Header 1

Our future, our universe, and other weighty topics


Showing posts with label molecular biology. Show all posts
Showing posts with label molecular biology. Show all posts

Monday, July 15, 2024

A Science Writer's Lame Excuses for Biologists Lying and Science Writers Lying

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 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. 
Some of these claims are documented in Table 1 of the paper here, where some authors count (in only June and July of the year 2000, in a single newspaper) 10 claims that DNA is a draft or script, 6 that it is a software program, 8 that it is a blueprint, 6 that it is a cook book (a recipe), and 12 that is a map. The same table shows similar claims being made abundantly in the leading scientific journal Nature; and Table 2 and Table 3 of the same paper shows similar claims being made abundantly in 2001 and 2003 in both the newspaper and Nature. 

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. 

Because of the lack of any justification for making the claims in the bullet list above, the biologists who have made such claims have been guilty of massive lying. Their deceits about DNA and genes have occurred over the course of 70 years. But now many scientists, doctors and science writers have confessed that there is no truth to the claims that DNA is a specification for making a human. A list of some of these confessions is found in the appendix of this post. 

You can describe the strange situation like this: the left hand of biology keeps lying about DNA and genes, while the right hand of biology is telling the truth. In which of these camps should we put science writer Phillip Ball? It's a little hard to tell. In the very mainstream publication The Guardian, science writer Phillip Ball said this about the Human Genome Project that ended in 2003, noting the failure of science figures to clean up their old misstatements about DNA after they were debunked by the Human Genome Project:

"But a blizzard of misleading rhetoric surrounded the project, contributing to the widespread and sometimes dangerous misunderstandings about genes that now bedevils the genomic age. So far, there have been few attempts to set the record straight. Even now, the National Human Genome Research Institute calls the HGP an effort to read 'nature’s complete genetic blueprint for building a human being' – the 'book of instructions' that 'determine our particular traits'. A genome, says the institute, 'contains all of the information needed to build and maintain that organism'. But this deterministic 'instruction book' image is precisely the fallacy that genomics has overturned, and the information in the genome is demonstrably incomplete. Yet no one associated with genomic research seems bothered about correcting these false claims...Plenty remain happy to propagate the misleading idea that we are 'gene machines' and our DNA is our 'blueprint'.

But in a recent essay on Aeon entitled "We Are Not Machines", Ball fails to give us the plain truth on this matter. In the middle of telling us that the narrative of biologists about DNA is "at best a partial and at worst a misleading picture," he describes a narrative about DNA claiming that "the genome contains the information needed to make a human." He then says this:

"This story is (for the most part) not wrong. It’s plenty good enough to give students a rough notion of how biology works. But its elisions, omissions and simplifications can create serious misconceptions about what genes are and do."

No, the claim that "the genome contains the information needed to make a human" is very much wrong, because the genome (in other words, DNA and its genes) does not have even a tenth of the information needed to make a human. The genome only specifies low-level chemical information, and that is only a tiny fraction of what you would need to know to make a human. The genome does not specify how to make anything bigger than a protein molecule. DNA does not specify anatomy. In fact genomes only half-specify how to make protein molecules, because DNA does not specify how to make the 3D shapes of protein molecules vital for their proper function.  Protein molecules are only the beginning of the vast hierarchical organization of a human body.  

Let us imagine a man who goes to a special library that is dedicated to fully teaching about the complexity and organization of the human body. Suppose the person has been commanded that he has to study all of the details and complexity of the human body. He might start by looking through books that describe proteins. A full description of the average protein molecule would require maybe 5 to 10 pages of information in a large book. First there would be a listing of all the amino acids in the protein, which would require several pages. Then there would be a diagram showing the three-dimensional shape of the protein.  A single book could not display all the details for more than about 100 types of protein molecules. So reading all of the protein books would require the man reading about 200 long books. This is because there are roughly 20,000 types of protein molecules in the human body. 

But reading all of those books would only be the beginning of the man's chore. For we would also have to study protein complexes. This would require reading about the complexities of all the thousands of protein complexes that may consist of dozens of different types of proteins.  So there would be many additional books the man would have to read. Then the man would have to read about all the different organelles in cells, and the structure of cells. This would not merely involve studying those phony childish cell diagrams like they have in biology books, those diagrams that depict cells as thousands of times simpler than they are. The man would have to study realistic cell diagrams. 

Such diagrams would have to be huge. We can imagine some special books in the library made up of large pocket-pages, with huge folded diagrams in such pockets. Taking out the diagrams, the man might spread them out to the size of a huge table. Each diagram would show the position of many thousands of organelles. There would be endless such diagrams to be studied. 

But the man's work would still not be done. Now he would have to study huge diagrams showing the unfathomable complexity of human biochemistry. We can imagine many special books in the library made up of pocket-pages, with huge folded diagrams in such pockets. Taking out the diagrams, the man might spread them out to the size of a huge table, and study many thousands of incredibly complex biochemistry diagrams, illustrating how fantastically hard-to-achieve functional results are achieved in the human body by the magnificently purposeful choreography of endless components acting together as smoothy and harmoniously as all the dancers and musicians in all the theaters of Broadway. 



Then the man would have to study endless more details, how cells combine to make organs and organ systems. How long would the total job take of studying all these details at the library? It would seem to take thousands of hours. 

In his Aeon essay Phillip Ball gives us no real sign that he understands the sky-high levels of organization and coordination and interdependent component teamwork  needed to make a human body.  But at least he seems to have perceived that there's something terribly wrong with biologists and the narratives they are telling. He describes them like this:

" Physicists are often keen to proclaim, at the drop of a hat, that ‘This changes everything!’ Biologists, on the other hand, while no slouches at drumming up media coverage for their own work, seem rather averse to big shifts in the discourse. ‘Well, we sort of knew that years ago,’ they will mutter – or alternatively: ‘That’s probably just a rare exception.’...Others said that, even if biology was indeed more complicated that we’d thought, what was to be gained by telling the public that? In other words: don’t upset the status quo....Finally, I suspect the narrative inertia reflects a general tendency in science whereby scientists get even more wedded to their metaphors than to their theories. Many biologists seem to have forgotten where the old metaphor of the genetic blueprint came from in the first place. The Harvard historian and philosopher of science Evelyn Fox Keller pointed out that it was never a notion compelled by the experimental evidence, but was merely a stopgap solution for our lack of knowledge about how the information in the genome (the genotype) was related to the visible traits of the organism (the phenotype)....Yet one can’t reasonably expect researchers to give up their metaphors unless they have others to replace them."

This quote only gives a part of the portrait Ball paints of biologists who keep telling us false claims, because they are clinging to misleading speech customs. The excuse given at the end of the quote is a lame one. It is misguided to claim that when scientists discover that a metaphorical explanation they have been using is untrue, they should be excused for continuing to lie by giving such an explanation, until they have some other more truthful metaphorical explanation they can give. 

We may wonder whether Ball is suggesting a rule such as "stick to your narrative of how something arises because of a particular physical explanation, no matter how badly that explanation is failing, until you can replace that narrative with a different and more successful narrative of how something arises because of a particular physical explanation."  That's a bad, dishonest rule. 

