30 November 2023

Dutch consumer organization 'De Consumentenbond': iPhone is more sustainable than Fairphone

According to the Dutch consumer organization 'De Consumentenbond', the iPhone is more sustainable than the Fairphone.

In my previous blog (Dutch) I gave a detailed analysis of how the Dutch consumer organization 'De Consumentenbond' tests the sustainability of smartphones. My focus was on the methodology of testing and the presentation of the results. Here I add a new surprising discovery and a summary of the analysis in my previous blog.

Strange results!
(adapted,©RGvT)

The smartphone test of De Consumentenbond is a one-dimensional ranking of 311 smartphones based on a large number of criteria. This results in one top-ranking smartphone: 'The Best in the test'. The winner is the iPhone. Most criteria they use have to do with technical performance and features such as camera, screen, sound, battery longevity, etc. Each property contributes with a fixed percentage to the total score (100%). The sustainability filter was introduced only this year on the website in tests of smartphones. Sustainability is defined by properties such as conflict minerals, child labour [6], durability, etc. These properties (if known) are listed for each phone and are given either a quantitative (if possible) or a qualitative value. Surprisingly, sustainability is not included in the ranking of the phones (0%). (see my previous blog). The result is that the 'Best of the test' is not (automatically) the most sustainable smartphone. In fact 'The Best of the Test' can by definition never be the most sustainable, because sustainability contributes only for a small percentage (if not zero!) to the total score. That is how 'De Consumentenbond' defines the total score. It is good to realize that this is a choice, not a test result.

Confusingly, as it happens, the iPhone got a 9.3 and the Fairphone got a 8.4 for Sustainability [1]. A counter-intuitive result. If true, than what was the point of bringing Fairphone to the market if all smartphones were already sustainably produced? It would be economic suicide for a start-up. This result is mind-blowing. It is contrary to what is generally accepted in the smartphone community, namely that the Fairphone is the most sustainable smartphone [2]. For example, the company Fairphone is a member of the Fair Cobalt Alliance. Apple is not a member. So, how does De Consumentbond arrive at this conclusion? In my previous blog I noted that a replaceable battery was not included in the Sustainability filter on the website, but it is present as a separate property. Again, this is a choice. Since the iPhone has no replaceable battery, this decision results in the inclusion of the iPhone in the group of sustainable smartphones. How wonderful! If they had chosen to include a 'replaceable battery' in the definition of sustainability, and implement it in the software on the website, than only 4 or 5 smartphones, including Fairphone, but excluding iPhone, would have ended up in the group of sustainable smartphones.

Repairability

Later I discovered yet another mind-blowing fact: Repairability is not included in the definition of sustainability. Even worse, the whole concept is absent [4]. Again, this is a choice, not a test result. Repairability means that the owner of the phone can replace modules. In the case of Fairphone no less than 11 modules. Clearly, repairability is connected with the modularity of the phone. Repairability and modularity are the most important sustainability features. If the owner can replace modules the phone will last longer. And that is good from a sustainability perspective. It is well-known that Apple has gone to extreme levels to make their phones un-repairable by design by gluing parts together so that the owner of the phone cannot replace them [3]. This is summarized in the discovery of smartphone expert Hugh Jeffreys:  'Astonishing Anti Repair Practices By Apple In the Last 15 Years' [3]. In 2009 Apple introduced the infamous anti-repair Pentalobe screw. On the other hand, it is no secret that Fairphone is the most repairable smartphone on the market [3]. It makes the Fairphone product unique. It is the raison d'être of the company.  Doesn't De Consumentenbond know this? They know this, because they published about the Fairphone back in 2016 in their magazine [1]. 

Conclusion

It is one of two things: either the testing of smartphones is a work in progress and De Consumentenbond struggles to include 'Sustainability' in a straightforward and consistent way in their tests, or, God forbid it, we see here a bias against sustainable smartphones disguised as a neutral, independent, objective, and quantitative test method. It doesn't help to add: "Our tests are professional". It is beside the point that the tests are being done in highly sophisticated professional labs. My point here is that a bias creeps in through the value they give to certain test parameters, the weight they give it in a percentage of the total, and/or the omission of parameters. Although I personally value sustainability very high, maybe the highest of all features, I do not ask 'De Consumentenbond' to do the same. However, I do expect from an organization that claims to be professional, a bias-free evaluation of all phones. And I do expect that it is easy to select the best sustainable smartphone from the test results.

 


Sources

Note [1] I am not allowed to quote any of the test results because they are for members only. Maybe I have revealed already too much. This makes it risky to discuss their method in public at all.

The Consumentenbond knew of the existence of the Fairphone back in 2016 (see my blog).

Marleen Bekker in
Consumentengids okt 2016.

The Consumentengids published an interview with a disappointed user of a Fairphone 1 (see picture above), she owned a Fairphone 1 but hesitated to buy a Fairphone 2 because its price (500 euro). The first fair phone was the most fair, but did not have the same features as other smartphones on the market at the time. They could have interviewed a happy Fairphone 2 user, but did not. In 2016 the Consumentenbond did not include any ethical criteria in their tests. Apparently, a fingerprint scanner was of higher value than ethical manufacturing practices.

[2] For example:

- Clove Technology Fairphone 5 - The World's Most Sustainable Phone (YouTube, 31 Aug 2023).

- TechAltar: Is Fairphone really fair? (YouTube, 13 Oct 2023) 

Is Fairphone really fair?
 

- Android authority: All smartphones, including iPhones, must have replaceable batteries by 2027 in the EU. July 13, 2023.

- Tweakers: (Dutch) Duurzaamheid gaat gepaard met offers. Fairphone 5 Review (16-09-2023)

- Fraunhofer Institute report 'Life CycleAssessment of the Fairphone 4', March 2022.

- Fraunhofer Institute: Keeping phones for 5 years cuts yearly impact on global warming by around 31%, finds Fairphone’s latest life cycle assessment May 03, 2022

- Fair Cobalt Alliance: members are Fairphone, Google, Tesla, LG. Not: Apple!

 

[3] Hugh Jeffreys (18 Sept 2022) iPhone 14 Pro Programmed To Reject Repair - Teardown and Repair Assessment. (youtube 16 min) Most detailed test of the unrepairability of the iPhone (swapping parts between two identical iPhones!). Recommended!

