19 December 2022

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

 

05 December 2022

NIA image recognition software has learned thousands of species but still classifies humans as Highland Cattle

Highland Cattle - Bos taurus var. highland
with 100.0% probability.

Highland Cattle - Bos taurus var. highland
with 100.0% probability.
©https://thispersondoesnotexist.com


Humans have a lot in common with Highland Cattle! Let me explain...

NIA (Nature Identification API ) is the image recognition software that helps identify animal and plant species at observation.org. It all started in 2019 as ObsIdentify and was introduced on the Dutch website waarneming.nl. It is also available as an app. The purpose is automatic identification of animals and plants. The identification of a species is always presented as a prediction, it is never the final answer. A human moderator always makes the final decision. It is especially useful for inexperienced users (and fun for the experienced users). Since its appearance NIA was trained with a growing database of thousands of validated pictures. One would expect that its success rate would steadily increase. which is probably the case. But, I don't yet have definitive data about NIA's performance. However, I have noticed that its predictions have changed in the past few years.

However, unexpectedly, it is still easy to fool the software with pictures of human faces. For example the above computer generated image of a person is classified as Highland Cattle with 100.0% probability. I find that fascinating. How is it possible that this successful software makes such weird errors? Naturally, it sometimes confuses ponies or horses with highland cattle, but human faces? They are in a completely different category. What feature in the human face could be the cause of these mis-identifications? Maybe hair? Compare these two images:

Highland cattle 19.9%
©https://thispersondoesnotexist.com

  
Highland Cattle 98.0% (modified picture)
©https://thispersondoesnotexist.com

Clearly, duplicating part of the girl's hair enhances the confidence of the 'Highland cattle' prediction from 19.9% to 98.0%. It doesn't matter that it is a distorted face. The specific pattern and color of the hair is enough. 

Apparently, other people find this fascinating too. Some people do not only test their selfies, but also unnecessarily save them to the database. The system does not reject human faces automatically, simply because it thinks they are animals. I found the following pictures among the Photos of the 'Highland Cattle' of observation.org:

Highland Cattle 24,2%

Highland Cattle 79.1%

Highland Cattle 33.0%

Highland Cattle 27,6%

These four pictures are identified as Highland Cattle albeit with low probability, except for the dog. Obviously, they have not yet been seen by moderators. Otherwise they would have been rejected, I guess.

We humans have a lot in common with Highland Cattle! The pictures are not hard to find. The website thispersondoesnotexist.com produces an infinite number of human faces. Many of them are identified as animals. Some of them with high certainty. Endless pleasure to find them.

I found a very carefully executed time-lapse of a young women with one picture every week during 2 years:

Hair Growth Time-lapse - 2 Years (youtube)

This is really a great idea, but the most surprising thing is that every picture is classified as 'Cattle' or 'Highland Cattle' by NIA (observation.org):

Cattle - Bos taurus 81.9%

NIA image recognition predicts Highland Cattle
- Bos taurus var. highland with 99.4% probability.

I tested 10 pictures of the time-lapse: all are 'Cattle' or 'Highland Cattle' with probabilities ranging from 32% up to 99.4%. Again: we humans have a lot in common with Highland Cattle! For example: hair.

The NIA algorithm makes mistakes a child would not make. So, is this a stupid mistake? No, not really. It just views the world differently. And, it hasn't been trained to recognize humans! It is very good at what it has been trained to do: recognizing wild animal and plant species. NIA would only be in serious trouble when it identifies a wrong animal or plant species with 100% certainty.

Most humans are very good at recognizing human faces. The average person can recognize 5000 human faces and superrecognizers up to 10,000 humans. But most humans are very bad at recognizing wild animal species. Exceptions are top observers such as Remco Hofland with 8694 species. At the Dutch website waarneming.nl top observers Ruud en Betty van Middelkoop have a list of 9522 species. So, I guess, NIA / ObsIdentify most 'know' at least 10.000 species...

 

 

For more pictures see this page!


 Update 12 Dec: small edit in text.

 

Other blogs about NIA


14 November 2022

De liegende pakketbezorger. PostNL: 'Bezorgen lukte niet'

'Bezorgen lukte niet'

'Bezorgen lukte niet, zending gaat naar PostNL punt'

We zaten zaterdag 12 november op een pakketje te wachten dat bezorgd zou worden tussen 10:55 en 12:55 uur. Tegen 13 uur staat er op de website PostNL: 'Af te halen vanaf: maandag. Bezorgen lukte niet, zending gaat naar PostNL punt.'

