Accounts of the history of science love to follow a convention of discussing some important discovery, and then telling how that discovery led to some important new understanding about nature. For example, we are often told about the discovery of the red shifts of galaxies, and how this led to the important conclusion that the universe is expanding. But some of the most important insights about nature follow from observation failures -- cases when things were not observed.
An example was Louis Pasteur's famous experiment regarding spontaneous generation. Pasteur took two goose flasks and filled them with broth. He heated them both to a high enough temperature to sterilize any microbes in them. One flask was left sealed, and the other other flask was left unsealed. The flasks were left for months. After months, the unsealed flask had developed microbes inside the broth. But the sealed flask had no such microbes. Tending to discredit claims of spontaneous generation, the experiment at least showed something very important: that life cannot easily arise from non-life. That was a very important insight. Now we understand some of the reasons why life cannot easily arise from non-life, such as the fact that even the simplest forms of life are extremely complex systems requiring a special arrangement of 100,000+ atoms, an arrangement so improbable that its chance occurrence would be like ink splashes writing many pages of well-written prose.
Another example of an important observational failure has been the failure of all attempts to receive radio signals from extraterrestrial civilizations. Scientists have been trying to receive such signals for more than 50 years, but have not got anywhere. The failure of such a search tells us something important: that our galaxy is apparently not abundant in technological civilizations that are eager to communicate with strangers. Apparently we don't live in a Star Trek type galaxy in which there's a civilized planet in roughly every parsec.
Another example of an important observational failure has been the failure of all attempts to detect in DNA anything like a blueprint, recipe or program for making a human body or any of its organs or any of its cells. DNA contains only low-level chemical information such as which amino acids make up particular proteins. The Human Genome Project was completed in 2003, and by now the genomes of more than 3000 species have been cataloged. No one ever found in any genome any such thing as a specification of anatomy or how to build an organ or even how to build a cell.
The implications of this observational failure are vast. The lack of high-level anatomical information in DNA and the lack of DNA instructions on how to build cells means that the origin of every adult human body is a miracle of organization a thousand miles over the heads of today's biologists. There is not a biologist in the world who can explain how it is it that a speck-sized zygote is able to progress to the state of vast hierarchical organization that is the human body, without telling us lies such as the lie that DNA has a blueprint or recipe or program for making the human body. The lack of anatomy information in DNA and the lack of cellular specifications in DNA is such a show-stopper for mechanistic biology that mechanistic biologists have dealt with the problem by lying to us for decades, telling us the phony myth that DNA has a blueprint or a recipe or a program for making a human body. For a long list of biology and medical authorities who have told us the truth about this topic (saying that DNA is no such thing as a blueprint, a recipe or program for making a human body or any of its cells), read my post here.
There is another observational failure of scientists that has the most gigantic implications: the failure of scientists to ever detect any such thing as addresses within the human body. The human body has no such thing as an internal coordinate system. There is no part of the body that has any such thing as an addressing system. There is no body addressing system. There is no brain address system. There is not even an addressing system within DNA. The lack of any address system in the human body has gigantic implications.
One implication of the lack of any addressing system in DNA is that scientists are unable to give any credible mechanistic explanation for the origin of any protein molecule.
Cells are constantly creating new proteins to replace proteins that disappeared because of the short lifetimes of proteins. The page here discusses the lifetimes of human proteins, and we see a reference to a scientific paper listing the average human protein as having a half-life of only 6.9 hours. A muscle protein might live for three weeks, but a liver protein might live for only a few days. To create new proteins, a cell uses a process called gene transcription. In this process a particular gene in DNA will be converted to a messenger RNA molecule that helps to build the new protein.
Cell transcription occurs quickly. The source here lists a time of ten minutes for a gene to be transcribed by a mammal, but another source lists a speed of only about a minute. The great majority of that is used up by the reading of base pairs from the gene, with typically more than a 1000 base pairs being read each time a gene is transcribed. The finding of the correct gene to read in DNA seems to occur in only seconds, not minutes, or at most a few minutes.
Descriptions of DNA transcription fail to explain a huge issue: how does a cell find the right gene in DNA so quickly? Human DNA contains more than 20,000 genes, each of which is just a section of the DNA. The DNA is like an extremely long necklace of many thousands of beads, and a typical gene is like a group of several hundred of those beads. We should actually imagine multiple such necklaces, because DNA is scattered across 23 different chromosome pairs. Now if genes had gene numbers, and DNA was a set of numbered genes in numerical order, it might be easy to find a particular gene. So if a cell knew that it was trying to find gene number 4,233, it could use a binary search method that would allow it to find that gene pretty quickly. Such a method might sound like Bob using a binary search method efficiently in the dialog below:
Jane: Okay, I picked a date in world history. Try to guess it.
Bob: Was it after the first century AD?
Jane: Yes.
Bob: Was it in the past thousand years?
Jane: Yes
Bob: Was it in the past 500 years?
Jane: No.
Bob: Was it between 1250 and 1500?
Jane: Yes.
Bob: Was it between 1375 and 1500?
Jane: Yes.
Using such a binary search method, Bob will find the correct year within several more guesses.
But no such method can be used within the human body. Genes do not have gene numbers that can be accessed within the human body, and DNA is not numerically sorted. DNA has no indexes that might allow a cell to find some particular gene that it was trying to find within DNA. So we have an explanatory "needle in a haystack" problem. Or we might call it a "needle in the haystacks" problem, because human DNA is scattered across 23 different chromosome pairs, as shown in the diagram below:
A scientific text tells us some information that makes this explanatory problem seem more pressing:
"One might have predicted that the information present in genomes would be arranged in an orderly fashion, resembling a dictionary or a telephone directory. Although the genomes of some bacteria seem fairly well organized, the genomes of most multicellular organisms, such as our Drosophila example, are surprisingly disorderly. Small bits of coding DNA (that is, DNA that codes for protein) are interspersed with large blocks of seemingly meaningless DNA. Some sections of the genome contain many genes and others lack genes altogether. Proteins that work closely with one another in the cell often have their genes located on different chromosomes, and adjacent genes typically encode proteins that have little to do with each other in the cell. Decoding genomes is therefore no simple matter. Even with the aid of powerful computers, it is still difficult for researchers to locate definitively the beginning and end of genes in the DNA sequences of complex genomes, much less to predict when each gene is expressed in the life of the organism. Although the DNA sequence of the human genome is known, it will probably take at least a decade for humans to identify every gene and determine the precise amino acid sequence of the protein it produces. Yet the cells in our body do this thousands of times a second."
We have here a very severe navigation problem. A cell is somehow able to find the right gene in only seconds or a few minutes when a new protein is made, even though DNA and chromosomes seem to have no physical organization that could allow for such blazing fast access to the right information. In an article on Chemistry World, we read this:
"How does the machinery that turns genes into proteins know which part of the genome to read in any given cell type? ‘To me that is one of the most fundamental questions in biology,’ says biochemist Robert Tjian of the University of California at Berkeley in the US: ‘How does a cell know what it is supposed to be?"
Biochemist Tjian has spoken just as if he had no idea how it is that a cell is able to navigate to the right place to read a particular gene in DNA. Later in the article we read this:
"For one thing, the regulatory machinery ‘is unbelievably complex’, says Tjian, comprising perhaps 60–100 proteins – mostly of a class called transcription factors (TFs) – that have to interact before anything happens. ....As well as promoters, mammalian genes are controlled by DNA segments called enhancers. Some proteins bind to the promoter site, others bind to the enhancer, and they have to communicate. ‘This is where things get bizarre, because the enhancer can sit miles away from the promoter,’ says Tjian – meaning, perhaps, millions of base pairs away, maybe with a whole gene or two in between. And the transcription machinery can’t just track along the DNA until it hits the enhancer, because the track is blocked. In eukaryotes, almost all of the genome is, at any given moment, packaged away by being wrapped around disk-shaped proteins called histones. These, says Tjian, ‘are like big boulders on the track’: you can’t get past them easily.... ‘Even after 40 years of studying this stuff, I don’t think we have a clear idea of how that looping happens,’ says Tjian. Until recently, the general idea was that the TFs and other components all fit together into a kind of jigsaw, via molecular recognition, that will bridge and bind a loop in place while transcription happens. ‘We molecular biologists love to draw nice model schemes of how TFs find their target genes and how enhancers can regulate promoters located millions of base pairs away,’ says Ralph Stadhouders of the Erasmus University Medical Centre in Rotterdam, the Netherlands. ‘But exactly how this is achieved in a timely and highly specific manner is still very much a mystery.’ "
Later in the article Tjian says he was shocked by the speed at which some of the process occurs. He expected it would take hours, but found something much different:
"The residence times of these proteins in vivo was not minutes or hours, but about six seconds!’, he says. ‘I was so shocked that it took me months to come to grips with my own data. How could a low-concentration protein ever get together with all its partners to trigger expression of a gene, when everything is moving at this unbelievably rapid pace?’ "
The rest of the article is just some speculation, which Tjian mostly knocks down, and the article itself calls "hand-wavy." We are left with the impression that no one understands how cells are able to instantly find the right gene.