Hugh Jeffreys (5 Nov 2023) Astonishing Anti Repair Practices By Apple In the Last 15 Years (youtube 13:19 min)

Hugh Jeffreys (29 May 2022) Apples Self Repair Program Is Not What It Seems (youtube 18:00 min)

Hugh Jeffreys (18 Jun 2023) New Laptop Brand Shocked Whole Computer Industry - Framework Laptop - Teardown And Repair Assessment.
This a review of the most repairable and upgradable Notebook on the planet. 

[4] A work in progress? The repairability of Notebooks.

De Dutch consumer organization 'De Consumentenbond' tested the repairability of 24 laptops/Notebooks in the December issue of the Consumentengids ('Repareren? Vergeet het maar!', page 16-19). The test did not include the Framework laptop (why?), although it is mentioned in the text. Repairability was included in the ranking (good!), but contributed only for 5%. Despite the lowest value for Repairability, Apple MacBook Air was 'The Best of the Test'! So, in practice repairability is not valued at all. The author Eric Verlooij wrote that repairability is fine, but the higher price as an obstacle (!). He is not alone. This is short-time thinking. He did not think of the consequences of an unrepairable laptop with a broken component.
See my blog: The Framework laptop: an upgradeable, modular, customizable, user-repairable laptop, 5 April 2022.


[5] Alex Alderson: Fairphone 5: World's most repairable smartphone survives savage durability tests. notebookcheck.net (Published 08/30/2023)


[6] 'De Consumentenbond' says of the Fairphone: 'Child labour' 'not tested', however Child labour is mentioned on these pages:

 

Previous blog

08 November 2023

Consumentenbond test duurzaamheid smartphones: Apple iPhone is duurzamer dan Fairphone!

Op de website van de Consumentenbond staan op dit moment de testuitslagen van 312 smartphones. Er is ook gekeken naar duurzaamheid. Wat blijkt? Apple iPhone is duurzamer dan Fairphone! Dat vinden wij vreemd. Reden om op onderzoek te gaan.

Fokke & Sukke vinden dat vreemd!
(aangepast,©RGvT)

De feiten

Dit zijn de testresultaten op de website van de Consumentenbond:

  • de 'Beste uit de Test' van 312 smartphones: Apple iPhone 15 (3 modellen).
  • de nieuwste Apple iPhones hebben duurzaamheidsscores van 9,1 tot 9,3
  • de nieuwste Fairphone 5 krijgt een 8,4 voor duurzaamheid. 
  • de website heeft een filter voor 'duurzamere keuze': dat levert 96 smartphones (30% van het totaal). Op 8 Nov: 95 smartphones.
  • bij de 'Beste uit de Test' telt 'duurzaamheid' voor 0% mee.
  • De 'Groen Keuze' wordt toegekend aan producten die op het testonderdeel duurzaamheid minimaal een 7 scoren.
  • De 'Groen Keuze' is (nog) niet toegekend aan smartphones, maar volgens hun eigen maatstaven zouden alle iPhones een Groene Keuze zijn. 

Consumentenbond Groene Keuze [4]. (bron)

Wat is duurzaamheid?

Duurzaamheid (iPhone 15 Pro Max) Screenshot 8 Nov 23 ©Consumentenbond

De definitie van 'Duurzaamheid' van de Consumentenbond bestaat uit 2 delen:

  • Duurzaamheid van het bedrijf: Conflictmineralen, Kinderrechten, Elektriciteit, Rapportage
  • Duurzaamheid van het product: Bestendigheid, Accessoires, Stroomefficiëntie, Verwisselbare batterij, eSIM, Bovengemiddeld, Duurzamere keuze.

Hoe wordt het duurzaamheids cijfer berekend?

Sommige onderdelen krijgen een cijfer, andere een vinkje. Kwantitatief en kwalitatief lopen door elkaar. Dat geeft problemen bij het berekenen van de score. Feitelijk kun je dan geen eindcijfer berekenen. Toch geeft de Consumentenbond een kwantitatief eindcijfer en er wordt niet uitgelegd hoe ze dat doen. Niet transparant en dus onbetrouwbaar.

De resultaten

Het blijkt dat de Apple iPhone 15 Pro Max niet alleen 'De Beste uit de Test' is, maar ook een ongekend hoog rapportcijfer van 9,3 voor duurzaamheid krijgt. Dat is opmerkelijk want Fairphone als bedrijf is in 2014 opgericht om een duurzame smartphone op de markt te brengen [5]. Dat was revolutionair in die tijd. Maar bij de Consumentenbond heeft Fairphone 5 nota bene een lager rapportcijfer van 8,4 voor duurzaamheid. Alle iPhones hebben 9,1 of hoger voor duurzaamheid.  Apple iPhone is duurzamer dan Fairphone?! Dat vinden wij vreemd [2].

Het blijkt dat iPhone op alle duurzaamheids punten beter scoort, behalve 'Accessoires' en 'verwisselbare batterij'. De iPhone heeft géén verwisselbare batterij, Fairphone wel [3]. Maar volgens hun eigen criteria is 'verwisselbare batterij' een van de duurzaamheidskenmerken! Het weglaten van 'verwisselbare batterij' uit de duurzaamheidsscore is dus de verklaring waarom iPhone zo hoog scoort. Ja, zo kan ik ook smartphones testen!

Duurzaamheid telt niet mee

Hoe het testoordeel wordt berekend.
Pop-up op website
©Consumentenbond.
NB: let op Duurzaamheid!

Het verwarrende is dat Duurzaamheid helemaal niet mee telt voor het predicaat 'Beste uit de Test'! (zie screenshot hierboven). Een telefoon kan dus 'de beste' zijn zonder dat duurzaamheid überhaupt wordt meegewogen. Waarom niet? De iPhone heeft de hoogste duurzaamheids scores en die staan ook vermeld bij de kenmerken van de smartphones op de website, maar dit telt kennelijk niet mee bij het eindoordeel. Op grond van die score zouden de iPhones het predicaat 'Groene Keuze' moeten krijgen. Maar geen enkele smartphone heeft dat predicaat. Verwarrend en onbegrijpelijk.


