The DNA delusion

The Library of Atlantis
July 6th, 2023  

The DNA delusion is the idea that a string of nucleic acids is responsible for almost all inherited features of an organism and moreover, that this is an established scientific theory supported by experimental evidence. Nothing like this is remotely true and the confusion arises from the conflation of two related but nevertheless different hypotheses.

The historical roots of the problem lie in the fact that there are two separate ‘theories’ of inherited characteristics which both use words such as ‘gene’ ‘, ‘genome’, ‘genotype’ and ‘phenotype’. Sometimes the words mean the same thing and at other times they have different meanings, thus allowing conflation of two separate conceptual frameworks and enabling discussions of the two as if they form a single coherent and proven theory.

 

William Johannsen (1957-1927) coined the terms phenotype and genotype in 1909 and referred to a gene as that ‘something’ which was responsible for inherited characteristics. No biological mechanism was identified, a gene was simply some repository of information that would find its ‘expression’ in the formation of a new organism looking fairly similar to its parents.

“No hypothesis about the nature of this ‘something’ should be postulated or supported by it .. The word ‘gene’ is completely free of any hypothesis ; it expresses only the established fact that in any case many traits of the organism are determined by specific, separable, and thus independent conditions.” – Wikipedia

Johann Friedrich Miescher (1844-1895) had discovered DNA in 1869 but after Crick and Watson characterised it as a double helix in 1953, scientists began to speculate that this could be something to do with inheritance and evolution.
DNA became, without any evidence, to be described as the ‘Book of Life’ or a ‘Blueprint for life’.

In their excitement, scientists began to describe segments of DNA now as ‘genes’ and to explain that the way that proteins were created from DNA as ‘expression’.

“Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, and ultimately affect a phenotype.” – Wikipedia

The problem here is that DNA sequences are described at best as ‘data’ as they don’t become ‘information’ until they are interpreted as having ‘meaning’. The interpretation process happens outside of the DNA strand itself, seems to be at liberty as to which portions of the DNA it chooses or discards and is even free to interpret the same piece of DNA in different ways depending upon many factors which are again outside of the DNA molecule itself.

The concept of information is somewhat abstract. You cannot see information and so the characterisation of DNA base pairs as ‘information’ is very much a matter of interpretation itself and rather prejudices the reader in favour of the thesis that is being put forward.

Since genes are ‘expressed’ differently according to context, one valid interpretation of this is that the DNA code of a gene is just ‘nonsense (just a sequence of CGAT bases) until it is interpreted functionally‘ – Denis Noble

 

 

Denis Noble (1936-) “Many of the problems with the Modern Synthesis in accommodating the new experimental findings have their origin in neo-Darwinist forms of representation rather than in experimental biology itself“
“The concepts therefore form a biased interpretive veneer that can hide those discoveries in a web of interpretation.“

In his paper “Evolution beyond neo-Darwinism: a new conceptual framework” Noble regards the problems neo-Darwinism as essentially un-fixable as the whole theory has become experimentally unfalsifiable and “All parts of the neo-Darwinist forms of representation encourage the use and acceptance of the other parts.” So any part of the theory really depends on the other parts and no single part has been or could be proved independently of the others.

“Neo-Darwinism is a gene-centred theory of evolution. Yet, its central notion, the ‘gene’, is an unstable concept. Surprising as it may seem, there is no single agreed definition of ‘gene’. Even more seriously, the different definitions have incompatible consequences for the theory..” – Noble

“Of course, no-one now thinks that there is a simple 1:1 relation (between genes and traits) , but the language of direct causation has been retained” – Noble

“In fact, it can be shown that, in the case of some of the central concepts of ‘selfish genes’ or ‘genetic program’, no biological experiment could possibly distinguish even between completely opposite conceptual interpretations of the same experimental findings” – Noble

 

Calico cats. It is claimed by some sources that every cell of the body contains the same DNA and that this DNA is responsible for determination of the entire phenotype. In the case of calico cats however this cannot be the case as we can see three different colours of fur ‘determined’ by the same genes.

The explanation given is that the DNA somehow contains sufficient information to create all three colours but that other developmental and ‘epigenetic’ factors are responsible for the geographic distribution of the colours. To put it more clearly, DNA is not the determinant of the coat pattern.

Similar considerations apply to eye colour: Heterochromia

 

 

XX/XY chromosomes. There is a strong statistical correlation between say XY karyotype and a male phenotype but correlation is not causality. In the paper by DelaChapelle a patient with XX chromosomes had a male phenotype, could function sexually and could produce sperm. The sperm were not viable and he had some feminisation of body shape.

In this case then something has ‘gone wrong’ with development and this is reflected in the karyotype. What we can say however is that most the information required to create a male human being is not dependent upon a Y chromosome. So where is this information held or how is it generated?

“Human ‘XX males’ are sterile males whose chromosomes seem to be those of a normal female.” – Page et al. (If the end result is a male then what is it about the chromosome that is particularly ‘female’?)

 

Control of sex development
“Most of the knowledge on the factors involved in sexual development came from animal models and from studies of cases in whom the genetic or the gonadal sex does not match the phenotypical sex.” – Anna Biason-Lauber

Sexual development is in two stages:

1. Sexual determination – gonad development at 3 weeks
2. Sexual differentiation – phenotypical development influenced by hormones from the gonads

“Generally speaking, factors influencing sex determination are transcriptional regulators, whereas factors important for sex differentiation are secreted hormones and their receptors.”

Interesting that there is actually no mention of genes, chromosomes or DNA in this sentence. It is observed that women who take testosterone do in fact develop masculinised features but nobody believes that testosterone contains sufficient information to create a male phenotype so it must be the case that both phenotypes are possible regardless of karyotype. Chromosomes are therefore responsible for neither sex determination nor differentiation.

From the paper we find also that a female phenotype can arise from XY chromosomes: “Patients present with normal female external genitalia, streak gonads, and XY karyotype“

DNA damage can result from both normal metabolic activities and environmental factors resulting in tens of thousands of individual lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can give rise to mutation and altered gene expression. Wikpedia

To rephrase: “Human DNA is continually changing“.

In fact identical twins have different DNA by the time they are born and they will continue to diverge throughout life. Each of us has potentially different DNA in each cell of our body. (Stefan Lanka)

The characterisation of altered DNA as ‘damage’ suggests that there is a semi-stable ‘known’ sequence of DNA that has been altered and that can therefore be ‘repaired’. But if DNA is the definitive repository of genetic information then how can this be so? Where is the backup data kept?

Organisms are very good at buffering themselves against genomic change.” – Noble.
In other words, we maintain our structural integrity somewhat independently of the content of our DNA.

So how do DNA forensics work?
We can infer from watching CSI that some part of the changing genome is stable enough to represent a single individual after being extracted from dried up blood. This sequence is sufficiently different from other people for identification but similar enough to family members to recognise them as such. Amazing.

“The forensic laboratory has no control over the amount of evidence left at a crime scene or the insults to which the biologic material may have been subjected. The analysis performed therefore must be validated carefully and documented extensively before use. Also, the interpretation will often be scrutinized more
stringently than routine clinical testing.” – Weedn

A Human chimera is someone with a distinct subset of cells that have a different genotype from the rest of the body. (Wikipedia) .So a female for example can incorporate cells from a male twin and live quite happily without realising it – until they get a DNA test that is..

• The Dutch sprinter Foekje Dillema was expelled from the 1950 national team after she refused a mandatory sex test in July 1950; later investigations revealed a Y-chromosome in her body cells, and the analysis showed that she was probably a 46,XX/46,XY mosaic female.
• In 1953, a human chimera was reported in the British Medical Journal. A woman was found to have blood containing two different blood types. Apparently this resulted from her twin brother’s cells living in her body. A 1996 study found that such blood group chimerism is not rare.
• In 2002, Lydia Fairchild was denied public assistance in Washington state when DNA evidence appeared to show that she was not the mother of her own children. A lawyer for the prosecution heard of a human chimera in New England, Karen Keegan, and suggested the possibility to the defence, who were able to show that Fairchild, too, was a chimera with two sets of DNA, and that one of those sets could have been the mother of the children.
• In 2002, an article in the New England Journal of Medicine described a woman in whom tetragametic chimerism was unexpectedly identified after she underwent preparations for kidney transplant. The transplant required the patient and her immediate family to undergo histocompatibility testing, the result of which suggested that she was not the biological mother of two of her three children.
• The DNA content of semen from an assault case in 2004 matched that of a man who had been in prison at the time of the assault, but who had been a bone marrow donor for his brother, who was later determined to have committed the crime.
• In 2008, a man was killed in a traffic accident that occurred in Seoul, South Korea. In order to identify him, his DNA was analyzed. Results revealed that the DNA of his blood, along with some of his organs, appeared to show that he was female. It was later determined that he had received a bone marrow transplant from his daughter.
• Another instance of treatment-related human chimerism was published in 1998, where a male human had some partially developed female organs due to chimerism. He had been conceived by in-vitro fertilization. (Note the assumption here that the female development was caused by the XX chromosomes in contrast to the sprinter who had plenty of XY chromosomes but still retained a female body type.)   

Evolution is said to be via random mutations of DNA and ruthless natural selection of the resulting (inherited) traits.

However, the thing that is selected for is essentially phenotype and this does not now appear to be very closely coupled to genotype, with transcription, translation and other epigenetic factors being equally or even more important. For Darwinian selection to work then, what is now needed is for these factors to be inherited somehow. We need transcriptional mechanisms to be somehow encoded in a stable form and to be passed down the generations – but DNA is assumed to be the genetic material.

Or as Denis Noble has put it: If we don’t have a model connecting genotype to phenotype then we don’t actually have a theory of evolution.

 

Mae-Wan Ho and her husband Peter Saunders have written extensively about genetics and evolution, reaching similar conclusions to Denis Noble:
“Much of the problem is that neo-Darwinism appears completely invincible to falsification by observations and experiments, so much so that many doubt if it is a scientific theory at all” – Ho, Saunders

The page on the The fluid genome has the following highlights:

• Macroevolution of form and function is ‘decoupled’ from the microevolution of gene sequences; there is no simple mapping from gene to phenotype
• Useful genetic mutations are not produced at random. Instead the same non-random gene sequences are repeatedly produced by external stimuli.
• The intrinsic dynamic structure of the epigenetic system is the source of non-random variations
• Information flows from top down and from the cytoplasm to the genes – the opposite way to that of the Central Dogma
• Natural selection plays little or no role in evolution especially in the evolution of major novelties
• Epigenetic novelties are common to all individuals in a population – evolution happens to everybody at once and not to a few select individuals
• Fluidity of the genome means that environment and organism are inseparable. Hence no variant is random with respect to the environment
• Physical and chemical forces that generate biological patterns are independent of natural selection and require their own explanation
• Morphogenesis is probably due to electrodynamic forces not ‘hox’ genes

Telegony is a process by which traits from a previous mate can be passed on to children of later mates. In one experiment, female flies who had mated with oversized males were able to pass on that characteristic to offspring of subsequent partners. So inheritance here is decoupled from the physical presence of DNA. See: Telegony

 

Summary

The almost magical properties that have been attributed to DNA actually preceded the description of the molecule and many have not been verified experimentally.

The picture painted by school text books, TV dramas and celebrity scientists is a long way from reality and is not supported by researchers or academics.

It seems to be typical of many papers on genetics that you can simply cross out all the references to genes and no real information is lost. Scientists stick to the idea that DNA contains genetic information and that all that needs to happen is that the instructions are followed correctly to get a complete human. However, on reading their own papers the impression is created that DNA hardly matters at all.

DNA is not the determinant of phenotype.

“Therefore, nucleic acid cannot possibly contain our inheritance! Ideas such as epigenetics (the theory of flexible heredity) are only desperate attempts to somehow justify and keep alive the old model of a material heredity in the form of genes.” – Stefan Lanka

But if DNA is not the material substance of inheritance then we are left with two burning questions:

1. What is the mechanism of inheritance?
2. What is DNA for?

We don’t know how life began and we don’t know how humans evolved, how development takes place or even how order is maintained once we reach adulthood. We don’t know how traits are inherited, how they are encoded or in what substance they persist.

 

References:

Evolution beyond neo-Darwinism: a new conceptual framework – Denis Noble
https://journals.biologists.com/jeb/article/218/1/7/13568/Evolution-beyond-neo-Darwinism-a-new-conceptual

What is life? – Erwin Schrödinger 1944

“Meaning of Life & the Universe: Transforming” – Mae-Wan Ho
 ISBN-10. 981310886X ; ISBN-13. 978-9813108868

Ten Years of the Human Genome – Mae-Wan Ho
https://www.i-sis.org.uk/tenYearsOfTheHumanGenome.php

Beyond neo-Darwinism – an epigenetic approach to evolution
https://www.researchgate.net/publication/22628078_Beyond_neo-Darwinism-an_epigenetic_approach_to_evolution

A theory of biological relativity: no privileged level of causation – Denis Noble
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262309/

Molecular Biology of the Cell (5th ed.). New York: WH Freeman. p. 963.
Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J (2004). 

Differences between germline genomes of monozygotic twins – Hako Johnson et al
https://www.nature.com/articles/s41588-020-00755-1.epdf

DNA Testing in the Forensic Laboratory – Weedn, Rogers, Henry
https://www.researchgate.net/publication/296390391_DNA_Testing_in_the_Forensic_Laboratory

Control of sex development – Anna Biason-Lauber
https://www.zora.uzh.ch/id/eprint/34770/31/Best_practice_190110-1.pdf

XX Sex Chromosomes in a Human Male. First case. Acta Med. Scand. 1964, 175 (Suppl. 412), 25–28.
Authors: DelaChapelle, A.; Hortling, H.; Niemi, M.; Wennstroem, J.
https://onlinelibrary.wiley.com/doi/10.1111/j.0954-6820.1964.tb04630.x

Chromosome Y-specific DNA in Related Human XX Males
Authors: Page, D.C.; de la Chapelle, A.; Weissenbach, J.
https://www.nature.com/articles/315224a0

Disorders of Sex Development: Classification, Review, and Impact on Fertility
Authors: Pedro Acién, Maribel Acién
https://www.mdpi.com/2077-0383/9/11/3555#

Rethinking DNA: Examining the Evidence featuring Dr. Tom Cowan:

Source: https://library-of-atlantis.com/2023/07/06/the-dna-delusion/