The Tangled Tree: A Radical New History of Life

The Tangled Tree: A Radical New History of Life

Nonpareil science writer David Quammen explains how recent discoveries in molecular biology can change our understanding of evolution and life’s history, with powerful implications for human health and even our own human nature. In the mid-1970s, scientists began using DNA sequences to reexamine the history of all life. Perhaps the most startling discovery to come out of t...

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Title:The Tangled Tree: A Radical New History of Life
Author:David Quammen
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Edition Language:English

The Tangled Tree: A Radical New History of Life Reviews

  • Jonna Higgins-Freese

    A large part of the book was about Carl Woese, a character who was odd, but about whom I really could not care. He used early, difficult sequencing techniques to identify the Archaea, an entirely separate form of life, different from bacteria, plants, and animals. But since this was already old news when I had Bio 101 in 1990-91, I already knew about the Archaea, and the details of its discovery and identification just weren't that riveting the way they're presented here.

    More interesting -- alth

    A large part of the book was about Carl Woese, a character who was odd, but about whom I really could not care. He used early, difficult sequencing techniques to identify the Archaea, an entirely separate form of life, different from bacteria, plants, and animals. But since this was already old news when I had Bio 101 in 1990-91, I already knew about the Archaea, and the details of its discovery and identification just weren't that riveting the way they're presented here.

    More interesting -- although, again, already known to me, and not that interesting in the details of its discovery, was the realization (in 1944) that it was DNA that could transform a benign bacterium into a virulent one, through "infective heredity." (225). The interesting part of that was how early this was known, how early we knew how difficult it would be to keep ahead of bacteria in the resistance area.

    But then things get interesting. I didn't know the overall phrase "horizontal gene transfer." Transformation, in the above sense, was one (transfer of genetic material from a dead bacterium to a live one). A second was conjugation, a sort of "sex" between bacteria. The other involves viruses carrying foreign DNA into the cells they infect, called transduction (227).

    Evidence of bacteria that were resistant to various antibiotics *before* the human populations in which they were found were exposed to those abx -- because they are derived from plant compounds in the first place

    Maurice Panisset, in _A New Bacteriology-, made "the case that all bacteria on Earth constitute a single interconnected entity, a single species - no, wait, maybe even a single _individual_ creature -- through which genes from all the variously named 'species' flow relatively freely, by horizontal gene transfer, fo ruse where needed" (252) (a "superorganism" idea related in spirit, but not particulars, to Margulis's Gaia hypothesis and the idea that mitochondria had once been free-living bacteria" (253)

    And when they started looking, scientists found horizontal transfer *everywhere* -- bacterial genes in fish and plants (255). Sea urchins one to another, though their lineages had been separate for 65 million years. E. coli to a fungus, brewer's yeast. (some microbes are eukaryotic -- so they come in three flavors, since there are also bacteria and archaea). Bdelloids (which have only females, having gone without sex for 25M years), scientists have "found all sorts of craziness that shouldn't have been there. More specifically, they found at least twenty-two genes" from bacteria, fungi, and plants. A few were still functional. 8% of bdelloid genes had been acquired from bacteria "or other dissimilar creatures" (258).

    One parasitic bacteria infects the germline (eggs) of insects, and has managed to get itself included in the host's genome -- one fruit fly has incorporated *the entire Wolbachia genome* into its own DNA (262). The same researcher found that bacterial DNA can be found in normal human genomes, but they are "210 times more common in tumor cells than in healthy cells" (263). "In leukemia cell genomes, they found stretches resembling the DNA of Acinetobacter bacteria, a group that includes infectious forms often picked up in hospitals. In the stomach tumor genomes, they found pieces suggesting Pseudomonas . . . " The genome of one cabbage-related plant is 18% bacterial. A fungus contains 850 genes from bacteria and archaea. The human genome contains 263,000 letters of bacterial DNA transferred from our mitochondria (endosymbiotic gene transfer) (294).

    And there's more: in one study, researchers looked at the genomes of 2,235 complete bacterial genomes, half o fthem closely associated with humans, along with their ecological (where on/in the body) and geographic (where in the world) provenance. They looked for close matches in the genes, which would "signal a relatively recent horizontal transfer event for that gene" (325). They found 10,770 incidents. What predicted transfer? "The shared ecology of the human gut, or the vagina, or the nasal passages, or the skin, was most conducive to horizontal transfer. The shared phylogeny of membership in the same bacterial lineage came second. The shared geography of the same continent was a weak third." (326)

    Dunning HOtopp's research faced "adamant resistance among a few influential biologists, including some Nobel Prize winners, to her and her colleagues' discoveries of HGT in the animal kingdom. 'No, it's got to be an artifact. You have to be able to explain it some other way.' Animals don't experience horizontal gene transfer, period. Humans, certainly not.

    "'Do you ever say to them, "Is that a faith-based statement?" I asked. What I meant was: it seemed almost as though the Weismann barrier had become a theological dogma.

    "She mused about that for a moment and allowed that some scientists did appear to be more religious about science than about religion. A touch of faith-based genomics? 'I think it is,' she said." (264).

    Jim Brown and Ford Doolittle looked at 66 different proteins "that are essential to all forms of life, and at the different variatns of those proteins as reflected in more than 1,200 different gene sequences, from a wide variety o fbacateria, archaea, and eukaryotes. They constructed an indvidiual tree for each of the sixty six proteins, showing how it had evolved into distinct variants within different lineages of creatures. Brown and Doolittle compared the variants, constructing an independent tree of descent for each. This exercise yielded a telling point: the trees didn't match. The logical conclusion was that genes have their individual lineages of descent, not necessarily matchin gthe lineage of the organism in which they are presently found. [As] Robert Feldman [said], "each gene has its own history." (281)

    And so the tree of life has been redrawn, more as a weird, tangled shrub or "reticulated tree" (285)

  • Kathleen

    National Book Award Longlist for Nonfiction 2018. Wow—where to start? Probably the most ‘blow your mind’ thing is that 8% of the human genome originated in virus genomes. This is just one of the insights resulting from scientists studying molecular phylogenetics, where the study of DNA and RNA in different species allows them to discover the evolutionary relationship among them. One such retrovirus genome fragment is found in placentas and helps to transfer nutrients between the mother and child

    National Book Award Longlist for Nonfiction 2018. Wow—where to start? Probably the most ‘blow your mind’ thing is that 8% of the human genome originated in virus genomes. This is just one of the insights resulting from scientists studying molecular phylogenetics, where the study of DNA and RNA in different species allows them to discover the evolutionary relationship among them. One such retrovirus genome fragment is found in placentas and helps to transfer nutrients between the mother and child. So—this is a retrovirus genome fragment that humans have benefitted from. However, other retroviruses aren’t so benevolent—they are found in some leukemias and HIV.

    How did viruses get into the human genome? Through a process call horizontal gene transfer (HGT). This is a process whereby genes pass on genetic material directly and is absorbed into the new DNA and can then be passed on vertically from parents to offspring. Not surprisingly, HGT is more prevalent in simpler life forms, like bacteria. So—remember the many bacteria species found in the human GI tract? Now, what happens when an antibiotic-resistant bacteria finds its way in your small intestine? There might be some cute little viruses there too. And they help to transfer that resistance to many of the other bacteria. The result is the avalanche of bacteria species that become resistant to that antibiotic.

    There are some biological forms that are particularly susceptible to HGT; things like rotifers. These guys look like microscopic sucking organisms and feed on bacteria, algal cells, small protozoans and organic detritus and are probably prevalent in our rain gutters. They absorb all sorts of genome bits and they have been shown to transfer those to fruit flies.

    In addition, Quammen covers the discovery in 1977 by biologist Carl Woese of a third domain of living organisms, which he called Archaea. These microorganisms were once considered a form of bacteria, but its cell walls are completely different, allowing it to live in extreme environments like hot springs and salty ponds. Further, its DNA is in some ways closer to the domain Eukarya (organisms like us with cells with a nucleus), than regular bacteria (Eubacteria).

    Be reassured, Darwin’s 1837 Origin of the Species is not dispelled. It just got more complicated. Highly recommend.

  • Angie

    This is a book at war with itself, trying to be many things at the same time. It is a well-written examination of evolution, the inadequacy of the standard tree metaphor for it, and the messiness of gene transfer. Quammen explores horizontal gene transfer and the uncertainty in what a species actually is, what an individual is (with all the little cells that live in us but don't share DNA). This is timely and fascinating stuff.

    It is also a biography of, and tribute to, Carl Woese. I hadn't known

    This is a book at war with itself, trying to be many things at the same time. It is a well-written examination of evolution, the inadequacy of the standard tree metaphor for it, and the messiness of gene transfer. Quammen explores horizontal gene transfer and the uncertainty in what a species actually is, what an individual is (with all the little cells that live in us but don't share DNA). This is timely and fascinating stuff.

    It is also a biography of, and tribute to, Carl Woese. I hadn't known of Dr. Woese before reading the book (I'm not a biologist), but he's the one who first expanded the types of life beyond the original two, to include archea. He was a pioneer in genomic evolution, i.e. studying how closely related organisms are by looking at their DNA. His story fits into what I otherwise see as Quammen's main point because his work and discovery complicated the idea of the tree of evolution and helped people to see the connections between very different forms of life. But Quammen spent a lot of time researching Woese, talking to people who knew him, trying to get the essence of the man, to the point that this becomes half a Worse biography and it takes away from his main point. The second half of the book is stronger than the first, because we get closer to modern history and the astounding discoveries made in the last 30 years or so, but with every new topic, Quammen returned to Woese, checking in to see what he thought of it. And, well, in most cases, Woese was a crotchety old man working to protect his legacy and feuding with anyone who disagreed with him. So yes, I very much feel like this weakened the book.

    Whole chapters about Woese could be removed and the book could be improved and shortened. But I still give it 4 stars because of how well they key chapters on gene transfer are written. I learned some things, and that's always a good thing. He also spends quite a bit of time introducing us to biologists working in these fields, and that's well done as well. He keeps returning to the tree metaphor, and that results in a couple rather amusing interludes regarding imaginative topiary hobbyists.

    His final chapter is the best, I think, and I wish it were the introduction. Maybe I would suggest reading it first. He says that he has worked to show us that three fundamentals of biology -- species, individuals, and the tree of evolution -- are misleading at best. He spends most of the time in the book on species, then on the tree, and least on individuals (although he recommends

    for more detail on that subject, and I can't agree more). And for that, I highly recommend the book. But it will help if you're either intrinsically interested in Woese or maybe skim over his biographical sections.

    I got a copy to review from Net Galley.

  • Dorothy

    In

    popular science writer David Quammen gives us the history of a field of study called "molecular phylog

    In

    popular science writer David Quammen gives us the history of a field of study called "molecular phylogenetics." Have I lost you already? Well, hang with me a bit longer; this is actually pretty interesting.

    In the late 1970s, a research team at the University of Illinois announced that they had identified a "third domain" of life. This "domain" was made up of single-cell microbes which they called archaea. They were genetically distinct from what were then the only two recognized lineages of life: prokaryotes, which include bacteria, and eukaryotes, which include plants and animals. This team was headed by Carl Woese, who Quammen calls "the most important biologist of the 20th century you've never heard of." (Even more interestingly for me, the team included as his chief assistant George Edward Fox, then a post-doctoral researcher and soon to be a researcher in biochemistry at the University of Houston, where he still serves.)

    Quammen spends a lot of time describing the life's work of Woese, who, in his telling at least, was the guiding force behind the discovery. Woese was undoubtedly a major contributor to the science of molecular phylogenetics, which essentially describes how evolution occurs at a molecular level and is not just vertical between parents and children but can also be horizontal (between species) through something called "horizontal gene transfer" (HGT). Unfortunately, late in life Woese turned into a bit of a crank who harbored resentments over slights - for example, the fact that he was overlooked for the Nobel Prize.

