The Vital Question, by Nick Lane - Part 2

Mitochondrion. Source: US NIH

" So what about sex, or the nucleus, or phagocytosis? [...] If each of these traits arose by natural selection – which they undoubtedly did – and all of the adaptive steps offered some small advantage – which they undoubtedly did – then we should see multiple origins of eukaryotic traits in bacteria. But we don't. This is little short of an evolutionary 'scandal'. "
Nick Lane – The Vital Question (2015)

In my previous post I commented on the first part of Nick Lane's book, which deals with the proton-motive force and the origin of life. This second post focuses on the second half of the book, which explores the origin of complex life (i.e. eukaryotic cells).

If the first half of the book was equally part history of the field and part new hypotheses, the second half leans clearly more towards hypothetical ideas – albeit including many facts, and backed with rigorous thinking. Lane's big idea is the following. Most traits that differentiate eukaryotes from prokaryotes (cell and genome sizes, nucleus, introns, sexual reproduction) ultimately follow from a single and singular event: the endosymbiosis event that created mitochondria. For Lane, the organelles that power respiration in all eukaryotic cells are the one special ingredient that permitted the development of cellular complexity.

The Vital Question, by Nick Lane

“In the end, respiration and burning are equivalent; the slight delay in the middle is what we know as life.”

This quote, from Nick Lane’s book The Vital Question (2015), is both poetic and true, which is the mark of great popular science writing. What Lane’s book attempts to do (and in my opinion succeeds in doing) is to radically change our perspective on life by showing us the crucial role played by energy. 

Lane is a biochemist at University College London and already the author of three books. I think there’s something to be said about popular science written by scientists, as opposed to science journalists, in the sense that they can sometimes achieve much more than educating. For example, they can fundamentally change our understanding of some topics (that certainly happened to me on some occasions). Actually, reading The Vital Question reminded me of reading Richard Dawkins’ The Selfish Gene many years ago, and Lane’s book did for me with biochemistry what Dawkins did with genetics and evolutionary theory: it opened a window into a fascinating new landscape. 

Principles of Microbial Diversity, by James Brown

Published by ASM Press

A new textbook on microbial diversity has just been published by ASM Press. Principles of Microbial Diversity is a relatively thin textbook (392 pages) that is intended for undergraduate students who need to follow a course on microbial diversity, hence filling a gap in the available teaching material. His author is James W. Brown, a professor at North Carolina State University.

The book is pleasant to read and richly illustrated by hundreds of micrographs. But what is quite original, and to me very justified, is the author's perspective, which is, in James Brown's own words in the preface, "phylogenetic and organismal, from the Carl Woese school".  I applaud that! Woese, as I discussed in a previous post, revolutionized biology by showing that we had until then totally ignored a whole distinct domain of life, the Archaea. This discovery was made through the careful analysis of the sequence of 16S rRNA gene (not an easy feat in the days of Woese's work). Because of this pedagogical and scientifical choice, Brown's book dedicates lots of pages to introduce phylogenetic concepts. Notably, he gives a didactic and useful explanation of how to construct a phylogenetic tree (Chapter 3). Brown explains his focus as follows (p. 351):

"In this book, the vantage point from which all of microbial diversity is viewed is the phylogenetic perspective. Other perspectives are possible and are very useful. Medical microbiology views the microbial world from the perspective of its influence on microbe-human interactions and human health. Environmental microbiology views the microbial world from the perspective of biogeochemical processes and ecosystems. […] However, the organizing principle of biology is evolutionary theory. The phylogenetic perspective is the view of biological diversity as the outcome of evolutionary history. This perspective is not exclusive of any other perspective on microbiology, but instead enriches these other perspectives."

Brown's textbook contribution is very welcome, and should find a place in each university's library.

Example of book photo. The eukaryote Arcella. Source: Wikimedia Commons

References:

• Brown, J. W. (2015) Principles of Microbial Diversity. ASM Press, Washington DC. 392 pages.

