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Our future, our universe, and other weighty topics


Friday, November 15, 2019

"DNA as Recipe" Is as False as "DNA as Blueprint"

In 1943 physicist Erwin Schrodinger speculated that the chromosomes of a cell “contain, in some kind of code-script, the entire pattern of the individual’s future development and of its functioning in the mature state.” Within a decade, DNA was discovered. But DNA never was found to be anything like some blueprint or recipe or code-script for making a human being. 

The Cambridge English Dictionary defines a blueprint as "a complete plan that explains how to do or develop something." DNA merely contains very low-level chemical information such as lists of the amino acids that make up the proteins in our bodies. Nowhere in DNA is there any of the following:
  1. a specification of the large-scale structure of the human body;
  2. a specification of the structure of any of the appendages of the human body such as legs or arms or heads;
  3. a specification of any organ system of the human body;
  4. a specification of any individual organ of the human body;
  5. a specification of any of the 200 types of cells in the human body;
  6. a specification of any of the organelles that are the building blocks of cells.
There are several different reasons why we know that DNA has no such things. The first reason is that human DNA has been very thoroughly analyzed through multi-year scientific projects involving very large teams of scientists, such as the Human Genome Project and the ENCODE project, and no such specifications have been found in DNA. For example, no one has found any place in DNA where it specifies that humans have two legs or two arms or one neck or two eyes or two ears or ten fingers. The second reason is that only one type of “language” has ever been found used by DNA, the very low-level “poor-man's language” of the genetic code, allowing nothing to be stated other than low-level chemical information such as the amino acids in proteins. Using this “poor-man's language” capable of only stating amino acids or other equally low-level chemical information, it is absolutely impossible to state things such as a complex three-dimensional structure or the anatomy of the eye or the anatomy of the human reproductive system.


DNA only specifies low-level chemical information

The third reason is that if a human DNA molecule were to contain a specification of a human, should a thing would be a fantastically complex instruction that could only be read and interpreted by something in the human womb capable of reading fantastically complex instructions. But nothing like that exists in the human womb. Blueprints are only useful because they are read by human agents smart enough to execute the complex instructions of the blueprints. If a blueprint existed in DNA, it would be something far more complicated than a blueprint for making a home. Such a thing would require some gigantically sophisticated “DNA blueprint reader” capable of reading and executing enormously complicated instructions. But no such thing exists in the human womb. We therefore absolutely cannot explain how a human progresses from a fertilized ovum to a newly delivered baby by imagining that a DNA blueprint or recipe has been read and followed.

Such facts prove in multiple ways that DNA cannot possibly be a blueprint or a program or a recipe for making a human. DNA actually contains less than 10 percent of what is needed to specify a human. A molecule containing all of the information needed to specify a human being would be more than 10 times larger than a human DNA molecule. What we know about the size of the genomes of different organisms is entirely inconsistent with claims that DNA is some kind of blueprint or recipe for making a human. In terms of total number of base pairs, the DNA of humans is more than ten times smaller than the DNA of many amphibians and flowering plants, as you can see in the visual here. We would expect the opposite to be true if DNA contained a blueprint for making a human.

But for decades, mainstream academia has deceived us about DNA, pushing the phony-baloney idea that DNA is some kind of blueprint or recipe or algorithm for making a human. I call this falsehood the Great DNA Myth. The false claim that DNA is a blueprint or recipe for making a human was denounced by Ken Richardson, formerly Senior Lecturer in Human Development at the Open University. In an article in the mainstream Nautilus science site, Richardson stated the following:

"Scientists now understand that the information in the DNA code can only serve as a template for a protein. It cannot possibly serve as instructions for the more complex task of putting the proteins together into a fully functioning being, no more than the characters on a typewriter can produce a story."

But the Great DNA Myth (that DNA is a blueprint or recipe for making a human) continues to be pushed by many, including the journal Science, the official publication of the American Association for the Advancement of Science. In September, 2019 the publication had a “special issue” entitled “Genotype to Phentotype.” The issue was designed to give us the idea that genotypes specify phenotypes, an idea that is dead wrong. The phenotype (or visually observable characteristics of an organism) is not specified by an organism's genotype (its DNA). DNA merely specifies low-level chemical information, not high-level structural information.

On page 1395 we are told a huge untruth by Zahn, Purnell and Ash, who stated, “The DNA within a human cell, known as the genotype, provides a blueprint to direct a host of processes for building an embodied organism.” Here we have the two biggest fables about DNA, the myth that it is a blueprint, and the myth that the passive chemical information repository that is DNA “directs” things, as if it were almost some intelligent agent. The fallacy of using words such as “directs” about DNA is debunked by biologist Richardson in his Nautilus article, and he also debunks the “DNA as blueprint” myth by stating, “there is no prior plan or blueprint for development.” 

Introducing some of the papers in the “special issue,” Zahn, Purnell and Ash state, “We examine cases in which various cells and traits are specified by DNA mutations or epigenetic changes.” But humans have 200 different types of cells, and DNA does not contain a specification of any one of them. The “special issue” has a paper with the misleading title, “Mapping human-cell phenotypes to genotypes with single-cell genomics.” But the paper does not at all describe how any cell phenotypes or structures are specified in DNA genotypes. It merely mentions some cases in which rare DNA mutations can affect a cell to produce a disease.  The paper has a visual which attempts to illustrate the idea of some mapping between genes and cell types, but it's just a speculative "something like this could exist" type of thing; and instead of listing specific genes, the genes listed in the mapping are listed as "Gene 1", "Gene 2", "Gene 3," "Gene 4," and "Gene 5." Such speculative illustrations do not constitute any case of showing that a cell type is specified by DNA or genes. 

At a biology "expert answers" site, we read an expert answer telling us that "DNA does not have instructions for how to build a cell," and also that DNA does not even specify how to make the mere membrane of a cell. DNA does not specify any type of cell, and does not even fully specify the things that are smaller than cells. Cells are built from smaller units called organelles, and even their structures are not specified by DNA. When we look at the lowest level of chemical structure, and look at proteins, we find that even those are not fully specified by DNA. DNA specifies the amino acid sequence of proteins, but not their three dimensional shapes.  The mystery of how proteins acquire such three-dimensional shapes is the unsolved problem of protein folding, which scientists have not solved despite decades of laborious efforts. Claims that the three-dimensional shapes of proteins are simply consequences of their amino acids sequences (listed in DNA) are disproved by the failure of ab initio methods to reliably predict the shapes of proteins from their amino acid sequences, and also by the dependency of a large fraction of protein molecules on other molecules (so-called chaperone molecules) in order to achieve their three-dimensional shapes.  A scientific paper about such ab initio protein structure prediction (which uses only the amino acid sequence) tells us, "Currently, the accuracy of ab initio modeling is low and the success is generally limited to small proteins." 

The Genotype to Phenotype “special issue” also very strangely includes a paper entitled “Microbiomes as source of emergent host phenotypes.” Talk about grasping at straws. Your microbiome is the set of all microbes living inside you, or the total DNA of all the microbes living inside you. You will not solve the problem that DNA does not contain a blueprint or recipe for making a human by trying to look for instructions for making a human inside the DNA of microbes living inside a human. The DNA of such microbes suffers from exactly the same limitations of human DNA, limitations which prevent it from being anything like a blueprint or a recipe for building large three-dimensional structures.

None of the papers in the Genotype to Phenotype “special issue” provide anything that should prevent us from thinking that Zahn, Purnell and Ash were feeding us baloney when they stated, “The DNA within a human cell, known as the genotype, provides a blueprint to direct a host of processes for building an embodied organism.” There is zero evidence that DNA is a blueprint for making a human, and we know of several reasons why it cannot be any such thing.  Given its physical limitations limiting it to listing low-level chemical ingredients, it is utterly impossible that DNA could do any such thing as directing or specifying even a single process, let alone "a host of processes."  The biochemical processes inside organisms are gigantically complex, far too complex to be specified or directed by the kind of minimalist "bare bones" poor-man's language that is the genetic code used by DNA,  capable of listing only sequences of low-level chemicals.  Below we see a description of one of these gigantically complex processes, from a biochemistry textbook. 


complicated biology process
Immensely complicated biochemistry of vision

On page 26 of the recent book The Developing Genome, Professor David S. Moore states, "The common belief that there are things inside of us that constitute a set of instructions for building bodies and minds -- things that are analogous to 'blueprints' or 'recipes' -- is undoubtedly false." Describing conclusions of biologist Brian Goodwin, the New York Times says, "While genes may help produce the proteins that make the skeleton or the glue, they do not determine the shape and form of an embryo or an organism." Massimo Pigliucci (mainstream author of numerous scientific papers on evolution) has stated  that "old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading." Neuroscientist Romain Brette states, "The genome does not encode much except for amino acids."