There's a much better rule of proper scientific behavior: when you discover that the boastful claims you previously made about having a good physical explanation of the origin of something are not sound, then confess your ignorance of the origin of such a thing, and start telling people, "I thought I understood how this enormously complex reality arises, but now I see that my explanation is not credible, and that I don't understand how it arises."  It is wrong and unethical to claim that boastful and failing claims of understanding something by some physical explanation must be maintained until they can be replaced by new boastful claims of understanding that thing by some new physical explanation. When the most popular explanation of something fails, healthy scientists should be saying things like, "We use to think we understood how this reality arose, but it's now clear that it's a complexity far over our heads, and that we don't understand  at all how such a reality arises." 

In the visual below, we see scientists who have placed themselves on pedestals. The pedestals were constructed by misleading statements. What are the first things such erring scientists should do? They should start by climbing off of their pedestals, and confessing all of the times they made statements and claims that were untrue or unbelievable. They should remove their self-devised crowns marked "Grand Lord of Explanation," and start confessing that their knowledge of nature is fragmentary. 

scientists on pedestals

Ball gives us another lame excuse for lying biologists who claim to understand things they don't understand, stating this: "It has also become much harder in recent years for scientists to admit to gaps in knowledge and understanding, which will be exploited by everyone ranging from creationists to climate-change deniers to anti-vaxxers as evidence that we shouldn’t believe a word they say." It is not a decent excuse for deception that if you stop such deception you will give some talking points to your opponents. Here Ball represents critics of Darwinism using the most misleading portrayal. He absurdly portrays them as people eager to say that we shouldn't believe a word that biologists say. To the contrary, intelligent design theorists are building their case very much on the truth of very many of the claims that biologists make, such as their  claims about the many types of intricate molecular machinery inside our body, their claims about the vast organization of organisms, their claims about the gigantic functional complexity of cells, and so forth. A typical intelligent design theorist is constantly citing the low-level facts discovered by biologists, while doubting some of the high-level causal claims such biologists make. 

Ball gives another excuse for science journalists continuing to tell false biology claims such as the "DNA is a body blueprint" claim: the very lame excuse that the reality is so complex that it cannot be fit into a short explanatory soundbite. He says this (very ridiculously insinuating that he understands "the real picture" of how human bodies arise, a miracle of organization that is actually a thousand miles over his head and the head of every biologist):

"But surely another reason for the near invisibility in the science media of the transformation in biology is that we now have a much harder story to tell. The idea that ‘genes make proteins, and proteins make us’ is easy to grasp. The real picture is far harder to capture in a sound bite. I suspect we hear so little about this new biology in part because many journalists (or their editors) take a look at the latest research on, say, gene regulation of chromatin remodelling or cell signalling and think: ‘I’m not going anywhere near that!’"  

This is no excuse. It presumes that journalists have to have a nice little mechanistic explanation when writing a science story. They don't have to have any such thing. Rather than giving us some little sketch and saying, "That's how it happens," a science journalist can tell us about the vast organization and mountainously complex functional biochemistry in  human bodies, and say, "We don't understand how such organization and vast functional complexity arises."  There are all kinds of metaphors that can be used to give a correct idea about a state of knowledge that is merely fragmentary. For example, you can use Isaac Newton's classic analogy that he was like a little child at the seashore examining a few seashells, while the great ocean of truth lie undiscovered before him.  Or you could give the analogy of some 1st century person transported to Times Square, seeing all kinds of engineering and technology beyond his understanding.  Or you can give the analogy like the one in the visual below, in which the sitting figure represents the current state of modern science, compared to the unsolved mysteries of reality. There is no rule that science stories have to give neat little explanations of how something very complex works or how scientists are starting to understand how something very complex works. 

unsolved science problems

Talking about metaphors used by scientists, Ball makes the very untrue claim that "metaphors aren’t the kind of thing you test at all." No, that's not true; there are all kinds of ways of testing whether a metaphorical statement is valid. For example, if someone says the brain is like a computer, I can test whether that metaphor is valid by listing some of the things a computer has, and checking whether the brain has such things. An example of trying such a test can be read here. 

At the end of his article, Ball asks, "So how now should we be speaking about biology?"  He starts out very strangely by quoting some biologist making the silly claim that the genome is "an organ of the cell." No, cells don't have organs; cells are the components of tissues, which are the components of organs. Saying the genome is an organ of the cell is every bit as silly as saying your distributor cap is the car inside your engine. 

Ball then gives us a puerile little sound bite that sounds like "new nonsense to replace the old nonsense." Struggling for an explanation of how human bodies end up so vastly organized (something that cannot be explained by genes, genomes or DNA), Ball claims this: "Our biomolecules appear to make decisions not in the manner of on/off switches but in loosely defined committees that obey a combinatorial logic, comparable to the way different combinations of just a few light-sensitive cells or olfactory receptor molecules can generate countless sensations of colour or smell. " This is nonsense.  Molecules don't understand things; they are not minds, they do not decide, and do not form committees.  And if a molecule had a mind it could never understand the proper decisions it would need to make to help achieve the goal of creating the state of stratospheric organization that is a walking, talking, eating, grasping human, something the molecule had never observed and could never get the faintest notion of.  What is going on when a body grows are endless examples on very many different scales of fantastically organized and functional arrangements of matter appearing.  Giving some metaphor evoking the variety of different color combinations does nothing to explain such reaching of accidentally unachievable states of fine-tuned functional organization.  The history of Darwinism is a history of people making very  misleading biology metaphors, and Ball's metaphor quoted above is the latest in this long clown parade.  
 
With the statement above, Ball ends up pitching some new "bottom-up" nonsense to replace the old bottom-up nonsense and lie of blueprint-containing genes building bodies.  What he should have said  at the end of his essay is something like: "We now know human bodies are gigantically more organized and exponentially more functionally complex than anyone ever dreamed a century ago, and no scientist understands how such vast heights of purposeful organization and fine-tuned  functionality arise." 

Misspeaking very badly, Ball tells us in his essay that "the more complex the organism, the fuzzier its molecular mechanisms have to be," because if "countless components interlock in precisely coordinated ways" our bodies would be "far too fragile."  That sounds like complexity denialism and component coordination denialism.  Enormously complex organisms such as humans have endless examples of the most precise molecular teamwork and coordination, and such organisms have endless examples of components that are interdependent in magnificently fine-tuned and precisely coordinated ways. An armchair argument that such results would leave you with organisms "far too fragile" cannot discredit the observed reality that such precise coordination and fine-tuned molecular teamwork really exists all over the place in the human body, in mountainous amounts, without humans being "far too fragile." 

Ball has written a book with the title "How Life Works," and has another book  that purports to tell us "how we are made," and another book that purports to tell us "how to understand ourselves and other beings, from animals to AI to aliens." With titles and subtitles so pretentious, it rather sounds as if Ball is trying  to crown himself as a grand lord of biological explanation, which may be a bit of a stretch for someone having no biology or psychology degree. Ball has not learned the lesson of humility he should have learned from his studies: that the origin of human bodies and human minds are realities a thousand miles over his head, and a thousand miles over the heads of today's biologists, who do not have any credible physical explanation for human minds or human memory, do not have any credible explanation for the appearance of very complex biological innovations,  and do not have any credible explanation for how there occurs the progression from a speck-sized zygote to the vast hierarchical organization that is an adult  human body. 

miracle of morphogenesis

The long bibliography of Ball's "The Book of Minds" shows an  "ignore everything spooky"  filter-bubble reading list that includes very few or none of the 50 top books one should read before writing a book with such a title, many of which can be found here. The bibliography is the kind of echo-chamber reading list someone might have if he couldn't bear to ever read a word conflicting with materialist orthodoxy. People with parochial reading lists so very narrow should not be regarded as very diligent and very thorough scholars of human minds and human mental phenomena. 

The deception that is committed by the advocates of materialism is several dozens of times greater than merely lying that human DNA (the human genome) contains a specification for how to make a human body. For a very long list of 60+ types of deceptions committed by such people, see my post here. 

Appendix: Since the lie that DNA is a blueprint or program or recipe for building bodies has so often been told, I will need to cite again a list I have compiled of distinguished scientists and other PhD's or MD's who have told us such an idea is untrue. Below is the list:
  • 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."
  • 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."

Wednesday, December 27, 2023

The Continent Explorers: An Analogy

On a distant planet in another solar system there was a single continent, inhabited on its eastern side by a proud race of seven-feet-tall beings. Their ideology held that they were the only inhabitants of their continent. But the western part of the continent had never been explored.  One day the inhabitants of the eastern side of the continent sent out an exploration expedition, with the goal of finally determining what was on the west side of the continent. The expedition was led by a famous scientist, and consisted of seven males and one woman. 

The scientist had predicted that no intelligent creatures would be discovered on the west side of the continent. But at one point in the long journey the explorers saw something that seemed to challenge such an idea. Traveling on a long flat plane, they seemed to see miles ahead of them what looked rather like a huge castle far away.

distant castle

"Look on the horizon!" exclaimed a woman. "I think that maybe that's some huge building, like a castle."

"Foolish woman!" said the scientist. "What you see on the horizon is merely a distant mountain, a mere accident of nature."

"I guess we'll find out for sure when we get closer," said the woman. 

The exploration party walked further towards the high object on the horizon.  Very soon a tragic event occurred. The scientist who was the expedition leader was attacked by a four-legged predator, and bled to death. The exploration party buried him, and then continued to walk on towards the interesting tall object on the horizon. 

Soon the woman noted that the tall object on the horizon now appeared to be even more clearly what looked like a high castle, not a mountain. 

"Look, the tall object on the horizon seems to be like some mighty castle," said the woman. "It can't be a mountain." 

"But the great scientist told us it was just a mountain, a mere accident of nature," said the scientist's assistant. "We must follow his wise teaching."

The exploration party walked further towards the high object on the horizon. The woman noted that the tall object on the horizon now appeared to be even more clearly some artificial construction. She noticed strange things she had never seen before on any building: electrical lighting. Her people had not yet invented electrical lights. 

"Look at those strange lights like none we have ever seen," said the woman. "This must be a work of great agency and artistry. It can't be a mountain." 

"But the great scientist told us it was just a mountain," said the scientist's assistant. "We must follow his wise teaching."

The exploration party walked further towards the high object on the horizon. The woman now noted that the tall object on the horizon appeared to have things she had never seen of nor heard of: elevators, helicopters and huge video screens on its outside. She could also see with her spy glass some great library that seemed to store vast amounts of information.

"Look at those astonishing wonders on the building," said the woman. "This is not only some work of great agency and artistry, but something far beyond anything our people could ever construct." 

"But the great scientist told us it was just a mountain, a mere accident of nature," said the scientist's assistant. "We must follow his wise teaching."

The situation described is an analogy for what has gone in biology since about the time of Charles Darwin. Around 1850 scientists seemed to see before them great evidence that the wonders of biology were not mere accidents of nature, but the work of some agency far greater than mankind.  Fine-tuned anatomical structures had been discovered abundantly. But in 1859 Charles Darwin introduced his theory that the wonders of biology were caused by purely natural processes such as random variations and the survival of the fittest. Introducing such a theory, Darwin was like the scientist of my story who sees in the far distance something that might be a castle or a mountain, and who says that it is merely a mountain, not anything the result of agency or design. 

The progression of the explorers closer and closer to the great castle is an analogy for the progression of biology in the 160 years since 1859. Just as the explorers in my story learned more and more about the castle as they walked closer and closer to it, biologists have learned more and more about the wonders of biology. Below is a table of what we now know.  The items in yellow are facts that Darwin never knew about during his lifetime.


HUMANS CONSIST OF HUMAN BODIES AND HUMAN MINDS.

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

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

The human skeletal system contains 206 bones.

ORGAN SYSTEMS CONSIST OF ORGANS AND SUPPORTING STRUCTURES.

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

ORGANS CONSIST OF TISSUES.


TISSUES CONSIST OF VERY COMPLEX AND VASTLY ORGANIZED  CELLS

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

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

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

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

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

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

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

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

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

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

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

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

ATOMS CONSIST OF MULTIPLE PROTONS, NEUTRONS AND ELECTRONS.

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


We are now in a situation where it is very clear that the wonders of biology are far greater in their hierarchical organization and fine-tuned dynamic complexity than anything that humans have ever constructed. An aircraft carrier is a less impressive work of fine-tuned organization than the human body. Humans know how to make aircraft carriers equipped with all of their aircraft. There is not a corporation in the world or a nation in the world that could construct from lifeless materials a living adult human body. It is notable that humans are completely incapable of creating machines that can reproduce themselves.  There is not a robot in the world capable of building from raw materials a robot just like itself. But self-reproduction is something that occurs throughout the world of biology, as does molecular machinery. 

Like the castle in my analogy, containing some vast library that the woman could spot with her spyglass, biological organisms contain vast libraries of functional information in their DNA. What we see in biological organism are massive numbers of engineering effects and endless examples of information-rich fine-tuned architecture. Such a reality makes nineteenth century explanations of biology origins sound like  old wives' tales. Ink splashes don't produce long functional essays telling how to perform complex tasks; accidents don't engineer things; and random variations don't create novel astonishing works of information-rich fine-tuned architecture. It is not true that we can explain such wonders of biology by a simple principle of "random variations occur, and nature saves the good stuff," because most of the good stuff we see  requires arrangements of atoms so improbable you would never get such good stuff from random variations.  The reason that would never happen is pretty much the same as the reason why ink splashes don't produce well-written essays telling how to do complex things. 

