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Friday, August 28, 2015

Human Evolution: Genes, Genealogies and Phylogenies by Graeme Finlay

Human Evolution: Genes, Genealogies and Phylogenies was published in 2013 by Cambridge University Press. The author is Graeme Finlay, a cancer researcher at the University of Auckland, Auckland, New Zealand.

I first learned about this book from a book review published in the journal Evolution (Johnson, 2014). It sounded interesting so I bought a copy and read it.

There are four main chapters and each one covers a specific topic related to genomes and function. The topics are: Retroviruses, Transposons, Pseudogenes, and New Genes. There's lots and lots of interesting information in these chapters including an up-to-date summary of co-opted DNA that probably serves a biologically relevant function in our genome. This is the book to buy if you want a good review of the scientific literature on those topics.

I was surprised to discover that there's no mention of junk DNA in this book even though most of the subject material is about junk. It's difficult to figure out exactly what point the author is making but I agree with the reviewer (Norman Johnson) that the tone is hyperadaptationist and that "the book would have benefited from a firmer footing in population genetic principles."

The emphasis in the book is on the co-opted functions of retrovirus, transposon, and pseudogene sequences. One gets the impression that the author favors the idea that these bits of DNA serve an important role in evolution and, therefore, don't count as junk DNA. This view is reinforced by his reference to John Mattick as a revolutionary thinker.
Human evolution over the past few million years has been profound. Striking innovations in our biology include bipedality and the increase in brain size. It has been suggested that this rapid evolution may correlate with, and may have been driven by, a high rate of retrotransposition. John Mattick has championed the paradigm that non-coding RNA has vital roles in the genetic regulation of complex organisms. He suggests that waves of Alu insertions into primate genomes have provided a substrate contributing to the versatility of transcriptional and epigenetic regulation, necessary for interactions between the environment and epigenetic regulation of the genome, and thus contributing to the development of cognitive function.

It is generally stated that half of our genome is derived from ERVs and TEs. The application of more-sophisticated software that allows identification of more degerated (fragmented)TEs has raised this estimate to two-thirds of our genome. TEs have expanded, modified and eloborated our ancestors' genomes at least as far back as genetic analysis can detect. Mattick's revolutionary theorising may be generalisable over biological history.
(pp. 130-131)
There are hints of human exceptionalism in those paragraphs but those hints become explicit in the last chapter: "What really makes us human?"
Biologically, we constitute a twig of the mammalian branch of the phylogenetic tree. It does not follow that we are merely another one of the millions of species that comprise that tree. Physically we are apes, genetically contiguouos with lemurs platypuses. It does not follow that metaphysically we are nothing but another kind of ape. (p. 266)
It seems strange to bring up metaphysics in this way but it's consistent with what Graeme Finlay wrote in the Prologue. It seemed strange then as well ...
Darwinism as science entails the random generation of variation screened by lawful natural selection, leading to biological adaptation and diversification. But when this mechanism is asserted to be either purposive or non-purposive, Darwinism is changed into a metaphysical consideration. Such deliberations may be properly carried out, but not as a scientific activity. For science is blind to the concept of purpose. Whether the process of natural selection entails no purpose (as a materialist might suppose) or is a means to an end, such as a creature that expresses the image of God (as a Christian might suppose) are equally metaphysical interpretations. Neither teleology nor a denial of teleology shoudl be accepted as an integral component of a scientific understanding. (p. 9)
I profoundly disagree. I think it's possible for science to investigate whether there's any evidence of purpose in evolution, especially the evolution of humans. So far, there's no scientific evidence that humans are special or that their evolution was preordained. Thus, we can tentatively conclude, scientifically, that evolution lacks purpose.

This is not just "metaphysics." The irony here is that Graeme Finlay seems to be making the argument that there's scientific evidence for purpose in human evolution.

I was wondering why a cancer researcher in New Zealand would feel compelled to write things like that so I looked him up on Google. Turns out that Graeme Finlay is active on BioLogos, the website founded by Francis Collins and funded by Templeton. The goal is to show that science and Christianity are compatible.

