Two Nobel Prizes contradicting each other: Watson and Crick versus Tomas Lindahl

In 1962 Watson, Crick and Wilkins received the Nobel Prize for the discovery of the structure of DNA. In 2015, Tomas Lindahl received the Nobel Prize for the discovery of DNA repair. The first prize symbolizes the beauty of the DNA molecule. The second Nobel Prize symbolizes the weaknesses of the same molecule. So, in a sense, these prizes contradict each other.

Watson-Crick versus Lindahl

How the beauty of DNA (and the Nobel Prize?) blinded scientists for the weaknesses of DNA. Surprise: later those weaknesses were awarded a Nobel Prize!

Why is DNA perfect? Because DNA structure has been proven chemically correct and because the structure gives for the first time a satisfactory explanation of heredity in the biological world. Two problems solved at once. Heredity requires a a stable structure. Since all life forms from bacteria to humans are based on DNA, and life is some 3 billion years old, DNA simply must be a stable structure.

But then came Swedish scientist Tomas Lindahl. He showed that the apparent stability of DNA is not based on its structure, but –totally unexpected – on enzymatic repair and proofreading! So, DNA only seemed stable. But when he started his research, repair-enzymes were unknown. Clearly, his idea contradicted known facts. To see how it could be that all biologists were blinded by the beauty and the logic of DNA, we must first look at some details of DNA structure. Here, I follow the description of Francis Crick in What Mad Pursuit (1988).

In 1950, three years before the discovery of the structure of DNA, chemist Chargaff had found in DNA from many different species the amount of base A equaled the amount of T and the amount of C equaled the amount of G. The relative amounts of AT and CG in species differ. Chargaff did not conclude anything from his data about the structure of DNA. For Watson and Crick it was crucial evidence for AT and CG base pairing. Furthermore, AT and CG base pairs have equal dimensions. So they fit perfectly in a regular double helix. This is important for a very long molecule. Furthermore, to fit in the double helix the four bases have to be in the correct tautomeric form [1]. The beauty of the DNA model is that the specificity of base pairing gives a mechanism for replication (making a copy of DNA). This is a crucial function in biology (cell division, heredity!). Base pairing guaranties an exact copy of a DNA string. So, a crucial biological property is explained with an elegant chemical structure and its properties. "This base pairing is the key feature of the structure [of DNA]" (Crick, 1988, p.166).

One problem remains: a mutation implies that a wrong base is incorporated, but how can mutations occur if base-pairing is always correct? In their second paper in Nature, Watson and Crick wrote: 

"We believe that the bases will be present almost entirely in their most probable tautomeric forms." ... "spontaneous mutation may be due to a base occasionally occurring in one of its less likely tautomeric forms." [2]

So, they explained mutation theoretically and in principle, but had no data about how often the bases were in the 'correct' or 'wrong' tautomeric form [4], [6]. Consequently, they had no idea how often spontaneous mutation occurs. Neither did they seem to care. They simply assumed it occurs in negligible frequencies. They ignored the problem. It apparently did not invalidate the structure as a carrier of hereditary information.

In the years after 1953 scientists were busy with experimental validation of the double helix model. This took some time. Furthermore, solving the genetic code (how the DNA code is translated into proteins) took some hard work too. The solution of these two problems created a solid foundation of molecular biology. It was a tremendous breakthrough. In fact it was a solid foundation for the whole of biological science including evolutionary biology. It seemed no important problems remained. Crick wanted to move on to other fields of research! 

But, than came Lindahl: 

"It was at the time a far-fetched idea that DNA might be unstable in the cellular environment. (Lindahl Nobel lecture )

Tomas Lindahl discovered the intrinsic fragility of DNA. This constituted no less than a paradigm shift. For example: could anyone predict on the basis of the structure of DNA that Uracil could be present in DNA? (it normally occurs only in RNA!). That specific enzymes exist that continuously scan DNA for the presence of Uracil? Also: oxidative damage (see Lindahl Nobel Prize lecture). Water is a damaging agent for DNA! For a complete overview see the Wikipedia article about the endogenous causes of DNA damage.

Thirty five years after the discovery of the double helix and twenty six years after the Nobel Prize, Francis Crick published What Mad Pursuit (1988). By that time Lindahl had already published several papers demonstrating DNA-repair enzymes, his first in 1974. Surprisingly, I found only 1 page about DNA error-correction [3] in What Mad Pursuit. Not important enough? It did not fit in his DNA-is-perfect-paradigm? Yes, Crick knew very well mutations exist. He did experimental work with phage mutants. The mutations he studied were created with chemical mutagens (acridine, proflavin). So, the damage came from outside DNA, not from the inside. It wasn't spontaneous damage. Those mutations were not a threat to the DNA-is-perfect-paradigm. But Lindahl showed that DNA is inherently unstable in its normal cellular environment. Certainly a revolutionary idea. The reason must be clear by now: DNA must be reliable to function as a carrier of genetic information. Evolution produced complex beings such as humans. How much evidence do you need?

Summary 

Life exists - so DNA must be stable

Life exists - so DNA must be repairable

Watson, Crick, and Wilkins received the Nobel Prize for the structure of DNA. Although they did not explicitly claim DNA is stable, it is implicit in the statement that DNA is the carrier of hereditary information and the structure explains why this is the case. The Nobel Prize in Chemistry 2015 was awarded to Tomas Lindahl, Paul Modrich and Aziz Sancar for DNA repair. Repair implies DNA on its own is not a stable molecule. Although the Watson-Crick model is not refuted, its assumed stability certainly has been refuted. I didn't find this contradiction clearly in the literature [5]. I wrote this blog because it is worth pointing out.

In a next blog I will reveal important consequences of the stability/instability of DNA. This blog resulted from shocking remarks in Kondrashov (2017) Crumbling Genome (see previous blog).

 

Notes

1. Tautomerism is a dynamic equilibrium between two compounds with same molecular formula. Crick did not elaborate on the frequency of right/wrong tautomeric forms of the bases. In his What Mad Pursuit he writes that "Jerry Donohue, who shared an office with us, told us that some of the textbook formulas were erroneous and that each base occurred almost exclusively in one particular form." (p.65). (Which from?). Please note: "almost exclusively"!
2. Watson, Crick (1953) Genetical Implications of the Structure of Deoxyribonucleic Acid, Nature, May 1953. This is the second publication of Watson and Crick.
3. and a rough estimate about error-rate. I will return to that in a next blog. 
4. It seems there are no data and there is no theory to predict the frequency of wrong base tautomeres after 70 years! See:  "calculating the position of tautomeric equilibria in nucleobases is certainly within the grasp of contemporary quantum chemistry, and semi-empirical parameters on which the positions of these equilibria might most sensitively depend could presumably be identified." page 354 in Fitness of the Cosmos for Life. CUP 2008 [added: 9 Jan 2023] 
   
5. Intelligent Design theorist Michael Denton (1998) triumphantly claims that DNA is a remarkably stable structure! I added a paragraph to my review of his Nature's Destiny. How the Laws of Biology reveal Purpose in the Universe on my DWD website. [added: 10 Jan 2023]
6. Hubert Yockey (1992) is the first author where I found a probability of mispairing of the AT and CG base pairs. In an aside on page 300 he calculates that "the probability that adenine will mispair to cytosine is about 10^-4 x 10^-4 = 10^-8." About the CG pair he writes: "...the base selected has a probability of about 10^-4 of being in the imino or enol tautometirc form that leads to mispairing."  (see: keto–enol tautomerism). [added: 11 Jan 2023]

 

 

Further Reading

• Nobelprize.org: DNA repair – providing chemical stability for life, 2015. This gives a popular explanation of DNA repair. Recommended.
• Watson, Crick (1953) Genetical Implications of the Structure of Deoxyribonucleic Acid, Nature, May 1953. This is the second publication of Watson and Crick. The first (the most famous) was published April 25.
• Francis Crick (1988) What Mad Pursuit, paperback. Is a popular account of the discovery of DNA in Crick's own words. Recommended.
• Tomas Lindahl (1993) Instability and decay of the primary structure of DNA, Nature, 1993. (Abstract). "Although DNA is the carrier of genetic information, it has limited chemical stability. Hydrolysis, oxidation and nonenzymatic methylation of DNA occur at significant rates in vivo." (free pdf).
• Deborah E Barnes, Tomas Lindahl (2004)  Repair and genetic consequences of endogenous DNA base damage in mammalian cells, Annu Rev Genet. (full text) (makes clear that oxygen, water and metabolites damage DNA in rest).
  
• Blog page with list of DNA blogs of the past 10 years (2012-2022). 

Happy New Year 2023 for all my blog followers!

 

Happy 2023 for all blog visitors!

Do we need to worry about the increasing number of deleterious genes in our genomes? Review of Alexey Kondrashov: Crumbling Genome

Alexey S. Kondrashov
Crumbling Genome

The title of the book is a good description of what the book is about: the negative effects of deleterious mutations on individual humans and human populations. Deleterious mutations (literally: 'causing harm or damage') reduce our fitness and wellness. That is worrying by itself, but a 'Crumbling genome', a genome that is slowly disintegrating, is plainly alarming. Furthermore, healing our genome is fraught with ethical dilemmas.

Alexey S. Kondrashov (2017) 'Crumbling Genome. The Impact of Deleterious Mutations on Humans'. Kondrashov is a population geneticist and Professor of Ecology and Evolutionary Biology at the University of Michigan. He published in Nature about deleterious mutations, the evolution of sexual reproduction, the rate of human mutation, and mutation load.

In evolutionary biology fitness is defined as the number of offspring. Deleterious mutations reduce fitness. According to Kondrashov, we mostly care about our wellness, not about the number of children. Mutations are natural, inevitable and spontaneous in every species. Natural selection eliminates bad mutations. But 'the problem' is that natural selection in the human species has become less severe since the Industrial Revolution due to improvements in living conditions (efficient food production, better healthcare, etc). Especially, advances in medicine led to a dramatic relaxation of selection against many mutations. That means that natural selection less efficiently removes deleterious mutations from the population. Inevitably, mutations accumulate. Eventually, in the course of many generations, this will cause "a meltdown of fitness and wellness". That is his Main Concern. Indeed, enough to worry about. Additionally, there is the paternal age effect: older fathers produce children with more mutations [2]. When parents have children at older ages this effect will increase.

The magnitude of the effect is unimaginably large: "The genotype of a healthy human carries at least ~1000 substantially deleterious alleles." [5]. At the same time "~3% of humans are born with a Mendelian disease". "I believe that the total mutational pressure [6] on the health of young people, due to the contribution of de novo [7] mutation to both Mendelian and complex diseases, is between 0.02 and 0.05." (chapter 13). "a 20-year old father transmits to his child ~25 de novo mutations, and a 50-year-old father transmits ~85 de novo mutations." (chapter 13). How many mutations are removed from the human population? Of the ~10.000 protein-coding gene variants only ~1000 are subject to a substantial negative selection (chapter 8). Still, this doesn't mean, they are completely removed. By definition, only lethal mutations are removed.

Wellness is an important concept in Kondrashov's book (chapter 12). He defines wellness in terms of disease, disability, less-than-excellent health and death. Deleterious mutations reduce wellness without killing people. The standard definition of 'deleterious mutation' is 'having lower fitness'. Despite this, 'fitness' is not his biggest concern.

Ethical dilemmas

Probably the most important chapters are chapter 14 in which Kondrashov discusses ethical issues and chapter 15 in which he discusses what we can do about the growing number of deleterious mutations. He avoids the mistakes of the past (eugenics) and adopts a humanist ethics. This means that every human being has the same dignity and rights. No state should interfere with fundamental human rights. But, a humanist ethics also implies that prospective parents have duties regarding the genetic health of children. An important  thought experiment: 

"Imagine, for the sake of argument, that there is a pill that reverts some, or even all, clearly and unconditionally deleterious alleles in my germline cells to their normal alleles, without any side-effects." (14.3)[1].