But our scientists keep senselessly claiming that the wonders of biology are not the product of intelligent agency, but mere accidents of nature, as accidental as mountains. They keep telling us that we must follow opinions of the scientist Darwin, reached around the year 1859. The scientists who do that are like the assistant scientist in my story, who asked the team to follow some opinion reached when the castle was a blur on the horizon, instead of forming an opinion based on what we now know to exist.  The assistant scientist in my story was advising the group: don't decide based on what you now see clearly, but decide based on what some dead guy thought when the picture was so much blurrier. And that is very much like what is going on when scientists tell us to not judge based on the current known realities of biology, but to follow some opinion first formed before we knew half of the relevant facts we now know. 

Saturday, September 9, 2023

Some Accidentally Unachievable Molecular Machines in Your Body

In order to help perpetuate their dogma that humans are accidents of nature owing our existence to lucky random mutations in the distant past, our biologists are very fond of using what I call shrink-speaking language: language that makes the endless towering cathedrals of biological complexity look like mere crumbs.  This involves many tricks of diminutive representation, such as:

  • Referring to gigantically organized human bodies as "bags of chemicals" or "carbon stuff" or "star stuff."
  • Referring to stratospheric leaps of biological organization and  functional complexity as mere "variants." 
  • Referring to enormous new bonanzas of unprecedented biological engineering (such as the Cambrian Explosion) as mere "diversification." 
Our biological professors have in effect received their marching orders that they are supposed to describe human bodies as something that nature might have accidentally produced. But there are some cases where they encounter so much fine-tuned organized and purposeful functional complexity that professors find it almost impossible to follow such orders. One such case is the case of extremely organized protein complexes that even our reductionist professors have repeatedly described as molecular machinery. 

Organisms such as ourselves involve hierarchically structured and enormously organized complexity that cannot be credibly explained by appealing to random mutations. What we have in a human body is enormously organized and fine-tuned complexity so immense that it can be called an enormous engineering effect. In his interesting book Cosmological Koans, the physicist Anthony Aquirre tells us about just how complex biological life is. He states the following on page 338:

"On the physical level, biological creatures are so much more complex in a functional way than current artifacts of our technology that there's almost no comparison. 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."

So if a lowly bacterium has a functional complexity comparable to a jetliner, what kind of functional complexity does a human body have? Functional complexity so great it can be called an enormously strong engineering effect. The human body includes many types of  molecular machines that are best classified as accidentally unachievable. Something is accidentally unachievable if there are no imaginable unguided accidental events that could cause its origin. 

I can explain the idea of something being accidentally unachievable with a simple example that is easy to understand.  A bridge across a shallow stream is something that is accidentally achievable. We can imagine some accidental arrangement of rocks that might make a kind of bridge across a shallow stream, and we can imagine some lightning bolt causing a tree to fall, making a bridge across a shallow steam. But a bridge across a very wide and deep river is something that is accidentally achievable. There is no conceivable series of accidents or unwilled natural events that could create a bridge over an average section of a wide river such as the Mississippi, which has an average width of one mile. 

Let us look at some of the most impressive cases of molecular machinery in your body, systems requiring so many thousands of well-arranged parts that they are reasonably called accidentally unachievable. Pay attention to the numbers given in the second columns of the tables below, numbers which tell how many amino acids parts have to be well-arranged to get the protein mentioned in each row. If the numbers were very low numbers such as 3 or 5 or 7, it might be excessive to state that the relevant molecular machines are accidentally unachievable. Instead, the actual numbers will be numbers in the hundreds or thousands, meaning that we will be constantly finding that individual protein components of these molecular machines each required hundreds or thousands of well-arranged amino acid parts (with a consequence that the total system required thousands of well-arranged amino acids, equivalent to tens of thousands of well-arranged atoms).  

Example #1: The Apoptosome 

apoptosme

(Image credit:  Wikipedia Commons, derived from Yuan et al. 2010, Structure of an apoptosome-procaspase-9 CARD complex)

Shown above is the apoptosome protein complex involved in programmed cell death. Note the references in the chart to propellers, which remind  us how much the complex resembles a product of engineering. Humans have more than 20,000 types of protein molecules, and the average protein molecule is a very special arrangement of more than 400 different amino acid parts. The arrangement of amino acids in each protein is as hard-to-achieve by chance as 400 accidentally typed characters making a paragraph of grammatical and functional prose. Extremely complex engineering arises in the form of protein complexes, in which different proteins (often useless by themselves) work together as team members to achieve some dramatic functional result. We see that in the visual above, where multiple instances of several different types of protein molecules come together to form an extremely complex structure consisting of thousands of well-arranged amino acid parts, and consisting of a total of tens of thousands of well-arranged atoms. A page describes the action of these individually useless proteins coming together to form a functional protein complex:

"The process of programmed cell death, also known as apoptosis, is highly regulated, and the decision to die is made through the coordinated action of many molecules. The apoptosome plays the role of gatekeeper in one of the major processes, termed the intrinsic pathway. It lies between the molecules that sense a problem and the molecules that disassemble the cell once the choice is made. Normally, the many subunits of the apoptosome are separated and inactive, circulating harmlessly through the cell. When trouble occurs, they assemble into a star-shaped complex, which activates protein-cutting caspases that get apoptosis started."

Another site that includes a 3D rotating animation of the structure shown above says this:

"The apoptosome is revealed as a wheel-like complex with seven spokes. On top of the wheel is a spiral-shaped disk that allows for docking and subsequent activation of proteases, which then target cellular components. When active, the apoptosome is revealed to be a dynamic machine with three to five protease molecules tethered to the wheel at any given time."

The "Apaf 1" part of this complex (APAF_HUMAN ) involves 1248 amino acids.   

Example # 2: The Spliceosome

spliceosome

At the site here, we read this about the human spliceosome: 

"The spliceosome is a complicated and formidable example of a multi-subunit molecular machine, with the pre-catalytic form being the largest spliceosomal complex, containing 5 RNA molecules and 65 proteins, in addition to a substrate mRNA precursor. The arrangement and activities of all of these has to be intricately coordinated, paradoxically to catalyse a rather simple chemical reaction."

The paper here describes the spliceosome as a highly dynamic machine, like some race car that has its parts changed or replaced by a pit crew as the race car stops for pit stops:

"Indeed, ∼45 proteins are recruited to the human spliceosome as part of the spliceosomal snRNPs, whereas non-snRNP proteins comprise the remainder. The composition of the spliceosome is highly dynamic with a remarkable exchange of proteins from one stage of splicing to the next. These changes are also accompanied by extensive remodeling of the snRNPs within the spliceosome."

Below are the number of amino acids involved in these parts, which I looked up using the UniProt online database (you can use the links to check the numbers I have given):

Protein

Number of amino acids

Conment

SF3A1

793

On Chromosome 22

SF3A2

462

On Chromosome 19

SF3A3

501

On Chromosome 1

PRPF3

683

On Chromosome 1

PRPF4

522

On Chromosome 9

PRP8

2335

On Chromosome 17

U5S1

972

On Chromosome 17

PRP31

499

On Chromosome 19

PRP4

522

On Chromosme 9

SNUT1

800

On Chromosome 11

SLU7

586

On Chromosome 5

RBM22

420

On Chromosome 5

FAM32A

112

On Chromosome 19

XAB2

855

On Chromosome 19

CACTIN

758

On Chromosome 19

PLRG1

514

On Chromosome 4

Altogether the structure shown above requires more than 9000 amino acids that have to be arranged in just the right way. The structure shown above is not specified in DNA, which merely specifies which amino acids make up each of the protein parts. The amino acid information needed to make the structure above (insufficient to specify the physical arrangement of the structure) is not at all contiguous in DNA. To assemble the structure above, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 45 loose pages hidden in random books of 46 tall, long bookcases in a public library. The table above shows that at least eight of the 23 human chromosome pairs would need to be accessed: Chromosome 1, Chromosome 4, Chromosome 5, Chromosome 9, Chromosome 11, Chromosome 17, Chromosome 19 and Chromosome 22. 

