Review of Nathaniel Jeanson: Replacing Darwin - The New Origin of Species

My review of the book will soon be published in Answers Research Journal together with comments from Jeanson. As soon as this happens, I will link to both.

In the meantime:

 

Supplementary material

Remember: Arguments in favour of evolution is always about patterns.

From Oct. 28. 2017 no correction will be made to the supplementary material.

This is because Jeanson is in the process of writing a reply. My review and Jeanson's reply will be published in the same volume of Answers Research Journal. It wouldn't be fair if I continued to correct this material, and Jeanson had no chance of responding.

Darwin didn't know Genetics

Jeanson postulates that because Darwin didn't know genetics, there is good reason to question his theory. Let’s see if that is even relevant?
Species are defined by their traits!
Traits are defined by genetics!
Darwin didn't know any genetics!
How then could Darwin write a book about the origin of species?
This seems like a legitimate question. But, consider the following premises:

If there are limited resources
if traits are inherited
if there is Variation in inherited traits
if some source of new hereditary variation exists
and if part of the inherited variation influence survival and, more importantly, reproduction

then some hereditary traits, those that support reproduction more than the alternative traits, will spread in a population. Others will disappear. Hence, the combination of hereditary traits in the population will change over generations. This is evolution in its most basic form: Descent with modification.
Darwin's bold idea was not only to suggest this process, but also to suggest that this process could go on forever, and that there is no limit to variation.
Evolution will take place whenever the premises are met, regardless of how heredity actually works.
Knowledge of the details of heredity isn't necessary!
But that doesn't mean that knowledge of genetics is irrelevant. It is not just necessary to suggest the theory of evolution.
The details of genetics has to be such that variation actually IS endless!
It has to be such that brand new traits actually CAN occur!
When investigated, the genetic variation within and among species has to reflect the expectations that can be made from descent with modification. Otherwise, evolution would have been disproven.
That's why genetics is such a relevant subject, when it comes to evolution.

Oct. 28. 2017

Strange Quotes

Skeletons of Okapi (left) and Giraffe (right)

Here is a few strange quotes from the book:

Chapter 3
Referring to the giraffe's long neck: "At the molecular level, major changes to the standard developmental pathway for vertebrae would be required to produce the giraffe’s signature structure."
Hardly. As is obvious from the picture, the neck of Giraffe is much longer than that of the Okapi. They are both from the family Giraffidae, and therefore the same kind. Apparently, a factor 2 change in neck-length is no problem within the Biblical timescale of 4400 years.

Chapter 3
“Could jellyfish become jaguars”
Why such a silly example. No biologist have ever suggested this. Evolution can only result in transformations that can be linked by multiple small differences. The Theory of Evolution does not state that all organisms can evolve into any other.

Chapter 10
"How can miracles have a place in science? If you’re an evolutionist, I would respond by pointing to Michael Behe's published work."
Michael Behe's ideas of 'Intelligent design' and 'Irreducible complexity' have never been accepted by 'secular' scientists. His books has been heavily criticized in 'secular' scientific journals. Referring to Behe as an example of a scientist that refer to miracles, only shows that Jeanson apparently is not aware of this fact.

Afterword
"If atheistic evolution is true ... " ... "How can you trust them [your eyes] to convey accurate information?"
If evolution is true all details in our anatomy is the result of selection through eons of time. Numerous small beneficial variation in our forefathers has been selected and added to beneficial variation in their ancestors. To what benefit would a variation in an eye be, if it didn't help survival and, ultimately, reproduction? None! How can a variation in the eye help survival? Only by giving a slightly more accurate picture of the world. Therefore, according to evolution, can we trust our senses. That they are not 100% accurate is understandable. Random variation cannot be expected to result in perfection.
Jeanson is taking selection out of the picture, and then saying: Look evolution doesn't work.
I don't know who first came up with this nonsense. I first came upon it when I heard Jason Lisle tell about his so-called 'Ultimate Proof of Creation'.

Oct. 28. 2017

Biogeography

Of 19 families of marsupials, 17 are endemic to Australia.
Jean Lightner, who, just as Jeanson, is an associate of Answers in Genesis, has identified all these families as separate biblical kinds in her overview of Mammalian 'Ark Kinds'. It is therefore relevant to ask how it comes that all these animals migrated from the Middle East to Australia, leaving no trace behind them, if the Biblical story of the Flood is true. Further, they were only followed by those placental mammals that has the best chance of traveling over the sea (Bats and Rodents). What a coincidence!

In South America, there are four endemic families of monkeys (no family of monkeys live in both S.A. and other areas). All four are recognized as separate 'kinds' by Jean Lightner, who recognize a total of 15 primate 'kinds'. Judged by mtDNA homology the S.A monkeys are closer related to one another than to other groups. This is refelcted in tha fact that they are menbers of the so-called 'Parvorder' (a group-level between family and order) Platyrrhini. According to Evolution, this is because all four originated from a single group of monkeys that made it to S.A. after it split from Africa by plate tectonics. According to Creation, they must have made it to S.A. separately after the end of the Flood. What a coincidence!

Correspondingly four of five 'kinds' of primates on Madagascar are Lemurs, Infraorder Lemuriformes: Cheirogaleidae; Lemuridae; Lepilemuridae and Indriidae. Lemurs are endemics of Madagascar. What a coincidence!

Reference to Ark Kinds: Answers Research Journal 5 (2012):151–204. Link

Oct. 28. 2017

Taxonomy

A little more details on the important difference between design and common descent.

