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Inside the Human Genome: A Case for Non-Intelligent Design

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Published on February 12, 2010, presumably in celebration of the 201st anniversary of the birth of Charles Darwin, "Inside the Human Genome: A Case for Non-Intelligent Design" is yet another book convincingly pointing out that the "modern" Creationist theory of Intelligent Design has no explanatory or predictive power, and therefore fails.

I don't recommend the Kindle edition though. The formatting of the tables and illustrations is very poor, and almost completely unreadable, and after a while I gave up on them. The text is very clear though. It would have been better if it had been formatted for the larger screen of the Kindle DX or the Kindle computer version.

Instead of examining biological structures that work very well and are very beautiful, John Avise examines plain ugly and barely functional elements of ID's latest poster child, DNA. He shows that DNA looks exactly the way it should, after a long process of evolution and tinkering, and not the masterwork of a loving and caring Intelligent Designer.

It's often forgotten, that for all its design faults, the vertebrate eye still works extremely well. Both Intelligent Design and Evolution have little trouble in explaining perfection or almost perfection.

John Avise, in less than 240 pages (in the Kindle version, the main text finishes 72% through the book before the "Notes and References"), discusses exhaustively the many design faults of the human genome. I'm not certain for whom this book is written. Certainly not the common run-of-the mill ID proponent who waxes enthusiastically over Stephen Meyer's 600+ page "Signature in the Cell". The information is presented in a very dense form, fact after fact, almost without respite.

To give two examples John Avise uses. In malarial areas, sickle cell trait provides increased resistance to malaria. Individuals are heterozygous for Haemoglobin S, a variant form of Haemoglobin A, and have a survival advantage. Individuals with sickle cell anaemia, homozygous for HbS, have a nasty and short life. They pay the price for the increased survival of heterozygotes, and the die is cast at conception. Hardly the deed of a loving and caring Intelligent Designer. So, the malarial parasite is intelligently designed, and the stop-gap measure of sickle cell trait is also intelligently designed, or at least according to ID.

He also discusses my favourite example of bad design, the mitochondrial genome. Mitochondria were originally symbiotic bacteria, and as such had a complete bacterial genome. Most of the mitochondrial genes have been moved out of harm's way to the nucleus, but the mitochondria still retains a circular bacterial chromosome, with a small number of genes, including 13 genes for components of the oxidative phosphorylation pathway. In mitochondria, exposed to free radicals of oxygen, they mutate at 5 to 10 times the rate of nuclear genes, so the end result is steadily decreasing energy production with ageing, and "brownouts" followed by "blackouts", and death.

The human genome contains 3 billion base pairs. Most of it is definitely "junk", without function. ID proponents have faith that all of it will eventually be found to have a function, but they are certain to be disappointed. Almost all genes consist of alternating exons (which code for the protein product) and introns (which don't). The trouble is, is that the the non-coding introns are 30 times as long as the coding exons. So the cell has to take a lot of effort transcribing a much larger mRNA molecule than necessary, and then has to expend a lot more effort splicing the non-coding RNA out to get a functional mRNA molecule. Not very efficient, and very wasteful. Bacteria have a much more efficient genome (actually, I wonder, does the Intelligent Designer love bacteria more than us?)

Towards the end, the author points out that Darwin liberated both science and theology with "Origin of the Species". No longer do religious people have to try to explain the theodicy of genetic defects, as the action of a loving and caring Creator.

The author finishes, with a re-writing of Darwin's famous conclusion to "Origin"; "... There is grandeur in this view of the genome, with its several powers, having perhaps been originally breathed by the Creator into one or a few primordial molecular forms; and ... from so simple a beginning most beautiful, sometimes most awful, but always wondrous genomic features have been, and are being evolved".

I think I still prefer the original, which still excites me whenever I hear it.

The author does an excellent job of presenting evidence against Intelligent Design at the genomic level. It's a relatively short book, packed with facts. As a biologist I was fine, but it may be slightly too technical for the casual reader.

Unfortunately the Kindle formatting was atrocious. I doubt that anyone actually checked it. Only the first chapter link works on the table of contents. And none of the endnotes are clickable. Plus many of the tables are broken up by text or unreadable. I feel bad for the author to have the publisher mangle his book like this.