Duurzaamheidsfilter

Verwisselbare batterij: 4 van de 95 Duurzamere keuzes!
screenshot 8 Nov 2023
©Consumentenbond
 
Het nieuwe duurzaamheidsfilter op de website levert 96 smartphones op van de 311 totaal (=30%). Op 8 november zie ik 95 smartphones: Apple (45), Fairphone (3), Google (5), Samsung (34), Sony (8). Best een groot aantal. Nadeel: het is onmogelijk om ze te sorteren op duurzaamheid. Er wordt gesorteerd op de 'eindscore' (waarin duurzaamheid niet mee telt!). Dus met dit filter kun je niet de meest duurzame smartphone selecteren. Maar dat is wel wat je verwacht van een duurzaamheidsfilter. 

Bovendien worden de kenmerken van duurzaamheid niet consequent toegepast in het duurzaamheidsfilter: 'verwisselbare batterij' telt op eens niet meer mee met als resultaat dat Apple, Fairphone, Google, Samsung, Sony duurzaam zijn, terwijl alleen Fairphone, Samsung en Shift een verwisselbare batterij hebben. Klopt dus niet.


Aanbevelingen

  • De test scores moeten volledig na te rekenen zijn, er mogen geen geheime factoren zijn die alleen de Consumentenbond kent
  • De duurzaamheids onderdelen moeten transparant zijn: er moet voor iedere fabrikant, product of testonderdeel een link staan naar de webpagina waar de informatie staat met datum van bezoek van die pagina. Alleen op die manier zijn beoordelingen controleerbaar.
  • Het duurzaamheidsfilter moet alle duurzaamheidskenmerken meenemen
  • Alle telefoons moeten onpartijdig beoordeeld worden, daarom mogen er geen subjectieve factoren binnensluipen.


Conclusie

Het is goed dat de Consumentenbond duurzaamheid probeert mee te nemen in haar testen. Maar: het is een raadsel waarom duurzaamheid nog steeds niet mee telt de 'Beste uit de Test' bij smartphones. Het is ook een raadsel waarom iPhones duurzamer zijn dan Fairphones. Het is een raadsel waarom het duurzaamheidsfilter niet 'verwisselbare batterij' meeneemt.

De berekening van de eindscores is een mengeling van kwantitatieve en kwalitatieve scores. Die kun je niet optellen en middelen. Deze methode is quasi objectief. Er wordt niet uitgelegd hoe daar mee om gegaan wordt. Zelfs als je je beperkt tot de kwantitatieve scores, dan kloppen de gemiddelden niet [2]. 

Het resultaat van dit alles is dat de testen van de Consumentenbond niet te controleren zijn. Er is geen verantwoording van hoe de Consumentenbond de duurzaamheid van een smartphone (product en en bedrijf) wordt vastgesteld.  Ze zijn ondoorzichtig en daardoor is de waarde van de testresultaten dubieus. De Consumentenbond neemt producenten de maat, maar wie neemt de Consumentenbond de maat? 

 

Postscript

Ondertussen heb ik een mail naar Jorien van Hoogen (Consumentenbond, expert duurzaamheid) gestuurd (9 nov 23). Het is me nog niet gelukt een bericht bij Fairphone of Fairphone Community achter te laten, want er zijn allemaal barrières en drempels ingebouwd. Als iemand anders een mogelijkheid ziet om Fairphone op de hoogte te brengen van dit blog, heel graag!  Ondertussen heb ik een 'formele' reactie van de Consumentenbond, maar nog geen inhoudelijke reactie. PS: ondertussen is het me gelukt om een bericht op het Fairhone forum 'The Industry' te posten (19 nov).  

Op 19 nov 2023 verscheen op de website van de Consumentenbond: De beste smartphone voor jou, door ons getest.  "Wij hebben 290 smartphones voor je getest". Laatste update van de test: 9 november 2023. Op 22 nov 23 waren 287 smartphones getest:

Duurzaamheid 22 Nov 2023 ©Consumentenbond
 
De papieren Consumentengids December 2023 heeft op pagina 8 een korte bespreking van de Fairphone 5.
Op 23 Nov zie ik 270 resultaten in de smartphone vergelijker, gisteren waren dat er 287, dus vandaag zijn er 17 minder. 


 

Noten

  1. De kosten van een beter milieu mogen niet volledig op het bordje van de consument komen? Dat is merkwaardig! Dus als consumenten energie slurpende apparaten kopen, moet de overheid en het bedrijfsleven hen daarbij helpen? subsidiëren? In tegendeel: de overheid zou energiezuinige apparaten moeten stimuleren! en energieslurpers belasten! (zie Consumentengids Nov 2023 pagina 58 Jorien van Hoogen). Noot staat niet meer in tekst.
  2. Ga je de berekening van de scores narekenen dan kloppen ze niet. De duurzaamheid heeft 2 onderdelen: duurzaamheid van het bedrijf en duurzaamheid van het product: 
    • duurzaamheid van het bedrijf = 9,8
    • duurzaamheid van het product = 8,3
      gemiddelde =  9,05 terwijl de CB geeft 9,3. Dat is dus te hoog.
    • het is onduidelijk hoe er geteld wordt als een item zoals Kinderrechten niet bekend is
  3. De batterij is nogal belangrijk: wat doen we met de iPhone van €1479 tot 1980 als de batterij degradeert? Een nieuwe smartphone is de enige optie als je de batterij niet kunt vervangen. De vervangbaarheid van de batterij zit niet in het duurzaamheidsfilter voor smartphones! Filter je bovendien op 'verwisselbare batterij' dan houd je maar 4 smartphones en daar zit dus geen  iPhone bij.
  4. Vorig jaar mei heeft de Consumentenbond het predicaat 'Groene Keuze' gelanceerd. Zie: Onze blik op duurzaamheid, 5 mei 2022.
  5. Het bedrijf Fairphone heeft sinds april 2015 een 'B-Corporation' certificaat. Dat vindt U op de website van het bedrijf dat de certificering uitvoert: B lab Europe. "A Certified B Corporation is a company that has voluntarily met the highest standards for social and environmental performance." Toegevoegd 12 nov 2023

 

Links

https://www.consumentenbond.nl/duurzaamheid/hoe-adviseren-wij-jou-bij-het-maken-van-een-duurzamere-keuze 

https://www.consumentenbond.nl/duurzaamheid#duurzaamproduct

https://www.consumentenbond.nl/smartphone/hoe-wij-testen

https://www.consumentenbond.nl/smartphone/fairphone-3

https://www.consumentenbond.nl/tablet/strengere-regels-voor-duurzame-productie-smartphones-en-tablets 

https://cloudfront.consumentenbond.nl/binaries/content/assets/cbhippowebsite/gidsen/digitaalgids/2023/nummer-6---november/dg202311p40-keuzehulp-duurzame-smartphones.pdf

https://www.greenpeace.org/nl/natuur/6855/groene-elektronicagids-2017/

https://www.fairphone.com/nl/over/over-ons/

https://www.consumentenbond.nl/tablet/strengere-regels-voor-duurzame-productie-smartphones-en-tablets

https://www.consumentenbond.nl/stofzuiger/reparatie-elektrische-apparaten

Mobile Phones: Ethical Comparison Ratings Table !!!