The CORUM database page here gives details on 39 different proteins involved in just one part of the spliceosome, a part called the spliceosome C complex. The CORUM database page here gives details on 38 different proteins involved in another part of the spliceosome, a part called the spliceosome pre-B complex. The CORUM database page here gives details on 43 different proteins involved in another part of the spliceosome, a part called the spliceosome B complex. The CORUM database page here gives details on 113 different proteins involved in another part of the spliceosome, a part called the spliceosome A complex. The CORUM database page here gives details on 139 different proteins involved in another part of the spliceosome, a part called the spliceosome E complex. The paper here says, "The spliceosome is composed of as many as 300 distinct proteins and five RNAs, making it among the most complex macromolecular machines known."

Example # 3: RNA Polymerase II

The page here discusses RNA polymerase:

"RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA. The enzyme RNA polymerase carries the weighty responsibility of creating all of these different RNA molecules...RNA polymerase is a huge factory with many moving parts".

There are three different versions of RNA Polymerase, RNA Polymerase I, RNA Polymerase II, and RNA Polymerase III. In a previous post I discussed the proteins that make up the RNA Polymerase III complex: more than a dozen proteins with amino acid sequences specified across ten or more different chromosomes, with the complex requiring thousands of well-arranged amino acids. Below are the number of amino acids involved in RNA Polymerase II, which I looked up using the UniProt online database (you can use the links to check the numbers I have given):


Protein

Number of amino acids

Comment

RPB1_HUMAN

1970

On Chromosome 17

RPB4_HUMAN

142

On Chromosome 2

RPB7_HUMAN

172

On Chromosome 11

RPB2_HUMAN

1174

On Chromosome 4

MED21_HUMAN

144

On Chromosome 12

RPB9_HUMAN

125

On Chromosome 19

RPB3_HUMAN

275

On Chromosome 16

RPB11_HUMAN

117

On Chromosome 7

RPAP3_HUMAN

665

On Chromosome 12

RPAB1_HUMAN

210

On Chromosome 19

RPAP1_HUMAN

1393

On Chromosome 15

RPAB5_HUMAN

67

On Chromosome 11

MED20_HUMAN

212

On Chromosome 6

RPAB3_HUMAN

150

On Chromosome 3

A0A3B3IRX3_HUMAN


2222

On Chromosome 12

MD13L_HUMAN

2210

On Chromosome 12

MED12_HUMAN

2177

On Chromosome X

MED13_HUMAN

2174

On Chromosome 17

MD12L_HUMAN

2145

On Chromosome 3

Requiring many more well-arranged amino acids than RNA Polymerase III, the RNA Polymerase II protein complex clearly requires more than 10,000 amino acids that have to be arranged in just the right way. The RNA Polymerase II structure is not specified in DNA, which merely specifies which amino acids make up each of the protein parts. The amino acid information needed to make RNA Polymerase II  is not at all contiguous in DNA. To assemble RNA Polymerase II, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 15+ loose pages hidden in random books of 46 tall, long bookcases in a library. The table above shows that at least eleven of the 23 human chromosome pairs would need to be accessed: Chromosome 2, Chromosome 3, Chromosome 4, Chromosome 6, Chromosome 7,  Chromosome 11, Chromosome 12, Chromosome 15, Chromosome 17, Chromosome 19, and Chromosome X.

Example # 4: Proteasomes 

The wikipedia.org article on proteasomes tells us this:

"Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds...In structure, the proteasome is a cylindrical complex containing a 'core' of four stacked rings forming a central pore. Each ring is composed of seven individual proteins."

A paper on this topic is entitled "Gates, channels, and switches: elements of the proteasome machine." We read this:

"The proteasome has emerged as an intricate machine that has dynamic mechanisms to regulate the timing of its activity, its selection of substrates, and its processivity. The 19-subunit regulatory particle (RP) recognizes ubiquitinated proteins, removes ubiquitin, and injects the target protein into the proteolytic chamber of the core particle (CP) via a narrow channel."

Another paper is entitled "The 26S Proteasome: A Molecular Machine Designed for Controlled Proteolysis." A page on the site of the Theoretical and Computational Group tells us this:

"Recycling of unneeded protein molecules in cells is performed by a molecular machine called 26S proteasome (Figure 1), which cuts these proteins into smaller pieces for reuse as building blocks for new proteins. Proteins that need to be recycled are labeled by tags made of poly-ubiquitin protein chains. The 26S proteasome machine recognizes and binds to these tags, pulls the tagged protein close, then unwinds it, and finally cuts it into pieces. As the cell's recycling machinery, the 26S proteasome is vital for a variety of essential cellular processes, including protein quality control, cell cycle regulation, adaptive immune response, and apoptosis....The 26S proteasome recruits, unfolds, and degrades poly-ubiquitin tagged proteins through a complex interaction clockwork of over 60 known protein subunits that is driven through ATP hydrolysis."

A scientific paper tells us this:

"The 26S proteasome is a multisubunit complex that catalyzes the degradation of ubiquitinated proteins. The proteasome comprises 33 distinct subunits, all of which are essential for its function and structure." 

Below is a depiction of the human 26S proteasome structure, one that labels some of its protein parts. We see three different views of the same protein complex, with different protein parts labeled (the Greek letters used stand for alpha and beta parts mentioned in the table below):

26s proteasome

Image credit: Xing Guo et. al, link.

Below are the number of amino acids involved in these parts, which I looked up using the UniProt online database (you can use the links to check the numbers I have given):

Protein

Number of amino acids

Coment

Proteasome subunit beta type-1

241

On Chromosome 6

Proteasome subunit beta type-2

201

On Chromosome 1

Proteasome subunit beta type-3

205

On Chromosome 17

Proteasome subunit beta type-4

264On Chromosome 1

Proteasome subunit beta type-5

263On Chromosome 14

Proteasome subunit beta type-6

239On Chromosome 17

Proteasome subunit beta type-7

248On Chromosome 20

Proteasome subunit alpha type-1

263On Chromosome 11

Proteasome subunit alpha type-2

234On Chromosome 7

Proteasome subunit alpha type-3

255On Chromosome 14

Proteasome subunit alpha type-4

261On Chromosome 15

Proteasome subunit alpha type-5

241On Chromosome 1

Proteasome subunit alpha type-6

243On Chromosome 14

Proteasome subunit alpha type-7

248On Chromosome 20


The structure shown above clearly requires several thousands of amino acids that have to be arranged in just the right way. The structure shown above is not specified in DNA, which merely specifies which amino acids make up each of the protein parts. The amino acid information needed to make the structure above (insufficient to specify the total structure) is not at all contiguous in DNA. To assemble the structure above, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 60 loose pages hidden in random books of 46 tall, long bookcases in a library. The table above shows that at least eight of the 23 human chromosome pairs would need to be accessed: Chromosome 1, Chromosome 6, Chromosome 7, Chromosome 11, Chromosome 14, Chromosome 15, Chromosome 17, and Chromosome 20.

