“Virusphere: From Common Colds to Ebola Epidemics: Why We Need the Viruses that Plague Us“, written by Frank Ryan, published in Europe by William Collins (a HarperCollins imprint) in March 2019 (hardback, 278 pages)

Ah yes, that was the subtitle of Michael Cordingley’s book (see my review of Viruses: Agents of Evolutionary Invention). With Virusphere, Ryan has written a book along largely the same lines, although it is a good deal more accessible than Cordingley’s. A good two-thirds of the book is a catalogue of disease and a history lesson in microbiology.

We are introduced to Charles Chamberland and Louis Pasteur’s germ-proof porcelain filter, which was vital in establishing that some disease-causing agents were very tiny indeed. Or the famous story of how in 1854 London, anaesthetist John Snow linked cholera to contaminated drinking water, ultimately leading to improvements in sanitation in cities. Or how we rid the world of smallpox.

But foremost it is an opportunity for Ryan to entertain the reader with facts and first-hand encounters with viral diseases: measles, flu, polio, norovirus, smallpox, hantavirus, HIV, Ebola, rabies. Some of these are the subject of dedicated books (e.g. Virus Hunt: The Search for the Origin of HIV/Aids, Ebola: Profile of a Killer Virus, and my review of Spillover: Animal Infections and the Next Human Pandemic), but in case you want to read just one book, Ryan has got you covered. It is not all horror stories though. His message that the vast majority of viruses are innocuous to humans and vital components of organisms and ecosystems is echoed by Rob Dunn regarding bacteria and insects (see my review of Never Home Alone: From Microbes to Millipedes, Camel Crickets, and Honeybees, the Natural History of Where We Live).

“The virus particles that burst out of an infected cell and linger in the environment, waiting for a new host? Ryan likens them to dormant seeds rather than inanimate matter.”

Ryan is an admirer of the thinking of Lynn Margulis and mentions her ideas on symbiosis and holobionts in several places (the latter term refers to the whole formed by two or more interacting partner species, see also Symbiosis as a Source of Evolutionary Innovation). The idea that viruses and hosts live in a symbiotic relationship – encompassing parasitism, commensalism, and mutualism – is an idea he has been pushing pretty relentlessly for a few decades now (see his previous books Virus X: Understanding the Real Threat of New Pandemic Plagues, Darwin’s Blind Spot: Evolution Beyond Natural Selection, or Virolution). He teases the reader with this idea from the start, but it is not until chapter 16 that he finally develops it. Judging from the many references each chapter suddenly receives (and the numerous notes I was taking), this is really where the book gears up.

Biologists have typically portrayed viruses as parasites that straddle the border between life and non-life. Ryan goes against that grain, preferring to pull viruses into the domain of the living. Yes, they depend on their hosts for their replication, but virtually all organisms (bar the rare autotrophic bacterium) depend on other living organisms in the web of life. The virus particles that burst out of an infected cell and linger in the environment, waiting for a new host? Ryan likens them to dormant seeds rather than inanimate matter. He ends the book making a case for considering viruses as the fourth domain of life (in addition to the three that Carl Woese defined, see my review of The Tangled Tree: A Radical New History of Life).

I went into this a bit sceptical, but Ryan gives some fascinating examples. Starting with a scene straight out of the pen of Matt Simon, that of a wasp injecting eggs into the living tissue of a caterpillar (see my review of Plight of the Living Dead: What Real-Life Zombies Reveal About Our World – and Ourselves), Ryan adds the observation that there is a third partner involved. To turn the caterpillar into a zombie larder requires a virus that is injected along with the wasp’s eggs. A nice example of mutualism, where both virus and wasp profit from each other. And what of the bacteriophages (viruses that infect bacteria) that release both a persistent toxin and a short-lived antitoxin? This leaves the host with no option but to accept the virus. If it kills the virus, it will succumb to the toxin.

“To turn [a] caterpillar into a zombie larder requires a virus that is injected along with the wasp’s eggs.”

We furthermore know that viral genes become incorporated in the genome of hosts. Especially retroviruses such as HIV-1 do this (more on those in Discovering Retroviruses: Beacons in the Biosphere). The striking bit, as Ryan explains, is that some of these inserts have been repurposed by hosts as regulatory regions to control the transcription of their own genes. And the research he mentions that shows that such retroviral material has been implicated in the evolution of the mammalian placenta caused me to do a double take on that paragraph. I’m afraid that Cordingley already blew my mind with the concept of viruses as quasispecies (something which Ryan mentions, but Cordingley did a better job of explaining). Curiously, Ryan, too, completely omits any mention of CRISPR (see my review of A Crack in Creation: The New Power to Control Evolution). This is another striking example of incorporation of viral DNA in the host’s genome, in this case post-infection to be used in future host immune responses.

