آلات الحياة

by David S. Goodsell (وليد الشارود)

عن مؤسسة الكويت للتقدم العلمي، صدر ترجمة لكتاب "آلات الحياة"، للمؤلف د.ديفيد س.جودسل، وترجمة د.وليد محمود الشارود. ويتناول الكتاب الآلات الحيوية بصورة مبسطة، وعلاقتها بالحياة والموت والصحة والمرض والشيخوخة والتنوع في صفات الكائنات الحية، ويربط بين فروع المعرفة في علوم الأحياء والكيمياء والفيزياء والنانوتكنولوجي، ويضع كل ذلك في نسق مبسط من فلسفة علمية تساعد القارئ على تفسير ما ملكه من معرفة، والتأمل فيما يمكن أن تحمله من مضامين.
عن المترجم
الدكتور وليد الشارود، يعمل أستاذاً مساعداً لتكنولوجيا الألبان بقسم الألبان- كلية الزراعة جامعة المنصورة. وهو حاصل على جائزة الإبداع العلمي في العلوم الأساسية من جامعة المنصورة في العام2012، وجائزة أحسن باحث عربي شاب في البيولوجيا والعلوم الحيوية الجديدة من أكاديمية العلوم في العالم النامي TWAS في العام 2009، وجائزة الجامعة التشجيعية من جامعة المنصورة في العام 2008، وجائزة أحسن رسالة ماجستير من جامعة المنصورة في العام 1999.

Genres: Science, Biology, Nonfiction, Art, Biography, Evolution, Textbooks

Unknown Binding

First published January 1, 1992

About the author

David S. Goodsell is an associate professor in the Department of Molecular Biology at the Scripps Research Institute in La Jolla, California.

Reviews

[Forrest · Rating 5 out of 5]

I passed 10th grade biology . . . barely.

My friend James and I had the two cutest girls in the class as lab partners. I can't remember their names, but they were both pretty gorgeous. I ended up in that lab group mostly because of James' charm and good looks. I was not particularly charming. I can prove it:

James and I hung out a fair amount. We had fun. You know, teenagers. So when it came time in our biology class to dissect pig fetuses, we had a good time with it. James made the incision and we had fun moving the pig into different . . . positions. One thing led to another and after a while we had the sliced-open pig dancing to Hello My Baby.

Problem is, its guts didn't want to stay inside.

And we had very slick formica tabletops.

So all kinds of innards spilled out during the chorus and splayed out across and off the tabletop, right into the laps of the girls in our lab group. They were not impressed.

Our teacher, who, it was rumored, was a cocaine addict (though no one could substantiate the claim), turned toward our table and shouted "James! Forrest! Get the hell out!"

So we did. We left the classroom and wandered the halls. I mean, it was kind of like permission, wasn't it?

The next day, we walked into the classroom and no sooner had we crossed the threshold than the teacher pointed at us and simply said "out"!

After a couple of days of this, he figured out that we were just wandering the halls, so for the rest of the semester, we were sent across the hall to spend time in another teacher's empty classroom. BIG mistake! We learned about science, alright. Like how many bags of gummy bears, stolen from the teacher's desk, did it take to fill up two teenage boys. Or whether the buoyancy of balloons on a windy day was enough to keep a teacher's metal in-basket aloft over the schoolyard (it wasn't). Or how many different topological forms could stacked desk chairs take.

The teacher passed us with a "D" so that he wouldn't have to have us in class again.

The joke was on him. I moved to England as soon as the school year was done. I later ran into James in England - he had moved there (to a different air base) a few months after I had gone. There was no chance that teacher would have ever had us as students again.

Fast forward to today. My middle son is studying microbiology at the University of Wisconsin - Madison. He wants to go to medical school and become a doctor. And I, because of my mis-spent youth, am playing catch up. I've always loved science, just sort of missed out on the whole formal training aspect of it (until I got to college). Now, I'm diving in. Heck, the only magazine subscription I have is to Discover Magazine.