Would you do that? Kondrashov argues that we have a moral obligation to take this hypothetical pill. The general reader will be interested in the very thoughtful discussion of the ethical aspects of how to prevent the birth of children with genetic diseases or how to prevent that deleterious alleles are increasing in the population. What can individuals do, what can governments do? Is it moral to produce children with a known disease risk? Is a mutation-less genome a realistic goal or is it a 'Mutation-less Utopia'? If it is an unrealistic goal, what can we do without Germline Genotype Modification? Kondrashov suggests that "It would be wise for governments to treat sperm storage as a public health issue." (young adults tend to have less mutations).

Another somewhat less ambitious but more focused approach, which I would prefer, is "removing mutagenic features from the human genome. This would substantially reduce the genomic rate of spontaneous deleterious mutations". An example is the "hypermutable CG sequences within protein-coding exons, which are responsible for up to 50% of pathogenic missense mutations causing Mendelian diseases."  (missense: one amino acid is replaced with another).  I also prefer this approach because it is a case of addressing mutagenic causes rather than the effects (mutations). It could be tried with the latest CRISPR-Cas9 method and in-vitro fertilization in mice or rats without causing any harm to the animal. (You don't feel mutations!). A similar approach would be improving DNA proofreading (copying fidelity) in somatic as well as in germline cells. If successful, couples who already are going to use vitro fertilization would be obvious candidates. A really easy and low-risk option would be exploiting the anti-mutagenic activity of for example Lavandula angustifolia (lavender) essential oil. Quoting Kondrashov: what is inherently wrong with active anti-mutagnesis?

Discussion

I think the concept 'deleterious mutation' is problematic and should be used carefully [8]. For example: "The genotype of a healthy human carries at least ~1000 substantially deleterious alleles". Then, what is 'healthy' and what is a 'deleterious mutation'? Furthermore, if the phenotypic effect of a 'deleterious mutation' depends on the rest of the genotype as well as on the environment, the concept of 'deleterious mutation' is even more problematic. It cannot simply be used to measure the health of the genome of a person. Another statement shows how complicated the concept 'deleterious mutation' is: "The genotype of an individual carries, on average, ~4 million derived alleles, thousands of which are substantially deleterious.". Should we really worry about deleterious alleles in our genomes, when healthy persons carry so many 'deleterious' alleles? Or should we redefine the concept 'healthy' person? As a consequence, nobody would be healthy anymore. It could be true. Even more confusing is the fact that some generally deleterious alleles have a conditional beneficence (genes associated with autism and schizophrenia). Furthermore, in 2016 Nature published an article with the title: "Why many ‘deadly’ gene mutations are turning out to be harmless." [4].

In chapter 15 Kondrashov expresses his and my own doubts: "Thus at the present level of understanding of the connection between genotypes and phenotypes, knowing your own complement of potentially disease-causing alleles can do more harm than good, by causing fruitless anxiety and encouraging unnecessary tests, without providing any medically actionable information." As mentioned above, there seems to be a discrepancy between the number of ~1000 substantially deleterious alleles per person and the fact that only between 2% - 5% of young people carry de novo mutations with cause Mendelian and complex diseases. With 1000 substantially deleterious alleles (in functional genes), we all should be sick, need medicines, or be admitted to a hospital. I wonder whether Kondrashov is too pessimistic in his estimates of the number of serious harmful mutations in our genome [5]. His Main Concern is 'only' the those mutations that do not reduce fitness, but do reduce wellness. Especially, because there are thousands of them in every human genome and they keep accumulating during the generations. Those thousands of deleterious mutations apparently can be tolerated. For now.  

It seems that we currently don't have enough knowledge to worry about deleterious mutations in our genome. In fact, I found many pages where Kondrashov admits that we do not know enough to conclude how bad deleterious mutations are for our wellness. And we don't know how much natural selection is relaxed since the Industrial Revolution. The book could be viewed as a stimulus to do more research. As it happens, after the book was published, a study in Nature appeared: 'A massive effort links protein-coding gene variants to health' [3]. That is precisely the kind of study we need!

Summary

The natural way deleterious mutations are eliminated is natural selection. Lethal mutations are eliminated automatically. The substantial deleterious but non-lethal mutations are not eliminated in humans. They accumulate in our genomes. They reduce our wellness. We could solve this with medicines and therapy, but this keeps the mutations in the population. A better solution would be somatic gene therapy or even better germline gene therapy. This creates ethical dilemmas. The concept 'crumbling genome' is not a well-defined scientific concept, but represents a paradigm shift in our view of the human genome.

 

Postscript 21 Dec 2022

After this post was published I noticed an article in Science: "Sequencing projects will screen 200,000 newborns for disease genes."  They wil test 200 rare, treatable genetic diseases. The test will only include well-studied genetic variants that are almost certain to cause symptoms before age 5. My comment: this is good for the children, but since it is postnatal screening, the mutant alleles will stay in the population. This is only screening, not (germline) genetherapy. 

Another Science article is about cancer gene therapy: Teen’s leukemia goes into remission after experimental gene-editing therapy: good for the patient, but it is somatic genetherapy and thus does not eliminate deleterious germline gene variants.

Notes

1. "If this is possible, couples should modify their germline genotypes in such a way that the child they will conceive is expected to have a substantially better life than a child conceived without any modification ..." (14.3)  
2.  "a 20-year-old father transmits to his child ~25 de novo mutations, and a50-ywar-old father transmits ~85 de novo mutations." (chapter 13)
3. A massive effort links protein-coding gene variants to health, Nature 25 October 2021. "The protein-coding portions of more than 450,000 individuals’ genomes have been sequenced, and analysed together with the individuals’ health data, revealing rare and common gene variants linked to various health-related traits."
   
4. Erika Check Hayden A radical revision of human genetics, Nature 12 October 2016
5. This is his summary of a publication 'Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing' (2012). However, the authors conclude: "However, our current best mean estimates of ∼400 damaging variants and ∼2 bona fide disease mutations per individual ... Apparently healthy individuals can, for a number of reasons, carry many disadvantageous variants without showing any obvious ill effects ...". So, in this case Kondrashovs estimates are too high.
6. 'mutational pressure': the steady-state rate of change of some characteristic of the population due to unopposed accumulation of mutations (chapter 6).
7. "A de novo mutation can occur in an egg or sperm cell of a parent, in the fertilized egg soon after the egg and sperm unite, or in another type of cell during embryo development." (source).
8. The idea that healthy people carry so many deleterious mutations has been proposed before by other scientists. For example in "A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes" (Science, 2012) the authors claim that "the average person has about 100 true loss-of-function alleles of which approximately 20 have two copies within an individual."  [That means the other 80 are in a heterozygous state. The 20 homozygous deleterious genes should cause 20 Mendelian diseases...!?]. The authors explain this as an "unexpected redundancy in the human genome." [but sooner or later this redundancy must be gone?]. This is an interesting remark: "...that strong negative natural selection is expected to act against the majority of variants inactivating protein-coding genes". Why has natural selection not removed these deleterious mutations? Maybe because these genes are not necessary anymore? for example: sour taste sensitivity. But this need not be valid for all variants. Added: 23 Dec 2022.
   

Related pages

• Gert Korthof: William Hamilton's worries about the future of the human genome is a page on my WDW website.
• Gert Korthof (2011) William Hamilton over de toekomst van het menselijk genoom (blog)
  
• Gert Korthof:  When The Tiger Comes, Freeze. What the Chinese whispers game tell us about evolution of complexity. A large part of Mendel's Demon (espcially chapter 4) is about mutation rate, error elimination and genome meltdown. (also on my WDW website).
• Homepage A. Kondrashov at the University of Michigan
  
• Wikipedia page (incomplete: this book is not mentioned!)
• See Google books for several pages for free.

 

 

Further Reading

• Evolution of the germline mutation rate across vertebrates, Nature, 1 March 2023. (important article). From the Abstract:
  
  • "Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent–offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes."