26 June 2023

Scientists say: 90% of your genome is junk. Have a nice day! Biochemist Laurence Moran defends junk DNA theory.

Larry Moran (2023)
'What's in Your Genome?
90% of Your Genome Is Junk'

"The scientist says: science has explained many things about the universe. Your life has no meaning. Have a nice day." [1]

Biochemist Larry Moran brings more bad news: 90% of your genome has no meaning! Even worse: the remaining 10% is not a finely tuned Swiss watch but prone to mistakes and errors! Have a nice day! 

This is really not good for your self-esteem: The Deflated Ego Problem, as Moran calls it. He himself doesn't seem to be worried at all. He, like many molecular biochemists and geneticists, had many years to get used to the idea and trying to understand it. They are comfortable with the idea that large genomes are full of junk DNA. Moran eliminated God and natural selection for 90%. Read the book and decide for yourself if he is right. This book is not the usual popular science book. Moran is not a science journalist. The book has a high density of facts and arguments and no anecdotes. It is a book length and systematic defense of the junk DNA view. Whether you agree or not with Moran, after reading the book your view of the human genome (and some other things) will never be the same again.

In 2012 a large international group of scientists, called the ENCODE consortium, claims that 80% of our genome has some biochemical function. Junk is still there, but they reduced it to 20%. Top science journals Nature and Science published their results and opinions and seem to agree. Moran strongly disagrees. He argues that long before scientists were able to sequence the first whole genome (that is before 2000) there was evidence that much of our genome simply must be junk. I was not aware of some of those facts (or have forgotten it?). Amazingly, the ENCODE scientists didn't know those facts either and accused the 'junk DNA scientists' of having based their claims on ignorance because you cannot assume that all that DNA is junk without a thorough investigation. But according to Moran, the opposite is true: the anti-junk scientists are ignorant of a lot of evidence. Clearly it is necessary to know the history of the field. Moran explains that history. Read it.


Natural selection

Evolutionary biology was forced to adapt to a constant stream of new discoveries in biochemistry and genomics. The author of What's in Your Genome? rejects the Darwinian view that every property of an organism must have a function and must have been selected by natural selection (a view called adaptionism or pan-adaptionism). Remarkably, he follows paleontologist S. J. Gould in his criticism of pan-adaptionism. Moran has the rather extreme view that "most of evolution has nothing to do with natural selection". I hope he meant to say: "most of evolution at the molecular level has nothing to do with natural selection." But, I am not sure. In defense of Darwin, I must say that Darwin was concerned with organisms and the goal of his theory was to explain adaptations of organisms. In Darwin's time there was next to nothing known about genetics, let alone of DNA. So, Darwinism explains features of organisms (beaks, claws, eyes, wings, brains) as adaptations created by natural selection. Potential readers of What's in Your Genome? must be aware that the book is not about the precious 10% of our DNA that makes us human. It is not surprising that a biochemist focuses on non-adaptive features of organisms. Especially a biochemist who defends that 90% of your DNA is non-functional. There is so much noise in biochemical reactions, they are very messy and there is so much needless complexity at the genomic and cellular level.

Again unsurprisingly, Moran has sympathy for the idea that mutation is a prime mover in  evolution, an idea called 'mutationism' and argued by Masatoshi Nei [3]. It is reasonable to claim that the 90% junk is explained by mutation and random drift and further that natural selection is powerless to remove the junk. However, it is unreasonable to extrapolate that to a general rule in evolution and call it mutationism. Let me illustrate that by a thought experiment of Masatoshi Nei approvingly quoted by Moran:

"Nei emphasizes the importance of mutation by asking us to consider a parallel universe - one with natural selection but no mutation and one with mutations but no natural selection."

In the first universe there will be no evolution, in the second there will still be evolution since new genes and new variants will appear and their frequency in the populations can increase by random genetic drift. This is Nei's explanation. But it is nonsense. It is a false dilemma. It is just as silly as asking which of the legs of a table is the most important. Evolution needs both mutation and natural selection. Secondly, Nei simply assumes organisms with functional genes at the start of his thought experiment. The thought experiment will not work if there are no organisms in the first place. How did those organisms originate? By random genetic drift? Genomes will mutate to extinction if the fitter genomes will not be amplified relative to the less fitter genomes. Any existing life form is proof that natural selection has created functional genes. In both hypothetical universes there would be no living organisms to start with. Conclusion: mutationism cannot possibly be a general theory of evolution. Despite his endorsement of mutationism, Moran knows that natural selection is indispensable as an important indication of function of a DNA or RNA sequence. The fact that specific sequences are conserved between species shows they are functional and must have been selected. Moran knows that.


Is junk DNA a burden?

Genome size distribution
 Figure 2.1
Chapter 2.
Note: birds (green) have smaller genomes than mammals (red)

A valid question is: why didn't natural selection remove most of the junk from our genomes? The amount of junk seems disproportionate. The standard explanation (also adopted by Moran) is: 'small population size'. Species with large population sizes have less junk (bacteria). Animals with smaller populations sizes have lots of junk. Is that a universal law? Is it the correct explanation? But what about birds? "Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA" [4]. Is that because they have larger population sizes or could it be that the energetic burden of large amounts of junk is too much for birds? Moran writes: "The pufferfish genome is only one-eighth the size of our genome, and the lungfish genome is 40 times larger than the human genome". Can this be explained by different population sizes? Are effective population sizes known? Are there 8 times as many pufferfishes than humans? Prokaryotic genomes range from about 500 kb to about 12 Mb [8]: does that correlate with population sizes? 

