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Our future, our universe, and other weighty topics


Monday, August 28, 2023

Professors Persist in "Proud Preston" Pretending

Let us imagine a young man named Preston who upon reaching the age of 22 declares himself to be totally self-sufficient. Let's suppose up until this time Preston has very much relied upon the help of his father. But upon reaching 22 Preston says, "I can now make my way in life without any more help from my parents."  Preston spends a few years writing a book. He submits the book to multiple publishers, and one of them agrees to publish it After eagerly awaiting its publication, the book becomes a success, making Preston a nice sum of money.  Quite a few people buy the book. Preston proudly declares in triumph, "Now I have shown that I am totally independent of my parents."

But one day in a book store, Preston spots a person who is buying his book, and asks him why the person is buying his book. The person confesses that he was paid money to buy the book. Preston goes to his father, who makes some confessions.  The father confesses that he bribed Preston's publisher to accept Preston's book for publication. The father also confesses that he had paid thousands of people to buy Preston's book, so that he could become a successful author. 

This enrages proud Preston. He had vowed at age 22 to become totally independent of his parents, but now it seems that his success has depended on the action of his father. At this point Preston vows never to see his father again. "He's dead to me!" Preston declares. Later this sentiment somehow evolves into an actual belief that his father is dead, even though there is no evidence backing up this claim. 

But while believing himself to be totally independent in the coming years and decades, there is a reason why proud Preston is not actually independent of his father: the monthly packages that Preston receives from his father. Every month Preston finds on his doorstep a very large box delivered by Amazon, a package he did not order. Each package is filled with all kinds of valuable things. Some times the package contains gold coins. Other times the package is filled with food. Other times the package is filled with items such as jewelry and electronics that Preston is able to easily pawn for cash, to help pay his rent.  Each package has some kind of slip of paper identifying it as a gift from Preston's father.  Not having much further success in his writing career, Preston's lifestyle very much depends on these monthly packages from his father. 

But while this continues to happen year after year, decade after decade, proud Preston continues to believe in his complete independence from his father, and also continues to believe that his father is dead. Preston maintains this belief by some remarkable set of mental gymnastics. Preston tells himself that each package he receives arrived merely because of a random computer error occurring at the Amazon headquarters. He keeps telling himself when he gets his monthly package, "There it is again, another computer malfunction." Proud Preston tells himself that software errors at the Amazon warehouses can result in the generation of a random address. Each time that he sees the paper slip in his monthly package identifying his father as the sender of the package, Preston says, "It's just a coincidence that the random name and random address generated by the computer error happens to match the name and address of my father."  Preston justifies this claim by saying, "These packages can't possibly be from my father, because my father is dead." 

Of course, this all results in proud Preston believing in a set of coincidences fantastically unlikely to occur. What would be the chance of someone getting month after month for many years a package having a slip saying that the package is from his father living at the father's last known address, when each of these paper slips were generated by a separate computer error matching the name and address of someone's father? Maybe 1 chance in 1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000. But proud Preston uses some mental gymnastics to prevent him from being bothered by this improbability. One of Preston's pieces of mental gymnastics goes like this:

"Sure, it would be incredibly improbable that someone like me would keep getting all these packages with paper slips saying they came from my father, purely because of random computer errors happening each time, which coincidentally listed my father as the sender.  But improbable things happen all the time! Imagine if you take a basket full of dice, shake the basket 10 times and pour the dice in a long line that stretches 40 meters. That would produce a sequence of about 1000 random numbers between 1 and 6. But the chance of getting that exact sequence would be 1 in 6 to the thousandth power. This proves that incredibly improbable things can happen very easily." 

Proud Preston's reasoning here is fallacious. The fallacy is that Preston forgot to distinguish between random chance producing results not resembling the product of design, and random chance producing results that do resemble a product of design. It is true that random chance can very easily produce incredibly improbable results that look random and do not resemble a product of intention or design. But is is not at all true that random chance can easily produce incredibly improbable results that resemble a product of intention or design. For example, if you have a large basket filled with letter cubes that each have a letter on one of the six cube faces, and you pour out such cubes in a long line, the chance that you will get a 20-meter string of characters that makes a coherent, grammatical, well-spelled English paragraph is less than 1 in 1,000,000,000,000,000,000. 

We can imagine proud Preston using another line of "mental gymnastics" reasoning to persuade himself that he could accidentally keep getting monthly packages with slips saying that they came from his father, even though each time it was merely caused by a separate random computer error. The reasoning would go like this:

"There are computer programs that prove that the most improbable-seeming intentional-looking results can be produced by pure chance. One program runs in a long loop. At the beginning of each iteration the program generates a random letter. Then the program checks whether the letter is a match at a particular position in the text of Shakespeare's play Hamlet. If a match occurs at that position, the letter is saved. After a number of loop iterations equal to the character length of the play Hamlet multiplied by the number of characters in the alphabet, the program generates the entire text of the play Hamlet. This shows that random chance can produce a long series that looks just like intentional results."

Proud Preston's reasoning here is very fallacious. The computer program Preston describes is a program that has random character generation as a kind of "window dressing." But the program is not at all a program showing the power of pure chance results. In each loop iteration the program checks the randomly generated character to see whether it is a match for a character in that position in the play Hamlet. The randomly generated character is saved only if there is a match in the position. Because of this, the resulting text is not at all random text. So the program Preston imagines does nothing to show the power of chance results to produce intelligent intentional-looking results. 

Such mental gymnastics might not be sufficient for Preston, so we can imagine him simply starting to lie, as part of the process of fooling himself about the packages he receives every month. We can imagine him starting to tell one of his friends some untrue claims such as, "It is well-known that many people get packages claiming to be from their relatives not because their relatives sent them, but purely because of computer errors at an Amazon warehouse." Once proud Preston started to tell such a lie, we can easily imagine it becoming a habit for him to tell this lie. He might not even think he is lying when he tells such a lie for the hundredth time. By then there may be a kind of "I've said it so many times it must be true" effect. 

We may also imagine that in addition to the monthly packages filled with expensive gifts, proud Preston also gets from his father a monthly letter. But Preston simply throws away the letters unread. Telling himself his father is dead, Preston concludes that these monthly letters can be explained by assuming delusions, fraud and hallucinations associated with the letter writers.  Before throwing away the letter unread each month, Preston shouts, "Delusions, hallucinations and fraud!"

Through such effects Preston might fool himself into accepting his idea that these monthly packages he keeps getting are all the result of mere computer errors rather than gifts from his father. This story I have given about proud Preston is pure fiction.  There is no such person. But very importantly, there are all over academia very many people who year after year keep thinking in a way very similar to the thoughts of proud Preston. 

These people are our professors of science. Just as Preston proudly declared about age 22 that he has no more dependence on his father, the science professors of academia have proudly declared that they have no dependence at all on any of the ideas of religion and no dependence on any idea of some divine reality higher than man. Just as Preston rashly decided to believe that his father is dead (without any good basis for such a conclusion), the professors of academia have rashly declared God to be dead, without any good basis for such a conclusion. And just as proud Preston kept getting unwanted evidence of his reliance on his father, science professors have kept getting more and more evidence of mankind's reliance on some higher superhuman causal reality that they would rather not believe in. 