Some material is irreducibly complex. I mean in genetics. There is only so far that an author can go in simplifying the material for a non-scientist like me before she ends up not even saying things that are accurate any more. So I sympathize with Avise's challenge in writing a book like this, but...I found some of his efforts to be more "popular" in his tone sort of amusing. I mean, he says that he is trying to produce a work for a "broad audience." Effort noted and appreciated, but then the next couple of chapters had between them perhaps four or five paragraphs that I could follow fully. And sometime's Avise helpfully provides a definition for a term that might not be familiar to the reader (ironically, it was more often than not these terms that I WAS familiar with...so perhaps one of his guiding principles was only to define the terms that were essential to an understanding of the overall subject matter even if in the context of other less-well-understood terms), followed by an onslaught of three or four paragraphs in a row of genetic arcana that I find it very hard to believe anyone without a solid grounding in genetics could follow.

Having said all that, I still think the book is valuable and I think it's compelling...even kind of fun in its way, because the genome and its workings are such a freak show. The chapters where Avise comes up for air and makes pronouncements on what we've just read are lucid and cogent. Avise plays painfully fair with theism, but I do wish he could have followed Jerry Coyne's example in "Why Evolution is True" and just not addressed much of the theistic stuff at all. It's not necessary to make some sort of atheistic rant or to try to make up some soothing excuses for theism either one. The science speaks for itself, quite loudly, and any dispassionate examination of the evidence can only lead one to conclude that an all-powerful, all-good being cannot be behind the human genome. As Avise says in the section on mitochondria, not only is the design of it suboptimal, it is ludicrous. 'Nuff said, frankly. Efforts at reconciliation with religion seem necessarily hollow once the truth of that sinks in.

There are other books that walk a similar path and are much easier to read. I'm thinking especially of Survival of the Sickest: A Medical Maverick Discovers Why We Need Disease, which has an interesting take on, for example, malaria. But for sophisticated, scientifically credible material one could use to counter the work of, for example, some recent books that try to make the claim that Intelligent Design is evident in DNA, "Inside" is invaluable. Not light reading, mind you, but invaluable.

Avise, a Distinguished Professor of Ecology & Evolutionary Biology at UC Davis, holds a PhD in Genetics, has written 20 books, and has authored/coauthored more than 300 scientific articles in his field.

He wastes no time and minces no words. From the very first paragraphs of his Preface, he challenges the basic premise of Intelligent Design. He says: "...explaining biological systems that are complex and function well is easy, at a cursory level." [but] "The greater conceptual challenge--for scientists and ID proponents alike--is to explain complex biological traits that show profound structural or functional flaws." [and] "Flawed biotic features nonetheless abound in species, including humans." Avise posits that while the original design may have been intelligent, subsequent flaws reflect implementations that are far from intelligent and are accordingly more reasonably attributed to evolution's non-sentient design.

ID rejects macro-evolution, thus requires special creations, which brings the issue of theodicy to the fore, placing on God the entire responsibility for all the suffering caused by design and implementation flaws. But by attributing genetic flaws to evolution's less than perfect implementations, God is placed at least one remove from responsibility for them.

In Chapter 1 Avise fleshes out his thesis that an error-riddled genome, as implemented, does not reflect intelligent design: implementation by evolution does, and evolution lessens the burden of theodicy.

In Chapters 2-4, Avise supports his contention that flawed biotic features abound. He notes the many inborn errors of metabolism that take countless lives, gratuitous genomic complexities that routinely compromise human health, byzantine mechanisms of gene regulation, and much more - and all these imperfections are consistent with evolutionary expectations, not intelligent design. While he describes only a few representative genomic flaws, he does provides numerous tables categorizing and enumerating many more, and cites other documents that describe yet more, such as the "Human Genome Mutation Database", which as of 2010 describes more than 100,000 mutations!

In Chapter 5 Avise details his argument from imperfection. Since his argument is based on microbiological data, he chooses, appropriately, to challenge Behe: "I will use Behe's 1996 treatise [Darwin's Black Box] as a touchstone for discussion because it remains the preeminent book-length endorsement of Intelligent Design from a professional molecular biologist."

Point by point, Avise shows evolution's non-sentient design is far superior to ID's special creations in explaining the diversity of life on earth. Behe was aware that there are "apparent" molecular imperfections, but tried to deflect an argument from imperfection on the basis that we can't know the mind of the designer and whether he would consider them imperfections. Avise notes: `Ironically, Behe's dismissal of the argument from imperfection in effect demolishes Intelligent Design as a testable scientific hypothesis..."

Regarding special-creations Avise says: "When fine details of molecular errors appear in phylogenetically related species, special-creation explanations for such errors are thus effectively eliminated (unless we suppose that a bumbling Creator made the same molecular mistakes time and again when directly forging different species)."

Avise finishes with a brief epilogue - essentially an apologetic for science.