Ryan’s writing has its stylistic idiosyncrasies. Introducing viruses, he asks how we can study such minuscule entities, suggesting “that there is an obvious guide […] whose perspective has only recently been opened up to us in wonderful detail through the deepest penetration of the living world by the enlightenment of modern scientific techniques” (p. 5). On parents who have children with a fever, Ryan remarks: “How natural that our hearts should falter with the beloved child temporarily tossing in a perspiring fever […]” (p. 33). I cringed a bit at his mention of readers as “ordinary folk”, which is only mildly better than the patronising “common man” I sometimes come across. Throughout the book, his colleagues are esteemed, distinguished, eminent; the ideas novel, astonishing, profound. I personally found it a bit grandiose and self-aggrandising in places. It will no doubt depend on your taste in writing what you make of that, but it distracted somewhat from my pleasure in reading this book.

Because, make no mistake, Virusphere is a fascinating book that is well structured, with short, absorbing chapters. As Ryan makes clear, in many areas we have only started scratching the surface, and the potential of new techniques such as metagenomics (the study of genetic material recovered directly from environmental samples, really useful to find viruses) still has to be fully appreciated. Whether future researchers will remember Ryan as a pioneer in the vein of Margulis remains to be seen, but Virusphere makes an engrossing and fervent argument that he is on to something.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Virusphere paperback, hardback or ebook

Other recommended books mentioned in this review:

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

“Viruses: Agents of Evolutionary Invention“, written by Michael G. Cordingley, published by Harvard University Press in June 2017 (hardback, 373 pages)

And let there be no mistake, viruses are unusual. They straddle the border between living and non-living matter. By themselves, they are inert collections of nucleic acids (either RNA or DNA), often, but not always, wrapped in a protein capsule. They don’t eat, they don’t breathe, they don’t move. For all intents and purposes, they are just another collection of macromolecules that make up the world. But give them a living host and they appear alive: invading, multiplying, and evolving. In the first few chapters, Cordingley highlights many peculiarities and traits that make viruses so important and unique in evolution, and I will highlight three of them here.

For one, they are numerous. Because viruses can infect all lifeforms, including microbes (themselves already very numerous) the virosphere contains an astronomical number of individuals at any given time. A conservative estimate of 10³¹ viruses is mentioned. This is a lot of genetic information for natural selection to work with. The viruses that infect microbes, bacteriophages, make up a large part of this and reproduce quickly due to the short generation time of bacteria.

Second, viruses literally inject their genetic material into cells, and some of it can and will be accidentally incorporated into the host’s genetic blueprint (its genome). This means genetic information is not only moving between generations – from parents to offspring during conventional reproduction – but also within generations in a sideways fashion, which is known as horizontal gene transfer. Quammen further explores the importance of this in The Tangled Tree: A Radical New History of Life, but consider for a moment that this mechanism is implicated in the speed with which bacteria can develop resistance to antibiotics, previously discussed in Superbugs: An Arms Race Against Bacteria. The incorporation of viral DNA in the host’s genome is directly causing mutations and generating variation on which natural selection can act.

“For all intents and purposes they [viruses] are just another collection of macromolecules that make up the world”

The final example I want to highlight are RNA viruses, such as the poliovirus. Replication of RNA, the single-stranded relative of double-stranded DNA, is notoriously messy. Error rates are as high as one per 1000 to 10,000 bases, compared to one per ten million bases for DNA viruses (a base is the unit of genetic information, consisting of an organic molecule known as a nucleotide – in DNA these occur in pairs, hence base pairs, which form the familiar double helix when strung together). This means that the individuals in a population of RNA viruses are so genetically diverse you can’t really call them conventional species anymore. Cordingley introduces the concept of quasispecies: diffuse groups of closely related but genetically distinct individuals. This hypervariability makes viruses particularly adept at adapting. When environments change, the genetic variation present in a population of “conventional” organisms is probably not enough to immediately supply an individual that is optimally adapted, so further evolution will happen. As environments are constantly changing, in reality this means that most “conventional” species are constantly lagging behind, chasing the evolutionary optimum. The hyperdiverse members of an RNA virus population, meanwhile, are far more likely to already have well-adapted members present when environments change, which will immediately be favoured in reproduction. I had not heard of this concept before, but it blew my mind when considering it.