The existence of huge amounts of useless DNA conflicts with the evolutionary principle "use it or lose it." (cavefish lost their eyes). Useless DNA is copied and repaired by a complex repair system at every cell division. "Most of our genome is transcribed"  also adds to the burden. These spurious transcripts must be removed by RNA quality control, surveillance and degradation machinery. Again, this adds to the burden. Introns have to be degraded. "Incorrectly spliced RNAs are rapidly degraded by enzymes that clean up mistakes": this adds to the burden as well. Furthermore, "Some pseudogenes will be transcribed and still produce a protein. This does not mean they have a biological function." Again this adds to the burden. I wished Moran had discussed these questions. Too easily he accepts the population size argument and doesn't take the burden problem serious. To me it seems appropriate to discuss the burden problem in a book length defense of junk DNA [12].

Null hypothesis or null dogma?

It's clear this is a polemical book. It is a very forceful criticism of ENCODE and everyone who uncritically accepts and spreads their views including Nature and Science. I agree that this criticism is necessary. However, there is a downside. Moran writes that the ENCODE research goals of documenting all transcripts in the human genome was a waste of money. Only a relatively small group of transcripts have a proven biological function ("only 1000 lncRNAs out of 60,000 were conserved in mammals"; "the number with a proven function is less than 500 in humans"; "The correct null hypothesis is that these long noncoding RNAs are examples of noisy transcription", or junk RNA"). Furthermore, Moran also thinks it is a waste of time and money to identify the functions of the thousands of transcripts that have been found because he knows its all junk. I disagree. The null hypothesis is an hypothesis, not a fact [9]. One cannot assume it is true. That would be the 'null dogma'. He writes: "We don't know how many lncRNA genes there are in the human genome."! Exactly! We simply must know all the functional elements in the human genome. We can't afford to be ignorant about that. We'll never understand disease. We never know the difference between humans and chimps if we don't know all the functional DNA in both genomes [7]. In the year 2000 the human genome sequence was published. That was also a huge project costing millions of dollars [10]. But we should have an inventory not only of protein coding genes, but of all non-coding genes, all regulatory sequences and simply all functional DNA in the human genome. It would be irresponsible and unacceptable to stop that kind of research simply because ENCODE claims too much. We should find a way to do it efficiently.

A book as this comes with a bias. For example the concept: "functional pseudogenes" is absent! "There are only 200 human pseudogenes that produce a protein". Only! Are they not important or interesting? John Avise thinks functional pseudogenes are important enough to be counted as a "conceptual breakthrough" [5]. Whereas ENCODE is too optimistic about the importance of 90% of our genome, Moran is perhaps a little bit too pessimistic. [11]


Coping with a sloppy genome?

The Deflated Ego Problem is not solved by claiming it isn't a problem. We need more than that. Let me try: there could be no junk DNA if there would be not enough functional DNA. It is the non-junk DNA that keeps us alive. Simply the fact that there is 9 times more junk than functional DNA, does not prove that the 90% is the most important part. It may be that natural selection has no power over the 90%, but it rules over the 10%. And the 10% is the most important part of our genome. Thanks to the 10% we have rather unique brains. We are the only species that invented science and write books and blogs. Thanks to the 10%. Apparently, the junk burden is compatible with life. For now. We have learned to live with introns. We are not alone, salamanders and lungfishes have much more junk DNA in their genomes. Junk DNA is not cancer. Junk DNA doesn't make us sick, it doesn't hurt. Even Einstein must have had 90% junk DNA in his genome! Nobody ever died of junk DNA, etc. etc. etc.

In my own scientific education I learned about polyploidy in plants (huge redundancy!), constitutive heterochromatin in chromosomes, introns (unexpected discovery!) and repetitive DNA (ALU). But at the time it wasn't called junk DNA. In 2011 I wrote against the ID-view of introns. Although I knew these facts, I was not aware of the magnitude. I knew bits and pieces, but Moran made the sum total and put a number on the amount of junk. In that sense Moran created a 'conceptual breakthrough' (in the words of John Avise). In the past, authors who published about junk DNA never made the 90% claim explicitly. Moran places it prominently in the title of his book. In my next blog I will discuss  about junk DNA in Evolution textbooks. I discovered that I have been a victim of the ENCODE propaganda [6] and it seems this happend to John Avise too.  Moran succeeded after a prolonged struggle against a tribe of  Wikipedia geniuses to create a Junk DNA Wikipedia page. His book is not (yet) listed on that page. The Dutch Wikipedia page Junk DNA says that 'junk' is an inappropriate word. 

Note: I have used the KOBO e-book version of the book which has full-text search capability (invaluable!).

Appendix 1

After reading the book I did a 'junk DNA' search in Nature and the results were surprising. Years before the ENCODE publications in 2012 a seemingly endless number of articles showed up attacking the junk DNA concept:

All articles are attacking or even ridiculing the 'junk DNA' concept before the ENCODE publication 2012. That Nature published the ENCODE results in 2012 did not quite come out of the blue. The problem is that Nature did not give its readers a balanced presentation of different views in the scientific community. It is a very one-sided point of view. Why? Finding functional DNA in junk DNA is newsworthy and finding no function is a negative result which will not get published. It seems a natural unbalance. The people who discovered treasures in the junk are the heroes and revolutionaries and get published and interviewed. Just as Moran describes in his book. Notwithstanding severe criticism, Nature continued to propagate the anti-junk worldview after 2012. That is even more amazing!

Appendix 2

After reading Moran's book, I found it helpful to compare it with John Avise's
Conceptual Breakthroughs in Evolutionary Genetics [2] because Avise emphasizes different scientific discoveries and interprets them differently. Moran has a rather extreme point of view and is dismissive of the results of other scientists who argue there is less junk in our genome and more functional DNA. According to Avise the following discoveries are conceptual breakthrough discoveries. I selected the relevant breakthroughs.  

Before the discovery of jumping genes scientists viewed the genome as a stable entity. Mutation did change the sequence of a gene, but not the order of the genes on a chromosome, and the total number of genes. Jumping genes changed that view. A stable genome became a dynamic genome. Next is the discovery of repetitive elements. They originate by copy and paste, but it is unclear what their function is, if any. Then came the subversive idea that many small mutations in DNA are ignored by natural selection because they do not affect fitness (neutralism theory). Not everything is useful. At that time it was thought that changes in protein coding genes are the most important drivers of evolution. But evidence began to accumulate that gene regulation of the protein coding genes was important in the evolution of eukaryotic species. The idea of gene regulation by RNA was a paradigm shift in molecular genetics. "Nearly all evolutionary geneticists now fully accept the idea that changes in the regulatory apparatus of eukaryotic genomes are central to much of adaptive evolution." Next revolution: human genomic uniqueness. Before this revolution, humans were extraordinarily distinct from all other creatures (Inflated Ego!). So, our genome must be unique. But then came the discovery that genes and proteins of humans and chimpanzees are remarkably similar. A shock for many people. The standard paradigm at that time was that most genes within any genome collaborate harmoniously for the benefit of the organism. But Selfish genes multiply within our genome much like viruses without benefit to the organism. We knew about selfish genes, but after the complete sequence of the human genome in 2000 the amount of selfish DNA was new. The view of a protein coding gene before the next revolution was an uninterrupted sequences of the 4 bases from a START to a STOP codon. The discovery of Split genes came as a shock. I remember this very well. It looked a crazy idea. Protein coding genes were interrupted with introns: pieces of DNA that are spliced out of the RNA transcript before producing a protein. Completely unnecessary complexity. Introns are junk DNA. They are not the exception, they are the rule. Even worse: introns are larger than the protein coding genes themselves! The total amount of useless introns in our genome is larger than the useful genes. It takes some time to get used to it. Now, they are in every textbook. The next unanticipated discovery was that RNA could catalyze biochemical reactions: Ribozymes. A task that enzymes (proteins) had a monopoly on. The point is that RNA wasn't just an intermediate between DNA and proteins anymore, it is a functional end product.

Additionally it was discovered that non coding RNAs play an important role in gene regulation: Regulatory RNAs. According to Avise the discovery of regulatory RNAs are a conceptual breakthrough. They come in two types: short micro-RNAs and long RNAs. According to Moran there are not many regulatory RNAs, but according to the ENCODE people there are thousands. Remember their claim: 80% of our genome is functional and Long non coding RNAs (lncRNAs) are a major player (?). Obviously, one cannot estimate the percentage of junk in a genome if one doesn't know the complete sequence. The Whole-Genome sequence, published in 2000, made it possible to calculate the percentage of junk in the complete genome. One last breakthrough I want to mention is Functional pseudogenes (a paradoxical concept!). Until that discovery pseudogenes were considered damaged copies of functional protein coding genes. Just junk. The conceptual revolution was that some pseudogenes appeared to regulate gene expression. 'Pseudogenes are not pseudo any more.'  At least not all.

Appendix 3

There is one scientist who back in 1994 published a book completely based upon the hypothesis that much of our genome is random DNA. He used the concept 'junk DNA'. His name is Periannan Senapathy and the full title of his book is: "Independent Birth of Organisms. A New Theory That Distinct Organisms Arose Independently From The Primordial Pond Showing That Evolutionary Theories Are Fundamentally Incorrect". In his own words:

"the genome would be mostly random DNA sequence with only small “islands” of genes scattered in an ocean of meaningless DNA. Such an architecture actually exists in the genomes of all living multicellular organisms, with the intergenic sequences termed “junk DNA.” "

Beautiful words! (with hindsight!). I reviewed the book here on my WDW website. I will blog about him soon with a focus on junk DNA:

Periannan Senapathy (1994) claimed that the human genome consists of more than 90% junk DNA 4 July 2023


Postscript 8 Nov 2023

Lesson from a 50% synthetic yeast genome:

"One such source [of instability] is large stretches of repetitive DNA that don’t code for anything, but that can recombine with each other through natural processes, causing major structural changes in the genome. The synthetic biologists want to have complete control of their engineered yeast, so the team combed through S. cerevisiae’s genome with computer programs to find highly repetitive regions — and then deleted them. These sequences are effectively “genome parasites”, Boeke says.". Nature 8 Nov 2023

So, there are talking about removing junk DNA because it is causing major structural changes in the genome. Those sequences must be highly non-adaptive or deleterious. If they are not neutral, why are they not removed from the genome by natural selection? Low population size can't be an explanation in yeast.




  1. Jonathan Marks (2003) "What it means to be 98% chimpanzee. - Apes, people, and their genes.". Listed on my WDW page here.
  2. John Avise (2014) Conceptual Breakthroughs in Evolutionary Genetics: A Brief History of Shifting Paradigms.
  3. Masatoshi Nei (2013) 'Mutation-driven Evolution', page 107. However, Nei himself writes: "Recent studies have shown that a substantial portion of noncoding DNA has some roles in the regulation" and he refers to the ENCODE Project Consortium 2012 !
  4. Chris Organ et al (2007) Origin of avian genome size and structure in non-avian dinosaurs, Nature.
  5. John Avise (2014): "Beginning in the 1980s, examples gradually came to light in which some "pseudogenes" played active roles, such as in regulating gene expression", Chapter 68 'Functional Pseudogenes',  (p.143).
  6. In my review of Senapathy's book Independent Origin I quoted ENCODE results several times without knowing how controversial they were!
  7. Moran writes only about differences in junk DNA between humans and chimps: "almost all the differences between the human and chimp genomes are due to the fixation of neutral mutations by random genetic drift." (chapter 4)
  8. Genome size
  9. It is not a fact, but the "90% of your genome is junk" is stated as a fact: it is in the title of his book! and is many times repeated in his book. [12 Jul 2023]
  10. "But sequencing the full genome was widely considered to be pointless, partly because around 95 percent of it was thought to be junk DNA.".
    Michel Morange (2020) 'The Black Box of Biology. A History of the Molecular Revolution', p.341.
  11. For example, this publication is absent in his book: Introns: The Functional Benefits of Introns in Genomes, Genomics & Informatics, 2015. Ideally, one should discuss publications against your own theory. [23 Jul 2023]
  12. Later I found a remarkable passage that shows Moran accepts the idea that junk could be a burden: "This evidence suggests that there has been selection for removing excess junk DNA from these introns in order to speed up gene expression." (chapter 6). So, Moran concludes from this that introns are mostly junk, and at the same time accepts that intron-junk is costly for highly expressed genes. Apparently, in this case natural selection is powerful enough to get rid of junk despite the small effective population size. But if population size is not a problem for removing junk DNA from introns, then the argument of population size doesn't seem to be valid anymore. The question arises: why hasn't most of the junk been removed from our genome? Is intron-junk  more costly than intergenic junk? [ 11 Aug 2023 ]. See also: Selection for short introns in highly expressed genes.


  1. Thank you, Dr Korthof for the thorough discussion of Moran's book.
    Interesting material, because openly professing mutationists are rare nowadays, unlike in the past (eg Bateson, Morgan, De Vries etc).
    I have a few questions to start with if you don't mind:
    Does Moran refer to the work of these pioneers, or is he relying solely on Nei?
    Does he further discuss mutationism as an alternative to adaptationism in his 'polemical book' - with examples, for example?

  2. Thank you for your comment.
    Actually, Moran does not tell us very much about 'mutationism'. This what he writes:
    "The idea that mutation is a prime mover in evolution is called 'mutationism', and in addition to Nei, there are other strong proponents of this minority view (e.g. Arlin Stoltzfus)."
    So, he does not explicitly endorse mutationism, but read this:
    "Mutationism is just one of many ideas that emphasize the randomness and unpredictability of evolution, and it fits nicely into the view that genomes are sloppy and not exquisitely designed like a Swiss watch."
    There is no mention of Bateson, Morgan, De Vries.
    Interestingly, Nei (2013) himself devotes several pages to De Vries!
    and Morgan and Bateson are also discussed.
    Let me give another example to illustrate the status of 'mutationism' as a general theory of evolution: humans have two legs: which leg is more important: the left or the right leg?

  3. Moran follows SJ Gould in his criticism of pan-adaptionism.

  4. thanks for the clarification.

    I think your quip about mutationism misses the point, but I admit it's a lot easier to make fun of adaptationism: it explains that evolution made our legs just long enough to touch the ground.

    "I think it would be a very good idea to stop further genomic surveys and start identifying which transcripts and putative regulatory elements are actually functional. I'd love to know the answer to that very important question", Moran writes. I couldn't agree more.

    A good recent example: Nature (2023). DOI: 10.1038/s41586-023-06356-2 Who is still waiting for discussions about junk and or adaptationist scenarios?

    By the way, you got the bit about null hypothesis wrong, as Moran explains.

  5. You wrote "I think your quip about mutationism misses the point" but you did not explain WHY.

    You quote Moran: "I think it would be a very good idea to stop further genomic surveys and start identifying which transcripts and putative regulatory elements are actually functional. I'd love to know the answer to that very important question", Moran writes."
    But you copied that from his blog! NOT FROM THE BOOK!
    Moran wrote that AFTER I wrote my blog!
    In his BOOK he writes:
    "The most likley result of all that investment is the realization that most transcription factor binding sites don't do anything; ...
    No responsible scientist is going to waste time on such fool's errand." (Chapter 10)
    That is the opposite. And that is a very clear statement. And I reacted to that statement on my blog above.
    Did you read the book?

  6. my comments simply refer to your blog and I try to be as up to date as possible

    explain what? I think your quip about 'mutationism' can't be serious, even though you call it an example.

  7. OK.
    There is one thing I regret not having explained more clearly in teh section Is junk DNA a burden? and that is: DNA repair: the insanity and absurdness that junk DNA and functional DNA are both subjected by sophisticated time-consuming and energy-consuming DNA repair processes! Think about it: junk DNA is repaired with the same accuracy as genes! Repairing junk DNA: what a waste! It seems impossible to discriminate between junk and functional DNA, otherwise evolution could have found a way to refrain from repairing replication errors in junk DNA and save time and energy. Maybe it is somehow possible if junk DNA can be recognized. It should be investigated!

  8. These are really outstanding points, and I think they are underscoring the relevance, if not to say the importance, of 'mutationism'.

    E.g. "faults in repairing DNA breaks that are caused by oxidative stress in the noncoding parts of the genome are directly involved in the development of neurological diseases", wrote Nuala Moran Sep. 30, 2022 in bioworld.com (I couldn't resist the temptation to quote his namesake instead of the original Nature article describing the discovery of a gene that sits at the heart of the repair process)!

    I could may be prompt the other Moran about these misses, so he can adapt his somewhat condescending review of your review of his book...

  9. Thank you Gert for your interesting blog about the new book of Moran. I remember very well the discussion following the publication of ENCODE.
    Maybe because of the video animations or maybe because of the beautiful drawings in the textbooks, we are convinced that the macromolecules operate in a neat and tidy way, like the drawings and videos about RNA-elongation or the walking dynein on microtubuli. This perfect and clean representation is probably not so realistic which is what several ‘unheard’ commenters on the publications of ENCODE were trying to say.
    One of the most eloquent blogs was the one of Mike White from The Finch&Pea who states the following:

    whatever bits of our genome we want to call functional are embedded within a very specific genomic context, and function produced by natural selection emerged within, and certainly depends on, that context.
    This is why computer analogies of our genome are bad. Our genome isn’t a giant control panel packed with millions of switches, blinking lights, buzzers, gauges, and chrome-plated knobs. Our genome is like Darwin’s tangled bank, an ecosystem filled with elements that have their own agenda in mind. Function is a fluid thing. Regulatory sites wink into and out of existence. Transposable elements pick up transcription factor binding sites, giving themselves an advantage, but they spread those sites around, occasionally leaving something that, with a tweak, turns out to be useful. Function emerges from, and disappears back into the seething genomic jungle.
    This is what biology looks like, and the failed media coverage of the genome this past month was so damaging because we lost a chance to tell people about biology.

    I haven't yet read Moran’s book. Your comparison of the relative importance of mutation and natural selection to evolution with the legs of a table is very well expressed and I do agree completely.

    The enormous quantities of junk DNA in organisms might simply be determined by dragging along 'old' discarded genes. The organism cannot get rid of them because they are an essential part of the chromosomes that must separate neatly during mitosis and meiosis and recombine in the case of the zygote. Perhaps that is the reason why the organisms cannot get rid of the junk. After all, they must be able to continue to mate with their peers, so they need, just like their partners, all their chromosomes with all the junk in them.
    Didn't Moran write about that in his book, or some other scientist that you know of?

  10. Hi Marleen. Yes, you are right: those idealized educational video animations are misleading in the sense that molecular processes are not deterministic but stochastic.
    It's nice to see you accept my table metaphor. I simplified it in a comment: Which of your legs is more important: the left or the right? An anonymous commenter discarded it as nonsense :-(

    You wrote: "...they are an essential part of the chromosomes that must separate neatly during mitosis and meiosis and recombine in the case of the zygote".
    I agree. A species is defined as a group of individuals who can reproduce within the group and not with members of other such groups.
    And indeed that is partly determined by meiosis. Having said that, I wonder whether small differences in genome size would be acceptable. So, the question is: what is the threshold of the amount of junk DNA that disturbs the meiotic pairing of chromosomes? It seems there must be some tolerance for small variation in total genome size because for example variable abundances of LINE-1 retrotransposons in different people.
    Maybe the reason why the organisms cannot get rid of the junk is that (1) only the deletion of small amounts of junk are possible in order not to disturb meiotic pairing and (2) small amounts of junk will not have a big enough impact on natural selection to get rid of it.
    An if successful, it should become a characteristic of all the members of the species. And that will take a lot of time.
    I think Moran isn't worried about the energetic and evolutionary burden of 90% junk. So he doesn't discuss it in his book.
    For a start: googling for "genome size variation within humans" and possibly in combination with "meiotic pairing" will help you further with this interesting problem.

  11. dag Gert, en ook Marleen,
    Ik heb met plezier je blog gelezen. Ik vond de reactie van Marleen zo goed, maar ook mooi verwoord, dat ik dat er onder wilde zetten … vanuit mijn intuïtie. Maar ik dacht, laat ik de reactie van Gert even afwachten.
    Wel, je gaat mee in de gedachtegang van Marleen, dus nu kan ik ook wel.

