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Tuesday, October 4, 2022

The Extended Evolutionary Synthesis Offers a Ragtag Hodgepodge

There is a technique you can use to create the impression of an explanation, without actually offering a credible explanation. I can call that technique the "ragtag hodgepodge" technique. If you don't have any single acceptable explanation for why something happened, you can offer a kind of potpourri or smorgasbord of factors that could help explain why the thing happened. Usually the more misty and shadowy and imprecise you are in presenting such a grab bag or hodgepodge of possible causal factors, the better it works. 

I can give an example of using this "ragtag hodgepodge" technique in ordinary life, set at a time before everyone had smartphones. Suppose John (the husband of Mary) has been sexually involved with John's co-worker at her apartment one Tuesday evening. John comes home to his apartment at 2:00 AM, to meet his upset wife. She says, "Why are you home so late?" She then immediately follows with, "And don't tell me you were looking late at the office, because I called you at 8:00, 9:00, 10:00 and 11:00, and you didn't answer your office phone." 

John could then offer this ragtag explanation:

"Well, someone can be at work without answering his phone. He might be visiting the bathroom, or talking at a colleague's desk, or in a meeting in another spot in the office. And don't forget that telephone systems sometimes fail. A little construction near the phone lines or some lightning can mess up things so that all the calls fail to get into the office. And someone who takes the train home can realize he forgot to bring enough money to get back, so maybe he has to walk all the way, coming home so much later than normal. Not to mention that someone can get hit on the head while being mugged walking home, and maybe then have to sit in the hospital for hours waiting for an MRI. And don't forget you banged your head on the kitchen cabinet last month, which might create a memory problem. Are you sure I wasn't here last night, or did you just forget seeing me?"

John has used the ragtag hodgepodge technique effectively. Without committing himself to any one explanation for his 2:00 AM appearance back home, he has raised so many hypothetical explanations that it will be difficult for his wife Mary to rebut them all. Maybe she'll just say "Sheesh!" and let John off the hook, silently going back to bed. 

The ragtag hodgepodge technique is used by something called the Extended Evolutionary Synthesis or EES.  The term is used for an explanatory program that offers to remedy the huge explanatory shortfalls of what is called the Modern Synthesis. Darwin never used any explanation saying much about genes. When genes and DNA started to be understood in the twentieth century, a belief system called the Modern Synthesis appeared. The main idea of this Modern Synthesis (basically the same as Neo-Darwinism) was that the appearance of new species and new biological innovations could be explained by changes in DNA and the genes that make up DNA. 

At the heart of the Modern Synthesis was a lie: the lie that DNA is some specification for making a particular organism. There are various ways in which this false idea is stated, all equally false:

  • Someone may describe DNA or the genome as a blueprint for an organism.
  • Someone may describe DNA or the genome as a recipe for making an organism.
  • Someone may describe DNA or the genome as a program for building an organism.
  • Someone may claim that DNA or genomes specify the anatomy of an organism. 
  • Someone may claim that genotypes (the DNA in organisms) specify phenotypes (the observable characteristics of an organism).
  • Someone may claim that genotypes (the DNA in organisms) "map"  phenotypes (the observable characteristics of an organism) or "map to" phenotypes.
  • Someone may claim that DNA contains "all the instructions needed to make an organism."
  • Someone may claim that there is a "genetic architecture" for an organism's body or some fraction of that body. 
  • Using a little equation, someone may claim 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. 

Weaker formulations of this false idea include claims that DNA is "life's instruction book" or "the key to life" or "the book of life" or "the secret of life." While such rather vague assertions are not as explicitly false as the statements in the bullet list above, such formulations are equally misleading, as they insinuate the false claims in such a bullet list. 

An example of a Darwinist biologist shamelessly making this untrue claim is the dead wrong statement made below by French biologist Francois Jacob on page 313 in his 1970 book "The Logic of Life: A History of Heredity":

"The formation of a man from an egg is a marvel of exactitude and precision. How can millions of cells emerge, in specialized lineages, in perfect order in time and space, from a single cell? This baffles the imagination. During embryonic development, the instructions contained in the chromosomes of the egg are gradually translated and executed, determining when and where the thousands of molecular species that constitute the body of an adult are to be formed. The whole plan of growth, the whole series of operations to be carried out, the order and the site of syntheses and their coordination are all written down in the nucleic-acid message." 

The last two sentences were a huge fiction, written decades before the Human Genome Project had even started to analyze the contents of DNA. Jacob's ideological motivation in telling this huge falsehood can be deduced from the quotation he gives at the very beginning of this book, where he quotes Diderot as saying this:

"Do you see this egg? With it you can overthrow all the schools of theology, all the churches of the earth." 