Finlay has posted an article on that site with the same title as his book: Human Evolution: Genes, Genealogies and Phylogenies. He explains how evolution is compatible with his belief in a Christian God.
So how did this demonstration of human evolution fit in with my Christian faith? The biblical concept of creation emphasized that all of reality is given existence by God. This biblical understanding was very important for the development of science during the Middle Ages, because it entailed that creation was ordered and behaved lawfully (and therefore was worthy of investigation). It also meant that the entire universe was creation, distinct from God (and therefore was amenable to investigation). The concept of an independent and lawful creation was foreign to polytheistic or pantheistic worldviews. On the biblical account, biological evolution is merely the history of life, and an aspect of God’s created world.

Old Testament scholars have shown that the creation stories in the book of Genesis were written to present a vision of the nature of God – in his peerless sovereignty, faithfulness, and goodness. This God was wholly different from the violent and petty gods of the ancient Babylonians or Canaanites. When read in this way, the Genesis stories may be seen as one of the greatest-ever revolutions in human understanding. Genesis used the literary forms of the day to introduce its readers to a rational God who cares for people – and whose faithfulness made science possible. Genesis is expressly about theology, not science.

Ultimately, of course, Christian faith comes from God’s revelation in Jesus of Nazareth. As David Hart states, Christianity is the only major religion that arose from a single historical claim. A lifetime of study can only emphasize the authenticity and power of this history. And I have a deep sense of satisfaction that the God who is revealed in human history is also the God of cosmic and biological history. All such histories run freely, but they follow channels that are constrained by divinely-ordained laws, and they have culminated in astonishing climaxes. Science reveals the universe, the solar system, and all living organisms to have an authentic history. In the same way, the Christian faith is irreducibly historical. The wonders of biological development and of Resurrection come from the same faithful God. That’s exhilarating.
It's okay to post stuff like this on BioLogos but I wish he would have kept even the softer version out of his book.

The books is a good read and very useful. References to human exceptionalism and gods detract from an otherwise valuable resource.

Johnson, N.A. (2014) Making sense of the human genome. Evolution 68: 3047-3049.


Bjørn Østman said...

What does 'lawful' mean in 'lawful natural selection' and 'lawful creation'?

Dave Carlson said...

Thanks for this! I'll add it to my (ever growing) list books to purchase when I'm not on a grad student stipend! :)

Beau Stoddard said...

Professor Moran, what would justify human exceptionalism claims?

Joe Felsenstein said...

I am not familiar with Finlay. From the book's subtitle, I would have guessed it was about coalescent genealogies of copies of protein-coding genes, or of stretches of noncoding sequence that occur in the same place in all primates. That is a fascinating subject -- you can get interesting information about the history of humans from coalescents. (Or about the history of any other life form).

But to have the book talk only about retroviruses, pseudogenes, transposons and new genes is strange. And all the strange terminology such as "legal" natural selection doesn't help. If anyone notices any illegal natural selection, please report it to the police.

Petrushka said...

The Flood was a historical claim. Basing a world religion on a single historical claim is balancing a pyramid on its point.

Imagine how the historical claims of the gospels would be treated if you left out the god parts and simply read them as a secular history of someone like Houdini, or of Uri Geller.

Mikkel Rumraket Rasmussen said...

An objective measure of exceptionalism, where humans occupy the top.

Petrushka said...


Larry Moran said...

Professor Moran, what would justify human exceptionalism claims?

Evidence that humans possess features that have no homolog in other species and could not possibly have arisen by natural processes.

Chris B said...

"This God was wholly different from the violent and petty gods of the ancient Babylonians or Canaanites. When read in this way, the Genesis stories may be seen as one of the greatest-ever revolutions in human understanding. Genesis used the literary forms of the day to introduce its readers to a rational God who cares for people – and whose faithfulness made science possible."

Did Finlay actually read Genesis?

Petrushka said...

