Wednesday, 4 April 2018

Blogging Graeme Finlay's "Human Evolution: Genes, Genealogies and Phylogenies" - Part 1

I've referred to Graeme Finlay's excellent book Human Evolution: Genes, Genealogies and Phylogenies in a number of previous posts. Finlay, who is a Senior Lecturer in Scientific Pathology at the Department of Molecular Medicine and Pathology, and Honorary Senior Research Fellow at the Auckland Cancer Society Research Centre, University of Auckland, New Zealand is well placed to comment on the subject, and also argues from the position of a convinced Christian. For the ant-evolutionist, dismissing him as either hostile to Christianity or uninformed is simply not an option.

Finlay argues that "from my perspective, [genetics] now constitutes the ultimate evidence for common descent and the definitive way of defining phylogenetic relationships", [1] an argument with which I am in complete agreement. Therefore, over the next few posts, I will be blogging through Finlay's book, showing in detail why molecular biology proves common descent beyond doubt.

The fundamental principle underlying the genomic evidence Finlay details is the concept of common mutations shared by human and ape derived ultimately from a common ancestral species in which this mutation first occurred. Finlay notes that his research in cancer led him to this conclusion:
I have spent years studying cancer cells. I have learned that cancers develop, in part, when particular mutations arise. Once a mutation arises in a cell, it is transmitted to all the descendents of that cell. The same complex mutation in the DNA of two or more cells establishes that those cells are related. They inherited that singular mutation from the same ancestor – the one in which the mutation occurred. A cell population descended from a single progenitor is called a clone. Clones and lineages of cells are identified by shared mutations. The same logic can be applied to evolution. Once I appreciated that genetic evidence establishes the clonal nature of oncogenesis (cancer development), I could appreciate the genetic evidence for phylogenesis (species development). (Emphasis mine) [2]
When I discuss this subject, I use the concept of genetic plagiarism as an analogy. If you were a teacher marking term papers, and discovered the same spelling errors in the same places, you would dismiss as unlikely the explanation that purely by chances these spelling errors occurred in the same place in different exam papers, and rightly assume that some of those papers had copied from another. This is exactly the same argument Finlay uses. He describes how when marking medical student reports he encountered both a novel misspelling of basal cell carcinoma and evidence of copying by other students:
One year I was marking the students’ reports of the visit, and was struck to read one student’s description of basal cell casanova – an expression that was singular and therefore memorable. But I subsequently came across two more students who wrote of basal cell ‘casanovas’. Here was a singular error shared by three students. Two students must have copied their work from another. I reviewed the three reports closely and confirmed that this was the case. (Emphasis mine) [3]
Just as the presence of a spelling error in two reports was proof of copying from an another report, the presence of a specific genetic error in many cancer cells is evidence of their descent from an ancestral cell in which the mutation first occurred:
When singular novelties in DNA – unique genetic ‘mistakes’ arising through random and often complex events – are shared by multiple cells, we may conclude that all those cells are descended from the one cell in which the mutation arose. This basic principle is familiar to everyone involved in the study of the clonal progression of cancers, or the clonal development of lymphocytes in immunity (as revealed by antigen receptor gene rearrangements). When singular complex mutations are shared by multiple individuals, then all those individuals are descended from the one individual (indeed the one reproductive cell) in whom that mutation occurred. And if singular mutations were shared by multiple species, then all those species are derived from the one species (indeed the one reproductive cell) in which each of those mutations occurred. (Emphasis mine) [4]
Finlay gives two examples of infectious cancers that demonstrate this concept. canine transmissible venereal tumour (CTVT), spread via copulation and devil facial tumour disease (DFTD), spread via bites. The latter a disease that affects Tasmanian Devils and could end up causing their extinction. Finlay points out that:
All the cells comprising each of these contagious tumours are descended from a single cancer cell (the most recent common ancestor that may have lived a long time after the tumour first arose). These infectious cancers are clonal. All CTVT cells are defined by a unique mutation that probably occurred in the founding cancer cell: the random insertion of a segment of DNA adjacent to the growth-controlling MYC gene. All DFTD cells are defined by a set of unique chromosome rearrangements. Such genetic markers arise uniquely, and all cells that now possess them acquired them by inheritance. Common ancestry is established by shared singular mutations. (Emphasis mine) [5]
Having outlined the concept, Finlay shows its utility in establishing human lineages by showing how molecular biology allowed us to solve the mystery of where the Romanovs, who were murdered in 1918, but whose final location remained unknown for most of the 20th century. Analysis of mitochondrial DNA and comparison with known relatives confirmed that bodies found in a grave in Yekaterinburg were those of the Romanovs.

Figure P1. DNA identification of the last Russian royal family A partial genealogy of the Russian Royal family, depicting females (circles), males (squares), individuals from whom mitochondrial DNA sequences were determined (bold outlines), and the Empress Maria Feodorovna and Queen Victoria mitochondrial sequence types (background shading).

This technique also allowed one final mystery to be solved. The remains thought to be those of Tsar Nicholas II had two populations of mitochondrial cells. While this could well have been a case of heteroplasmy, where there are multiple mitochondrial DNA populations in a cell or individual, the possibility that the DNA sample was contaminated had to be excluded. If one could find the same example of heteroplasmy in a known relative of the Romanovs then one could demonstrate that the remains were indeed that of Tsar Nicholas II. Finlay continues:
To resolve this mystery, the remains of the Tsar’s brother, the Grand Duke Georgij, who died in 1899, were exhumed and DNA recovered from a leg bone. The Grand Duke’s mitochondrial DNA also showed the same pair of mitochondrial DNA molecules, one of which had a C, and the other a T, at base position 16,169. The heteroplasmy was no longer an embarrassment, but a convincing demonstration of the authenticity of the Tsar’s DNA. The issue was settled when DNA from a bloodstained shirt (that the Tsar wore during a failed assassination attempt) showed the same C/T pair of 16,169 markers (Figure P2). [6]
Figure P2. A heteroplasmic marker establishing the authenticity of the Tsar’s remains A small segment of mitochondrial DNA sequence is shown. The shaded area shows that the Tsar’s and Grand Duke Georgij’s tissues contained two populations of mitochondrial DNA molecules, one with a C, and the other with a T, at position 16,169. The population of DNA molecules with the C was lost during transmission to living descendants of the Tsar’s mother (‘maternal relatives’).

Mutations, as Finlay notes, allow us to delineate lineages. [7] The rest of the book is devoted to how this 'casanova phenomenon' proves overwhelming evidence for human evolution and details the nature of our evolutionary tree. Finlay makes no apology for the large number of examples he employs:
I have provided an abundance of examples for two reasons. Firstly, I find each example to be a source of sheer fascination, because of its precise information content and its compelling evidential power. The question of whether large-scale evolutionary change has occurred has been resolved by appeal to a source of historical information that we all carry around with us. Secondly, I want to provide some feeling for the sheer mass of data available. The supreme information-bearing molecule in the known universe, DNA, provides millions of genetic markers for historical reconstruction. [8]
I too share Finlay's fascination with the subject, and also agree that in this case, proving a large number of cases helps emphasise to the interested reader just how overwhelming the evidence for human-ape common ancestry from the genomic data is. Over the next few posts, I will be showing just how compelling this evidence is.


1. Graeme Finlay. Human Evolution: Genes, Genealogies and Phylogenies (2013: Cambridge University Press) p 14
2. ibid, p 15
3. ibid, p 15
4. ibid, p 15
5. ibid, p 16
6. ibid, p 17
7. ibid, p 18
8. ibid, p 19