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| Jonathan Wells: The Human Eye: Evolution’s Hardest Problem |
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| Jonathan Wells (Sep 19, 1942 – Sep 19, 2024) |
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| Richard Dawkins |
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| blueprint of a house |
The problem is that the blueprint is a two-dimensional ground plan with all the rooms, doors, windows, gas, water, electricity and so on. It is a kind of miniature house on paper, it is a final product. But DNA in a fertilized egg cell is not a miniature animal. The three-dimensional structure arises gradually during development. Every knowledgeable biologist rejects the blueprint metaphor for the workings of DNA. So does Dawkins. So far, so good.
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"DNA is a program or recipe for making a body." (2 min 36 sec) |
Immediately after rejecting the blueprint metaphor, Dawkins explains that DNA is a program or a recipe for making a body. Is that any better? This metaphor does not use an animal blueprint as the starting point. Instead, the body is gradually built by a genetic developmental program. The 'program metaphor' looks appropriate because a computer program as well as biological development are deterministic processes which follow a fixed sequence of steps and seem to have inbuilt goals [2].
The DNA-is-a-program metaphor is still wrong. Very wrong, indeed. Yes, metaphors can be wrong and misleading. Although there seem to be programs in animal and plant development, the program is not located in DNA. DNA is not a program. Where is the program? Scientists have sequenced thousands of genomes with high accuracy. They never found a program. I am serious. What did they find? They found thousands of protein coding genes which are interrupted with nonsense DNA (introns) located as small islands in large oceans of meaningless DNA. The protein coding genes are accompanied by a variable number of regulatory sequences (ON/OFF switches). Furthermore, the genes are arbitrarily distributed over a variable number of chromosomes (in humans: 46 chromosomes). There is no rhyme or reason to the order or distribution of the genes over chromosomes [3]. Genes are not located in the order in which they are executed. The genome is not logically and efficiently structured like a computer program. A computer program is a highly structured set of routines and subroutines, and does not contain superfluous code. On the other hand, the organization of animal and plant genomes is excessively complex [8] and balances on the edge of chaos. No human engineer would have designed such a mess [5]. DNA is not the place to look for a program.
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| "it's a fairly long chain of causation from DNA to embryology," (12:59 min in video) This is proof of his DNA-centric view of life! [9] |
The regulatory sequences are recognition sites for proteins [6]. They are sequences of A, T, C, G, just like protein coding sequences. They do not actively 'regulate' anything. They have to wait for proteins passing by. So, although their name 'regulatory sequences' suggests that they actively regulate gene expression, they are waiting to be read just like QR-codes:
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| QR codes are data |
A QR code is not a program. QR codes are data. QR codes must be read by specific software.
A genome is a very large collection of data, not a program. A genome is not even remotely like a computer program. An unstructured collection of protein-coding genes, RNA-coding genes and regulatory sequences and a lot of meaningless nonsense (also called a 'genome') does not constitute a program. I am serious [4]. This is not trivial. Unexpectedly, Dawkins' failed computer program metaphor delivers a new argument against gene-centrism! Thank You. DNA is not the control centre which controls the cell. Then, who is in control? Who or what decides which proteins are synthesized and when and how much? Something must be in control, otherwise it will end in chaos. One starts to realize that it must be the system as a whole: the cell. The needs of the cell determine which genes are switched on or off. Is the cell in rest, is it growing, or is it dividing? [7]. All this should be obvious by now. Why do biologists still talk as if DNA is the control centre? Bad metaphors lead to bad ideas. Scientists should eliminate bad theories. Have a nice day!
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| https://evolution.berkeley.edu/reviewing-dna/ [1] |
A short explanation of the above question:
I deliberately kept this post as short as possible, with just the necessary facts and arguments, in order to focus on the central question! Think about this! Once you see the inconsistency in the reasoning, you can't unsee it!
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| Richard Dawkins (1976) The Selfish Gene |
The Selfish Gene Theory in short:
"Thus Richard Dawkins introduces us to ourselves as we really are - throwaway survival machines for our immortal genes. Man is a gene machine: a robot vehicle, blindly programmed to preserve its selfish genes." (blurb from the publisher).
"The replicators which survived were the ones which built survival machines for themselves to live in." [1-4]
Clearly, this is a gene-centric theory of life and evolution. Bodies are temporary throw-away vehicles to replicate genes. Viewed in this way, there are several problems that are not at all, or not adequately addressed in either the popular press or by Dawkins himself.
I have 5 objections:
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| -1- |
The first objection to the selfish gene theory is that genes cannot act without the help of the cell, and in case of multicellular organisms cannot act without the help of the organism. The central dogma of systems biology reads: The cell reads the DNA code. The cell decides when and which genes to read. The organism ('vehicle' in Dawkins terminology) uses the genes in its genetic library to build itself. DNA itself does not contain a program for building an organism. DNA only contains the code for producing proteins. That's a huge difference. The cell uses the library of genes to look up the exact specification of a protein and synthesizes it. Enzymes transcribe, translate, replicate and repair DNA. The cell has all the resources (building blocks for DNA, machinery, energy) for the transcription, replication, translation and repair of DNA. The cell has the power and ultimate control. DNA 'self-replication' does not exist. The cell replicates DNA with the help of enzymes. That's not all. An even more shocking fact for the reputation of DNA: the cell manipulates DNA. Specific enzymes turn off/on genes by attaching a methyl group to the DNA base Cytosine (methylation) or removing a methyl group (demethylation). So, genes do not turn themselves on/off. It is clear by now: DNA on its own is totally helpless. DNA is a dead molecule. DNA never initiates anything. DNA never leaves the cell nucleus. How could DNA be a cause?
But enzymes are helpless too, in the sense that they are unable to replicate themselves. They need the specific information encoded in genes to get synthesized. So, genes and enzymes are interdependent. Their very existence depends on each other. It makes no sense to single out one component of a system as being 'selfish'. If there are selfish genes, one could as well say, there are selfish enzymes. Those enzymes, for example: DNA-replicases, helicases, primases and ligases, want to replicate DNA, because their own specification is encoded in that DNA. So, indirectly those enzymes ensure their existence in the next generation. If genes are immortal, so are enzymes. Again: it makes no sense to single out one component of a system as being 'selfish' or as being 'the cause', or as being 'immortal'.
(this paragraph has been improved Jan 31)
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| -2- |
The second objection starts with an uncontroversial observation: the earth is populated by complex bodies. If selfish genes want to maximize the number of copies in the next generation, and use bodies as temporary vehicles, why do we see highly complex vehicles instead of relatively simple single cells? (bacteria). Single cells leave more descendants in shorter time, so more copies of their genes are produced. A bacterium can multiply in 30 minutes. In contrast, large, complex bodies take longer to grow and leave fewer descendants. What a waste of time! For example, in the human species, the female is only about 20% of the year fertile; it takes 9 months to grow a baby; it takes about ten years for the newborn to reach sexual maturity, and the number of offspring is significantly smaller compared to mice, flies, bacteria. Why are there eukaryotes at all? The selfish gene theory should predict single cells (prokayotes) as the outcome of evolution.
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| -3- |
The third objection is: the existence of DNA-repair genes refutes the idea that genes are selfish. DNA-repair enzymes repair DNA replication errors. They repair errors in all genes, irrespective of what the genes 'do', if anything. They do not do what one would expect of 'selfish genes': selfishly and selectively repair errors in their own genes. Repair enzymes are blind with respect what the genes 'do'. Hence, DNA-repair genes behave altruistically. This is a new and profound objection to the selfish gene theory.