In my story it was not merely that Preston discovered evidence of his very great dependence on his father in the past. It was also that Preston kept getting evidence (which he tried to sweep under the rug) of his continued dependence on his father; because he kept getting the packages from his father every month. Does this part of the story correspond to anything that goes on in nature? Yes, it very much does. 

Citing failures such as the dismal failure of Darwinism to credibly explain the enormous organization and information-rich fine-tuned complexity of more than 20,000 types of protein molecules in the human body, many people think that human existence would never have occurred were it not for fortunate interventions or some purposeful activity by some higher power long ago. Such thinkers will typically or very often assume that humans have no current dependence on any such power. But nature suggests a very different story. The shocking story suggested by nature is the radical idea of the continuous biological dependence of the human species on some superhuman organizing principle far beyond human understanding. There are four reasons why nature very strongly suggests such an idea.

(1) The origination of every adult human body is a miracle of organization utterly beyond the understanding of science. Without resorting to lies such as the lie that DNA is a blueprint or recipe or program for building a human body, no scientist can tell a credible tale of how a speck-sized zygote is able to progress to become the enormously organized state of the human body. 

(2) The continued existence of every human depends on the continual occurrence of protein folding, a phenomena by which string-like polypeptide chains (sequences of amino acids) fold into very complex 3D shapes necessary for the function of protein molecules. Scientists cannot credibly explain how protein folding occurs. Don't be fooled by untrue headlines claiming that some AlphaFold2 software "solved the protein folding problem." Such software did no such thing, but merely made progress at a very different problem, the problem of predicting the 3D shape of a protein from its amino acid sequence. That problem is properly called "the protein folding prediction problem," not the protein folding problem. The protein folding problem is still very much unsolved.  Scientists simply do not know why it is that proteins form the complex folded three-dimensional structures needed for them to perform their function.  Such a structure is not specified in DNA, which merely specifies the one-dimensional string or sequence of amino acids used by a protein.  Protein folding occurs continuously in the human body, and the existence of each of us depends on it. You would die within a month if protein folding stopped in your body. So your continued existence depends on the continued occurrence of thousands of types of protein-folding miracles of organization which scientists can't explain. Claims sometimes made that protein folding occurs because of "energy minimization" are not credible. What is called Levinthal's Paradox is that while protein folding occurs with blazing speed, if such a thing were to occur by trial-and-error searching for a minimum energy, it would require eons.  A scientific paper states this, using the term "conformation" to refer to the 3D shapes needed for protein function:

"The problem of protein folding is one of the most important problems of molecular biology. A central problem (the so called Levinthal's paradox) is that the protein is first synthesized as a linear molecule that must reach its native conformation in a short time (on the order of seconds or less). The protein can only perform its functions in this (often single) conformation. The problem, however, is that the number of possible conformational states is exponentially large for a long protein molecule. Despite almost 30 years of attempts to resolve this paradox, a solution has not yet been found."

(3) There is another way your continued existence depends on the continued occurrence of a miracle of organization which scientists can't explain: the miracle of protein complex formation. A large fraction or most proteins in the body only function if they are team members within groups of proteins called protein complexes. How do these protein complexes form? Scientists have no credible explanation. DNA does not specify which proteins belong to particular protein complexes. When they attempt to explain how protein complexes form, scientists engage in vacuous hand-waving such as using the empty phrase "self-organization" or vague, empty phrases such as "signal cascading." Scientists have no explanation for the formation of the more complex protein complexes, which are so complex that scientists refer to them as "molecular machines." Examples of such machines (each requiring many types of proteins arranged in just the right way) include the proteasome and the spliceosome. The continued existence of each of us is very much dependent on the continuous formation of such protein complexes in the human body. But scientists have no credible explanation as how the more complex protein complexes appear.  Here are some relevant quotes:

  • "The majority of cellular proteins function as subunits in larger protein complexes. However, very little is known about how protein complexes form in vivo." Duncan and Mata, "Widespread Cotranslational Formation of Protein Complexes," 2011.
  • "While the occurrence of multiprotein assemblies is ubiquitous, the understanding of pathways that dictate the formation of quaternary structure remains enigmatic." -- Two scientists (link). 
  • "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). 

Astonishingly, the different types of proteins that make up very complex protein complexes have their amino acid sequences stored not contiguously in DNA, but in very scattered parts of DNA scattered across many different chromosomes. I have given examples in the post here,  showing how the proteins that make up the spliceosome, the RNA polymerase III protein complex and the 26s proteasome have their amino acid sequences stated in very diverse chromosomes in the human body, with the amino acid sequences of each of these protein complexes being scattered across more than 10 different chromosomes, rather than being stated contiguously in DNA. I will give similar examples in a future post. An analogy for the assembly of such protein complexes would be a landowner who has across his acres of land 26 big open boxes of letter cubes, an "A" box, a "B" box, a "C" box, and so forth.  Imagine every day very many of the letter cubes mysteriously migrate from the boxes, and form on the ground very many purposeful useful sentences, with the effect continuing day after day, year after year. That gives you an idea of the kind of purposeful assembly going on with protein complexes. 

(4) Our existence depends on the continued reproduction of cells in our body.  While some types of cells in our bodies (such as neurons) do not reproduce, many types of cells in our bodies frequently reproduce; and the existence of each of us depends on a continual occurrence of cell reproduction. Every time a eukaryotic cell in our body reproduces, it is an event beyond the understanding of science. Cell reproduction does not occur by the reading of a DNA blueprint specifying a cell's very complex structure. The structure of no cell is specified in DNA, which merely specifies very low-level chemical information such as which amino acids make up a protein. The cells in our body are fantastically complex things. The complexity of a cell has been compared to the complexity of a jet aircraft or a factory. So how are our cells able to reproduce? Our scientists cannot credibly explain it. A scientist can no more explain the reproduction of a cell than he could explain a modern automobile splitting into two to become two equally functional automobiles; and a typical cell in our body has a complexity and organization comparable to that of an automobile. Although they have classified various stages in cellular reproduction such as anaphase and prophase, our scientists cannot even credibly explain what causes the reproduction of any eukaryotic cell in the human body.  (A search on the biology preprint server for papers with "kidney" in the title returns 250 matches, but searching for  papers with "cell reproduction" in the title returns only one match.)  Diagrams of the stages of cell reproduction make cell reproduction look a thousand times simpler than it is,  since they depict cells with only a few organelles, even though eukaryotic cells have hundreds or thousands of organelles of quite a few different types.  M. Pitkanen (who has a PhD in theoretical physics) has written the following about cell division:

"Replication is one of the deepest mysteries of biology. It is really something totally counterintuitive if cell is seen as a sack of water plus some chemicals. We have a lot [of] facts about what happens in the replication at DNA level but how this miracle happens is a mystery. At cell level the situation gets even more complex."