In the review, I mention batteries, wires, LEDs, artificial polymers and metal alloys.
The problem goes further than just the common use of these things. One model of Airplane, Ferry, Bus and Car could use an upholstery constructed of, say, 10% rayon and 90% nylon. Another model of Airplane, Ferry, Bus and Car could use an upholstery constructed of, say, 90% rayon and 10% nylon. In living organisms, a corresponding violence of the hierarchical pattern would hardly be possible. When you look at e.g. structure of the cell membrane, it follows large taxonomical groups.
The structure of the eye of Vertebrates differ from that of Mollusks by the arrangement of retina and nerve cells. Arthropods have yet another arrangement. Other arrangements can be found in various other phyla, always following the taxonomical groups.
Why does the skeleton of Whale flippers resemble that of land Mammals rather than that of Shark fins? All examples where evolution put restrictions on the 'design'.

Another objection to Jeanson's model is that there is no 'natural' hierarchy of vehicles. His major groups are 'Powered' and 'Non-powered'. But why not 'Military' and 'Civilian', or 'For transportation of people' and 'For transportation of goods'?
Contrary to this, Evolution immediately suggests a natural hierarchy: That based on descent. Today descent is mostly evaluated by comparing DNA-sequences for two reasons: DNA is the ultimate source of variation; and the details of information in DNA is much larger than in any other group of characters.
In practice it is a problem that not all genes suggest the same phylogeny. This is due mainly to the stochastic process of mutation. Dealing with more genes at the same time (as in mtDNA) mostly solves the problem.

Oct. 28. 2017

Genetic diversity

In the review, I suggest that data from the GenBank database could be used to test Jeanson's idea that the majority of genetic variation within families is due to original created variation. Cats are among the 'Kinds' that, according to the Bible, were present at the Ark in only one pair. Therefor a maximum of four alleles of each gene could be present in this original pair. This should be traceable in the current variation within the cat family.

The picture present the sum of differences in 15 nuclear genes.
Colors show homology. Low homology: blue. Medium homology: white. High homology: red.
To squeeze these results into four groups (the squares) reveals that at least 79 mutations must have occurred. According to creationism 4400 years has passed since the Flood, so there is a maximum of 4400 generations (No cats start breeding before they are two years old on average) between the most distantly related species. 79 mutations in 4400 generations in a sequence of 8696 nt correspond to 1 mutation in 500.000 nt per generation. In humans, according to Jeanson, the corresponding number is 1:40 million (78 mutations per generation in genome of 3.1 billion nt). Cats would have to have an almost 80 times higher mutation rate than humans. At best an extremely bold prediction.

I also comment on the mtDNA of the Great Apes. Humans and Chimps differ by 1500 nt. Between each of those two and Gorillas there are about 1700 differences. Between these three and Orangutans, there are more than 2000 differences. This pattern is exactly what you would expect if Human and Chimps (and Bonobos) share a unique common ancestor, Gorillas, Human and Chimps share a somewhat older common ancestor and all the species share an even older common ancestor.

Jeanson makes a number of other analyses on the mtDNA. In all cases, he fails to include selection, though this can be shown to be a very real phenomenon. To understand this you have to know that mutations in protein coding genes fall into two categories: synonymous mutations that does not alter the resulting protein, and non-synonymous that does alter the protein. Due to the way DNA is translated into protein, about 21% of all mutations are synonymous. I compared two of the most different Human mtDNAs (GenBank numbers EF184607 and FJ168742) and counted the non-synonymous to synonymous differences. 35 of 55 = 64% were synonymous. If more distant mtDNA sequences are compared (Modern Human: KC345974 and Denisovan: FR695060) 85% are synonymous. This tells us that non-synonymous mutations are under stronger selection than synonymous. Selection is important, and Jeanson should include it.
Jeanson doesn't accept the mtDNA sequences from Neanderthals and Denisovans. He claims that the sequences are unreliable, partly because the DNA has been degraded or contaminated. I have urged him to confront the relevant scientists, but he refuses to do so for reasons I don't think is valid.
If mtDNA from Denisovans is unreliable, the mistakes in the sequence should be expected to be randomly distributed, when counted as synonymous vs, non-synonymous substitutions. A short look at the results mentioned above show that this is far from the case. To dismiss Denisovan mtDNA as unreliable is thus unfounded.

To learn to do such calculations here . Scroll down to the fourth and fifth slide from the bottom.

Reference on the cat-example: Science vol. 311 (2006) p. 73-77

For Jeanson's arguments on ancient Human DNA. Look here.

Oct. 28. 2017

Speciation

In chapter 6 Jeanson deals with the question of speciation. How fast can it go. Jeanson argues that because hundreds of breeds of Horses have been produced in just a few thousand years, then surely the much smaller number of species in the families, from which these animals come, could have formed in equally short time. Strangely, he makes no attempt to quantify his claims. Strange because a method for doing so is right in front of his eyes: The mtDNA that he uses in other arguments.
As soon as such attempts are made, the problems appear. A few calculation on mtDNA from dogs will illustrate the problem. Between mtDNA from domesticated Dogs and Wolfs are about 170 differences. The dog family falls into two large groups, here represented by the Gray Fox (Urocyon cinereoargenteus) and the Dhole (Cuon alpinus). The mtDNA of the groups has between 2400 and 2600 differences. Not taking selection and differences in generation time into account, this means that the dog family is about 15 times older than the domestication of dogs from their Wolf ancestors. Taking selection into account will make this difference even larger. Generation time of Dhole and Grey Fox is 5 and 3 years respectively (Source). The generation time of domesticated dog probably vary, but I sincerely doubt it can be longer than that on average.
It should be noted that six genera and several species are missing in the list of mtDNA from the dog-family. Therefor it might be that the most different mtDNA is yet to be identified.

Oct. 28. 2017