Dit is een leugen. Wij waren de hele ochtend thuis.

Het is dus een valse beschuldiging aan ons adres. Steeds heeft er op de website PostNL track and trace gestaan: bezorgtijd tussen 10:55 en 12:55 uur.

Wij bezorgen het vandaag tussen 10:55 en 12:55

Wij hebben niet gekozen voor bezorgen bij een afhaalpunt. Wij wilden het thuis bezorgd hebben. En we waren thuis. De bel deed het. Er stond geen keiharde muziek aan. We waren niet in de tuin.

Ik denk dat de pakketbezorger dacht: Als ik al die pakketjes bij het afhaalpunt deponeer, hoef ik niet al die adressen af. En ben ik veel sneller klaar.

Maar als PostNL eerst zegt dat het pakketje thuis bezorgd wordt, dan is dat de tweede leugen. Of moet ik zeggen: 'onjuiste informatie'? We hebben dus onnodig thuis zitten wachten. Ook de webshop geeft onjuiste informatie over de bezorging.

Ik erger mij hier ontzettend aan. Als liegen bij PostNL de nieuwe standaard wordt, dan kunnen ze ook beweren dat het pakketje WEL thuis bezorgd is, terwijl de bezorger het gestolen heeft. Als je liegen accepteert is het hek van de dam. Een kleine leugen maakt een grotere leugen makkelijker.

De derde 'leugen', of moet ik zeggen 'onjuiste informatie', is beweren dat het pakketje pas maandag af te halen is, terwijl het zaterdagmiddag al bij het afhaalpunt (supermarkt) ligt.

Ik heb dit ook in het feedback formulier van PostNL als feedback gegeven. Ik ga ook aan de leverancier van het pakketje mailen dat PostNL een onbetrouwbare pakketbezorger is en dat ze die niet meer moeten inschakelen. 

Heeft U ook dergelijke ervaringen? Laat het weten.

 

De bezorger die bij het verkeerde adres aanbelde

15 nov 22

De reactie van de leverancier HomeWizard op mijn mail is teleurstellend. Het interesseert ze allemaal niet wat er fout is gegaan, want de klant heeft uiteindelijk (via een omweg) toch het pakje gekregen. Het maakt hen niet uit dat je een artikel hebt gekocht waar van zij zelf aangeven dat het thuis bezorgd zou worden, en dat de bezorger heeft gelogen. Ze willen niet van een leugen spreken: 

"Mogelijk heeft de bezorger bij het verkeerde adres aangebeld bijv."

Pardon? Een bezorger die bij het verkeerde adres aanbelt, constateert dat niemand open doet en vervolgens het pakketje bij een afhaalpunt deponeert? Een analfabeet? En dat is normaal? En dat is acceptabel gedrag? *)

Van 'klantvriendelijkheid' hebben ze bij HomeWizard nog nooit gehoord. Excuses voor het ongemak kan er bij HomeWizard niet af. HomeWizard: als dit het nieuwe normaal is, wees dan eerlijk en zet op uw website dat het pakketje niet altijd thuis bezorgd wordt omdat de bezorger bij het verkeerde adres kan aanbellen. Of kies een betrouwbaardere pakketbezorger om uw mooie producten mee te verzenden.

*) de straatnaam staat op een standaard straatnaambord aan het begin van de straat, en alle huizen zijn van duidelijk leesbare huisnummers voorzien. Er waren geen obstakels op straat of bij de voordeur.


U hoeft zich niet te identificeren

Het meisje van het afhaalpunt zei: hier staat: U hoeft zich niet te identificeren. En ik kreeg het pakje mee door alleen mijn naam te noemen. Een half uur later kreeg ik de mail van PostNL die als bewijs moest dienen:
Met dit bewijs kun je het ophalen
 
Het kan dus niet waar zijn dat ik het pakje zonder identificatie kon ophalen. Het meisje was behulpzaam. En verzon een leugentje. Laten we maar zeggen: een geluk bij een ongeluk.