The facts of biology strongly suggest the idea that there must exist some continuous biological agency working perpetually with enormous intelligence and unfathomable power to produce many of the known effects of biology such as vast levels of biological organization far beyond explanation by mechanistic chemistry. We can refer to such activity using the term "continuous biological agency" or by using the acronym GOAL, which stands for Global Organizing Activity of a Life-Force.  The continuous dependency of humans on such an agency may be described as a continuous transcendent dependency

The failure of attempts to explain the origin of human bodies by bottom-up low-level chemical factors is the most gigantic shortfall, as great as the shortfall of someone who tries to explain the continued phenomenon of large building construction by evoking little principles such as "stuff sticks together" or "bricks can pile up."  To have a credible hypothesis of the origin of enormously dynamic physical states of vast organization such as the human body,  we must assume a purposeful top-down organizational effect. Given a lack of anything in a human body that explains the full reproduction of a human (not to be confused with mere pregnancy), it is utterly insufficient to assume that such a purposeful organizational effect merely acted in the past. We should assume that such a purposeful organizational effect acts continuously throughout all of our lives, and acts across all parts of the planet in which large superbly organized organisms exist.  A good acronym to describe such a reality is the acronym GOAL, which stands for Global Organizing Activity of a Life-Force. Such an acronym is suitable, given the dramatically teleological and purposefulness of such an agency. 

We need to postulate such a GOAL force acting not just long ago but every day. One reason is that across the globe inside millions of pregnant women there is unfolding every day the mysterious process of morphogenesis, the progression from a speck-sized egg to a full-sized baby.  Nothing understood by chemists or biologists can explain such miracles of organization occurring in bodies in which DNA does not specify any high-level structural information.  Other reasons for postulating such a GOAL force include three other reasons listed above: (1) the continued occurrence in the human body of protein folding needed for our existence, (2) the continued formation of protein complexes of very high complexity (called molecular machines), and (3) the continued occurrence of cell reproduction needed for our existence. None of these things is credibly explained by "bottom up" chemical explanations or by DNA. 

Because of such continuous dependencies, each of one of us has a continual dependence on some purposeful causal reality beyond himself, just as Preston in my story had a dependence on the monthly packages from his father. The science professors who try to sweep these dependencies under the rug and deny our dependence on something superhuman beyond ourselves are like the proud Preston of my story. And such professors often resort to reasoning as bad as some of the reasoning Preston used. 

The utterly fallacious reasoning of Preston quoted above mirrors fallacious arguments by the apologists of materialism. You might think that a publication like Scientific American would never resort to reasoning as fallacious as the computer program argument of Preston that I quote above. But very similar reasoning appeared in an article in Scientific American in 2002, and many writers in that magazine keep linking to the article that used such bad reasoning. Read here for a discussion of that article and a refutation of its reasoning.  And just as Preston made a fallacious argument that confused the likelihood of random chance producing results that did not look like intentional results with the likelihood of random chance producing results that did look  like intentional results, science professors have often made equally fallacious arguments. 

In my story Preston helped to prop up his silly idea that all of his packages were arising by "counterfeits of chance" by inventing and repeating the untrue claim that such "miracle of luck" events were often reported by others. Equally big lies have repeatedly come from the mouths of science professors. One of the biggest is the phony-baloney claim that DNA has a blueprint or recipe or program for how to construct a human body. DNA has no such thing. Read my post here for a discussion of some of the now-dead science professors who taught such a lie, along with many quotes by science and medical authorities telling us that such a claim is not true. 

But, you may object, surely our science professors do not believe in miracles of luck as improbable as those imagined by proud Preston. To the contrary, such professors believe in miracles of luck almost infinitely more improbable. Address labels (including a name and address) have a total of about 40 characters; and if we count the number of uppercase letters and the ten possible digits, there are 36 possible values in each character position of an address label. The chance of a random computer output of 40 characters exactly matching a particular person's name and address is a probability of about 1 in 36 to the 40th power, which is probability of roughly 1 in 10 to the 62nd power. There is every reason to believe that the origin of an average new type of protein molecule by unintentional processes would require even greater luck than this. There are twenty possible amino acids used by proteins, and the average eukaryotic protein molecule has a length of more than 450 amino acids. Very generously assuming that only half of these amino acids have to exist for the protein molecule to have its function, we end up with a probability of a new type of functional protein molecule originating by unguided processes as something like 1 in 20 to the 225th power, which is about 1 in 10 to the 292nd power.  The improbability of unguided processes producing a particular new type of functional protein molecule turns out to be very vastly greater than the improbability of 40 random letters and numbers exactly matching a particular person's name and address. While proud Preston believed (after 30 years of getting the monthly packages) in no more than about 360 of his "miracles of luck," the person believing in a Darwinian origin of protein molecules has to believe in vastly more miracles of luck: more than 20,000 such miracles of luck to get all the proteins in the human body, and countless millions of such miracles of luck to get all the proteins in all the animal kingdom.  

But, you may object, surely our science professors can't have committed "mental gymnastics" as bad as proud Preston did.  You may say, "Surely our science professors could not have made a claim as silly as Preston's claim that all of his monthly packages resulted from coincidental computer errors at Amazon's warehouse." But the truth is that very many science professors have spoken in ways every bit as silly as that. Such authorities have asked us to believe that all of the 20,000 types of proteins in our body resulted from miracles of luck. Believing in that requires much greater credulity than believing in some miracle of luck occurring once a month. 

But what about the monthly letters from his father that proud Preston kept throwing away unread, while derisively saying, "Delusions, hallucinations, and fraud"? Is there a parallel to that in the behavior of academia's scientists? There surely is. Preston's behavior in throwing away the letters unread reminds me of how mainstream professors almost all refuse to seriously study the hundreds of years of written evidence for the paranormal. Such professors try to dismiss such evidence as delusions and hallucinations and fraud. But what about all the similarities in accounts of the paranormal? For example, those having out-of-body experiences so often report floating parallel to their bodies, about a meter or two above their bodies. And reports of near-death experiences have a remarkable degree of similarity. For example, a study of those in Iran having near-death experiences reports accounts remarkably similar to US accounts, despite all the cultural and religious differences in the two countries. Our "proud Preston" professors refuse to seriously study such matters, saying to themselves angrily things such as "It's all just delusions, fraud, hallucinations and coincidence!" 

scientist overconfidence
The "proud Prestons" of academia

The proud Preston of my story believed in some fantastically unlikely coincidences, but at least he only imagined hugely improbable events occurring on a single planet, without "going cosmic" in his "sweep things under the rug" effort. But for the proud Prestons of academia, things are much worse. Nowadays they have the dilemma that physics and cosmology have discovered a universe of incredible fine-tuning. There are all sorts of "coincidences" suggesting our universe was purposefully created to allow the existence of beings such as us, such as every proton having an electric charge that is the very precise opposite of the electric charge of every electron (an exact matching that must occur to thirty or more decimal places for planets to hold together).  Evoking some imaginary infinity or near-infinity of our universes they call the multiverse, our professors have responded by saying, "Why all that 'cosmic fine-tuning' just means that we must live in the luckiest universe in the multiverse!" Preston did some pretty bad mental gymnastics, but nothing as bad as this; for Preston's mental gymnastics weren't cosmic-sized.  Engaging in such stochastic speculations, and ignoring a mountain of important testimony and many mountains of purposeful teleology within biology, our professors smugly declare themselves to be "intellectually fulfilled."  

