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Sunday, February 18, 2018

Human genome books

& Junk DNA

I'm trying to read all the recent books on the human genome and anything related. There are a lot of them. Here's a list with some brief comments. You should buy some of these books. There are others you should not buy under any circumstances.

The Deeper Genome: Why there is more to the human genome than meets the eye
by John Parrington
Oxford University Press (2015)
ISBN 978-0-19-968873-9

John Parrington is an Associate Professor in Molecular and Cellular Pharmacology at the University of Oxford (UK). He claims that most of our genome is functional (not junk) based largely on the results of the ENCODE study. He ignores most of the scientific evidence in favor of junk DNA. This is a very bad book [Georgi Marinov reviews two books on junk DNA] [John Parrington discusses genome sequence conservation].

Junk DNA: A journey Through the Dark Matter of the Genome
by Nessa Carey
Columbia University Press (2015)
ISBN 978-0-231-53941-8

Nessa Carey is former researcher in epigenetics. She is currently a science writer based in the United Kingdom. She claims that recent discoveries have revealed that most of the mysterious “dark matter” of the genome (formerly junk DNA) is actually required for the regulation of gene expression. This book is even worse than Parrington’s [Georgi Marinov reviews two books on junk DNA] [Teaching about genomes using Nessa Carey's book: Junk DNA] [Nessa Carey doesn't understand junk DNA]. It's even worse than the book written by ID proponent Jonathan Wells (see below). In fact, it's a classic example of everything that's wrong with modern science writing [On explaining science to the general public].

The Myth of Junk DNA
by Jonathan Wells
Discovery Institute Press (2011)
ISBN 978-1-9365990-0-4

Jonathan Wells has a Ph.D. in Molecular & Cell Biology from the University of California, Berkeley. He is a leading advocate of intelligent design. According to Wells, the idea that most of our genome is junk is a myth promoted by Darwinian scientists. The science in this book is far superior to the first two books on the list. Wells acknowledges and deals with the main evidence for junk DNA but he still reaches the wrong conclusion [The Myth of Junk DNA by Jonathan Wells].

Human Evolution: Genes, Genealogies and Phylogenies
by Graeme Finlay
Cambridge University Press (2013)
ISBN 978-1-107-04012-0

Graeme Finlay is a professor in the Department of Molecular Medicine and Pathology at the University of Auckland, Auckland, New Zealand. This is an excellent book on retroviruses, transposons, pseudogenes, and new (de novo) genes. Those topics are very well described at a fairly sophisticated level with an emphasis on their adaptive roles. Junk DNA is not discussed even though most of the sequences Finlay discusses are junk. The emphasis is on the possible evolutionary significance of co-opted sequences of pseudogenes giving the impression that they aren't junk [Human Evolution: Genes, Genealogies and Phylogenies by Graeme Finlay]. I agree with Norman Johnson when he says that the book is hyperadaptationist in tone [Making sense of the human genome].

Ancestors in Our Genome: The new science of human evolution
by Eugene E. Harris
Oxford University Press (2015)
ISBN 978-0-19-997803-8

Eugene Harris is a professor of Biological Sciences and Geology at City University of New York, New York (USA). He has written an excellent analysis of modern human evolution from a molecular evolution perspective. His description of some complex techniques; such as selective sweeps and coalescence are very good. His explanation of the difference between gene trees and species trees is excellent. The science is well above the level of some of the dumbed-down books at the top of this list. This is the best book I've ever read on the subject of random genetic drift. Harris understands that most of our genome is junk. Buy this book.

Inside the Human Genome: A case for non-intelligent design
by John C. Avise
Oxford University Press (2010)
ISBN 978-0-19-539343-9

John Avise is a molecular evolutionary biologist at the University of California, Irvine. His goal in this book is to demonstrate that our genome is sloppy and disorganized. It doesn’t look like it was intelligently designed. Avise writes from the perspective of someone who is opposed to intelligent design creationism but favors accommodation between science and religion. He is non-committal, but skeptical, about the view that most of our genome is junk DNA [Shoddy But Not "Junk"?]. The book is pretty good if you're looking for evidence to refute Intelligent Design Creationists. It's a whole lot better than his more recent book on 70 breakthroughs or paradigm shifts in biology [John Avise doesn't understand the Central Dogma of Molecular Biology].

Drawing the Map of Life: Inside the Human Genome Project
by Victor K. McElheny
Basic Books (2010, updated in the paperback edition 2012)
ISBN 978-0-465-02895-5

Victor McElheny is a science writer based in the United States. He has written an entertaining, and accurate, account of the Human Genome Project from an historical perspective. The book does not cover the implications of the genome sequence and it does not explain the science behind the work. McElheny thinks that the results of the human genome sequence were revolutionary—especially the surprisingly small number of genes. He thinks there’s very little junk DNA.

