Problems a Hundred Miles Over Our Heads

While scientists often boast about how much they know, the truth is that human knowledge is merely fragmentary. The English expression "over your head" means something that is beyond your understanding. There are very many fundamental problems that are a hundred miles over the heads of today's scientists. The diagram below illustrates the situation.

Let me explain the diagram by explaining why each of the listed problems is many miles over the heads of today's scientists. 

The problem of explaining minds, memory and psychical phenomena. The first cloud in the diagram mentions the mountain-sized problem of explaining human minds and human memory. The problem is gigantic and very much over the heads of today's scientists, both because of the huge variety of human mental experiences and human mental capabilities, and because of the many brain physical shortfalls that exclude the brain as a credible explanation for most such capabilities and experiences. 

A scientist trying to play "fake it until you make it" 

Morphogenesis problems (super-hard because of DNA limitations).  If someone defines a fertilized human egg as a human being, a definition that is very debatable, you might be able to say, "I understand the physical origin of a human being," and merely refer to a sperm uniting with an egg cell as such an origin.  But a more challenging question is whether anyone understands the physical origin of an adult human being. 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, a state of great organization, 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."

There is a more specific account often told to try to explain the origin of an adult human body. The account goes something like this:

"Every cell contains a DNA molecule that is a blueprint for constructing a human, all the information that is needed. So what happens is that inside the body of a mother, this DNA plan for a human body is read, and the body of a baby is gradually constructed. It's kind of like a construction crew working from a blueprint to make a building."

The problem with this account is that while it has been told very many times, the story is just plain false, as many scientists have confessed. There is no such blueprint for a human being in human DNA. We know exactly what is in human DNA. It is merely low-level chemical information such as the sequence of amino acids that make up polypeptide chains that are the starting points of protein molecules. DNA does not specify anatomy. DNA is not a blueprint for making a human. DNA is not a recipe for making a human. DNA is not a program or algorithm for making a human. 

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 many types of smaller structural units called organelles. DNA does not even specify how to make such low-level organelles. 

The chart below diagrams the hierarchical organization of the human body, and what part of that organization is explained by DNA:

Partially because so few of these layers are explained by DNA or its genes, the problem of explaining morphogenesis (the formation of a full human body) is a problem very far over the heads of scientists. 

Problem of explaining vast levels of biological organization. Below are some categories of innovations. These categories are not mutually exclusive.

Name	Description	Example(s)
Type A Innovation	Innovation requires all of its parts to have any functional benefit	Mousetrap, probably some biological units
Type B Innovation	Innovation requires almost all of its parts before any functional benefit	Jet aircraft, many protein molecules. Suspension bridge. Television, digital computer.
Type C Innovation	Innovation requires most of its parts before any benefit	Cells, most protein molecules, an automobile (which doesn't need its roof, doors or seats or car hood or bumper to be functional), electric fan (which gives some benefit even if the cage and stand are missing), cardiovascular system
Type D Innovation	Innovation requires a series of sub-components, each of which is useless until mostly completed.	Office tower. Each floor provides a benefit. But the construction of each floor requires many new parts, and no floor is useful until mainly completed. Also porcupine barbs (each barb is useful).
Type E innovation	Innovation may have some use in a relatively simple fractional form, but then requires many more parts organized in the right way to achieve a higher level of usefulness	Vision systems (?)
Type F innovation	Innovation requires an arrangement of several complex parts before becoming useful, with at least 25% of its part existing and well-arranged until functionality is achieved
Type G innovation	As each small simple part of the innovation is added, usefulness is slightly increased	Roof insulation, but almost nothing in the world of biology.

Darwinism may be able to explain some Type G innovations. But most of the impressive innovations in biology seem to be Type B innovations or Type C innovations. Innovations of that type are not credibly explained by any of the ideas of Darwinism, including the idea of so-called natural selection. Some of the reasons why Darwinism and gradualism are not credible explanations for most of the more complex innovations in natural history and biology are explained in my post "Anatomically Uninformative DNA, Nonfunctional Intermediates and Useless Early Stages Are Why Gradualism Does Not Work" which you can read here. 

Part of the reason why biological systems are beyond the explanation of scientists is the very great interdependence of the components of such systems, illustrated by the diagrams below:

Origin of life problem. Everything we have learned about the very great organization and complexity of even the simplest living things suggests that the natural origin of life should be impossible, and should be as unlikely as a thrown deck of cards accidentally forming into a house of cards consisting of 52 cards. The concept of abiogenesis (that life can naturally arise from non-life) is a concept with zero observational and experimental support. Scientists have had no luck in trying to create a living thing in experiments simulating the early Earth, and have failed to create even a single protein molecule in such experiments. Below are some relevant quotes by scientists:

• "The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions (Appendix A), an event that could not have happened within the time frame of the Earth except, we believe, as a miracle (Hoyle and Wickramasinghe, 1981, 1982, 2000). All laboratory experiments attempting to simulate such an event have so far led to dismal failure (Deamer, 2011; Walker and Wickramasinghe, 2015)." -- "Cause of Cambrian Explosion - Terrestrial or Cosmic?," a paper by 21 scientists,  2018. 
• "Biochemistry's orthodox account of how life emerged from a primordial soup of such chemicals lacks experimental support and is invalid because, among other reasons, there is an overwhelming statistical improbability that random reactions in an aqueous solution could have produced self-replicating RNA molecules."  John Hands MD, "Cosmo Sapiens: Human Evolution From the Origin of the Universe," page 411. 
• "The ongoing insistence on defending scientific orthodoxies on these matters, even against a formidable tide of contrary evidence, has turned out to be no less repressive than the discarded superstitions in earlier times. For instance, although all attempts to demonstrate spontaneous generation in the laboratory have led to failure for over half a century, strident assertions of its necessary operation against the most incredible odds continue to dominate the literature." -- 3 scientists (link).
• "The interconnected nature of DNA, RNA, and proteins means that it could not have sprung up ab initio from the primordial ooze, because if only one component is missing then the whole system falls apart – a three-legged table with one missing cannot stand." -- "The Improbable Origins of Life on Earth" by astronomer Paul Sutter. 
• "Even the simplest of these substances [proteins} represent extremely complex compounds, containing many thousands of atoms of carbon, hydrogen, oxygen, and nitrogen arranged in absolutely definite patterns, which are specific for each separate substance. To the student of protein structure the spontaneous formation of such an atomic arrangement in the protein molecule would seem as improbable as would the accidental origin of the text of Virgil's 'Aeneid'  from scattered letter type." -- Chemist A. I. Oparin, "The Origin of Life," pages 132-133.

Matter-antimatter asymmetry problem. Let us imagine the early minutes of the Big Bang about 13 billion years ago, when the density of the universe was incredibly great. At that time the universe should have consisted of energy, matter and antimatter. The energy should have been in the form of very high energy photons that were frequently colliding with each other. All such collisions should have produced equal amounts of matter and antimatter. For example, a collision of high energy particles with sufficient energy creates a matter proton and an antimatter particle called an antiproton. So the amount of antimatter shortly after the Big Bang should have been exactly the same as the amount of matter. As a CERN page on this topic says, "The Big Bang should have created equal amounts of matter and antimatter in the early universe." But whenever a matter particle touched an antimatter particle, both would have been converted into photons. The eventual result should have been a universe consisting either of nothing but photons, or some matter but an equal amount of antimatter. But only trace amounts of antimatter are observed in the universe. A universe with equal amounts of matter and antimatter would have been uninhabitable, because of the vast amount of lethal energy released when even a tiny bit of matter comes in contact with a tiny bit of antimatter.

