Monday, July 23, 2018

Why DNA Cannot Be a Specification of a Human

The discovery of DNA was one of the great triumphs of science. But ever since this discovery there has been a strange trend which we may call “DNA inflation” or “DNA exaggeration.” The trend has been to carelessly describe DNA in ever more grandiose terms, regardless of the actual facts.

One very common claim is that DNA is a blueprint that lays out the complete specification of the human body. Another common claim is that DNA is a recipe (or a library of recipes) for making an organism. It is also sometimes claimed that DNA is like a computer program for generating our bodies.

But such statements are not warranted by the facts. Judging from the facts, we must conclude that while DNA uses a code of symbolic representations (the genetic code), DNA is not a blueprint for making a human, is not a recipe for making a human, and is not a program or algorithm for making a human. The facts indicate that DNA is not anything close to a complete specification of an organism, but that DNA is instead something much simpler, mainly just a kind of database (or a collection of ingredient lists) used in making particular parts of an organism.

To get an idea of the true nature of DNA, it is a good idea to adopt a conceptual model of DNA. In science, a model is a somewhat simplified representation that helps us understand a more complicated reality. A classic example of a model is the Bohr model of the atom, in which the nucleus of an atom is compared to the sun, and the electrons in an atom are compared to planets that revolve around the sun. The atom is actually more complicated than such a situation (given the weirdness of quantum mechanics), but the Bohr model is still useful to help us get a basic grasp of what an atom is like. The Bohr model is essentially accurate, because just as the great majority of a solar system's mass exists at its center in the sun, the great majority of an atom's mass exists at its center in the atomic nucleus.

Now, what model can we use to grasp the basic nature of DNA? A good model to use is what we may call the chain-of-colored-beads model. Let us imagine a long chain of colored beads, in which there are about twenty possible bead colors, and each bead stands for a particular type of chemical called an amino acid. That is exactly how DNA works. We can imagine that one of these colors means kind of “Start.” The amino acids are the constituents of proteins. So after one of these “Start” beads appears in the chain, there is then a sequence of colored beads, with each color representing one of the twenty amino acids. Altogether the long “chain of beads” that is DNA specifies the ingredients of thousands of different proteins.

A particular snippet or section of DNA will correspond to a chain of amino acids that is the starting point of a protein. The visual below illustrates this schematically.

polypeptide chain

Now, once we have adopted this useful “chain of colored beads” model to help us understand the nature of DNA, we can understand the limitations of DNA. What type of information can be specified with such a “chain of colored beads”? Only simple linear information, what is called one-dimensional information. As two scientists state, "Genes are merely a means of specifying polypeptides," the one-dimensional chains like those depicted above. 

An example of one-dimensional information is a telephone number, a social security number, or a stock ticker tape. Such information can always be presented with a single line or row, although some types of one-dimensional information might require a long line or row. A more complicated type of information is what is called two-dimensional information. Such information requires both rows and columns. An example of two-dimensional information is the information in a calendar or a spreadsheet.

Another more complicated type of information is called three-dimensional information. Three-dimensional information specifies something that can only be described using the dimensions of length, width, and depth. An example is the information specifying the three-dimensional structure of a car.


Now, what type of information would be required to specify the physical layout of a three-dimensional body such as the human body? To specify such a thing, you would need three-dimensional information, information involving length, width and depth. But there is no way that such three-dimensional information could exist in DNA, which has merely one-dimensional information.

In fact, it seems that in order to make a complete biological specification of an organism, you would need not just three-dimensional information, but four-dimensional information. Time is often regarded as the fourth dimension. We can describe four-dimensional information as information that involves not merely aspects of length, width, and depth, but also an aspect of time.

Why would you need four-dimensional information to specify an organism such as a human? For one thing, it is not true that humans just pop into existence as adults. Instead, there is a long series of transitions between the earliest state of a newly fertilized egg, and that of a full-grown human. A full human specification would have to specify each of these states. So the specification would need to use the fourth dimension of time to specify this temporal progression in human forms.