The Logic of Life, by François Jacob

The Logic of Life (La logique du vivant) opens with the following quote by the French philosopher and Enlightenment figure Denis Diderot:

"Do you see this egg? It's with it that we overturn all theological schools and all temples on Earth".

[All translations in this post are mine.]

The choice of a 18th century thinker for the epigraph prefigures a lot of this book, which was published by the late Nobel laureate François Jacob in 1970. The book—subtitled "a history of heredity"—thus proves to be of great erudition and cites the original work of, among many names, Paré, Montaigne, Paracelse, Descartes, Galilée, Harvey, Réaumur, Buffon, Redi, Leibniz, D'Holbach, La Mettrie, Lamarck, Linné, Geoffroy Saint-Hilaire... and I haven't even mentioned the 20th century references yet! Excusez du peu!

This story of heredity truly is a huge endeavor, spanning about four centuries of philosophical and scientific attempts to understand what kind of stuff we're made of. Articulated in long chapters that correspond to conceptual milestones ("visible structure", "organization", "time", "gene", "molecule", and "integron"), the book follows the chronological development of our biological knowledge (which was part of "natural philosophy") with plenty of referenced sources and with a quality of writing that is hardly matched today.

Microbe Hunters by Paul de Kruif

‘Microbe Hunters’, as I have often been told, is a classic reading in microbiology—one of those books that can inspire the beginning of a career. In this book, written in 1926, American microbiologist and author Paul de Kruif proposes to acquaint us with the great pioneers of microbiology, from Leeuwenhoek to Ehrlich, via Pasteur, Koch, Roux and several more. 

I gave it a try, and I must confess that at first I was a bit taken aback by the quite unusual style of the author: extremely enthusiastic, overly lyric, made to immerge us in the life of the protagonists with a plethora of details that may or may not be true.  I can’t remember reading anything quite approaching the surprising and unusual tone of Microbe Hunters. Here’s an example describing Spallanzani’s early experiments (p. 34):

“What’s this?” [Spallanzani] cried. Here and there in the gray field of his lens he made out an animalcule playing and sporting about—these weren’t large microbes, like some he had seen—but they were living little animals just the same.

“Why, they look like little fishes, tiny as ants,” he muttered—and then something dawned on him— “These flasks were sealed- nothing could get into them from the outside, yet here are little beings that have stood a heat of boiling water for several minutes!”

[…] It was a great day for Spallanzani, and though he did not know it, a great day for the world.

But as I was reading further I grew accustomed to this prose, and, to my own surprise, I started to enjoy it! It is indeed difficult not to share de Kruif’s enthusiasm for these great men of the past and, even though I would take the author’s factual accuracy with more than a grain of salt, the book really makes you want to learn more about the personal life of these pioneers.

The Invisible Gorilla by Chabris and Simons

UK edition, published by Harper

The invisible gorilla and other ways ourintuition deceives us, by psychologists Christopher Chabris and Daniel Simons, is a wonderful book that contains a lot of food for thought for scientists – and actually for everybody. 

There is little chance that you missed this viral video, dating back from just before the turn of the millennium: two teams, dressed either in white or in black, play basketball, and you are supposed to count how many passes the white team manages to do. If you never saw that, watch it here before reading. OK, that was the one and only spoiler alert!

In the middle of the video, a student wearing a gorilla suit walks through the players, thumps her chest, and leaves. I didn’t see the gorilla, just as half of the people who watch the video, because I was too focused on counting the white team passes. With this video, Chabris and Simons showed us that we wrongly take certain things for granted, such as our ability to notice everything that enters our field of view. They write in their introduction (p. ix):

“We all believe that we are capable of seeing what’s in front of us, of accurately remembering important events from our past, of understanding the limits of our knowledge, of properly determining cause and effect. But these intuitive beliefs are often mistaken ones that mask critically important limitations on our cognitive abilities.”