A large part of the book deals with human viruses and the diseases they cause: influenza, HIV-1 and AIDS, ebolavirus, cross-species infections and animal reservoirs of viral zoonoses (i.e. diseases that can be transmitted from animals to humans), and the unique world of retroviruses. Most of these topics have been the subject of dedicated books (e.g. Virus Hunt: The Search for the Origin of HIV/Aids, Ebola: Profile of a Killer Virus, and my review of Spillover: Animal Infections and the Next Human Pandemic), though not yet retroviruses. This group *must* nestle themselves into the host’s DNA before they can replicate, which means they are by definition heritable. In contrast, most other viruses will use their host for their own replication, but if the host survives and reproduces, the viral DNA is not passed on to the host’s offspring. Skalka writes more about these unique viruses in Discovering Retroviruses: Beacons in the Biosphere.

“the concept of quasispecies […] blew my mind”

In all these chapters, the focus is on the mechanics of these viruses and the particular evolutionary viral tricks they use. While introductions are light and terminology and concepts are explained, the reading quickly gets technical, sometimes to the point that I felt I was reading a journal paper rather than a popular science book. Although I found Viruses an incredibly fascinating book, I can’t say it is easily accessible. A basic understanding of microbiology is a must to really get the most out of this book. The lack of a glossary doesn’t help, but probably the biggest drawback is the complete absence of illustrations. The many complicated and often theoretical concepts could have been made much more accessible by illustrations. A Crack in Creation: The New Power to Control Evolution is a shining example of illustrating concepts in bacterial and viral genetics. Given the diversity of topics covered here, the number of required illustrations would perhaps have been prohibitive.

Speaking of A Crack in Creation, given what we now know about the incorporation of viral DNA in the host’s genome post-infection to be used in future immune responses, I was surprised to find no mention of CRISPR in this book whatsoever. Not even in the chapter on using viruses as human tools that covers such topics as the use of viruses in vaccines, as biological control agents, or as agents to combat cancer. It seems like an odd omission in an otherwise very thorough and wide-ranging book.

Though not a popular science book such as, say, A Planet of Viruses, Cordingley nevertheless provides an up-to-date and detailed account of the evolutionary power and prowess of viruses that should appeal to biologists with an interest in evolution or microbiology.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Viruses hardback or ebook

Other recommended books mentioned in this review:

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

“Superbugs: An Arms Race Against Bacteria“, written by William Hall, Anthony McDonnell, and Jim O’Neill, published by Harvard University Press in April 2018 (hardback, 246 pages)

Superbugs: An Arms Race Against Bacteria is a small book written by two economists and a public policy professional, and follows on their work on the independent Review on Antimicrobial Resistance, which was commissioned by former UK prime minister David Cameron and published in May 2016. The book chronicles the rise of resistant bacteria (you may have seen headlines mentioning MRSA, which is a microbe resistant to methicillin), and why this rise has happened. Part of the failure to develop new antibiotics has to do with the complexity of the science. But far more important are economic and political problems. A combination of the long time required before a drug is approved due to the trials that are needed and the limited duration of patents on these drugs means that it is economically not attractive for pharmaceutical companies to invest in researching new ones.

The second part of the book outlines the solutions proposed by the authors to address this problem. They cover what incentives are required to stimulate drug development, how to prevent disease transmission, how to reduce the use of unnecessary antibiotics in humans, and the need to tackle the abuse of antibiotics in the livestock sector. That last point might come as a surprise to many readers, or so claim the authors. However, I think that animal welfare campaigners have been tabling this topic for long enough for it not to be a particular secret anymore. The reason that the overuse of antibiotics in livestock is so problematic is that these are very similar to the ones used in humans, which means that we are shooting ourselves in the foot – this is another way to encourage evolution of drug-resistant bacteria.

Throughout the book, the authors include quotes and fragments of interviews they have had with scientists and policymakers, providing interesting viewpoints. Lucidly written, the book is far from alarmist, but the situation it sketches is very alarming nevertheless. Whether the solutions proposed here can be put into practice in a timely manner (if at all) remains to be seen. But this is one of those books that you hope will end up in the hands of politicians, for they need to understand the severity of the threat we are facing. One only has to think back to the 2013-2014 Ebola crisis (see Ebola: Profile of a Killer Virus) to realise how difficult it is to control disease outbreaks once they occur. Beyond that group, this book is an excellent primer and overview of the what, how, why, and the “what now” of antibiotics and resistant bacteria that should be widely read.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Superbugs hardback, ebook, audiobook or audio CD

Other recommended books mentioned in this review:

“Defending Biodiversity: Environmental Science and Ethics”, written by Jonathan A Newman, Gary Varner, and Stefan Linquist, published by Cambridge University Press in October 2017 in paperback and hardback (441 pages)

After some definitions and an overview of the environmentalist agenda (i.e. those things that environmentalists want to achieve), the book is split into two parts. The first half analyses arguments of instrumental value (i.e. the usefulness of biodiversity to humans), while the second half analyses arguments of intrinsic value (i.e. the value of biodiversity in and of itself, without considering its usefulness).