Tweakers: Is dit de duurzaamste telefoon ooit? - Fairphone 5 Review. 15 Sep 2023. Geeft een goed overzicht van de voor- en nadelen.

 

Vorige blogs over Consumentenbond

20 October 2023

I discovered the beautiful Humming-bird Hawk Moth (Kolibrievlinder) hovering above flowers in a Dutch garden

Humming-bird Hawk Moth visiting flowers
31Aug 23 SRX06805A.JPG©Gert Korthof


This summer I was photographing butterflies in De Tuinen in Demen gardens, The Netherlands. These gardens have literally hundreds of flowering plant species. Unexpectedly, I found myself chasing a Humming-bird Hawk Moth, Macroglossum stellatarum (Dutch: Kolibrievlinder) hovering above the flowers. 

The butterfly was quite difficult to capture because it constantly moved from one flower to the next, and never sat down on a flower. Typically, they hover a few centimeters above a flower and stick their tongue out to enter a flower and quickly move to another flower. This is a very unique behaviour for a butterfly. Most butterflies sit down on a flower for some time. This exotic butterfly certainly deserves its name: it behaves like a hummingbird! It is really acrobatic to enter such a long tongue into flowers while hovering.

Later, when selecting the best pictures, I discovered the long tongue. At that moment I remembered the cover illustration of Mark Ridley's Evolution textbook:

cover Mark Ridley Evolution 3d edition

Ridley writes [1] that Darwin had seen specimens of the orchid Angraecum sesquipedale which has a very long spur. A nectar spur is a hollow extension of a part of a flower. Darwin speculated that a butterfly with a very long tongue must exist. But at the time he did not know such a species. Twenty years later such a butterfly was discovered: the hawk moth Xanthopan morganii pollinating an orchid. The butterfly I photographed, Humming-bird Hawk Moth, is not the same as the one on the cover of Ridley's Evolution. It is another genus. but it belongs to the same family [2]. The plant species my Humming-bird hawk moth visited is not an orchid. Now it gets interesting. Did my butterfly visit the 'wrong' flowers? There are no flowers present that fit the tongue of my Humming-bird Hawk Moth? Upon further inspection of my pictures I noted that the flowers also had a rather long spur:

Size of flower spur indicated with arrow.
31Aug 23 SRX06798A.jpg©Gert Korthof

But this spur is certainly not as long as Darwin's orchid. So, the particular plant species and my Humming-bird Hawk Moth don't seem highly adapted. They did not co-evolve.

This is a mystery. Are there plant species in the Netherlands or elsewhere in Europe which are better adapted to the Humming-bird Hawk Moth? Plant species with a very long spur? I don't know. More observations are needed. In the Netherlands our butterfly is often seen on a common garden plant: Buddleja davidii (butterfly bush, vlinderstruik) native to China and Japan. The problem is that in observation.org and waarneming.nl it is not required to identify the plant species when submitting an observation of a butterfly [3]. It is difficult to identify the plant species from the pictures. Above that, waarneming.nl discourages users to upload non-native plant species and it could be that precisely cultured garden varieties are visited by the Humming-bird Hawk Moth!

Another unique feature of this 'moth' are the eyes. They are looking at you:

He is looking at you!
SRX06802.jpg©Gert Korthof

It looks like a human eye!

Then its wings: rather exceptionally for a moth, its wings have orange patches!

Finally, another mystery: what about pollination? Since it doesn't sit down on a flower, the only point of contact is its tongue! Clearly, this is a wonderful and unique butterfly, or should I say a moth?

 

Additional nice pictures

https://waarneming.nl/observation/290848030/

https://waarneming.nl/observation/290782391/


Sources

 

Notes

  1. Mark Ridley (2004) Evolution, third edition, page 617. Ridley discusses the case in the paragraph 22.3 'Insect-plant coevolution'. But also that the case is more complex than just the coevolution of insect tongue length and flower spur length.
  2. Family: Sphingidae (pijlstaarten) is a very species rich family and the genus Macroglossum has nearly a hundred species.
  3. Buddleja davidii  (vlinderstruik), Lavandula species (lavendel), geranium, Valeriana spec (rode valeriaan), Phlox, Verbena officinalis (ijzerhard) are visited by the Humming-bird Hawk Moth.

13 September 2023

The true history of junk DNA (2)

Francis Crick
What Mad Pursuit.
paperback 1988

"The originator of the central dogma, Francis Crick, was well aware of genes that didn't encode protein. They don't figure into the central dogma." (Laurence Moran (2023) What's in your genome, chapter 8 paragraph 'Revising the central Dogma?') (my bold)

Exactly: They don't figure in the Central Dogma! That is precisely the problem! Crick omitted noncoding DNA from the Central Dogma. Had he included it in his scheme, a lot of confusion could have been prevented.

Central Dogma, from: Francis Crick, What Mad Pursuit, page 168.

Crick could have added an arrow from RNA to for example 'RNA genes'. He did not.

RNA genes added to Central Dogma (©GK)

In this blog I want to explore possible reasons for this omission. They have to do with the historical scientific context of the time that Crick proposed his central dogma. I hope this will show that scientists misinterpreting the Central Dogma are not fools and that Crick himself overlooked non-coding DNA when drawing his Central Dogma diagram. But first a second quote from Laurence Moran:

"Many scientists have a very different view of the central dogma. They were taught, incorrectly, that the real meaning of the central dogma is that DNA makes RNA makes protein and the only function of DNA is to encode protein ... They were somehow led to believe that there was only one kind of gene, namely, protein-coding genes." (Moran, 2023, What's in your genome, Chapter 8) (my bold)

Well, it is certainly not a mystery why many scientists were led to believe that there was only one kind of gene: there is only one kind of gene in Crick's illustration of the Central Dogma.