 

09 November 2022

De boekhandel en de elektrische auto. Drogredenen en inconsequent denken!

Ik was aanwezig bij een boekpresentatie van het boek van Geert Buelens (2022) Wat we toen al wisten. De vergeten groene geschiedenis van 1972. Het boek gaat over de geschiedenis van de milieubeweging in Nederland vanaf het jaar 1972. In dat jaar verscheen het beroemde The Limits to Growth van de club van Rome. Na afloop stelde iemand een vraag. Het was eigenlijk geen vraag maar twee opmerkingen. En het onderwerp, de elektrische auto, was niet aan bod geweest in de lezing.

De 'vraag' was:

  1. "die mensen die elektrische auto's kopen doen dat alleen maar omdat het goedkoper is"
  2. "de milieukosten voor het produceren van de elektrische auto's haal je er pas over 20 jaar uit."


DENKFOUT 1: vraagsteller gaat uit van een valse tegenstelling: het is volgens haar óf-óf. Fout. Want het kan ook én-én zijn. Die mensen kunnen het zowel om het geld als om het klimaat doen. Het één sluit het ander niet uit. Een voorbeeld: besparen op energie gaat meestal samen met kostenbesparing. 


DENKFOUT 2: Als je in een elektrische auto rijdt met de verkeerde motieven dan is het slecht voor het milieu. Fout. Want, motieven kunnen niet slecht zijn voor het milieu. Wat, als die elektrische rijder het wél om het klimaat deed? Is het dan wel OK? Of zijn elektrische auto's sowieso slecht voor het milieu zoals vraag 2 suggereert? In dat geval maakt het helemaal niet uit welke motieven die mensen hebben. Motieven zijn helemaal niet relevant voor het milieu effect.


DENKFOUT 3: Alle elektrische rijders hebben dezelfde motieven. Fout. Er zijn in Nederland 300.000 elektrische personenauto’s [1]. De meerderheid van elektrische rijders laadt hun auto op met eigen zonnepanelen. En langs de Nederlandse snelwegen staan snelladers die volledig op zonne-energie werken.  Er zijn dus elektrische rijders die de juiste motieven hebben én rijden op duurzame energie.

 

DENKFOUT 4: de keuze voor de elektrische auto framen als een privé zaak. De keuze wordt dus geherdefinieerd als een zaak van persoonlijke motieven. En dan ook nog als foute motieven. Maar het bevorderen van duurzaam vervoer en het terugdringen van fossiele brandstoffen is een Overheidsbeleid [2]. Denk aan subsidies voor elektrische auto's (geen wegenbelasting en aankoopbelasting). Hebben de bedrijven die ruim 107.000 publieke laadpalen in Nederland hebben geïnstalleerd ook verkeerde motieven?

 

GEBREK AAN VERDER DOORDENKEN: de vraagstelster wordt niet aan het denken gezet door haar eigen vraag. Als elektrisch rijden goedkoper is, waarom blijft iedereen dan doorrijden in fossiele brandstof auto's? Zijn die dan beter voor het milieu? En hoe kan het eigenlijk dat elektrische auto's goedkoper zijn? (ze zijn goedkoper in gebruik, niet in aanschaf). Is het slecht om in een auto te rijden die efficiënter omgaat met energie? 


INCONSEQUENT DENKEN (1): omdat de milieukosten voor het produceren van de elektrische auto's 'pas na 20 jaar terugverdiend zijn', kun je beter benzine of diesel rijden. Fout: een fossiele auto stoot zijn hele leven CO2 en giftige gassen uit. Die milieuschade wordt alleen maar groter in de loop der jaren en wordt dus nooit 'terugverdiend' [3],[4].


INCONSEQUENT DENKEN (2): berijders van fossiele auto's hoeven geen verantwoording af te leggen, maar elektrische rijders moeten dat wel. Dat is niet consequent. Fossiele auto's stoten schadelijke uitlaatgassen uit zoals CO2 en stikstofoxiden. Fossiele rijders moeten daar verantwoording van afleggen [3].

 

Ik was nogal teleurgesteld door de anti-elektrische auto houding van iemand die beroepshalve de hele dag tussen de boeken zit! Zij zou beter geïnformeerd moeten zijn! Boek: 13 misverstanden over elektrische auto’s !


 

Noten

  1. Aantal elektrische auto’s verdrievoudigd, RAI, 22 september 2022
  2. Het is een ad hominem aanval, het gaat niet om de personen (en hun motieven) maar om Europees beleid: EU-verbod op de verkoop van nieuwe benzine- en dieselauto's vanaf 2035. En: Europees Parlement: laadstations moeten om de 60 kilometer beschikbaar zijn. En: Vanaf 2035 moeten alle nieuwe auto’s in de hele EU emissieloos zijn (boek: Elektrisch rijden – ja of nee?), en Nederlands beleid (2023): je krijgt plm 3000 euro subsidie voor de koop van een elektrische auto en voor een tweedehands elektrische auto 2000 euro. Bij een apk dieselauto's wordt altijd getest of een diesel een goed werkend roetfilter heeft (RVO). Dus: hoezo een privé zaak?
  3. Heeft ze zich ooit afgevraagd hoe schadelijk benzine en diesel auto's voor mens, milieu en klimaat zijn? Ooit gehoord van de sjoemeldiesel affaire? (zie: wikipedia artikel). Zie ook: 'Dieselrijders zijn jarenlang misleid door Volkswagen (Consumentgids december 2022 pagina 46). Het gaat om: Volkswagen, Citroën, Dacia, DS, Mercedes-Benz, Opel, Peugeot en Renault. Zie ook: Stellantis US arm pleads guilty to fraud and conspiracy in diesel emissions investigation.
  4. De terugverdientijd van een elektrische auto voor het milieu begint bij ongeveer 2,5 jaar Vereniging Zakelijke Rijders.

  

Vorige blogs

  1. Volkswagen's misdaad tegen de volksgezondheid en het milieu 25 september 2015 
  2. 5 okt 15 Greenpeace waarschuwde al in 2011 voor 'The Dark Side of Volkswagen' 
  3. In ruil voor sponsoring maakt Vogelbescherming reclame voor sjoemelsoftware fabrikant Volkswagen 29 februari 2016

 

25 October 2022

Solar eclipse 25 Oct 2022

Solar eclipse 25 Oct 2022

video created with SONY RX10 IV max zoom 600mm
ISO speed rating 80 (that is very low!)
It was cloudy weather, but the clouds functioned as a 'sunscreen' to protect the camera and at the same time it created a beautiful effect!
 
original video on YouTube  ©Gert Korthof
 
Solar eclipse. ©GertKorthof


picture:

underexposure: -2 EV (-2 stops)

exposure time: 1/25600 sec (extremely short)

ISO speed: 80 (very low)

local time: 11:46 (Amsterdam time zone)

Please note that I did not use a solar filter (I don't have one). This could be dangerous for your camera! Thanks to the clouds I could take pictures without damaging the camera. I am going to investigate which solar filter I could use for the next solar eclipse!



geographic visibility of solar eclipse (NOS)
(not visible in North and South America)

 

Vorige zonsverduistering

Zonsverduistering 10 juni 2021 groot succes! Sony A580 met eclipsfilter in 55-300 mm lens 10 juni 2021

18 October 2022

Johnjoe McFadden: Life Is Simple: How Occam's Razor Set Science Free and Shapes the Universe.

Johnjoe McFadden (2021)
Life Is Simple

The book Life is Simple by biochemist and molecular biologist Johnjoe McFadden is not about life, but is a history of Western science viewed from Occam's perspective. William of Occam was a thirteenth century theologian and inventor of what is now known as 'Occam's razor'. I really have to blog about this useful and entertaining book.

Occam's razor is the preference for the simplest solutions to scientific problems; theoretical entities should not be multiplied beyond necessity; plurality should not be posited without necessity; it is vain to do with more what can be done with less. This seemingly simple principle of parsimony revolutionized theology, philosophy and science. McFadden selects various scientific revolutions of the past six centuries to illustrate Occam's Razor in action.

Occam used his razor to strip away everything in medieval philosophy except God's omnipotence. Furthermore, he claimed that the only way to gain knowledge is through experience and observation. Not by syllogism. For Occam, this was another important distinction between science and religion. Science, he maintained, yields probabilities, not proof. A very modern understanding! Despite all this Occam never doubted the existence of God, nor the central tenets of Christianity. Only faith gives us access to theological truths, he wrote. Remarkably, McFadden does not comment on the fact that Occam did not apply his razor to the question whether God was a necessary entity in our worldview and whether the elimination of the God hypothesis could simplify our view of the universe.

A good example of the application of Occam's razor is the replacement of the geocentric model with the heliocentric model of our solar system. Copernicus argued that

"accepting that the earth rotates every day, rather than the sun, moon, planets and stars,  provides a much simpler cosmos." (214/687, ch 7).


(wikipedia)
In the geocentric model each planet has its own epicycle:

 

Epicycles of Mercury, Venus, Mars, Jupiter, Saturn
©Vliegende Schotels en andere Raadsels van het Heelal,1978

Copernicus eliminated five planetary epicycles and by placing the sun in the center of the system he removed all epicycles, thereby simplifying the whole solar system.

Furthermore, "Ptolemy's geocentric system could not explain why Mercury and Venus are always seen to be closest to the sun at sunrise and sunset". He added an arbitrary rule to account for this. But Copernicus positioned "Venus and Mercury to a position between the earth and the sun so that they became inner planets. In this position, their closeness to the sun in the sky is simply due to their closeness to the sun in reality. In this way, an arbitrary feature of the complex model becomes an inevitable consequence of its simple alternative." Furthermore, the mysterious behaviour of Mars, Jupiter and Saturn was explained in the heliocentric model by positioning them beyond the orbit of the earth: they became the outer planets.  This is a very convincing demonstration of the usefulness of Occam's razor. Although I knew the Copernican revolution, and I knew that heliocentrism was a simpler theory, I never made the connection with Occam. I never had any knowledge of the life and work of William of Occam. His philosophical approach reminds me of modern philosophers Gilbert Ryle and Alfred Ayer (see notes).

McFadden did a great job. He revisits the big revolutions in science and shows how Occam's razor is at work, whether or not the scientists involved acknowledge this. The writing style is certainly not dry or academic. There are a lot of anecdotes that contribute to the story and make one continuing reading. 

Galileo mentions Occam several times in his early lecture notes, and argued that "the single daily rotation of the earth is much simpler and more natural than having the sun, moon, planets and the stars rotating around the earth every day." (298/687). A perfect example of Occam's razor at work. Many of the most important scientists in the history of science were following Occam. McFadden writes: "The razor had made its way from the thirteenth century, via the via moderna, through to Leonardo, Copernicus, Kepler, Galileo, Boyle and now to Newton to become a central plank of modern science." (Ch11). Add to this list: Hobbes who took Occam's reductionist approach further than anyone previously dared and Lavoisier's dismissal of phlogiston. In biology the vital spirit was shown to be an entity beyond necessity. 

Life's razors

Occam was ahead of his time. Amazingly, he described a form of natural selection! He wrote that animal properties such as teeth might have arisen by chance and be retained because 'the animals survive'. Really amazing! But Darwin made the supernatural watchmaker superfluous. 

In chapter 14 McFadden reveals some rather remarkable facts about Darwin and Wallace. In 1855 Alfred Russel Wallace wrote a paper 'On the law which has regulated the introduction of new species'.  At the time he was collecting specimen for a living in Indonesia. He sent the manuscript to the editor of a British natural history magazine. The subject was the same as the one Darwin had been working on for the past 20 years. Wallace proposed that any theory about the origin of new species should explain nine bio-geographic and paleontological facts. Next he formulated a general law that captured all those facts, the Sarawak law. It was a descriptive law, without causal mechanisms. But it was a revolutionary idea. Never had such a law been formulated before. It was 4 years before Darwin published his Origin of Species. McFadden interprets the Sarawak law as an example of Occam's principle. I did not know about that manuscript. And McFadden rightly believes that it should be far more widely recognized as key to the development of the theory of evolution. In 1858 Wallace (still in Indonesia) wrote a letter to Darwin with his explanation of the Sarawak law: natural selection. This letter and the subsequent events are well-known. Except the following: "Despite Darwin's habit of keeping nearly all his letters, all those written to Darwin by Wallace, Hooker, Huxley or Lyell during that crucial year of 1858, including Wallace's original Ternate paper manuscript, have been lost." Have been lost! Very mysterious! Could that be an accident or is it intentionally 'lost'? The work of Wallace surely deserves further study. McFadden concludes that "natural selection is probably the most Occamist reduction of a multitude of arbitrary facts into a simple law."