A Brief History of Everyone Who Ever Lived: The Stories in Our Genes
by Adam Rutherford
Weidenfeld & Nicholson (2016)
ISBN 978-0-297-60937-7

Adam Rutherford is a science writer with a Ph.D. in developmental genetics. While working at Nature in 2012 he was a prominent member of the team that helped hype the ENCODE results. His current view of the human genome is that we just don't know what most of it is doing. He doesn't spend any time at all on the evidence for junk DNA, nor does he explain how controversial the topic is. Nevertheless, the other parts of the book are excellent, especially the parts on our ancestors. I recommend it in spite of it's shortcomings.

The Mysterious World of the Human Genome
by Frank Ryan
William Collins (2015)
ISBN 978-0-00-754906-1

Frank Ryan is a physician, a science writer, and a leading member of The Third Way. His book purports to explain the human genome but it does nothing of the sort. Instead, Ryan has fallen for every bit of hype, and every "revolution," that has been promoted in the past 17 years since publication of the human genome sequence (e.g. alternative splicing, pervasive transcription, epigenetics, etc.). He rejects junk DNA, misinterprets the Central Dogma, and doesn't understand what a gene is. It's no wonder that the genome appears "mysterious" to someone like Frank Ryan since he ignores most of the relevant scientific literature while focusing on the "fact" that recent discoveries have challenged everything we thought we knew [Another failure: The Mysterious World of the Human Genome.

The Gene: An Intimate History
by Siddhartha Mukherjee
Scribner (2016)
ISBN 978-1-4767-3350-0

This is a very big book by Siddhartha Mukherjee. You might recognize the name—he's a physician who won a Pulitzer Price for an earlier book: The Emperor of all Maladies: A Biography of Cancer. In spite of the title of his latest book, you will get through 592 pages without knowing what a gene is and many other things [What is a "gene" and how do genes work according to Siddhartha Mukherjee?] [Siddhartha Mukherjee tries to correct his book]. Mukherjee is not interested in the human genome because his focus is on genes, genetic disease, and the future of genetic manipulation. Mathew Cobb has reviewed that part of his book [On the heredity trail].

Herding Hemingway's Cats: Understanding How Our Genes Work
by Kat Arney
Bloomsbury Sigma (2016)
ISBN 978-1-4729-1004-2

Here's what I wrote earlier about this book [Herding Hemingway's Cats by Kat Arney]. "Kat Arney is a science writer based in the UK. She has a Ph.D. from the University of Cambridge where she worked on epigenetics and regulation in mice. She also did postdoc work at Imperial College in London. Her experience in the field of molecular biology and gene expression shows up clearly in her book where she demonstrates the appropriate skepticism and critical thinking in her coverage of the major advances in the field." Buy this book.

The Society of Genes
by Itai Yanai and Martin Lercher
Harvard University Press (2016)
ISBN 978-0-674-42502-6

Itai Yanai is a professor at new York University, School of Medicine (New York, NY, USA) and Martin Lercher is a professor at Heinrich Heine University in Düsseldorf, Germany. I like this book because the authors get their facts right and they understand evolution, drift, and junk DNA. Unfortunately, this advantage is somewhat tainted by an over-emphasis on the cooperative nature of protein-coding genes—the society of genes. This gives rise to a somewhat adaptationist view of evolution and a misplaced admiration of Richard Dawkins and The Selfish Gene. Don't let this dissuade you from buying this book because there's lots of other good stuff in it. I recommend it.

The Age of Genomes: Tales from the Front Lines of Genetic Medicine
by Steven Monroe Lipkin with John R. Luma
Beacon Press (2016)
ISBN 978-0-8070-7458-9

Steven Monroe Lipkin is a clinical geneticist at Cornell Medical College in New York. This is a book about the limitations of genetics and why we have to be cautious about analyzing our genome. I highly recommend this book because it debunks some of the myths surrounding genetic testing. The author doesn't have much to say about the gross organization of human genome since he focuses on protein-coding genes.

Postgenomics: Perspectives on Biology after the Genome
edited by Sarah S. Richardson and Hallam Stevens
Duke University Press (2015)
ISBN 978-0-8223-5922-7

This book is a series of 12 essays by different authors discussing "new ways of thinking" about biology in light of recent advances in genomics. Some of the essays are ridiculous, such as Evelyn Fox Keller's diatribe against junk DNA and praise of John Mattick. Some of the essays are brilliant, such as the one by Rachel Ankeny and Sabina Leonelli on the importance of genome curation. Most of them are somewhere in between. There's no serious discussion of junk DNA and the controversy over function. The general tone of the book is that the human genome sequence contained lots of surprises and revelations and we still don't know what most of it does. This is the standard myth propagated in the popular press.

