Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA Hardcover – March 17, 2020

I'm reviewing and comparing two books on horizontal gene transfer (HGT). I've cross posted this also on the reviews for Quammen's book.Shubin, Neil. 2020. Some Assembly Required: Decoding Four Billion Years of Life, from Ancient Fossils to DNA. New York: Pantheon Books.Quammen, David. 2018. The Tangled Tree: A Radical New History of Life. New York: Simon & Schuster.I was familiar with both authors. Shubin’s Your Inner Fish and The Universe Within sit on my bookshelf. I’ve enjoyed Quammen’s The Boilerplate Rhino, Wild Thoughts from Wild Places, and The Song of the Dodo of which I can find only the first, the later two lost to a thinning of my library.There is some overlap between the two books in both style and focus. Through historical narrative, the science emerges from stories about the scientists who made these discoveries. Both focus on the relatively new fields of horizontal gene transfer (HGT). While Quammen’s discussion is far more extensive, both introduce us to Lynn Margulis and her revolutionary idea that all multi-celled life - plants, animals, and fungus - evolved from a primitive eukaryote cell created when a bacteria entered an archaea and they started working as a team. Both also discuss the implications of Nobelist Barbara McClintock’s jumping genes.Shubin’s book is similar to his previous two. Science is explained in a 200 page narrative. Shubin takes a traditional Darwinian approach with considerable focus on multi-celled plants (e.g., corn) and animals (e.g., dinosaurs, flies, humans) and vertical gene evolution. The focus on HGT is on the impact of ancient viral and bacterial genes that entered the genome of more complex species. Ten percent of our human genome consists of these sequences. In some cases these insertions have little or no impact. But some are important. One HIV like insert known as Arc DNA appears in all land animals, fish don’t have it, and is used by our brains to enhance memories.Quammen’s book is unlike his previous ones. Those were collections of short “sort of” related topics. This book is long, detailed, and has one focus. It is all about HGT and largely ignores classic Darwinian generational evolution. It is far more focused on the scientists’ biographies than the science itself, especially Carl Woese, who is not even mentioned by Shubin. It isn’t completely devoid of the science. Rather the science comes largely in terms of the scientific debates surrounding theory and data.And there are some little nuggets on how HGT impacted multi-celled life, including humans. For example, a mystery is how female mammals can carry their young to term without their body rejecting the fetus as a foreign invader. It turns out we have genes called syncytin that create proteins that help build the placenta and allow food and waste to move between mother and fetus. The big surprise is that these genes did not evolve as “mistakes” during classic linear evolution. Rather, these genes were inserted into the mammal genome by invading retroviruses. A key reason viruses of any kind are able to flood your body is because they fool or turn off your immune response. In the case of syncytin genes, our genome tamed this feature that allows mammals to carry their young inside the female body.It is estimated that 8 to 10% of the human genome is of viral origin. While both books were interesting and worth a read, I’d like to read a book with less biography and more focus on what impact those viral insertion have contributed to our species.

Some Assembly Required, Decoding 4 Billion Years of Life from Ancient Fossils to DNA, 2020,Neil ShubinHow did an ancient fish crawl onto land and begin terrestrial life? This has been a controversial question for biology since the time of Darwin. Darwin was prescient in saying major transitions are “often accompanied by a change of function”. Shubin answered the question in his 2005 book “Your Inner Fish”. Way before fish walked on land, they had developed a ballast system much like the ballast tanks on submarines. Connected to the esophagus of most fish are small air sacs. When a fish wants to be nearer the surface it pushes it’s mouth above water and inflates the air sacs. Maybe you have seen fish doing this? Over time fish in oxygen depleted bodies of water expanded these air sacs into alternate lungs. What happened to the gills once these fishlike animals began life on land? In the case of many mammals they formed the inner ear structure and in humans also the structure of the voice box.Since decoding the genome in 2000 progress in the science of genetics and paleontology has been nothing short of astounding. The cost of decoding a genome has decreased form the 3.8 billion in 2000 to just a few hundred dollars today. This has enabled the decoding of thousands of animal species, ancient human DNA, bacteria, and viruses. In the human genome we have discovered that only 2% is made up of our own genes. 10% is made up of ancient viruses that at one time infected our ancestors. 60% is duplications made up of “jumping genes gone wild”. A recent astounding discovery was that the genetic program that makes the human placenta is a genetic sequence from a virus incorporated into the mammalian genome in the transition from egg laying to placental birth. The protein that makes neuron connected memory possible also is derived from a virus invader. Amazingly both have components very similar to HIV virus. I guess we can’t be too negative on viruses, no?What is the other 28% of our genome? These are the are linear molecular programs, consisting of on-off switches, that design and construct all complex multicellular creatures. They operate much like a digital computer. Working as a field engineer on ballistic missile submarines in the 1960’s, I was responsible for a piece of gear that checked out the missile before launch. It consisted of thousands of discreet switches that ran a group of linear subroutine programs that verified each component was working before signaling successful completion and ready for launch. What the HOX and PAX genes do in building complex bodies is somewhat similar. Each structure such as a leg, fin or hand is created by a series of switches activated in linear order to produce the required proteins in an ordered sequence. What has been discovered is that these programs are remarkably similar in all creatures ranging from flies to fish to reptiles to humans. Using Crispr, a gene editing program, researchers have changed the locations of these programs resulting in bizarre outcomes such as legs growing out of a fly’s head. As Shubin eloquently relates: “The genome at every level resembles a musical score in which the same musical phrases are repeated in different ways to make vastly different songs. In fact, if nature was a composer, she would be one of the greatest copyright violators in history- everything from DNA to entire genes and proteins is a modified copy of something else”.What has been discovered in the last 20 years has changed the conception of humankind’s place in the universe. We can no longer be seen as somehow special or separate from the rest of life. We are a continuation of biological evolution as a product of and deeply connected to all life on Earth.As Shubin concludes “The poet William Blake wrote of seeing “the universe in a grain of sand and a heaven in a wildflower”. When you know how to look, you can see billions of years inside the organs, cells, and DNA in all living things and relish our connections to the rest of life on the planet”.For those of you who have read “The Tangled Tree” by David Quammen you will love this book as a perfect follow on. While that book detailed the evolution of the complex cell, this book details the evolution of complex bodies. JACK

Made things easy to understand although I wish he would have gone more in depth. Also he mention something completely wrong that Australia marsupial evolved isolated for 100 million years is false. Marsupials from Australia originated from South America that had crossed and lived in Antarctica who later drifted or swam over about 50 million years ago after Australia had split from Antarctica

Fantastic read. It will walk you through the series of biological processes driving evolution, all well-threaded with cool anecdotes and stories behind the pertinent discoveries. Should be included in high school biology curricula and more importantly, to teach how life mechanisms change over time.

Neil does a great job again. He takes time to expound on hox genes and how the human anatomy is formed in reference to our DNA. This book almost feels like a part 2 to "your inner fish", where he is giving more background into what inspired him to author his ideas in the first place. In your inner fish, he touches on genetics, but it almost felt out of left field for fossil gurus. I think this book takes those early ideas and brings them back full circle for readers, thereby creating a more complete understanding of the collective and corroborating sciences backing our evolutionary history.On another note, Neil, bring us more bones!

book quality is normal but content is very rich

As a high school student with little to no knowledge of paleontology , this is a great introduction to this field of study . Author explains things in lucid words and delves deeper making it an enjoyable read . Thank you.

A well-written book about the evolution of living beings based on Paleonthology and Molecular Biology data that will surprise most readers. I made several notes about interesting facts narrated in this essay that I didn't know and would like to remember.

This book hit all the right spots for me. It was well written, contained a lot of interesting facts and ideas, told the stories of many interesting people and how they contributed to the understanding of evolution, but most importantly, got me looking at things I already knew in a new light. If you are interested in evolution and want to deepen your understanding this is an excellent book. If you sometimes have to argue with people who say 'such-and such a thing could not possibly have evolved by natural selection, then it is an essential addition to your arsenal.

Like in his earlier book, Your Inner Fish, Neil Shubin takes the reader by the hand and guides one through the intricacies of evolutionary development. Starting with St.George Jackson Mirvat's, on the surface, very reasonable critique of Darwin's theory he shows how this can be disposed of by the study of the development of the embryos of different species which, at the ouset, look very similar. Very clear and enjoyable read.