Below are some relevant quotations by scientists or scientist organizations:

• "One cannot ignore the deep, unanswered question concerning the origin of the baryonic component because baryons and antibaryons should have annihilated almost completely, leaving only a negligible abundance today. Yet we observe a far greater concentration than the standard model of particle physics  and the first and second laws of thermodynamics should have permitted. So where did baryons come from?"  Astronomer Fulvio Melia, "A Candid Assessment of Standard Cosmology," 2022.
• "We believe the big bang produced the same amounts of matter and antimatter. These should have annihilated each other, leaving a universe made of electromagnetic radiation and not much else.” -- Professor Stefan Ulmer, a scientist at CERN (link). 
• "The Big Bang should have created equal amounts of matter and antimatter in the early universe. But today, everything we see from the smallest life forms on Earth to the largest stellar objects is made almost entirely of matter. Comparatively, there is not much antimatter to be found." -- "The matter-antimatter asymmetry problem," a page on the CERN web site describing the European Organization for Nuclear Research projects (link).

The matter/antimatter asymmetry problem is one scientists have made no progress in solving. It seems to be a problem a hundred miles over their heads. 

Problem of explaining the origin of universe. Scientists have no testable theory as to what caused the origin of the universe in the Big Bang. Every attempt that has been made to suggest a natural explanation for the Big Bang has been the thinnest speculation. The problem of what caused the Big Bang is a hundred miles over the heads of scientists. 

Cosmic fine-tuning problem.  Life is possible in our universe because of many seemingly fine-tuned features and fundamental constants. All attempts to naturally explain such fine-tuning have failed.  In particular:

• Faced with an undesired case of very strong fine-tuning involving the Higgs boson or Higgs field, scientists wrote more than 1000 papers speculating about a theory called supersymmetry which tries to explain away this fine-tuning; but the theory has failed all experimental tests at the Large Hadron Collider.  

• Faced with an undesired result that the universe's expansion rate at the time of the Big Bang was apparently fine-tuned to more than 1 part in 1,000,000,000,000,000,000,000, scientists wrote more than a thousand speculative “cosmic inflation” cosmology papers trying to explain away this thing they didn't want to believe in, by imagining a never-observed earliest instant in which the universe expanded at an exponential rate. But the "cosmic inflation" theories are unverifiable. Because of the density of the earliest years of the universe, we can never observe the first thousand years of the universe's history. The main prediction of these "cosmic inflation" theories has been that there would be observed something called primordial b-modes. Gigantic sums have been spent looking for these primordial b-modes, but all attempts have failed. 

• Scientists tried to explain away cosmic fine-tuning by speculating about a multiverse, an imagined infinity or near-infinity of universes. All such speculations do nothing to explain cosmic fine-tuning, for reasons I explain in my posts here and here. 

Below are some relevant quotations by scientists:

• "We conclude that a change of more than 0.5 % in the strength of the strong interaction or more than 4 % change in the strength of the Coulomb force would destroy either nearly all C [carbon] or all O [oxygen] in every star. This implies that irrespective of stellar evolution the contribution of each star to the abundance of C or O in the ISM would be negligible. Therefore, for the above cases the creation of carbon-based life in our universe would be strongly disfavoured." -- Oberhummer, Csot, and Schlattl, "Stellar Production Rates of Carbon and Its Abundance in the Universe."
• "The cosmological constant must be tuned to 120 decimal places and there are also many mysterious ‘coincidences’ involving the physical constants that appear to be necessary for life, or any form of information processing, to exist....Fred Hoyle first pointed out, the beryllium would decay before interacting with another alpha particle were it not for the existence of a remarkably finely-tuned resonance in this interaction. Heinz Oberhummer has studied this resonance in detail and showed how the amount of oxygen and carbon produced in red giant stars varies with the strength and range of the nucleon interactions. His work indicates that these must be tuned to at least 0.5% if one is to produce both these elements to the extent required for life."  -- Physicists B.J. Carr and M.J. Rees, "Fine-Tuning in Living Systems." 
• "The Standard Model [of physics] is regarded as a highly 'unnatural' theory. Aside from having a large number of different particles and forces, many of which seem surplus to requirement, it is also very precariously balanced. If you change any of the 20+ numbers that have to be put into the theory even a little, you rapidly find yourself living in a universe without atoms. This spooky fine-tuning worries many physicists, leaving the universe looking as though it has been set up in just the right way for life to exist." -- Harry Cliff, particle physicist, in a Scientific American article.
• "If the parameters defining the physics of our universe departed from their present values, the observed rich structure and complexity would not be supported....Thirty-one such dimensionless parameters were identified that specify our universe. Fine-tuning refers to the observation that if any of these numbers took a slightly different value, the qualitative features of our universe would change dramatically. Our large, long-lived universe with a hierarchy of complexity from the sub-atomic to the galactic is the result of particular values of these parameters." -- Jeffrey M. Shainline, physicist (link). 
• "The overall result is that, because multiverse hypotheses do not predict the fine-tuning for this universe any better than a single universe hypothesis, the multiverse hypotheses fail as explanations for cosmic fine-tuning. Conversely, the fine-tuning data does not support the multiverse hypotheses." -- physicist V. Palonen, "Bayesian considerations on the multiverse explanation of cosmic fine-tuning."
• "A mere 1 percent offset between the charge of the electron and that of the proton would lead to a catastrophic repulsion....My entire body would dissolve in a massive explosion...The very Earth itself, the planet as a whole, would crack open and fly apart in an annihilating explosion...This is what would happen were the electron's charge to exceed the proton's by 1 percent. The opposite case, in which the proton's charge exceeded the electron's, would lead to the identical situation...How precise must the balance be?...Relatively small things like atoms, people and the like would fly apart if the charges differed by as little as one part in 100 billion. Larger structures like the Earth and the Sun require for their existence a yet more perfect balance of one part in a billion billion." -- Astronomy professor emeritus George Greenstein, "The Symbiotic Universe: Life and Mind in the Cosmos," pages 63-64. 
• "What is particularly striking is how sensitive the possibility of life in our universe is to a small change in these constants. For example, if the constant that controls the way the electromagnetic field behaves in a vacuum is changed by four percent, then fusion in stars could not produce carbon....Change the cosmological constant in the 123rd decimal place and suddenly it's impossible to have a habitable galaxy." --  Marcus Du Sautoy, Charles Simonyi Professor for the Public Understanding of Science at Oxford University, "The Great Unknown," page 221. 
• "The evolution of the cosmos is determined by initial conditions (such as the initial rate of expansion and the initial mass of matter), as well as by fifteen or so numbers called physical constants (such as the speed of the light and the mass of the electron). We have by now measured these physical constants with extremely high precision, but we have failed to come up with any theory explaining why they have their particular values. One of the most surprising discoveries of modern cosmology is the realization that the initial conditions and physical constants of the universe had to be adjusted with exquisite precision if they are to allow the emergence of conscious observers. This realization is referred to as the 'anthropic principle'...Change the initial conditions and physical constants ever so slightly, and the universe would be empty and sterile; we would not be around to discuss it. The precision of this fine-tuning is nothing short of stunning. The initial rate of expansion of the universe, to take just one example, had to have been tweaked to a precision comparable to that of an archer trying to land an arrow in a 1-square-centimeter target located on the fringes of the universe, 15 billion light years away!" -- Trinh Xuan Thuan, Professor of Astronomy, University of Virginia, “Chaos and Harmony”  p. 235.

