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The Tangled Tree: A Radical New History of Life
Goodreads Choice Award
Nominee for Best Science & Technology (2018)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 this new field—the study of life’s diversity and relatedness at the molecular level—is horizontal gene transfer (HGT), or the movement of genes across species lines. It turns out that HGT has been widespread and important. For instance, we now know that roughly eight percent of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection—a type of HGT.
David Quammen chronicles these discoveries through the lives of the researchers who made them—such as Carl Woese, the most important little-known biologist of the twentieth century; Lynn Margulis, the notorious maverick whose wild ideas about “mosaic” creatures proved to be true; and Tsutomu Wantanabe, who discovered that the scourge of antibiotic-resistant bacteria is a direct result of horizontal gene transfer, bringing the deep study of genome histories to bear on a global crisis in public health.
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 this new field—the study of life’s diversity and relatedness at the molecular level—is horizontal gene transfer (HGT), or the movement of genes across species lines. It turns out that HGT has been widespread and important. For instance, we now know that roughly eight percent of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection—a type of HGT.
David Quammen chronicles these discoveries through the lives of the researchers who made them—such as Carl Woese, the most important little-known biologist of the twentieth century; Lynn Margulis, the notorious maverick whose wild ideas about “mosaic” creatures proved to be true; and Tsutomu Wantanabe, who discovered that the scourge of antibiotic-resistant bacteria is a direct result of horizontal gene transfer, bringing the deep study of genome histories to bear on a global crisis in public health.
480 pages, Hardcover
First published August 14, 2018
About the author
David Quammen
69 books1,791 followersDavid Quammen (born February 1948) is an award-winning science, nature and travel writer whose work has appeared in publications such as National Geographic, Outside, Harper's, Rolling Stone, and The New York Times Book Review; he has also written fiction. He wrote a column called "Natural Acts" for Outside magazine for fifteen years. Quammen lives in Bozeman, Montana.
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Displaying 1 - 30 of 718 reviews
September 6, 2018
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.
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.
September 7, 2018
Meticulously researched, but Quammen’s ability to frame a complex scientific theory in a captivating story is lacking. Pick up The Tangled Tree if molecular phylogenetics is what makes your heart go pitty-pat.
September 17, 2018
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.
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.
November 7, 2018
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.
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.
January 2, 2021
The Tangled Tree is an up-to-date account of evolution, or, it is the evolution of our scientific understanding of evolution. The principals of Darwinian evolution still stand, however, the details have been reworked. Starting from mid-1970s, new discoveries are powered by genetics and DNA sequencing, and mostly in the field of molecular phylogenetics.
Several topics covered in the book:
-- The discovery of Archaea as a separate kingdom by a group of scientists lead by Carl Woese
-- The discovery of Mitochondrion and Chloroplast as captured bacteria; they may have been captured by ancient eukaryotic organisms, or co-evolved from some even more ancient life form into today's eukaryotic organisms as we know of
-- Horizontal gene transfer (HGT) in natural world is much more common than scientists used to think
-- HGT played and still plays a very important role in bacteria evolution
-- We human (and other animals on earth) contain "alien" genes too. About 8% of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection—a type of HGT.
-- A brief mention of CRISPR gene editing
Mostly because of HGT, life on earth is not a clear branched tree. Instead, it is a tangled 3D web.
The book contains 84 chapters. It is repetitive at times and could be better organized. The author covers a lot of scientists. It's a mini-biography of Carl Woese. Another important scientist discussed is Lynn Margulis. The author does not spare us the less glorious side of scientific research. Be prepared to read the ugly competition and conflict in the academia world.
I like the philosophic question the author brought up in the end: what are species, category and individual? How different you and the human being sitting next to you? What makes a human human?
Several topics covered in the book:
-- The discovery of Archaea as a separate kingdom by a group of scientists lead by Carl Woese
-- The discovery of Mitochondrion and Chloroplast as captured bacteria; they may have been captured by ancient eukaryotic organisms, or co-evolved from some even more ancient life form into today's eukaryotic organisms as we know of
-- Horizontal gene transfer (HGT) in natural world is much more common than scientists used to think
-- HGT played and still plays a very important role in bacteria evolution
-- We human (and other animals on earth) contain "alien" genes too. About 8% of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection—a type of HGT.
-- A brief mention of CRISPR gene editing
Mostly because of HGT, life on earth is not a clear branched tree. Instead, it is a tangled 3D web.
The book contains 84 chapters. It is repetitive at times and could be better organized. The author covers a lot of scientists. It's a mini-biography of Carl Woese. Another important scientist discussed is Lynn Margulis. The author does not spare us the less glorious side of scientific research. Be prepared to read the ugly competition and conflict in the academia world.
I like the philosophic question the author brought up in the end: what are species, category and individual? How different you and the human being sitting next to you? What makes a human human?
March 25, 2019
I was very disappointed with this book. It is not what it boasts of being (book blurb "There's no one who writes about complex science better than David Quammen").
As a biologist who was taught the usual prokaryote/eukaryote tree in college (a long time ago) I was excited that someone was setting out to explain archaea, the "third domain" for me --Here Quammen is mostly bent on Carl Woese, whose life was dedicated to putting archaea on the map. The author goes a bit further, but not in any cogent way, to talk about horizontal gene transfer (HGT). HGT is not really Woese's story at all so that was really messy! But in truth, I found the all the science superficial at best, and the relatedness of one chapter to another was sketchy. I barely have a feel for archaea after reading every one of the 400+ pages. HGT and CRISPR-cas I know much more about - and I found his coverage of it rudimentary. In truth, every chapter is 4 pages or less. This is an excuse for the author to never go into any depth - each short chapter starts with a completely irrelevant description of some peripheral scientist's career, who s/he knew, what gossip was up about them before going into a small snippet of their science.
Which brings me to my conclusion that Quamman is mostly interested in gossip. How people looked, who knew who, what was scientifically explosive. He could have walked into any lab to see a bacteria, but he had to fly to some restricted facility to see some special bacteria (I can't remember what it was) which I'm sure looked exactly the same in a frozen plug in liquid nitrogen as any e coli in a zillion labs. This flight/story/bacteria had no point. The book jumped the shark for me when he went into a description of what a pike was - in describing a very peripheral scientist's character as pike-like (or something).
Quamman tries to make Woese out to be some mythical guru - but I sure wasn't convinced. He did things in his biological career to colleagues that were frankly ungenerous and cruel. His hatred of Darwin - who fergodssakes is dead - was pathological (like Trump yelling about McCain). The absence of his wife in the story suggests either Quannum just didn't bother, or there was something even more terrible afoot. Frankly I see very little to admire in Woese, or his career - at least as related by this author.
Why did I keep reading? I was waiting for the archaea - I'd paid for the hardback - I thought maybe i'd learn something about HGT. I didn't. I wouldn't recommend this book to anyone interested in science. I'm surprised that that it's gotten such high praise.
As a biologist who was taught the usual prokaryote/eukaryote tree in college (a long time ago) I was excited that someone was setting out to explain archaea, the "third domain" for me --Here Quammen is mostly bent on Carl Woese, whose life was dedicated to putting archaea on the map. The author goes a bit further, but not in any cogent way, to talk about horizontal gene transfer (HGT). HGT is not really Woese's story at all so that was really messy! But in truth, I found the all the science superficial at best, and the relatedness of one chapter to another was sketchy. I barely have a feel for archaea after reading every one of the 400+ pages. HGT and CRISPR-cas I know much more about - and I found his coverage of it rudimentary. In truth, every chapter is 4 pages or less. This is an excuse for the author to never go into any depth - each short chapter starts with a completely irrelevant description of some peripheral scientist's career, who s/he knew, what gossip was up about them before going into a small snippet of their science.
Which brings me to my conclusion that Quamman is mostly interested in gossip. How people looked, who knew who, what was scientifically explosive. He could have walked into any lab to see a bacteria, but he had to fly to some restricted facility to see some special bacteria (I can't remember what it was) which I'm sure looked exactly the same in a frozen plug in liquid nitrogen as any e coli in a zillion labs. This flight/story/bacteria had no point. The book jumped the shark for me when he went into a description of what a pike was - in describing a very peripheral scientist's character as pike-like (or something).
