Among the DNA sequences co-opted by bacteria is the famous gene-frag-family known as CRISPR. You’ve heard of it, and you probably know what it does. Briefly, genetic scientists can use the innate power of CRISPR to manipulate other DNA to “repair” or modify in situ DNA sequences in living organisms. Got a genetic disease? No problem. We get the good genetic sequence, and then use the CRISPR based technology to replace all your bad DNA with the good DNA.

Now, of course, that doesn’t really work this way, and CRISPR technology has had fairly limited success so far. But there have been successes, and CRISPR is generally regarded as the Next Great Hope in the future of genetic therapy.

But now there may be a problem. Among the bacteria that use a CRISPER sort of sequence are two that are fairly nasty and common human pathogens. These are Staphylococcus aureus and Streptococcus pyogenes. In fact, the specific CRISPER sequences that genetic scientists use to do the CRISPR thing, come from these specific bacteria.

So, think about this for a moment. If CRISPER is used by bacteria to do any of their dirty work, and the bacteria are common human pathogens, is it possible that some humans have built up an immunity to the CRISPER sequences, perhaps putting them off limits for future CRISPR therapy?

Yes.

From the abstract of a recent paper:

Based on the fact that these two bacterial
species cause infections in the human population at high frequencies, we looked for the presence of pre-existing adaptive immune responses to their respective Cas9 homologs, SaCas9 (S. aureus homolog of Cas9) and SpCas9 (S. pyogenes homolog of Cas9). To determine the presence of anti-Cas9 antibodies, we probed for the two homologs using human serum and were able to detect antibodies against both, with 79% of donors staining against SaCas9 and 65% of donors staining against SpCas9. Upon investigating the presence of antigen-specific T-cells against the two homologs in human peripheral blood, we found anti-SaCas9 T-cells in 46% of donors. Upon isolating, expanding, and conducting antigen re-stimulation experiments on several of these donors’ anti-SaCas9 T-cells, we observed an SaCas9-specific response confirming that these T-cells were antigen-specific. We were unable to detect antigen- specific T-cells against SpCas9, although the sensitivity of the assay precludes us from concluding that such T-cells do not exist. Together, this data demonstrates that there are pre-existing humoral and cell-mediated adaptive immune responses to Cas9 in humans, a factor which must be taken into account as the CRISPR-Cas9 system moves forward into clinical trials.

This could be a problem. Maybe it is time to look for CRISPR sequences in other more obscure bacteria.

This is all new, and the ultimate meaning of it all remains to be seen. Stay tuned!

Let’s start off with a kid’s book: Grandmother Fish: a child’s first book of Evolution by Jonathan Tweet.

From the blurb:

Grandmother Fish is the first book to teach evolution to preschoolers. While listening to the story, the child mimics the motions and sounds of our ancestors, such as wiggling like a fish or hooting like an ape. Like magic, evolution becomes fun, accessible, and personal. Grandmother Fish will be a full-size (10 x 8), full-color, 32-page, hardback book full of appealing animal illustrations, perfect for your bookshelf. US publishers consider evolution to be too “hot” a topic for children, but with your help we can make this book happen ourselves.

I reviewed the book here before it first came out. This was a kickstarter project, and it may be currently unavailable commercially, but if you click through to the kickstarter project you can probably get a copy of it.

The most recent book to come across my desk is Don Prothero’s The Story of Life in 25 Fossils: Tales of Intrepid Fossil Hunters and the Wonders of Evolution. I’ve got a review of Prothero’s book in my draft file, so look for that post coming out over the next few days.

One might ask, “how do you choose 25 fossils, among so many choices, to represent evolution?” Well, Don cheated a little by mentioning more than 25 fossils. Also, you really can’t do this. Don selected fossils using several criteria, but one basis for his choice was the availability of rich historical information about a fossil’s discovery, interpretation, and effect on our thinking about evolution. And, he covers all of that.

Don is one of those rare authors who is both an expert scientist and a great writer, with a proven ability to explain things in a way that is not watered down yet totally accessible.

Here’s a selection of the many other books written by Prothero:

• Abominable Science!: Origins of the Yeti, Nessie, and Other Famous Cryptids

• After the Dinosaurs: The Age of Mammals (Life of the Past)

• Catastrophes!: Earthquakes, Tsunamis, Tornadoes, and Other Earth-Shattering Disasters

• Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet

• Rhinoceros Giants: The Paleobiology of Indricotheres (Life of the Past)

• Evolution: What the Fossils Say and Why It Matters by Prothero, Donald R. 1st (first) Edition [Hardcover(2007)]

Evolution: The Whole Story is an astonishing book that needs to be on the bookshelf of anyone interested in evolution. The work is edied by Steve Parker, but authored by nearly a dozen experts in various subfields of fossils and evolution, so it is authoritative and scholarly. At the same time, it is very accessible and enjoyable. This is not a book you read from cover to cover, though you could. Feel free to skip around, and you;ll find yourself looking stuff up all the time.