In a 2016 scientific paper, three scientists state the following:

"It is now clear that the genome does not directly program the organism; the computer program metaphor has misled us...The genome does not function as a master plan or computer program for controlling the organism; the genome is the organism's servant, not its master."

In the book Mind in Life by Evan Thompson (published by the Belknap Press of Harvard University Press) we read the following on page 180: "The plain truth is that DNA is not a program for building organisms, as several authors have shown in detail (Keller 2000, Lewontin 1993, Moss 2003)."  Scientist Jean Krivine presents here a very elaborate visual presentation with the title, "Epigenetics, Aging and Symmetry or why DNA is not a program." Scientists Walker and Davies state this in a scientific paper:

"DNA is not a blueprint for an organism; no information is actively processed by DNA alone. Rather, DNA is a passive repository for transcription of stored data into RNA, some (but by no means all) of which goes on to be translated into proteins."

Rejecting the "DNA as blueprint" and "DNA as human specification" ideas, biologist Rupert Sheldrake has written the following:

"DNA only codes for the materials from which the body is constructed: the enzymes, the structural proteins, and so forth. There is no evidence that it also codes for the plan, the form, the morphology of the body."

Geneticist Adam Rutherford states that "DNA is not a blueprint." A press account of the thought of geneticist Sir Alec Jeffreys states, "DNA is not a blueprint, he says."  B.N. Queenan (the Executive Director of Research at the NSF-Simons Center for Mathematical & Statistical Analysis of Biology at Harvard University) tells us this:

"DNA is not a blueprint. A blueprint faithfully maps out each part of an envisioned structure. Unlike a battleship or a building, our bodies and minds are not static structures constructed to specification."

When we ponder the vastly dynamic nature of the human organism, we may more fully understand the absurdity of trying to explain human morphogenesis by pushing a myth of "the DNA blueprint is read." Blueprints are used to create static things such as buildings.  But a human organism is gigantically dynamic, with a vast horde of diverse cellular activities occuring in most of our flesh.  Each cell is as complex as a factory, and to specify a human (with 200 cell types) you would need (among other things) not merely to specify the structure of each of those 200 cell types, but an intricate description of the activity and processes within those cells.  Such a specification would be as complex as one that not only specified the physical layout of 200 factories, but also one that specified the dynamics of the manufacturing processes and material movements inside such 200 factories. We can think of all too many reasons why such vast complexities could never be specified by a molecule merely listing low-level chemical ingredients.  

Some concede that DNA is not a blueprint, but then say that DNA is a recipe. It is just as false and misleading to claim that DNA is a recipe as it is to say that DNA is a blueprint.  Let's start with the definition of "recipe." The Cambridge English Dictionary defines "recipe"  as "a set of instructions telling you how to prepare and cook a particular food, including a list of what foods are needed for this," giving no other definition. DNA does not tell us how to prepare and cook a food, so it is absurd to be calling DNA a recipe. 

A recipe is not a mere list of ingredients, but a set of assembly instructions on how to make some edible food using those ingredients -- instructions such as "mix for 2 minutes on medium speed of mixer," "chop up almonds and pour them into mixing bowl," "pour mixture into a cake cooking pan," and "bake for 35 minutes at 375 degrees." DNA specifies chemical ingredients, but does not specify any steps or algorithm for using such ingredients to assemble complex things such as cells or organs or reproductive systems or organisms. So it is false to say that DNA is a recipe, unless you merely say that DNA is a recipe for making the low-level chemical units called polypeptide chains.  Because it contains no high-level assembly instructions, DNA is neither a recipe nor a program for making a human, any organ system of a human, any organ of a human, any appendage of a human, or any cell type of a human. 

The Great DNA Myth that DNA is a blueprint or recipe or program for building organisms is not some careless error comparable to someone clumsily saying that there are only 7 planets in the solar system. The claim that DNA is a blueprint or recipe for building organisms is a falsehood typically told by certain people who need to tell this particular falsehood to defend unbelievable claims they wish to defend.   I will leave for another post a discussion of the ideological motivations for this misinformation that has been peddled for decades by esteemed authorities in academia.  

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