Biosphere Shouts From 100 Directions About Its Purposeful Agency, But Mainstream Stays Deaf to Such Clues

 When I read a previous article written by science writer Phillip Ball at Quanta Magazine, an article on DNA, I felt like writing a post in response that would be entitled "Pondering DNA, Phillip Ball Drops the Ball" (a reference to fumbling). Phillip Ball is a writer who has figured out that the long-told story about DNA and its genes simply isn't true. But he seems to have completely failed to realize the enormous implications of such a thing. 

As an explanation for how human bodies arise, "DNA as body blueprint" was always a childish myth, both because DNA has neither any body blueprint nor any cell blueprint, and also because blueprints have no power to build things (as explained below). 

Not long after DNA was discovered about the middle of the twentieth century, scientists and science writers began spreading a false idea about DNA: the idea that DNA contains a specification for building an organism such as a human.  There are various ways in which this false idea is stated, all equally false:

• Many described DNA or the genome as a blueprint for an organism.
• Many said DNA or the genome is a recipe for making an organism.
• Many said DNA or the genome is a program for building an organism, making an analogy to a computer program.
• Many claimed that DNA or genomes specify the anatomy of an organism. 
• Many claimed that genotypes (the DNA in organisms) specify phenotypes (the observable characteristics of an organism), or that the genotype is a "map" of the phenotype. 
• Many claimed that phenotypes (the observable characteristics of an organism) are "expressions" of genotypes (the DNA in organisms). 
• Many claimed that genotypes (the DNA in organisms) "map"  phenotypes (the observable characteristics of an organism) or "map to" phenotypes.
• Many claimed that DNA contains "all the instructions needed to make an organism."
• Many claimed that there is a "genetic architecture" for an organism's body or some fraction of that body. 
• Many claimed that DNA or its genes "guide," "direct" or "control" the nine-month process by which a zygote progresses to become a full-sized human baby. 
• Using a little equation,  many claimed that a "genotype plus the environment equals the phenotype," a formulation as false  as the preceding statements, since we know of nothing in the environment that would cause phenotypes to arise from genotypes that do not specify such phenotypes. 

All of these claims were false. DNA is no such thing as a blueprint, recipe or program for making an organism or any of its organs or any of its cells or any of the organelles that make up such cells.  At the post here I have a list of 40+ statements by 50+ experts (almost all scientists and doctors) who confess that DNA is no such thing as a program, blueprint or recipe for making an organism. 

Phillip Ball has realized that the long-told story about DNA and its genes simply is not true.  In the very mainstream publication The Guardian, Ball said this about the Human Genome Project that ended in 2003, noting the failure of science figures to clean up their old misstatements about DNA after they were debunked by the Human Genome Project:

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

So Ball has realized that the long-told "DNA as body blueprint" story is bunk. The subtitle of his article "Why the Human Genome’s Tangled Physicality May Confound AI" is "Our genetic heritage is not a blueprint or an algorithm, as many biologists have imagined, but something else entirely." Ball discusses some of the enormous complexity of the processes involving DNA.   But Ball has failed to realize the gigantic implications of the fact DNA and its genes don't tell how to make anything bigger than protein molecules.  The problem is that once you get rid of the old lie that DNA is a blueprint for building bodies, organs and cells, you have no mechanistic explanation for how bodies, organs and cells get built. That explanatory failure explodes the pretensions of today's biologists, showing that their boasts of understanding the origin of the human species are groundless legends.  The truth is that scientists understand neither the origin of the human species, nor the origin of any full human body, nor the origin of any human mind. 

Ball gives us a little new bunk to replace the old bunk, saying, "Our cells are, in effect, making complex decisions about how to use their genes — both the information they contain and the structure they assume."  Cells don't make decisions; people make decisions.  If a cell had understanding, it would have no understanding of anything beyond itself. So we can never explain how human bodies get constructed by some idea of cells making a decision. A stem cell would not have any idea of what type of cell to become and where in the body to go to in order to serve the grand final purpose of helping to construct a mobile perceiving organism with a cardiovascular system and a digestive system and arms and legs and a vision system. 

Ball fails to perceive what the main explanatory problem is regarding the origin of individual human bodies. That problem is what I call the missing specifications problem. The missing specifications problem is the problem that the arising of adult human bodies requires at least six extremely complex specifications that are nowhere to be found in the human body. 