So I heard and read a bit about this book and I must say that it's outstanding. Yes, it could use a little bit more depth, but it's a primer, really, a layman's introduction to cells and how they work on the molecular level. Very cool stuff. Some very scary stuff. HIV, for instance, is brutal on the molecular level, snipping out strands of a cells RNA and replacing them with its own, making itself virtually undetectable by the body's defense mechanisms. It's nasty stuff. I learned a lot about how cells work, particularly those in the human body. Did you know that the reason rigor mortis sets in is that the body, upon death, releases calcium from each muscle cell, which causes the muscles to contract. Normally, the living cells would almost instantaneously reabsorb the calcium, causing the muscles to relax, but the reabsorbing mechanism is shut off upon death. The calcium eventually reabsorbs and the body does relax, but only after a while. Or did you realize that the reason spicy foods are used as a sort of folk remedy for colds is because rhinovirus (i.e., the common cold) resides most comfortably in the mouth and nose, where there is not much acidity. Many spicy foods are highly acidic, which breaks down the cell walls of the rhinovirus, exposing its guts to the world, much like my experimental pig.

The illustrations are extremely helpful for me, a visual learner. Now, since I've "seen" how cells work, I can get on with some more specific studies and add some scientific rigor to my studies. Someday, I'd like to take a shot at some DIY biology.

And, in case you're wondering, James and I lost contact a long time ago, but I did find this little bio about him a couple of years ago. Seems he was someone very important on the USS New Orleans, a ship capable of delivering a battalion of 700 fully-armed marines into battle in short order.

If that doesn't scare you, nothing will.

PS: It got scarier. James is now the Chief Petty Officer of the US Navy. I'm sure he's great at his job, but it still cracks me up.

[Old Man JP · Rating 5 out of 5]

Absolutely fascinating! Goodsell discusses the mind-boggling complexity of cells, explaining the actions that occur for even the simplest task. Over fifty years ago, when I was in college, I don't remember studying anything like this in my biology classes and I was a biology major. The advancements that have been made in science are astounding. There is an overload of information in the book but Goodsell's writing is very accessible and easy to understand and the book is filled with wonderfully drawn illustrations to help clarify the subject. In our everyday world it seems to us that turning a page in the book we're reading is the simplest thing we can do but when you see what is actually happening at the cellular level it seems almost impossible.

[Raed · Rating 3 out of 5]

LIFE STORY:
Some remote clumps of rock and metal, ice and organic molecules would fall together to make place called Earth, or that life would arise and thinking beings evolve who would one day capture a little of that galactic light, and try to puzzle out what had sent it on its way.

"The Universe is created for us! We’re at the center!", Right ???

If it is right then Keep looking at the mirror until the idiot appears.
(The idiot always hides in the unlikely of places.)

[Matilda (booksinwildplaces) · Rating 5 out of 5]

5 stars - beautiful

I picked up this book a little while ago because I came across some of the beautiful illustrations David produced online. These illustrations are dotted throughout the book and break up the different themes and concepts nicely, providing an in-depth look at what makes up our cells and life.

This is a great introductory book for people both with or without a scientific background, and delves into molecular and cellular biology, microbiology, immunology and other physical sciences. It is very readable and doesn't expect any prior knowledge. As someone who has a background in science, it feels a bit like revision reading this book. Nevertheless, it was a very enjoyable read and I would recommend this to others. This would also make a great present for high-school/first-year university students interested in science.

[Douglas Summers-Stay · Rating 4 out of 5]

This is a book about molecular cell biology for non-experts in the field. What really distinguishes it are the excellent illustrations. Most books illustrate the interior of a cell with a kind of simplified toy version (and I include my own models of a cell in that characterization). Even the most accurate illustrations I've seen in the past leave out a lot of the stuff inside a cell to make it easier to see what is going on. But this book doesn't pull any punches. Half the illustrations are computer rendered molecules with every atom in the proper place. The other half are watercolors-- but every atom is still in its proper place! The shading is greatly simplified and the molecules are color coded to make it possible to make some sense of it all, but every molecule is there, crowding each other, overlapping, squashed together. In one illustration he even includes all the water molecules. This gives a different set of insights into what is really happening in a cell. The bi-lipid layer, for example, is usually illustrated as neatly lined up little clothes-pins, all waiting in line. But here they are shown wrapping around each other like a nest of snakes, with only their heads pointed outward.
My last class on biology was my freshman year of college, but I was able to follow along just fine. It's surprising how much I remembered. He gives a lot of good analogies. Imagine a room full of grains of rice, he says. That's how many cells are in your fingertip. It's also roughly how many proteins are in a cell. They are all jostling each other like a vast crowd in an airport, all going in different directions at once, but because reactions happen so fast at that scale, within a few seconds every loose protein in the cell has bumped into every other one several times.