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| -5- |
The fifth objection: the selfish gene theory seems to predict selfish genes within genomes, not cooperative genes. It seems to predict a war of genes within a genome, since every gene wants to become the dominant gene. Yet, the 'selfish' genes of an organism are housed together with all other selfish genes in the same body (vehicle). In other words: they are all in the same boat! The problem is that genes housed in bodies can do nothing on their own. A single gene cannot build an organism. Even the most simple single-cell organisms need thousands of cooperating genes to build the 'vehicle'. The totality of all genes is called the genome. Only a complete genome can be the basis for building an organism. If one gene in a genome replicates significantly more than all the other genes in the same genome (a selfish gene), that could result in the death of the organism. Consequently, it would result in the death of that selfish gene and all the other genes. There is only one option for the 'selfish' genes to survive: cooperate! So, a genome necessarily is a community of cooperating genes. Paradoxically, in order to build their vehicle, those 'selfish' genes need to be altruistic towards all the other genes in the same vehicle. Remember this: The best cooperators build the best vehicles!
The Selfish Gene theory is an extreme form of gene-centrism. The book The Selfish Gene became a bestseller because it resonates with our perception of human nature. The book seems to explain the urge to survive, to have sex, and to have children of one's own. The story that genes make survival machines is intuitively easy to comprehend. But it is misleading. It is wrong. It is not what really happens in the cell. The truth is more complicated than that. Genes do not have the power to control anything. From the perspective of the organism, DNA is nothing more than a storage medium and a vehicle of inheritance. Organisms want to make identical or at least very similar copies of themselves. To make that possible they use DNA. It makes no sense to single out one component of a system as the most important, as Dawkins did. Maybe, in a sense we are programmed to reproduce, but that cannot be attributed solely to genes. If evolution is all about the replication of genes, then why complex bodies? Why sex? They are unnecessary to get genes copied. Bacteria do that much better and faster without complex bodies and sex.
22 Feb 2026
Strange things happen at female meiosis. In female animals, three of the four meiotic products are typically eliminated by extrusion into polar bodies, and only one cell develops to produce an ovum. Contrary to male meiosis, which produces 4 functional haploid spermatids. Does The Selfish Gene theory predict that 3 of the 4 meiosis products in females are discarded? Those 3 are not transmitted to the next generation, but contain a full haploid set of chromsomes. The Selfish Gene theory predicts that all genes (and alleles) maximize their transmission to the next generation. Concluding, the Selfish Gene theory predicts asexual reproduction, which is rare. Additionally, sexual reproduction is common, but the details of female sexual reproduction don't allow for a straightforward explanation by The Selfish Gene theory [6].
If that is not enough trouble, "around 30 percent of early pregnancies fail before the embryo implants in the body of the mother, with another 30 percent around that time." [5]. Apparently, reproductive output is not maximized!
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| Zwartkop. 25 Jan 2026 Sylvia atricapilla |
Overwinterende zwartkop (mannetje)
Overwintering Blackcap (male)
25 January 2026
Op 17 februari 2021 had ik een vrouwtje Zwartkop in de tuin! Zie dit blog. Op 8 februari 2021 weer een vrouwtje Zwartkop.
Er zijn vandaag 25 januari in Nederland 11 automatisch of handmatig goedgekeurde waarnemingen van zwartkoppen, waarvan 9 met foto's, waarvan 3 vrouwtjes en 3 mannetjes herkenbaar op foto. In totaal zijn er in Nederland in de maand januari 187 goedgekeurde waarnemingen van de zwartkop. De provincies Utrecht, Zuid- en Noord-Holland hadden de meeste waarnemingen; de 3 Noordelijke provincies hadden de minste.
Maandag 26 januari 09:27 hij zit er weer! op de drinkbak! Op 3 februari zag ik hem weer. De dagen er na eet hij ook van een appel.
Het is bijzonder dat zwartkoppen overwinteren, want het zijn, net als andere kleine zangvogels zoals tjiftjaf en fitis, insecteneters en trekvogels.
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The Music of Life. |
The amazing thing is that Noble's criticism doesn't contain controversial facts. His facts are all mainstream scientific facts. The facts are not the problem. It is just that the views about the precise role of DNA in organisms in mainstream science literature is an inaccurate description of what is really going on in a cell. Noble doesn't deny the importance of DNA. It is the routine mainstream science writing about DNA that is wrong. The way mainstream science writes about DNA is based on a bad habit that crept unnoticed into the literature after the discovery of the structure of DNA in 1953, and culminated in Richard Dawkins' The Selfish Gene in 1976.
The book The Music of Life is about systems biology. It is about putting together rather than taking apart, integration rather than reduction. DNA is important, but is not 'the control centre of the cell'. The genome is not a privileged level of causality in biological systems. The genome is on a 'lower' level than the cell. The cell or the organism is 'the system'. The genome is part of the cell, and the cell is part of the organism. The genome only functions within a system. Reducing the cell to its genome is reductionism. Reductionism as a method to discover the parts of a system is necessary and should not be replaced by anything else. The system level must be built on successful reduction.
According to Noble, DNA as a biological molecule does not do much. The real players are the proteins. DNA is in comparison rather passive. (How could a passive part control anything?). I think that Noble's statement:
'the cell reads the DNA code'
could be called 'the central dogma of systems biology or cell biology'. This statement must be printed in a bold, large font in every biology and evolution textbook. It is a perfect antidote to the DNA-centric worldview. Here, the cell is the active part. The cell is the system. From this principle, it follows that we must describe the genome as a database (or an archive, library, toolbox, memory ) that is transmitted to the next generation, rather than a 'program' that creates organisms. How could a database with protein-coding genes create an organism? There must be an organizing principle. Something has to choose which genes are to be read in which cells (in a multicellular organism like us). Our worldview influences how we describe what happens in a cell. So, the language we use to describe DNA is important. The language that scientists use, reveals the underlying worldview: DNA-centric or cell-centric.
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| Richard Dawkins: The Selfish Gene |
That is in particular true for expressions such as 'The Selfish Gene'. The way Noble analyses 'The Selfish Gene' idea is enlightening and new to me. 'The Selfish Gene' idea is in fact not a scientific theory at all, Noble says. No empirical test could possibly distinguish between 'selfish genes' and the opposite view 'genes as prisoners'. The genes are prisoners because they are trapped in huge colonies locked inside highly intelligent beings [5]. They are inside you and me; we are the system that allows their code to be read. The selfish genes do not create us, body and soul. Their preservation is totally dependent on our efforts to reproduce. We are the ultimate rationale for their existence. Additionally, Noble mentions that Dawkins agrees with him that the 'selfish gene' idea is not a scientifically testable hypothesis. I didn't realize that. Despite the fact that the selfish gene metaphor is not a scientific hypothesis, it continues to influence scientific research, thinking and writing. However, if it is an arbitrary view, then it doesn't deserve to be the standard view in biology and evolution. Noble presents us with an eye-opening alternative view.
I think, contrary to Noble, that there is a fact that can distinguish between the DNA-centric and cell centric view. That fact is that DNA as a molecule is passive. How could a passive molecule create you and me? A molecule that for every 'action', such as transcription, replication, recombination, repair or whatever, requires enzymes [6]. In my view, this fact contradicts Dawkins' selfish gene view, because that view implicitly claims that genes actively control the actions of the organism. To be precise Dawkins says: we are robots obeying the commands of the selfish genes. I consider that claim as falsified. A database cannot dictate anything. Consequently, a theory of how an individual is created from a fertilized egg is far from complete by summing up all the necessary protein-coding and regulatory genes in the genome. The genes in our genome are an inventory that is necessary, but far from sufficient. Question: how do thousands of individual protein-coding genes and proteins create an individual? [7]. These are fundamental questions in biology which tend to be ignored by the standard gene-centric selfish gene account.