DNA and its genes only specify low-level chemical information, such as which amino acids make up a particular protein. DNA and its genes do not specify how to make anything larger than a protein molecule. In fact, DNA and its genes fail to even fully specify how to make a folded protein molecule of any particular type. To be functional, protein molecules require complex special three-dimensional shapes. DNA and its genes do not specify how such shapes arise.  The problem of how the special three-dimensional shapes of proteins arise is the unsolved problem known as the protein folding problem (not to be confused with a different problem called the protein folding prediction problem, which deep learning software has made some progress on). 

3D shape of a folded protein molecule

The "sister problem" of the protein folding problem is the protein complex origination problem, the problem of how proteins form into complex special teams so well-engineered and fine-tuned they are often called "molecular machines." No substantial progress has been made on that problem, as some scientists confess in quotes at the end of this post. Below we see one such protein complex, consisting of hundreds of protein molecules teaming up to become a special functional component. 

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

So how does there arise over nine months of pregnancy a full human body, consisting of so many layers of physical organization above the layer of mere protein molecules? How does a mere speck-sized zygote (existing just after impregnation) progress to become a state of organization a billion times more impressive, the full organization of a human body? Such an origination is a miracle of organization a hundred miles over the heads of today's scientists. Their failure to explain this problem (the problem of morphogenesis) is a failure that makes a mockery of all claims that they understand the origin of the human species. If you do not understand the origin of any individual human body, you do not understand the origin of the human species. 

Given the utter lack of anything in a speck-sized zygote or the surrounding mother's womb that can sufficiently explain the progression from such a speck-sized object to a full human body, and given the lack of any credible explanation for the more impressive phenomena of human minds and human memory (none of which are credibly explained by brains), reality compels the inference that every human being arises because of transcendent agency. Nature never told us or even suggested that the universe is self-explanatory; nature never told us or even suggested that biological life is self-explanatory; nature never told us or even suggested that human bodies are self-explanatory; and nature never told us or even suggested that bodies or brains explain human minds.  Nature never told us or even suggested that the laws of nature are even a hundredth of what is needed to produce a human being.  We must postulate a purposeful agency acting throughout the biosphere to produce the stupendous wonders of biology, which mechanistic science is light-years away from explaining. I sometimes have used the acronym GOAL for such a transcendent agency. GOAL stands for Global Organizing Activity of a Life-force. The pillars of such an inference are shown in the diagram below. For a long explanation of why the pillar clues compel the two inferences listed at top, read my post here. 

By "transcendent agency" I mean purposeful intelligent agency beyond anything currently understood by humans.  The nature of such agency is mysterious. 

In another Quanta magazine article, Phillip Ball considers the issue of biological agency. He fails to address the issue with much insight, but at least inadvertently documents how clue-blind today's biologists are on this topic. His subtitle immediately goes astray, referring to, "The idea of ‘biological agency’ — that life devises its own goals and behaves accordingly." That is not a sensible definition of "biological agency."

We can give three sensible definitions of "biological agency":

(1) Organismic agency: the ability of organisms to act in ways that they will or decide to act, something that is the same as volition. There are endless mysteries of organismic agency, including the basic mystery of how any organism is able to choose a particular action (something not explained by anything we know about brains), and also endless mysteries of why organisms choose the particular path that they do (such as endless mysteries involving hard-to-explain instincts). 

(2) Component agency: the tendency (throughout the biosphere) for components in all layers of biology to act towards the achievement of purposeful goals (such as organization and homeostasis) that make possible the origination and continuation of biological organisms. 

(3) Morphogenetic agency: the agency driving the progression (over nine months) from a speck-sized zygote to a full human body. 

Today's scientists have no credible material and mechanistic explanation for any of these three types of agency. For example, no neuroscientist can explain why a human being may choose one type of life direction or one type of career rather than another. Such things can be explained by referring to minds and persons and personalities, but cannot be explained in terms of brains or neurons. 

In regard to component agency and morphogenetic agency, the explanation failures of biologists are gigantic and everywhere. Scientists lack any credible explanation of so simple a thing as how human cells are able to reproduce; they lack any credible explanation of the most basic mental processes such as thinking and memory; scientists lack any convincing explanation of how proteins are able to fold into the 3D shapes needed for their function; scientists are unable to explain how so many useful protein complexes (often called "molecular machines") are able to form; and since DNA is not a specification for making a human, or any organ, cell or organelle, scientists lack any credible explanation for the nine-month progression from a speck-sized zygote to an adult human. For a long discussion of some of these huge mysteries that physics, chemistry and biology have gigantically failed to solve, read my post "Problems a Hundred Miles Over Our Heads" here, and also read my posts here and here. 