Those crazy Babylonians, whose god tried to kill everyone in a flood.

Dazz said...

Question should be, how much more evidence do you need to accept what we are Beau? Give it a try, I promise you won't suddenly feel the urge to climb trees, eat bananas all day, or go killing and raping people randomly

Beau Stoddard said...

Dazz, it doesn't fit the professors criteria but the fact we're having this conversation is exceptional to me. I'm not here to argue science I just ask questions. I've admitted numerous times I'm a dunce compared to %99 of those who comment on this page. That being said I'm smart enough to know you're not on the same level as these gentleman either. Lay off the snark sir intelligence by association isn't what you may perceive it to be.

judmarc said...

I'll say this much about "this God:" To the extent that notions of gods acting in the world comprised a sort of proto-science, i.e., an attempt to explain the phenomena ancient peoples observed, monotheism might be seen as an attempt at a sort of Grand Unified Theory. To that extent, it deserves some admiration as an intellectual achievement of that era.

Dazz said...

The same Epic of Gilgamesh they borrowed from in the garden of Eden and other biblical passages. They ripped off all those Babylonian myths, and not only they can't give them credit for it, they even have the audacity to consider it all original.

And then there's the resurrection thing:

They couldn't even bother making up something original for their central myth? smh

At least mormons have the golden plates and the scientologists the Galactic Confederacy, the aliens and stuff.

Dazz said...

I have openly admitted here that I'm not a biologist and I am nowhere near as knowledgeable in the field as the pros, and pretty much everyone here.
Anyway, mine was an honest question. It may sound snarky to you but I've heard christians claim they would have no reason not to kill and rape if they believed they're "just animals".

anthrosciguy said...

I was curious about the term "lawful" and couldn't find anything definitively outlining the usage, but doing a search for the word on the Biologos website returns 3 pages of results where it seems to be used in the same way.

Beau Stoddard said...

I apologize Dazz took your comment the wrong way.

Piotr Gąsiorowski said...

The Oxford English Dictionary has some examples illustrating the use of lawful in the meaning 'describable or governed by laws of nature', e.g.

1939. Newton and others have found confirmation even for their religious beliefs in the lawful character of physical phenomena.

The source is this issue of Nature. I have no free access to it, but it contains three "research articles" on science and religion, and I'm pretty sure the quotation is from one of them. My impression is that this rare usage can be traced back to theologians and philosophers.

anthrosciguy said...

It seemed to me to be a piece of theology jargon when I first read it; the Biologos search results reinforced that. My snarky side says it's a way to try to shut off criticism by simply stating the statement is settled and beyond argument.

Piotr Gąsiorowski said...

Sorry, I messed up the link. Here's the correct one:

Rolf Aalberg said...

Dazz said: I've heard christians claim they would have no reason not to kill and rape if they believed they're "just animals".

Well, but do they also say that they don't love themelves or their family, and have no concern whatsoever for other people - or animals, and therefore they don't even keep pets, and would not hesitate to commit murder on the spot were it not for the risk of being rewarded with imprisonment or execution?

In short, they are not human, the only reson they are not asocial, criminal misanthropics is the risk of reataliation?

Dazz said...

Not really. It's a known statistical fact that coercion and punishment doesn't help reduce criminality. Democracies with the lowest crime index are always those with high level of social equality and education, and of course, the least religious ones too (South Korea, Japan, Scandinavian countries...).

Just for the record, I don't think that any of those who claimed they would kill and rape if it wasn't for their religious faith would actually do it, and I'm sure they do love they're families and most of them are good people. But it's baffling that they really believe they would do all that. Goes to show how deluded they are

Dazz said...

*their families* ouch!

Piotr Gąsiorowski said...

Worse than that: they project this belief on actual atheists, concluding that the latter are evil sociopaths (and liars, should they claim otherwise). See Barry Arrington's mantras at UD.

Dazz said...

If projection was an Olympic discipline christians would win every time. Problem is they would never take the medals because they would project their projection and claim some atheist won instead XD