The book is divided into major sections, and each section has a series of short pieces on this or that fossil, group of fossils, type of life system, method for studying fossils, etc. There is a running sidebar on the bottom of many pages giving “key events” in evolutionary history of the group of life forms under consideration The book is VERY richly illustrated, with detailed keys to the illustrations. Many of the illustrations are broken down into “focal points” that expand significantly on the illustrations’ details. There are countless additional inserts with more information. The book itself is beautiful, intriguingly organized, and it is full of … well, everything. The book is very well indexed and sourced, and has helpful, up to date, phylogenies and chronological graphics.

The Biology Book: From the Origin of Life to Epigenetics, 250 Milestones in the History of Biology (Sterling Milestones) by Michael Gerald and Gloria Gerald is a compendium of biological topics and key moments in the history of biological science, organized in a sort of chronological framework. Major groups (the insects, the amphibians), major ideas (Pliny’s Natural History, Ongogeny and Phylogeny), key physiological and developmental concepts (meiosis, mitosis, many topics in endocrinology), key fossils (like the Coelocanth) and so on are discussed, very nicely illustrated. This is almost like having a gazillian short articles from Natural History Magazine (or similar) all in one book. There are 250 biological “milestones” in all. The charming part of the book is that a milestone can be an evolutionary event, an extinction episode, the emergence of a great idea, or a particular discover. And, as noted, these are ordered across time, as well as one can, from the beginning of life to a selection of the most recent discovery. The book effectively combines history of biology (and related sciences) and the biological history itself.

Life’s Greatest Secret: The Race to Crack the Genetic Code by the well respected scientist and historian Matthew Cobb is a carefully and clearly written history of the discovery of the nature of DNA, covering a lot more than, and since, Watson and Crick. It is extremely well sourced, indexed, and supported, and very readable.

This is the detailed and authoritative work on all the elements that came together to understand the genetic code. Don’t talk about the discovery and understanding of DNA any more until you’ve read this book. From the publisher:

Life’s Greatest Secret mixes remarkable insights, theoretical dead-ends, and ingenious experiments with the swift pace of a thriller. From New York to Paris, Cambridge, Massachusetts, to Cambridge, England, and London to Moscow, the greatest discovery of twentieth-century biology was truly a global feat. Biologist and historian of science Matthew Cobb gives the full and rich account of the cooperation and competition between the eccentric characters—mathematicians, physicists, information theorists, and biologists—who contributed to this revolutionary new science. And, while every new discovery was a leap forward for science, Cobb shows how every new answer inevitably led to new questions that were at least as difficult to answer: just ask anyone who had hoped that the successful completion of the Human Genome Project was going to truly yield the book of life, or that a better understanding of epigenetics or “junk DNA” was going to be the final piece of the puzzle. But the setbacks and unexpected discoveries are what make the science exciting, and it is Matthew Cobb’s telling that makes them worth reading. This is a riveting story of humans exploring what it is that makes us human and how the world works, and it is essential reading for anyone who’d like to explore those questions for themselves.

Extinction and Evolution: What Fossils Reveal About the History of Life is a an updated version of a classic book about evolution and extinction written by one of the scientists who developed our modern way of thinking about evolution and extinction (especially the extinction part).

Eldredge’s groundbreaking work is now accepted as the definitive statement of how life as we know it evolved on Earth. This book chronicles how Eldredge made his discoveries and traces the history of life through the lenses of paleontology, geology, ecology, anthropology, biology, genetics, zoology, mammalogy, herpetology, entomology and botany. While rigorously accurate, the text is accessible, engaging and free of jargon.

Honorable Mentions: Older books that are great and may now be avaialable for much reduced prices.

I really liked The Great Transition: Shifting from Fossil Fuels to Solar and Wind Energy as an expose of a particular time period and major event in geological history. Greenhouse of the Dinosaurs: Evolution, Extinction, and the Future of Our Planet by Prothero is a classic, again, looking at a fairly narrowly defined moment in prehistory. You can get it used for about five bucks.

The Fossil Chronicles: How Two Controversial Discoveries Changed Our View of Human Evolution by Dean Falk is a great book focusing on one key human fossil. This is a personal story as well as a scientific one. Again, available used for a song.

Have you read Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body yet? I’m sure you’ve heard about it. It is still a great read, and you can get it used cheap.

The only book I would recommend that uses the “paleolithic” to advise you on diet and exercise is The Paleolithic Prescription: A Program of Diet and Exercise and a Design for Living.