Physicist Charles S. Cockell: "DNA and its entourage". The Genetic Code is non-random.

Evolution is the transformation of species into slightly modified species. The origin of species is solved in principle. However, the origin of life is a fundamentally different problem. Darwin avoided discussing the origin of life. It is the hardest problem of biology and it still has not been solved yet. Whereas the details of evolution can be described as a puzzle, the origin of life must be characterized as an intractable problem.

A crucial step (although not the first step) in the origin of life was the invention of DNA and the Genetic Code. DNA has become a defining property of life. But how DNA acquired its meaning is still a mystery. How could a relatively chemically inert non-enzymatic molecule (DNA) become useful, even indispensable, for life? DNA itself could not have been involved in the origin of life (Think about this...). There must have been something before DNA. 

In the literature the Genetic Code is usually presented as a table in which all 64 combinations of 3 bases A, T, C, G are 'associated' with 20 Amino Acids. These associations could be made in many different ways. Nature got stuck to one system of associations called the Genetic Code table. In the book The Equations of Life: How Physics Shapes Evolution, Chapter 7 'The Code of Life', physicist Charles S. Cockell notices that the Genetic Code table is non-random. This is an important observation. The assignments of base triplets to Amino Acids (AAs) is non-random. When looking at the table It is immediately clear that there is a pattern. Secondly, there is redundancy: many Amino Acids are coded by more than one base triplet. But there is also a pattern. This is all known very well.

However, Cockell also notices that there is something special about nature's choice of the twenty Amino Acids. There are many more natural Amino Acids available than those twenty. So, why those twenty? Random? Accident? Or are they the most suitable for their task? He refers to a publication [1] that argues for a non-random choice. The authors reasoned that there are 3 properties of Amino Acids that are important for constructing a protein: (1) the size of an Amino Acid, (2) the charge, (3) hydrophobicity (repelling water). Together those properties determine how the protein behaves and what it can do. In principle proteins could be constructed from one or a few Amino Acids. But most useful proteins consist of a diverse mixture of amino acids. Proteins are defined by a unique sequence of AAs to fold into a complex 3D shape. Also, it is not useful to have many AAs with the same hydrophobicity, or the same size or the same charge. The best toolkit for life would have an even distribution of AA properties that does not overlap too much. To test for optimality the authors tested a set of fifty AAs found in the Murchison meteorite. The reason? They assumed that AAs found in the meteorite would represent the set of AAs found on the early Earth. What they found was astonishing, writes Cockell:

"When they compared the twenty amino acids used by life with a million alternative bundles of amino acids randomly chosen from the fifty in the meteorite, the twenty used by life had better coverage and combinations of all three of the key factors than did any other set. ... they seemed to be selected by evolution to give a wide range and even distribution of properties that might be useful in proteins." ... Of a much expanded set of seventy-six AA, not a single group out of a million possible alternatives outperformed the natural set.". (chapter 7). 

Cockell concludes that the twenty AAs used by life are not random. That was new to me. But there is one important aspect Cockell doesn't mention: the AAs must also be suitable to be attached to a transfer RNA (tRNA) and to be processed by the ribosome. This is a crucial property. It is the biochemical implementation of the Genetic Code table. There could be differences in suitability. This must be investigated. Furthermore, all AAs are associated with 1 or more triplet codons (redundancy). The question is: how is the association made between a base triplet codon and the AA? And how did that originate in the first place? The structure of tRNAs does not show a direct chemical bond between codon and AA. Is it a random choice? That could certainly be the case because AAs and triplet codons (bases A, T, C, T) are different chemical compounds, yet they are somehow connected. Or is there a logic in the associations? Is there a pattern? Much research has been done to solve this question. No definitive answer yet. Cockell does mention this. But at least he pointed out a new aspect of the origin of life and the Genetic Code table to me.  