I found the first half of the book easily accessible and understandable, as this takes a look at the empirical data in favour of conservation. Four arguments are examined: ecosystem functioning and stability (e.g. soil fertility or air quality that is provided by functional, highly biodiverse ecosystems), the precautionary principle (when in doubt, let’s err on the side of caution and conserve a species), agricultural and pharmaceutical benefits, and nature-based tourism.

There has especially been a lot of empirical work done on ecosystem functioning, but closely examining the data shows that most work is done on artificially created grassland communities that are very species-poor. It is very hard to extrapolate from these findings, and they have little relevance to support the idea of more biodiversity supporting better ecosystem functioning (this is just one of a raft of problems the authors highlight).

The precautionary principle is often touted in favour of proper ecological risk assessments or quantitative cost-benefit analyses. Furthermore, the precautionary principle is usually invoked to stop something from happening (usually human action that could lead to biodiversity loss), without ever asking what the benefit is from said action, and the cost if said action is prevented.

Agricultural and pharmaceutical benefits only apply to a very small number of plants that are already well protected, leaving much biodiversity out of the picture. And as far as nature-based tourism is concerned, the link between biodiversity and the enjoyment people get out of it is weak.

I only highlight some of the findings that struck me as particularly relevant or surprising, but the authors analyse each topic in much more detail. Furthermore, in many cases, a corollary of each argument is that if you apply it consistently, it would suggest actions that many environmentalists would oppose. For example, the idea that biodiversity supports ecosystem functioning could be an argument for species introductions, or causing local extinction of a species if it benefits the ecosystem. Actions most environmentalists would baulk at.

“Most people would agree that it is important to conserve wildlife and the environment it lives in. But can you clearly articulate why?”

The second half examines arguments that biodiversity has intrinsic value. I’ll be honest with you, this is where the book largely lost me. Now, I have no formal background in philosophy. The introductory chapter to this section is aimed at people like me who are not familiar with how ethical theories and principles are defended. The different chapters look at sentientism (the idea that the lives of all sentient animals, including humans, have intrinsic value), biocentric individualism (the lives of all organisms, sentient or not, have value), ecoholism (ecological wholes such as species and ecosystems have intrinsic value), Aldo Leopold’s land ethic (his book A Sand County Almanac has had a large influence on modern environmentalism), and the importance of aesthetic value. Here, too, the authors provide analyses of what some of the weak points are of each of these arguments, but I feel ill-equipped to summarise them.

The overall conclusion is that none of the arguments that environmentalists normally put forward address all the points on their agenda. Combining arguments doesn’t necessarily make things better as some of them are in conflict with each other. This does leave me wondering how we can improve our arguments in favour of biodiversity conservation. The book doesn’t provide clear answers. Largely, I think, because these answers are not yet apparent. Where the instrumental values are concerned, reading between the lines, Defending Biodiversity highlights what sort of research we would need to do, and what sort of data we would need to gather in order to answer such questions. For the intrinsic values debate the authors highlight that theories have not been fully developed yet, and that this is still an area of ongoing effort.

The academic discipline of environmental ethics, which examines the ethical arguments of how humans ought to treat the natural environment, has been around for a few decades. This book seems to me to be the first to try and build a bridge to the practical discipline of biodiversity conservation practised by environmentalists. My impression is that this book would be an excellent textbook for a course on environmental ethics, where you read each of these chapters and discuss them in a group setting, led by an environmental philosopher. I could see how, in such a setting, a biologist like myself with little formal training in philosophy could get more out of it. As it stands, reading it is interesting, but the book feels like an opening salvo. It highlights many problems, which is valuable, but it provides few answers or directions to better answers. I understand that this book wants to engender reflection, but I’m a bit worried that practising biologists and conservationists reading the book will finish it feeling lost for both answers and a way forward.

Disclosure: The publisher provided a review copy of this book. The opinion expressed here is my own, however.

Defending Biodiversity paperback, hardback or ebook

Other recommended books mentioned in this review: