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Question: is this music? Are the above symbols on a piece of paper music? What do you think? My answer: of course not! It is encoded information. Only a specially trained person is able to read and translate that information into sounds with the help of specially designed devices. On their own, these ink stains are not music.
Question: do the symbols on a piece of paper cause music? Are they the cause of music? My answer: of course not! The ink dots on a piece of paper are not the cause of the sounds we call music. Those symbols are dead and meaningless ink stains in themselves. One needs a person with specific knowledge of how to read and translate the symbols on paper. Furthermore, that person needs a special designed instrument. Do the hands cause the music? Or does the instrument cause the music? Or our ears? Or our brains? It is impossible to point to one cause. It is everything together. It is clear that here we have a chain of causal factors.
DNA centrism
"The basic principle is that if genes were abundantly available in the primordial pond, they could have randomly assembled to form various genomes, each capable of forming an organism." [1]
This is the most concise and extreme expression of DNA-centrism I know of. It is almost a definition of DNA-centrism in the context of the Origin of Life. The statement claims that life started with DNA. All you need is DNA and the organism will develop from it. On the other hand, in biology DNA-centrism means: DNA creates the organism. DNA is the cause of the organism. DNA controls every biological function in the organism. DNA-centrism in the context of Mendelian genetics is almost by definition gene-centrism because Mendelian genetics is not interested in the molecular details of how a gene affects the phenotype of the organism. For Mendelian genetics, the inner workings of an organism are a black box.
Now, let us ask the same questions about DNA as we did above about the musical notes on a piece of paper: does DNA cause an organism to develop, grow, breath and live? Of course not! Try it yourself: place a complete genome in a physiological saline solution in a Petri dish at 37°C and wait. Nothing will happen! But why? Because this is an unnatural environment? But if DNA has the power to create an organism, why does DNA do that? Apparently, DNA hasn't the power to create an organism. Apparently, the genome has to be in a cell and needs all the machinery to read and translate the information in the genome. Conclusion: it only seems that DNA is the cause of an organism because it is always in the right environment. We always assume the right environment.
Compare this with the musical notes on paper: we are used to associating musical notes on paper with the sounds of music. Change a note (mutation) and the music changes (phenotype). But the musical notes on paper define, but do not create music. The right environment is required to create music [2]. We need a change of perspective to see this.
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Duck-Rabbit illusion (wikipedia) Does DNA control the cell, or does the cell control DNA? |
We need a change of perspective because we have become the victims of the illusion that DNA itself controls everything. We forget that the cell controls the expression of genes. My eyes were opened at the moment that I realized that our DNA is a parasite in the same manner as a virus is a parasite. A virus is completely dependent on its host for its replication. A DNA genome is completely dependent on its host cell for its replication. DNA is replicated by the cell. DNA does not replicate itself. The cell delivers the resources for replication. The only difference with the virus is that 'our' DNA usually is for the benefit of the individual in which it is housed, whereas the virus DNA is detrimental to its host. But that does not give DNA special powers. In the Duck-Rabbit illustration above, the duck is DNA-centrism and the rabbit is cell-centrism. It is difficult to change perspective. It is even more difficult to see both perspectives at the same time. Since the birth of genetics, scientists always saw the duck (DNA controls the organism). Now it is time to see the rabbit. And when we have succeeded, we should try to see both. That takes some effort. But it is worth it because a scientific theory should not depend on one perspective.
But what about genetic diseases?
Genetic disease seem to be a very strong argument against my position and for DNA-centrism. What is the cause of Cystic Fibrosis? The answer: Cystic Fibrosisis is caused by a mutation in the CFTR gene. What is the cause of Huntington's Disease? Answer: HD is caused by a mutation in the Huntingtin gene. What is the cause of Duchenne Muscular Dystrophy? DMD is caused by a mutation of the dystrophin gene. What is the cause of Sickle cell disease? Sickle cell disease is caused by a mutation in the HBB gene. A clear case for DNA-centrism?
No. On closer inspection, it appears that genetic diseases are an argument against DNA-centrism. This is because all cells in our body have the same genome. If the fertilized egg (zygote) has a mutation, all cells in our body necessarily have that mutation. Yet, genetic diseases tend to affect specific organs in our body: blood, brain, muscles, heart, lungs, intestines, eyes, ears, etc. How could that be if all cells harbour exactly the same genome? Answer: it is the difference in expression of genes. Do genes express themselves? Of course not. Factors outside DNA trigger gene expression. Additionally, genetic diseases often start at different ages. For example, symptoms of Huntington's Disease typically appear in middle-aged people. How could that be? The genome doesn't change with age. Again: gene expression changes with age, not the gene itself. This is an argument against DNA-centrism because these examples show that DNA is passive, and factors outside DNA cause gene expression in specific organs at specific times. To understand this correctly, the whole cell should be in the centre ('cell-centric view of life').
Origin of Life
The DNA-centric view of life spectacularly fails in the context of the Origin of Life. That's a hint that should make us think again. Life didn't and couldn't start with DNA. That is because DNA is a dead and meaningless molecule. It has no activity on its own. That is the famous vicious circle: the enzymes that transcribe and translate DNA must be present before those very enzymes can be produced.
Another powerful reason why DNA-centrism is wrong is that DNA is only one of the three components that constitute life:
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| Tibor Gánti model of life [3] |
- chemical motor system: metabolism that produces the energy to run and maintain the organism
- chemical boundary system: cell membrane that separates the inside from the outside of the cell
- chemical information system: the hereditary material (DNA)
Not one of the subsystems is dominant, all three determine the living organism. One subsystem is a chemical system and nothing more.
This blog is an attempt to summarize my position, not a review of the literature. My position does not downplay the importance of DNA [4], I emphasize the passive role of DNA. This does not contradict any facts. However, my position appears non-mainstream due to sloppy language use in the scientific literature [5].
Acknowledgements
Susan checked my English. Thanks!
Notes
- Periannan Senapathy (1994) 'Independent Birth of Organisms. A New Theory That Distinct Organisms Arose Independently From The Primordial Pond Showing That Evolutionary Theories Are Fundamentally Incorrect'. Introduction page 5.
- Don't push the analogy with musical notation too far! Music is an event with a clear beginning and an end in time. It is produced by starting to read and translate the first note on paper, and to continue until the last note and stops there. Music or a book have a beginning and an end. This is not the way an organism is produced from a DNA genome. The genome has no beginning and end. There is no 'first' gene to start with in order to produce an organism. Secondly, the sheet music doesn't include instructions to build a musical instrument. On the other hand, there is a useful similarity here: musical notation on paper is a handy way to store and copy 'music'. Just like DNA.
- Tibor Gánti (2003) The Principles of Life. (my review)
- Philip Ball (2024) downgrades DNA to an extreme degree. For example, he relegates the 1962 Nobel Prize for DNA to a footnote. A blunder. (see my blogpost). In that blog post, I have already made many of the same points I make in this post.
- For example: "Central to this are enhancers and promoters, DNA sequences that dictate the location, timing, and intensity of gene expression." in A tighter grip on gene expression, Science 3 Jul 2025. Note: "dictate", "timing". Especially, 'timing' is mysterious. How do DNA sequences dictate timing? I asked the author. No reply. I think this is a sloppy language caused by a DNA-centric view. [ 11-11-25 ]
Thanks Gert for your interesting blog about cell centrism.
ReplyDeleteTalking about the music made by an orchestra you say: It is impossible to point to one cause. It is everything together. It is clear that here we have a chain of causal factors.
This illustrates (in my view) the strength of your argument. You cannot point at one part of the system (playing music) as THE causal factor. But talking about a "chain of causal factors" indicates also the main weakness of your view. The process of playing music, the functioning of a living cell is not "a chain" but "a network of causal factors". And of course this network has inputs and outputs.
But the network concept is essential, indicating that all components need each other to get a well-functioning system. It also clarifies the circularity: later in the blog you talk about "the famous vicious circle".
And cell centrism is not new, see my book (De kosmos en het leven, een Meesterwerk, p. 35) for my view. And think of the book of Franklin Harold (2014), giving a passionate plea for a cell centered view, p. 27. ‘I am but one of a cohort of skeptics who suspect that the gene-centered view of life is incomplete and fundamentally misleading; and in the following section we shall spell out the deficiencies and ask what should take its place.’
Excellent! You must know the book by Dennis Noble I guess, he uses the very same music metaphore as the title of his book. The suggestion DNA should be considered as parasite amounts to a game changer, though estimates of the percentages of dna that are of viral origine, still vary a lot: the jury still seems to be out- as far as I know.
ReplyDeleteRolie, thanks for your helpful comment. Yes, I did use the phrase "chain of causal factors", but I didn't want to exclude networks. That was not my intention. You have understood what I wanted with the metaphor. However, for me, networks are conceptually harder to work with because they are extremely complicated. I don't have an easy-to-understand and easy-to-work-with metaphor for networks. For me, the music metaphor works well.
ReplyDeleteYou wrote, "cell centrism is not new". Yes, it is in your book. And I did buy the eBook Franklin Harold (2014) 'In search of cell history', and added the book to my Introduction page with some useful quotes.
Thanks [Anonymus] for your nice comment. Yes, I know Dennis Noble 'The Music of Life', but I think he uses the music metaphor in a different way and for a different purpose. He is rather extreme anti-DNA. But we can't deny the importance of DNA and genes and genomes in evolution because that's the main thing that is transmitted to the next generation, and evolution is all about transmitting genes to the next generation. I can't say the same for proteins, and networks. What is in an egg or sperm cell?!
ReplyDeleteYou wrote "The suggestion DNA should be considered as parasite ...". I did not want to imply that all (or most of) of our genes are of viral origin, but that our DNA and DNA in general is passive. DNA has not the power to replicate itself, it depends on the resources (building blocks, energy, enzymes) of the host cell. Just like a virus depends on the host. It is about the behavior, the capacities of DNA. It does not matter that it is 'our DNA'. DNA is a passive molecule. Indeed, that is also a change of perspective!
The viral origin of our dna is a major issue, think ‘ descent with modification’ or take f.e. the origin/evolution of the placenta.
ReplyDeleteGert you wrote: “DNA has not the power to replicate itself, it depends on the resources (building blocks, energy, enzymes) of the host cell. Just like a virus depends on the host. It is about the behavior, the capacities of DNA. It does not matter that it is 'our DNA'. DNA is a passive molecule. Indeed, that is also a change of perspective!”
ReplyDeleteThis text nicely illustrates why the parasite-metaphor is incorrect in y eyes. Indeed DNA on its own is a passive molecule just like the DNA or RNA of viruses. But there is a crucial difference: viruses don’t make any contribution to the cellular machinery that makes DNA work in the production of all kind of biomolecules. While many, if not all, cellular processes depend on DNA information. Therefore cellular DNA cannot be ascribed as parasitic.
And all these interdependent cellular processes illustrate what I meant by the concept of networks. DNA is nothing but a passive molecule without the cooperation with many cellular processes, but at the same time these processes would not occur without proper DNA instructions.
Using the music metaphor DNA has a leading role just like the partiture. Of course you need the orchestra and all the instruments, etcetera but the partiture mainly defines what kind of music you get. So does DNA, it partly or mainly defines what kind of organism you get. Not fully, because of epigenetics, chemical and physical self-organization etc. Especially epigenetics may be compared to the interpretation of the partiture by the director.
You see, Gert, I like the music metaphor.
Rolie, I agree, the music metaphor is to a large extent useful. However, I maintain that DNA is to a large extent parasitic: 1) 90% of your genome is junk, useless ballast. 2) most mutations are deleterious, not good for you! 3) some mutations are strongly correlated with cancer. Evidently not good for you! In all 3 cases DNA doesn't care! DNA is blind.
ReplyDeleteGert, what you say about mutations is right, but aren't mutations and gene duplications one of the fundamental pillars of Darwinism?
ReplyDeleteAnd it is not a surprise that DNA "doesn't care" or "DNA is blind". You apply human categories to molecules and so on. DNA is just as blind as electrons are, or as gravity is. They operate according to fundamental rules which we call laws of nature.
And I won't restart our former discussion about junk DNA.
Fact is that the DNA-strings of our cells contain indispensable information for our bodies and lives. Calling that parasitic is not justified. And it might bring you back to gene centrism and to the selfish genes of Dawkins. But may be you restrict the lable "paracitic" to what you call junk DNA. But as you discussed in your previous blog: random DNA can be the source of ORFs and therefore the source of new genes - not by duplication but de novo.
Rolie, thanks for your comment. I agree on most of your comment. You wrote "Fact is that the DNA-strings of our cells contain indispensable information for our bodies and lives. Calling that parasitic is not justified."
ReplyDeleteYes, DNA contains useful, even indispensable information for the survival of the cell or the organism. Absolutely! On the other hand DNA-on-its-own is useless, good for nothing, a meaningless dead molecule. The reason: DNA itself has no resources: no energy, no building blocks, it can't replicate, transcribe, translate itself. DNA cannot produce proteins on-its-own. DNA is useful only *in* a living cell and useful *for* a living cell.
Now, I do understand if you object to the description 'parasitic' for this situation. But please, do you at least agree that every DNA genome in the living world is a passive entity. It is not active, it can't do anything.
Why is this so important? It is important to accept this because (1) it is true, (2) the Origin of Live! DNA can never be the start of something! DNA cannot be the start of life! The properties of DNA didn't change since the Origin of Life. Since the origin of DNA until today, DNA is still the same passive molecule! Remember what biochemist Nick Lane has said again and again: "genes did not invent metabolism, but the reverse."
Gert, just to be sure: of course DNA cannot function outside the cell. But isn't that the case for many cellular components? Anyway, all particles, atoms and molecules exercise there potentiality just in relationship to other things.
DeleteThat's why I emphasized the network concept. All you need is interaction. To be left alone makes no sense in the universe, not for electrons, not for DNA, not for human beings.
So being a passive molecule doesn't make DNA a kind of parasite.
And yes, I agree that the origin of life cannot start with one kind of molecule like DNA. In my view life began with some sort of chemical network, a network with feedback loops.
note on 'passive' viral dna, a quick update:
ReplyDelete1. https://www.nature.com/articles/d41586-025-03203-4#:~:text=Research%20suggests%20that%20ancient%20viral,of%20their%20activity%20is%20limited. to wit: our knowledge of their activity is limited.
2. Science Advances DOI: 10.1126/sciadv.ads9164
3. Cell. DOI: 10.1016/j.cell.2024.12.013
Hi [Anonymous], thanks for your references:
ReplyDeleteAncient viral DNA helps human embryos develop
https://www.nature.com/articles/d41586-025-02970-4
A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage
https://www.science.org/doi/10.1126/sciadv.ads9164
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development
https://pubmed.ncbi.nlm.nih.gov/39837330/
Rolie, thanks for your comments, it made me thinking!
ReplyDeleteRolie wrote: "Anyway, all particles, atoms and molecules exercise there potentiality just in relationship to other things."
Yes, physical objects consist of interacting particles I suppose, but (1) they are dead!!! (2) they do not have heredity! The property of heredity (DNA) is the prime distinguishing property of living things.
Rolie: "That's why I emphasized the network concept. All you need is interaction".
You mean Stuart Kauffman autocatalytic networks?
but what is the difference between dead and living objects?
Life works with only very specific molecules, not any atom and molecule will do. It took billions of years to evolve single cells, and multicellular life, and again for eukaryotes.
If "All you need is interaction" then intelligent apes could have evolved a billion years earlier. Why did humans not develop from the first cell?
Rolie: "So being a passive molecule doesn't make DNA a kind of parasite."
You have an emotional attitude against the word 'parasite". I use the word in a descriptive way.
Parasite dna, aka ‘junk’, aka viral dna: see refs
ReplyDelete......and aka transposons
ReplyDeleteGert and anonymous, it seems we don't understand each other.
ReplyDeleteWith my reference to electrons etc. I hoped to illuminate my point - without success.
In short what I wanted to say:
1. From the fact that DNA on its own is "dead" you cannot conclude that it is parasitic. Every biomolecule would be parasitic if that was right.
2. From the fact that viral RNA is included in eukaryotic DNA you cannot conclude that the (e.g. human) DNA would be parasitic.
And, my thinking about parasites starts with this definition:
A biological parasite is an organism that lives at the expense of a host, from which it obtains food and shelter.
Does DNA live at the expense of the cell? Or is it an indispensable part of it?
Rolie: all the refs i mentioned in my quick update show that you cant dismiss dna, let alone dna of viral origin as ‘parasitic’, or junk or what metaphore you’d prefer
ReplyDeleteHi anonymous, I have no doubts that parts of our DNA are of parasitic origin. Some of them even have been "transformed" into functional genes.
ReplyDeleteBut a parasitic origin doesn't mean that the (whole) DNA is a parasitic. According to the above given definition that is wrong.
May be endosymbiose theory can be helpfull. This theory posits that organelles such as mitochondria and chloroplasts were once free-living bacteria that invaded larger cells and became an indespensible part of those larger cells. As far as I can see, those invasions are comparable to parasitic actions of a virus. But we don't call mitochondria parasites, isn't it?
Rolie, thanks for the excellent endosymbiosis example.
ReplyDeleteIn a sense, a genome has a symbiotic relationship with the rest of the cell because it stores the specification of all the proteins which in turn keep the whole cell up and running... but this kind of symbiosis or cooperation can sometimes go wrong...
Roli: right! Endosymbiosis might be the apt term, given the role of viral dna in the origin/evolution of the placenta- or in transposons, for that matter.
ReplyDeleteGert and Anonymous, nice to see that we agree. So our conclusion might be: a virus or bacteria invades a cell for its own benefit, but finally the invader becomes a cooperator with an important function for the benefit of the host (and therefore itself).
ReplyDeleteWould that be an indication that cooperation is an important factor in evolution, together with competition?