On page 100 of the very interesting work "Theory of Directed Evolution" scientist Alexey V. Melkikh asks this:
"How does a protein during genome regulation find its only place on the DNA molecule? If it is based on the key-lock principle, how does the protein not confuse its binding site with someone else's? How many erroneous attempts at linking should it make until it finds its site? Why does it not get stuck in someone else's deep potential hole? All these processes should drastically reduce the efficiency of genome regulation."
The question I raise in this section of this post is a question raised, but never answered, by the latest (32nd) edition of Harper's Illustrated Biochemistry, which states this:
"The question 'How does RNAP [RNA polymerase] find the correct site to initiate transcription?' is not trivial when the complexity of the genome is considered....The situation is even more complex in humans, where as many as 150,000 distinct transcriptions sites are distributed throughout [three billion base pairs] of DNA."
The textbook gives us a very detailed discussion of things such as promoters, but the discussion fails to answer the question of how this "finding the needle in a haystack" could occur so quickly.
The lack of any addressing system within DNA means that the fast construction of a protein molecule is something beyond any mechanistic explanation. Furthermore, the lack of any addressing system within the body implies that the arrival of a protein molecule at a suitable place within a cell is beyond mechanistic explanation.
Let us consider how fantastically complex human cells are. Humans cells are constantly misrepresented by profoundly misleading diagrams that make them look many thousands of times simpler than they are. A typical human cell has thousands of times more organelles than depicted by a typical cell diagram. A human cell is so complex it has been compared to a city. For newly constructed protein molecules to do their jobs, they must arrive at the right places. An analogy might be a worker who arrives at a city to start working. He can't just start working anywhere. He has to arrive at the right place in the city, to do his specialized job. Workers can successfully arrive at the right place to their jobs because cities have addresses. So, for example, a worker may be told to start working at 353 Maple Street on August 8.
But cells have no addresses, and no coordinate system. So it can't be that a protein molecule arrives at the right place in a cell because it was told to go to some particular address in a cell. So how do protein molecules arrive at the right places in cells? Mechanistic biology has no general explanation to offer.
There's another similar problem of equal immensity: the problem of how newly constructed cells arrive at the right places in the human body. Consider the origin of a human body. The beginning of human development is a single cell called a zygote. That somehow progresses to become the vast state of hierarchical organization that is the human body. Along the way, something like 200 types of cells must originate, each in massive numbers. All those cells must find the right places to exist. It doesn't do a body any good, for example, if heart cells end up in the foot or liver cells up in the stomach.
How do cells find the right place to go to? Mechanistic biology has no credible answer to offer. Part of the reason a mechanistic answer is impossible is the lack of any addresses in the body.
We may consider some of the difficulties. On a two-dimensional surface, there are two ways in which addresses might work. In the first way, no map is needed, but the addresses must be numerically ordered. For example, in general (with some exceptions) you don't need a map to navigate around in Manhattan. That borough of New York City is sensibly organized so that streets are numbered in numerical order. So if you are on, say, 2nd Avenue and 14th street, you do not need a map to navigate to 5th Avenue and 22nd Street. Conversely, a city may have streets in no numerical order. In that case, to find a particular house there must exist both street addresses and maps people can use to find a particular street. You can't just use simple math to navigate your way to Roosevelt Avenue and Maple Street.
Now, in a human body growing from a speck-sized zygote to a baby of ten pounds and eventually an adult of maybe 180 pounds, it would never be practical to use numerically ordered addresses; and such numerical addresses don't exist in the body. So what you would need for a cell to navigate around in the human body would be something like both addresses that are not numerically ordered, and also a map storing all the addresses. But neither of these things exist in the body. Organelles in cells don't have addresses; cells don't have addresses; and particular spots of the body don't have addresses. So how could a cell ever find the right place to go to in the body? Mechanistic biology has no credible answer.
There are are two additional reasons why the problem of cells finding the right locations in the body and protein molecules finding the right locations in cells is actually far greater than I have suggested above:
(1) Instead of requiring merely navigation to the right place on a flat surface (like a person navigating to the right address in a city), the problem of navigating to the right place in a cell or the body is exponentially more difficult, because we are dealing with three-dimensional space rather than a flat two-dimensional space.
(2) City streets are conveniently designed with sidewalks and streets allowing you to go anywhere you want, but cells and bodies are filled with existing matter blocking navigation, and existing flow pathways making it all the more harder for protein molecules and cells to find the right places. An analogy might be a city in which very heavy traffic, blocked roads and streets, and a raging flash flood makes it so much harder to get around to where you are trying to go.
For reasons such as these, a lack of addresses in the body crushes the credibility of mechanistic biology as an explanation for the origin of the human body. The lack of addresses in the body also crushes the credibility of mechanistic psychology, the idea that human mind and memory can be explained as mechanistic brain processes.
Humans routinely display the ability to instantly recall learned information, given a name, date or image. So, for example, if you say "death of Lincoln," I will instantly be able to recite various facts about the death of Abraham Lincoln, such as that it occurred because John Wilkes Booth shot Lincoln through the back of his head at Ford's Theater on April 15, 1865. If we believe that a memory is stored in some tiny little spot in the brain, such as storage spot 186,395 out of 950,000, then we have the problem: how was the brain able to instantly find that exact tiny spot where the memory was formed? This difficulty is a "show stopper" for all claims that a memory is stored in one exact spot of a brain, an insuperable difficulty.
We cannot get around such a difficulty by imagining that a brain uses the type of things that a book or a computer use to allow instant retrieval. Books and computers use information addressing, sorting and indexes to allow instant access of a particular data item. The brain has neither addressing nor indexes nor sorting. Unlike houses that have street addresses, neurons don't have neuron numbers or any other addressing system. Storing a memory in a brain would be like throwing a little 3" by 5" card into a giant swimming pool filled to the top with a million little 3" by 5" cards. Just as it should take you a very long time to find a specific piece of information stored in such a swimming pool, it would take you a very long time to find in the brain some particular piece of learned information, if it was stored in one tiny spot, like a book stored in one spot on the shelves of a huge library.
You do not at all get around this difficulty by suggesting the idea that a memory or a piece of learned information is scattered or distributed in multiple locations across the brain. The main difficulty is explaining instantaneous recall. If a brain has to search scattered storage locations in the brain, that would not be any easier than finding a single storage location; it would instead be harder. We would then have the same problem: how is it that those exact locations can instantly be found? Similarly, if a family is somewhere in New York City, and you don't know their address, without an electronic device you won't be able to find the family very quickly; and it's not going to be any easier if the family is scattered across three different apartments in different parts of the city, which would make finding the family even harder. You do not solve a "how was the needle instantly found in the haystack" problem by converting it to the even harder problem of "how were just the right few needles instantly found in multiple haystacks?" Moreover, the idea of a brain instantly bringing together scattered fragments to instantly make a unified conceptual whole creates an "instant reassembly" problem that would be an additional explanatory nightmare, with such a thing being some miracle of instant assembly as implausible as someone instantly assembling cut-up pieces of a photo after the pieces had been scattered in pages of different books on different bookshelves.
This "speed of human recall" problem becomes much worse when we consider that brain signals have an average transmission speed much slower than the "100 meters per second" figure that is commonly given (which is the fastest speed that any nerve signal can travel over any part of the brain) A typical brain signal traveling from one part of a brain to another would have to pass across many chemical synapses, and each time that happens there would be a delay. The effect of cumulative synaptic delays would mean that brain signals must typically travel from one area of a brain to another at a sluggish speed of something like about one centimeter per second or less. Even if a brain somehow knew exactly where to find some information it needed, the retrieval of such information would be too slow to explain instant human recall.
The failure to ever observe addresses in the brain is one of only two observation failures that crush the credibility of mechanistic psychology. The second failure is the failure to ever observe human learned information by microscopic observation of the brain.
Despite microscopically studying more than 14,000 brains (a large fraction of which were cryogenically preserved within a day after death), scientists are unable to read any memory from any of these brains, and are also unable to find any evidence of some neural code that could be used to translate learned information into brain states. The brains are saying "storing memories is not something brains do," but our scientists refuse to listen to what the brains are telling them.
Below is a diagram from the paper "Materials Advances Through Aberration-Corrected Electron Microscopy." We see that since the time the genetic code was discovered about 1953, microscopes have grown very many times more powerful. The A on the left stands for an angstrom, a tenth of a nanometer (that is, a ten-billionth of a meter).
Currently the most powerful microscopes can see things about 1 angstrom in width, which is a tenth of a nanometer. How does this compare to the sizes of the smallest units in brains? Those sizes are below:
Width of a neuron body (soma): about 100 microns (micrometers), which is about 1,000,000 angstroms.
Width of a synapse: about 20-30 nanometers, about 200-300 angstroms.
Width of a dendritic spine: about 50 to 200 nanometers, about 500 to 2000 angstroms.
Clearly the resolution of the most powerful microscopes is powerful enough to read memories stored in neurons or synapses, if such memories existed. And more than 14,000 brains have been microscopically studied in recent years. The failure to microscopically read any memories from human brain tissue is a major reason for thinking that brains do not store human memories.
Besides failing to find specific memories and items of learned knowledge by microscopically examining brains (such as the information that the New York Yankees belong to the American League of US baseball), scientists can find no evidence of a mechanism for storing learned information in brains. If such a mechanism existed, its fingerprints would be all over the place. Since humans can learn and remember so many different types of things (sights, sounds, feelings, facts, beliefs, opinions, numbers, smells, tastes, physical pains, physical pleasures, music, quotations, and so forth), any brain mechanism for storing all of these things would have a massive footprint in the brain and in the genome. No sign of any such thing can be found. The workhorses that get things done in the body are proteins, and humans have more than 20,000 types of proteins. No one has ever identified a protein that helps to write a memory of experiences or numbers or words to the brain or neural tissue, in any kind of way that helps explain how memories or knowledge could be stored in brains. Of course, you can find studies maybe showing that protein XYZ was used when someone learned something, but that does nothing to show a mechanism of memory storage.
There is a very important lesson to be learned here. For insight into the true nature of things, pay the greatest attention not merely to what scientists have discovered, but also to what they have not discovered.
Let's define "morphogenesis" as the process that leads from a tiny speck-sized zygote to the full organization of a human body. The topic of morphogenesis tends to be senselessly ignored by philosophers of mind. The topic of morphogenesis is of very great relevance to the issue of whether brains make minds. A hazard of making a deep study of the topic of morphogenesis is that the literature on the topic is infested with lies, mainly the lie that DNA (the human genome) is a blueprint or program or recipe for making a human body. DNA and its genes are no such thing. DNA merely specifies low-level chemical information such as which amino acids make up a protein.
The diagram below gives us an idea of what DNA and its genes do and do not specify. The internal parts (but not the 3D shape) of a protein molecule is specified by a gene in DNA.
Once we sweep away the "DNA is a body blueprint" myth, we get closer to the shocking truth: the physical origin of every adult human body is a miracle of organization a thousand miles over the head of every scientist. Although the main reasons for thinking that our minds and memory cannot be explained by neural causes are separate from considerations of morphogenesis, the truth that our bodies are beyond any "bottom-up" mechanistic explanation helps to bolster the idea that our minds and memory are beyond any "bottom-up" neural explanation. For more on why that is so, read my post here.
You were told for much of your life the lie that the gigantic wonders of bodily organization kind of "bubble up" from genes that are mere lists of amino acids. That was a big lie of biologists eager to crown themselves as grand lords of explanation. You were also told for much of your life the falsehood that the innumerable wonders of the human mind are caused by a kind of bubbling up of largely random electrical and chemical activity from mere noisy neurons. That was a big myth told by biologists eager to crown themselves as grand lords of explanation. When you understand how you were misled by the first of these myths, you will be more likely to perceive how you were misled by the second of these big myths. It was a similar deal in both cases: scientists putting themselves on pedestals by peddling self-serving unwarranted achievement legends, telling socially constructed tall tales that do not hold up to critical scrutiny and the most careful pondering of the relevant facts.
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