From this quote, we can surmise what was going on in the mind of Francois Jacob, who scorned all religion as a "farce":

(1) He got the idea that if a blueprint or program for making humans was to be found in a human egg, that this would be a devastating blow against religion, one that would help "overthrow all the schools of theology, all the churches of the earth" by somehow showing that the physical origin of each human was a purely mechanistic affair that required no assistance (directly or indirectly) from some divine power or some intelligent agency beyond human understanding.

(2) Not content to wait for the discovery within DNA of such an anatomy blueprint or program for constructing humans, Jacob simply made the false claim that such a thing had already been discovered in a "nucleic acid message" (DNA) in the human egg. 

There is no truth to the claim that DNA is a specification for anatomy.  DNA has been throroughly analyzed by large research projects such as the Human Genome Project and the ENCODE project, and no such specification was ever found in it. DNA merely specifies low-level chemical information such as which sequences of amino acids make up polypeptide chains that are the starting points of protein molecules.  Many biology and chemistry and medical authorities have confessed this reality that DNA does not specify anatomy, and I quote dozens of such confessions at the end of the post here. Some of those authorities advance something they called the Extended Evolutionary Synthesis or EES. 

Typically those speaking in support of this Extended Evolutionary Synthesis will confess very frankly that genetic variation is not adequate to explain the origin of species and the origin of biological novelties. Their approach is to offer a ragtag hodgepodge to explain the wonders of biology. Random genetic variation is only one item in that smorgasbord.

A long recent statement of the EES is "Extended Evolutionary Synthesis: A Review of the Latest Scientific Research" by Lynn Chiu of the Department of Evolutionary Biology of the University of Vienna, which you can read here. In Figures 18 and Figure 19 of that document we are told via two diagrams that the Extended Evolutionary Synthesis offers these items to explain the marvels of biology::

  • Genes
  • Developmental bias
  • Bio-physics
  • Phenotypic plasticity
  • Symbiosis and microbes
  • Niche construction and behavior
  • Culture and society
  • Extra-genetic molecules

This is very much a hodgepodge, a smorgasbord, a potpourri of items that fails to explain the vastly impressive wonders of biology. 

hodgepodge

A hodgepodge

Let's look at each of these items individually:

Genes

Genes are some of the wonders of biology. A particular gene is a sequence of nucleotide base pairs that specify the hundreds of amino acids needed for a particular protein molecule to exist.  Human DNA consists of about 20,000 genes, which help to allow the existence of up to 100,000 different types of protein molecules in the human body. A particular gene can be read in several different ways, so the number of different types of proteins in the human body is several times greater than the number of genes in our DNA. 

Neo-Darwinism (the Modern Synthesis) fails to credibly explain DNA, and fails to credibly explain the genes that make up DNA. Each gene is a very special  arrangement of hundreds of parts that we would never expect to arise by any Darwinian process. The average number of amino acids in a human protein molecule is about 470, although very many types of protein molecules contain more than 700 amino acids. Since the number of amino acids used by living things (20) is about the same as the number of characters in the English language (26), you can get a rough idea of the improbability of a successful gene originating by considering that such a thing has roughly the same improbability as about 470 randomly typed characters (typed by a monkey) being a grammatical and meaningful and useful paragraph of English prose. Just as we would never expect a typing monkey to ever produce a good meaningful, grammatical and well-spelled paragraph of 470 characters (even if there were billions of typing monkeys typing for billions of years), we would never expect random mutations to produce a useful gene corresponding to a functional useful protein molecule. 

The Extended Evolutionary Synthesis offers no new explanation for genes or protein molecules, so nothing new is going on when the list above offers "genes" as part of an explanation for how we got here. Genes belong on the list of things that have not been credibly explained by scientists, so you're cheating if you put "genes" as an item on your list of explanatory factors explaining super-organized organisms such as humans. As a scientific paper states, "Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity." Also, since neither DNA nor the genes in it specify anatomy or how to build cells, organs or bodies, you do not even get to first base in explaining the origin of anatomical innovations and wondrously complex cells by listing "genes" as part of your explanation. 