Quamman tries to make Woese out to be some mythical guru - but I sure wasn't convinced. He did things in his biological career to colleagues that were frankly ungenerous and cruel. His hatred of Darwin - who fergodssakes is dead - was pathological (like Trump yelling about McCain). The absence of his wife in the story suggests either Quannum just didn't bother, or there was something even more terrible afoot. Frankly I see very little to admire in Woese, or his career - at least as related by this author.
Why did I keep reading? I was waiting for the archaea - I'd paid for the hardback - I thought maybe i'd learn something about HGT. I didn't. I wouldn't recommend this book to anyone interested in science. I'm surprised that that it's gotten such high praise.
March 15, 2020
Popular science writer Quammen states that "three counterintuitive insights, three challenges to categorical thinking about aspects of life on earth" are among the most essential points of this book.
The book covers the science, in a way I found pretty easy to understand, but it's essentially a group biography of the large cast of scientists who played roles in the history of evolutionary science. Given how many fascinating figures feature in this story and their many contributions, I think it was a mistake for Quammen to cast microbiologist Carl Woese in a starring role; neither his science nor his personality seem to warrant such treatment, nor did the book benefit from it.
I can't give an unqualified recommendation, e.g. readers more current on developments in evolutionary science probably can pass, but it was a good read for me because I learned quite a bit.
Species: it's a collective entity but a discrete one, like a club with a fixed membership list. The lines between this species and that one don't blur.Unaware that these ideas are now considered wrong, I was interested in Quammen's review of how our understanding of evolution has been significantly revised by research on DNA, RNA and the discoveries of, among other things, archaea and horizontal gene transfer (HGT), mostly all since I took high school biology in the 1970s.
Individual: an organism is also discrete, with a unitary identity. There's a brown dog named Rufus, there's an elephant with extraordinary tusks, there's a human known as Charles Robert Darwin.
Tree: inheritance flows always vertically from ancestor to descendant, always branching and diverging, never converging. So the history of life is shaped like a tree.
Now we know that each of those three categoricals is wrong.
The book covers the science, in a way I found pretty easy to understand, but it's essentially a group biography of the large cast of scientists who played roles in the history of evolutionary science. Given how many fascinating figures feature in this story and their many contributions, I think it was a mistake for Quammen to cast microbiologist Carl Woese in a starring role; neither his science nor his personality seem to warrant such treatment, nor did the book benefit from it.
I can't give an unqualified recommendation, e.g. readers more current on developments in evolutionary science probably can pass, but it was a good read for me because I learned quite a bit.
February 1, 2019
Really interesting stuff. Unless you are fresh off a molecular biology class, you will struggle to keep up with the terminology, but Quammen does a great job of simplifying things and clearly illustrating the implications of each new development and breakthrough.
You do not need to have a strong biology background to enjoy 'The Tangled tree', but you should know going in that the scientific studies covered here focus almost entirely on bacteria and archaea, rather than plants and animals. The final chapter ties everything together and focuses on what this all means for humans. Where do we come from and where do we go from here. 'The Tangled Tree' doesn't necessarily answer these questions, but Quammen gives us a good idea of the possibilities.
The good news is that you can now think of yourself as a super-organism rather than an individual. Feels kinda nice.
You do not need to have a strong biology background to enjoy 'The Tangled tree', but you should know going in that the scientific studies covered here focus almost entirely on bacteria and archaea, rather than plants and animals. The final chapter ties everything together and focuses on what this all means for humans. Where do we come from and where do we go from here. 'The Tangled Tree' doesn't necessarily answer these questions, but Quammen gives us a good idea of the possibilities.
The good news is that you can now think of yourself as a super-organism rather than an individual. Feels kinda nice.
Read
September 7, 2018I 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.
March 19, 2020
The “tree of life” is an ancient metaphor. Even Aristotle wrote about a scala naturae or “natural ladder of ascent,” a hierarchical depiction of the relationships between the objects of the world. In his notes Darwin sketched a tree-like diagram, an early speculation about all living things connected by diverging lineages, the basis for his theory of evolution.
Quammen neatly folds this historical context into a narrative that links research at the cellular and molecular level to a startling new understanding of evolutionary process, an understanding that could no longer be depicted by a tree. The familiar model of evolutionary process is of course that of natural selection. Random genetic mutations nudge changes that favor some new characteristics over others in sync with gradually changing environmental conditions.Old species lines die out; new ones flourish. The idea of new species was in itself revolutionary. In the past, species were considered unchanging entities. That viewpoint was endorsed by centuries of theology.
Darwin, Mendel and Linnaeus. Those are the three big names I learned in grade school. But back in the 17th century, Leeuwenhoek had observed single-celled life forms. Were these the primordial basis of all life? A closer look revealed some fascinating problems. Microbes come in all sorts of shapes and structures. They inhabit even the most hostile environments. Some microbes, bacteria, even lacked a nucleus. This was also the case for blue-green algae now known as cyanoalgae. Were cyanoalgae plants or animals?
In 1956 microsomal particles called ribosomes were observed via the electron microscope. Protein blueprints were transmitted from DNA via messenger RNA. In a cellular organelle called the ribosome, the message was decoded. Those decoded instructions directed the construction of a specific protein. A researcher named Carl Woese was curious. Could comparisons of the composition of RNA indicate the lineal relationships between various bacteria? He made this study his life's work. His lab developed a technique for identifying the proteins comprising tiny fragments of structural RNA. On examining the structural RNA fragments of methanogens, microbes that oxidized hydrogen and carbon dioxide, he found unique RNA sequences that did not resemble either microbes with nuclei (eukaryotes) or bacteria (microbes lacking nuclei (prokaryotes)). He proposed a 3rd “Kingdom”: archaea. Other physiological anomalies supported this construct. Archaea had a unique lipid chemistry and cell wall construction. The revolution was just beginning!
The second major contribution that overturned conventional wisdom came from the research of Lynn Margulies. In 1970 she published “The Origin of Eukaryotic Cells.” Other cell organelles include mitochondria and chloroplasts. How did they come into being? Margulies proposed that a cell could absorb but only partially break down a bacterial cell. The bacteria's genetic material could be repurposed in a process called endosymbiosis. More questions. How often could this happen? Which organelles could this process account for? Were these bacterial remnants the genetic material found floating in the cytoplasm rather than the nucleus? Was this the process that produced bacteria from Woese's archaea? In addition to the “3rd Kingdom,” HGT (Horizontal gene transfer) became part of the lexicon of evolution theory.
Quammen details the painstaking experiments conducted to prove these hypotheses. He adds biographical details gathered not only from research papers but from interviews with researchers' colleagues. Those details add an element of drama to his narrative. He succinctly summarizes in memorable prose the key accomplishment of a number of scientists. Robert Whittaker, a plant ecologists, “began to challenge a canonical principle in his branch of science: the idea that plant communities are stable, highly integrated associations, with consistent species compositions, clear boundaries, and hard reality as units, almost as though they were living organisms....He showed that plant communities are loose associations, not integrated units, with blurry boundaries and a 'low degree of reality.'” (p.187) Lynn Margulies: “'The evolutionary pattern is a web –the branches fuse, like when algae and slugs come together.'” (p.158) James Brown and Ford Doolittle compared 66 proteins and showed how they evolved within different lineages. “The logical conclusion was that genes have their individual lineages of descent, not necessarily matching the lineage of the organism in which they are found.” (p.281) Nigel Goldenfeld and Carl Woese boldly asserted: “'Among microbes, HGT is pervasive and powerful....The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment.' Because of that genetic fluidity, the two men argued, the concept of 'species' is useless among bacteria and archaea.” (p.330)
All too often scientific discovery is condensed into lists of researchers, dates and so-called breakthroughs. Quammen captures the dynamic quality of scientific research. He is even able to insert some elements of humor into these endeavors. Quammen conveys a sense of excitement, prompting the reader with new questions that arose after each seemingly definitive experiment. These questions give his narrative momentum. At the same time, he keeps each chapter brief as if knowing his reader needed to catch a breath before moving forward.
Quammen neatly folds this historical context into a narrative that links research at the cellular and molecular level to a startling new understanding of evolutionary process, an understanding that could no longer be depicted by a tree. The familiar model of evolutionary process is of course that of natural selection. Random genetic mutations nudge changes that favor some new characteristics over others in sync with gradually changing environmental conditions.Old species lines die out; new ones flourish. The idea of new species was in itself revolutionary. In the past, species were considered unchanging entities. That viewpoint was endorsed by centuries of theology.