Example # 5: The ATP Synthase Complex

Another example of accidentally unachievable molecular machinery in the human body is the ATP synthase protein complex. It's a very complex molecular motor system described in a paper entitled "ATP Synthase: Motoring to the Finish Line." The paper refers to this complex as a "sophisticated molecular machine."  We read this: "ATP synthase is an unusually efficient rotary motor that synthesizes ATP at rates exceeding 100 molecules per second."  Another scientific page tells us this:

"ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an indispensable role in our cells, building most of the ATP that powers our cellular processes....Why have two motors connected together? The trick is that one motor can force the other motor to turn, and in this way, change the motor into a generator. "

ATP Synthase
ATP Synthase (image source: link)

Below are some of the components of ATP synthase, as listed in the UniProt database.

Protein

Number of amino acids

Comment

ATP5E_HUMAN

51

On Chromosome 20

ATP8_HUMAN

68From Mitochondrion

ATP6_HUMAN

226From Mitochondrion

ATP5S_HUMAN

215On Chromosome 14

ATP5J_HUMAN

108
On Chromosome 21

ATP68_HUMAN

58On Chromosome 14

ATP23_HUMAN

246On Chromosome 12

ATP51_HUMAN

69On Chromosome 4

ATP5H_HUMAN

161

On Chromosome 17

ATPPK_HUMAN

94

On Chromosome 7

ATPB_HUMAN

529

On Chromosome 12

ATPD_HUMAN

168

On Chromosome 19

ATPA_HUMAN

553

On Chromosome 18

AT5G1_HUMAN

136

On Chromosome 17

ATPG_HUMAN

298

On Chromosome 10

ATP5G2_HUMAN

141

On Chromosome 12

ATPO_HUMAN

213

On Chromosome 21

AT5G3_HUMAN

142

On Chromosome 2

AT5F1_HUMAN

256

On Chromosome 1



ATP Synthase seems to require thousands of amino acid parts arranged in just the right way, which amounts to a special arrangement of tens of thousands of atoms. The arrangement of the parts of the ATP Synthase complex is not specified in DNA, which does not specify which proteins are parts of particular protein complexes. To assemble the structure above, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 19 loose pages hidden in random books of 46 tall, long bookcases in a public library. The table above shows that at least 12  of the 23 human chromosome pairs would need to be accessed: Chromosome 1, Chromosome 2,  Chromosome 4, Chromosome 7, Chromosome 10, Chromosome 12, Chromosome 14,  Chromosome 17, Chromosome 18, Chromosome 19, Chromosome 20 and Chromosome 21.

Example # 6: The Origin Recognition Complex/Replicative Helicase Complex

Mammalian cells are so complicated they have been compared to factories or jet aircraft. The reproduction of most cells in the human body is a miracle of replication beyond the understanding of today's science. Scientists have confessed that they do not know what causes the fantastically complex process of cell reproduction. Scientists merely understand phases of such a process, and what components play a role in the process. 

One of those components is called the origin recognition complex. The wikipedia.org article on this protein complex says this: "The origin recognition complex (ORC) is a highly conserved six subunits protein complex essential for the initiation of the DNA replication in eukaryotic cells." The ORC complex works as a team with a "replicative helicase" complex consisting of the six bottom rows on the table below. So the wikipedia.org article on the ORC complex lists all of the items in the table below as the items in the complete complex. Below are some details of these subunits:

Protein

Number of amino acids

Comment

ORC1

861

On Chromosome 1

ORC2

577

On Chromosome 2

ORC3

711

On Chromosome 6

ORC4

436

On Chromosome 2

ORC5

435

On Chromosome 7

ORC6

252

On Chromosome 16

Cdc6

560

On Chromosome 17


Mcm2

904

On Chromosome 3

Mcm3

808

On Chromosome 6

Mcm4

863

On Chromosome 8

Mcm5

734

On Chromosome 22

Mcm6

821

On Chromosome 2

Mcm7

719

On Chromosome 7


Science writer Amber Dance skillfully describes the operations of the unit above:

"The average dividing cell must copy—perfectly—3.2 billion base pairs of DNA, about once every 24 hours. The cell’s replication machinery does an amazing job of this, copying genetic material at a lickety-split pace of some 50 base pairs per second. Still, that’s much too slow to duplicate the entirety of the human genome. If the cell’s copying machinery started at the tip of each of the 46 chromosomes at the same time, it would finish the longest chromosome—No. 1, at 249 million base pairs—in about two months. 'The way cells get around this, of course, is that they start replication in multiple spots,' says James Berger, a structural biologist...'But that poses its own challenge,' says Berger, 'which is, how do you know where to start, and how do you time everything?' Without precision control, some DNA might get copied twice, causing cellular pandemonium... It takes a tightly coordinated dance involving dozens of proteins for the DNA-copying machinery to start replication at the right point in the cell’s life cycle...Kicking off the process is a cluster of six proteins that sit down at the origins. Called ORC, this cluster is shaped like a double-layer ring with a handy notch that allows it to slide onto the DNA strands, Berger’s team has found...Once ORC has settled onto the DNA, it attracts a second protein complex: one that includes the helicase that will eventually unwind the DNA. Costa and colleagues used electron microscopy to work out how ORC lures in first one helicase, and then another. The helicases are also ring-shaped, and each one opens up to wrap around the double-stranded DNA. Then the two helicases close up again, facing toward each other on the DNA strands, like two beads on a string."

The molecular machinery shown above clearly requires more than five  thousand amino acids that have to be arranged in just the right way. The structure of the molecular machinery described above is not specified in DNA, which merely specifies which amino acids make up each of the protein parts. The amino acid information needed to make the structure above (insufficient to make the 3D structure) is not at all contiguous in DNA. To assemble the structure above, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 14 loose pages hidden in random books of 46 tall, long bookcases in a library. The table above shows that at least nine of the 23 human chromosome pairs would need to be accessed: Chromosome 1, Chromosome 2, Chromosome 3, Chromosome 6, Chromosome 7, Chromosome 8, Chromosome 16, Chromosome 17 and Chromosome 22.

Example # 7: The Nuclear Pore Complex

The nuclear pore complex or NPC is a large protein complex found in the "nuclear envelope" that is the outer boundary of the nucleus inside human cells.  A science research press release tells us this: "

"For structural biologists, the human NPC is a challenging yet exciting 3D puzzle, with around 30 different proteins each present in multiple copies. This amounts to around 1000 puzzle pieces, which form a round core with surrounding flexible parts."