Again a new and interesting fact: in 1867 J. D. Campbell noted in his Reign of Law that Darwin had in fact not explained the origin of new species. A criticism repeated many times by Darwin critics and evolutionary biologists in the years thereafter. Again an issue that deserves further study.

In chapter15 about heredity and genetics McFadden points out the DNA, the genetic code and mutation are a perfect example of explaining the diversity of life on earth with a few simple concepts. Indeed, DNA and the genetic code are universal for life on earth. However, I disagree with his claim that the genomes of biological species are very nearly as simple as they can be. They are not (pseudo-genes, junk DNA, introns, Alternative splicing, X-inactivation, mitochondrial-DNA, etc).

The Cosmic Razor

In Part IV The Cosmic Razor McFadden addresses the laws of physics, Einstein, general relativity and quantum mechanics. He concludes that Einstein made the universe less complex and more simple. All this is evidence of "the unreasonable effectiveness of Occam's razor."

In his final, and I would say speculative, chapter 'The Simplest of All Possible Worlds?' McFadden concludes that the universe is close to being as simple as it could be while remaining habitable.

This book is a dazzling tour through the history of science and the universe. It is also well-researched. McFadden is as equally at ease with theology, philosophy, biology, physics and astronomy as with the history of those sciences. The unifying theme is Occam's razor. I think it is a successful project. But an unfinished project, I think, because there are so many facts and issues that demand further exploration.

While reading Life is Simple I remembered that theologian Richard Swinburne based his argument for the existence of God on the same principle as science does: the simplicity principle or Occam's razor. Swinburne mentions Occam. But instead of demolishing the God hypothesis, Swinburne exploits it to argue that God is the most simple explanation of the universe! Far simpler than the materialist explanation. Not what one would expect. Is this a bogus or an ingenious claim? I have to read Swinburne's book again and find out. I would like to know McFadden's opinion about this! McFadden did not discuss whether Occam's razor would eliminate God.

Why am I so interested in the history of science? I think the history of science, as it is described by McFadden, gives us hope. There are things in this world that show progress in the long run despite a relapse to barbarism and war. Bombs, tanks and kamikaze drones can destroy cities and people, but cannot destroy scientific knowledge. That at least may give us hope.


Update 11-11-22

Sabine Hossenfeld video Dit the Big Bang happen?

In this video she uses Occam's Razor without identifying it as such.

the simpler the better (here)
"The simplest explanation that we have found is the standard model for cosmology, which is based on Einstein's equations. The requirement that an explanation is simple is super important. It's because without it we can't do science at all."

A simpler theory is better, because Occam's razor. (youtube)


Update 3 Jan 2023

"While Occam's razor is a useful tool in physical sciences, it can be a very dangerous implement in biology. It is thus very rash to use simplicity and elegance as a guide in biological research. While DNA could be claimed to be both simple and elegant, it must be remembered that DNA almost certainly originated fairly close to the origin of life when things were necessarily simple or they could not have got going. (...) The genetic code is a very good example of what I mean. Who could possibly invent such a complex allocation of the sixty-four triplets? Surely the comma-free code was all that a theory should be. An elegant solution based on very simple assumptions – yet completely wrong."

(p.138-139 Francis Crick (1988) What mad pursuit.)

 

Notes

I bought this eBook at KOBO bookstore because of its exceptional price: € 3,99 and the intriguing title.  I found out that McFadden is also the author of Quantum Evolution. Life in the Universe (which I listed on my website) and Life on the Edge. The Coming of Age of Quantum Biology.

The influence of Occam on Gilbert Ryle: "he claimed that much of his philosophical work amounted to "Occamizing" (the reference is to William of Occam and his so-called "Occam's razor," which states that the best explanation is the simplest, the overly-complicated concepts and work of other philosophers." (source).

About A. J. Ayer se: Ayer, Alfred Jules (1910–1989) (encyclopedia.com) and:  A.J. Ayer And The Elimination Of Metaphysics in which Ockam is discussed. 

I reviewed Richard Swinburne (1997) Is there a God? on my WDW website. But after reading McFadden I have to reread it and find out how Swinburne uses Ockam to prove God.

Website JohnJoe McFadden