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Thinking Like a Phage: The Genius of the Viruses That Infect Bacteria and Archaea
It isn't easy to be a phage. First, what is a phage? A phage is a virus that infects Bacteria. To succeed, a phage must encounter, recognize, and enter a particular type of bacterial cell, then coerce it to make more phages rather than more cells. Of course, the cell resists this hostile takeover in numerous ways, all of which the successful phage overcomes. The triumphant phage then proceeds with its replicative business. In this engaging book, Merry Youle relates some of the tactics used by 21 pheatured phages to outwit their host and successfully maintain their own lineage generation after generation.
This ongoing contest of wits is a matter of life and death for both players. A phage chromosome arriving in its intended host cell is met by the cell's state-of-the-art defenses. Unless it dodges or neutralizes every one, it will be chopped into a nutritious snack for the cell. If the phage survives, it then quickly diverts the cell's machinery to production of more phages, rather than more cells. Under skillful phage supervision, manufacture of phage components proceeds at top speed, with all parts produced when needed and in the quantities required. As the pieces come off the assembly line, they self-assemble into sophisticated transport packages, each carrying a phage chromosome and capable of delivering it into a new host cell. When a new crop of progeny is ready - perhaps 25, 100, or more of them - the phage ruptures the cell to free them all and send them out into the world in quest of hosts of their own. Overall, a balance is maintained so that both the phages and their hosts thrive.
Many phages have the option to instead follow a different script. When they arrive in a host, they can opt to delay immediate hostile takeover and to instead form a coalition with the host for mutual benefit. In this case, as the cell grows and divides, the phage is replicated and inherited by both daughter cells. This can continue for many generations. However, if the cell encounters life-threatening difficulties, the phage ends the alliance and switches to rapid replication. Cell rupture and release of the new generation follows quickly.
Each step of the way presents challenges that test the ingenuity of the phages. In this book, tales of phage prowess are accompanied by pertinent electron micrographs; every chapter is enlivened by informative illustrations created by San Diego fine artist Leah Pantéa. The writing focuses on strategies and underlying principles, with a minimum of jargon. Since some knowledge of molecular biology is required to appreciate phage wizardry, a primer of the needed basics is provided for those unfamiliar with that subject. Thus, these phage adventures can be enjoyed by a wide audience.
Despite being the most abundant life form, the phages - being much smaller than even the microbes they infect - elude our everyday perception.
This ongoing contest of wits is a matter of life and death for both players. A phage chromosome arriving in its intended host cell is met by the cell's state-of-the-art defenses. Unless it dodges or neutralizes every one, it will be chopped into a nutritious snack for the cell. If the phage survives, it then quickly diverts the cell's machinery to production of more phages, rather than more cells. Under skillful phage supervision, manufacture of phage components proceeds at top speed, with all parts produced when needed and in the quantities required. As the pieces come off the assembly line, they self-assemble into sophisticated transport packages, each carrying a phage chromosome and capable of delivering it into a new host cell. When a new crop of progeny is ready - perhaps 25, 100, or more of them - the phage ruptures the cell to free them all and send them out into the world in quest of hosts of their own. Overall, a balance is maintained so that both the phages and their hosts thrive.
Many phages have the option to instead follow a different script. When they arrive in a host, they can opt to delay immediate hostile takeover and to instead form a coalition with the host for mutual benefit. In this case, as the cell grows and divides, the phage is replicated and inherited by both daughter cells. This can continue for many generations. However, if the cell encounters life-threatening difficulties, the phage ends the alliance and switches to rapid replication. Cell rupture and release of the new generation follows quickly.
Each step of the way presents challenges that test the ingenuity of the phages. In this book, tales of phage prowess are accompanied by pertinent electron micrographs; every chapter is enlivened by informative illustrations created by San Diego fine artist Leah Pantéa. The writing focuses on strategies and underlying principles, with a minimum of jargon. Since some knowledge of molecular biology is required to appreciate phage wizardry, a primer of the needed basics is provided for those unfamiliar with that subject. Thus, these phage adventures can be enjoyed by a wide audience.
Despite being the most abundant life form, the phages - being much smaller than even the microbes they infect - elude our everyday perception.
310 pages, ebook
Published May 1, 2017
26 people are currently reading
111 people want to read
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Displaying 1 - 4 of 4 reviews
July 6, 2017
This is a remarkable book about a remarkable subject, although it's not going to be for everyone. Merry Youle gives us chapter and verse on phages, the remarkably diverse range of viruses that specialise in making use of bacteria (and archaea) as their hosts. These incredibly prolific viruses range from the classic 'moon lander' structures to strange blobs and filaments. Some simply reproduce in a bacterium then destroy it, while others can keep their host alive indefinitely. But they are all worthy of our interest.