Why did Crick not add RNA genes to his diagram? It is important trying to understand the historical context at the time that Crick proposed his Central Dogma. Traveling back in time is not easy, therefore I use Crick's own account in What Mad Pursuit.

The central problem of biology at the time was: How could genes possibly construct all the elaborate and beautifully controlled parts of living things? It was known that each chemical reaction in the cell was catalyzed by enzymes. This is a defining property of life on earth. Furthermore, it was known before 1953 that enzymes are proteins. Crick realized that the key problem in biology was to explain how proteins were synthesized. In the 1940s a very influential hypothesis was proposed, the 'One gene - one enzyme' hypothesis. The next question was: How do genes control the synthesis of proteins? (Chapter 3 The Baffling Problem, page 33). Obvious today, but at the time it was a problem at the frontiers of science. Further, it was also known at the time that proteins were made of about 20 different amino acids. 

After the discovery that DNA consisted of a sequence of bases, the next question emerged: what is the precise relation between genes and proteins? Crick proposed the Sequence hypothesis: the sequence of bases in DNA is a necessary and sufficient condition for the sequence of amino acids in proteins. Crick:

"Rereading it, I see that I did not express myself very precisely, since I said "...it assumes that the specificity of a piece of nucleic acid is expressed solely by the sequence of its bases, and that is sequence is a (simple) code for the amino acid sequence of a particular protein." This rather implies that all nucleic acid sequences must code for protein which is certainly not what I meant." (Francis Crick, What Mad Pursuit, Chapter 10, page 108).

Then Crick explains that other parts of the DNA sequence could be used for control mechanisms (today: gene regulation) and he even mentions producing RNA for purposes other than coding (today: RNA genes). Crick concluded: "I don't believe anyone noticed my slip, so little harm was done." (page 109). Unfortunately, Crick underestimated the long lasting influence of the famous Central Dogma diagram.

According to Moran the meaning of the Central Dogma diagram is that the information in proteins cannot get out again. That, indeed, is what Crick himself says (page 109). Unfortunately, the Central Dogma diagram is a weird way to illustrate the non-existence of a specific type of information flow. It is as if one wants to illustrate the absence of something with the absence of something in an illustration. It isn't manifest. It seems rather impossible to me to do that [2].

In my view the point of the Central Dogma was to illustrate (albeit in a partial way) the solution of the central question of the time and indeed of all times: how can genes specify proteins? Crick himself expressed this clearly:

"I shall… argue that the main function of the genetic material is to control (not necessarily directly) the synthesis of proteins." [1] (my bold)

The Sequence hypothesis isn't a hypothesis anymore, and it isn't at the frontiers of science anymore, but 'The Sequence' is still and will always be one of the defining characteristics of life on earth [3]. This is certainly not an outdated idea from the pas. Life as we know it is impossible without enzymes (=sequences) and without genes (=sequences) coding for them. 

The 'protein universe' is very much at the frontiers of science, new protein structures are discovered today [4].

 

 

Appendix (1)

All the following concepts are about protein synthesis:  
  1. Mendelian genes specify discrete phenotypic characters (with the benefit of hindsight).
  2. The Sequence Hypothesis states that the sequences of DNA bases specify the sequence of amino acids in proteins. (Chapter 10 Theory in Molecular Biology)
  3. The Central Dogma states the direction of flow of information from DNA to RNA to protein and not back from proteins (chapter 10)
  4. The Genetic Code Table specifies which 61 DNA base triplets which amino acid ('sense' codons) and 3 base triplets which specify STOP chain ('nonsense' codons) Chapter 8 and Appendix B.
  5. The Adaptor Hypothesis  (Crick, Chapter 8 page 95) (the implementation of the Genetic Code in specific molecules: tRNA) doesn't make sense without protein synthesis.
     

 

Appendix (2)

The terminology used to describe genes makes only sense (!) in relation to protein synthesis: 

  • sense, nonsense, missense
  • sense, anti-sense strand
  • positive-sense, negative-sense 
  • coding strand, template strand
  • coding, noncoding
  • translation
  • STOP/START codons
  • the Genetic Code Table
  • triplets
  • in-frame/out of frame
  • ORF: Open Reading Frame
  • mRNA: messenger DNA
  • tRNA: transfer RNA
  • rRNA: ribosomal RNA

Also, the concepts: promoter (DNA sequence to which proteins bind) and enhancer (DNA sequence to which specific proteins bind) make only sense (!) in the context of protein synthesis, direct or indirectly, because they promote or enhance gene expression of protein-coding genes (mainly). Using these concepts implies protein synthesis on the basis of DNA sequences.  

However, there are concepts not (directly) related to protein synthesis: base pairing, double helixtranscription, directionality, replication.


Appendix (3)

I wonder whether there is a total absence of any coding signature in non-coding RNA genes. I found it difficult to find clear information about it. For example: do START and STOP codons occur in RNA genes? If so, do they have any effect? Do non-coding RNA genes have a triplet structure? Do single base deletions or insertions have similar effects on RNA genes as on protein-coding genes? (they don't disturb the reading frame). Are there functional RNAs completely independent and unrelated to protein (synthesis)? How did RNA genes originate? Did those they originate from coding sequences or from random sequences?



Notes

  1. Matthew Cobb (2017) 60 years ago, Francis Crick changed the logic of biology, PLOS BIOLOGY. Please note "(not necessarily directly)", this is a very ingenious way of including the indirect way of controlling protein synthesis: via enhancers and promoters. (added 22 sep 2023).
  2. Elsewhere Crick designed another diagram which prevents the dilemma of illustrating the absence of something, see: Larry Moran (2007) Basic Concepts: The Central Dogma of Molecular Biology blog.
  3. See for example my review of Tibor Gánti (2003) 'The Principles of Life'. 
  4. ‘A Pandora’s box’: map of protein-structure families delights scientists,  Nature 13 Dec 2023.

 

Previous blogs


31 July 2023

The true history of junk DNA

"By the late 1960s, knowledgeable scientists were used to the idea that genes occupied only a small part of the genome, and in 1974 the editor of the journal Cell, Benjamin Lewin, was expressing the consensus view of the experts when he wrote that the C-value Paradox could be resolved by assuming that much of the genome is composed of nonfunctional repetitive DNA (junk DNA)." (Chapter 2 of Laurence Moran (2023) What's in your genome.)