 

Problem of explaining cell reproduction:  Cells like humans have are enormously complex things.  We have been misled by diagrams that depict cells as having only a few organelles. Most types of human cells have thousands of organelles, of many different types. Human cells are so complex that they have been compared to factories or cities.  How are cells so complex able to reproduce? Scientists cannot explain it. Although the problem of cell reproduction is a million times simpler than the problem of human morphogenesis, even the problem of explaining how cells reproduce is a hundred miles over the heads of scientists.  Typically consisting of many hundreds or thousands of types of proteins, which each has its own special arrangement of hundreds or thousands of amino acids, a human cell can be compared in complexity to an automobile. But suppose you saw an automobile split to become two separate automobiles. That would be a miracle of origination that would confound and baffle you. Human cell reproduction is an event just as baffling as an automobile splitting into two working automobiles. 

Why is there something rather than nothing.   The utter non-existence of the universe is perfectly conceivable, and involves no contradiction. If there had never existed any universe, such a counter-factual state of utter nonexistence would be the simplest possible state of existence, and would have involved zero explanatory problems.  So why is there something rather than nothing? The problem is one a hundred miles over the heads of scientists. 

Problem of explaining the paranormal.  Humans have systematically observed and studied the paranormal for roughly 200 years. The explanatory problems of explaining the paranormal are endless. They include the problem of explaining all of these things:

• The accounts of very many thousands of reliable witnesses who had near-death experiences, often reporting the most vivid and life-changing experiences at a time when their heart had stopped and their brain waves had shut down, something that should have prevented any experience according to "brains make minds" dogmas. 
• The accounts of very many people reporting out-of-body experiences in which they observed their own bodies from a position meters away (discussed here, here, and here). 

• The many cases in which medical personnel who did not have such experiences verified the medical resuscitation details recalled by people who had near-death experiences, who recalled medical details that occurred when such people should have been completely unconscious because their hearts had stopped.
• Abundant cases of dying people who reported seeing dead relatives.
• Very many cases of people who saw an apparition of someone they did not know had died, with the witness soon learning the person did die at about the time the apparition was seen (discussed in the 18 posts here). 
• Very many cases when multiple witnesses reported seeing the same apparition (discussed in my series of posts here). 
• The very careful research of people like Ian Stevenson who documented countless cases of children who claimed to recalk past lives, and found that their accounts often checked out well, with the details of the “past lives” being corroborated, with the children often having birthmarks corresponding to the deaths they recalled, and with the children often recognizing people or places they should not have been able to recognize unless they had the reported past life.
• A great abundance of reports in the nineteenth century of spiritual manifestations such as mysterious raps that spelled out messages, tables moving when no one touched them, tables half-levitating when no one touched them, and tables fully levitating when no  one touched them (discussed in the series of posts here).  
• Spectacular cases in the history of mediums, with paranormal phenomena often being carefully documented by observing scientists, as in the cases of Daniel Dunglas Home, Eusapia Palladino, Leonora Piper, and Indridi Indridason.
• Two hundred years of evidence for clairvoyance in which people could observe things far away or observe things when they were blindfolded or observe things in closed containers such as locked boxes. 
• Abundant photographic evidence for mysterious orbs, including 800 photos of mysterious striped orbs, orbs appearing with dramatically repeating patterns, and orbs appearing with dramatically repeating patterns while falling water was being photographed. 
• Abundant reports of mysterious orbs being seen with the naked eye, described in the 120+ posts here.
• A great abundance of anecdotal evidence for telepathy, with large fractions of the human population reporting telepathic experiences. 
• More than a century of solid laboratory evidence for telepathy, including cases discussed here, here, and here.  
• A great abundance of evidence for a phenomenon of materialization, involving the mysterious appearance of tangible human forms. 
• Extremely numerous cases in which living people report hard-to-explain events and synchronicity suggesting interaction with survivors of death.

Mainstream scientists typically take a "head in the sand" approach when faced with the problem of explaining such things. Their typical attitude is a clear hint about how the problem of explaining the paranormal is a hundred miles over their heads. 

Protein and protein complex origination problem.  There are three aspects of this problem.

Problem of explaining the origin of proteins.  In 2019 computer scientist David Gelernter published a widely discussed book review entitled "Giving Up Darwin." He commented on the improbability of the natural origin of a new type of functional protein:

"Now at last we are ready to take Darwin out for a test drive. Starting with 150 links of gibberish, what are the chances that we can mutate our way to a useful new shape of protein? We can ask basically the same question in a more manageable way: what are the chances that a random 150-link sequence will create such a protein? Nonsense sequences are essentially random. Mutations are random. Make random changes to a random sequence and you get another random sequence. So, close your eyes, make 150 random choices from your 20 bead boxes and string up your beads in the order in which you chose them. What are the odds that you will come up with a useful new protein?...The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20¹⁵⁰. In other words, many. 20¹⁵⁰ roughly equals 10¹⁹⁵, and there are only 10⁸⁰  atoms in the universe. What proportion of these many polypeptides are useful proteins?"

Gelernter tells us that the ratio of long useful amino acid sequences (compared to useless amino acid sequences that will not be the basis of functional proteins) is incredibly small. He cites a paper by Douglas Axe estimating that the ratio is something like 1 in ten to the seventy-fourth power, or about 1 in 10⁷⁴ . 

Gelernter states this:

"Try to mutate your way from 150 links of gibberish to a working, useful protein and you are guaranteed to fail. Try it with ten mutations, a thousand, a million—you fail. The odds bury you. It can’t be done."

The phrasing of the middle sentence is a great understatement. What it should be is something like "Try it with a million mutations, a billion, a trillion, a quadrillion, a quintillion—you fail." If you have some result that you can only get about 1 in 10⁷⁴ attempts, then you can try 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 times, and you still very probably do not succeed.  According to the paper here, "we arrive at a figure of 4×1021 different protein sequences tested since the origin of life." The problem is that isn't enough tries to get even one success, if you're talking about proteins of average length.  If you have some result that you can only get about 1 in 10⁷⁴ attempts, then 4×1021 tries will not give you a 1 in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 chance of a single success.

Gelernter misstated the average number of amino acids in a protein. He states, "A protein molecule is based on a chain of amino acids; 150 elements is a 'modest-sized' chain; the average is 250." No, according to the 2012 scientific paper here, "Eukaryotic proteins have an average size of 472 aa [amino acids], whereas bacterial (320 aa) and archaeal (283 aa) proteins are significantly smaller (33-40% on average)." Mammals like us have eukaryotic proteins, so the average human protein has about 472 amino acids, almost twice as many as the number Gelernter cited. 