In summary, the preceding is just a taste: Avise delivers much, much more. He provides a passionate defense of science in general and evolution theory in particular. In the process, he demonstrates that ID is without scientific merit and is of questionable religious merit, being unsupportive of religion relative to theodicy.

In one of its pivotal confrontations, the New Testament shows a wry Jesus responding to the challenge of critics concerning what defference to give to Rome (and along with it, temporal human authority).

By way of reply, Jesus holds up a coin (presumably showing the face of Tiberius Caesar) and asks whose face is on it. Noting the reply that the image depicts Caesar, Jesus famously suggests that followers render to Caesar that which is Caesar's and that to God, which is God's.

I think Professor Avise's book can best be understood as making a much similar point, albeit with respect to science.

And though fundamentalist's may certainly differ, the liberation from having to force religion to explain natural phenomenon and thereby be placed in competition with it, dissaudes it from its more proper historical mission. And what is that proper role of religion? By its own religious texts, much of the message of organized religion concerns itself with proseltyzing moral values rather than imparting factual truths (separate and apart of course that those facts which specifically relate to its myth of beginning). In this sense, I think the particularly religious as well as the majority stream can welcome this book as a breath of fresh air.

But for the mainstream, this book is fascinating reading. Contrary to what one may think, an examination of our genetics clearly shows a more Rube Goldberg structure than one bearing the imprint of some mastermind intelligent designer. The points Avise makes in support of this thesis do run to the very technical but fortunately he periodically reduces his more complex explanations to more simple layman's language.

And significantly, the examples Avise points out are merely the tip of the iceberg to show the often flawed and self destructive ways in which our genetics can fail us.

This book's central message, namely, that the outcome of evolutionary processes is not a supposed perfection of design but the suboptimal result of tinkering under all types of restrictions (physical, chemical, environmental, etc), is excellent (though not new). It focuses on the many molecular errors and bizarre genomic arrangements, a clear blow to the intelectually bankrupt and dishonest "intelligent design" crowd and their curren brand of "élan vital", now dubbed "irreducible complexity". The prose flows smoothly as in the author's other books: his erudition, passion for and knowledge of the subject is engaging. However, the reader must have some pretty good knowledge of basic genetics as many concepts are tossed around concerning details of DNA structure and function, the cell and complex population genetic

notions such as random drift, and many others. Maybe an appendix reviewing these basics would have been helpful (and the inclusion of more figures).

Now, what really dissapointed me was the type of politically correct surrender to the religious viewpoint at the end of the book. The author claims that the inevitable genetic mistakes and the ensuing human suffering, resulting from evolutionary less-than-perfect design could be viewed as a solution to the theodicy (aka, "the problem of evil") and, hence, as an incentive for religious people to accept Darwinism! First off, the acceptance of Darwinism should come from the fact that it provides the best known naturalistic and evidence-based explanation of a host of biological facts, unifying the whole of Biology and providing ever-new research questions. Evolutionary theory is on a par with, say, Newtonian physics, or Relativity Theory, or Quantum Physics. It's an ongoing scientific theory, always incomplete, always in need of development and re-checks and testing and, fortunately, full of open problems. And it's doing pretty well.

Moreover, accepting Darwinism doesn't solve the problem of evil at all, it just shifts it elsewhere, to a hidden (useless?) deity, which somehow is supposed to be solely concerned with "moral and spiritual issues". This NOMA-style conciliatory non-sense is nothing but a pathetic surrender to religious groups, whose anti-science pressure in the US is quite strong. Point is that Darwinism was/is another major blow to the religious world-view and this should be stated clearly and without fear. Of course, people have the inalienable right to their religious beliefs and it's up to them to conciliate within themselves the blatant contradictions that science presents to their worldview. But this kind of politically-correct happy ending, after debunking the ID non-sense throughout the book, is self-defeating and a bit schizophrenic.

The author lays out his purpose for this book early on (Page ix): "Here I hope to introduce readers with diverse educational and philosophical backgrounds to astounding and often unsuspected molecular features of the human genome and the relevance of these scientific findings to the question of underlying deign."

Using genetic data, he raises questions about the extent to which intelligent design or non-intelligent design reigns. He notes the messiness of the genome and the many defects associated with it. He attempts to demonstrate how natural selection can readily explain the genome.

A reasoned argument, and it is made reasonably. Unlike Dawkins, he does not spend a great deal of time criticizing religion. And that is to the good, in my view. Still, proponents of Intelligent Design are unlikely to change their views as they read this book. But it is accessible to nonscientific readers and will prove a useful resource to understand the genome.

Mostly a rant against God and why did he create so many mistakes. Hoping it would be more scientific, I was disappointed.