Darwin, Mendel and Linnaeus. Those are the three big names I learned in grade school. But back in the 17th century, Leeuwenhoek had observed single-celled life forms. Were these the primordial basis of all life? A closer look revealed some fascinating problems. Microbes come in all sorts of shapes and structures. They inhabit even the most hostile environments. Some microbes, bacteria, even lacked a nucleus. This was also the case for blue-green algae now known as cyanoalgae. Were cyanoalgae plants or animals?
In 1956 microsomal particles called ribosomes were observed via the electron microscope. Protein blueprints were transmitted from DNA via messenger RNA. In a cellular organelle called the ribosome, the message was decoded. Those decoded instructions directed the construction of a specific protein. A researcher named Carl Woese was curious. Could comparisons of the composition of RNA indicate the lineal relationships between various bacteria? He made this study his life's work. His lab developed a technique for identifying the proteins comprising tiny fragments of structural RNA. On examining the structural RNA fragments of methanogens, microbes that oxidized hydrogen and carbon dioxide, he found unique RNA sequences that did not resemble either microbes with nuclei (eukaryotes) or bacteria (microbes lacking nuclei (prokaryotes)). He proposed a 3rd “Kingdom”: archaea. Other physiological anomalies supported this construct. Archaea had a unique lipid chemistry and cell wall construction. The revolution was just beginning!
The second major contribution that overturned conventional wisdom came from the research of Lynn Margulies. In 1970 she published “The Origin of Eukaryotic Cells.” Other cell organelles include mitochondria and chloroplasts. How did they come into being? Margulies proposed that a cell could absorb but only partially break down a bacterial cell. The bacteria's genetic material could be repurposed in a process called endosymbiosis. More questions. How often could this happen? Which organelles could this process account for? Were these bacterial remnants the genetic material found floating in the cytoplasm rather than the nucleus? Was this the process that produced bacteria from Woese's archaea? In addition to the “3rd Kingdom,” HGT (Horizontal gene transfer) became part of the lexicon of evolution theory.
Quammen details the painstaking experiments conducted to prove these hypotheses. He adds biographical details gathered not only from research papers but from interviews with researchers' colleagues. Those details add an element of drama to his narrative. He succinctly summarizes in memorable prose the key accomplishment of a number of scientists. Robert Whittaker, a plant ecologists, “began to challenge a canonical principle in his branch of science: the idea that plant communities are stable, highly integrated associations, with consistent species compositions, clear boundaries, and hard reality as units, almost as though they were living organisms....He showed that plant communities are loose associations, not integrated units, with blurry boundaries and a 'low degree of reality.'” (p.187) Lynn Margulies: “'The evolutionary pattern is a web –the branches fuse, like when algae and slugs come together.'” (p.158) James Brown and Ford Doolittle compared 66 proteins and showed how they evolved within different lineages. “The logical conclusion was that genes have their individual lineages of descent, not necessarily matching the lineage of the organism in which they are found.” (p.281) Nigel Goldenfeld and Carl Woese boldly asserted: “'Among microbes, HGT is pervasive and powerful....The available studies strongly indicate that microbes absorb and discard genes as needed, in response to their environment.' Because of that genetic fluidity, the two men argued, the concept of 'species' is useless among bacteria and archaea.” (p.330)
All too often scientific discovery is condensed into lists of researchers, dates and so-called breakthroughs. Quammen captures the dynamic quality of scientific research. He is even able to insert some elements of humor into these endeavors. Quammen conveys a sense of excitement, prompting the reader with new questions that arose after each seemingly definitive experiment. These questions give his narrative momentum. At the same time, he keeps each chapter brief as if knowing his reader needed to catch a breath before moving forward.
October 22, 2018
5 stars for how fascinating this theory is and 1 star for the book. The book is just a bunch of short bios about a bunch of scientists from Darwin to the present who have contributed to misunderstanding and then understanding better, the history of evolution. The big breakthroughs are covered at the end and they are huge breakthroughs and super fascinating. But maybe skip the book and listen to the radio lab episode with the author or read the Times review. The good stuff is covered there.
Shelved as 'not-interested'
April 20, 2019Here's the review that made me cancel my hold on this one:
https://www.goodreads.com/review/show...
Also https://www.goodreads.com/review/show... Both 2 star reviews, and Tony has been a reliable source for me in the past.
OK, and my two previous tries of Quammen books were duds, too. So I guess he's not the pop-science writer for me!
https://www.goodreads.com/review/show...
Also https://www.goodreads.com/review/show... Both 2 star reviews, and Tony has been a reliable source for me in the past.
OK, and my two previous tries of Quammen books were duds, too. So I guess he's not the pop-science writer for me!
August 28, 2018
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)
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)
December 21, 2018
More accurately biographies of the scientists who made the discoveries.
Read only if you are interested in their hair color or waist size.
At least 2/3 of the book reviews basic science that would already known by readers.
Read only if you are interested in their hair color or waist size.
At least 2/3 of the book reviews basic science that would already known by readers.
September 7, 2019
Horizontal gene transfer, reticulated trees ('a tangle of rising and crossing and diverging and converging limbs'), molecular phylogenetics (study of evolutionary relatedness using molecules as evidence), mutation, natural selection and horizontal gene transfer replacing Darwin's omissive theory, 'the idea of the tree of life, the great arboreal image of relatedness and diversification.'
"The tree of life is more tangled. Genes don't move just vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms of life, and some have come sideways into our own lineage—the primate lineage—from unsuspected nonprimate sources."
"The logical conclusion is that genes have their individual lineages of descent, not necessarily matching the lineage of the organism in which they are presently found. It was the same thing Robert Feldman would soon tell the reporter Elizabeth Pennisi: 'each gene has its own history.'"
(A reticulated tree, or net, which might more appropriately represent life's history", by W. Ford Doolittle.
Variation doesn't "come mostly from the tiny random mutations that seem sufficient to neo-Darwinists. 'Rather,' [Margulis and Dorion wrote], 'the important transmitted variation that leads to evolutionary novelty comes from the acquisition of genomes.' It comes from symbiosis, the real origin of species."
"'As a cell design becomes more complex and interconnected, [Woese wrote], 'a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty'—meaning parent-offspring inheritance, with modest variation, as distinct from horizontal gene transfer—'can and does assume greater importance.' At that critical borderline, the Darwinian Threshold, evolution as Darwin understood it begins."
"The concept of species is useless among bacteria and archaea. With genes flowing sideways, information moving across boundaries, and energy flowing upward from cells through communities and environments, the concept of an organism—an isolated creature, a discrete individual—seemed less valid too."
"Among such simpler microbial creatures...horizontal gene transfer is far more important, in quantity and consequences, than imagined previously. Its impacts could be understood in four ways. First, new genes received by sideways transfer, from a different lineage or species, may allow a population of microbes (the recipient bug and its offspring) to colonize an entirely new ecological niche. Second it may allow organisms to acquire a new sort of adaptation abruptly, without passing through the dangerous stage of being only half adapted to one situation or another. Third, this transformation happens fast compared with incremental mutation, which proceeds slowly. Fourth, HGT is a 'font of innovation', bringing drastically new genetic possibilities, new supplies of variation, on which natural selection can act. All four kinds of impact are interrelated and represent overlapping perspectives on the same phenomenon."
"Linnaeus also gave a half column to what he called Paradoxa: a wild-card assemblage of mythic chimeras and befuddling but real creatures, including the unicorn, the satyr, the phoenix, dragon..." (One enthusiastic vote here to bring the classification of Paradoxa back!)
"The tree of life is more tangled. Genes don't move just vertically. They can also pass laterally across species boundaries, across wider gaps, even between different kingdoms of life, and some have come sideways into our own lineage—the primate lineage—from unsuspected nonprimate sources."
"The logical conclusion is that genes have their individual lineages of descent, not necessarily matching the lineage of the organism in which they are presently found. It was the same thing Robert Feldman would soon tell the reporter Elizabeth Pennisi: 'each gene has its own history.'"
(A reticulated tree, or net, which might more appropriately represent life's history", by W. Ford Doolittle.
Variation doesn't "come mostly from the tiny random mutations that seem sufficient to neo-Darwinists. 'Rather,' [Margulis and Dorion wrote], 'the important transmitted variation that leads to evolutionary novelty comes from the acquisition of genomes.' It comes from symbiosis, the real origin of species."