Developmental Bias

On pages 20, 21 and 22 of her long document on the Extended Evolutionary Synthesis, evolutionary biologist Lynn Chiu attempts to explain a concept of "developmental bias," without discussing anything that substantially explains the wonders of biology or the wonders of morphogenesis. She kind of wanders all over the place, and we are left with the idea that it means something like bad results are excluded because they don't work. That does nothing to explain how you would get incredibly improbable arrangements of matter that we would never expect blind nature to produce.  Similarly, if I imagine a book editor who reviews the output from 1000 typing monkeys, discarding all of their pages that are unintelligible, that does nothing to explain how intelligible results would result from typing monkeys. The idea of "developmental bias" seems to be little more than "only successful results succeed," which doesn't explain why incredibly improbable successful results would occur.  The little ragtag examples offered by Chiu on page 20 (beetle horns) and on page 22 (the spots on a butterfly wings) are very feeble examples, not being one of the million most impressive results in biological innovations. Developmental biology and morphogenesis are actually the most gigantic problems for Darwinists, who have no credible explanation for how a speck-sized egg is able to progress to become a trillion-times more organized adult organism, with the lack of such an explanation making a mockery of their claims to understand the origin of species. If you don't understand the origin of any adult individual, you should not be claiming to understand the origin of a species. This shortfall of Darwinism becomes clear once the lie of "DNA as human anatomy blueprint" is recognized. 

Bio-physics

In her section of bio-physics starting on page 23 of her document, Chiu, starts to make some "give you the wrong idea" statements:

  • She speaks in a "give you the wrong idea" manner by saying "it is the physical properties of cells that determine how they move, stick together, stop, or separate from each other." To the contrary, we have no understanding of how cells form such incredibly complex and biologically necessary arrangements as an organism progresses from a speck-sized zygote to the incredibly organized state of a large adult; and such fantasitcally fine-tuned arrangements are not at all explained by "the physical properties of cells." For example, there is nothing in the physical properties of eye cells that explains how such cells organize into the enormously organized state of an eye; and there is nothing in the physical properties of heart cells that explains how such cells organize into the enormously organized state of a heart.
  • She states, "Stuart Newman has long championed that biology should take seriously the importance physical factors such as adhesion, surface tension, viscosity, phase separation, gravitational effects, etc., that determine organismal form (Newman and Frisch 1979; Newman and Comper 1990; Newman 1994)." Such factors do not at all "determine organismal form," but merely have some effect on organismal form. 
  • Giving an example of vacuous talk, she claims "the major morphological motifs or features can be explained as the natural result of their unique physical properties and mechanisms," which is just saying X is explained by Y, where Y is simply a synonym for X. "Features" means the same as "physical properties and mechanisms," and you haven't explained anything by saying that features are the "natural results" of "physical properties and mechanisms." That's as empty and non-explanatory as saying a person can be explained as being the "natural result" of a human being. 
People offering such trivial explanations for the mountainous levels of fine-tuning and functional organization in biological organisms often engage in "make the cathedral seem like crumbs" talk that ignores the reality of biological complexity, which is depicted in the table below:

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.


TISSUE CONSISTS OF CELLS.

There are roughly 200 types of cells in the human body, each a different type of system of enormous organization.

CELLS TYPICALLY CONSIST OF COMPLEX MEMBRANES AND THOUSANDS 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 protein molecules that work together to achieve a function that cannot be achieved by only one of the proteins in the complex.

PROTEIN MOLECULES CONSIST OF HUNDREDS 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.

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+ 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.



Phentoypic Plasticity 

Chiu starts talking about phenotypic plasticity on page 25 of her document, and defines it as "when organisms exhibit different shapes, sizes, or any number of other traits and features in different environments."  That does not do anything substantial to explain how fantastically organized of arrangements of matter should arise in bodies with DNA that does not specify such arrangements. Chiu provides no impressive example of phenotypic plasticity explaining anything. The main example she gives (on page 26) is some feeble example involving goats having a birth defect so that they only have two legs. A recent paper on phenotypic plasticity offers these unimpressive ragtag examples: "Examples of phenotypic plasticity include, but are not limited to, temperature dependent sex determination in reptiles (Whiteley et al, 2021), behavioral and physical dimorphism in dung beetles (Emlen, 1997) and caste polyphenism in social insect populations (Weiner and Toth, 2012)." 

Symbiosis and Microbes

Chiu's explanation of this concept (beginning on page 28 of her document) does nothing to help explain the incredibly organized bodies and enormously gifted minds of humans. She does little more than repeat the tall tale that Lynn Margulis did something to explain the origin of eukaryotic cells, an idea that is not credible. Such a triumphal legend has been socially constructed because of the utter inadequacy of Darwinism as an explanation for a transition from prokaryotic cells to vastly more organized eukaryotic cells. 

