New evolution textbook as birthday present for Darwin

 

EVOLUTION
Futuyma, Kirkpatrick 5th ed. OUP hardback 2023
615 pages plus 83 pages index, literature.

A new evolution textbook for Darwin's birthday 12 Feb 2023. 

The publication of a new evolution textbook is a rare event. The textbook displayed above is now the most recent evolution textbook. The previous edition (4th) was also published together with Mark Kirkpatrik in 2017 (5 years ago). It is the longest-running series of Evolution textbooks. Futuyma published his first evolution textbook in 1979. For a visual overview of all evolution textbooks see the homepage of my WDW website. And here on the Introduction page they are listed with short descriptions.

The emphasis of this textbook is on organisms and species. Human evolution gets considerable attention (50 pages). The largest section is about mechanisms: mutation and variation, natural selection, genetic drift. There is a large section devoted to the History of Life (122 pages). I like the presence of a chapter about genome evolution. There is some attention to philosophical issues, and a chapter about Evolution and society. The numerous color illustrations make it a pleasure to browse. 

I was mystified and disappointed that there was no illustration of the molecule all life is based upon; the carrier of hereditary information. This molecule and its mechanisms of action are described in as few words as possible. As if this molecule is of minor importance in evolution. However, its discovery was rewarded which a Nobel prize! I am talking about DNA. Portraits of many evolutionary biologists are present, but Watson and Crick are missing. I also found the space devoted to the origin of life minimalistic.

A welcome feature of this edition is that most chapters have a final What We Don't Know section. The message is: evolutionary biologists have not yet solved all evolutionary puzzles. Critics take note!

 

I will update this first impression either here or on my WDW website.

Erich von Daniken (2022) 'Evolution is Wrong. A Radical Approach to the Origin and Transformation of Life'

Erich von Daniken (2022)
'Evolution is Wrong'

I was curious what Erich von Daniken's arguments against evolution are, and how good his knowledge and understanding  of evolution is. Surprisingly,  he gives a reasonably accurate but short account of the discovery of DNA. 

He even mentions Phoebus Levene [4], but writes that Levene used a 'supermicroscope' and that later his discoveries were confirmed with an electron microscope (wrong). He accurately but incompletely describes Chargaff's discoveries and also that Watson & Crick's double helix model was based on Chargaff. Unfortunately, Von Daniken doesn't mention the crucial fact that Chargaff discovered that the amounts of A roughly equal the amounts of T in DNA, and the same holds for C and G. Most importantly, he misses the crucial feature of DNA: AT and CG form pairs. And that's the crux of genetic information. He is often distracted by asides and story telling. On another page he knows that "the order of the four bases" is important and "only certain basic bases fit into the sequence ... Others cannot dock at all" without mentioning AT and CG pairs! So, strictly speaking, he didn't get the most important feature of DNA, but he is close. 

As is often done by non-biologists, he mistakes the concept 'genetic code' for the genome (the total of DNA in a cell or of a species). This is wrong. The genetic code is the way the information in DNA is translated into proteins. That is: how 64 base triplets code for 20 amino acids. And that can be done in a million ways. As a consequence of this misunderstanding he never wonders how DNA works and what it does. He is completely unaware of the fact that the genetic code cannot be derived from biochemical laws. It has an arbitrary character. The genetic code of all life on earth is unique to life on earth. It is not an universal law. And this explains why he doesn't see a problem with aliens injecting DNA in humans. This could only be meaningful if the alien DNA had the same genetic code (in the scientific sense) as life on earth. The smallest difference in the genetic code could create an obstacle. Significant deviations from our genetic code, makes 'injecting alien DNA' pointless, even pathogenic.

Not surprising, he quotes the panspermia theory of Fred Hoyle and Chandra Wickramasinghe, because according to this theory the first DNA came from space. He also fully accepts and defends Intelligent Designer Michael Behe's Darwin's Black Box. In Von Daniken's view Intelligent Design means aliens. Aliens created DNA and had sex with humans. Or something like that.

His description of Darwin is short but factual without any Darwin bashing. He includes an illustration of Darwin's finches (!) in the book. So far so good. But, the only occurrence of the concept of 'natural selection', crucial for Darwin's theory of evolution, is in a quote: "A Scientific Dissent from Darwinism [1] ..."  (Intelligent Design!). I found one occurrence of "Darwin's selection (choice)". That's all. As often happens he uses 'survival of the fittest' in stead of 'natural selection'.

