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Our future, our universe, and other weighty topics

Saturday, January 19, 2019

The Myths and Mystery of Morphogenesis

For decades scientists and science writers have been pushing the false claim that DNA is some kind of blueprint or recipe for making an organism. But in the mainstream science magazine Nautilus a scientist has “fessed up” in great detail that this idea is bunk. The confession is in a long post entitled “It's the End of the Gene As We Know It,” by biologist Ken Richardson.

Richardson quotes physicist Erwin Schrodinger as saying this in 1943 about the chromosomes: that they “contain, in some kind of code-script, the entire pattern of the individual’s future development and of its functioning in the mature state.” In 1943 this idea was purely a speculation. But in a few years DNA was discovered, and some claimed that Schrodinger's idea had been confirmed. 

DNA does contain a code-script of a sort, and it uses a system called the genetic code in which chemicals in DNA (called nucleotide base pairs) stand for amino acids that make up proteins. But under such a system there is only a very limited capacity for specification. DNA (and the genes that make up DNA) can only specify the amino acids that make up proteins, and the contents of RNA molecules. When scientists discovered the genetic code used by DNA, they only discovered an extremely limited “poor man's language” completely incapable of specifying complex three-dimensional structures such as the layout of a human body or the structure of an eye or the layout of the human reproductive system. 

We can compare the genetic code used by DNA to a tiny little “sandwich language” in which the only words are the names of sandwich ingredients: words such as “bread,” “tomato,” "salami," “cheese,” and “ham.” With such a tiny little language, you can specify any number of sandwiches, but you can't specify something like the anatomy of an eye or the anatomy of a mammal. Similarly, with its “poor man's language,” DNA can specify the linear arrangement of amino acids in a protein, and the contents of RNA molecules, but that's about it.

Completely ignoring the inherent physical limitations of DNA, scientists and scientific writers have for seventy years been peddling what I call the Great DNA Myth. It is the myth that DNA (and the genes in it) are a blueprint or a recipe or a program for making an organism. Describing how this myth has been told, and suggesting a counter-trend, Richardson states the following:

In scientific, as well as popular descriptions today, genes 'act,' 'behave,' 'direct,' “control,' 'design,' 'influence,' have 'effects,' are “responsible for,' are 'selfish,' and so on, as if minds of their own with designs and intentions. But at the same time, a counter-narrative is building, not from the media but from inside science itself.”

Shortly after saying this Richardson states the following, negating the very claims that he has just assured us are so widespread:

"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."

Richardson is correct in what he has said about DNA, which cannot be a blueprint or a specification for the body plan of an organism. But he has left us with a glaring inconsistency between what he says “scientists now understand” and what he has previously stated that scientists are saying, making it sound as if scientists are feeding us bunk that is inconsistent with what they understand.

Richardson approvingly quotes biologist Denis Noble as saying, “DNA is not a cause in an active sense” and that DNA “is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires.” This is correct, and if we think of DNA as mainly a chemical ingredient list we will be getting on the right track. Ingredient lists don't cause things to be built, and don't contain either blueprints or recipes for making complex visible structures. A recipe always includes assembly instructions that go beyond an ingredient list. “Three eggs” is not a recipe for making a three-egg omelet.

Richardson tells us some things that contradict the “DNA is a blueprint” dogma. He tells us, “Increasingly, we are finding that, in complex evolved traits—like human minds—there is little prediction from DNA variation through development to individual differences.” Contradicting the idea that DNA specifies an organism, Richardson states the following:

"Conversely, it is now well known that a group of genetically identical individuals, reared in identical environments—as in pure-bred laboratory animals—do not become identical adults. Rather, they develop to exhibit the full range of bodily and functional variations found in normal, genetically-variable, groups. In a report in Science in 2013, Julia Fruend and colleagues observed this effect in differences in developing brain structures."

Richardson tries to make it sound as if the idea that DNA or genes are a blueprint or recipe for making a human is an idea that is mainly discredited by recent developments in the past few decades. Such a narrative is rather a half-truth. It is certainly true that some things that have occurred in the past few decades have strongly discredited the idea that DNA is a blueprint or recipe for making a human. Some of these things have been: (1) the complete failure of massive DNA analysis projects such as the Human Genome Project and the ENCODE project to find in DNA or genes any such thing as a blueprint or recipe for making a human or any organ of a human or even any cell of a human; (2) the discovery (to quote Richardson) that “there is no correlation between the complexity of living things and the number of genes they have,” and that organisms such as a simple rice plant have twice as many genes as humans.

But there is a reason why it is a half-truth to make it sound as if the idea that DNA or genes are a blueprint or recipe for making a human is an idea that is mainly discredited by recent developments in the past few decades. The reason is that extremely strong reasons for rejecting this idea have existed for about seventy years, since the time of the discovery of DNA. The first such reason is that the genetic code used by DNA only allows for proteins or RNA to be specified, and is completely insufficient for stating complex three dimensional structural information such as how to construct a human being. The second such reason is that there does not exist anything in the human body capable of interpreting such instructions if they happened to exist in DNA. Very complex instructions require a very complex instruction reader, and there is no such thing in the womb of a human body. If DNA happened to have the incredibly complex instructions needed to build a human, there would be nothing in a womb capable of reading instructions so complex and executing them.

So from the time DNA was discovered, there were the strongest reasons reasons for rejecting the whole “DNA is a blueprint for a human” idea. So why was such an idea taught so many times? It's because it was a pillar of Neo-Darwinism, the “modern synthesis” which attempts to explain the origin of biological innovations by saying they occurred entirely because of changes in genomes (that is, changes in DNA). When we have a proper idea, that DNA is merely a chemical database, the legs are pulled out from under the table of Neo-Darwinism. Richardson quotes biologist Denis Noble as saying this about Neo-Darwinism (which is also called “the modern synthesis”): “The modern synthesis has got causality in biology wrong.”

The full quote by Noble (from this interview) is as follows:

"I think that as a gene-centric view of evolution, the modern synthesis has got causality in biology wrong. Genes, after all, if they’re defined as DNA sequences, are purely passive. DNA on its own does absolutely nothing until activated by the rest of the system through transcription factors, markers of one kind or another, interactions with the proteins. So on its own, DNA is not a cause in an active sense. I think it is better described as a passive data base which is used by the organism to enable it to make the proteins that it requires."

Shockingly, in the same interview, this distinguished biologist refers to speciation (the origin of a new species), and says, "So I go along with the view that there has been no really clear proof that speciation occurred via gradual mutation followed by selection." Here we have an admission that the central dogma of modern Darwinism has "no really clear proof." Noble here mirrors what was stated in the book Evolution and Ecology: The Pace of Life by Cambridge University biology professor K. D. Bennett. Bennett says on page 175, "Natural selection has been shown to have occurred (for example, among populations of Darwin's finches), but there is no evidence that it accumulates over longer periods of time to produce speciation in the Darwinian sense." 

Once we correctly realize that DNA cannot be a specification for a human, and does not store a human body plan, the question that immediately comes to mind: where is it that the human body plan comes from? Richardson gives us some biological double-talk to try to explain this, but his explanation makes no sense at all.

Here is what Richardson says about the process of human development:

"Within hours, the fertilized egg becomes a ball of identical cells—all with the same genome, of course. But the cells are already talking to each other with storms of chemical signals. Through the statistical patterns within the storms, instructions are, again, created de novo. The cells, all with the same genes, multiply into hundreds of starkly different types, moving in a glorious ballet to find just the right places at the right times. That could not have been specified in the fixed linear strings of DNA. So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA."

Richardson is right that this miracle of organization cannot be explained by the "bad old myth" of a DNA blueprint that causes a baby to form form an egg (for DNA is not like a blueprint, and blueprints don't build things).  But Richardson is not credible at all in asserting that “there is no prior plan or blueprint” behind morphogenesis and embryonic development. Claiming that human beings arise from “statistical patterns” that create instructions “on the hoof” is a new myth no more credible than the old myth that babies appear from a fertilized ovum because the womb is reading a DNA blueprint. A much better thing to say is that there must be some human specification or body plan, and that we do not know where it exists, or how it is used so that a full-grown baby grows from a fertilized egg.

Inexplicable by any reductionist or "bottom-up" explanation, the development of a human body from a fertilized egg strongly suggests that there is some unfathomable "top-down" effect causing biological organisms to assume their forms -- some gigantic facet of reality beyond our ken.  As for the idea that  instructions created "on the hoof" (an expression meaning "without thought or preparation") might act "far more intelligently," that makes no sense whatsoever.  Instructions created "on the hoof" by mindless chemical units would be random nonsense, not something "far more intelligent."

A recent Science Daily article reveals that scientists have not actually observed any chemical or biological instructions giving rise to the tissues and organs in a body, contrary to what Richardson has insinuated. The article states, "As cells divide to form tissues and organs in multicell organisms, they move to where they belong, informed by a series of cues that scientists have yet to observe or fully understand."  Notice the phrase "have yet to observe" in that sentence. 

To try to explain his bad new myth of morphogenesis,  Richardson uses analogies which don't make any sense in the context of his account. He compares cells that billions of times move in just the right way at just the right time to a "glorious ballet."  But ballet dancers don't produce a glorious ballet like The Nutcracker by "talking to each other" during their dance, or free-wheeling it in some spontaneous "on the hoof" manner;  they follow the instructions of a choreographer who has planned out their dances. Richardson also suggests the analogy of an orchestra working without a conductor. That analogy does not fit his claims, as orchestras work from sheet music previously designed by a composer.  A symphony orchestra in which musicians are playing their instruments "on the hoof" would produce just noise, not an organized symphony. 