Adam and the Genome: Reading Scripture after Genetic Science
by Dennis R. Venema and Scot McKnight
Brazos Press (2017)
ISBN 978-8158-7433-948

There are two parts to this book. The first part is written by Dennis Venema, a Christian evangelical who teaches biology at Trinity Western University in Langley, British Columbia (Canada). He is an active member of BioLogos. His goal is to show that biology is compatible with Christianity and incompatible with Intelligent Design Creationism.1 He presents the science in a very straightforward and readable format that I greatly admire. Moreover, he gets it right, including evolution and the fact that our genome is full of junk. If you want a good overview of modern molecular genetics then this is the book to buy. The second part of the book is written by Scott McKnight, a professor of New Testament at Northern Baptist Theological Seminary in Lombard, Illinois (USA). Its purpose is to explain why the science in the first part of the book is compatible with the Biblical story of Adam and Eve. This is apologetics at its worst. I did not enjoy this part of the book.

Making Sense of Genes
by Kostas Kampourakis
Cambridge University Press (2017)
ISBN 978-1-107-12813-2

The best short review of this book is supplied by the author in the last chapter.

"Here is the take-home message of this book: Genes were initially conceived as immaterial factors with heuristic values for research, but along the way they acquired a parallel identity as DNA segments. The two identities never converged completely, and therefore the best we can do so far is to think of genes as DNA segments that encode functional products. There are neither 'genes for' characters nor 'genes for' diseases. Genes do nothing on their own, but are important resources for our self-regulated organism. If we insist in asking what genes do, we can accept that they are implicated in the development of characters and disease, and that they account for variation in characters in particular populations. Beyond that, we should remember that genes are part of an interactive genome that we have just begun to understand, the study of which has various limitations. Genes are not our essences, they do not determine who we are, and they are not the explanation of who we are and what we do. Therefore we are not the prisoners of any genetic fate. This is what the present book has aimed to explain."

Most of the book is an essay against genetic determinism in the style of Richard Lewontin. If you are interested in that argument then you should read this book. If you are interested in real facts about genes and the history of gene definitions then you will be sorely disappointed because the author has fallen for the ENCODE hype. Similarly, if you want to know about genomes and junk DNA don't read this book. The author takes his cues from Junk DNA by Nessa Carey and The Deeper Genome by John Parrington. Kampourakis' view of the genome makes no sense [see Making Sense of Genes by Kostas Kampourakis].

DNA Is Not Destiny: The Remarkable Completely Misunderstood Relationship between You and Your Genes
by Steven J. Heine
W.W. Norton & Company, New York/London (2017)
ISBN: 978-0-393-24408-3

Steven Heine is a Professor in the Department of Psychology at the University of British Columbia (Vancouver, B.C., Canada). He has written a book about the perils of DNA testing and his main thesis is that the results of such tests are bound to make you fell unhappy because you will learn that you have a higher risk of several nasty diseases. He warns us that the science behind these predictions is not nearly as solid as the testing companies would have you believe but his main point is the psychological impact of the test results. He claims that we are not conditioned to put the results into the proper perspective because we are pre-conditioned to adopt a very fatalist view of our genetic makeup [see DNA Is Not Destiny by Steven J. Heine].

1. As you might imagine, the Intelligent Design Creationists are not happy about this. In recent months they have attacked Dennis repeatedly on their websites [e.g. Adam and the Genome and Citation Bluffing]. This is strange since we are told repeatedly that ID has nothing to do with Christianity or god(s) or Genesis.


rems said...

Thank you very much for the book recommendations Professor Moran. There is an ongoing discussion between Dennis Venema and Richard Buggs wondering if coalescence methods have dismissed the possibility that there were only two humans at some point of history.

John Harshman said...

Well, that was useful. I'll almost certainly read Harris's book.

I almost certainly won't read Wells's book, but I'm very curious: how does he "deal with" the evidence for junk?

Georgi Marinov said...

He doesn't. It is a much better scientifically book than the first two, but that is because it does not get its biochemistry and history wrong as they do (especially the second one).

But in terms of arguments for junk DNA it mostly deals with them by omission, and just parades licnRNAs, alternative splicing, and other stuff like that as evidence against junk DNA.

Joe Felsenstein said...

Larry, my condolences on having to read all these. This is a very useful set of reviews, so than you.

Joe Felsenstein said...

typo: ... so thank you.

John Harshman said...

Then why does Larry say "Wells acknowledges and deals with the main evidence for junk DNA..."?

Georgi Marinov said...

He mentions the Ohno, Doolittle & Sapienza, and Orgell & Crick papers, and other stuff like that.

But I wouldn't call that properly dealing with the evidence for junk DNA.

Larry Moran said...

I didn’t say he “properly” deals with the evidence. Read my blog posts on Wells’ book.

Rupinder Sayal said...

Prof. Moran, thank you very much for these succinct reviews. These pretty much cover the most recent works on genomics. There are more coming soon, like Carl Zimmer's "She has her mother's laugh", and David Reich's "Who we are and how we got here". I'll be interested in knowing your views on these books when they are out.

Tom Mueller said...

Two seemingly interesting books - a review