The wikipedia.org article on this complex states that it consists of "456 individual protein molecules, and 34 distinct nucleoporin proteins." So the complex apparently requires 34 types of protein molecules. The article tells us that the "principal function of nuclear pore complexes is to facilitate selective membrane transportation of various molecules across the nuclear envelope." This mean that nuclear pore complexes have the extremely complex job of acting like gatekeepers, letting the right kind of molecules get into the nucleus of the cell, and keeping out the wrong type of molecules.  The article tells us that there are typically about 1000 of the nuclear pore complexes in every cell. We read of some impressive functionality of these nuclear pore complexes:

"Notably, the nuclear pore complex (NPC) can actively mediate up to 1000 translocations per complex per second. While smaller molecules can passively diffuse through the pores, larger molecules are often identified by specific signal sequences and are facilitated by nucleoporins to traverse the nuclear envelope."

The article tells us that a nuclear pore complex has a molecular weight of about 110 megadaltons. A dalton is the mass equal to a twelfth of the mass of a carbon atom. A protein complex of 110 megadaltons would have the mass of about 9 million carbon atoms. Apparently the proteins that make up this complex are particularly complex proteins. Below are the exact numbers (we may assume that there are multiple instances of such proteins in a nuclear pore complex). 


Protein

Number of amino acids

Comment

NUP98_HUMAN

1817

On Chromosome 11

NU153_HUMAN

1475

On Chromosome 6

NUP93_HUMAN

819

On Chromosome 16

NU107_HUMAN

925

On Chromosome 12

NU205_HUMAN

2012

On Chromosome 7

NU160_HUMAN

1436

On Chromosome 11

NU214_HUMAN

2090

On Chromosome 9

NUP85_HUMAN

656

On Chromosome 17

NUP50_HUMAN

468

On Chromosome 22

NUP88_HUMAN

741

On Chromosome 17

NU133_HUMAN

1156

On Chromosome 1

NU155_HUMAN

1391

On Chromosome 5


The molecular machinery shown above clearly requires more than 12,000 amino acids that have to be arranged in just the right way, which amounts to a special arrangement of more than 100,000  atoms. The structure of the molecular machinery described above is not specified in DNA, which merely specifies which amino acids make up each of the protein parts. The amino acid information needed to make the structure above  is not at all contiguous in DNA. To assemble the structure above, among other wonders of construction a human body must magically gather genetic information scattered across many different chromosomes in the nucleus, like someone quickly finding just the right 34 loose pages hidden in random books of 46 tall, long bookcases in a library. The table above shows that at least nine of the 23 human chromosome pairs would need to be accessed: Chromosome 1, Chromosome 5, Chromosome 6, Chromosome 7, Chromosome 11, Chromosome 12, Chromosome 16, Chromosome 17 and Chromosome 22.

nuclear pore complex
The nuclear pore complex (credit: Protein Data Bank, link)

Six Reasons These Molecular Machines And Their Behavior Are Accidentally Unachievable

There are six main reasons why we must regard the molecular machines described above as accidentally unachievable.

Reason #1: Chance processes such as Darwinian evolution could never produce the genes needed to make the proteins that make up such molecular machines (the gene origination problem). To perform the task a particular protein molecule performs, a type of protein molecule typically requires some specific fine-tuned gene, an amino acid sequence with most or nearly all of the protein's actual amino acid sequence, a chain of hundreds or thousands of amino acids specially arranged to produce a functional effect. Evolutionary biologist Richard Lewontin stated, "It seems clear that even the smallest change in the sequence of amino acids of proteins usually has a deleterious effect on the physiology and metabolism of organisms." A biology textbook tells us, "Proteins are so precisely built that the change of even a few atoms in one amino acid can sometimes disrupt the structure of the whole molecule so severely that all function is lost." And we read on a science site, "Folded proteins are actually fragile structures, which can easily denature, or unfold." Another science site tells us, "Proteins are fragile molecules that are remarkably sensitive to changes in structure." A paper describing a database of protein mutations tells us that "two thirds of mutations within the database are destabilising."  Those who think that functional folded protein molecules could gradually arise (getting longer and longer from a small size) will be dismayed to read this statement in a 900+ page textbook on protein chemistry: "Polypeptides less than about 70 amino acids in length should not fold because they should not be able to bury a large enough number of hydrophobic amino acids to overcome the configurational entropy of their random coils." Folding is required for most functional protein molecules. 

Accordingly, we cannot explain the origin of genes through some gradualism approach that imagines that first there was one tenth of the gene that was useful for one purpose, and then there was two tenths of the gene that were useful for some other purpose, and then finally we got the version of the gene that humans now have.  Human genes with only half of their base pairs or a third of their base pairs are not useful, and their corresponding protein molecules are not useful with half of their amino acids. 

But how hard would it be to get by chance or random mutations an amino acid sequence that would be the core of a useful protein molecule? That depends on the number of amino acids in the protein. Here we run into a simple principle that is the bane of all theories of accidental biological origins: the principle that a simple linear increase in the number of parts that must be well-arranged results in an exponential or geometric increase in the unlikelihood of such an arrangement occurring by chance. A small increase in the number of parts quickly results in what is called a combinatorial explosion, in which the number of possible combinations skyrockets. This is why computer security experts often tell you to use at at least 14-characters for the password of any financial account.  If you change your password from 7-characters to 14 characters, that doesn't make it merely twice as hard for a hacker trying all combinations to break into your account; instead it is is roughly 10,000,000,000 times harder. 

The chart below shows some of the relevant mathematics. If you doubt these numbers, you can verify them using the Large Exponents Calculator here. Since there are 20 different amino acids used in protein, you use 20 in the first row of such a calculator. Numbers such as E+6 refer to powers of ten. So 3.2 E+6 means 3,200,000; 1.024 E+13 means 10,240,000,000,000; and E+26 means 1 followed by 26 zeros. The bottom of the chart is a number of combinations equal to about 1 followed by more than 2600 zeros. 


Number of amino acids in a molecule

Number of possible combinations of the molecule's amino acids

5

3.2 E+6

10

1.024 E+13

20

1.048576 E+26

40

1.099511627 E+52

80

1.208925819 E+104

160

1.461501637 E+208

320

2.135987035 E+416

640

4.562440617 E+832

1280

2.081586438 E+1665

2000

1.148130695 E+2602


We can see from the chart above that the odds become utterly prohibitive once you start to get amino acid lengths much longer than about 160. Even if you very generously assume that a particular protein molecule only needs to have half of its amino acid sequence matching its actual sequence (an assumption too generous because of what we know about the sensitivity of protein molecules to small changes), you still have a case where we should never expect chance processes to produce successful amino acid sequences (corresponding to functional protein molecules) as long as 320 amino acids. 

In most of the protein complexes described above, we have some very complex proteins consisting of very long amino acids chains that we should never expect to have arisen by chance or Darwinian processes, never in the entire visible universe even given billions of years. Specifically:

  • One of the complexes (the spliceosome) had a protein consisting of 2335 well-arranged amino acids.
  • Another of the complexes (the apoptosome) had a protein consisting of 1248 well-arranged amino acids. 
  • The nuclear pore protein complex had one protein requiring 2090 well-arranged amino acids, and another protein requiring 2012 well-arranged amino acids, along with three other types of proteins each requiring more than 1000 well-arranged amino acids.
  • The origin recognition complex/replicative helicase complex required 7 types of proteins that each required more than 700 well-arranged amino acids. 
  • The RNA polymerase II protein complex described above had five types of proteins each requiring more than 2000 well-arranged amino acids, and three other types of proteins each  requiring more than 1000 well-arranged amino acids.
I could say much more about why proteins with amino acid sequences as long as this are not explicable by Darwinian processes, but that would involve repeating too many of the points in a previous post. See my previous post here for quite a long discussion on why it is not credible to suppose that fine-tuned amino acid sequences of this length ever could have arisen through any type of natural selection.  

Reason #2: we lack any explanation as to why very complex proteins would fold correctly. To be functional, proteins have to fold in just the right way, to achieve very complex three-dimensional shapes. But we don't understand how this folding occurs. DNA specifies only the linear sequence of the amino acids that make up a protein, not the complex 3D shape of a protein. Don't be fooled by press accounts claiming that the AlphaFold2 software did something to solve the protein folding problem. Such software did not produce any progress in solving the protein folding problem (the problem of how proteins are able to fold into the complex 3D shapes needed for their function). Such software merely produced progress in a different problem: the protein folding prediction problem, which is the problem of predicting the 3D shape of a protein from its amino acid sequence. 

One maneuver is an appeal to what is called Anfinsen's Dogma, a claim that the 3D shape of a protein is entirely a function of its amino acid sequence. Such an appeal is futile because it is a "rob Peter to pay Paul" affair rather like "solving" your college tuition burden by charging your tuition on your credit card.  If Anfinsen's Dogma were true, then genes would all-the-more-enormously have to be "just right" to allow for a properly folded 3D protein molecule; and in that case the gene origination problem becomes exponentially worsened.  The person who appeals to Anfinsen's Dogma lessens the protein folding problem at the expense of exponentially worsening the gene origination problem  (the problem of how 20,000+ suitable genes ended up in human DNA).    Appealing to Anfinsen's Dogma seem to make Reason #2 of these six reasons seem less convincing, at the expense of making Reason #1 seem enormously and exponentially more convincing. Such an appeal produces no net progress in making molecular machines like those above seem accidentally achievable. 

I may note that there are very good reasons for rejecting Anfinsen's Dogma, such as the very massive reliance of protein folding on helper molecules called chaperone proteins, which show that the 3D shapes of proteins are not a simple function of their amino acids sequences as Anfinsen's Dogma claims. 

Reason #3: we have no credible physical explanation for how  a transcription event could promptly find the right gene to make a particular protein (a "needle from the haystack" type of event). Cells are constantly creating new proteins to replace proteins that disappeared because of the short lifetimes of proteins. The page here has a chart showing the lifetimes of human proteins, and we see a bar graph showing most of the proteins have a half-life between about 10 hours and 70 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 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. 

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  (that is, DNA that codes for ) are interspersed with large blocks of seemingly meaningless DNA. Some sections of the  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  genomes, much less to predict when each  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  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.


Reason #4: chance processes would never produce the arrangements of proteins like those found in the molecular machines listed above. What we must never forget is that a protein complex involves three types of organization:
  • The one-dimensional organization of amino acids found in the sequence of amino acids that makes up a protein;
  • the three-dimensional organization of such a sequence to make a complex folded three-dimensional shape needed for a particular protein molecule to function properly;
  • the entirely different three-dimensional organization needed for the proteins of a protein complex to fit together in the right way to make a physical arrangement so complex that it may be called a "molecular machine."
How is it that protein molecules form into protein complexes consisting of multiple protein molecules? Some may guess that DNA is read to determine which type of proteins should team up with other proteins to make particular protein complexes.  But that does not happen. DNA does not specify which proteins belong to particular protein complexes. In fact, the tables above show that the genes corresponding to the proteins that make up the protein complexes are typically found in widely scattered chromosomes. That would seem to be the opposite of what would happen if DNA was specifying that particular protein molecules should team up with other types of protein molecules to make particular kind of protein complexes. 

So what explanation do biologists give for how protein complexes form? Their attempts at explanations consist of little more than hand-waving.  They mainly appeal to chance collisions of molecules floating around in the human body. This is no more credible  than claiming that tornadoes passing through junkyards can create automobiles out of the spare parts that are lying around the junkyards. 

A very important point here is that vast wonders of molecular assembly are happening continuously in the human body. Every week very many of the molecular machines described above (and countless others not described) are being assembled in your body. And as I have shown above, such molecular machines are built using amino acid sequences from very scattered chromosomes So we have an effect no more explainable by chance collisions than tornadoes building cars out of junk scattered in diverse places of a junk yard. And such an effect is constantly occurring in your body, in massive numbers. 

There is no way to explain this by trotting out some Darwinist phrase such as "very lucky things can happen given a million years of chance events."  We are not talking here about some miracle of genetic luck that occurred once in an eon. We are talking about miracles of complex purposeful assembly that are occurring in massive numbers every single day in your body. Darwin doesn't do anything to get the materialist out of this jam. 

The statements below are indications that scientists simply have no credible explanation as to how very complex protein complexes (like those discussed above) can form from their constituent protein parts:

  • "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. 

Reason #5: once assembled, such molecular machines act as if they knew where to go, which would not happen by accident . It is not merely the assembly of such molecular machines that defies anything we should expect to occur accidentally. It is also the behavior of such molecular machines, in the sense that they always seem to act exactly as if they knew where to go to. For example, the nuclear pore complex molecular machines go to just where they are needed (the nuclear membrane), and the splicesome and RNA polymerase II complex go to appropriate places in the cell.  To have an analogy for the whole storyline of the construction and target reaching of such molecular machines occurring accidentally, we would have to imagine something like tornadoes passing through junkyards, constructing many cars, and also blowing the cars to just the right places to pick up a million scattered people who needed rides.  How accidentally unachievable would that be? 

molecular machines acting like motors

Reason #6: such molecular machinery behavior occurs massively every day.  If something occurs only very rarely, we might regard is as accident. For example, if you come to your door with a friend, and realize you lost your  key, and your friend suggests he tries his key on your door, and his key opens your door, you may regard this as a lucky coincidence, having seen such a thing only once in your life. But when some type of lucky thing occurs all the time in massive numbers, in some way you cannot account for, chance and coincidence are no longer reasonable explanations. 

How often does there occur in your body the assembly and correct positional targeting of the molecular machines I have listed above? Billions or trillions of times every day. For example, very many  instances of the nuclear pore complex discussed above are needed in the construction of a new cell, and it has been estimated that the human body makes 300 billion new cells every day. What would be the chance of the totality of such daily feats of construction occurring accidentally? Something like the chance of a winter ice storm constructing a thousand-mile-high ice arch stretching all the way from Europe to North America.