"'As a cell design becomes more complex and interconnected, [Woese wrote], 'a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty'—meaning parent-offspring inheritance, with modest variation, as distinct from horizontal gene transfer—'can and does assume greater importance.' At that critical borderline, the Darwinian Threshold, evolution as Darwin understood it begins."
"The concept of species is useless among bacteria and archaea. With genes flowing sideways, information moving across boundaries, and energy flowing upward from cells through communities and environments, the concept of an organism—an isolated creature, a discrete individual—seemed less valid too."
"Among such simpler microbial creatures...horizontal gene transfer is far more important, in quantity and consequences, than imagined previously. Its impacts could be understood in four ways. First, new genes received by sideways transfer, from a different lineage or species, may allow a population of microbes (the recipient bug and its offspring) to colonize an entirely new ecological niche. Second it may allow organisms to acquire a new sort of adaptation abruptly, without passing through the dangerous stage of being only half adapted to one situation or another. Third, this transformation happens fast compared with incremental mutation, which proceeds slowly. Fourth, HGT is a 'font of innovation', bringing drastically new genetic possibilities, new supplies of variation, on which natural selection can act. All four kinds of impact are interrelated and represent overlapping perspectives on the same phenomenon."
"Linnaeus also gave a half column to what he called Paradoxa: a wild-card assemblage of mythic chimeras and befuddling but real creatures, including the unicorn, the satyr, the phoenix, dragon..." (One enthusiastic vote here to bring the classification of Paradoxa back!)
July 28, 2018
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 I Contain Multitudes: The Microbes Within Us and a Grander View of Life 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.
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 I Contain Multitudes: The Microbes Within Us and a Grander View of Life 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.
August 12, 2020
Dopo aver letto "Spillover", che riguardava i salti di specie dei virus, questo è un repotage a più ampio spettro perché racconta della perseveranza e della tenacia con la quale gli scienziati hanno speso la propria vita professionale alla ricerca delle origini della vita.
Ciascuno ha provato a disegnare il proprio albero dove il tronco corrisponde ai primi organismi capaci di trasmettere le informazioni e replicarsi.
Il risultato è che le grafie diventano sempre più complesse dal momento in cui si introduce la filogenetica molecolare che mette in mostra l'evoluzione orizzontale con scambi di materiale genetico tra specie e speci diverse, in aggiunta a quello verticale determinato dal codice che passa dai genitori ai figli.
Il racconto storico, che parte dai pionieri della biologia fino alla contemporaneità, è entusiasmante e procede con le intuizioni, la ricerca, la serendipity e la tecnologia capace di esaminare e di confrontare tra loro una enorme quantità di dati genetici per arrivare a delle scoperte veramente sorprendenti.
Consiglio la lettura perché, se anche alcune nuove conoscenze sono state divulgate dai media, qui se ne dà ragione portando il lettore a una visione organica della disciplina senza appesantirla di elementi troppo tecnici.
Ciascuno ha provato a disegnare il proprio albero dove il tronco corrisponde ai primi organismi capaci di trasmettere le informazioni e replicarsi.
Il risultato è che le grafie diventano sempre più complesse dal momento in cui si introduce la filogenetica molecolare che mette in mostra l'evoluzione orizzontale con scambi di materiale genetico tra specie e speci diverse, in aggiunta a quello verticale determinato dal codice che passa dai genitori ai figli.
Il racconto storico, che parte dai pionieri della biologia fino alla contemporaneità, è entusiasmante e procede con le intuizioni, la ricerca, la serendipity e la tecnologia capace di esaminare e di confrontare tra loro una enorme quantità di dati genetici per arrivare a delle scoperte veramente sorprendenti.
Consiglio la lettura perché, se anche alcune nuove conoscenze sono state divulgate dai media, qui se ne dà ragione portando il lettore a una visione organica della disciplina senza appesantirla di elementi troppo tecnici.
February 16, 2019
New advances in genetic research are facilitating a massive rewrite of the story of life. Peeking inside DNA and RNA is changing our understanding of how life developed.
We’ve always been taught that bacteria came first, then plants arose, and finally animals. The new evidence is scrambling this traditional view. Research suggests that animals came before plants. These animals then on-boarded a chloroplast and thus could generate their own energy supply. The big realization is that bacteria, archaea, viruses, animals and plants have all been swapping huge amounts of genetic code throughout time.
As a matter of fact, the entire “tree of life” metaphor is proving to be a misnomer. 8% of human genetic code comes from viruses. How did it get there? Sneaky viruses found a back door into our genome using a process called horizontal gene transfer (HGT). Genes don’t need to be transferred from parent to offspring. Other life forms have regularly commandeered our ancestor’s DNA and melded their abilities with our own.
We might think this is a really bad thing. Viruses like HIV that modify host DNA can bring on fatal consequences. Most of the time this scrambling of the genetic code had benign or detrimental effects on the host. However this merging also facilitated the development of some wickedly handy human traits.
Retroviruses that attacked our distant ancestors found a way to assure their survival by modifying the host’s DNA. This assured the invading virus would not be attacked by the host’s immune system. Well it turns out the same viral DNA fragments found their way into human placentas and assured that a mother’s immune system didn’t attack a developing fetus as an external invader. Thank you retroviruses for facilitating the evolution of live birth.
Another surprising thing I learned was that our ancestors were also mightily shaped by symbiosis. For example, a cell would ingest or be invaded by an outside organism. The two organisms would discover they were a stronger pair if they teamed up. For example, one creature might be good at energy conversion; the other might be great at locomotion. The previously individual organisms would then meld into a single entity.
Quammen takes us through all sorts of strange organisms that defy classification such as a tiny organism that finds oxygen toxic, breathes hydrogen and exhales methane. A snail exists that uses photosynthesis to produce energy - a creature that’s part plant, part animal.
Finally, one of the most interesting things that I learned was the mechanics of DNA extraction. After a lifetime of watching news footage of lab technicians using those long glass syringes to inject strange liquids into gelatin, I finally understand how that whole procedure works.
Quammen is a very skilled writer with a limber vocabulary. He made an intimidating topic like biochemistry approachable for non-scientists like myself.
We’ve always been taught that bacteria came first, then plants arose, and finally animals. The new evidence is scrambling this traditional view. Research suggests that animals came before plants. These animals then on-boarded a chloroplast and thus could generate their own energy supply. The big realization is that bacteria, archaea, viruses, animals and plants have all been swapping huge amounts of genetic code throughout time.
As a matter of fact, the entire “tree of life” metaphor is proving to be a misnomer. 8% of human genetic code comes from viruses. How did it get there? Sneaky viruses found a back door into our genome using a process called horizontal gene transfer (HGT). Genes don’t need to be transferred from parent to offspring. Other life forms have regularly commandeered our ancestor’s DNA and melded their abilities with our own.
We might think this is a really bad thing. Viruses like HIV that modify host DNA can bring on fatal consequences. Most of the time this scrambling of the genetic code had benign or detrimental effects on the host. However this merging also facilitated the development of some wickedly handy human traits.
Retroviruses that attacked our distant ancestors found a way to assure their survival by modifying the host’s DNA. This assured the invading virus would not be attacked by the host’s immune system. Well it turns out the same viral DNA fragments found their way into human placentas and assured that a mother’s immune system didn’t attack a developing fetus as an external invader. Thank you retroviruses for facilitating the evolution of live birth.
Another surprising thing I learned was that our ancestors were also mightily shaped by symbiosis. For example, a cell would ingest or be invaded by an outside organism. The two organisms would discover they were a stronger pair if they teamed up. For example, one creature might be good at energy conversion; the other might be great at locomotion. The previously individual organisms would then meld into a single entity.
Quammen takes us through all sorts of strange organisms that defy classification such as a tiny organism that finds oxygen toxic, breathes hydrogen and exhales methane. A snail exists that uses photosynthesis to produce energy - a creature that’s part plant, part animal.
Finally, one of the most interesting things that I learned was the mechanics of DNA extraction. After a lifetime of watching news footage of lab technicians using those long glass syringes to inject strange liquids into gelatin, I finally understand how that whole procedure works.
Quammen is a very skilled writer with a limber vocabulary. He made an intimidating topic like biochemistry approachable for non-scientists like myself.
February 8, 2019
Oh so boring, so so boring.
Some writers know how to turn scientific data into a popular knowledge, and can make you even have fun as well as make you learn new things. They can make amazing accessible magic from the deep knowledge without completely losing the essence of it. Most cannot. And then they end up with a very detailed or technical book, or with an extremely flat book that is mainly populistic.
Astrophysics for People in a Hurry by Neil deGrasse Tyson is one of the books that in my opinion loses the science on the way to popularity. This book had the opposite problem. The author does not want to lose anything, and instead loses any interest that could be found in the book or in the topic.
For strong people that really want all the details it might be great. I found myself skimming and not interested. 2 stars for me.
Here are two rare cases that are magical:
The The Gene: An Intimate History by Siddhartha Mukherjee did a really good job and I highly enjoyed It. The The Immortal Life of Henrietta Lacks by Rebecca Skloot did an outstanding job. I can't recommend this book enough!
Some writers know how to turn scientific data into a popular knowledge, and can make you even have fun as well as make you learn new things. They can make amazing accessible magic from the deep knowledge without completely losing the essence of it. Most cannot. And then they end up with a very detailed or technical book, or with an extremely flat book that is mainly populistic.
Astrophysics for People in a Hurry by Neil deGrasse Tyson is one of the books that in my opinion loses the science on the way to popularity. This book had the opposite problem. The author does not want to lose anything, and instead loses any interest that could be found in the book or in the topic.
For strong people that really want all the details it might be great. I found myself skimming and not interested. 2 stars for me.
Here are two rare cases that are magical:
The The Gene: An Intimate History by Siddhartha Mukherjee did a really good job and I highly enjoyed It. The The Immortal Life of Henrietta Lacks by Rebecca Skloot did an outstanding job. I can't recommend this book enough!
August 11, 2018
Comprehensive, exhaustive, entertaining, at times gossipy, and altogether wonderful! If more science books were so rich with stories of the scientists, more students might be riveted to classes in genetics and evolutionary biology.
I cannot imagine the years of research that must have gone into the writing of this book. Interviews with authors living or then-living, now-dead, bring to life the drama and controversies and obstacles that beset even a rational scientist. Never mind scientific objectivity; emotions, and ambitions, fly high in humans of every field of endeavor.
I have hundreds, literally hundreds, of passages in my Kindle, highlighted, waiting for me to share, but there is that disclaimer about not sharing an ARC because this isn't the final version. So let me just say Karl Woese. O Karl!
I wanted to understand the sideways evolution thing. I wanted to be a doctor, back in the day; then a coroner, at least; but my fascination for science was never paired with a mind capable of grasping the mathematical intricacies. Which reminds me of Karl Woese, turning to a mathematician, not a biologist, to help prove a theory he had been working on forever.
Later, I might take the time to pull passages and rave, rave, rave over the details. If you find them too much, you can always skim past some of the biographical information and cut to the chase, the science, but then you may not find enough science left over. I'm thinking I need to find a Genetics for Dummies book that sticks to the science, skims past the personalities, and helps me tell someone what the heck I just read. Sadly, I am not able to sum it up off the top of my head. Books like this, I have to revisit, repeatedly, before it sinks in.
Oh, I know people who can read a chapter once, never give it a second glance, and score 100% on a test over the chapter. I am not one of those people. (Dr. Mat Weekly, can you copy some of your brain cells and do a genetic transfer over to mine?)
Yes, I'm thinking of getting him a copy of this book, but I'm not sure I want to hear how elementary and "easy" it is for people who really have the brains to fathom the stuff I love reading about.
This is a great book. I need to kee re-reading it, and I may need to find an easier book to explain it all, but this is still great! The narrative tone reminds me of Sam Kean (no relation to Carol Kean). Now, Sam writes in a way that doesn't overwhelm me, and he tends to keep his books a wee bit shorter and to the point.
But, again, if this one offers too much, skim past the bonus material and hone in on the meat and marrow.
I cannot imagine the years of research that must have gone into the writing of this book. Interviews with authors living or then-living, now-dead, bring to life the drama and controversies and obstacles that beset even a rational scientist. Never mind scientific objectivity; emotions, and ambitions, fly high in humans of every field of endeavor.
I have hundreds, literally hundreds, of passages in my Kindle, highlighted, waiting for me to share, but there is that disclaimer about not sharing an ARC because this isn't the final version. So let me just say Karl Woese. O Karl!
I wanted to understand the sideways evolution thing. I wanted to be a doctor, back in the day; then a coroner, at least; but my fascination for science was never paired with a mind capable of grasping the mathematical intricacies. Which reminds me of Karl Woese, turning to a mathematician, not a biologist, to help prove a theory he had been working on forever.
Later, I might take the time to pull passages and rave, rave, rave over the details. If you find them too much, you can always skim past some of the biographical information and cut to the chase, the science, but then you may not find enough science left over. I'm thinking I need to find a Genetics for Dummies book that sticks to the science, skims past the personalities, and helps me tell someone what the heck I just read. Sadly, I am not able to sum it up off the top of my head. Books like this, I have to revisit, repeatedly, before it sinks in.
Oh, I know people who can read a chapter once, never give it a second glance, and score 100% on a test over the chapter. I am not one of those people. (Dr. Mat Weekly, can you copy some of your brain cells and do a genetic transfer over to mine?)
Yes, I'm thinking of getting him a copy of this book, but I'm not sure I want to hear how elementary and "easy" it is for people who really have the brains to fathom the stuff I love reading about.
This is a great book. I need to kee re-reading it, and I may need to find an easier book to explain it all, but this is still great! The narrative tone reminds me of Sam Kean (no relation to Carol Kean). Now, Sam writes in a way that doesn't overwhelm me, and he tends to keep his books a wee bit shorter and to the point.
But, again, if this one offers too much, skim past the bonus material and hone in on the meat and marrow.
August 30, 2018
It’s ok but I wish it had more technical details.
The people stories are ok but less valuable than the science
The people stories are ok but less valuable than the science
September 4, 2018
There is no one correct way of dividing a world, identity is fleeting and reification leads to oversimplification. All of that is within this book as the author looks at where the incredibly interesting world of microbiology stands today and what it means for understanding our current understanding of the world we find ourselves in. I have read many stimulating books on the early 20th century development of quantum physics and gravitational theory and this book has that feel to it and lays out the recent and just as exciting history of why micro and molecular biology’s recent discoveries about whom we are and where we came from is just as exciting.
I have to expand on my first sentence above because it might not be obvious how this book embraces that sentence in such a succinct way. First, ‘no correct way of dividing the world’, Darwin’s greatest realization was that there is no absolute ‘nature of things’ in and of themselves (i.e. ‘a unique world structure’ or an unique ontological foundation), essences are human imposed order on to the world, and for his theory to work ‘species’ needed a fluid nuanced definition and its own inherent truth was a myth (‘essences’ and species are not things they are human constructs). Even though Darwin titles his book ‘On the Origin of Species’ he dances around the meaning of the word ‘species’ because without fluidity he can’t get to evolution by way of natural selection.
Second ‘identity is fleeting’, the individual under consideration might not always be as obvious as common sense dictates. The author gave the example by asking is it the ant, the colony or all of the colonies that make the entity worthy of consideration, and the author made note of the ship of Theseus and its paradox as related to self identity of the individual. In other words, if we were to analyze every single oyster would we understand the oyster? Or as Nietzsche once mockingly said by way of criticizing philosophy ‘would we be any nearer to the truth of understanding women by asking every woman what they want’. Or, moreover, are bacteria best thought of as individuals or can they be thought of in their totality as one? Descartes takes the world away from us with his cogito by literally assuming it away, but Kierkegaard, Nietzsche and Heidegger think we are not separate from the world and the world needs to be considered in order to understand our Being.
The third item from my opening sentence is on ‘reification’. Is the map actually the thing? Or in the case for this book is the ‘tree of life’ such as nature demands it, or do we as humans make nature fit our model, the tree of life. I love Darwin and I love his book and I love when people say that they accept ‘evolution by way of natural selection’ as the best description to explain how life developed over the eons, but in reality the truth is more nuanced and especially for the first 3 billion years of life on earth and even in our more recent history (check out what the author tells the reader about the placenta and what we think we know about it!).