[Michael · Rating 5 out of 5]

Written for a person like me - no real experience in molecular biology beyond school bio and pop culture. Amazing illustrations.

[Reinhardt · Rating 5 out of 5]

Fascinating, informative, and beautiful.

I learned more about cell mechanism in these 160 pages than in years of reading. Clear illustrations that are tightly linked to the text show in a visual way how the processes in cells work. It is filled with huge words - I mean huge - which usually means I’m getting completely lost in the vocabulary. Not here. The close link to the illustration and the very clear writing make learning almost automatic. Visualizing the processes is a game changer.

If you have any interest in cell mechanisms, how cells make proteins, build structures, reproduce and die, how DNA works at the molecular level, how vitamins, poisons and pain relievers work at the molecular scale, this is the book

[Stijn · Rating 4 out of 5]

An impressive overview of the field of molecular Biology. It goes into much less detail than The Processes of Life goes, but manages to give a broad intuition that has to leave one in awe for what is going on in our bodies. Who knew!?

I feel that precisely the combination of starting with the dense The Processes Of Life and following up with this one works very well (and that ordering might be precisely the reason this one catches on so well: most of the needed vocabulary one already encountered).

[Dimitri Yatsenko · Rating 5 out of 5]

Textbooks on physiology are replete with cartoons of interacting molecules that attempt to convey only the relevant information without preserving detail, proportion, or scale. "The machinery of life" is a simple and visual primer to cellular physiology that conveys an accurate sense of proportion and relation between the major molecular ingredients of life.

[Ludvig Wärnberg Gerdin · Rating 5 out of 5]

An amazing read. Easy to follow, builds from the most fundamental parts of atoms and molecules to viruses and programmed cell death. With only about 150 pages I think this is a must to pick up for everyone.

[Sebastian · Rating 4 out of 5]

This is an adult picture book where Goodsell gives us an electron microscope's view of life at the cellular / molecular level. It's fun.

The content itself is largely a review of things you might learn from biology class. So, a few takeaways I thought about while reading:
- Our intuitions break at a low Reynold's number. It's kind odd to try and envision it, but viscous friction dominates inertial effects on the scale of a cell. Bacteria stop moving the nanosecond their flagella stop spinning as a result.
- Cells are very crowded. I think localization of enzymes and substrates is an underrated area of study. I would imagine you can really change the kinetics of a reaction by playing with localization.
- I am bearish on connectome projects. Why? Pages 106-107 -- I think there are tons of hidden variables that a connectome doesn't measure. It's the same overhype people applied to the genome. Useless? Hardly. But things like the basement membrane in a synapse, relative concentration of acetylcholinesterase... this stuff surely matters when we think about how the brain works as a system. One would think.
- Cytidine and Thymine bases absorb UV radiation which can result in mutations. We could probably engineer organisms with a different system of encoding genetic information that doesn't get corrupted. That would be cool. (we could also create tRNAs with novel amino acids and increase the variety of enzymes nature can evolve).
- I also think it would be pretty interesting to try and engineer a mammal with circular DNA like bacteria. You probably have to put in some new defenses against cancer. But telomeres are finnicky. I wonder what would happen.
- How does a virus like poliovirus replicate its RNA while ribosomes are bound up to it? Seems like they'd get in the way. Maybe the polymerase has higher affinity to the RNA or something. But then it seems like you'd be kicking off the ribosome all willy nilly.

Living things are pockets of space where entropy seems to run in reverse (Schroedinger: "living things avoid decay into equilibrium"). I can't help but find it mindblowing every time I think about how rare it is to be anything at all in this universe.

[Kinan Diraneyya · Rating 3 out of 5]

I appreciate how much effort was spent creating this book, but I have to admit that it didn't work as well as planned.