Niche Construction

Chiu defines niche construction like this: "Niche construction occurs when organisms (plants and animals alike) affect their evolution or that of others by modifying environments through their metabolism, activities, choices, or behavior (Odling-Smee et al. 1996; Laland et al. 2016)."  The motley ragtag examples she gives of this are not impressive:

"Termite mounds, beaver dams, earthworm tunnels, nests and burrows, etc., are all classic examples of niche construction. Other examples include the manipulation of penguin group temperature through huddling, the maintenance of stable food sources through migration, or as mentioned before, the manipulation of light intensity on plant leaves through plasticity."

Whatever is being talked about (and it sounds like little more than mere environmental modification), it does nothing to explain how fantastically organized arrangements of matter could occur. Chiu provides no impressive examples of any biological features that can be explained as resulting from niche construction. 

Culture and Society

Chiu starts talking about culture on page 35 of her document, and talks about it for a few pages, failing to mention anything that can be of much help in explaining the wonders of biology. The human example she gives is an unimpressive one: mere lactose tolerance.  Human bodies and minds have a thousand stunning wonders, and that is not one of them. The main example she gives of "culture and society" shaping evolution outside of humans is some very dubious and "small potatoes" claim involving the assertion that "that some bottlenose dolphins in Western Australia created and transmitted the cultural trait of using sponges as foraging tools, which protects them against more harmful prey and thus led to a shift in their diet and food sources." 

Extra-genetic molecules

When Chiu used this phrase she was apparently referring to epigenetics. Epigenetics is the study of things such as methlyation molecules that can turn off particular genes. But epigenetics cannot explain impressive biological novelties. To get some new biological inventions such as a wing or an arm or an eye or an organ, you need many things, such as 

(1) New protein molecules, each of which involve hundreds of amino acids arranged in just the right way.

(2) Correct folding of these protein molecules, something not yet explained.

(3) In many cases, the origination of new types of cells, things many times bigger than a mere protein molecules.

(3) The origination of some new very complex structure such as an organ or limb or eye, something that cannot be explained by mere DNA changes, because DNA does not specify anatomy. 

None of this can be explained by the rather incidental effects produced by methylation molecules and similar things studied in epigenetics.  You don't get a new organ or a new limb by some chemical thing such as DNA methylation that serves as a mere "off switch" for genes.  Similarly, a flying bomber aircraft can "turn off" particular houses or buildings in a city, but such a bomber sure cannot construct new skyscraper towers.  

A paper in a well-known scientific journal tell us, "At present, evidence for epigenetic inheritance in human populations is sparse." Elsewhere we read an expert saying this: "While we have more than 20,000 genes in our genome, only that rare subset of about 150 imprinted genes and very few others have been shown to carry epigenetic information from one generation to another." Referring to the DNA methylation that is at the heart of epigenetics, another scientific paper states, "Most DNA methylation is also likely to be without significant biological function."

EES Seems to Give Us the Same Old Misleading Language, Plus a Few Minor "Odds and Ends"

In Figure 24 Chiu gives us a diagram entitled "The cause of evolution, according to the EES." The two lines below are an equivalent of this diagram on page 45 of her document, using the terms used in that diagram:

Genetic change+gene expression+developmental processes+environmental change = phenotypic variants.

Phenotypic variants +developmental bias+niche construction+mutation+natural selection+random drift+gene flow = phenotypic evolution.

We have here a continuation of two of the worst linguistic offenses of Neo-Darwinism (the Modern Synthesis). The first is the use of the "make the cathedral look like crumbs" phrase "phenotypic variants." What is that evolutionary biologists mean by this phrase? They mean minor changes but also things such as going from a microbe to a mouse, or going from a mouse to a man. Such changes involve miracles of physical organization many times more impressive than a transition from a purely natural forest to a city consisting of 1000 four-story wood houses including plumbing and electricity. Such changes also involve almost infinitely complicated wonders such as the arising of human minds and their countless capabilities. Calling such things "phenotypic variants" is ultra-diminutive language as misleading as using the phrase "atomic variations" to refer to a modern new city rising up from an uninhabited desert, or using the phrase "molecular rearrangements" to refer to cities being blown up by atomic bombs.  

The second linguistic offense is the continued use of the misleading term "natural selection," which does not actually refer to selection (selection being a choice made by conscious agents).  What faith should we have in EES theorists if they continue to use the same misleading language of the Neo-Darwinists?

Maximizing a use of shrink-speaking ultra-diminutive language, Chiu has in her long document used the term "variants" 32 times and the term "variations" 18 times, very often (it seems) to refer to changes both big and small, including dramatic new biological innovations and things such as the appearance of new species unlike any the world had seen before. Such language is misleading. When I search for the definition of "variant" Google gives me this definition: "a form or version of something that differs in some respect from other forms of the same thing or from a standard." Every single time nature gives us any type of  new biological innovation, it is not some "other form of the same thing" but the appearance of a new type of thing.  The term "variation" or "variants" is never honestly used in referring to impressive biological innovations that involve the appearance of dramatically new types of things. 

Chiu's Figure 24 makes rather clear that the Extended Evolutionary Synthesis has nothing very new to offer to explain the appearance of biological innovations. The things listed as causing "phenotypic variants" (genetic change, gene expression, developmental processes, environmental change) are just things already appealed to by Neo-Darwinists (advocates of the so-called Modern Synthesis). None of them are capable of explaining either anatomical structural innovations or mental innovations in organisms, mainly because genes do not specify anatomy, and do not do anything to explain mental capabilities. The phrase "genetic change" does nothing to explain the origin of genes. Each of the roughly 20,000 genes in our genome is a function-enabling arrangement of hundreds of parts that should never have occurred from any known natural process. Because a protein molecule corresponding to a gene will typically be nonfunctional if half of its components are removed, there is generically no credible Darwinian explanation for the origin of a gene. 

It seems that not once in Chiu's 85-page document does she do anything to tell us about the gigantic levels of complexity and organization in living things. She fails to describe either genes or protein molecules, and fails to mention the hierarchical organization of matter in organisms. Failing to mention nucleotides, she fails to mention that an average gene consists of about 1000 well-arranged nucleotide pairs. Failing to mention amino acids, she fails to mention that an average protein molecule consists of about 470 well-arranged amino acids, each consisting of many atoms. You would never know from reading her document that human bodies have more than 20,000 different types of complex inventions inside them (the more than 20,000 different types of protein molecules in our bodies), that each type of protein molecule has thousands of well-arranged atoms, and that humans have 200 types of cells (each something of such intricate functional complexity it has been compared to a jet aircraft or a factory). So it commonly is with evolutionary biologists, who seem so often to operate under a principle of "conceal the complexity, overlook the organization, and hide the hierarchical."

When a Program Has Been Caught Massively Lying, Your Goal Should Not Be to Extend It 

The Extended Evolutionary Synthesis fails to offer much of anything that fixes the massive explanatory failures of the Modern Synthesis (in other words, Neo-Darwinism). All that it offers are a professorial potpourri: a hodgepodge consisting of a few miscellaneous "odds and ends" that do not add up to an explanation for how we got here, physically or mentally. 

The Modern Synthesis (in other words, Neo-Darwinism) was built upon one of the worst deceits ever spread: the fictional notion that in DNA there is a blueprint or recipe or program for building organisms. Given so massive a deceit, why is that EES theorists propose that we should be extending the Modern Synthesis? Extensions should be built for things that are healthy. Extensions should not be built for rotting structures. You don't fix a sandwich all infected with botulism by adding a few new slices of meat or cheese. The Modern Synthesis is like such a sandwich, because it's all infected with lies and misleading claims, mainly the lie that DNA is a specification for building a human. 

There is no quick solution to the unsolved problem of explaining human origins, something that may take many centuries. But a good way to at least start going down the right road would be:

(1) Thoroughly renounce the lies at the heart of mainstream biology, such as the lie that DNA is a specification for building humans, and the lie that scientists have got an understanding of how human minds do things by studying brains (something that has not at all occurred for reasons discussed here). 

(2) Thoroughly list all of the things that biologists do not understand and the reasons they do not understand them, including how novel genes arise, how protein molecules reach the 3D shapes needed for their function, how cells originate, how cells find suitable positions in bodies, how organs originate, how the overall structure of a human body originates, how humans form memories, how humans recall much relevant nformation after hearing a single word, and how human minds originate.

(3) Thoroughly study all of the observations and facts that are very relevant to explaining the origin of humans, observations and facts that biologists have largely failed to study, such as anomalous phenomena, paranormal phenomena and the full spectrum of human capabilities and human mental experiences.

(4) Stop using misleading ultra-diminutive "make the cathedrals look like crumbs" language such as merely referring to enormous wonders of biological innovation as "phenotypic variants," and start giving honest descriptions of the stratospheric levels of organization and functional complexity in all large organisms.

(5) Stop using deceptive dehumanizing language that makes humans sound like mere minor variations of apes, and recognize the oceanic mental gulf between human beings and all other organisms.

(6) "Wake up and smell the coffee" by recognizing what nature is screaming to us in a very loud voice: that gigantically organized  organisms are intrisincally, massively and fundamentally teleological, with such teleology thoroughly permeating most aspects of their physical origination.

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