The power plant that produces the universal currency of life by creating ATP (little battery like energy sources) by way of the cells mitochondria and are within all living creatures that have complexity with structure and that are more complicated than bacteria or archaea or fungi or blue-green algae and which are not plants (i.e. get their energy directly from the sun through chloroplast) for each and every eukaryote that has ever lived (humans are eukaryotes since we are made up of cells that usually have a nucleolus and organelles and mitochondria) or are alive today that original event of endobiosis happened only once in the history of the world (endobiosis is a big theme within this book and will be explained in great detail for the observant reader). The fact that event only happened once as stated in this book always floors me and anyone who thinks that the galaxy or the universe is teeming with complex intelligent life first needs to explain why that event only happened once on earth as far as we know today.
The chapters on Lynn Margulis were fascinating and illustrated why this book was so very fun to read. First, I had no idea she was Carl Sagan’s first wife. She latched on to a concept that was only on the fringes of microbiology and made it mainstream. Scientists in general hate nothing more than to have their paradigms be overturned while an individual scientist likes nothing more than to challenge the status quo and overthrow a paradigm. Science knows itself by correcting itself. Lynn Margulis took what was known within footnotes and mostly obscure corners (including, most probably, a Russian pedophile) and popularized HGT (horizontal gene transfer) and gave it a pedigree that was lacking. Margulis is a scientist worth knowing and remembering, and oddly, she couldn’t help herself in later days by goofingly thinking 9/11 was an inside job or thinking HIV did not cause Aids (fringe thinking also, but wrongheaded).
I had previously read Margulis’ book ‘The Five Kingdoms’, and therefore I have a bias towards how she sees the world and it explains why I think archaea are different from bacteria and prokaryote is the wrong label for them. I would recommend that book not to read but to look at the beautiful pictures of single cell life, and one day when you happen to be in a used book store do yourself a favor and pick it up at least to glance through.
Overall this book doesn’t make a definitive statement on how many life kingdoms there are and how the tree of life should be designed. That’s a feature not a bug with this book because in the end there aren’t absolutely correct ways of categorizing the world or if there are we don’t know it when we get it right. I don’t want to give away the punch line in this book, but the very last sentence of this book made me laugh out loud, and will make you laugh too.
I have to expand on my first sentence above because it might not be obvious how this book embraces that sentence in such a succinct way. First, ‘no correct way of dividing the world’, Darwin’s greatest realization was that there is no absolute ‘nature of things’ in and of themselves (i.e. ‘a unique world structure’ or an unique ontological foundation), essences are human imposed order on to the world, and for his theory to work ‘species’ needed a fluid nuanced definition and its own inherent truth was a myth (‘essences’ and species are not things they are human constructs). Even though Darwin titles his book ‘On the Origin of Species’ he dances around the meaning of the word ‘species’ because without fluidity he can’t get to evolution by way of natural selection.
Second ‘identity is fleeting’, the individual under consideration might not always be as obvious as common sense dictates. The author gave the example by asking is it the ant, the colony or all of the colonies that make the entity worthy of consideration, and the author made note of the ship of Theseus and its paradox as related to self identity of the individual. In other words, if we were to analyze every single oyster would we understand the oyster? Or as Nietzsche once mockingly said by way of criticizing philosophy ‘would we be any nearer to the truth of understanding women by asking every woman what they want’. Or, moreover, are bacteria best thought of as individuals or can they be thought of in their totality as one? Descartes takes the world away from us with his cogito by literally assuming it away, but Kierkegaard, Nietzsche and Heidegger think we are not separate from the world and the world needs to be considered in order to understand our Being.
The third item from my opening sentence is on ‘reification’. Is the map actually the thing? Or in the case for this book is the ‘tree of life’ such as nature demands it, or do we as humans make nature fit our model, the tree of life. I love Darwin and I love his book and I love when people say that they accept ‘evolution by way of natural selection’ as the best description to explain how life developed over the eons, but in reality the truth is more nuanced and especially for the first 3 billion years of life on earth and even in our more recent history (check out what the author tells the reader about the placenta and what we think we know about it!).
The power plant that produces the universal currency of life by creating ATP (little battery like energy sources) by way of the cells mitochondria and are within all living creatures that have complexity with structure and that are more complicated than bacteria or archaea or fungi or blue-green algae and which are not plants (i.e. get their energy directly from the sun through chloroplast) for each and every eukaryote that has ever lived (humans are eukaryotes since we are made up of cells that usually have a nucleolus and organelles and mitochondria) or are alive today that original event of endobiosis happened only once in the history of the world (endobiosis is a big theme within this book and will be explained in great detail for the observant reader). The fact that event only happened once as stated in this book always floors me and anyone who thinks that the galaxy or the universe is teeming with complex intelligent life first needs to explain why that event only happened once on earth as far as we know today.
The chapters on Lynn Margulis were fascinating and illustrated why this book was so very fun to read. First, I had no idea she was Carl Sagan’s first wife. She latched on to a concept that was only on the fringes of microbiology and made it mainstream. Scientists in general hate nothing more than to have their paradigms be overturned while an individual scientist likes nothing more than to challenge the status quo and overthrow a paradigm. Science knows itself by correcting itself. Lynn Margulis took what was known within footnotes and mostly obscure corners (including, most probably, a Russian pedophile) and popularized HGT (horizontal gene transfer) and gave it a pedigree that was lacking. Margulis is a scientist worth knowing and remembering, and oddly, she couldn’t help herself in later days by goofingly thinking 9/11 was an inside job or thinking HIV did not cause Aids (fringe thinking also, but wrongheaded).
I had previously read Margulis’ book ‘The Five Kingdoms’, and therefore I have a bias towards how she sees the world and it explains why I think archaea are different from bacteria and prokaryote is the wrong label for them. I would recommend that book not to read but to look at the beautiful pictures of single cell life, and one day when you happen to be in a used book store do yourself a favor and pick it up at least to glance through.
Overall this book doesn’t make a definitive statement on how many life kingdoms there are and how the tree of life should be designed. That’s a feature not a bug with this book because in the end there aren’t absolutely correct ways of categorizing the world or if there are we don’t know it when we get it right. I don’t want to give away the punch line in this book, but the very last sentence of this book made me laugh out loud, and will make you laugh too.
August 4, 2020
It’s fine, I guess. It’s a nice summary of evolution and the ancestral trees of organisms, but I’m just not sure it delivers on the premise its title promises.
What about this perfectly adequate “history of life” is at all “new” or “radical”? The information contained here will be familiar to the modern reader, though Quammen goes into a little more detail than the average reader has on hand.
If it had presented itself as just another overview of Mendel and Darwin, I’d say it had done its job. I was expecting more new research, something I had never heard of.
Quammen's book Spillover was much better. And also, eminently more relevant in the pandemic.
What about this perfectly adequate “history of life” is at all “new” or “radical”? The information contained here will be familiar to the modern reader, though Quammen goes into a little more detail than the average reader has on hand.
If it had presented itself as just another overview of Mendel and Darwin, I’d say it had done its job. I was expecting more new research, something I had never heard of.
Quammen's book Spillover was much better. And also, eminently more relevant in the pandemic.
March 20, 2019
4 stars.
Update: 3-20-19 at 12:53 Eastern Standard Time
I will be rereading this book. A friend and I used to talk about this subject in depth. I also read books and watch documentaries similar to this book ( due to this friend) in the before I join Goodreads Era. Some stuff I did not have in my notes, some of them I had to reread to grasp. Regardless, this was fun and educational!
🐾🇺🇸
Update: 3-20-19 at 12:53 Eastern Standard Time
I will be rereading this book. A friend and I used to talk about this subject in depth. I also read books and watch documentaries similar to this book ( due to this friend) in the before I join Goodreads Era. Some stuff I did not have in my notes, some of them I had to reread to grasp. Regardless, this was fun and educational!
🐾🇺🇸
September 2, 2018
Wow. A lot has changed since I took AP Biology in 1985-6! Back then it was classic Darwin and prokaryotes and eukaryotes, and the reason some bacteria were antibiotic resistant was because they were descended from the few survivors with some random mutation that gave them resistance. ALL WRONG. ALL CHANGED.
This book was absolutely fascinating (if you like history of science) and biology and thinking about how we come to be where we are, biologically speaking. If you've never heard of molecular phylogeny or horizontal gene transfer, as I hadn't, the book provides clear and compelling explanations. I did ask my 17YO son if he'd been taught these things last year in his own AP Bio class, and I'm happy to report he was. Knowledge marches onward, though author Quammen is very clear that science is a messy, egotistical business, as are all endeavors involving human beings.
This book was absolutely fascinating (if you like history of science) and biology and thinking about how we come to be where we are, biologically speaking. If you've never heard of molecular phylogeny or horizontal gene transfer, as I hadn't, the book provides clear and compelling explanations. I did ask my 17YO son if he'd been taught these things last year in his own AP Bio class, and I'm happy to report he was. Knowledge marches onward, though author Quammen is very clear that science is a messy, egotistical business, as are all endeavors involving human beings.
September 13, 2018
"Science itself, however precise and objective, is a human activity. It's a way of wondering as well as a way of knowing. It's a process, not a body of facts or laws. Like music, like poetry, like baseball, like grandmaster chess, it's something gloriously imperfect that people do. The smudgy fingerprints of our humanness are all over it." - David Quammen in The Tangled Tree
In The Tangled Tree, 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 100 trillion bacterial cells! (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.
November 26, 2018
David Quammen has written a great book, wrapped in a pretty good one. I rarely give 5-star reviews, and from me a 3-star review actually means "I liked it", just like the goodreads scale advises. Nonetheless, I have given Quammen's books 5 stars on more than one occasion, and never less than 4. Until now.
Keep in mind, 3 stars from me means "I liked it", and I did like it. In fact, there was a 5 star book inside this one, a book about the ways in which a metaphor as old as the idea of evolution itself (or older) has been laid low in the last couple decades. That idea, is the metaphor of the "tree of life"; the idea that species split from common ancestors like the branches of a tree go from trunk to branch to twig.
One of the things I liked about "The Tangled Tree" is that Quammen shows us the actual visuals, from pre-evolutionary thinkers like Edward Hitchcock (Quammen describes his drawing of the "tree of life" as being "like a windbreak of tightly placed Lombardy poplars") to Darwin himself (his tree the only visual of any kind in "The Origin of Species") to Ernst Haeckel's "great oak" in the late 19th century. You can see the idea being developed, as each thinker looked at the illustrations of the ones before them and said, "I think it should be a bit more like..."
Then, we enter the 20th century, and midway through things take an abrupt turn into a more complicated theory. In some ways, it's like when you realize that the relatively simple, 3- or 4-generations back "family tree" cannot possibly continue back to the beginning. After 30 generations, you would have over a billion ancestors, yet the entire earth's human population did not reach that level until the early 19th century. The simple idea of a "tree" works for a while, but because your great-great-great-grandmother might also be your great-great-great-great-grandmother on another line, eventually, as you work your way back it becomes more of a web than a tree.
There were a few early radical thinkers who floated the idea of blurry lines between one species' DNA and another's, but the one who by all accounts really pushed the idea into the mainstream of biological thought was Lynn Margulis. Quammen gives her a fair portion of the middle book, even including a picture of himself and Lynn Margulis. Margulis championed the idea that things like mitochondria and chloroplasts, which we now call "organelles" inside the cells of animals and plants, were once independently living cells. One living thing entered another, neither as parasite nor as food, and both lived, and their descendants were fused as well. This idea was challenging, not least because it is hard to see how it would be possible to draw a "tree of life", when two branches turn into one, instead of the other way around. Margulis is not the person who ends up hijacking the book, though, and now we come to the problem.
Carl Woese was a researcher who worked at the University of Illinois at Urbana/Champaign, which coincidentally is where I studied Electrical Engineering in the late 1980's. In fact, I suppose he was doing some of his most important work not long before I got there, although I knew nothing of it. He was one of the early researchers to get down to the detailed work of sequencing RNA from a variety of different "bacteria" (as they were all called then), and use that data to try to piece together what was more closely related to what.
It so turned out that the ribosomal RNA that Woese had chosen to focus on, in order to piece together the tree of life, were almost uniquely well suited to the task, but by that some token poorly suited for showing the limitations of the "tree" metaphor. Some parts of our genetic code can be tinkered with, and they do nothing observable (these used to be called "junk" DNA). Other parts are more important, but still there are many ways to get the job done, and a modification to one is unlikely to be fatal. Ribosomes, though, are pretty crucial, and if you mess with those then there is a good chance you would die an early death (perhaps before you are even born). Thus, there is little chance of surviving if, say, a random virus comes and inserts different DNA in that spot.
Because, it turns out, that happens. Woese helped the world to achieve an earlier revolution in understanding, that there are multiple urkingdoms ("domains") of bacteria. It was a further confirmation that our cells are composed of a fusion of different types of (not closely related) cells, so different that the term "bacteria" cannot be used for both of them (we call the other one "archaea" now).
This is an important part of the story Quammen is there to tell us, but he just can't let Woese go. He does move on, to the next generation of scientists who discovered "horizontal gene transfer", that process where a virus enables a piece of DNA to move from one species into another. But, he cannot refrain from repeatedly circling back to Woese, even though by this point in the story he is mostly carping from the sidelines.
The fact is that Quammen has set himself a difficult task, here, to tell us a story of how ideas change over time in a scientific field which has, in recent decades, become increasingly technical and difficult to explain. I understand that the tragic flaw of Woese, the revolutionary caught in a second revolution that goes too far for him to follow, adds a human element that Quammen wanted to use to spike our interest. But, the reality is, there is far too much Woese in this book.
Because of this, the latter part of the book takes on a gloomy, somewhat depressing cast, as we approach the end of Woese's life. The reality is that the research into horizontal gene transfer, and how to replace a "tree of life" with a "web of life", is in an enormously exciting phase right now. The data is coming faster and faster, and the ability to sort through it is being developed alongside, and we are practically guaranteed to have our understanding of how life evolved, and how it continues to evolve, changed in the near future. The end of this book, should not have been gloomy, it should have been bursting with excitement.
Nonetheless, Quammen does a good job of taking us through a host of technical topics, in a way that makes it readable and enjoyable. If the technical explanation is that halophiles lack the normal peptidoglycan walls, he will tell us, "we get technical again, but I'll keep it simple: weird lipids". He uses diagrams freely, and he is able to give us the simplest essence of a topic in a way that allows one to follow the plot, when it would be all to easy to get lost in twenty-syllable jawbreakers. Quammen is, in fact, very good at his job.
Maybe just ignore some of the later anecdotes of an exasperated Woese growling at the kids to get off his lawn.
Keep in mind, 3 stars from me means "I liked it", and I did like it. In fact, there was a 5 star book inside this one, a book about the ways in which a metaphor as old as the idea of evolution itself (or older) has been laid low in the last couple decades. That idea, is the metaphor of the "tree of life"; the idea that species split from common ancestors like the branches of a tree go from trunk to branch to twig.
One of the things I liked about "The Tangled Tree" is that Quammen shows us the actual visuals, from pre-evolutionary thinkers like Edward Hitchcock (Quammen describes his drawing of the "tree of life" as being "like a windbreak of tightly placed Lombardy poplars") to Darwin himself (his tree the only visual of any kind in "The Origin of Species") to Ernst Haeckel's "great oak" in the late 19th century. You can see the idea being developed, as each thinker looked at the illustrations of the ones before them and said, "I think it should be a bit more like..."
Then, we enter the 20th century, and midway through things take an abrupt turn into a more complicated theory. In some ways, it's like when you realize that the relatively simple, 3- or 4-generations back "family tree" cannot possibly continue back to the beginning. After 30 generations, you would have over a billion ancestors, yet the entire earth's human population did not reach that level until the early 19th century. The simple idea of a "tree" works for a while, but because your great-great-great-grandmother might also be your great-great-great-great-grandmother on another line, eventually, as you work your way back it becomes more of a web than a tree.
There were a few early radical thinkers who floated the idea of blurry lines between one species' DNA and another's, but the one who by all accounts really pushed the idea into the mainstream of biological thought was Lynn Margulis. Quammen gives her a fair portion of the middle book, even including a picture of himself and Lynn Margulis. Margulis championed the idea that things like mitochondria and chloroplasts, which we now call "organelles" inside the cells of animals and plants, were once independently living cells. One living thing entered another, neither as parasite nor as food, and both lived, and their descendants were fused as well. This idea was challenging, not least because it is hard to see how it would be possible to draw a "tree of life", when two branches turn into one, instead of the other way around. Margulis is not the person who ends up hijacking the book, though, and now we come to the problem.