    Science is a human activity and humans are notably imperfect.

    One of the most intriguing offshoots of this new science for me is what it does to the old concepts (at least since Darwin) of species, individuals, and the evolutionary tree of life.

    First of all species: We think of species as being discrete, separate, identifiable. In reality, each "species" is a mosaic of species. Each living being is not so much a species as a community of species which live together in symbiotic relationships.

    Which brings us to the individual: Humans, for example. By the estimate of one research group, each human body contains 37 trillion human cells and

    (Another study puts the ratio closer to 1/1.) We are host to other fellow travelers as well - nonbacterial microbes like virus particles, fungal cells, archaea, and other teeny bits of life. And all of these play their role in helping us to function. In helping us be human. These "others" that are a part of us make up an estimated 1% - 3% of our body mass.

    And about that tree: As Darwin drew it, it has distinct branches and twigs, but this isn't really how evolution works. In fact, the branches and twigs are all tangled and grown together, so that one species - human, for example - may be composed of more than 10,000 actual species living in our guts, our hair, our mucus membranes, our skin...

    Have I blown your mind now?

    This is truly an amazing story and Quammen does a commendable job of telling it in a way that can be (at least partially) understood by a reader with scant scientific training. He also gives us the personalities of the scientists who pioneered the new field, but one could argue that he is too gentle with them at times. Woese did turn quite paranoid late in life and grew to hate Charles Darwin, feeling that Darwin was hogging all the acclaim that he (Woese) deserved. And then there was Lynn Margulis, one of the women researchers who featured prominently in the book. She made important contributions early on, but she, too, turned quite dark at the end of her life, becoming a 9/11 truther. Quammen tends to present these as sort of lovable quirks of personality.

    Still, a fascinating book, divided into mercifully short chapters which make it easier to absorb. Moreover, each chapter ends in something of a cliffhanger that makes you want to keep turning those pages. And so I did and was surprised when it ended at 65% on my Kindle. The rest is all acknowledgements, notes, and bibliography.

  • Charlene

    I feel so disappointed. It was like being a kid and getting a half eaten chocolate Santa on Christmas as your only gift. This seems like a book half written. When I got the the end, I just sat there in completely disbelief. Some parts of this book are exceptional. For example, this is an incredibly detailed and informative history of how scientists and the public came to understand the tree of life, how our understanding changed to see it as a web, and finally, merely a starting point with no sh

    I feel so disappointed. It was like being a kid and getting a half eaten chocolate Santa on Christmas as your only gift. This seems like a book half written. When I got the the end, I just sat there in completely disbelief. Some parts of this book are exceptional. For example, this is an incredibly detailed and informative history of how scientists and the public came to understand the tree of life, how our understanding changed to see it as a web, and finally, merely a starting point with no shape. In many ways, biology mimics physics in this regard. Newton gave us the laws of the universe that work very well on the larger scale, but when you dig deeper, it is clear that the very small has quantum rules all its own. A similar thing is going on with the tree of life. The tree Darwin played around with works very well for later evolved species. We can, with great success, trace our ancestry back to earlier branches. However, when we get to the earliest species on the tree, archaea and bacteria, there was so much horizontal gene transfer (bacteria and archaea swapping genes instead of handing them down through generation) that we cannot trace a universal common ancestor. This story needed to be told. The only problem is, this story really wasn't told completely! And what a shame. Parts of this story never made it onto the page. This seems to be because Quammen wanted to focus on a biography of Carl Woese. Woese was a pioneer who discovered archaea and fought for their place on the tangled tree. He went to war with giants like Lynn Margulis, George Fox, and so many others. All of that was essential to include. However, there was a shocking turn of events when Quammen wrote about visiting Bill Martin (who he refers to as William F. Martin, and not Bill, which seemed odd to begin with). It was almost as if Quammen didn't really understand the work Martin has devoted his life to. Quammen talked about endosymbiosis being a single event; so he understood that part of Martin's research. He even discussed hydrothermal vents, but not in relation to Martin's work and discussed it so very briefly and it was clear he wasn't making the connections he was supposed to. He wrote about Martin and then *immediately* discussed that Woese guess that the RNA world is the correct hypothesis of how the first cells came to assemble. Did this just not come up when he spoke with Martin? I find that almost impossible to fathom. I find Qaummen not having read Martin, Russell, or Lane's work on the origin of life almost an impossibility. But yet, it seems he really wasn't familiar with it. Quammen went so far as to say he thought Woese was probably right about the RNA world. He then said that other people disagree but didn't say *how* they disagree. He never talked about Martin, Russell, and Lane's work (among others) who accounted for the energy needed for the cells to assemble. He never quite showed an understanding of how the hydrothermal vent hypothesis (or other processes that focus on the laws of thermodynamics and can show how free energy was available for the assembly of RNA, DNA, amino acids, fats, etc) challenge the RNA world hypothesis (and for damn good reason). I kept thinking, "Oh he must be saving Martin's objections to the RNA world for later in the book." Later never came.