Youle picks out around 20 variants who will star throughout the book. They are what she refers to as the 'pheatured phages', reflecting a slightly cringe-making tendency to go for fake 'ph' spellings on a regular basis. And should you read the book end to end you will find out a huge amount about them. You will also delight in the illustrations, which range from watercolour-enhanced diagrams to detailed sketches of complex virion structures to electron microscope scans and computer-drawn structural diagrams. There are lots of these illustrations, many of them in colour, making parts of the book a visual treat.
If this book is to be used by biology students to get the information they need on phages, it's wonderful. It is simply the most fun introductory textbook I've ever seen - and if I were reviewing it as a textbook, I would give it more stars. As popular science, though, it falls down a bit. Youle doesn't handle Feynman's biology challenge well. Famously, when studying biology in his spare time, the great American physicist said '"[...] no wonder I can catch up with you so fast after you've had four years of biology." They had wasted all their time memorizing stuff like that, when it could be looked up in fifteen minutes.'
We are simply bombarded, both in the text and in endless footnotes, with definitions for page after page. (And even those probably aren't enough, as some of the terms used that won't be familiar to the general reader aren't defined.) To be for the rest of us, the idea is as much as possible to avoid jargon, not to define it at length. There's simply far too much information we really don't want to know.
Having said that, there are parts of the book that are still digestible to the non-biologist. For example, Yule gives her 'pheatured phages' nicknames like Lander, Fickle and Skinny' to avoid the awful names they tend to be given. But there's still plenty here that isn't accessible.
It depends, then, what you are looking for. If you want an introduction to phages for biology students, this is truly wonderful, but for the general reader it's far too heavy going.
Youle picks out around 20 variants who will star throughout the book. They are what she refers to as the 'pheatured phages', reflecting a slightly cringe-making tendency to go for fake 'ph' spellings on a regular basis. And should you read the book end to end you will find out a huge amount about them. You will also delight in the illustrations, which range from watercolour-enhanced diagrams to detailed sketches of complex virion structures to electron microscope scans and computer-drawn structural diagrams. There are lots of these illustrations, many of them in colour, making parts of the book a visual treat.
If this book is to be used by biology students to get the information they need on phages, it's wonderful. It is simply the most fun introductory textbook I've ever seen - and if I were reviewing it as a textbook, I would give it more stars. As popular science, though, it falls down a bit. Youle doesn't handle Feynman's biology challenge well. Famously, when studying biology in his spare time, the great American physicist said '"[...] no wonder I can catch up with you so fast after you've had four years of biology." They had wasted all their time memorizing stuff like that, when it could be looked up in fifteen minutes.'
We are simply bombarded, both in the text and in endless footnotes, with definitions for page after page. (And even those probably aren't enough, as some of the terms used that won't be familiar to the general reader aren't defined.) To be for the rest of us, the idea is as much as possible to avoid jargon, not to define it at length. There's simply far too much information we really don't want to know.
Having said that, there are parts of the book that are still digestible to the non-biologist. For example, Yule gives her 'pheatured phages' nicknames like Lander, Fickle and Skinny' to avoid the awful names they tend to be given. But there's still plenty here that isn't accessible.
It depends, then, what you are looking for. If you want an introduction to phages for biology students, this is truly wonderful, but for the general reader it's far too heavy going.
March 8, 2021
"There isn't much that I have learned
Through all my foolish years
Except that life keeps runnin' in cycles"
-Lyrics from Frank Sinatras Cycles
Bacteriophage (/bækˈtɪərioʊfeɪdʒ/) also known informally as a phage (/feɪdʒ/), is a virus that infects and replicates within bacteria and archaea.
Since they really can't live or replicate on their own, they're not somewhere between life and death, but rather somewhere between life and non-life, existing in that fuzzy grey area where their "life"-style easily escapes the very definition of life.
This book is like a mini-series played out over 8 episodes.
Cinematography
The pictures in the book ranges from artistically water colored renderings of biochemical environments and detailed pencil drawings of phages to electron microscope pictures, with nothing in between. I like this sharp dichotomy, that reflects the books' both accessible and technically rigorous nature.
Story
In the first episode we're introduced, cursory, to the phages (characters) and their environment (the basics of biochemistry / microbiology).
After this we plunge into episode 2.
Like the last sentence in Finnegans Wake connects to the very first, making the book circular, so every phage phage life is cyclical and there isn't any "real" natural starting point. However, Merry Youle has been kind enough to chose one for us; the point at which a phage has just entered the prokaryote. Here we're starting to get our characters into some real interesting scenarios, showing just how crafty they are, these biochemical wizards.
The rest of the book continues in this vein, showing how our different characters overcome various dramatic challenges, and how the villains (the bacteria) try to counter the phage strategies.
It all ends on a seemingly happy note, with the author noting that a symbiosis between the phages and the bacteria could be more beneficial than the purely lytic (i.e., bacteria destroying) lifestyle. But as the quote for the last episode notes:
"Politeness is the poison of collaboration." - Edwin Land
And indeed, the collaboration only lasts as long as the phage can sense that the bacteria is thriving.