It may be that 'knowledgeable scientists' in the late 1960s knew that much of the genome is composed of junk DNA, but the 'consensus view' was not widely known in all sub-disciplines of the biological research community. Maybe the journal Cell was not read in the evolutionary biologist community. Probably, those experts were experts in a different field with its own journals and conferences.

Eli C. Minkoff (1984) Evolutionary Biology.

I checked the oldest textbook I have, Minkoff (1984) Evolutionary biology. There is no 'junk DNA' and no 'non-coding' DNA in the index, despite the 'consensus view'. Yes, there are tRNA and rRNA (p.16), but these RNAs are not labeled as 'non-coding RNA' or 'non-coding DNA'. They are in the business of producing proteins. They are the very embodiment of the genetic code. Therefore, it would be somewhat counterintuitive to call them 'non-coding'. Yes, there is 'genetic drift', neutral mutations, 'neutralism versus selectionism', 'genetic load', 'mutational load' in his book, but Minkoff did not connect these concepts with 'non-coding DNA'. The concept is absent anyway. 'Centromere' is mentioned once casually (p.19), I could not find 'telomere'. Anyway, 'centromere' is not labeled as 'non-coding DNA'. Why is non-coding DNA absent from the book? 

I think I found part of the answer in the following passage:

"One of the fundamental tenets of modern synthetic theory of evolution is that natural selection operates on the phenotype rather than the genotype. No genetic change can be influenced by natural selection unless it first produces some phenotypic change. It is largely for this reason that modern evolutionary biologists must be aware of the manner in which phenotypes are controlled." (p.114)
This was an eye-opener for me. The phenotype is the most important, the genotype is important only in so far it has an effect on the phenotype. Who cares about DNA that does nothing? Evolutionary biology has the task of explaining the organism.

A second foundational paradigm I found here:

"Proteins are among the most important of all biological molecules. (...) The great intricacies of living systems are all the result of enzyme-controlled activities (...) enzymes are therefore the chemical basis of life". (p.17).

Taken together these two principles explain the mindset of evolutionary biologists in those days. If they did know about non-coding DNA, it simply had no relevance to the goals of their daily research. On page 37 there is a table labeled as 'The Genetic Code for Translation of mRNA Codons into Amino Acid sequences'. The famous table. It makes sense in this context, because the Genetic Code is the link between DNA and proteins. The reason for the existence of the Genetic Code is to produce proteins. The Watson-Crick structure of DNA plus the chemical structure of the four bases is present in the book. Minkoff knows the necessary biochemistry. Unfortunate exception: introns and splicing are absent! Introns were discovered in 1977.

There is one isolated and thus mysterious remark which vaguely suggests something like 'non-coding DNA':

"Not all of the genotype is transcribed and translated into a portion of the epigenotype, nor are all the transcribable genes ever transcribed at the same time." (p.114) ['epigenotype' = "the polypeptides that result from the immediate transcription and translation of the genotype"]

That's all. Probably, Minkoff was vaguely aware of non-coding DNA. But why include it in his textbook? He did not elaborate the concept because in his opinion it was simply not relevant or nothing was known about it. DNA which is not transcribed and translated has nothing to contribute to the phenotype of the organism, consequently nothing to biology and evolution. It doesn't fit in the evolutionary biology paradigm of that time [1].

So, that is the 'true history' of non-coding DNA based upon Minkoff (1984) and that was taught to biology students at that time. He did not say that non-coding equals junk, but by omitting non-coding DNA, he implied that non-coding DNA is unimportant. If one makes statements about the history of junk DNA, one has to investigate the evolutionary biology textbooks, especially older ones. Minkoff was an eye-opener for me. I checked more evolutionary biology textbooks: 8 out of 17 do not have 'non-coding DNA' in the index.

"As Sandwalk readers know, there was never a time when knowledgeable scientists said that all non-coding DNA was junk. They always knew that there was functional DNA outside of coding regions." (Sandwalk)

I think one has to take into account that there are different scientific disciplines with their own paradigms, leaders, journals, conferences, and networks. 

Thanks for reading. Have a nice day!

 

Notes

  1. On page 18 he writes: "there are other sequences in each DNA molecule that do not appear to determine the amino acid sequence of any polypeptide. Some of these may function as "spacers", and others are believed to function as regulatory genes, which control the transcription of other genes." (page 18, chapter 2: Basic Principles of Genetics). Here he describes non-coding regulatory genes! He doesn't realize that these non-protein-coding DNA sequences must have indirect effects on the phenotype, and consequently are important for evolutionary biology! In the subsequent development of evolutionary biology, the evolutionary importance of regulatory genes became evident.  Added: 21 Aug 2023

 

Previous posts

  1. Junk DNA in the Evolution textbooks (2) from 1996 to 2023 26 Jul 23
  2. Junk DNA in the evolution textbooks. Bergstrom and Dugatkin 2023 12 Jul 23
  3. Periannan Senapathy (1994) claimed that the human genome consists of more than 90% junk DNA. 4 Jul 2023
  4. Scientists say: 90% of your genome is junk. Have a nice day! Biochemist Laurence Moran defends junk DNA theory 26 Jun 23

26 July 2023

Junk DNA in the Evolution textbooks (2) from 1996 to 2023


 

    Futuyma, Kirkpatrick (2023)  Evolution.

fifth edition        

In the previous blog I discussed Bergstrom and Dugatkin Evolution, third and first edition. Today I continue my investigation of 'junk DNA' in the Evolution textbooks with a textbook by Douglas Futuyma and Mark Kirkpatrick (2023) Evolution also published this year

Although "junk DNA" does not occur in the index, on page 86 (chapter ' Mutation and variation'), the authors state: "In humans for example, 98% of the DNA does not code for any gene product." Note: they do not say 'protein product', but 'gene product'. However, the capture of figure 10.13 states: "Less than 2% is devoted to protein-coding sequences." (p.274). So, if that is what they mean by 'gene product' the 98% is OK. They explain these matters in an excellent and up-to-date chapter about genes and genomes (chapter 10). On page 281 the authors ask:

"Does that mean the 98% of our genome that is noncoding is actually junk? We are still far from having a clear answer to this fundamental question. (...) some of the resulting "junk" now plays key roles in regulating gene expression, and the cell's metabolism has coevolved with the total quantity of DNA in the nucleus. (...) Like an addict and his drug, eukaryotes may not be able to break their dependence on a bloated genome. But their is good news in this story. When ancient eukaryotes acquired large amounts of of noncoding DNA, it opened new options for the evolution of gene regulation. That, in turn, may have enables the origin of complex life-forms, including ourselves." (p.281)

In the end-of-chapter section called 'What We Don't Know' (by the way, a nice feature!):

"Also debated is the fraction of the eukaryotic genome that has a function. One large-scale study estimated that 80% of the human genome has a function." [the reference is the ENCODE publication in Nature, 2012]. "That estimate, however, has been criticized as far too high, and many evolutionary biologists would agree that perhaps only about 10% of our genome has a definite function" (p.281).