Let's do some simple math to show the difference here between the right numbers. A reasonable assumption is that every functional protein needs to have at least half of its amino acid sequence just as it is, or the molecule will not perform its function. (There are reasons for thinking that the fraction is actually much larger than 50%, given the high fragility of protein molecules, and their extreme sensitivity to small changes.)  So given that there are twenty amino acids used by living things, the probability of getting a random amino acid sequence serving the purpose of a particular protein can be very roughly estimated as 1 in 20n, where n is half the length of a protein's amino acid sequence. If we have a protein with a sequence of 250 amino acids, this equals a probability of about 1 in 20125, which is the same as about 1 in 10162. But if we have a protein with a sequence of 472 amino acids, this equals a probability of roughly 1 in 20236, which is the same as about 1 in 10307.  

Humans have 20,000+ types of protein molecules, and the animal kingdom has many millions of types of protein molecules. But the relevant math calculations (like those above) tell us that no type of functional protein ever should have naturally originated in the history of Earth. Darwinism does not remove this problem, or even significantly reduce it. Here are two relevant quotes by scientists:

• "A wide variety of protein structures exist in nature, however the evolutionary origins of this panoply of proteins remain unknown."  -- Four Harvard scientists, "The role of evolutionary selection in the dynamics of protein structure evolution." 
• "Tawfik admits the issue of a first protein is 'a complete mystery' because it reveals a paradox: enzymatic function depends upon the well-defined, three-dimensional structure of a protein scaffold, yet the 3D structure is too complex, too intricate, and too coordinated to arise without simpler precursors and intermediates....Tawfik soberly recognizes the problem. The appearance of early protein families, he has remarked, is 'something like close to a miracle.'....'In fact, to our knowledge,' Tawfik and Tóth-Petróczy write, 'no macromutations ... that gave birth to novel proteins have yet been identified.' " -- Tyler Hampton, quoting Dan  S. Tawfik, professor in a Department of Biological Chemistry (link). 

Problem of explaining protein complex formation. A large fraction of all types of proteins are useless unless they act as team members within teams of proteins that are called protein complexes. But scientists do not understand how protein complexes are able to form into such useful teams of proteins. The problem is not explained by DNA and its genes, which do not specify the structure or makeup of any protein complex. You may realize how huge the explanatory problem is when you study how scientists are calling many of these protein complexes "molecular machines" because they so strongly resemble something purposefully constructed. We see below one example, one including propeller-like parts. 

Below are some relevant quotes:

• "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.
• "While the occurrence of multiprotein assemblies is ubiquitous, the understanding of pathways that dictate the formation of quaternary structure remains enigmatic." -- Two scientists (link). 
• "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). 
• "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.

Problem of explaining protein folding. Proteins are almost always useless unless they have a specific three-dimensional shape.  Different types of proteins have different three-dimensional shapes. But how do such shapes arise? Scientists do not understand this. This unsolved problem is called the protein folding problem.  One attempt at solving the problem has been to advance what is called Anfinsen's Dogma, the claim that the amino acid sequence of a protein forces it to be some particular three-dimensional shape. But there has never been any good evidence to support Anfinsen's Dogma, and there are strong reasons for believing that it cannot be correct.  The case against Anfinsen's Dogma is made in two of my posts that you can read here.  It is sometimes claimed that the AlphaFold2 software did something to help solve the protein folding problem, but such claims are not correct. That software instead merely did something to help solve a different problem, one called the protein folding prediction problem.  The protein folding problem is still unsolved, and there are no good prospects of it being solved. 

Homochirality problem.  Chemicals such as amino acids and sugars can be either left-handed or right handed. A left handed amino acid looks like a mirror image of the right-handed amino acid, and a right-handed sugar looks like the mirror image of the left-handed sugar. Homochirality is the fact that in living things essentially all amino acids are left-handed, and all sugars in DNA are right-handed. But when such things are synthesized in a laboratory, or produced in experiments simulating the early Earth, you see equal amounts of left-handed and right-handed amino acids and equal amounts of left-handed and right-handed sugars.

Based on the fact that it is just as easy for left-handed amino acids to form in the laboratory as right-handed amino acids, and just as easy for left-handed sugars to form in the laboratory as right-handed sugars, we would expect for there to be a symmetry in the handedness of amino acids, with an equal amount of left-handed and right-handed amino acids. We would also would expect a symmetry in the handedness of sugars, with equal amounts of left-handed sugars and right-handed sugars. But what we see is an asymmetry, with living things having only left-handed amino acids and right-handed sugars in DNA. This characteristic of earthly life is called homochirality. 

I can give an analogy for why homochirality is such a mystery. Let us imagine a very large box filled with 5000 cards, each displaying one of the letters in the alphabet. On one side of each card is a letter. For example:

On the back side of each card is the mirror image of the letter on the front side of the card. For example:

Now, let us suppose that someone dumped this large box of cards from the top of a tall building. Imagine that the cards fell to the ground, forming a set of useful instructions that was 5000 letters long, and that none of those letters were the mirror  images of the letters in the alphabet. 

We would have two gigantic difficulties in explaining this outcome.  The first problem would be in explaining how we accidentally got a useful and intelligible set of instructions 5000 characters long.  The second problem would be in explaining how the 5000 cards all ended up showing the card side with the regular English letter, with none of them showing the mirror image of the letter on the opposite side of the card. 

The origin of life is as hard-to-explain as the falling cards event just described.  It would be easier to explain if scientists had an explanation for homochirality, but they do not. 

For twenty other posts on this blog on the topic of the tininess of human knowledge, use the link here, and continue to press Older Posts at the bottom right. 

The Missing Specifications Problem in Biology

Most biologists have heard of a problem called the missing heritability problem. It is has to do with a huge discrepancy in the degree to which traits are heritable, depending on different methods used to calculate heritability.  Speaking about issues related to this missing heritability problem, this Guardian article quotes a psychologist saying the following:

"It’s the best kept secret of modern science: 16 years of the Human Genome Project suggest that genes play little or no role in explaining differences in intelligence. While genes have been found for physical traits, such as height or eye colour, they are not the reason you are smarter (or not) than your siblings. Nor are they why you are like your high-achieving or dullard parents, or their forebears."

But this "missing heritability problem" is not at all "the best kept secret of modern science." There's another type of "missing something" problem that is much bigger and more important than such a "missing heritability problem." The problem I refer to may be called the "missing specifications problem."  The missing specifications problem is the problem that the arising of adult human bodies seem to require at least six extremely complex specifications that are nowhere to be found in the human body. 

Not long after DNA was discovered about the middle of the twentieth century, scientists and science writers began spreading a false idea about DNA: the idea that DNA contains a specification for building an organism such as a human.  There are various ways in which this false idea is stated, all equally false:

• Many described DNA or the genome as a blueprint for an organism.
• Many said DNA or the genome is a recipe for making an organism.
• Many said DNA or the genome is a program for building an organism, making an analogy to a computer program.
• Many claimed that DNA or genomes specify the anatomy of an organism. 
• Many claimed that genotypes (the DNA in organisms) specify phenotypes (the observable characteristics of an organism).
• Many claimed that phenotypes (the observable characteristics of an organism) are "expressions" of genotypes (the DNA in organisms). 
• Many claimed that genotypes (the DNA in organisms) "map"  phenotypes (the observable characteristics of an organism) or "map to" phenotypes.
• Many claimed that DNA contains "all the instructions needed to make an organism."
• Many claimed that there is a "genetic architecture" for an organism's body or some fraction of that body. 
• Many claimed that DNA or its genes "guide," "direct" or "control" the nine-month process by which a zygote progresses to become a full-sized human baby. 
• Using a little equation,  many claimed that a "genotype plus the environment equals the phenotype," a formulation as false  as the preceding statements, since we know of nothing in the environment that would cause phenotypes to arise from genotypes that do not specify such phenotypes. 

There was never any justification for making any such claims. The only coding system that has ever been discovered in DNA is a system allowing only low-level chemical information to be specified.  That coding system is known as the genetic code, and it is merely a system whereby certain combinations of nucleotide base pairs in DNA stand for amino acids.  So a section of DNA can specify the amino acids that make up a protein molecule. But no one has ever discovered any coding system by which DNA could specify anything larger than a protein molecule. 

The Genetic Code

No one ever discovered any coding system in DNA by which parts of DNA can specify high-level anatomy such as the arrangement of parts in an organ, or a skeletal structure, or an overall body appearance.  No one has even discovered any coding system in DNA by which the structure of cells can be specified.  The human body has at least 200 types of cells, and the structure of none of these cell types is specified by DNA. DNA does not even specify the structure of organelles that are the building components of cells.

If you ponder the simple fact that blueprints don't build things, you can start to get an idea of how nonsensical is the claim that a human arises because a DNA blueprint is read.  Blueprints have no power of construction.  When buildings are built with the help of blueprints, it is because intelligent agents read the blueprints to get an idea of what type of construction work to do, and because intelligent agents then follow such instructions. But there is nothing in the human body below the neck with the power to understand and carry out instructions for building a body if they happened to exist in DNA. 

Consider what goes on when you read a web page at a complicated site such as www.facebook.com or www.buzzfeed.com.  What occurs is a very complicated interaction between two things: (1) a web page that is rather like a blueprint for how the page should look and act, and (2) an extremely complicated piece of software called a web browser, which is rather like a construction crew that reads the web's page blueprint (typically written in HTML), and then constructs very quickly a well-performing web page.  If the web browser did not exist, you would never be able to get a well-performing web page.  The construction of a three-dimensional human body would be a feat trillions of times more complicated than the mere display of a two-dimensional web page.  Just as it is never enough to have just a web page without a web browser,  having some DNA blueprint for building a body would never be enough to build a body.  You would also need to have some "body blueprint reader" that would be some system almost infinitely more complicated than a web browser, in order for a body as complex as a human body to get built.  

We have no evidence that DNA contains any instructions for building cells or anatomy, and we also have no evidence for the existence of any such thing as a "body blueprint reader" in the human body, capable of reading, understanding and executing incredibly complicated instructions for building a human body. When you consider the amount of organization in a human body, you may start to realize the gigantic absurdity of thinking that a human specification can be found in some molecule merely listing low-level chemical information. 

Let us look at some of the specifications that are not found in DNA or its genes.  The human body relies very much not just on 20,000+ types of protein molecules, but also thousands of teams of protein molecules known as protein complexes. But DNA and its genes do not specify how to make such protein complexes. The specification shortfall is illustrated in the schematic visual below. In this diagram and all similar diagrams in this post, the red "missing" word means merely "missing in the human body" rather than entirely nonexistent. 

At least a long book would be required for such a specification of how to make the protein complexes used by human bodies. It is now well-known that protein complexes often make up components so complex that they are often called "molecular machines."  Such molecular machines often resemble human machines, by having features such as motor-like parts or propeller-like parts.  An example of one of the very many extremely organized protein complexes in the human body is shown below. The structure has many moving parts.  

Another example of an extremely organized protein complex is shown below. The diagram (made by a scientist) refers to some of the parts as "propellers."

Another example of an extremely organized protein complex is shown below. 

See my post here which discusses some of the more complex protein complexes used in human bodies. There are many cases in which the human body uses some type of protein complex requiring many different proteins arranged in some special way to achieve some astonishing piece of engineering that is often called a molecular machine.  The failure of scientists to understand how these protein complexes form is shown by the quotes below:

•  "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.
• "While the occurrence of multiprotein assemblies is ubiquitous, the understanding of pathways that dictate the formation of quaternary structure remains enigmatic." -- Two scientists (link). 
• "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). 
• "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.

Let us look at some more of the specifications that are not found in DNA or its genes.  The human body relies very much on cell organelles. Organelles are the basic building components of cells. Contrary to the misleading diagrams that make cells look thousands or millions of times simpler than they are, the more organized cells in the human body require thousands of different organelles of quite a few different types.  But nowhere does DNA or its genes tell how to make any type of organelle. The specification shortfall is illustrated in the schematic visual below.

Looking at the diagram below, from the scientific paper here, you might be able to get some idea of how complex and long a specification would be needed to specify organelles. A ribosome is the smallest type of organelles in a cell. But in its tiny size it manages to have a factory for making different proteins.

Below are some other types of cell organelles:

By looking at the number in the second column of the table below,  derived from a table on this page of the Human Protein Atlas, you can get an idea of how complex each organelle is. The larger the number in the second column, the more complex that organelle is. Lysosomes are relatively simple organelles, but organelles such as mitochondria and plasma membranes are vastly more complex. Each type of protein requires a special arrangement of hundreds of amino acids, which altogether involves a special arrangement of thousands of atoms. The more complex organelles in cells require a special arrangement of more than a million atoms. The arrangement involved is as special and as hard-to-achieve by chance as the arrangement of characters in a lengthy essay such as this blog post. 

ORGANELLE TYPE	NUMBER OF TYPES OF PROTEINS IN EACH ORGANELLE
Intermediate filaments	163
Actin filaments	237
Focal adhesion sites	138
Microtubules	262
Microtubule ends	6
Cytokinetic bridge	159
Midbody	53
Midbody ring	25
Cleavage furrow	1
Mitotic spindle	93
Centriolar satellite	194
Centrosome	396
Mitochondria	1121
Aggresome	19
Cytosol	4883
Cytoplasmic bodies	73
Rods & Rings	20
Endoplasmic reticulum	542
Golgi apparatus	1163
Vesicles	2238
Peroxisomes	23
Endosomes	17
Lysosomes	19
Lipid droplets	39
Plasma membrane	2074
Cell Junctions	330
Nucleoplasm	6166
Nuclear membrane	276
Nucleoli	1075
Nucleoli fibrillar center	311
Nucleoli rim	151
Nuclear speckles	493
Nuclear bodies	588
Kinetochore	6
Mitotic chromosome	74
Total number of types of proteins used in human cell organelles	13147

Then there are cells themselves. Cells like those in the human body are fantastically organized things. Human cells are so complex they have been compared to factories or cities in their complexity. Most of the cells in the human body somehow manage to achieve the marvel of cell reproduction. Given the number of well-organized parts in a cell, every time a human cell reproduces it is a marvel comparable to an automobile splitting up to become two different working automobiles. Obviously some great plan is needed to construct all of the different types of cells in the human body. But no such plan can be found in DNA or its genes, which know nothing about how to make a cell. The missing specification is illustrated schematically below:

Here is a relevant quote from a physicist Anthony Aquirre, from his "Cosmological Koans," page 338:

"The most elaborate and sophisticated human-designed machines, while quite impressive, are utter child's play compared with the workings of a cell: a cell contains on the order of 100 trillion atoms, and probably billions of quite complex molecules working with amazing precision. The most complex engineered machines -- modern jet aircraft, for example -- have several million parts. Thus, perhaps all the jetliners in the world (without people in them, of course) could compete in functional complexity with a lowly bacterium." 

Then there are organs. Organs such as eyes and ears and hearts and lungs and livers are enormously complex. But DNA and it genes have no specification for making any organ in a body. The situation is schematically depicted below:

In Table 1 of the paper "A comprehensive functional analysis of tissue specificity of human gene expression," we have the following list.  In the paper the table has the same title as below.  The genes referred to are not the total number of genes used in a particular organ or body part, but the "tissue-specific genes" used only by that organ or body part. So, for example, there are apparently 22 genes used only by the liver, and 484 genes used only by the testis.  Each gene corresponds to a different type of protein, typically with a unique arrangement of several hundred amino acid parts. The "housekeeping" genes are genes not used only by one organ or body part. The table helps give us an idea of how complex human organs are. 

 

Table 1: Number of housekeeping and tissue-specific genes

Housekeeping 2374

Liver 22

Skeletal muscle 37

Fetal liver 16

Testis 484

Placenta 38

Bone marrow 63

Skin 75

Adrenal gland 13

Prostate 14

Trachea 16

Small intestine 35

Peripheral blood lymphocytes 49

Mammary gland 16

Tonsil 24

Thymus 4

Spleen 14

Fetal kidney 5

Thyroid 7

Brain 34

Heart 26

Lung 16

Salivary gland 17

Ovary 15

Pancreas 20

Fetal thymus 8

Colon 9

Spinal cord 24

Retina 190

Kidney 17

Uterus 12

Fetal brain 61

Average 43.8

Average, somatic tissues 30.9

A specification for an organ would include not just a specification of how to construct the organ, but also a specification of how to perform the enormously complex biochemistry needed for the organ to properly function. For example, here is a description of some of the biochemistry needed for the proper working of an eye, taken from a biochemistry textbook:

1. "Light-absorption converts 11-cis retinal to all-trans-retinal, activating rhodopsin.
2. Activated rhodopsin catalyzes replacement of GDP by GTP on transducin (T), which then disassociates into T_a-GTP and T_by.
3. T_a-GTP activates cGMP phosphodiesterase (PDE) by binding and removing its inhibitory subunit (I).
4. Active PDE reduces [cGMP] to below the level needed to keep cation channels open.
5. Cation channels close, preventing influx of Na⁺ and Ca2⁺; membrane is hyperpolarized. This signal passes to the brain.
6. Continued efflux of Ca²⁺ through the Na⁺-Ca2⁺ exchanger reduces cytosolic [Ca²⁺].
7. Reduction of [CA²⁺] activates guanylyl cyclase (CG) and inhibits PDE; [cGMP] rises toward 'dark' level, reopening cation channels and returning V_m to prestimulus level.
8. Rhodopsin kinase (RK) phosphorylates 'bleached' rhodopsin; low [Ca²⁺] and recoverin (Recov) stimulate this reaction. Arrestin (Arr) binds phosphorylated carboxyl terminus, reactivating rhodopsin.
9. Slowly, arrestin dissociates, rhodopsin is dephosphorylated, and all-trans-retinal is replaced with 11-cis-retinal. Rhodopsin is ready for another phototransduction cycle."

Then there are organ systems. Some organs require elaborate systems much more complex than the organ itself. For example, the nervous system has not just a brain but also nerves that are spread out throughout the body, and exist abundantly in the spine. And hearts cannot do anything in isolation, but require a huge system of arteries, veins and capillaries to achieve the circulation of the blood.  But DNA and its genes do not specify either how to make organs or organ systems. The missing specification is depicted in the visual below:

Finally, building a body such as a human body requires a specification for the structure of the overall organism.  Such a specification would include things such as a specification of the skeletal structure (consisting of 200+ different bones in humans, and how they are connected), and a specification of the overall body structure, including muscles, arms, legs, hands, feet, fingers, toes and the head (as well as the arrangement of organs on the head).  The specification would include all of the many things needed for the human body to result in a mobile human capable of walking, running, swimming and jumping. No such specification is to be found in DNA or its genes. The situation is depicted by the visual below:

Appealing to a dubious claim of self-organization, a web page on a college biology department states, "We still only poorly understand how all these tiny molecules self-organize into much larger organelles, cells, and organisms." At least the statement lets us know how such things are not explained by anything found in DNA or genes. 

Do you think that a large mobile body such as a lion's body or a human body could just pop up without there being any kind of specification for such a body? Consider all of the functional  interdependence of the items below, and you may change your mind. 

Our biologists have senselessly failed to recognize the gigantic problem of these missing specifications.  Many of our biologists have lied and misled us about what is in DNA, by speaking as if DNA was a blueprint or program or recipe for making a human. But many other scientists have told us the truth about what DNA and its genes are not. Some of the statements of these biologists are below:

• On page 26 of the recent book The Developing Genome, Professor David S. Moore states, "The common belief that there are things inside of us that constitute a set of instructions for building bodies and minds -- things that are analogous to 'blueprints' or 'recipes' -- is undoubtedly false."
• Biologist Rupert Sheldrake says this "DNA only codes for the materials from which the body is constructed: the enzymes, the structural proteins, and so forth," and "There is no evidence that it also codes for the plan, the form, the morphology of the body."
• Describing conclusions of biologist Brian Goodwin, the New York Times says, "While genes may help produce the proteins that make the skeleton or the glue, they do not determine the shape and form of an embryo or an organism." 
• Professor Massimo Pigliucci (mainstream author of numerous scientific papers on evolution) has stated  that "old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading."
• Neuroscientist Romain Brette states, "The genome does not encode much except for amino acids."
• In a 2016 scientific paper, three scientists state the following: "It is now clear that the genome does not directly program the organism; the computer program metaphor has misled us...The genome does not function as a master plan or computer program for controlling the organism; the genome is the organism's servant, not its master.
• In the book Mind in Life by Evan Thompson (published by the Belknap Press of Harvard University Press) we read the following on page 180: "The plain truth is that DNA is not a program for building organisms, as several authors have shown in detail (Keller 2000, Lewontin 1993, Moss 2003)."
• Developmental biologist C/H. Waddington stated, "The DNA is not a program or sequentially accessed control over the behavior of the cell."
•  Scientists Walker and Davies state this in a scientific paper: "DNA is not a blueprint for an organism; no information is actively processed by DNA alone...DNA is a passive repository for transcription of stored data into RNA, some (but by no means all) of which goes on to be translated into proteins."
• Geneticist Adam Rutherford states that "DNA is not a blueprint," a statement also made by biochemistry professor Keith Fox. 
• "The genome is not a blueprint," says Kevin Mitchell, a geneticist and neuroscientist at Trinity College Dublin, noting "it doesn't encode some specific outcome."
• "DNA cannot be seen as the 'blueprint' for life," says Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, who says, "It is at best an overlapping and potentially scrambled list of ingredients that is used differently by different cells at different times."  
• Sergio Pistoi (a science writer with a PhD in molecular biology) tells us, "DNA is not a blueprint," and tells us, "We do not inherit specific instructions on how to build a cell or an organ." 
• Michael Levin (director of a large biology research lab) states that "genomes are not a blueprint for anatomy," and after referring to a "deep puzzle" of how biological forms arise, he gives this example: "Scientists really don’t know what determines the intricate shape and structure of the flatworm’s head."
• Ian Stevenson M.D. stated "Genes alone - which provide instructions for the production of amino acids and proteins -- cannot explain how the proteins produced by their instructions come to have the shape they develop and, ultimately, determine the form of the organisms where they are," and noted that "biologists who have drawn attention to this important gap in our knowledge of form have not been a grouping of mediocrities (Denton, 1986; Goldschmidt, 1952; B. C. Goodwin, 1985, 1988, 1989, 1994; Gottlieb, 1992; Grasse, 1973; E. S. Russell...Sheldrake, 1981; Tauber and Sarkar, 1992; Thompson, 1917/1942)."
• Biologist B.C. Goodwin stated this in 1989: "Since genes make molecules, genetics...does not tell us how the molecules are organized into the dynamic, organized process that is the living organism."
• An article in the journal Nature states this: "The manner in which bodies and tissues take form remains 'one of the most important, and still poorly understood, questions of our time', says developmental biologist Amy Shyer, who studies morphogenesis at the Rockefeller University in New York City."
• Timothy Saunders, a developmental biologist at the National University of Singapore says, "Fundamentally, we have a poor understanding of how any internal organ forms.”
• On the web site of the well-known biologist Denis Noble, we read that "the whole idea that genes contain the recipe or the program of life is absurd, according to Noble," and that we should understand DNA "not so much as a recipe or a program, but rather as a database that is used by the tissues and organs in order to make the proteins which they need."
• A paper by Stuart A. Newman (a professor of cell biology and anatomy) discussing at length the work of scientists trying to evoke "self-organization" as an explanation for morphogenesis states that "public lectures by principals of the field contain confidently asserted, but similarly oversimplified or misleading treatments," and says that "these analogies...give the false impression that there has been more progress in understanding embryonic development than there truly has been." Referring to scientists moving from one bunk explanation of morphogenesis to another bunk explanation, the paper concludes by stating, "It would be unfortunate if we find ourselves having emerged from a period of misconceived genetic program metaphors only to land in a brave new world captivated by equally misguided ones about self-organization."
• Referring to claims there is a program for building organisms in DNA, biochemist F. M. Harold stated "reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading." Referring to  self-organization (a vague phrase sometimes used to try to explain morphogenesis), he says, "self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm." 
• Writing in the leading journal Cell, biologists  Marc Kirschner, John Gerhart and Tim Mitchison stated, "The genotype, however deeply we analyze it, cannot be predictive of the actual phenotype, but can only provide knowledge of the universe of possible phenotypes." That's equivalent to saying that DNA does not specify visible biological structures, but merely limits what structures an organism can have (just as a building parts list merely limits what structures can be made from the set of parts). 
• At the Stack Exchange expert answers site, someone posted a question asking which parts of a genome specify how to make a cell (he wanted to write a program that would sketch out a cell based on DNA inputs).  An unidentified expert stated that it is "not correct" that DNA is a blueprint that describes an organism, and that "DNA is not a blueprint because DNA does not have instructions for how to build a cell." No one contradicted this expert's claim, even though the site allows any of its experts to reply. 
• A paper co-authored by a chemistry professor (Jesper Hoffmeyer) tells us this: "Ontogenetic 'information,' whether about the structure of the organism or about its behavior, does not exist as such in the genes or in the environment, but is constructed in a given developmental context, as critically emphasized, for example, by Lewotin (1982) and Oyama (1985)."
• Biologist Steven Rose has stated, "DNA is not a blueprint, and the four dimensions of life (three of space, one of time) cannot be read off from its one-dimensional strand."
• Jonathan Latham has a master's degree in Crop Genetics and a PhD in virology. In his essay “Genetics Is Giving Way to a New Science of Life,” a long essay well worth a read, Latham exposes many of the myths about DNA. Referring to "the mythologizing of DNA," he says that "DNA is not a master controller," and asks, "How is it that, if organisms are the principal objects of biological study, and the standard explanation of their origin and operation is so scientifically weak that it has to award DNA imaginary superpowers of 'expression'” and 'control' to paper over the cracks, have scientists nevertheless clung to it?"
• An interesting 2006 paper by six medical authorities and scientists tells us that "biochemistry cannot provide the spatial information needed to explain morphogenesis," that "supracellular morphogenesis is mysterious," and that "nobody seems to understand the origin of biological and cellular order," contrary to claims that such order arises from a reading of a specification in DNA. 
• Keith Baverstock (with a PhD in chemical kinetics) has stated "genes are like the merchants that provide the necessary materials to build a house: they are neither the architect, nor the builder but, without them, the house cannot be built," and that "genes are neither the formal cause (the blueprint), nor the efficient cause (the builder) of the cell, nor of the organism."
• Evolutionary biologist Richard Lewontin stated, "DNA is not self-reproducing; second, it makes nothing; and third, organisms are not determined by it." Noting that "the more accurate description of the role of DNA is that it bears information that is read by the cell machinery," Lewontin lamented the "evangelical enthusiasm" of those who "fetishized DNA" and misspoke so that "DNA as information bearer is transmogrified into DNA as blueprint, as plan, as master plan, as master molecule." In another work he stated "the information in DNA sequences is insufficient to specify even a folded protein, not to speak of an entire organism." This was correct: DNA does not even specify the 3D shapes of proteins, but merely their sequence of amino acids. 
• In 2022 developmental biologist Claudio D. Stern first noted,  "All cells in an organism have the same genetic information yet they generate often huge complexity as they diversify in the appropriate locations at the correct time and generate form and pattern as well as an array of identities, dynamic behaviours and functions." In his next sentence he stated, "The key quest is to find the 'computer program' that contains the instructions to build an organism, and the mechanisms responsible for its evolution over longer periods." Since this was written long after the Human Genome Project had been completed, he thereby suggested that no such instruction program had yet been discovered in the genome (DNA). 
• A 2024 article says, "Martínez Arias, 68, argues that the DNA sequence of an individual is not an instruction manual or a construction plan for their body...The Madrid-born biologist argues that there is nothing in the DNA molecule that explains why the heart is located on the left, why there are five fingers on the hand or why twin brothers have different fingerprints."
• Two scientists said this: "We see no valid use for definitions of the genotype and phenotype in terms of blueprints, programs, or sets of instructions, and their realizations or manifestation....The program/manifestation metaphor is factually misleading, because it suggests that the genotype uniquely determines an organism’s phenotype. However, as is well known, all it does is specify an organism’s norm of reaction to environmental conditions (Rieger et al., 1991,Lewontin, 1992)."
• A 2022 paper in the journal Science (one authored by more than ten scientists) says this: "Although the genome is often called the blueprint of an organism, it is perhaps more accurate to describe it as a parts list composed of the various genes that may or may not be used in the different cell types of a multicellular organism....The genome in and of itself does not provide an understanding of the molecular complexity of the various cell types of that organism."
• A Duke University biologist and a Cornell University biologist have confessed this: " No information about the overall architecture of these body parts is present in the cells and tissues of the parts themselves, or in each organism’s genes."  

Have these scientists recognized the enormity of the missing specifications problem, and its implications? Have these biologists realized that the missing specifications problem is an issue that overthrows the mechanistic and Darwinian knowledge boasts of biologists? In general, they have not. You might compare such scientists to some tower builder trying to build a ten-story structure, who realizes one day that his second floor and his foundation cannot support the weight of the third, fourth and fifth floors he has already built. The implication is that the tower is destined to collapse, but the tower builder fails to put two and two together to come to that conclusion.  Similarly, the missing specifications problem ultimately implies that the boasts of mechanistic and reductionist and Darwinist biologists are doomed to collapse, at least in the sense of a credibility collapse. But most of the scientists quoted above probably have not realized that yet. 

The diagram below illustrates the levels of organization in a human body, and which levels are not specified by anything in DNA or its genes. The diagram is one way of illustrating the missing specifications problem. 

The diagram above (and the first visual of this post) actually fail to fully represent the missing specifications problem, because neither of these visuals mentions that protein molecules are only half-specified by DNA and its genes. DNA and its genes specify which amino acids make up particular proteins, but  DNA and its genes do not specify the three-dimensional shapes of protein molecules, something necessary for their function. The claim that the three-dimensional shapes of protein molecules is an inevitable consequence of their amino acid sequence is a claim known as Anfinsen's Dogma. But this claim is not well-supported by observations, and there are strong reasons for rejecting it, as I discuss in my posts here. Scientists attempting to reproduce the experiment of Anfinsen trying to support his dogma have failed to reproduce his results, as I discuss in those posts.  Claims that the protein folding problem was solved by the AlphaFold2 software are incorrect. That software merely made some progress with a different problem: the protein folding prediction problem, the problem of how to predict the 3D shape of a protein from its amino acid sequence. The protein folding problem (the problem of how 3D shapes arise from 0ne-dimensional sequences of amino acids) is very much unsolved, and this is one aspect of the missing specifications problem. 

Whenever results can all be easily explained as accidents or chance effects, and whenever results do not require any very special and very improbable arrangement of parts that achieve functional ends, or when results are achieved only once or a few times, there may be no need to say that there must be a specification of the results somewhere. For example, the wind forms snow into random types of snow drifts, and there is no need to postulate that there are snow drift specifications. But whenever a result is achieved a huge number of times, and involves a very special arrangement and organization of very many parts of many different types that is necessary for achieving a functional end, and whenever so special and hard-to-achieve a functional organization of very many parts of many types is accidentally unachievable, then we should say: there must be a specification somewhere.  Each of the levels of organization listed above is a level of organization that is accidentally unachievable, and each of these levels of organization must be matched by some specification existing somewhere. But none of these specifications exist in the human body. 

 

Large biological organisms such as humans somehow get constructed according to the most elaborate and purposeful plans, but most of those plans can be found nowhere in the human body. And even if such plans were to be ever found in the human body,  they would not explain the physical construction of a human body so organized and internally dynamic, both  because the plans would be too complex for anything in the human body to understand, and because plans don't build things.  For example, blueprints do not build houses -- houses get built because intelligent house builders read blueprints and get ideas on how to build houses. 

The implications of the missing specifications problem are so large they can scarcely be overstated.  The person who very deeply ponders the missing specifications problem at sufficient length will tend to eventually suspect that biology is radically and thoroughly teleological from top to bottom, that claims of mostly accidental biological origins are gigantically incorrect, and that earthly biology must be driven by some purposeful agency beyond human fathoming, with such agency working continuously, rather than merely as some "way back when" type of thing. The probability that such suspicions are anathema to the great majority of biologists is no reason for avoiding such ideas, if deeply pondering the facts and their implications compel us to move in the direction of such ideas. The complete failure of neural explanations to credibly account for the main aspects of the human mind is something that should embolden us when pondering the need for a drastic rethinking of long-standing but never-justified claims in biology. 

There are two ways in which materialists try to prevent you from understanding the missing specifications problem. The first way is to make deceptive statements about DNA and genes, including false claims that DNA is a blueprint, recipe or program for making bodies. The scientist statements quoted above refute such deceptive claims. The second way in which materialists try to prevent you from understanding the missing specifications problem is to misrepresent the vast amount of hierarchical organization and internal dynamism and fine-tuned functional complexity of human bodies. This consists of various tricks to fool you into thinking that human bodies are a million times simpler than they are. Among these tricks are the tricks of publishing cell diagrams that depict cells  as a million times simpler than they are, or diagrams depicting protein molecules as hundreds of times simpler than they are, or diagrams or statements that fail to mention protein complexes or organelles or cells, leading people to think the very incorrect idea that organism bodies or cells are directly made from proteins, or profoundly misleading statements describing your body as "star stuff" using the term "stuff" referring to something disorganized . The main trick of this type is just a failure of adequate description, so that people are never educated about how their bodies are feats of precise engineering more impressive than any objects humans have constructed. 

Humans know how to make cities. There is not a nation or a corporation in the world that could ever construct a living human body even as small as a baby from low-chemical materials, or get even a tenth of the way to such a goal. Given the missing specifications described above, every time a new human body comes fully into existence, it is a miracle of construction far more impressive than a million piles of bricks, pipes, doors and boards magically turning into a city, when there are no builders around,  No appeal to evolution can overcome this difficulty, because Darwinian evolution refers to what supposedly occurred over the span of many generations long ago, not what happens during the nine months of a human pregnancy. 

Below are some relevant quotes:

• "Yet while these are several examples of well-understood processes, our study of animal morphogenesis is really in its infancy." -- David Bilder and Saori L. Haigo1, "Expanding the Morphogenetic Repertoire: Perspectives from the Drosophila Egg." 
• "Fundamentally, we have a poor understanding of how any internal organ forms." -- Timothy Saunders, developmental biologist (link).
• "An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place -- development -- is only understood in the roughest of outlines." -- Five scientists (link). 
• "Biochemistry cannot provide the spatial information needed to explain morphogenesis...Supracellular morphogenesis is mysterious...Nobody seems to understand the origin of biological and cellular order."  -- Six medical authorities (link).
• "Despite the centrality of multicellularity and cell differentiation to animal biology, their origins are little understood." -- Two cell biologists (link). 
• "We have little understanding of the processes that allow cells to become different." -- Two scientists, 2019 (link).