So our TV show really features a kind of band of phage anti-heroes, which is en vogue these days anyway.
Loose associations with information technology concepts
During my reading of the book, I couldn't help but notice the many concepts used by the phages that have been used in programming and computer architecture. To list just a few:
- Obvious one: They both run on digital information.
- Phages (programs) are often OS (bacteria) specific.
- Some phages sets a time (watchdog timer) and sensors the environment. It resets the timer (kicks the watchdog) every time a certain event is satisfied, or let all hell run loose if it is not reset within time (application closes / resets).
- CRISPR systems in the bacteria functions just like an anti-virus program (which it literally is), with a database that is continually updated when new viruses are found (just like how any computer AV program works!).
- DNA is clearly a von Neumann architecture, with the DNA (instructions) being able to modify (repair / restore / transpose) itself.
Book is recommended, if you prefer when all the technical details are not left out. In that case this is a very rewarding read!
Through all my foolish years
Except that life keeps runnin' in cycles"
-Lyrics from Frank Sinatras Cycles
Bacteriophage (/bækˈtɪərioʊfeɪdʒ/) also known informally as a phage (/feɪdʒ/), is a virus that infects and replicates within bacteria and archaea.
Since they really can't live or replicate on their own, they're not somewhere between life and death, but rather somewhere between life and non-life, existing in that fuzzy grey area where their "life"-style easily escapes the very definition of life.
This book is like a mini-series played out over 8 episodes.
Cinematography
The pictures in the book ranges from artistically water colored renderings of biochemical environments and detailed pencil drawings of phages to electron microscope pictures, with nothing in between. I like this sharp dichotomy, that reflects the books' both accessible and technically rigorous nature.
Story
In the first episode we're introduced, cursory, to the phages (characters) and their environment (the basics of biochemistry / microbiology).
After this we plunge into episode 2.
Like the last sentence in Finnegans Wake connects to the very first, making the book circular, so every phage phage life is cyclical and there isn't any "real" natural starting point. However, Merry Youle has been kind enough to chose one for us; the point at which a phage has just entered the prokaryote. Here we're starting to get our characters into some real interesting scenarios, showing just how crafty they are, these biochemical wizards.
The rest of the book continues in this vein, showing how our different characters overcome various dramatic challenges, and how the villains (the bacteria) try to counter the phage strategies.
It all ends on a seemingly happy note, with the author noting that a symbiosis between the phages and the bacteria could be more beneficial than the purely lytic (i.e., bacteria destroying) lifestyle. But as the quote for the last episode notes:
"Politeness is the poison of collaboration." - Edwin Land
And indeed, the collaboration only lasts as long as the phage can sense that the bacteria is thriving.
So our TV show really features a kind of band of phage anti-heroes, which is en vogue these days anyway.
Loose associations with information technology concepts
During my reading of the book, I couldn't help but notice the many concepts used by the phages that have been used in programming and computer architecture. To list just a few:
- Obvious one: They both run on digital information.
- Phages (programs) are often OS (bacteria) specific.
- Some phages sets a time (watchdog timer) and sensors the environment. It resets the timer (kicks the watchdog) every time a certain event is satisfied, or let all hell run loose if it is not reset within time (application closes / resets).
- CRISPR systems in the bacteria functions just like an anti-virus program (which it literally is), with a database that is continually updated when new viruses are found (just like how any computer AV program works!).
- DNA is clearly a von Neumann architecture, with the DNA (instructions) being able to modify (repair / restore / transpose) itself.
Book is recommended, if you prefer when all the technical details are not left out. In that case this is a very rewarding read!
June 14, 2019
An excellent book. I love science books from time to time, and this ones definitely a good example of a science book in its best form. Its informative, well written and easily digestible in its journey through the world of phage biology as it uses a selection of the little viruses to showcase how they can operate and how odd some of them can get. It also oozes passion and its clear how interesting the author finds the subject matter-something further brought home by the lovely artwork. If you're not versed in science at all...this book might be a bit of a hefty read, as it goes into some heavy biological topics though I think it explains them well enough that you'll be able to get a foothold and understand things well enough. And if you are well versed in biology and want to learn more about phages, this is definitely a good place to start to get an understanding of them. Very much looking forward to Phages in Community, and would highly recommend giving this book a looksie if you want something science focused to read.
June 21, 2020
Fascinating book, I came to love the subject
I am a nerd and this is a beautiful nerd book. I don’t have a lot of background in microbiology but I learned so much from this book. The author’s love of her subject really come through. Protists run the world and phages run protists.
I look forward to Phages in Community, the companion book Merry Youle promises us.
I am a nerd and this is a beautiful nerd book. I don’t have a lot of background in microbiology but I learned so much from this book. The author’s love of her subject really come through. Protists run the world and phages run protists.
I look forward to Phages in Community, the companion book Merry Youle promises us.
Displaying 1 - 4 of 4 reviews