Science fiction meets microbiology: Vitals by Greg Bear

I can’t think of many sci fi books in which microbiology is the core element of the story—actually I can only think of one, the excellent Andromeda Strain of Michael Crichton, which deals with viral infection from outer space. As to Greg Bear, author of Vitals (2002), he had the brilliant idea of putting bacteria on center stage with, as we shall see, pretty good intuitions. 

Bear is an accomplished American science fiction writer. His short story Blood Music won both a Nebula and a Hugo Award, and his Darwin’s Radio won a Nebula Award for Best Novel in 2000. He’s considered a ‘hard SF’ writer, since science has a prominent place in his fictions (which is, by far, not a prerequisite in science fiction). 

Vitals tells the story of twin brothers, Hal and Rob Cousins, who happened to be microbiologists (the story is mainly told through the point of view of Hal, but we learn about Rob via another POV character). The Cousins brothers are in their late twenties and already very successful scientists. Hal had a tenure track position in Stanford, however, at the beginning of the book we learn that he has been fired due to a redistribution of resources at Stanford. So now he’s going rogue, that is, he’s looking for rich patrons to subsidize his research and he's renting lab space for his own use—a situation that I thought unrealistic, but I read something similar recently in Science, so... Good news for Hal, his trade is the prolongation of human life, a topic that has the ear of many rich old men. In the first pages of the book we thus meet Hal on a mission to seek the secret of eternal life in the deep ocean floor…

Of Flies, Mice, and Men by François Jacob

Published by Harvard University Press

It is thanks to François Jacob that I began to understand what evolution meant at the molecular level, when I read his wonderful book Le jeu des possibles (The possible and the actual), more than ten years ago. And “Evolution is tinkering”, Jacob’s catchphrase, is with me ever since. 

Jacob, now 92 years old, began his scientific career after fighting in World War II, and studied lysogenic phages in bacteria at the Pasteur Institute in Paris. There he met Jacques Monod, starting one of the most fruitful collaboration of the 20^th century. Their work on genetic regulation in E. coli culminated in a Nobel Prize in 1965. In addition to their revolutionary contribution to molecular biology, Jacob and Monod also wrote books of great importance and large outreach, notably Chance and necessity (Monod) and The logic of life (Jacob).  

Of flies, mice, and men¹ (1998) is his last book to date, a personal journey across biology that spans several decades. The different chapters feel a little bit disconnected, because apparently they were first written as lectures for different occasions, but the book is very enjoyable. Jacob is one of these great scientific figures with a real literary culture, one who can invoke Dino Buzzatti and ancient greek myths, the poets Paul Valéry and John Keats, or Tolstoy. 

The Naked Ape by Desmond Morris

First American edition, 1967

"There are one hundred and ninety-three living species of monkeys and apes. One hundred and ninety-two of them are covered with hair. The exception is a naked ape self-named Homo sapiens. This unusual and highly successful species spends a great deal of time examining his higher motives and an equal amount of time studiously ignoring his fundamental ones. He is proud that he has the biggest brain of all primates, but attempts to conceal the fact that he also has the biggest penis, preferring to accord this honour falsely to the mighty gorilla. He is an intensely vocal, acutely exploratory, over-crowded ape, and it is high time we examined his basic behaviour."

Desmond Morris is a wonderful writer, and I think this shows in the first paragraph of his best-seller book "The Naked Ape" (1967), reproduced above. I hadn't read it for at least ten years, and this second reading (but first time in English) was as enjoyable as the first one.

The Naked Ape—subtitled A zoologist's study of the human animal—is Morris' attempt to teach us some anthropological and biological facts about ourselves, and this in a very clear and funny way. Morris is a British scientist who studied animal behavior at Oxford. He later worked at the London zoo  and he has participated to many radio and television programs. Last but not least, he's the author of many popular science books! (You can read his full biography and find his complete works on his personal website.)

A Planet of Viruses by Carl Zimmer

Published by University of Chicago Press

This is popular science writing at its best: concise, edifying and not condescending. But I did not expect less from Carl Zimmer, a seasoned science writer and the author of many books (e.g. Microcosm, Soul Made Flesh, Evolution:Making Sense of Life), as well as a contributor to many high profiles newspapers and magazines (e. g. NYT, Time, Scientific American). On top of that he's a widely read blogger (The Loom).

You can tell that it is good when you would recommend the book to a non-scientist, and at the same time you find plenty in the book to enjoy for yourself.

A Planet of Viruses is a short book, so don’t expect an exhaustive treatise on viruses. But if the scope is narrow, it is due to clever choices that help keep the book focused.  For instance, Zimmer doesn’t discuss the molecular details so much. We won’t learn here about RNA vs. DNA viruses, single vs. double stranded, and so forth. Neither will we learn the elaborated tricks of viral replication or the taxonomy of viruses – but textbooks are just for that, aren’t they?

Naming Nature by Carol Kaesuk Yoon

Published by W. W. Norton & Company

For a book that aims at a large readership, Naming Nature (2009) dares to explore a topic that seems anything but sexy at first sight: taxonomy. But we know better and we won’t turn away from the book, since the act of naming and classifying organisms is of course a very exciting activity! (No, I’m not kidding.)

In her book, Carol Yoon recapitulates the history of the discipline and presents the main scientific actors who contributed to the advance of taxonomy. She thus tells us about important figures:  Linné (Carolus Linnaeus), who is considered the founder of modern taxonomy, and who notably popularized the use of the binomial nomenclature (Felis catus and Escherichia coli, to name two lovable examples); Charles Darwin, who needs no introduction, and who revolutionized taxonomy by showing that species were not immutable; Ernst Mayr,  one of the main architects of the modern synthesis of evolutionary theory; Linus Pauling, the Nobel laureate chemist who had the brilliant idea of classifying organisms by looking at the amino acid sequence of hemoglobin; and Carl Woese, microbiologists’ modern hero, who classified organisms by looking at their DNA sequence and turned the tree of life topsy-turvy. Nothing new to me here, but, after all, this book is not written for biologists.

On the other hand, I learned facts that I was ignorant of (and this seems to be an inexhaustible category of facts...). For instance, I learned that it was Julian Huxley (member of a family in which each member is either a literary or a scientific genius) who coined the term ‘systematics’ and proposed to use it in place of taxonomy.

The science and art of David Goodsell

Portion of an E. coli cell. Image courtesy of David Goodsell.

At the University of Lausanne, when I was a biology student, our great professor Jacques Dubochet tried to instil in us some sense of the physics at play in the biological world. He would ask us questions such as: “So, how thick is the plasmic membrane?” or “How fast will a protein diffuse in the cell?”.  And we would be like: “Huhhh….” So I’m convinced my former professor must be a great fan of the work of David S. Goodsell.

David Goodsell is associate professor of molecular biology at the Scripps Research Institute in La Jolla, California. He is an expert in the structure of biomolecules, and he uses computer simulations to illustrate molecular organizations and interactions.  But what makes his work truly unique is the use of classic watercolor painting to represent cells and their compartments: anything from a bacterium to the Golgi apparatus of a eukaryotic cell, nerve synapses or even viral particles. At odds with the oversimplistic representations of cellular organization that many biologists enjoy, David Goodsell’s drawings offer a real sense of what the biophysical world is. And did I mention they were beautiful too? His website—Molecular Art/Molecular Science—is a great resource to learn more about his work.

The Logic of Chance by Eugene Koonin (continuation)

Published by FT Press

In the first part of this post, I insisted on living organisms (viruses, bacteria, eukaryotes) and their evolutionary history. 

Here I want to look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an evolutionary outlook that is based on an analogy with the physical world. Central, for instance, is stochasticity, as a force shaping the genomic evolution. Equally important, in Koonin’s view, are the statistical principles that govern the interactions between all genes within a genome (he likens the collection of all genes in a genome to the ideal gas model in physics). Thus, genes are influenced by a number of statistical rules. On this line, even though it is apparently not possible to define “laws of genomics”, certain regularities can be identified, such as the proportion of different functional classes of genes within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems biology, while revealing an extremely complex, multifaceted picture of evolution, at the same time allow us to derive powerful and simplifying generalizations. It is tempting to offer yet another version of the famous phrase: Nothing in evolution—and in population genetics—makes sense except in light of statistical physics.”

The Logic of Chance by Eugene Koonin

Published by FT Press

About fifteen years ago, a revolution started in the biological sciences, which goes by the name whole genome sequencing. I don’t have memories of the announcement of the first bacterial genome in 1995 (I was in high school and not really following biology news…), but at the time of the human genome project I was a biology student at the University and I remember very well when the paper describing the human genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was that it was a technical revolution, not a conceptual one. After all, I thought, the sequence information revolution already took place in the seventies, when Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny. 

I revised this feeling, thanks in part to the excellent book of Eugene Koonin, The Logic of Chance (2011)—subtitled the nature and origin of biological evolution—and published by Financial Times Press (yes, they do have a science catalog!).

Francis Crick and Directed Panspermia

Francis Crick. Photo Marc Lieberman

Every biologist knows that Francis Crick is the co-discoverer of the structure of DNA. What is less known, probably, is the fact that Crick was a proponent of a theory that stands at the border of science, the theory of directed panspermia.

In 1973, Crick (together with chemist Leslie Orgel) published an article describing the theory, and in 1981 he dedicated a full book to directed panspermia, entitled Life itself. 

According to Crick, the idea of panspermia – which means “seeds everywhere” – was proposed by the physicist Arrhenius at the end of the 19^th century. Arrhenius suggested that life on Earth originated from space, that our world was seeded by spores of micro-organisms traveling between planets. 

But because the radiations in space were thought to be too intense for the spores to survive, Crick and Orgel postulated a variant of the theory in which spores were transported by an interplanetary spaceship sent by an alien civilization!

Kingdoms or domains?

I view taxonomy – the classification of organisms – at the same time as the most useless and the most useful science. Useless because we know that all life forms are related to one another, and therefore the categories that we create to separate them are arbitrary (with the exception of the distinction at the species level). Most useful, since naming and organizing things seem necessary if we are to claim any knowledge. And isn't it a true pleasure (I almost dare to write "bliss") to point at a plant, a mushroom or an animal (if the latter doesn't move too fast) and be able to name it? 

I learned my share of taxonomy as a student, but I also forgot quite a bunch… At least I remember that I got a good grade at my zoology exam (I had to talk about the subphylum Chelicerata!), based on a course by one of the best professors I ever had, Peter Vogel. 

Taxonomy, which is part of Systematics (the study of biological diversity), proposes a hierarchy from the most particular to the most general: Species, Genera, Families, Orders, Classes, Phyla… (In the classic evolutionary taxonomy, classification is mostly based on morphology, while modern molecular systematics compares the sequence of amino acids in proteins or of nucleotides in nucleic acids.) But, what about higher (more global) levels of classification? 

The endosymbiotic theory of Lynn Margulis

Published by Basic Books

Lynn Margulis passed away last November, sadly. She was renowned for the endosymbiotic theory of evolution, which is now part of biology textbooks. She had a wonderful insight: the mitochondria and chloroplasts that are found in eukaryotic cells were, in distant past, free-living bacteria. Thanks to at least two distinct endosymbiosis events, they were incorporated—and not digested—in the eukaryotic ancestor. They became responsible of key functions within the new association, namely respiration and photosynthesis. These symbionts persisted until at some point they were indistinguishable from their host, and all merged to become one new organism, a eukaryotic cell. 

Recently I found a copy of her book Symbiotic Planet (1998) in my usual second-hand bookshop in Davis. It is a short book in which Margulis deals with the scientific idea that has occupied her during most of her career: the serial endosymbiosis theory (or SET). The author sums up the book as follows (p.33):

In short, I believe that most evolutionary novelty arose, and still arises, directly from symbiosis.

The Human Zoo by Desmond Morris

Back in the days when I was a biology student in Lausanne I had a great time reading Desmond Morris' best seller The Naked Ape (1967), in which the British zoologist discusses what sort of curious social animals we are—and he does so with a lot of wit and humor.  

The Human Zoo (1969) is his follow-up book, thus when I found a copy of it in a second-hand bookshop I happily bought it (probably equally motivated by the lovely vintage yellow cover!). Newer editions are available, as you can see in the author's bibliography.

The Human Zoo still deals with the human animal, but this time the focus is on the social ties that we develop between each other and the sort of society in which we live. The underlying question is: How beings used to living in tribes of at most hundreds of individuals can cope with our modern society and its super-tribes of millions? The city, writes Morris, is not a concrete jungle, it is a human zoo. In the modern life and its crowded places, we tend to behave as animals in captivity.

Jacques Monod and the origins of molecular biology

A beautiful model or theory may not be right; but an ugly one must be wrong. 
Jacques Monod 

 Published by ASM Press

After his work on bacterial growth, I'm now reading about Monod's later career and the discoveries that contributed to the creation of molecular biology. And for that purpose, I warmly recommend the revised edition of "Origins of molecular biology – A tribute to Jacques Monod", published at ASM Press. In this book, Agnes Ullmann and André Lwoff (two former collaborators of Monod) have compiled a collection of essays by colleagues and peers who recall their memories of the great scientist (among whom François Jacob, Francis Crick, Salvador Luria and many others). The book should be praised for providing a mosaic view that tells both the story of the science and the story of the man. And what a man! Bacterial growth kinetics, messenger RNA, enzymatic repression, lac operon, allosteric proteins… A Nobel prize received in 1965 (together with André Lwoff and François Jacob) rewarded their «discoveries concerning the genetic regulation of enzyme and virus synthesis». But, although the book portrays Jacques Monod as an extraordinary man and a great scientist, this is no hagiography, and the darker sides of his personality are evoked as well. 

The role of textbooks in biology

"Hey, this is textbook knowledge, you should know that!"

This is what I would be told, if I were to ask a stupid question about microbiology in the laboratory. (And for the record, I believe that such things as "stupid questions" do in fact exist.) 

"Textbook knowledge" is often used to define the core knowledge that a biologist (or any scientist, as far as I can tell) should possess as a result of her education. When I was an undergraduate biology student, we used to talk about "the Campbell" and "the Alberts" to refer to our textbooks of general biology and molecular biology, respectively, and today I talk of "the Brock" to mention a reference textbook in microbiology. Textbooks are not only useful to students; personally, I often find relevant information in them, although most of my readings are scientific papers. 

A textbook should provide you with the background knowledge sufficient to operate in the current state of your discipline. (Although, of course, some will be more general or conversely will be more specific than others, depending on their goals.) 

The University of Chicago Press (Image source)

The reason I want to write about textbooks here is a consequence of my reading of "The structure of scientific revolutions" (1962), the landmark book by science philosopher Thomas Kuhn. Together with Popper, Kuhn is among the most famous philosophers of science: he coined the term "paradigm shift", which is not only a fascinating concept, but also a very catchy idea. Scientists like to use it often and in many different contexts. (Probably too often in my opinion, since paradigm shifts do not take place that frequently—if they take place at all.) 

Kuhn's book is an excellent read because it is rather concise (my edition is about 200 pages, with a 30 pages postscript) and almost devoid of jargon, which makes it very engaging. My only regret was maybe that I felt I already knew too much of it, since Kuhn's ideas have been widely explained and discussed. For instance, I remember reading a very good recapitulation of Kuhn's theses in a French translation of Alan Chalmers' book "What is that thing called science?". Nonetheless, a lot of fascinating details were still to be found.