Apart from uncritical acceptation of Michael Behe and the Intelligent Design movement, he manages to refer to Hans-Joachim Zillmer Die Evolutions-Lüge. If you start accusing your opponents of lies, then you stop thinking scientifically. He also uses and quotes from Reinhard Junker, Siegfried Scherer (1998) Evolution, Ein Kritisches Lehrbuch. The book has been criticized thoroughly by evolutionary biologist Gerdien de Jong on this blog [2]. Von Daniken says about the book: "excellent work"!!!  However it is not an evolution textbook as Gerdien de Jong explained. There is no evolution textbook mentioned in Evolution is Wrong. So, he knows 'evolution is wrong', but did not read any of the many professional or popular evolution textbooks. There are hundreds of them! [3]. I recommend the excellent and popular book Jerry A. Coyne (2009) "Why Evolution Is True". This is a very complete overview, but it is not a textbook in the sense that for example the structure of DNA, Mendelian and molecular genetics are explained. If only Von Daniken had read this book, he would have known the arguments and facts in favour of evolution. I think he is able to understand everything in the book provided he takes the trouble to study it carefully. Another example of his one-sided reading habits is the fact that he read Dawkins Der Gotteswahn (The God Delusion) in stead of the famous The Selfish Gene. He would have learned a lot about evolution if he had read it. It is available in German: Das egoistische Gen.

 

Conclusion

I was curious about Von Daniken's knowledge of evolution and DNA in his recent Evolution is wrong. I must conclude that his knowledge is fragmentary; there are some surprising bits of knowledge: Evo-Devo, genetic toolkit, CRISPR, genetic knockout, and some fragments of the history of science, but he misses crucial insights and facts.

Notes

1. "We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life" (Intelligent Design credo)
   
2. Gerdien de Jong: Der geist der stets verneint. Weglaten, verkeerd weergeven, verdraaien, misleiden, 15 December 2010. We have created a website devoted to the Junker & Scherer book with a few English abstracts.
   
3. I have collected all the current evolution textbooks and introductions to evolution on my webpage Introduction to the evolution literature. I could not find a German translation of Coyne's book, so Daniken has to read it in English!
4. P. Levene discovered and described all the components of DNA, but Watson and Crick (1953) did not refer to him. This demands an explanation. I have to find out what's going on. [29 Jan 2023]
   

 

This is a tweetblog: a short blog to report news quickly without all the details of a full review. I have used the KOBO ebook. I discovered today that for the first time I can read my books in the browser, that is in full color! and on my computer screen! (logged in with my KOBO account). All KOBO e-readers are black and white. So, this is a huge step forwards.

I am working on an extended version which will appear on my WDW website.

 

Update 22 Feb 2023

A full review of von Daniken's book Evolution is wrong has appeared on my website Was Darwin Wrong?

See also my blog: Seks met aliens. Literatuur bij het Skepter artikel. 30 May 2023

Famous Watson-Crick base pairing is by far insufficient for DNA copying fidelity

"Despite its beauty, Watson-Crick complementarity is absolutely insufficient to ensure an acceptable fidelity of replication, even with perfect raw materials.  ... Fortunately, fidelity of nucleotide attachment depends not on complementarity, but on active involvement of DNA polymerases." Kondrashov [1]

These statements changed my thinking about DNA dramatically and definitively. More than Tomas Lindahl did. Perhaps because Kondrashov contrasts replication fidelity so clearly with the A:T and C:G base complementarity.

I always had the idea that A:T and C:G base pairing was the crucial feature of DNA and that it was a necessary and sufficient condition for the double-helix structure, replication, transcription and translation. In a restricted sense this is still true, but it is certainly not the whole story. It is a necessary component of life, but it needs help. Lots of help! In the background hundreds of enzymes are constantly working to correct base mis-pairings and replication errors. Kondrashov gives a detailed description of the known enzymes that are involved.

Don't be mistaken, I still agree with the central importance of DNA in biology: 

"The model of the DNA structure built by James Watson and Francis Crick certainly is one of the central discoveries in twentieth-century biology and the entire history of biology." Eugene Koonin [2].

Just as Mendeleev’s periodic table of elements created a foundation in the science of chemistry, so does the structure of DNA create the foundation of biology. DNA as a carrier of genetic information draws the line between living and non-living systems. With the invention of DNA, evolution took off and created millions of species from the most simple to the most complex. Bacteria are based on DNA. Humans are based on DNA. And everything between is based on DNA. DNA seems to have an unlimited potential.

But again, DNA cannot even 'self-replicate' without enzymes. DNA on its own is just a large non-living chemical macro-molecule. It becomes useful only when it is transcribed and translated into proteins ... with the help of enzymes. DNA needs help. Curiously, it created the help itself! Let me introduce the self-building crane as a metaphor for DNA creating its own helpers:

How to build a crane

How to build a crane? A crane can be built by a second crane. But, how to build that second crane? An ingenious solution is a self-building crane which does away with the second crane requirement. It only needs building blocks. The crane can pick them up, integrate them and it grows. Gradually. Similarly, DNA does not need external help. DNA can copy and repair itself with helper enzymes which are encoded in DNA itself.

 

Why are DNA polymerases needed anyway?

It is not immediately clear from Watson & Crick's model why special enzymes such as DNA-polymerases are needed, since the AT and CG base-pairs are formed naturally and spontaneously. Wrong base pairs are excluded by the base pairing rules. Wrong base pairing, for example A with C or T with G, does not fit in the double helix. So, the strong suggestion is that the base-pairing rules are enough for DNA replication. The fidelity of DNA-replication is completely based on the base pairing rules. 

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material " Watson & Crick

In 1953 Watson and Crick had absolutely no idea of the insufficiency of the base-pairing for DNA-replication. Their double-helix DNA structure, base pairing and replication were prime examples of beauty and simplicity. "The idea of errors and repair didn’t occur to them, because it wasn’t thought to be necessary” ! [4]

The fact is that enzymes such a s DNA-polymerase are required. Without DNA-polymerases, DNA-replication would produce a 1000-fold higher error rate.  Without DNA-polymerase, the error rate would be 1% (10^-2). With DNA-polymerase the error rate is down to 1 in 100,000 bases (10^-5) [1]. That is still too high. Several mechanisms bring the error rate down even further.

 

How could DNA have started life without enzymes?

Rolie Barth wrote in a comment to the previous post: "But still I think that physical and chemical mechanisms might play an important role in keeping DNA-structure and information stable, because DNA storage functioned before repair systems were operational. Logically the latter evolved using functioning genes, isn't it?"

Exactly! Good thinking! If the error rate of DNA replication is so high, how could DNA have been replicated reliably without all those enzymes? A chicken and egg problem:

1. DNA needs a lot of proofreading and repair enzymes  
2. these enzymes are encoded in DNA
3. this makes DNA longer (more complex, more genes, more information)
   
4. that means more DNA must be maintained
   
5. this requires better and/or more enzymes
6. etc ...
   

In other words: Eigen paradox [3]:

The error threshold (or critical mutation rate) is a limit on the number of base pairs a self-replicating molecule may have before mutation will destroy the information in subsequent generations of the molecule.

So, it seems you need a long DNA molecule with many high fidelity replication enzymes encoded in its DNA to produce high fidelity DNA replication. A vicious circle. What came first? But I see no reason why copying fidelity could not be improved in a gradual way step by step. It need not have increased a thousandfold in one step! Under favorable environmental conditions (climate, food) natural selection could improve the proofreading and repair machinery step by step. Furthermore, one doesn't need a separate proofreading enzyme, because DNA polymerase has also proofreading activity [5]. Ultimately, it all depends how many genes and how much junk is in your genome. A genome of 1 million functional base pairs can tolerate an error rate of 1:1,000,000 but a genome of 1 billion functional base pairs will degenerate quickly with the same error rate.

 
Conclusion: the above statement of Kondrashov about the insufficiency of base complementarity was an absolute eye-opener for me. My view of DNA as the perfect solution to the problem of heredity was shattered. Lindahl gave the first blow. But I was only really blown away by Kondrashov's statement. For me it is nothing less than a paradigm change.

Yes, DNA is the biggest revolution in biology, and yes, Watson & Crick got it right, but: (1) despite Watson & Crick, DNA replication fidelity is too low without the help of enzymes, (2) this requirement immediately creates a problem for the evolution of complex life based on DNA. In a future blog a will deal with that!

 

 

Notes

1. Chapter 5 'Struggle for Fidelity', in: Kondrashov, 2017, Crumbling Genome.
2. Eugene Koonin (2011) The Logic of Chance, p.21 hardback.
   
3. Geen leven zonder DNA-repair. De Lindahl paradox en de Eigen paradox. (blog 21 October 2015) (Dutch). See Wikipedia article: Error threshold.
   
4.  According to Phil Hanawaltin in the New Scientist: Running repair keeps DNA in order, 15 March 2003.
5. see wikipedia article DNA polymerase: DNA polymerase with proofreading ability.

 

Further Reading

• DNA repair – providing chemical stability for life, The Noble Prize in chemistry 2015:  

"Besides base excision repair, nucleotide excision repair, and mismatch repair, there are several other mechanisms that maintain our DNA. Every day, they fix thousands of occurrences of DNA damage caused by the sun, cigarette smoke or other genotoxic substances; they continuously counteract spontaneous alterations to DNA and, for each cell division, mismatch repair corrects some thousand mismatches. Our genome would collapse without these repair mechanisms."

• Rais A. Ganai, Erik Johansson (2016) DNA Replication—A Matter of Fidelity (overview).

• De Nobelprijs Chemie 2015 is gegaan naar een drietal pioniers op het gebied van DNA reparatie ('DNA-repair'), my blog (in Dutch)

  In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible.

• See complete video: How Tower Cranes Build Themselves on youtube.

 

 

Previous DNA post

• Non-Watson-Crick base pairs that you won't find in the textbooks and Wikipedia, 13 Jan 2023

 

Selection of DNA posts

• DNA: A selection of the most important posts 2012 - 2023, blog page.