 ______

In this blog I did focus on the origin of the Genetic Code. The origin of the Genetic Code is in fact the origin of DNA-based life: bacteria, animals and plants. It is also the origin of protein and enzyme based life. The origin of DNA and proteins are strongly intertwined. DNA on its own has no use and proteins can not exist without DNA. DNA cannot self-reproduce, it needs enzymes. But proteins cannot self-reproduce either. A specific protein consists of a unique sequence of Amino Acids. Unique proteins do not self-assemble spontaneously. The only way to reproduce such a unique sequence is on the basis of another unique sequence: the unique base sequence in DNA. In other words: DNA and proteins depend on each other. This not a promising situation to start life. Hence, the hypothetical RNA world was developed (which is not without its own problems!). Keep in mind: the origin of the Genetic Code is not the same as the origin of eukaryotes. Bacteria are also DNA- and protein-based life forms. All life on earth uses the same Genetic Code, including viruses.

Physicist Charles Cockell used the expression "DNA and its entourage" [2]. And that is a misleading description. I hope readers recognize this as DNA-centric thinking. The cell and the cellular machinery are not an "entourage"! It is an equally important part of the cell! DNA is not the master of the cell! The cell is not the servant of DNA!

Notes

1. Gayle, Freeland (2011) Did evolution select a nonrandom "alphabet" of amino acids? Astrobiology 
2. "An entourage is a group of attendants, assistants, or close associates who accompany and work for an important or famous person". 

 

Previous DNA blogs

• If the blueprint of the embryo is not in DNA, then where is it? Alfonso Martinez Arias. A very convincing argument for the cell-centric view of life 14 March 2026
• Richard Dawkins admits: DNA is *not* a blueprint! But Dawkins still got another metaphor wrong! 16 February 2026
• Think about this:  09 February 2026
• Gene-centrism is bad biology. Here is why. 17 December 2025
• What is DNA-centrism? Why is it wrong? 10 November 2025 

Douglas Hofstadter argued against the DNA-centric view in his famous book 'Godel, Escher, Bach'

GÖDEL, ESCHER, BACH (1988)

"As development of an organism takes place, can it be said that the information is being "pulled out" of its DNA? Is that where all of the information about the organism's structure reside;

DNA and the Necessity of Chemical Context

In one sense, the answer seems to be yes, thanks to experiments li Avery's [1]. But in another sense, the answer seems to be no, because so much of the pulling-out process depends on extraordinarily complicated cellular chemical processes, which are not coded for in the DNA itself. The DNA relies on the fact that they will happen, but does not seem to contain a code which brings them about. Thus we have two conflicting views on the nature of the information in a genotype. One view says that so much of the information is outside the DNA that it is not reasonable to look upon the DNA as anything more than a very intricate set of triggers, like a sequence of buttons to be pushed on a jukebox; another view says that the information is all there, but in a very implicit form.

Now it might seem that these are just two ways of saying the same thing, but that is not necessarily so. One view says that the DNA is quite meaningless out of context; the other says that even if it were taken out context, a molecule of DNA from a living being has such a compelling inner logic to its structure that its message could be deduced anyway. To put it as succinctly as possible, one view says that in order for DNA to have meaning, chemical context is necessary; the other view says that only intelligence is necessary to reveal the "intrinsic meaning" of a strand of DNA."

Quote from chapter 6 'The Location of Meaning'. 

 

My copy of Douglas Hofstadter's famous book 'Gödel, Escher, Bach' (Dutch translation, 1985) stood gathering dust on my bookshelf for some 30 years. A few days ago when I was searching for artwork of M. C. Escher in Hofstadter's book, I unexpectedly came across arguments against the 'DNA-centric view' of life. I have blogged about DNA-centrism many times over the past several months. It is extraordinary to find the same ideas you have been developing in a book that was written 47 years ago. As far as I can see, Hofstadter was not participating in an ongoing discussion among biologists about DNA-centrism. He wrote his ideas as part of an investigation of formal languages. DNA was an example of such a language. Probably the two mutually exclusive points of view –'DNA-centric' and 'cell-centric'– did not exist at the time. Likely, mainstream biology was DNA-centric. For example, Hofstadter writes: "Gunther Stent has characterized the nucleus as the 'throne room' of the cell, with DNA acting as the ruler." (page 509). Hofstadter wrote this in passing and without further comment! Stunning remark! If this isn't DNA-centrism, then I don't know what is! Hofstadter accepts it as if it were merely a neutral description of what DNA is. Probably it reflects mainstream scientific thinking at the time.