cosmic fine-tuning

When we examine the topic of mind and memory, we find that mostly the explanations of our professors fail and flop. They try to explain all mental activity by evoking brain activity. A sufficiently diligent study of the brain and its many physical shortfalls leads to the conclusion that this idea cannot be correct.  There is no way to credibly explain such basic mental phenomena as self-hood and consciousness and understanding and insight and abstract idea creation through any imaginable theory of the brain. Nor is there any way to explain the wonders of human memory phenomena by any known facts about the brain. We know from human construction of machines that can store and instantly retrieve data the type of things a device needs to have to be a device for permanently storing and instantly retrieving learned information in a reliable way: things such as systems for encoding learned information, addressing, very fast and reliable signal transmission, indexing, read/write heads and storage systems for permanently storing information. The human brain has no such things.  And mind and memory can persist with little damage when there is massive brain damage (as discussed here and here). A sufficiently diligent study of the shortfalls of the brain and the wonders of human mental phenomena will lead to the idea that the human mind (including memory) must have some source that transcends the human body. Such an idea meshes very well with the idea that our bodies arise and persist because of some transcendent reality.   

To read more about the philosophical justifications of some of the claims made here, read my posts here and here and here

I may note that professors have some maneuvers to try and make some of the teleological effects described here look less impressive; but such maneuvers are typically futile. 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).  There is no overall decrease in the reliance on the transcendent.  It's similar to the situation in regard to the cosmologist's "primordial cosmic inflation" theory, which "robs Peter to pay Paul" by seeming to lessen the required fine-tuning of the universe's initial expansion rate at the Big Bang (something like 1 in ten to the fiftieth power) at the price of introducing a wildly speculative theoretical regime requiring fine-tuning all over the place, with no net reduction in fine-tuning requirements.  The known massive reliance of protein folding on chaperone proteins is another reason why Anfinsen's Dogma is not credible. 

Another maneuver made by professors to reduce some of the difficulties mentioned above is to offer some idea of intermediate assembly stages of fantastically complex molecular machines in the body, claiming this as a kind of "mechanistic explanation." But in general you do little to reduce the unlikelihood of accidentally unachievable assemblies by showing there were intermediate stages rather than everything instantly assembling all at once. For example, you would not credibly explain wind storms forming junkyard junk into cars if you claimed the windstorms first formed an engine and then formed a chassis, rather than all the parts assembling into a car all at once. After reading claims of step-by-step assemblies of protein complexes, we are still left with the question: with thousands of proteins floating around in the body, why do we seem to get mainly purposeful assemblies of such proteins (protein complexes needed for our existence) rather than the random assemblies of such molecules we would expect chance collisions to produce? The answer isn't DNA, which doesn't specify which proteins belong to particular protein complexes. 

Thursday, August 24, 2023

Some Recommended Online Reading

The site www.archive.org is an invaluable resource for scholars of psychic phenomena and the paranormal. Using the site, you can find very many books written by witnesses of the paranormal and scholars of the paranormal.  The full text of very many of these books can be read by a user who does not even bother to register at the site.  Examples of such books are below:

Life After Death
       Cover of a book mentioned above

If you take the time to register at www.archive.org, which does not take long, the door will be opened to a huge number of more modern books, which you can "borrow" on an hourly basis simply by pressing a Borrow button after logging in. By clicking on the Borrow button after registering, you will be able to read important works on the paranormal such as these: 

An aspect of www.archive.org that I particularly like is that there are individual URLs for each page.  So if a scholar is citing page 347 of some book, he can include a link that takes the reader exactly to that specific page. 

Other sources of information about psychical phenomena are listed below: 

  • The  Psi Encyclopedia of the Society for Psychical Research (available here).
  • The much older 1932 Encyclopedia of Psychic Science by Nandor Fodor available here
  • The book-length document on ESP evidence here, "Extrasensory Perception: Research Findings" by John Palmer, which includes in white text below the book a book-length document ("Notes on the Paranormal") on evidence for the paranormal, written by Ben Steigmann. The latter document contains very many links to online original source materials on psychical research. 
  • The video here and here seem to provide modern evidence for clairvoyance. 

My very long post "Candid Confessions of the Scientists" contains links to very many papers and books by scientists who challenged the most prevalent thinking in fields such as chemistry, neuroscience, biochemistry,  physics, natural history and cosmology. Many of that post's links can be followed for illumination on such topics. My very long post "120+ Types of Paranormal or Anomalous Experiences" contains countless links to interesting papers and books on that topic.  Below are books or articles on topics such as biology and cosmology and psychology:

  •  Cosmo Sapiens: Human Evolution From the Origin of the Universe by John Hands. The book is discussed in my post here
  • A Fortunate Universe: Life in a Finely Tuned Cosmos by astrophysics professor Geraint F. Lewis and astronomy postdoctoral researcher Luke A. Barnes. The book is discussed in my post here
  • Why Us? How Science Rediscovered the Mystery of Ourselves by physician James Le Fanu.  The book is discussed in my post here
  • "Using statistical methods to model the fine-tuning of molecular machines and systems" by Steinar Thorvaldsen and Ola Hössjer. This peer-reviewed paper in the mainstream Journal of Theoretical Biology discusses very well the evidence for fine-tuning in biology and physics. 
  • "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists" by Bruce Alberts. This peer-reviewed scientific paper is essential reading for students of biological complexity. 
  • "The Fine-Tuning of the Universe for Intelligent Life" by Luke A. Barnes.  This paper (also available here) is a lengthy peer-reviewed paper discussing the evidence for fine-tuning in physics and cosmology. 
  • "Giving Up Darwin" by computer scientist David Gelernter.  Trying to explaining the reasons why Darwinian ideas cannot explain the appearance of proteins,  Gelernter does a good job, but actually underestimates the difficulties.  He lists the average amino-acid length of a protein as 250, but eukaryotic proteins (like those in our body) actually have an average of about 472 amino acids, according to the paper here; and achieving proteins of that size by unguided processes is more than a billion trillion quadrillion times harder.  

Sunday, August 20, 2023

Scientific American's Very Bad Nonsense on Protein Evolution

 In 2002 Scientific American published an article by John Rennie, who was then an editor in chief of the magazine. The article was entitled "15 Answers to Creationist Nonsense." Full of misstatements and appallingly bad reasoning, the article was an attempt to discredit all of the critics of Darwinism. Because articles in Scientific American keep linking to this 2002 article, it may be appropriate for someone to point out some of the ridiculous errors and sophistry it contained. I may note that Rennie's article didn't qualify as any type of expert statement, as he has a mere BS in biology.