    There is too much missing in this extremely important story to rate this book well. How we view the tree is extremely important. So, I appreciate how much detail was included. There are incredible sections about the work of Margulis. She really got her due in this book. Quammen wrote about the things she got right and what she got wrong, but he had equal respect for her and her male peers. I don't find this is always the case and was extremely happy to see how he managed her story. His sections of horizontal gene transfer were some of the most important sections included in this book (but probably could have been done better). His depiction of the many fights people had over the tree (is it a web, 5 kingdoms, 3 domains), and if we should even call archaea bacteria (no, we should not) were great. The sections on Darwin, and even Woese hatred for Darwin, were wonderful. Jumping genes and how they created a womb were all top notch, and things the public really needs to know. Quammen even included exciting little tidbits, such as how sponges can be both a multicellular organism and yet a single cell organisms if the environment dictates (but this really lacked the wow factor that other writers have managed to capture) or the tale of wolbachia, one of my very favorite bacteria, who control the sex of the new wolbachia produced (again, told in much more captivating manner by Ed Yong, who Quammen recommends reading, as do I).

    But none of his spectacular writing made up for the loss of what was missing from this story. I appreciate that Quammen chose this topic at all. But, I was left feeling like I do when I read a NYT science article that picked up the ball and ran with it before it was ready. When I finished this book, I found myself wishing, so desperately, that Nick Lane had chosen to write about this subject. It would have been a much better (more complete) book.

  • Radiantflux

    99th book for 2018.

    This is a captivating history of the changing ideas surrounding the evolutionary tree life, from Charles Darwin to the latest findings in computational phylogenetics. Quammen writes really well and the story and it's complications are fascinating. However, the books flowed is damaged as Quammen attempts to write a second book - a biography of Carl Woese - within the first which breaks up the flow and distracts from the central story of the book.

    Without all the needless addit

    99th book for 2018.

    This is a captivating history of the changing ideas surrounding the evolutionary tree life, from Charles Darwin to the latest findings in computational phylogenetics. Quammen writes really well and the story and it's complications are fascinating. However, the books flowed is damaged as Quammen attempts to write a second book - a biography of Carl Woese - within the first which breaks up the flow and distracts from the central story of the book.

    Without all the needless additional information on Woese I would have rated the book higher (did I really need to know over many pages that in his last years he hated Darwin and thought he missed out on a Nobel? Or that he liked to host BBQs and liked to pontificate about subjects when drunk?). Somehow Woese becomes THE central figure in this book, the reasons for which Quammen never bothers to explain.

    Worth a read, but could definitely have used a more proactive editor.

    3-stars.

  • Hannah Greendale

    Meticulously researched, but Quammen’s ability to frame a complex scientific theory in a captivating story is lacking. Pick up

    if molecular phylogenetics is what makes your heart go pitty-pat.

  • Conor

    Horizontal gene transfer is a thing!

    Darwin is overrated!

    This book was fine but pretty niche!

  • Faith

    I guess what I really wanted was a magazine article with conclusions. This had much more biographical information than I wanted. Actually, it had much more of everything than I wanted. I assume that I am not the correct audience for this book.

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