gelernter as basically zero)  is very, very many orders of magnitude smaller than Gelernter suggests.  As four Harvard scientists stated in a paper"A wide variety of protein structures exist in nature, however the evolutionary origins of this panoply of proteins remain unknown."  
  • Scientists lack any credible explanation for how protein molecules get the three dimensional shapes needed for their function.  DNA merely specifies which amino acids make up particular protein molecules, and does not specify the three-dimensional shapes that such molecules must have to function properly. How do protein molecules form into such shapes? That is the long-standing problem called the protein folding problem, and it has never been solved. Don't be fooled by false claims that some AlphaFold2 software solved the protein problem. Such software merely made progress on a different problem, called the protein folding prediction problem. The quotes below tell us the truth on this matter:  (1) "In real time how the chaperones fold the newly synthesized polypeptide sequences into a particular three-dimensional shape within a fraction of second is still a mystery for biologists as well as mathematicians."   -- Arun Upadhyay, "Structure of proteins: Evolution with unsolved mysteries," 2019. (2) "The problem of protein folding is one of the most important problems of molecular biology. A central problem (the so called Levinthal's paradox) is that the protein is first synthesized as a linear molecule that must reach its native conformation in a short time (on the order of seconds or less). The protein can only perform its functions in this (often single) conformation. The problem, however, is that the number of possible conformational states is exponentially large for a long protein molecule. Despite almost 30 years of attempts to resolve this paradox, a solution has not yet been found." -- Two scientists, "On a generalized Levinthal's paradox," 2018. 

  • Scientists lack any credible explanation of how protein complexes  are able to form. This is the problem of why it is that protein molecules so often form into very organized protein complexes, teams of protein molecules needed for the protein molecules to be functional. Such complexes are often so organized they are called "molecular machines." We cannot explain their formation merely be referring to DNA. Neither DNA nor its genes specify which protein molecules belong to particular protein complexes, nor do they specify how the intricate arrangement should occur. Here are some relevant quotes: (1) "The majority of cellular proteins function as subunits in larger protein complexes. However, very little is known about how protein complexes form in vivo." --Duncan and Mata, "Widespread Cotranslational Formation of Protein Complexes," 2011. (2) "While the occurrence of multiprotein assemblies is ubiquitous, the understanding of pathways that dictate the formation of quaternary structure remains enigmatic." -- Two scientists (link). (3) "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). (4) "Protein assemblies are at the basis of numerous biological machines by performing actions that none of the individual proteins would be able to do. There are thousands, perhaps millions of different types and states of proteins in a living organism, and the number of possible interactions between them is enormous...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." -- Steinar Thorvaldsen and Ola Hössjerm, "Using statistical methods to model the fine-tuning of molecular machines and systems,"  Journal of Theoretical Biology.
  • Scientists lack any credible explanation of how any adult human body is able to appear. The physical structure of an adult human being is a state of organization many millions of times more complex than a mere fertilized speck-sized egg cell.  (A human egg cell is about a tenth of a millimeter in length, but a human body occupies a volume of about 75 million cubic millimeters.) So you don't explain the physical origin of an adult human being by merely referring to the fertilization of an egg cell during or after sexual intercourse.  We cannot explain the origin of an adult human body by merely using words such as "development" or "growth." Trying to explain the origin of an adult human body by merely mentioning a starting cell and mentioning "growth" or "development" is as vacuous as trying to explain the mysterious appearance of a building by saying that it appeared through "origination" or "construction."  If we were to find some mysterious huge building on Mars, we would hardly be explaining it by merely saying that it arose from "origination" or by saying that it appeared through "construction." When a person tries to explain the origin of a human body by merely mentioning "growth" or "development" or "morphogenesis," he is giving as empty an explanation as someone who tells you he knows how World War II started, because he knows that it was caused by "historical events." The claim that you can explain the origin of a human body by imagining a reading of a DNA blueprint for making a human body is a lie long told by biologists and chemists. As many scientists have confessed, no such blueprint or recipe or program for making a human body exists in DNA.  As discussed here, not only does DNA not specify how to make a human, DNA does not even specify how to make any organ or appendage or cell of a human. There are more than 200 types of cells in human beings, each an incredibly organized thing (cells are so complex they are sometimes compared to factories or cities).  DNA does not specify how to make any of these hundreds of types of cells. Cells are built from smaller structural units called organelles. DNA does not even specify how to make such low-level organelles. 
  • Scientists have made no real progress in understanding the origin of life. No experiments realistically simulating early Earth conditions have ever been able to produce life from non-life. No experiments realistically simulating early Earth conditions have ever been able to produce the building blocks of one-celled life (organelles) from non-life. No experiments realistically simulating early Earth conditions have ever been able to produce the building blocks of the building blocks of one-celled life (functional protein molecules) from non-life.  No experiments realistically simulating early Earth conditions have ever even been able to produce the building blocks of the building blocks of the building blocks of one-celled life (biologically relevant amino acids) from non-life.  It was widely claimed that the Miller-Urey experiment produced the building blocks of the building blocks of the building blocks of one-celled life (biologically relevant amino acids) from non-life. But such claims were false.The Miller-Urey experiment never realistically simulated early Earth conditions, for reasons explained here

So where does this leave Reville's claim that scientists understand "the general nature of life"? It leaves that claim as an unfounded boast. Scientists do not understand any such thing. As biologist Denis Noble recently said, "It’s time to stop pretending that, give or take a few bits and pieces, we know how life works." 

Given the complexities discussed above, we should laugh hard at this ridiculously lame statement by Reville trying to persuade us that scientists understand "the general nature of life":

"The hierarchical structure of the world, from the simplest to the most complex, is traditionally categorised as follows: mineral, vegetable, animal, human. Each level displays all properties of the simpler level beneath but in addition displays a property/properties not present belowThus, the human body is made of matter, is living, conscious and self-aware. The animal body is similar but lacks self-awareness. The plant body is made of matter, is living but lacks consciousness and self-awareness. Minerals are made of matter but are not alive, conscious or self-aware."

No, that is not a correct description of the hierarchical structure of the world. That is an extremely ridiculous statement trying to make the hierarchical structure of biology sound enormously less complex and organized than it is. Below is a correct description of the  hierarchical structure of biology. 


HUMANS CONSIST OF HUMAN BODIES AND HUMAN MINDS.

Human minds have displayed a vast number of capabilities, many of which mainstream scientists fail to properly study.

HUMAN BODIES MAINLY CONSIST OF ORGAN SYSTEMS AND A SKELETAL SYSTEM.

The human skeletal system contains 206 bones.

ORGAN SYSTEMS CONSIST OF ORGANS AND SUPPORTING STRUCTURES.

Examples of organ systems include the circulatory system (consisting of much more than just the heart), and the nervous system consisting of much more than just the brain.

ORGANS CONSIST OF TISSUES.


TISSUES CONSIST OF VERY COMPLEX AND VASTLY ORGANIZED  CELLS

There are more than 200 types of cells in the human body, each a different type of system of enormous organization. Cells are so complex they have been compared to factories with many types of manufacturing devices. 

CELLS TYPICALLY CONSIST OF VERY COMPLEX MEMBRANES AND THOUSANDS OR MILLIONS OF ORGANELLES.

  • A cell diagram will typically depict a cell as having only a few mitochondria, but cells typically have many thousands of mitochondria, as many as a million.

  • A cell diagram will typically depict a cell as having only a few lysosomes, but cells typically have hundreds of lysosomes.

  • A cell diagram will typically depict a cell as having only a few ribosomes, but a cell may have up to 10 million ribosomes.

  • A cell diagram will typically depict one or a few stacks of a Golgi apparatus, each with only a few cisternae. But a cell will typically have between 10 and 20 stacks, each having as many as 60 cisternae.

ORGANELLES CONSIST OF VERY MANY PROTEIN MOLECULES AND PROTEIN MOLECULE COMPLEXES.

There are some 100,000 different types of protein molecules in the human body, each a different type of complex invention. Protein molecule complexes are groups of different types of protein molecules that work together as team members to achieve a function that cannot be achieved by only one of the proteins in the complex. Very many protein complexes have so many parts working together dynamically that such complexes are now being called "molecular machines." 

PROTEIN MOLECULES CONSIST OF HUNDREDS OR THOUSANDS OF WELL-ARRANGED AMINO ACIDS, EXISTING IN A FOLDED THREE-DIMENSIONAL SHAPE.

Small changes in the sequences of amino acids in a protein are typically sufficient to ruin the usefulness of the protein molecule, preventing it from folding in the right way to achieve its function.  See "The Fragility of Fine-Tuned Protein Molecules" section of the post here for quotes stating this. 

AMINO ACIDS CONSIST OF ABOUT 10 ATOMS ARRANGED IN SOME SPECIFIC WAY.

Some amino acids have 20 atoms. Given 10+ atoms in amino acids, and an average of about 470 amino acids per human protein molecule, a human protein molecule contains an average of about 5000+ very well-arranged atoms. Amino acids in living things are almost all left-handed, although amino acids forming naturally will with 50% likelihood be right-handed.

ATOMS CONSIST OF MULTIPLE PROTONS, NEUTRONS AND ELECTRONS.

A carbon atom has 6 protons, 6 neutrons, and 6 electrons.


The visual below correctly describes the hierarchical nature of life, and it is a reality almost infinitely harder to explain than the "mineral-vegetable-animal-human" tiers that Reville claimed as a description of the "hierarchical structure of the world.

pyramid of biological complexity

We then have from Reville an extremely misleading triumphalist narrative in which he describes increasing scientific discoveries that 
"cumulatively explained the secret of life in the mid-20th century." No,  what was discovered in the mid-20th century was mainly just DNA (and its genes) and the enormous complexity of protein molecules.  Such discoveries raised many more questions than they answered.  Calling DNA "the secret of life" (as if biological life has only one secret rather than hundreds of deep unanswered questions) is one of the most misleading speech customs of biologists and chemists.  Reville gives us the groundless claim that "The entire history of science fully justifies expectation that analogous scientific investigations will eventually unveil how consciousness and self-awareness gradually developed through biological evolution and how these processes work at a molecular level." No, there is no basis for any hope that the human mind will be understood by further investigations at a molecular level. 

What Reville is attempting here is a fallacious kind of reasoning that someone might fallaciously but more effectively use by saying something like this:

"Isn't it amazing the progress science has made? In the twentieth century scientists learned how to blow up entire cities by splitting atoms. Scientists have made all kinds of amazing discoveries such as discovering the chemical composition of distant stars and the velocities of distant galaxies. Now scientists can view things as small as a billionth of meter.  Science is so very powerful, so surely it will be able to figure out how brains produce minds." 

This would be a fallacious argument for at least two reasons. First, successes in the past do nothing to justify optimism about successes at vastly difficult undertakings in the future. Second, successes in understanding the material do nothing to justify optimism about successes in understanding the immaterial, something like the human mind.  But at least the argument quoted above is one that appeals to real accomplishments. Scientists did actually figure out how to blow up entire cities by splitting atoms, and did discover the chemical composition of distant stars and the velocities of distant galaxies. Reville's argument has the same two weaknesses of the argument above, with an additional fallacy that he is appealing to supposed accomplishments of biologists that never actually occurred. Biologists never actually discovered "the basic nature of life" in the sense of understanding any of the unanswered questions in my bullet list above. There did not ever occur any discoveries that "cumulatively explained the secret of life in the mid-20th century."  Every major discovery that was made simply deepened the mysteries of how species could have originated, deepened the evidence for accidentally unachievable organization in the human body, deepened the mystery of how a human body can originate, and deepened the mystery of how a cell can reproduce. If you got the opposite impression, it was because boastful scientists constructed many a groundless triumphal legend, and made very many misstatements about what they had accomplished, very frequently claiming to understand deep mysteries a thousand miles over their heads. 

Reville then uses one of the most witless arguments of materialists: the claim that we can explain the human mind as an emergent property. The argument (so often used before) will typically give an example involving water, and that is just what Reville does.  Water is composed of hydrogen and oxygen, and neither has any such property as wetness. But when oxygen and hydrogen are combined to make water, then we have something with the property of wetness. It is claimed that such a property could never be predicted by just analyzing hydrogen or just analyzing oxygen.

According to Reville, this example shows that amazing new properties can arise when matter combines in different ways. He suggests that human consciousness is simply such a property, a property that just arises from certain complex combinations of matter such as we find in the brain.

But this reasoning is absurd.  The human mind is not a property of the brain or a property of the body. In general, a property is a simple intrinsic characteristic of something, which can be completely expressed by giving a single number. For example, the properties of a rock are hardness, weight, height, width, length, and depth. Each of these simple properties can be expressed by a single number. (You may not think hardness can be expressed by a number, but there is something called the Mohs scale used to numerically express the hardness of rocks). We might also think of the color of the rock as being a property, although that requires a simplification (since the rock will actually be multiple colors). If one makes such a simplification, then that color can also be expressed as a single number, such as a number on a color scale. Even wetness can be expressed by a single number (we might, for example, create a wetness scale of 1 to 10, and reasonably assign liquid water a value of 10, and a thick soup a value of about 5).

But the human mind is not a simple characteristic that can be numerically expressed by a number. When we consider all of the very many facets of the human mind (memory, intelligence, personality, emotions, will, self-hood, spirituality, creativity and dozens of other facets or functions), we certainly do not have anything like a simple characteristic that can be expressed by a number. The human mind is also something mental, something much different from a physical property such as width, weight, or wetness. Below are two images showing aspects of human mental experience, normal and anomalous.

aspects of the human mind
types of paranormal experience
So much more than just "consciousness" or "awareness of surroundings"

In light of such facts, the argument of the emergentist falls apart. It may sound persuasive to make this shallow, sketchy comparison:

"When we combine hydrogen and oxygen, we see the emergence of a new, unexpected property of 'wetness.'  This can help explain how our consciousness could suddenly arise from the combination of certain types of neurons."

But it does not at all sound convincing to make this deeper, more complete comparison.