Figure 10.13. (p.274). Adapted from Gregory (2005)


This seems a fair and correct description of the status of the scientific evidence. What I miss in figure 10.13 is the difference between functional and non-functional DNA (perhaps an unreasonable demand!). The functional sequences outside protein coding sequences will be hidden in the 98%. 'Functional RNA' is not present in the book. One can find a comprehensive treatment of functional and nonfunctional RNA in Moran (2023) (see my blog 26 June).

"Alternative splicing is a major mechanism used by eukaryotes to increase organismal complexity " (p.274). 

Is it really 'a major mechanism'? This is a controversial statement because there is no quantitative estimate of its importance. Futuyma and Kirkpatrick do not mention non-coding tRNA (transfer RNA), but ribosomal RNA (rRNA) is present (p.269).  However, both are not introduced as good examples of non-coding DNA (they do not code for proteins but are functional). 

Note [3] about Futuyma, 1st edition, 1979


 

Nicholas Barton et al (2007) Evolution 

 

 

 

 

 

Nicholas Barton et al (2007) Evolution has a very good discussion of junk DNA, selfish DNA, C-value, non-coding DNA. Fortunately, they also pay attention to the disadvantages of a big genome (p.597). For example, in insects metamorphosis requires rapid cell division and is harder when massive amounts of DNA must be replicated. It shows that natural selection can downsize large genomes. Which is good to know! It brings the burden of large genomes back into focus. This is important:  transposons can by accident acquire a new function. They do not give an estimate how often this happens. "Introns are frequently considered to be junk DNA. However, comparative sequence analysis has revealed that the sequence of some introns is highly conserved, suggesting that functional constraints have played a role in evolution." (p.220). "Overall, about 18% of nucleotides are conserved in introns and intergenic regions, compared with 72% within exons" (546). "Such studies suggest that in that in multicellular eukaryotes, at least as much non-coding as coding sequence is maintained by selection." (p.547). If all possible alternative splicing possibilities are taken into account, species such as humans can make millions of different proteins, even though they each have only 25,000 protein-coding genes. Alternative splicing provides a significant source of novelty for diversification" (p.221). This is regarded as controversial by some. Transposable elements have sometimes been co-opted to aid their host (p.598). Sometimes pseudogenes acquire new functions. These views contrast with those of Laurence Moran (2023). Further research is necessary.

 

 










  Freeman, Herron (2007) Evolutionary Analysis

 

 

 

 

The most recent edition of Freeman and Herron is the fifth edition (2013). I don't have that edition, I used Evolutionary Analysis 4th edition (2007). There is no 'junk DNA' and no 'non-coding DNA' in the index. Unexpectedly and paradoxically, transposons –a prime example of selfish genetic elements– are discussed in chapter 15 'Phylogenomics and the molecular basis of ADAPTATION'. 

But first, read this stunning remark (remember, this book was published before ENCODE 2012):

"In humans only about 1.2% of the genome codes for proteins." (p.576)

They do not comment on this remarkable statement. It is an isolated statement from an unknown source. However, they do state that the "extra" DNA responsible for the C-value paradox consists of transposable elements: "In the human genome, for example, over 44% of the DNA present is derived from transposable elements (p.576). What about the remaining 54%? They do not tell. Unknown?

Fortunately, the authors discuss the burden of these genomic parasites. It costs the cell time, energy and resources to replicate a genome with a lot of transposons (p.577). Funny remark: transposons are present in the genome in "often appallingly large numbers"! Such an emotional remark is really funny for a textbook! Good to know: transposons are not 100% non-coding DNA, because they encode the enzyme transposase. They have further important information: defense mechanisms against transposons (!), and: "work by John Moran (!) (1999) suggested that transposition events in eukaryotes may occasionally result in mutations that confer a fitness benefit." (p.581-583). They conclude:

"Even though most transposable elements function as genomic parasites and most transposition events result in deleterious mutations, it is increasingly clear that at least some transposition events result in important new genes or other changes that have a positive impact on the fitness of organisms." (p.584).

My conclusion: there is no 'junk DNA' and no 'non-coding DNA' in the index, and more puzzling, there is also no discussion of introns and splicing. That is a serious omission for an evolution textbook. The origin of introns is a longstanding evolutionary mystery. However, they have interesting things to say about transposable elements. According to Laurence Moran 37% of our genome consists of introns and according to Futuyma, Kirkpatrick (2023): 26% (see figure above). Obviously, without introns Freeman and Herron don't have a complete overview of non-coding DNA and can't calculate the sum total of functionless DNA in our genome. Yet, they know that 1.2% of the genome codes for proteins! I guess that Freeman and Herron are optimistic about the possibility of finding more useful elements in the uncharted parts of the human genome and therefore avoid the concept 'junk DNA'. Reasonable.



 

Strickberger's Evolution Fourth edition 2008




 

Strickberger's Evolution is a famous evolution textbook. The first edition was published in 1990. The fifth edition appeared in 2013. The most recent edition I have is the fourth edition (2008) authored by Brian Hall and Benedikt Hallgrimsson (I don't know whether Strickberger participated in this edition). 'Junk DNA' [1] and 'non-coding DNA' are not in the index. However, 'junk DNA', 'selfish DNA' and 'C-value paradox' are discussed in the text.

"According to some molecular biologists, many transposable elements and other forms of repeated sequences contribute little, if any, function to their host cells. Because the DNA replication process cannot discriminated between functional and nonfunctional sequences, it replicates any introduced sequence. Transposon DNA and repeated sequences may therefore perpetuate parasitically as either "junk" or "selfish" DNA. (p.221).

