Molecular and Genome Evolution by Dan Graur

Over the last two weeks, I have been reading Dan Graur’s book titled “Molecular and Genome Evolution”. This is a fantastic book that everyone should read before starting to work on any genome-related project. For the benefit of our readers, I will share some comments in this short post. If time permits, I will later follow up with a longer post on the book.

My curiousity about Graur’s book grew after he posted a section from it on his blog. In that post, he discussed many competing hypotheses about the origin of eukaryotes. That well-written and thought-provoking post got me interested in finding out what other gems were hidden in his book.

Unfortunately, finding a copy in the university libraries had been very difficult, and I might have had better luck searching through rare books’ collections. Even the University of Washington, which claims to excel in “genome sciences,” does not have Graur’s book in their library. Believe it or not, I even visited the main library of the University of Houston, Graur’s own institution, to read his book and was unsuccessful. Strangely, both copies in their library got stolen !!! Back in Washington, I finally managed to borrow it from a college library of our neighboring state.

The topic of genome evolution covered in his book is highly relevant. These days almost every scientific paper in molecular biology starts with the genome of some organism. That means every researcher in the field needs to know their genomes well. Yet, no serious book exists covering the core evolutionary observations on the genome sequences. Typically, the existing biochemistry or molecular biology textbooks get tweaked a bit to include a ‘genome’ section or a chapter. That leads one to conclude that nothing important has been discovered through the sequencing of thousands of genomes since mid-1990s.

To make matters worse, many popular science books on genomes got published, and reading them can seriously diminish your ability to do scientific research. Most often these books glorify ‘the human genome’ presented without any evolutionary context. Given that even Mark Zuckerberg includes one such book in his recommended reading list, it is safe to conclude that genomes are ‘understood’ by every non-scientist, yet most scientists know little about them.

A proper book on the genomes should focus on evolution and address the core question - “how do the genomes of various organisms evolve to match the evolution of their biological/physiological properties”? That question has many interesting ramifications. For example, are the genomes of “complex” or “primitive” organisms also “complex” or “primitive”? Do closely related or similarly looking organisms have similar genomes? How fast do the genomes of organisms diverse from each other? Do more “complex” organisms have more genes? And what really are the genes for that matter?

Graur’s informative, well-researched and clearly written book addresses all those topics and a lot more. It is a proper science book, and that means it covers hypotheses, not hypes. That task is not easy, because Graur had to sort through many competing explanations for various observations regarding the genomes, and then present them in a simple language. The amount of intellectual work going into this book has been incredible. The only other comprehensive book written for the genomic era that I can think of is by Isabelle Peter/Eric Davidson (reviewed here and here). These books are complementary, and I expect both of them to eventually be the standard textbooks for a genome-centered modern biology.

I will write another blog post providing more in-depth coverage of different chapters of Graur’s book. Let me quickly mention a few things I enjoyed so far.

The most attractive feature of “Molecular and Genome Evolution” is that it is written by a single author. Apart from two short contributed chapters at the end, 573 out of 613 pages were written by Graur himself. Lately, I got tired of reading books written by committees, because they often contain inconsistent or contradictory sections at times right next to each other. In contrast, Graur’s book is consistent throughout, both in style and, more importantly, in scientific discussions.

Secondly, the book has an entire chapter devoted to mobile elements. This contrasts with traditional molecular biology textbooks, where the genomes are presented as mostly static. Apart from the Nobel prize late in her life, Barbara McClintock’s does not get much credit in the textbooks. We are still stuck with the conceptual model of mostly static genomes, and that impacts proper evolutionary understanding of the biochemical processes at the genomic level. In contrast, the core message coming out of Graur’s book is that the genomes are highly dynamic, often within multiple cells of the same living organism. This point has been made clear in almost all chapters from 6-11, and all relevant mechanisms for genome evolution such as whole genome duplication, horizontal gene transfer, molecular tinkering and mobile elements were covered in depth.

Apart from the genomes, I enjoyed Graur’s discussion of neutral evolution. Evolution tends to build a Rube Goldberg machine, where complexity does not always mean engineering efficiency and in fact may be the opposite. In a system engineered by humans, combination of more parts tends to suggest better design. For example, a bridge made of thousands of steel and concrete pieces is definitely safer than a single piece of wood spanning two sides of a waterway. That is not how evolution at the molecular level works. Instead a protein complex with many components may simply be a Rube Goldberg machine, i.e., an elaborate scheme to complete a simple task.

Last, but not the least, Graur’s book tests even better, because its serious topics are served with sprinkling of his wonderful sense of humor. Here are a few examples -

1. “Thus, the human EDARV370A allele is most probably responsible for the rarity of DD-cup bras in East Asian lingerie shops” - (page 502).

2. “the possibility remains that vertebrates (including readers of this book) may in fact be crytooctoploids, and the fish they consume cryptohexadecaploids!” - page 337.

3. Figure 4.27 on page 157 shows why Albert Einstein is more “primitive” than a fruitfly.