Hofstadter is a computer scientist and investigated coded messages, and the concept of information and meaning. It appears he had a detailed knowledge of what DNA is and how it functions. In chapter 16 Hofstadter gives detailed description of the structure of DNA, the Genetic code [2], transcription, translation, proteins, Transfer RNA and Ribosomes. Furthermore, he understood that knowing the Genetic Code, that is how a particular DNA sequence is translated in to a protein, is far from sufficient to understand how a genotype is translated in to a phenotype [1]. This truth still holds today! 

An important question for Hofstadter was: 

Where is the meaning of a coded message located? 

Applied to DNA, attempts to answer this question yield important insights. Interestingly, he proposed two possible answers: the intrinsic and extrinsic view of meaning. The intrinsic view means that DNA has 'a compelling inner logic' that enables an intelligent (extraterrestrial) investigator to decode the DNA message. This sounds rather vague. Hofstadter doesn't explain what 'inner logic' means [4], [5]. The extrinsic view is that the meaning of DNA is not stored in DNA itself, but that "extraordinarily complicated cellular chemical processes" are required.

Although he never rejects the intrinsic meaning hypothesis explicitly, I conclude from his statement "extraordinarily complicated cellular chemical processes, which are not coded for in the DNA itself", that he favours the extrinsic view. This is further confirmed by the heading "DNA and the Necessity of Chemical Context" and this (charming!) statement: 

"they [an extraterrestrial civilization] might to try to deduce from its chemical structure what kind of chemical environment it seemed to want, and then supply such an environment." (under the section heading How Universal Is DNA's Message?). (page 183).

Another wonderful statement:

"On the other hand, DNA is itself a passive molecule which undergoes manipulation at the hands of various kinds of enzymes; in this sense, a DNA molecule is exactly like a long piece of data, as well." (page 542) (my emphasis). I love this. This is exactly what I argued on several previous blogs. And: "But most of the 'living' in a cell goes on outside of the nucleus, namely in the cytoplasm..." (page 512). Well said! I fully agree. In other words: DNA is dead, the cell is alive! However, Hofstadter does not note there is a certain degree of contradiction between DNA 'sitting on a throne' and being dead.

Bootstrap problem

Continuing with the intrinsic and extrinsic point of view. There is a problem with the distinction. The tRNAs contain the translation key of DNA to protein. Since the information for producing tRNAs is stored in DNA (necessarily, because it must be inherited), one could say that the meaning of DNA is intrinsic to DNA. That's OK. However, in order for that information in DNA to be used, it must first be read by cellular machinery. Hofstadter is aware of the problem [3]: "... there is no way for the DNA to hoist itself by its own bootstraps. Some amount of knowledge of the Genetic Code must already be present in the cell beforehand." (page 519) (my italics). Excellent remark! Remarkable insight! However, it appears that the concepts intrinsic and extrinsic meaning are ambiguous. In one sense, DNA has an intrinsic meaning because DNA encodes for tRNAs, but on the other hand the meaning is extrinsic because machinery outside DNA is necessary to get the whole process started. In other words: a bootstrap problem [6]. The information is there, but one can not get it out!

Think about this: 47 years ago a smart computer scientist clearly understood that a DNA 'message' is meaningless without its cellular context! So, the cell-centric view is certainly not a modern invention. It was kept alive in the fringes of science. Hofstadter did not fully realize that his anti DNA-centric views contradicted the prevailing view of DNA as 'the Ruler on the throne'. Since Watson and Crick (1953) DNA-centrism has experienced stormy growth. Today, more and more scientists reject the DNA-centric view of life.

Notes

1. My note: Avery (1944) was the first to demonstrate that DNA and not protein was the vehicle of heredity.  
2. The Genetic Code table is on page 515. Furthermore: "The curious
   fact is that the Genetic Code is stored-where else?-in the DNA itself." (page 517). 
3. quote: "(Warning: Understanding this "language" would not at all be the same as cracking the Genetic Code, something which took place in the early 1960s. ... The cracking of the Genetic Code was a vital step on the
   way to extracting the meaning of DNA strands, but it was only the first on a long path which is yet to be trodden.)" page 168.
4. An argument against the intrinsic meaning of DNA is: the genetic code is a rather arbitrary association of 61 base triplets with 20 Amino Acids and 3 base triplets with STOP signals. Hofstadter did not mention this in this book. But 3 years later, in his 1982 Scientific American "Metamagical Themas" column, titled "Is the genetic code an arbitrary one, or would another code work as well?" Hofstadter argued that the genetic code is not fundamentally dictated by chemical necessity, suggesting that many other codes could theoretically work. (answer by Google AI!). The conclusion must be: there is no compelling logic in DNA. 
5. A further problem with 'intrinsic meaning': how to find the translation keys in a code script with the length of billions of symbols? The code for the tRNAs are scattered all around DNA and there are many duplicate keys. In other words: how to locate the meaning of DNA?! That's the fundamental question.

 

Sources

The paperback edition is still available on Amazon. The PDF of the book can be found on several websites, such as this one. I discovered the Dutch translation of the book at my bookshelves, which so it appears was a birthday present. 

Previous blogs

• If the blueprint of the embryo is not in DNA, then where is it? Alfonso Martinez Arias. A very convincing argument for the cell-centric view of life 14 March 2026
• Richard Dawkins admits: DNA is *not* a blueprint! But Dawkins still got another metaphor wrong! 16 February 2026
• Think about this:  09 February 2026
• Gene-centrism is bad biology. Here is why. 17 December 2025
• What is DNA-centrism? Why is it wrong? 10 November 2025 

 

 

Utrechts Landschap: Brandrode runderen beschermen, slachten en opeten + reclame voor vlees maken

Brandrode runderen op landgoed Sandwijck

Een verhaal over het behoeden voor het uitsterven van een oud runderras, én het slachten van diezelfde runderen. 

Infobord op landgoed Sandwijck (NB: vlinder!)

  

Het ras was bijna uitgestorven!

  

Vlees van eigen koeien!

Stier (L) en koe (R) van de Brandrode runderen
De lang gerekte bouw valt op. Dit zijn geen 'hobby-koetjes'

 

Het Utrechts Landschap beheert natuur in de provincie Utrecht. Op één van die terreinen worden 'Brandrode runderen' gehouden. Het is een oud runderras dat niet meer gebruikt wordt in de intensieve veehouderij. Er wordt mee gefokt en er worden jaarlijks kalveren geboren. Volgens het UL passen ze goed in het landschapsbeheer. Ze mogen hun hoorns behouden, en de kalveren mogen het eerste weideseizoen bij hun moeder blijven. Deze runderen worden ouder dan in de moderne veehouderij gebruikelijk is volgens het UL. Tenslotte lees ik: "de maatschap verkoopt vlees van eigen koeien". 

Maar kun je echt blijven beweren dat je de dieren respectvol behandelt, terwijl je ze ook slacht? Een oud runderras tegen uitsterven behoeden én ze tegelijk ook slachten? Eerst vertroetelen, dan de kogel. Some we love, some we hate, some we kill, some we eat. Opvallend genoeg, komt het woord 'slachten' niet voor op de informatieborden. Er worden géén dieren gedood, er wordt alleen maar vlees van eigen koeien verkocht! Dat noem ik verhullend taalgebruik [1]. Bij verhullend taalgebruik heb je iets te verbergen. In dit geval dat je ze slacht. Vlees is namelijk geen wol! Een andere verhullingstechniek is: grappen maken. Een vrijwilliger grapte bijvoorbeeld: één van de Brandrode runderen heeft zichzelf vrijwillig opgeofferd! Zo'n grap verhult de ongemakkelijke waarheid dat het uiteraard niet 'vrijwillig' is. Een respectloze houding. Volgens het UL worden ze ouder, maar wat gebeurt er als ze bejaard zijn? Bejaardentehuis? Begraven? In de natuur gelegd voor de wolven? Of ...? 

Wat het UL kennelijk niet weet is, dat die runderen in een groep, in familieverband leven. Het zijn sociale dieren. Alsof ze niet merken dat een groepsgenoot, dochter, zoon, vader of moeder plotseling is verdwenen. Alsof ze hun groepsgenoten niet missen. Alsof sociale dieren elkaar niet herkennen. Alsof het domme dieren zijn. Is het misschien te ongemakkelijk om over dit soort vragen na te denken als je heel graag hun vlees wilt eten? [4].

Als je runderen gaat houden, dan ben je een veehouder! Als je dieren fokt en slacht, ben je geen natuurbeschermer maar veehouder en slager! Dat past niet bij een natuurbeschermingsorganisatie.

Ik heb het Utrechts Landschap hierover gemaild en er op gewezen dat ze reclame maakten voor vlees (zie borden hierboven). En dat dit niet meer van deze tijd is vanwege de eiwittransitie (3). Er kwam wel een reactie, zelfs van de directeur, maar ze toonde geen enkel begrip voor mijn standpunt. Een organisatie die in deze tijd nog reclame maakt voor vlees, kan niet meer rekenen op onze steun.

kleine edit 26 maart. 

 

Wildernisvlees!

'Wildernisvlees' is vlees van dieren (runderen, paarden) die in het wild of semi-wild leven in natuurgebieden, zoals die beheerd door Utrechts Landschap en beheerd door FREE Nature, waarbij het vlees wordt verkocht als een duurzaam natuurproduct uit gebiedsbeheer, met afhaalpunten zoals op Landgoed Oostbroek in De Bilt (let op: dit stopt per 1 jan 2026.

Op 8 januari 2026 is Landgoed Oostbroek en de Blauwe Kamer van het Utrechts Landschap nog steeds afhaalpunten zijn van wildernis vlees: Afhaalpunten wildernis vlees.

 

Bestelformulier wildernisvlees jan 2006

Nevenactiviteit van de Slagerij het Utrechts Landschap: het vlees van die dieren die je beschermt verkopen: veel anonieme namen zoals 'gemengd pakket', 'stoofvleespakket', 'vlugklaarpakket', 'tartaar', 'beefburgers', 'verse worst', 'rundergehakt', 'rundertong', 'gemengd paard'. Behalve 'paard' en 'rund', van welk dieren is dit vlees afkomstig? Ree? Wild zwijn? Hert? Je wilt/mag het niet weten! Hoe zijn ze aan hun eind gekomen? Geschoten door jagers? Verkeersslachtoffer?

  

Noten

1. "Taal moet onthullen. ... Niet om de realiteit te vervormen of haar mooier voor te doen dan ze is, maar juist om zichtbaar te maken wat we anders zouden missen." Iris Murdoch (1919-1999). (Filosofie Kalender).
2. Juridisch: de wet definieert 'moord' specifiek als het doden van een mens door een mens. Het doden van een dier door een mens wordt niet aangeduid als 'moord', maar valt onder wetgeving inzake dierenwelzijn of dierenmishandeling.  
3. Eiwittransitie (overstap van dierlijke naar plantaardige eiwitten) en: Voedingscentrum over eiwitten. 
4. "My own research on the ‘meat paradox’ shows how people reconcile caring about animal welfare with enjoying eating meat: when reminded of animal suffering, they resolve the tension by downplaying the mental capacities of animals." from Nature book review of Animate: How Animals Shape the Human Mind Michael Bond Picador (2026) by Brock Bastian. 26 mrt 26

 

Bronnen

• "Let op: het afhaalpunt bij De Bilt stopt per 1 januari 2026. In de december levering van 2025 kunt u dus voor het laatste op deze locatie afhalen." geraadpleegd 8 jan 2016. 
• https://www.freenature.nl/nl/afhaalpunten/de-bilt-landgoed-oostbroek 
• https://www.freenature.nl/nl/wildernisvlees
• https://nos.nl/video/2595333-mee-op-jacht-naar-wild-vlees-dat-steeds-populairder-wordt 
• https://www.freenature.nl/nl/afhaalpunten/overzicht 

 

Vorige blogs Utrechts Landschap

• Een sfeervolle avondwandeling met een zeer relaxte ree 31 mei 2025
• Utrechts Landschap: stop met boeren in natuurgebieden! Bewaar de rust! 30 mei 2022
• Very disturbing agricultural activity in Utrechts Landschap nature reserve Moersbergen, The Netherlands. 24 mei 2022
• Utrechts Landschap schaft twee elektrische auto's aan. 1 jul 2020