Important information is present in Box 12.1 'Quantitative DNA measurements'. In connection with the ENCODE project the following paragraph contains intriguing thoughts which I quote in full:

"According to Bird [1995], eukaryotes were able to circumvent such "noise" by a nuclear membrane that separates transcription from protein translation, allowing only translatable messenger RNA sequences to filter into the cytoplasm, and by tightly folding the DNA of functionally unnecessary genes into nontranscribable confirmations, using nucleosomes and their histones. To these transcription-repressing mechanisms, Bird claims that vertebrates added DNA cytosine methylation, formerly used mostly to suppress genomic parasites such as transposons." (p.260). (my bold)

Especially the concept transcription-repressing is intriguing because according to the ENCODE project and Laurence Moran there is pervasive transcription in the cell and most of it is noise! This would disprove the success of transcription-repressing mechanisms? Apparently, the mechanism fails spectacularly. 

My own thoughts are that maybe because transcription is restricted to the nucleus and those RNA transcripts are not exported to the cytoplasm, and consequently are not translated, large-scale transcription can be tolerated by the cell. This assumes that protein synthesis is more costly than transcription. I admit that it is still a burden, but the burden has been halved.

In contrast to Freeman, Herron (2007), in this book 'introns', the "Introns early - Introns late-hypothesis" and alternative splicing are present. Interestingly, they describe introns as mobile DNA sequences that can splice themselves out, acting like transposon-like elements.

Brian Hall and Benedikt Hallgrimsson do not favor the concept 'junk DNA'. It is obvious from this remark: "various biologists have been tempted to consider some or many such sequences as forms of "selfish DNA'." (p.262).

 

 


Stephen Stearns, Rolf Hoekstra (2005) Evolution, an introduction, second edition, paperback.

Relevant topics are 'jumping genes', 'transposons', 'introns', 'B-chromosomes'. Not found in other textbooks: B-chromosomes are not transcribed and do not contain information vital to the organism, they are genomic parasites (p.362). This fits the definition of junk DNA, although Stearns and Hoekstra do not use the concept. They make an interesting remark about transposons: several mechanisms have evolved to suppress the deleterious effects of active transposons (p.363). I would like to know more about them! "In humans they [transposons] may account for 45% of the genome". "Transposons illustrate genomic conflict between selection favoring mutants that increase the replication rate of transposons and selection favoring the suppression of transposons through stronger replication control." (p.363). They have a chapter about Genomic Conflict. There is no new edition of this textbook.



Mark Ridley (2004) Evolution, 3rd Edition

Non-coding DNA is listed in the index under 'DNA, non-coding' [2]. One relevant paragraph 2.4: 'Large amounts of non-coding DNA exist in some species'. The human genome contains 5% maybe up to 10% of genes. "The function of non-coding DNA is uncertain. Some biologists argue that it has no function and refer to it as "junk DNA". Others argue that it has structural or regulatory functions." "Most non-coding DNA is repetitive." (p.27). Alternative splicing is mentioned (gene slo), but there is no diagram of exon-intron structure of a gene (!). The existence of genes coding for RNA (rRNA, tRNA) is mentioned in a footnote ("some genes code for RNA" ! p.25). Further information in Chapter 19 'Evolutionary Genomics' is about the evolutionary history of transposable elements ("About 45% of the human genome is derived from transposable elements", p.567). I am a little disappointed, I expected more of Ridley. Please note, that the draft Human Genome sequence was published in 2001. No definitive conclusions possible at that time. There is no new edition.



Finally (for now...), John Archibald (2018) 'Genomics: A Very Short Introduction', Oxford University Press, 135 pages, has a succinct description of the ENCODE project in the paragraph "Jumping genes and 'junk' DNA" (p.50-53): "The ENCODE project's broadest and most controversial claim is that 80 per cent or more of the human genome has a biochemical function. "



Peter Skelton 'EVOLUTION. A biological and palaeontological approach' (1993, 1994, 1996)

 

[ added 29 July ]

 

 

I ignored this book because I did not expect it would contain junk DNA. Surprise. In chapter 3: Heredity and Variation, the C-value paradox is explained and illustrated with the well-known genome size diagram of various groups of organisms (Fig. 3.5). It immediately stands out that all salamanders and lungfish have bigger genomes than all mammals, birds and reptiles. The C-value paradox is explained by differences in the amount of various repetitive sequences, and polyploidy. Bats and birds have a high metabolic rate and their genome size is lower than other mammals (p.84). ln 1977 introns were discovered. There is a diagram (Fig. 3.9) of gene structure (intron-exon structure). This figure shows introns with smaller sizes than exons. Unfortunately, students get the false impression that these are the right proportions. However, introns are generally larger than exons.  Alternative splicing is described (p.90). Transposons are explained (p.92). Conclusion: despite this book appeared before the publication of the human genome in 2001, the ingredients of 'junk DNA' are present. So, it doesn't matter that the word 'junk DNA' isn't used.

 

Conclusion: The word 'junk DNA' is absent in the index and in the text of 4 of the 9 textbooks I investigated. However, if 'junk DNA' is not in the index of a textbook, it always pays to search for transposons, introns, jumping genes, selfish DNA, pseudogenes or C-value paradox. This review of evolution textbooks is not exhaustive (I could not check all editions of all textbooks). Those listed here are the most interesting and give sometimes additional useful insights and different points of view. Some are pre-2012, some post-2012, but all except Skelton are post-2001. In general authors know that less than 2% of our DNA codes for proteins, but are not sure about the rest. I agree. Nobody can claim to know exactly how much of our genome is useless junk. Even assuming that 90% of our genome is junk, there is no solid answer to the question why is there so much junk in our genome, and why it hasn't been eliminated.

 

Not discussed here is John Parrington (2017) 'The Deeper Genome. Why there is more to the human genome than meets the eye'  (OUP paperback). This is a must read. He gives very interesting examples of beneficial non-coding DNA derived from transposons, and has a point of view other than that of Moran (2023). I hope to blog about it in the future.

Thank you for reading!


Notes

  1. Later I found 'junk DNA' listed under 'Deoxyribonucleic acid' - "junk DNA" in the index! [30 Jul 23]
  2. Non-coding DNA is listed in the index under 'DNA, non-coding' [30 Jul 23]
  3. Futuyma (1979) Evolutonary Biology (1st edition). page 439: "Nonetheless, there is an enormous amount of redundancy in the genome, and its significance is obscure. In may animals as much as 60% of the genome seems to consists of short (less than 300 nucleotide pairs) repeated sequences, some present in thousands of, even a milion, copies". That's all. (personal communication Gerdien de Jong) [1 Aug 23]