Another reason why a full human specification would need to be four-dimensional is that human beings are not static objects, but intensely dynamic objects. Think of all the dynamic activity occurring every day in your body. Blood and electricity is flowing about, proteins are being synthesized according to specific time tables, cells are being born and dying according to other time tables, and so forth. A single snapshot of the state of a human body is not at all sufficient to capture this dynamic activity. You would need to have a specification that is four-dimensional. Similarly, if someone from some small island in the Pacific had no idea of what a city was, you would never specify what a city was by just showing some maps. You would need to somehow specify the motion occurring in the city: the subways moving, the cars moving, the people moving, the water flowing through pipes, and so forth.

But DNA can only specify one-dimensional information. So it is very absurd to maintain that a biological specification of humans is in the one-dimensional information of DNA.

The table below lists on the left various types of information that would be needed to have a full biological specification of an organism, and on the right whether or not such information can be specified in DNA.

Type of information Can it be specified in DNA?
Linear amino acid sequence of a protein molecule Yes
Three-dimensional shape of a protein molecule No
Exact location where a protein is located in body No
Layout of a cell organelle No
Layout of a cell No
Layout of a tissue type No
Layout of an organ No
Layout of an organ system No
Layout of a full body plan No
Structure progression from simplest tiniest form to fully grown form No
Dynamic behavior inside an organism during a particular month or year No

Some would disagree about the answer I have given in the third row, and claim that the three-dimensional shape of a protein molecule is purely a consequence of its sequence of amino acids. If this were true, scientists would have long ago solved the protein folding problem, and would be able to predict the three-dimensional shapes of proteins from their one-dimensional sequence of amino acids. But after decades of trying to do this, the protein-folding problem is still unsolved, and (as discussed here) scientists still cannot accurately predict the 3D shapes of large proteins from their amino acid sequences.

The fact that DNA can only store one-dimensional information is a decisive reason for rejecting all claims that DNA even half-specifies the human organism. There are two other reasons for rejecting such claims. The first is that no one has found any information in DNA corresponding to human body plan information. The human genome has been thoroughly studied through massive projects such as the Human Genome Project and the ENCODE project. No one has found any gene information specifying a human body plan, a structural plan for a cell, a structural plan for an organ, or a structural plan for an organ system.

The second reason is equally enormous. It is simply that there exists nothing in the human body that could interpret a specification of human biology, if such a thing existed in DNA. Consider computer code. Such code can only work because there is an enormously sophisticated piece of software called an interpreter or compiler that is smart enough to read such complex instructions. If it were to happen that DNA stored instructions for making a human, contrary to the evidence, we would only explain human development if we imagined that somewhere in our biology was some enormously sophisticated machinery or functionality capable of reading such highly complex instructions and executing them. But no such functionality has ever been discovered.

Is it accurate to say that there are recipes in DNA? No it is not. A recipe includes an ingredient list, and a set of instructions explaining how to make a particular meal or dish using those ingredients. DNA has lots of ingredient lists specifying the ingredients of proteins. But nowhere does DNA specify a series of instructions for assembling a protein molecule, a cell, an organ, an organ system, or a full body. Protein molecules have three-dimensional shapes that they assume for unknown reasons. Such shapes are not specified in DNA.

At the end of this post (in which I cite additional very weighty reasons for rejecting the claim the DNA is a specification of a human), I quote eight different scientists (mainly biologists) who state that DNA is not a recipe or blueprint for making a human, or anything like a specification of the human form.  

So where is it that biological shapes and structures come from? This is a gigantic unknown, which stands as a dramatic contradiction of all attempts to explain biology in mechanistic or materialistic terms. We do not know where the 3D shapes of protein molecules come from. We do not know where the shapes of cells come from. We do not know where the structure of tissues comes from. We do not know where the shapes of organs come from. We do not know where the shapes of organ systems come from. We do not know where the overall body plan of an organism comes from. We therefore have a strong reason to suspect that such things are mysterious inputs from some unfathomable reality outside of an organism.

The reality of DNA is something very inconsistent with the claims about DNA made by many a science book, where we hear about DNA as a blueprint for the body or DNA as some recipe for making a human. In my next post I will look at one of these books, and the false and wildly inconsistent claims the book makes about DNA. We will see that the tall tales that the book tells about DNA are five different claims that are all inconsistent with each other, resulting in a kind of DNA mythology that is “all over the map.” 

Postscript: The genome is an organism's DNA, while the phenotype is the set of observable characteristics of an organism (such as its external appearance and internal arrangement of organs). In the mainstream book "Frontiers in Ecology, Evolution and Complexity," a scientist states the following:

At the beginning of the 21st century, biology confronted an uncomfortable fact: despite the increasing availability of whole genome sequence data, it was not possible to predict, or even clarify, phenotypic observations. In fact, we now know that there is not sufficient information in the linear DNA of the complete genomes to recover and/or understand the diverse phenotypic states of an organism. 

In statements such as this, scientists "fess up" that the idea of DNA as a human specification is not true.  Another example can be found in this paper written by several scientists, in which we read this: "Because genes code for proteins, there are no 'genes for' phenotypes per se, including behavioral phenotypes."  Here is another example. "DNA cannot be seen as the 'blueprint' for life," says Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland.  He says, "It is at best an overlapping and potentially scrambled list of ingredients that is used differently by different cells at different times."  Sergio Pistoi (a science writer with a PhD in molecular biology) tells us, "DNA is not a blueprint," and tells us, "We do not inherit specific instructions on how to build a cell or an organ." Michael Levin (director of a large biology research lab) states that "genomes are not a blueprint for anatomy," and after referring to a "deep puzzle" of how biological forms arise, he gives this example: "Scientists really don’t know what determines the intricate shape and structure of the flatworm’s head."

Agustin Fuentes, a professor of anthropology, states the following:

"Genes play an important role in our development and functioning, not as directors but as parts of a complex system. 'Blueprints' is a poor way to describe genes. It is misleading to talk about genes as doing things by themselves."

Two other scientists "fess up" in a similar way when they write the following about genes in the journal Nature: "Population genetics is founded on a subset of coding sequences that can be related to phenotype in a statistical sense, but not based on causation or a viable causal mechanism."

Regarding the DNA as blueprint idea a wikipedia.org article entitled “Common misunderstanding of genetics” lists the claim that “Genes are a blueprint of an organism's form and behavior” as one of the “common misunderstandings of genetics.” Jonathan Latham has a master's degree in Crop Genetics and a PhD in virology. In his essay “Genetics Is Giving Way to a New Science of Life,” a long essay well worth a read, Latham exposes many of the myths about DNA being a blueprint or master controller, and points out DNA does not even fully specify a protein. He states, "It is habitually, but lazily, presumed that DNA specifies all the information necessary for the formation of a protein, but that is not true." 

Ian Stevenson M.D. cited quite a few biologists pointing out the genes and DNA cannot determine the form of an organism:

"Genes alone - which provide instructions for the production of amino acids and proteins -- cannot explain how the proteins produced by their instructions come to have the shape they develop and, ultimately, determine the form of the organisms where they are. Biologists who have drawn attention to this important gap in our knowledge of form have not been a grouping of mediocrities (Denton, 1986; Goldschmidt, 1952; B. C. Goodwin, 1985, 1988, 1989, 1994; Gottlieb, 1992; Grasse, 1973; E. S. Russell...Sheldrake, 1981; Tauber and Sarkar, 1992; Thompson, 1917/1942)."

Biologist B.C. Goodwin stated this in 1989: "Since genes make molecules, genetics...does not tell us how the molecules are organized into the dynamic, organized process
that is the living organism."  paper by Stuart A. Newman (a professor of cell biology and anatomy) discussing at length the work of scientists trying to evoke "self-organization" as an explanation for morphogenesis states that "public lectures by principals of the field contain confidently asserted, but similarly oversimplified or misleading treatments," and says that "these analogies...give the false impression that there has been more progress in understanding embryonic development than there truly has been." Referring to scientists moving from one bunk explanation of morphogenesis to another bunk explanation for it, the paper concludes by stating, "It would be unfortunate if we find ourselves having emerged from a period of misconceived genetic program metaphors only to land in a brave new world captivated by equally misguided ones about self-organization."

Referring to claims there is a program for building organisms in DNA, biochemist F. M. Harold stated "reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading." Referring to  self-organization (a vague phrase sometimes used to try to explain morphogenesis), he says, "self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm." Geneticist Adam Rutherford states that "DNA is not a blueprint," a statement also made by biochemistry professor Keith Fox.

Physician James Le Fanu states the following:

"The genome projects were predicated on the reasonable assumption that spelling out the full sequence of genes would reveal the distinctive genetic instructions that determine the diverse forms of life. Biologists were thus understandably disconcerted to discover that precisely the reverse is the case. Contrary to all expectations, there is a near equivalence of 20,000 genes across the vast spectrum of organismic complexity, from a millimetre-long worm to ourselves. It was no less disconcerting to learn that the human genome is virtually interchangeable with that of both the mouse and our primate cousins...There is in short nothing in the genomes of fly and man to explain why the fly has six legs, a pair of wings and a dot-sized brain and that we should have two arms, two legs and a mind capable of comprehending the history of our universe."

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."

Writing in the leading journal Cell, biologists  Marc Kirschner, John Gerhart and Tim Mitchison stated"The genotype, however deeply we analyze it, cannot be predictive of the actual phenotype, but can only provide knowledge of the universe of possible phenotypes." That's equivalent to saying that DNA does not specify visible biological structures, but merely limits what structure an organism can have (just as a building parts list merely limits what structures can be made from the set of parts). paper co-authored by a chemistry professor (Jesper Hoffmeyer) tells us this: "Ontogenetic 'information,' whether about the structure of the organism or about its behavior, does not exist as such in the genes or in the environment, but is constructed in a given developmental context, as critically emphasized, for example, by Lewontin (1982) and Oyama (1985)." Biologist Steven Rose has stated, "DNA is not a blueprint, and the four dimensions of life (three of space, one of time) cannot be read off from its one-dimensional strand." "DNA is not a blueprint for an organism," states Templeton Prize-winning physicist and astrobiologist P. C. W. Davies. On page 26 of his book Biology as Ideology: The Doctrine of DNA, biologist Richard C. Lewontin stated this:

"We are not determined by our genes, although surely we are influenced by them...Even if I knew the complete molecular specification of every gene in an organism, I could not predict what that organism would be....Even if I knew the genes of a developing organism and the complete sequence of its environments, I could not specify that organism."

A 2024 article says, "Martínez Arias, 68, argues that the DNA sequence of an individual is not an instruction manual or a construction plan for their body...The Madrid-born biologist argues that there is nothing in the DNA molecule that explains why the heart is located on the left, why there are five fingers on the hand or why twin brothers have different fingerprints." 

Two scientists said this:

"We see no valid use for definitions of the genotype and phenotype in terms of blueprints, programs, or
sets of instructions, and their realizations or
manifestation....The program/manifestation metaphor is factually misleading, because it suggests that the genotype uniquely determines an organism’s phenotype. However, as is well known, all
it does is specify an organism’s norm of reaction to environmental conditions (Rieger et al., 1991, Lewontin, 1992)."

A 2022 paper in the journal Science (one authored by more than ten scientists) says this: "Although the genome is often called the blueprint of an organism, it is perhaps more accurate to describe it as a parts list composed of the various genes that may or may not be used in the different cell types of a multicellular organism....The genome in and of itself does not provide an understanding of the molecular complexity of the various cell types of that organism." A Duke University biologist and a Cornell University biologist have confessed this: " No information about the overall architecture of these body parts is present in the cells and tissues of the parts themselves, or in each organism’s genes."

PostscriptThe term "body plan" is a profoundly misleading term that biologists love to use, a term that opens the door to deceptions about DNA. In biology literature the term "body plan" has a very limited meaning, something vastly different from a complete plan for constructing an organism. According to a scientific paper "a body plan is a suite of characters shared by a group of phylogenetically related animals at some point during their development." The wikipedia.org article on "body plan" tells us this: "body planBauplan (German plural Baupläne), or ground plan is a set of morphological features common to many members of a phylum of animals." 

According to this definition, all chordates (including men, bears, dogs and fish) have the same body plan. So when biologists talk about "the human body plan" they
are merely referring to the common characteristics of all chordates, including men, bears, dogs and fish:  basically just the existence of a backbone and bilateral symmetry (having the same things on both sides of the body).  They are not referring to the structure of the 200 types of cells in the human body, or the structure of internal organs, and are not referring to the dynamic intricacies of human physiology. But anyone hearing the term "body plan" will think the term referred to a complete specification of a human body.  So, most misleadingly, biologists may say that this or that "determines the body plan," when all they mean is the beginning of a bilateral organism with a backbone, something a thousand times simpler than the final product of the internally dynamic and enormously organized human body.  This is as misleading as someone saying that he has built a starship, when he has merely built a boat in the shape of a star.  

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