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| Professor Dave Explains: Denis Noble is a clown [1] |
Contrary to what 'Professor Dave' claims: Denis Noble is not a clown! Don't let the loudmouths scare you away from reading The Music of Life and benefit from his insights. He is a serious and intelligent scientist. Don't be distracted by statements he made later in life.
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| Video Consumentenbond 28 nov 2025 bovenste telefoon: anoniem; onderste: Apple, Samsung |
Hier begint het onderdeel repareerbaarheid smartphones:
"Op het energie etiket staat ook de repareerbaarheidsklasse. Deze is bijvoorbeeld hoger als een reparateur minder stappen nodig heeft om een onderdeel te vervangen en dit met gangbaar gereedschap kan doen. Dat is natuurlijk niet helemaal hetzelfde als een reparatiewinkel vlakbij jouw huis, die een probleem met je smartphone snel en goedkoop oplost. Daarom kan het zo zijn dat je met een minder bekende smartphone in de hoogste reparatie klasse, minder makkelijk terecht kunt bij een reparateur, dan met de meest verkochte Samsung en Apple telefoons. Ook al zou de reparatieklasse op het energie etiket lager zijn."
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| Repareerbaarheidsklasse op etiket |
De smartphone expert in de video beweert dus dat je met een smartphone in de hoogste repareerbaarheidsklasse minder makkelijk terecht kunt bij een reparateur dan bij de meest verkochte Apple en Samsung telefoons. Hij zegt het niet, en hij laat het niet zien, maar Fairphone behoort tot de hoogste repareerbaarheidsklasse A. Toch suggereert hij dat je beter een iPhone of Samsung kunt kopen met een lagere repareerbaarheidsklasse (C), omdat je dan bij een 'reparatiewinkel om de hoek' terecht kunt. En met een Fairphone kun je niet terecht bij een reparatiewinkel om de hoek? Verbluffend! Hij slaagt er dus in om een voordeel om te toveren in een nadeel! Het voordeel van de hoogste repareerbaarheid wordt omgetoverd in een nadeel! Hoe krijg je het voor elkaar! Hij snapt dus kennelijk niet dat je een Fairphone zelf kunt repareren! Dat is het hele idee van repareerbaarheid! Je hoeft helemaal niet naar een 'winkel om de hoek'! Je kunt alle onderdelen online bestellen en zelf de onderdelen zoals batterij, camera, USB-C poort, achterkant, display, etc. vervangen met een iFixit schroevendraaier. Zelfs van de oudere toestellen zoals Fairphone 4 en Fairphone 5 zijn er onderdelen te bestellen. Zoals Fairphone zelf op hun website schrijft:
"Je telefoon is helemaal de jouwe. Je kunt hem dus ook zelf repareren. Met de iFixit Schroevendraaier is je Fairphone repareren kinderspel."
Ik vraag me af: kan zo'n 'winkel vlakbij jouw huis' die onderdelen niet zelf bij Fairphone bestellen? Iedereen kan dat, dus dat zou zo'n reparatiewinkel ook moeten kunnen, toch? En als zo'n winkel meer tijd kwijt is aan het repareren van een slecht repareerbare telefoon, zou het kunnen dat die reparatie dan ook meer kost? Kan het zijn dat die gespecialiseerde reparatiewinkels noodzakelijk waren om dat de meerderheid van de telefoons slecht repareerbaar zijn?
[3 jan 2026]
Heel toevallig moet volgens de Consumentenbond de repareerbaarheid van smartphones precies liggen op het niveau dat Apple en Samsung nu hebben. En die hebben een slechte repareerbaarheid. Toevallig hebben de meeste mensen een Apple of Samsung. Maximale repareerbaarheid is volgens de Consumentenbond alleen maar lastig.
Hiermee gaat de Nederlandse Consumentenbond tegen de belangen van de consument in. Een maximaal repareerbare telefoon, en in feite ieder apparaat, is in het belang van de consument. Dat heet: "right to repair" [7,8].