They aren't winging it

Trying to explain a hundred biological wonders like the extremely intricate functional anatomy and biochemistry of the eye by citing "statistical patterns" is rather amusing.  Evoking "statistical patterns" to explain something is the kind of empty bluff people use when they don't have an explanation for something, as illustrated in the conversation below.

Jim: Why did Trump win the 2016 election?
Dave: That was just statistical patterns.
Jim: And why did the stock market crash in 2008?
Dave: That was also just statistical patterns.
Jim: And how do such beautiful spiral galaxies form in space?
Dave: Once again, statistical patterns explain it.
Jim: And why do really bad wars start up a few times in a lifetime?
Dave: Again, it's just statistical patterns.
Jim: Why, Dave you're a genius! You can explain almost anything.

I may note that Richardson does a rather poor job of accounting for the lineage of his “DNA cannot be a blueprint or recipe” assertions. He rather makes it sound as if such a thing is a fairly recent development. But the transparent absurdity of claiming that DNA is a recipe or blueprint or program has long been pointed out by various critics of biological orthodoxy. The idea that DNA is not a blueprint or recipe or program for making a human, and cannot account for human development, was forcefully argued at length in my February 2016 post “The Gigantic Missing Link of Biological Life.” But a much earlier statement of the idea can be found in a 1987 paper by contrarian biologist Rupert Sheldrake, who stated 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. To see this more clearly, think of your arms and legs. The form of the arms and legs is different; it's obvious that they have a different shape from each other. Yet the chemicals in the arms and legs are identical. The muscles are the same, the nerve cells are the same, the skin cells are the same, and the DNA is the same in all the cells of the arms and legs. In fact, the DNA is the same in all the cells of the body. DNA alone cannot explain the difference in form; something else is necessary to explain form."

Sheldrake attempts to account for morphogenesis and embryonic development by speculating that there is a gigantic facet of reality overlooked by humans, something he calls morphic resonance.  He seems to imagine morphic resonance as some natural reality outside of a human body where the body plan is stored. That may or may not be the right explanation. But I think Sheldrake is on the right track in assuming that we can only account for the development of a human baby from a fertilized egg by postulating some gigantic additional reality beyond the human body to account for such an effect. 

When a child has learned how a human egg is fertilized through sexual intercourse,  people say that such a child has learned how babies originate. But the child has not actually learned such a thing.  For neither any children nor any adults can actually explain how babies originate in the sense of explaining how a fertilized egg is able to progress to become a baby.  

Nearly a century ago, the physician Gustave Geley stated that the facts of morphogenesis and embryonic development force upon us the idea that biological changes in an organism must come from some directing exterior force or "dynamism" outside of the body. He stated the following:

"In order to understand all these—the mystery of
specific form, embryonic and post-embryonic development,
the constitution and maintenance of the personality,
organic repair, and all the other general problems of
biology—it is necessary and sufficient to accept a notion,
which is certainly not new, but is placed in a new light,
the notion of a dynamism superior to the organism and
conditioning it....This is a concrete idea —that of a directing and centralizing dynamism, dominating both intrinsic and extrinsic contingencies, thchemical reactions of the organic medium, and the influences of the external environment."

Nothing we have learned in the many decades since these words were written makes the idea obsolete, and the concept still seems as necessary as when Geley suggested it, because chemistry within a developing body is utterly insufficient to explain the morphological progression of that body from an ovum to an adult. 

We take for granted the miracle of morphogenesis simply because we observe it happening invariably.  It's a rather a rule that anything that is observed invariably occurring will always be taken for granted, no matter how inexplicable or seemingly providential such a thing may be. Let us imagine a strange planet on which there are many volcanoes. But let us suppose that on this odd planet instead of volcanoes ejecting rocks and lava randomly all over the place, volcanoes only eject rocks and lava that conveniently form into habitable houses, some multi-storied.  On such a planet the scientists would probably regard such a thing as just being a "law of nature" rather than some wonderful blessing.  On that planet we might hear conversations like this:

Professor: So when volcanoes erupt, they shoot out lava and rocks that always conveniently form into habitable houses and buildings. We call this law of nature "the law of convenient volcanoes." 
Pupil: My father says that such a law is a sign of some purposeful intelligence working for our behalf. 
Professor: Superstitious nonsense! The "law of convenient volcanoes" is simply the way blind nature has always worked. No doubt such a law of nature prevails on all inhabited planets. 

Similarly, today's earthly scientists, who have no real explanation for how a human progresses from an ovum to an adult, typically assume that a similar wonder occurs on many other planets to produce full-grown extraterrestrial beings. 

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