No one can understand how badly scientists have failed to explain organismic agency unless he makes a deep study of topics such as brain physical shortfalls, a topic Ball never seems to have studied. No one can understand how vast is the explanatory gap involving component agency and morphogenetic agency unless he makes a thorough study of the endless stupendous marvels of purposeful construction that occur during human development and also every day in the human body. No one can be properly informed about the topic of biological agency if a writer discussing that topic is failing to discuss the marvels of organization occurring on so many different levels within the human body. But Ball makes little or no mention of such a reality. Guys like him almost always do a very bad job of explaining the vast levels of organization and dynamism within the bodies of organisms such as humans, just as they do a very bad job of explaining the extent of human mental powers and human mental capabilities. The reason is that the better such things are explained, the less likely you will be to believe in hand-waving vacuous sound bites such as Ball's claim that there are  "decision-making circuits in the brain." 

Below are some relevant quotations by scientists:

•   Scientists Walker and Davies state this in a scientific paper: "DNA is not a blueprint for an organism; no information is actively processed by DNA alone...DNA is a passive repository for transcription of stored data into RNA, some (but by no means all) of which goes on to be translated into proteins."
• Geneticist Adam Rutherford states that "DNA is not a blueprint," a statement also made by biochemistry professor Keith Fox. 
• "The genome is not a blueprint," says Kevin Mitchell, a geneticist and neuroscientist at Trinity College Dublin, noting "it doesn't encode some specific outcome."
• "DNA cannot be seen as the 'blueprint' for life," says Antony Jose, associate professor of cell biology and molecular genetics at the University of Maryland, who says, "It is at best an overlapping and potentially scrambled list of ingredients that is used differently by different cells at different times."  
• "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.
• "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). 
• "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." -- Two scientists, "On a generalized Levinthal's paradox," 2018. 
• "How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive tools to predict the final native structure of proteins, we still lack a predictive framework for how [amino acid] sequences dictate folding pathways....Almost seven decades of experimental and theoretical inquiry have not revealed a 'folding code' at the amino acid level, i.e., rules endowed with the generality and predictive power required to connect amino acid sequence to how the protein attains its structure....Machine learning made it possible to identify weak correlations to generate the structure most likely to correspond to a sequence. This tour-de-force effort has largely solved the problem of predicting protein structure from sequence...but with a key limitation: the algorithm that predicts the structure is a complex black box of pattern recognition that casts little light on the process of folding and that tells us nothing about why only some sequences fold, or how physics and evolution are coupled." -- Five scientists in the year 2025 (link). 
• "The real challenge—that remains unanswered after more than 50 years of research in the structural biology field—is understanding the mechanisms that lead proteins to fold into their native state. The reason for these difficulties is that the central question of the protein folding problem remains unresolved: specifically, how a sequence of amino acids encodes its folding pathways." -- Scientist Jorge A. Vila, 2025 (link). 
• "Yet while these are several examples of well-understood processes, our study of animal morphogenesis is really in its infancy." -- David Bilder and Saori L. Haigo1, "Expanding the Morphogenetic Repertoire: Perspectives from the Drosophila Egg." 
• "Fundamentally, we have a poor understanding of how any internal organ forms." -- Timothy Saunders, developmental biologist (link).
• "An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place -- development -- is only understood in the roughest of outlines." -- Five scientists (link). 
• "Our understanding of how our organs form is still in its infancy" -- A research project abstract written by scientists (link). 
• "Biochemistry cannot provide the spatial information needed to explain morphogenesis...Supracellular morphogenesis is mysterious...Nobody seems to understand the origin of biological and cellular order."  -- Six medical authorities (link).  "
• "Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how these individual actions coordinate over a macroscopic number of cells to grow complex structures with exquisite functionality is unknown." - Five scientists (link). 
• "However, our understanding of the molecular and physical basis of morphogenesis in plants or in any other eukaryotic system [e.g. mammals] is still in its infancy due to the complexity and non-linearity of processes involved in morphogenesis dynamics (or Morphodynamics)." -- A description of a 2017-2021 scientific project, presumably written by scientists (link). 
• "Understanding morphogenesis in vertebrate tissues in development and disease poses one of the most significant challenges in the life sciences. Despite the impressive technical advances aimed at cellular and subcellular characterization and manipulation over the past half century, a clear picture of how form is created still remains in its infancy." -- Four scientists in 2025 (link). 
• "We don't know what dark matter is, we don't understand how the brain works or consciousness, we don't understand morphogenesis, we don't understand the origin of life." -- Physics PhD Michael Nielsen (link).