First, let us consider the title. Rennie commits the mudslinging so commonly used by Darwinists: that of using the term "creationist" to refer to critics of Darwinism. Inextricably intwined with the term "biblical creationist," the term "creationist" is a term used to try to insinuate that someone is a fundamentalist. None of the arguments that Rennie discusses (none of the 15 statements he tries to rebut) has anything to do with scripture or the Bible, and such arguments and points are typically not made by fundamentalists, but by students or  scholars of biological complexity. By calling such people "creationists" Rennie seems to be deliberately creating an inaccurate impression about the type of reasoning he will criticize, which has nothing to do with the Bible.  The title of the article contains the word "creationist" in super-giant letters ten times taller than the article's small font, to help emphasize the mudslinging shaming effect. 

Let's look at some of the statements that Rennie disputes. He discusses 15 different statements that sound something like may have been made by Darwinism critics. The statements appear as boldface section headers in his article. If we ignore the one statement appearing as a question, we find that not a single one of the remaining 14 statements is obviously untrue or clearly nonsensical. Every one of them sounds like something that could be reasonably argued or that might be true. 

Let's look at some of the low points of Rennie's discussion. 

(1) His rebuttal of the statement "evolution is only a theory." Rennie uses the standard Darwinist nonsense here of claiming that scientists use the word "theory" in a way different from the way ordinary people use the word. He says this:

"Many people learned in elementary school that a theory falls in the middle of a hierarchy of certainty—above a mere hypothesis but below a law. Scientists do not use the terms that way, however. According to the National Academy of Sciences (NAS), a scientific theory is 'a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.' ”

This claim long made by Darwinists simply is not true. Scientists use the word "theory" the same way that ordinary people use the word. For example, they use the term "string theory" to refer to a totally speculative physics theory that has no evidence to support it; and scientists use the term "MOND theory" for a gravity theory most of them don't believe in. Scientists also use the term "Everett many worlds theory" to refer to a physics speculation that is utterly groundless, and also the worst nonsense humans have ever thought up. There is a fact of evolution (microevolution) and a theory of evolution (including ideas such as the idea that all animals have a common ancestor, and that random mutations are the main cause of biological innovations). The fact of evolution is a fact, and the theory is a theory. In general, when scientists use the term "theory" they refer to things that are not yet proven, contrary to the claim Rennie makes. 

(2) His rebuttal of a claim "evolution cannot explain how life first appeared on Earth."

This claim that "evolution cannot explain how life first appeared on Earth" is absolutely correct, and has been conceded by countless scientists and Darwinists. So why on Earth is Rennie claiming this as one of his examples of supposed "nonsense"?  Doing that severely damages the credibility of his article. What is very much nonsense  is the first statement in Rennie's rebuttal of this claim. He states, "The origin of life remains very much a mystery, but biochemists have learned about how primitive nucleic acids, amino acids and other building blocks of life could have formed and organized themselves into self-replicating, self-sustaining units, laying the foundation for cellular biochemistry." Everything in that statement after "remains very much a mystery" is untrue, and is not supported by any laboratory experiments realistically simulating early Earth conditions. 

I may note that "could have" claims are in general very weak responses to "never would have" objections referring to prohibitive odds. For example, if you make the unbelievable claim that you threw a deck of cards into the air and all of the cards luckily formed into a triangular house of cards, you do not effectively rebut someone saying that such a miracle of luck "never would have" happened by merely saying that it "could have" happened.  The miracle of luck needed to accidentally get life from non-life is something vastly more improbable than the luck of someone throwing a deck of cards into the air, and them all forming into a triangular house of cards. Such a house-of-cards thing would require the favorable arrangement of only 52 parts, while even the simplest self-reproducing cell would require the favorable arrangement of something like 100,000 amino acid parts. 

The next statement Rennie makes is also misleading. He states, "Astrochemical analyses hint that quantities of these compounds might have originated in space and fallen to Earth in comets, a scenario that may solve the problem of how those constituents arose under the conditions that prevailed when our planet was young." Nucleic acids have never been found in any comet, and only a few of the twenty amino acids used by living things have ever been found in space, with the quantities being only negligible trace amounts such as 1 part in a billion.

The truth about this matter was described by Karl Popper, who materialists love to cite:

"What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated...The code cannot be translated except by using certain products of its translation. This constitutes a really baffling circle: a vicious circle, it seems, for any attempt to form a model, or a theory, of the genesis of the genetic code. Thus we may be faced with the possibility that the origin of life (like the origin of the universe) becomes an impenetrable barrier to science..."

Nothing has been done to solve this problem, which is only one of many insurmountable problems in coming up with a theory of life's accidental or natural origin. In a 2018 paper about 20 scientists stated the following:

"The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions (Appendix A), an event that could not have happened within the time frame of the Earth except, we believe, as a miracle (Hoyle and Wickramasinghe, 198119822000). All laboratory experiments attempting to simulate such an event have so far led to dismal failure (Deamer, 2011Walker and Wickramasinghe, 2015)." 

(3) His attempt at rebutting the claim "Mathematically, it is inconceivable that anything as complex as a protein, let alone a living cell or a human, could spring up by chance." 

The claim stated is a very weighty one because of the known very high complexity and very high organization of protein molecules. Functional protein molecules consist of very well-arranged sequences of hundreds or thousands of amino acids, arranged in just the right way to produce some particular biological function. It is necessary that a functional protein molecule have a sequence of amino acids close to its actual sequence for the protein molecule to achieve its hard-to-achieve folding and have the function that it has. Given that there are twenty amino acids used by living things and twenty-six characters in the English alphabet, and given that the sequence of amino acids in a protein is as well-arranged as the characters in a paragraph or page of functional grammatical text, a good analogy would be to compare a protein molecule to a long well-written paragraph or page correctly explaining how to accomplish some particular task. Because there are more than 20,000 types of protein molecules in the human body, the amount of functional instructions in each of our bodies is as great as in a bookshelf containing ten long technical manuals describing how to accomplish very specific tasks. 

Trying to rebut the claim quoted above, Rennie starts out by making the claim below containing some misleading language:

"Chance plays a part in evolution (for example, in the random mutations that can give rise to new traits), but evolution does not depend on chance to create organisms, proteins or other entities. Quite the opposite: natural selection, the principal known mechanism of evolution, harnesses nonrandom change by preserving 'desirable' (adaptive) features and eliminating 'undesirable' (nonadaptive) ones."

To the contrary, Darwin's theory of natural selection has the most gigantic dependence on chance, as Darwin himself conceded in The Origin of Species, when he stated, "Natural selection can do nothing until favourable variations chance to occur." Rennie's statements above contradict each other. First he says that "chance plays a part in evolution," and then he says that "evolution does not depend on chance."  Rennie inaccurately states that natural selection  "harnesses nonrandom change," when in fact Darwinism has always been based on the idea of so-called natural selection capitalizing on lucky random changes,  also called random mutations or random variations. 

What is going on in Rennie's language is a sleazy word trick, one deployed by Darwinists to try to make random evolution sound nonrandom. The word trick works like this: you imagine a purely blind, mindless random process, imagine it producing a stream of random outputs, and then imagine it occasionally producing some miracle of luck that results in something useful; and when you then get such a result you call that result "nonrandom" simply because it is useful.  That is just the most ridiculous type of misleading word trick.  The Cambridge Dictionary gives this as its first definition of "random": "happening, done, or chosen by chance rather than according to a plan." According to that definition, all of the results of Darwinian evolution are random, because they never occurred according to a plan. 

Next Rennie gives us a piece of sophistry that I offer as Exhibit A that Scientific American has no shame in arguing for materialism, and is willing to publish nonsense about as glaring and as bad as anyone can state.  He writes this:

"As long as the forces of selection stay constant, natural selection can push evolution in one direction and produce sophisticated structures in surprisingly short times. As an analogy, consider the 13-letter sequence 'TOBEORNOTTOBE.' A million hypothetical monkeys, each typing out one phrase a second on a keyboard, could take as long as 78,800 years to find it among the 2613 sequences of that length. But in the 1980s Richard Hardison, then at Glendale College, wrote a computer program that generated phrases randomly while preserving the positions of individual letters that happened to be correctly placed (in effect, selecting for phrases more like Hamlet's). On average, the program re-created the phrase in just 336 iterations, less than 90 seconds. Even more amazing, it could reconstruct Shakespeare's entire play in just four and a half days."

Let's very carefully consider the computer program Rennie has discussed, claiming it as an analogy for natural selection.  As a long-time computer programmer, I know the exact components such a program would have. The program would have these parts:

(1) A target text consisting of some very well-arranged sequence of characters (such as the text of a Shakespeare play) that could only have been produced by an intelligent agent. 

(2) A random character generator.

(3) An "accumulating successful text" string variable (analogous to a notebook) consisting only of characters that have matched the correct character of the target text at a particular position. 

(4) An integer variable that that keeps track of the length of the "accumulating successful text" variable (or a function that gives the character length of such a variable).

(5) A utility that is able to run in a loop that keeps checking the intelligently designed target text for a match to see whether the latest randomly generated characters matches the character at a particular  position in the human written text, the integer variable position mentioned in (4). So, for example, if so far the "accumulating successful text" string variable has 1000 characters, then the utility keeps generating random characters until one of the random characters matches the target text at position 1001.  Then that random character is added at the end of the "accumulating successful text" string variable. 

Yes, using this type of computer program, you can create copies of intelligently designed human-written target text fairly quickly. But such a program is nothing like Darwinian evolution, and nothing like natural selection. This is because the intelligently designed computer program requires the pre-existence of the human-written intelligently designed target text, and neither natural selection nor Darwinian evolution has any such thing. For example, before anything like a successful rhodopsin protein molecule came into existence,  natural selection didn't have target text to try to match.  And neither natural selection nor Darwinian evolution ever do anything like letter-by-letter target matching. 

What Rennie has done here is something as about as appalling a piece of sophistry and bad reasoning as you could possibly make. He has described a human-written program for copying intelligently designed human-written text in a roundabout inefficient manner (one having randomness as some mere window-dressing),  and has tried to pass that off as something showing the feasibility of generating  intelligent-seeming novel purposeful creations by the blind mindless processes of random mutations or natural selection or Darwinian methods.  This is every bit as nonsensical as someone claiming that an automobile proves that Darwinian evolution can produce complex innovations. 

Rennie gives us no further reasoning to defend against the proposition that proteins are too complex and well-arranged to have arisen through Darwinian processes.  The claim is a very solid one that has never been refuted or even substantially damaged. What we have learned about the sensitivity of protein molecules to small changes (that they typically will become nonfunctional after only very small changes) only reinforces such a claim. Such a claim is also reinforced by what we have learned about protein complexes: that a large fraction of proteins are useful only as team members of "molecular machine" protein complexes far more complex than a protein, complexes often requiring more than a dozen different proteins be arranged in just the right way.  The CORUM database of protein complexes currently lists 3637 human protein complexes,  each of them protein teams requiring multiple types of proteins to do their job.  The 2020 paper here says protein complexes have between 2 and 116 proteins, with a median of 13 proteins per complex. 

You can't redeem Rennie's train-wreck reasoning here by appealing to some principle that each time an amino acid that is part of its final functional sequence is added to a protein,  that would be like the "matching the right character in the right position" happening in the programs Rennie refers to.  To argue that would be committing the "every tiny step in the right direction gives a benefit" fallacy that is one of the principle fallacies of Darwinists.  The average protein molecule requires nearly 500 well-arranged amino acids to be functional, and it is not at all true that each little addition of one more amino acid would produce a benefit.  Benefits occur when a functional threshold is reached, requiring a minimum number of well-arranged parts to achieve a functional end, often very many well-arranged parts.  For example, a bridge that only takes you 10% across a wide river has not reached its functional threshold, and is a mere suicide machine that will you dump you at the bottom of the river; and ditto for bridges across wide rivers that  only cross 30% or 50% of the river's width.   About a majority of proteins we can say: their individual origin would have no beneficial effect on an organism because the proteins are team members of complex systems that require multiple types of proteins (often dozens) working together in just the right way, in purposeful very complex "molecular machinery" arrangements we would never expect chance or Darwinian evolution to produce.  

To perform the task a particular protein molecule performs, a type of protein molecule typically requires an amino acid sequence with most or nearly all of its actual amino acid sequence, a chain of hundreds or thousands 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." 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. 

The number of cross-dependencies among proteins is gigantic. A large fraction of all proteins only serve a benefit when they act as team members of protein complexes consisting of something like 5, 10 or 20 different types of proteins. Also a large fraction of all proteins cannot fold correctly unless they are assisted by other types of specialized proteins called chaperones; and there are hundreds or thousands of types of such chaperone proteins, with these chaperone proteins making up 10% of the total mass of proteins in the bodyAccording to the source here, twenty to thirty percent of protein molecules require chaperone proteins. The mere existence of a type of protein molecule does nothing to improve an organism unless many other requirements are met, such as having sufficient numbers of that type of molecule exist in the body in the right place and at the right time. With so very many cross-dependencies in the world of proteins, and with proteins being so easily disabled or destabilized by small changes, and with so many interconnected requirements for a new type of protein molecule to be useful, nothing could be more fallacious than to assume something like that an uncompleted protein produces a survival or reproduction benefit when it does something like move from having 35% of its final amino acid sequence to having 36% of its final amino acid sequence.  At such a time no functional threshold would have been met. 

What Darwinists frequently forget is that so-called "natural selection" (a misnomer term) can only "select for" inheritable changes that produce an improvement in survival or reproduction.  There's a very simple formula to remember for any biological component that has not yet reached a functional threshold: "no benefit yet = no natural selection." 

protein cross-dependencies

The truth on this matter was told us by four Harvard scientists who stated this: "A wide variety of protein structures exist in nature, however the evolutionary origins of this panoply of proteins remain unknown."  Darwinism does not have credible explanations to offer for any of the 20,000+ types of protein molecules in our body.  For an intelligent discussion of the question of the difficulty of explaining the origin of proteins,  see the lengthy peer-reviewed paper "Using statistical methods to model the fine-tuning of molecular machines and systems" by Steinar Thorvaldsen and Ola Hössjer in the Journal of Theoretical Biology. That year 2020 paper tells us in Section 4.1 that for a "typical functional protein" the probability of its appearance is less than 1 in 10 to fiftieth power.  The paper gives very much precise support to the claim that the odds against protein origin by Darwinian evolution are utterly prohibitive, and helps show that such a claim is not at all nonsense as Rennie claims. 

For a fairly good discussion of why our knowledge of protein complexity discredits Darwinism as an explanation, see the 2019 book review "Giving Up Darwin" by computer scientist David Gelernter, who does a good job of explaining things but rather "pulls his punches" by understating the complexity of protein molecules (which have more than twice as many amino acids as Gelernter states)

(4) His attempt at rebutting the claim that "living things have fantastically intricate features—at the anatomical, cellular and molecular levels—that could not function if they were any less complex or sophisticated," and that "the only prudent conclusion is that they are the products of intelligent design, not evolution."

This is a very weighty claim, and Rennie does nothing of substance to rebut it. He just very lazily appeals to the groundless legend that Darwin did something to explain the origin of vision, stating this:

"The eye's ability to provide vision depends on the perfect arrangement of its parts, these critics say. Natural selection could thus never favor the transitional forms needed during the eye's evolution—what good is half an eye? Anticipating this criticism, Darwin suggested that even 'incomplete' eyes might confer benefits (such as helping creatures orient toward light) and thereby survive for further evolutionary refinement. Biology has vindicated Darwin: researchers have identified primitive eyes and light-sensing organs throughout the animal kingdom and have even tracked the evolutionary history of eyes through comparative genetics."

The idea that Darwin did something to explain  vision is one of the many groundless legends of Darwinism.  The existence of mere light-sensing organs in organisms in phyla other than the phylum humans belong to (Chordates) does nothing to explain the appearance of vision systems in the Chordates phylum that humans belong to,  because (1) such mere light-sensing organs are found in phyla not believed to be ancestors of the phylum of humans, and (2) we now know that such mere light-sensing organs are not at all simple things (as Darwin supposed) but fantastically complex structures requiring all kinds of fine-tuned molecular and cellular organization before yielding any function, and (3) there is such a gulf between such mere light-sensing organs and mammal vision systems that it's like the difference between a 1960's hand calculator and a 21st-century digital computer. 

Far from having "vindicated Darwin" on this matter, the facts discovered by biologists have done quite the opposite. By now it has been shown that vision requires many thousands of times more of a fine-tuned arrangement of parts than Darwin ever dreamed, with most of that being in the intricate biochemistry required for vision.  Moreover, organisms don't see by mere eyes: they see by virtue of fantastically intricate vision systems consisting of eyes, fine-tuned protein molecules requiring hundreds of well-arranged parts, optic nerves, and incredibly complex brain parts. 

You don't show that some accidentally achievable thing could arise by accident by showing that there could be incomplete versions of something that could still have benefits.  For example, pull out the seats and the kitchen of a 747 jet, and you have an incomplete jet that still could have benefits, and could still fly. But that does nothing to show that big aircraft like 747 jets can form by natural processes.  Modern biology has discovered 20,000+ types of complex inventions in the human body (20,000+ different types of protein molecules) that each has more well-arranged parts than Darwin ever thought an eye had. Darwinists have no credible tale to tell of how such proteins arose, except for bad efforts like the baloney computer program analogy Rennie gave (discussed above). 

Stating "we know absolutely nothing about the evolution of the eye of the vertebrate," and saying "in mammals, all sense organs evolved almost simultaneously," a French biologist told us in 1977 the truth about Darwin's futile attempt to explain the origin of eyes:

"Darwin (1859) devotes four a half pages of the 'Origin of the Species' to the eye and its genesis, possibly thanks to innumerable mutants, to natural selection, and to time. But we note that he does not overcome any of the obstacles raised against his doctrine by 'reality.' "

(5) His attempt at rebutting the claim that "recent discoveries prove that even at the microscopic level, life has a quality of complexity that could not have come about through evolution."

The statement is a justified one, if by "evolution" you mean blind Darwinian evolution. In recent decades scientists have discovered in the human body very many fantastically complex protein complexes that scientists themselves are calling "molecular machines." We now know that in our bodies are a vast number of different types of molecular machines, many requiring many thousands of well-arranged parts to function properly.  Below is a quote from a very widely cited peer-reviewed paper written in 1998:

"We have also come to realize that protein assemblies can be enormously complex. Consider for example the spliceosome. Composed of 5 small nuclear RNAs (snRNAs) and more than 50 proteins, this machine is thought to catalyze an ordered sequence of more than 10 RNA rearrangements as it removes an intron from an RNA transcript. As cogently described in this issue of Cell by 18, these steps involve at least eight RNA-dependent ATPase proteins and one GTPase, each of which is presumed to drive an ordered conformational change in the spliceosome and/or in its bound RNA molecule. As the example of the spliceosome should make clear, the cartoons thus far used to depict protein machines (e.g.Figure 1) vastly underestimate the sophistication of many of these remarkable devices. Given the ubiquity of protein machines in biology, we should be seriously attempting a comparative analysis of all of the known machines, with the aim of classifying them into types and deriving some general principles for future analyses."

Rennie fails to rebut claims that evolution theory has no credible explanation for such things. He mentions only two examples: the bacterium flagellum and the blood clotting system.  Appealing to dubious speculations, he attempts to explain such things by claiming some of their parts could have existed beforehand. 

But you don't show that some fantastically improbable arrangement of parts is accidentally achievable by showing that some of the parts could have existed beforehand. Whenever we have anything that requires very many well-arranged parts that have to be just right or almost just right for the thing to work, then we have something that is not reasonably attributed to accidental processes, even if all of the parts existed in scattered places.  Consider the case of a junkyard that has scattered around it all of the parts needed to make an automobile. Accidental processes will never construct an automobile from such parts. After an extinction of mankind, you could have a billion years of floods and earthquakes and tornados and hurricanes, and there would be no chance that such things would ever construct a car from car parts scattered around in junkyards. There's a very simple rule that prohibits such things: the rule that the improbability of getting an accidental invention increases exponentially with the number of well-arranged parts required. Once you get beyond very simple things, the odds against an accidental invention very rapidly become prohibitive, something that would never occur in the history of the universe. We face such prohibitive odds all over the place when we consider the molecular machines that are required all over the place for the human body to work. 