    Wat die intuïtie van mij dan betreft: als ik plaatjes zie, of filmpjes (nog meer) van wat zich in een cel afspeelt (Cees Dekker heeft eens in een tv-programma zo’n filmpje laten zien) , of in een molecuul, of, nog gecompliceerder, in een atoom, dan weet ik altijd één ding: zo ziet de werkelijkheid er niet uit.
    Het is uiteraard een model van de werkelijkheid, maar volgens mij moeten we het woord model hier goed verstaan: het is niet hét model van de werkelijkheid, maar het is het model van hoe de onderzoeker de werkelijkheid begrijpt.

    Dus, zoals Marleen Mike White aanhaalt: Our genome is […] an ecosystem filled with elements that have their own agenda in mind.

    Toch zit ik, als ik dit zo opschrijf, wel met een probleem.
    Want er is determinisme. En dat zie je aan de korenaren en de zonnebloemen … die hier op dit moment om mij heen in grote getale opkomen en opbloeien.
    Korenaren groeien hun graankorrels in een aarvorm - en dat gaat nooit mis. Er zijn zware korenaren, lichte korenaren, maar nooit graan dat in een soort halve maan tevoorschijn komt.
    Er zijn volle zonnebloemen, soms bijna lege zonnebloemen - maar ik heb nog nooit zonnepitten zich als een korenaar zien manifesteren.

    Dus, iedereen zijn eigen agenda, okay - maar mooi toch dat er uitkomt wat de evolutie er als bouwplan heeft ingestopt, lang geleden.

  12. Hoi Leonardo, ja dat klopt mutaties en variaties blijven binnen de soortsgrenzen. Maar wat dacht je van een behaarde baby, of een baby met een staartje, een extra tepel, of een extra vinger, extra ribben? Voor meer en heftiger (!) voorbeelden zie: Armand Marie Leroi (2003) Mutants. On Genetic Variety and the Human Body.

    1. http://no-footnote-to-plato.eu/ruimte_tijd/Sunday, July 9, 2023 at 7:50:00 AM GMT+2

      Dank voor de voorbeelden. En je hebt gelijk er zijn nog heftiger: ik herinner mij in ieder geval een baby met twee hoofden. Ik zou haast zeggen: dat zijn uitzonderingen die de regel bevestigen.

      Maar ik keek iets verder bij die tekst van Mike White … filled with elements that have their own agenda in mind. Het doet mij namelijk sterk denken aan de vraag: hebben wij een vrije wil. Vandaar dat ik het woord determinisme gebruikte.

      Of wij die vrije wil hebben blijft in het verborgene (al heb ik er wel een antwoord op, maar dat is hier niet zo belangrijk). Maar ik denk toch dat die eigen agenda en die eigen gedachten van z’n levensdagen niet zal leiden tot een evolutionaire sprong omdat er ineens iets heel anders tevoorschijn komt na de paring, iets heel onverwachts, iets nog nooit gezien.

    2. Leonardo: Vrije wil!? Als ik slaperig of moe ben, is dat niet uit vrije wil en ik kan wel willen om niet moe te zijn, maar dat lukt niet. Als ik heel nodig naar de wc moet, is mijn vrije wil niet sterk genoeg om dat tegen te houden. Als ik honger heb kan ik dat vrijwillig een tiidje negeren, maar tot een bepaalde grens. Wat ik echt 100% uit vrije wil doe daar ben ik nog niet echter.
      the genome is "filled with elements that have their own agenda in mind": dat is een uitspraak zeer geschikt voor filosofische analyse. "their own agenda" = 'selfish' elements = een metafoor die je figuurlijk moet lezen. "in mind": is ook een metafoor want een DNA element heeft natuurlijk geen 'mind'. Maar als je denkt van wel, laat maar horen ;-)

    3. haha, Gert,
      Wat betreft naar de wc moeten: des te ouder je wordt, des te minder vrije wil je krijgt

    4. grrrr... daar heb je een pijnpuntje te pakken :-(
      Daarentegen levert de tegenwoordige jeugd hun vrije wil vrijwillig in: ze zijn verslaafd aan smartphone, Instagram, twitter, whats-app en misschien wel aan party-drugs...


  13. Evolutionary biologist Zach B. Hancock interviews Larry Moran on his youtube channel:

  14. I watched the video last night. Very exciting! It is indeed very strange that it is simply assumed that there is no more junk DNA after ENCODE. I myself am still from the junk era. However, this is not the reason why this "paradigm-SHAFT" should not be accepted. It simply has not been shown that there is no junk. At most, it has been shown that there is a high degree of non-specific binding, as Laurence Moran also says.

  15. Yes, the video is worth watching even if you have read the book. It is helpful to see the author explaining and defending several of the claims in his book.
    Marleen: "I myself am still from the junk era." Long ago I learned about 'introns' and was shocked! I learned about repeat sequences and thought that is really strange. I learned about selfish DNA. But I never added it all up to 90%! Did you realize that at the time?
    Marleen: "paradigm-SHAFT": I don't understand the word SHAFT, it means nothing to me, so it isn't helpful at all.
    Marleen: "It simply has not been shown that there is no junk." It has not been shown or proved that 90% is junk! It is a hypotheses! It is NOT a fact, nonetheless the "90% of your genome is junk" is stated as a fact: it is in the title of his book! and is many times repeated in his book. Both are hypotheses, it is an open-ended problem. You can only prove '90% is junk" if you have deleted 90% of your genome and are still alive! haha!

  16. Gert,

    It is the case that junk DNA was considered real by almost everyone during a certain period of time that runs around the 1960s to the 1990s. I haven't kept track of it, but as soon as I can get to my old books, I'll check it out. But one can also check out the Wikipedia article on junk DNA (and its history) that L. Moran (User:Genome42) contributed to.
    In 1940 people already had good reasons to assume that a large part of our DNA should not be functional (Genetic Load).


    The conclusion that a significant part of our DNA is junk was made before DNA was discovered as a molecule and historically preceded the much later option (ENCODE) that as much as 80% of our genome has a function. Seen in this way, it is not the junk camp that has to again prove that 90% junk exists, but the camp that opposes this with proof.
    As I'm sure Moran's book makes clear, junk DNA refers to non-coding DNA and that's all the tRNAs, rRNAs and various transposons and so on. It is therefore clear that you cannot do without it.
    Why it's important to Moran that junk DNA is acknowledged probably has to do with his strong aversion to anything adaptationist. The adaptationists say that junk DNA cannot exist because natural selection leaves all "beneficial" traits and non-functional DNA, that must be replicated with every cell division, is not part of it. So junk DNA in a way supports the neutral theory.
    I would like to know how the genetic load problem is bypassed in the case where our DNA is 80% functional.

  17. Hi Marleen, apparently you have studied the problem seriously. I have consulted the textbook Srb, Owen, Edgar (1965) 'General Genetics' second edition, which was prescribed when I entered my biology study in 1971. We learned genetics from that book. There is no 'non-coding DNA', no 'introns', 'no junk DNA', no transposons in the index! How could it be? In stead it was the time of 'the one gene - one enzyme hypothesis'. Hypothesis! Scientists at the time were busy proving that genes coded for enzymes!!! and how they did it. They just produced the genetic code table. There is no 'neutral mutation' let alone 'neutralism theory' in the index! Nothing of the sort.
    In another textbook Stent, Calendar (1978) 'Molecular Genetics. An introductory narrative' 'noncoding DNA' is not in the index, neither 'introns', 'neutralism' let alone 'junk DNA'!
    Do you have textbooks from the 70s with those concepts discussed?

    1. Het allereerste artikel over neutrale mutaties was Kimura in 1968, en het eerste artikel met veel impact was King & Jukes 1969. Het idee non-coding DNA bestond wel, maar alleen als promoters, en andere regulerende elementen, zie lac-operon van E. coli. Operon staat wel in Srb. 'Genes in pieces' is van1978. 'junk dna' is van 1970 of 1971. Gen duplicatie was bekend, in 1970 - al die hemoglobines bv.
      De 1970's zijn te vroeg voor dit soort termen in leerboeken: die hebben toch gauw 5 jaar vertraging.
      Minkoff 'evolutionary biology' is van 1983 en heeft neutral mutation, en is verder heel traditioneel, met ook nog iets van een overzicht van het dierenrijk.
      Van 1970 tot minstens 1975 was er een nogal vurig debat over neutrale mutaties vs selectie op enzym variatie. Toen waren electroforetische verschillen in loopsnelheid van verschillende enzymen het meest moleculaire populatiegenetica werk. Iets van genen weten kon alleen door het mappen van mutanten.
      Het is makkelijk te vergeten hoe snel de wereld gaat)
      (Vergelijk: de AppleII begon zijn opmars in 1980 of 1981; in 1982 was er een klein tekstverwerk programmaatje dat fouten kon verbeteren en wel 8 (nou j zoiets) woorden kon verplaatsen. De grote tekstverwerkers van de secretaresses hadden 11 inch discs en 8kb capaciteit ...

    2. Misschien dat 'junk-DNA' voor het eerst in een leerboek verscheen in 1991, in Li & Graur, Fundamentals of Molecular Evolution, in een bespreking van de C-value paradox. LI & Grauar geven 4 hypothesen: alles functioneel, junk, selfish en strucctureel. Li & Graur schrijven "There is very little evidence for the first hypothesis". Ze geven de voorkeur aan de tweede. Dan Graur is ook actief geweest tegen ENCODE.

    3. Gerdien schreef "promoters, en andere regulerende elementen, zie lac-operon van E. coli.":
      dat soort noncoding DNA was bekend, maar (1) het was functioneel, (2) niet-functioneel noncoding DNA was niet of nauwelijks bekend. En zeker was niet bekend de totale hoeveelheid in het DNA.
      In Bruce Alberts ... James D. Watson (1983) Molecular Biology of the Cell, komt junk DNA niet voor in de index, maar op pagina 26 weten ze:
      "Yet it seems that only a small fraction of this DNA -perhaps 1% in human cells- carries the specifications for proteins that are actually made."
      Nog extremer dan Moran!
      Heb jij als medewerker in de jaren 70 AppleII computer gebruikt? Ik heb zelf geen actieve herinnering dat ik ooit computers heb gezien op het lab in die tijd. Gebruikte je hem uitsluitend als tekstverwerker of kon je er ook rekenwerk mee doen? Waarschijnlijk werden toen pocket calculators gebruikt, nu vrijwel uitgestorven...

    4. In de jaren 70 was er geen Apple computer op het lab. De eerste AppleII is gekocht in 80 of 81, ik weet niet precies wanneer. Ik gebruikte hem om berekeningen te doen voor dingen als selectie en aantalsregulatie. De AppleII was voor berekening, en je moest zelf programmeren in BASIC. Er waren geen voorgekookte programma’s voor bv statistiek: SPSS ging nog op de mainframe. Tekstverwerking kwam na rekenen. Ik weet zeker dat ik in 1982 voor het eerst met een klein tekstverwerkprogramma werkte, ik dacht op de Apple, en niet op de grote tekstverwerker van de secretaresses (waar wp eigenlijk niet aan mocht zitten; secretaresses zijn ook uitgestorven). 1982, want het was een stukje voor Trouw tegen creationisten, naar aanleiding van een tentoonstelling in Blijdorp waar creationisten een stand hadden.

  18. I think dr Korthof's issue see July 2, 2023 at 9:58:00 AM GMT+2 , is relevant in the 'junk' discussion

  19. Ik kan pas morgen bij mijn boeken komen en weet dus nu nog niet of er in ‘mijn tijd’ (1987) al geschreven werd in de studieboeken over junk-DNA. In het boek “Evolution” van N.H. Barton uit 2007 staat bijzonder veel vermeld over junk-DNA, al blijven de definities vaag. Maar dat is dan ook een relatief jong boek.

    Intussen heb ik een artikel uit 2016 van Dan Graur gelezen. De titel is “Rubbish DNA: The functionless fraction of the human genome” dat te vinden is op


    waar de PDF ook gedownload kan worden. Het is duidelijk dat Graur enorm kwaad is op het ENCODE-project en de auteurs, die volgens hem lijken op de ergste young-earth creationists!
    Hij definieert junk-DNA redelijk duidelijk en maakt een onderscheid tussen biochemische activiteit (ENCODE) en biologische functie (evolutionary biologists). Het artikel is zeer de moeite waard om te lezen. Behalve de definities, laat het ook wat van de geschiedenis van het concept zien. Het is dan inderdaad moeilijk te geloven dat, met alle ontdekkingen die sinds 1930 gedaan zijn, ENCODE er in een ogenblik in zou slagen al de argumenten waarom junk-DNA aanwezig is in ons genoom omver te werpen.

  20. Ger,

    Vandaag heb ik eindelijk kunnen kijken in mijn boeken, die trouwens minder oud zijn dan ik me herinnerde. In geen van de drie wordt expliciet over ‘junk DNA’ gesproken.

    In Molecular Biology of the Gene van Watson at al. 4th edition uit 1987, wordt er kort geschreven over introns en hoe deze een voordeel kunnen opleveren voor het organisme. Meer niet.

    In (de Italiaanse versie van) An Introduction to Genetic Analysis van Griffiths et al. uit 1996 wordt uitgebreid vermeld dat er ook DNA zonder functie bestaat. Onder andere over niet codificerend functioneel DNA zoals telomeren en centromeren. Dan wordt Spacer DNA genoemd, ofwel DNA waar men de functie niet van kent.

    In Molecular Cell Biology van Lodish et al. uit 1996 wordt ‘extra DNA’ genoemd waarvan gezegd wordt dat het junk-DNA is maar dat de auteurs deze term niet willen gebruiken (p.307)

    Ik heb uitgebreid geblogd over junk DNA. Het woord junk DNA en het concept vormen geen enkel probleem voor mij.

  21. Marleen, thanks for both comments.
    The evolution textbook N.H. Barton 2007 you mentioned is in fact a surprising modern book, it is not really outdated. I am working now on a new blog which includes Barton et al. It is the only Evolution textbook I know written by 5 authors.
    Thanks for 'Rubbish DNA: The functionless fraction of the human genome'! It is huge, like a book! 87 pages pdf. Graur mentions Popper (he has not been forgotten! still popular among scientists!).
    About ENCODE: it is absolutely important to separate their DATA and their INTERPRETATION and not focus exclusively on their interpretation of the data. The data deserve careful examination, should be investigated and compared with other species (chimpanzee!). We could gain insights from the pervasive transcription data about evolution, origin of life, eukaryotes versus prokaryotes, etc. Their data should certainly not be thrown in to the rubbish bin! They contribute to the genetic load and metabolic costs of an organism. We should understand them!

    I include Watson Molecular biology of the Cell (1983) in my new blog.
    Here is Griffiths et al 8th edtion English complete pdf:

    Lodish et al. Molecular Cell Biology fifth edition is also available as pdf.
    'junk DNA' is not present, but 'noncoding DNA' many times.

    Do you have a link to your blogpost about junk DNA?


  22. Thank you Gert for all the information.

    The blogposts in which I blogged about junk DNA can be found under this link:


    The last blogpost with no less than 137 comments is this:


    I have to read them all again to know what was going on at the time.

    Maybe I'll come back to it. In the mean time I wait for your next blogposts

  23. Marleen,
    I totally forgot about your blogpost about ENCODE. I see I was involved in the discussion too (for a small part). Many comments are heated and very strong opinions! I also forgot my own blog about ENCODE:
    ENCODE project is een mijlpaal, maar 80% functioneel dna roept vragen op, 18 Sep 2012. I reread the piece, and I think they are accurate.


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