Carl Woese was a researcher who worked at the University of Illinois at Urbana/Champaign, which coincidentally is where I studied Electrical Engineering in the late 1980's. In fact, I suppose he was doing some of his most important work not long before I got there, although I knew nothing of it. He was one of the early researchers to get down to the detailed work of sequencing RNA from a variety of different "bacteria" (as they were all called then), and use that data to try to piece together what was more closely related to what.
It so turned out that the ribosomal RNA that Woese had chosen to focus on, in order to piece together the tree of life, were almost uniquely well suited to the task, but by that some token poorly suited for showing the limitations of the "tree" metaphor. Some parts of our genetic code can be tinkered with, and they do nothing observable (these used to be called "junk" DNA). Other parts are more important, but still there are many ways to get the job done, and a modification to one is unlikely to be fatal. Ribosomes, though, are pretty crucial, and if you mess with those then there is a good chance you would die an early death (perhaps before you are even born). Thus, there is little chance of surviving if, say, a random virus comes and inserts different DNA in that spot.
Because, it turns out, that happens. Woese helped the world to achieve an earlier revolution in understanding, that there are multiple urkingdoms ("domains") of bacteria. It was a further confirmation that our cells are composed of a fusion of different types of (not closely related) cells, so different that the term "bacteria" cannot be used for both of them (we call the other one "archaea" now).
This is an important part of the story Quammen is there to tell us, but he just can't let Woese go. He does move on, to the next generation of scientists who discovered "horizontal gene transfer", that process where a virus enables a piece of DNA to move from one species into another. But, he cannot refrain from repeatedly circling back to Woese, even though by this point in the story he is mostly carping from the sidelines.
The fact is that Quammen has set himself a difficult task, here, to tell us a story of how ideas change over time in a scientific field which has, in recent decades, become increasingly technical and difficult to explain. I understand that the tragic flaw of Woese, the revolutionary caught in a second revolution that goes too far for him to follow, adds a human element that Quammen wanted to use to spike our interest. But, the reality is, there is far too much Woese in this book.
Because of this, the latter part of the book takes on a gloomy, somewhat depressing cast, as we approach the end of Woese's life. The reality is that the research into horizontal gene transfer, and how to replace a "tree of life" with a "web of life", is in an enormously exciting phase right now. The data is coming faster and faster, and the ability to sort through it is being developed alongside, and we are practically guaranteed to have our understanding of how life evolved, and how it continues to evolve, changed in the near future. The end of this book, should not have been gloomy, it should have been bursting with excitement.
Nonetheless, Quammen does a good job of taking us through a host of technical topics, in a way that makes it readable and enjoyable. If the technical explanation is that halophiles lack the normal peptidoglycan walls, he will tell us, "we get technical again, but I'll keep it simple: weird lipids". He uses diagrams freely, and he is able to give us the simplest essence of a topic in a way that allows one to follow the plot, when it would be all to easy to get lost in twenty-syllable jawbreakers. Quammen is, in fact, very good at his job.
Maybe just ignore some of the later anecdotes of an exasperated Woese growling at the kids to get off his lawn.
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May 11, 2019Дарвін (і інші довший час по ньому) уявляли еволюційне дерево як вертикальну послідовність. Потім у 1970-ті виявилося, що окремі гілки еволюційного дерева не тягнуться окремо вгору, а перетинаються в ході horizontal gene transfer, часто між доволі різними видами. Ця книжка розглядає історію того, як формувалася концепція дерева життя у різних дослідників (скільки в нього гілок? Чи вони перетинаються?), і наводить приклади цього самого горизонтального перенесення (органели в кожній клітині – це захавані на раніших етапах еволюції мікроорганізми; в нашому ДНК ціла купа заграбастаного ДНК від давніх вірусів; поширення опірності до антибіотиків серед сучасних бактерій і т.д.). Нічогісінько не знаю про тему, тобто по суті нічого сказати не можу, але аудіокнига начитана невимовно заспокійливим голосом:)
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January 8, 2019I enjoyed the other three books by Quammen that I've read, but had difficulty getting into this one. Seemed like a really hard slog and too focused on material of little interest to me. Bailed after fifty pages or so.
January 22, 2019
Summary: Fascinating material presented in an approachable way, but overall organization was lacking.
Many of you who enjoy natural history will have read about Charles Darwin. You may already know that he originated the tree of life as a way of visualizing the process of evolution. This story starts with that tree and covers several major discoveries that have caused to review our view of that tree. In particular, the author covers horizontal gene transfer (transfer of genetic material between individuals in ways that aren't from parent to child) and the discovery of a new taxonomic group, the Archaea.
This might sound like a dense topic, but the author actually writes in an extremely approachable way. He occasionally made fun of his own scientific jargon. While I wish he had explained the value of such jargon for concise, precise communication, he still made me laugh out loud. Short chapters didn't hurt the readability either. The author also did a great job explaining why we should care about all this. He draws you into his sense of curiosity about the origins of life and what it means to be human. He also brought to life the human side of the scientific endeavor. He conveyed the day-to-day experience of doing research. He showed how personality clashes can shape scientific discourse. He did a pretty good job covering a controversial female scientist fairly. And as a scientist, I found the depiction of doing genetics in the 60s and 70s delightfully quaint. Researchers spent decades doing work you could now do in hours! Programming in fortran! On punch cards! It was fun.
On a less positive note, I found the organization disjointed. My understanding of the author's focus, based on the intro, was on the two discoveries I described above - horizontal gene transfer and the Archaea - and how they impact the tree of life. Each of the topics I mentioned did get a section - the history of the tree concept; horizontal gene transfer; and the discovery of the Archaea. However, two later sections jumped back in time to the history of the tree concept in a way that jolted me out of the story. I would have preferred to get all of the history of these trees together, chronologically. There were also two sections on other types of DNA transfer where I could see a connection to the author's discussion of trees, but he didn't make that connection clearly or well. Finally, the last section was really only connected to itself or the rest of the book by a focus on Carl Woese, the scientist who discovered horizontal gene transfer. It seems possible the author should have explicitly structured the story around him, because in retrospect, he was the through line.
I'm not surprised this book made it onto the National Book Award longlist with this readable take on important scientific updates. I'm also not surprised it didn't make the shortlist though, as the organization let it down.This review was originally posted on Doing Dewey
Many of you who enjoy natural history will have read about Charles Darwin. You may already know that he originated the tree of life as a way of visualizing the process of evolution. This story starts with that tree and covers several major discoveries that have caused to review our view of that tree. In particular, the author covers horizontal gene transfer (transfer of genetic material between individuals in ways that aren't from parent to child) and the discovery of a new taxonomic group, the Archaea.
This might sound like a dense topic, but the author actually writes in an extremely approachable way. He occasionally made fun of his own scientific jargon. While I wish he had explained the value of such jargon for concise, precise communication, he still made me laugh out loud. Short chapters didn't hurt the readability either. The author also did a great job explaining why we should care about all this. He draws you into his sense of curiosity about the origins of life and what it means to be human. He also brought to life the human side of the scientific endeavor. He conveyed the day-to-day experience of doing research. He showed how personality clashes can shape scientific discourse. He did a pretty good job covering a controversial female scientist fairly. And as a scientist, I found the depiction of doing genetics in the 60s and 70s delightfully quaint. Researchers spent decades doing work you could now do in hours! Programming in fortran! On punch cards! It was fun.
On a less positive note, I found the organization disjointed. My understanding of the author's focus, based on the intro, was on the two discoveries I described above - horizontal gene transfer and the Archaea - and how they impact the tree of life. Each of the topics I mentioned did get a section - the history of the tree concept; horizontal gene transfer; and the discovery of the Archaea. However, two later sections jumped back in time to the history of the tree concept in a way that jolted me out of the story. I would have preferred to get all of the history of these trees together, chronologically. There were also two sections on other types of DNA transfer where I could see a connection to the author's discussion of trees, but he didn't make that connection clearly or well. Finally, the last section was really only connected to itself or the rest of the book by a focus on Carl Woese, the scientist who discovered horizontal gene transfer. It seems possible the author should have explicitly structured the story around him, because in retrospect, he was the through line.
I'm not surprised this book made it onto the National Book Award longlist with this readable take on important scientific updates. I'm also not surprised it didn't make the shortlist though, as the organization let it down.This review was originally posted on Doing Dewey
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