We know from our life experience that accidents don't produce complex inventions. Such a principle is not nonsense, but a sound principle derived from a lifetime of experience. Any careful mathematical analysis will abundantly confirm such a "gut feel" intuition, and abundantly support the principle that accidental effects cannot produce complex inventions. For an example of such reasoning, see the lengthy peer-reviewed year 2020 paper "Using statistical methods to model the fine-tuning of molecular machines and systems" by Steinar Thorvaldsen and Ola Hössjer.

failure of Darwinism

Protein molecules are in the light blue and dark purple wedges

The believer in ideas of accidental origins of biological innovations is faced with endless thousands of "too hard to get the needed parts" problems on his left hand, and endless thousands of "too hard to arrange the parts usefully" problems on his right hand. So, for example, it's too hard for unguided processes to get non-racemic amino acids needed for the origin of protein molecules, too hard for unguided processes to get the amino acids arranged in the right way to make the countless types of fine-tuned protein molecules needed for types of molecular machines or organelles or cells, and too hard for unguided processes to arrange such protein molecules in a useful way for you to get the required molecular machines and organelles and cells. Generically, you do not help such difficulties by merely suggesting that before some magnificent biological innovation appeared, some of the too-hard-to-get parts may have already existed; because by doing that you're just moving some of the "miracle of luck" from one point in natural history to another, not reducing the overall improbability.  Similarly, you wouldn't show that you could have produced a triangular house of 52 cards by throwing a deck of cards into the air, if you merely said that the full house of cards didn't appear all at once, and that you threw half of the pack in the air last week and half of the pack into the air today. 

It is very strange that Rennie cites the human blood clotting system as something to try and rebut the claim that human biochemistry is too complex to have appeared through blind Darwinian evolution. That system is a marvel of fine-tuned intricacy requiring the coordinated interaction of about 24 proteins, which altogether require about 12,000 well-arranged amino acids that have to be just right, something that requires a fine-tuned arrangement of more than 100,000 atoms. Rennie merely makes the feeble far-fetched speculation that the proteins of the human blood-clotting system "involve the modification and elaboration of proteins that were originally used in digestion." Rennie mentions some scientist who supposedly thinks this, but fails to mention or link to any scientific paper or article by such a scientist, just as if he had no decent evidence to support such a claim. The idea sounds preposterous, as blood clotting is vastly different from digestion (blood clotting involving a building up from liquids and digestion involving a breaking down of solids or semi-solids). And when the odds are prohibitive, you don't show that miracles of chance could have happened by merely speculating that they happened earlier in the history of life. 

Below is a quote from a French biologist describing how utterly inadequate Darwinist ideas are for explaining the human blood clotting system:

"Take, for example, regulation of the coagulation of blood, a highly complex phenomenon to which biologists seems to have given little thought...The lip of the wound (damaged tissues) become the site of chain reactions ending in the formation of a clot. This is possible because there preexist in the blood reaction agents or their precursors whose end effect is to coagulate certain proteins of the blood plasma...Such a process forms a complex whole; a lack of a substance arises, an enzyme is affected, and the system will not work. One does not see how it can have formed by successive chance effects supplying a protein or an enzyme in any random order. Besides, we know that the effects of mutations on the system are disastrous and form the lengthiest chapter in blood pathology. The system has become functional only when all of its components have come together and adjusted themselves to each other. The Darwinian hypothesis compels us to postulate a preparatory period during which selection acts upon something that does not, physiologically speaking, yet exist. Under the necessary conditions, the action can only have been prophetic!"

And very strangely it is this very marvel-of-fine-tuning blood clotting system which Rennie offers while attempting to rebut the claim that "life has a quality of complexity that could not have come about through evolution." It's like someone offering his 10-speed bicycle as proof that complex machines can accidentally arise. 

(6)  The appeal to the faulty principle of "methodological naturalism."

People following bad policies often try to describe their bad policies as a principle. And so Rennie evokes a principle they call "methodological naturalism."  Rennie describes this principle like this: "A central tenet of modern science is methodological naturalism—it seeks to explain the universe purely in terms of observed or testable natural mechanisms." There is no such principle of modern science. In general, human psychological phenomena cannot be explained "in terms of observed or testable natural mechanisms." Scientists frequently encounter things they do not understand and cannot credibly explain in terms of "observed or testable natural mechanisms," including endless mysteries of the mind, endless mysteries of paranormal phenomena, and the very fact of subjective experience. The proper thing for a scientist to do when encountering such phenomena is to study the phenomena and say "I can't credibly explain this yet," rather than always trying to implausibly explain things by evoking "observed or testable natural mechanisms" when such mechanisms fail to credibly explain things.  A perfect example is the Big Bang that gave birth to the universe. There is no observed or testable mechanism that can explain such a thing, and there never will be. And when cosmologists who study the universe introduced the idea of dark matter and dark energy, they were not using "observed or testable natural mechanisms." Neither dark energy nor dark matter are mechanisms, neither have been observed, and you can't test something until you have observed it. It's mostly the same for the "primordial cosmic inflation" so beloved by cosmologists, which is something never observed and which cannot be tested.  

Rennie would have us believe in macroevolution, but believing in such a thing would not be an example of explaining "the universe purely in terms of observed or testable natural mechanisms." Allegedly occurring over vast lengths of time, macroevolution cannot be observed or tested, unlike microevolution that can be observed in a human lifetime.  And macroevolution as described by Darwinists is not a mechanism. The Cambridge Dictionary defines a mechanism as "a way of doing something that is planned or part of a system," and the idea has strong connotations of physical parts working together to produce an effect at a particular time (as when we talk about the mechanism of blood circulation). Appealing to lucky mutations scattered over eons is not a case of describing a mechanism.  Last year a doctor and a professor put it this way:

"Macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10−50) when based on selection by survival of the fittest...Microevolution is probabilistically realistic; macroevolution is not, and this is documented empirically."   

"Methodological naturalism" as evoked by materialists effectively amounts to the foolish principle of "claim that everything in biology and cosmology and physics is accidental no matter how enormously designed it looks, and claim that everything you see is material-caused no matter how much it looks like something that cannot have a material cause." That amounts to a foolish "don't follow the evidence when it conflicts with your beliefs" kind of principle that is the opposite of being scientific.   

We also have in Rennie's article this nonsensical-sounding claim: "Whales had four-legged ancestors that walked on land." The fossils typically cited to back up this speculation have estimated ages relatively close to each other, making such fossils ineffective as evidence to support such a claim (as a paleontologist points out). Using his trademark vacuous reasoning tactic of merely saying something like "I see no difficulty" to try to establish the most far-fetched claims, Darwin stated this in the original edition of his main work: "I  can  see  no difficulty  in  a  race  of  bears  being  rendered,  by  natural selection,  more  and  more  aquatic  in  their  structure and  habits,  with  larger  and  larger  mouths,  till  a  creature was  produced  as  monstrous  as  a  whale." Darwin struck the statement from a later edition of the same work, as if he were ashamed of it. 

It is interesting that while Rennie's article title refers to "nonsense," the only clearly nonsensical nonsense found in the article is nonsense reasoning or nonsense claims made by Rennie himself. Giving us no quotations from named Darwinism critics, Rennie shows in this article no signs of having carefully read the thinkers he is criticizing, no signs of having very carefully and deeply studied biological organization or biological complexity, and no signs of familiarity with the relevant probability mathematics.  But his article with such glaring falsehoods and such appallingly bad reasoning is still being linked to by many a Darwinist. Is it that an article as bad as his is the best they can find to defend Darwinism?