"When we combine hydrogen and oxygen, we see the emergence of a new, unexpected property of 'wetness,' which is a simple, physical property that can be expressed by a single number. This can help explain how certain combinations of physical neurons could produce human mentality that is not physical, extremely diverse, and is enormously complex and multifaceted, and not capable of being expressed by a single number."

Obviously the latter argument does not work. Our minds are not at all a property. They are far too complicated, multifaceted, and multi-functional to be a property, which is a simple physical thing, like a single facet of something. And it makes no sense to use some analogy involving a tangible property of wetness to try to explain intangible aspects of minds. 

An additional reason for rejecting "mind is a property" reasoning comes from near-death experiences. In these experiences a person will often report floating above his body, and looking down on it. A property is something that cannot be separated from the object with which it is associated. So it would be absolutely nonsensical to say something like, “The rock is on the left side of the room, but the length of the rock is on the right side of the room,” just as it would be nonsensical to say, “I have your bicycle in my garage, but I have the weight of your bicycle in my kitchen.” But judging from near-death experiences, it is possible for a human mind to be separated from the brain, at least briefly. Since properties can never be separated from their associated objects, such experiences supply an additional reason for thinking that the human mind cannot be considered a property of the brain.

Reville makes a common mistake of reductionists at the beginning of his deliberation on such a topic: the mistake of posing a "problem of consciousness." Such a mistake involves bungling reductionist shrink-speaking in which the extremely multifaceted and enormously complex reality of the human mind is described using the minimalist word "consciousness," which serves to depict the human mind as a mere shadow of itself.  We do not have some mere problem of explaining why humans are aware of their surroundings. We have the almost infinitely bigger problem of explaining why there occurs all of the rich phenomena of human minds, which add up to being a reality enormously larger than mere "awareness of surroundings." Under any realistic consideration of the human mind, all attempts to explain the human as a property seem ridiculous in the extreme.  A property is a one-dimensional thing that can be described with a single number. The human mind is something enormously deeper and more diverse and more multifaceted than some mere property. 

"Consciousness" defined as mere "awareness of surroundings" would be a suitable term to use for the mental experiences of an ant. Purporting to explain human minds by describing them as mere things with awareness of surroundings (some shadow-like thing that might be a mere property) is as grotesque a trick and glaring a fallacy as purporting to explain human bodies by the shrink-speaking sophistry of describing them as mere "oblong shapes with protrusions" and claiming that it is real easy for nature to make such shapes, such as when such shapes arise from puddle splashes.  The person who depicts a human as "some consciousness" is like some person who describes World War II as "some noise."

The rest of Reville's article consists of some comments against panpsychism. Skepticism about panpsychism does nothing to justify optimism that neuroscientists will be able to explain minds. Reville gives us not one valid reason for being optimistic that further investigations into matter will be able to explain consciousness, self-hood or the human mind. His very field (biochemistry) actually gives us the strongest basis for doubting such a claim. 

What we see by deeply studying biochemistry are the most enormously impressive engineering effects throughout the human body. Inside your body is a vast army of chemical components so complex and so well-organized that mainstream scientists have for a long time been calling them "molecular machines." The extremely abundant existence of such accidentally unachievable molecular machines and countless other examples of extremely impressive engineering effects in the human body provide (with many other lines of evidence) an extremely strong basis for believing that the physical structure of every adult human body is something that will forever be unexplainable by bottom-down physical causes, and can only be the result of top-down causal agency.  If our bodies must have arisen from some mysterious top-down agency, then it is all the more plausible to assume that our minds must arise from some mysterious top-down agency. 

But the main reasons for suspecting that scientists will never be able to explain minds by studying brains comes not from biochemistry but from neuroscience itself. Neuroscientists have discovered many very serious brain physical shortfalls which exclude the brain as an explanation for the human mind and human memory, as discussed here.  Sadly, our neuroscientists are failing to pay attention to the implications of their own discoveries, and such scientists keep paying lip service to dogmas of their belief community that are excluded by the low-level findings of neuroscientists themselves. 

Notably, our biochemist makes not one single mention of anything in biochemistry that might explain minds or mental phenomenon.  That should surprise no one. Biochemistry involves equations like the one below, in which the things on the left of the arrow are material inputs, and the things on the right of the arrow are material outputs:

6CO2+6H2O→C6H12O6+6O2

But there could never, ever be any sensible chemical equation looking like this:

C12H18O12+6O2→ My thoughts about whether God exists

We should have little confidence in anyone claiming that the problems of human societies will be solved by scientists unless such a person is a scholar of human societies. Similarly, we should have no confidence in any person predicting that the problems of explaining humans minds will be solved by investigations into matter unless such a person is a scholar of the human mind and human mental experiences, a topic of oceanic depth. In general biochemistry professors such as Reville are specialists who are not scholars of human minds and human mental experiences. 

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