The book filled with amazingly detailed (and seemingly very accurate) micro shots that gives a great idea about how things look on a molecular scale, however, reading the related paragraphs and connecting their points to what is in the image (which is only done by tiny black letters hidden in the many details of that image) is often a huge pain, many of these points are yet only naked scientific names like "protein OmpA".



I have read books made for common readers (which I am) before, and I pretty sure they did a better job at explaining concepts and mechanisms without this extensive use of terms, in my opinion, a book like this one should be talking about how things work, not what is responsible for making them work this way.

After all, the book doesn't say how or why protein FhnA transfers the ions of iron, it just says: here is the protein that does this process, its scientific name is the follwing, it is located there and this is how it looks like. Why would I want to know that? I just want the general idea on what is happening!

Now it still gives a general idea on what is happening, and it deserves some praise, but I believe there are books out there that do the job more efficiently.

[Michael Scott · Rating 5 out of 5]

TODO full review:
i The Machinery of Life is a book about the cell and its processes, focusing on visualization. The book covers the main molecular machines; the main processes of living, aging, and dying; the (prokaryote) bacterial cell; the (eukaryote) human cell; the specialization of cells constructing the human body; and viruses, toxins, and antiviruses and antitoxins. Overall, amazing drawings, and a simplistic but very interesting introduction to cell biology, written in accessible language but with conceptual depth. Take it as a helpful university refresher.

Key insight: I liked everything about this book, including how short it was--read it in just a few hours, as preparation for my excursion into the borders of the sciences around the theory of evolution. The detailed visuals are for novices such as myself absolutely essential to understanding how cells work. Also, the excitement: Ever wanted to zoom 40,000,000x into a part of a cell? Wonderful!

Trivia: The author is an associate professor of molecular science and graphic artist of the same topic, and has helped redesign the education part of the RCSB Protein Data Bank. (The RCSB is one of the entities collectively curating over 100,000 descriptions of key atomic structures in molecular science; see for example the structure, reports, data, and 3d objects available about Hemoglobin 2hhb. In plain English, David S. Goodsell is the kind of scientist with real impact on our society.

Some details:
+++ High quality, high resolution, high zoom-in (max. 40,000,000x, Figure 2.5, 3.1, 7.3);
+ 30,000,000x used once, to depict instability of ATP (Fig.3.7);
++ 20,000,000x used for detailed molecular machines, mainly in Chapter 2, and for detailed use of vitamins, mainly in Chapter 9: DNA vs. RNA views (Fig.2.4), protein structure (Fig.2.7), lipid bilayers (Fig.2.9), polysaccharids (Fig.2.10), ATP reaction (Fig.3.8, combined with a 5,000,000x view of the result), cytochrome c oxydase ued in respiration (Fig.7.7, combined with a 5,000,000x view of the result), Vitamin A use to sense light (Fig.9.2, combined with a 5,000,000x view of the result), use of Vitamin B in enzymes (Fig.9.3, combined with a 5,000,000x view of the result), Vitamin D production from cholesterol (Fig.9.4, combined with a 5,000,000x view of the result), cell-killer cyanide (Fig.9.5, combined with a 5,000,000x view of the result), Cytochrome P450 used to eliminate poison from the body (Fig.9.6, combined with a 5,000,000x view of the result), use of Penicillin to eliminate bacteria (Fig.9.8, combined with a 5,000,000x view of the result), drug resistance in HIV (Fig.9.9);
++ 10,000,000x used to emphasize transformations of and links between enzymes/proteins, show views of smaller components such as sterols;
+++ I liked very much the 1,000,000x and 5,000,000x zoomins, for cell-level views and for views of enzymes/proteins/molecular machines (esp. in Chapter 9), respectively; Figure 3.5, on forming the mature protein for human insulin);
+ the smallest zoom, 1,000x, is used once, but with good reason: to depict muscle tissue (Fig.6.1), whose operation which cannot be understood only from visualizations of individual cells (albeit, Chapter 6 hosts plenty of more zoomed-in figures, down to the Sarcomere micron-level contraction, which I suspect is a 40,000,000x zoom).

[Michiel · Rating 4 out of 5]

This book gives someone a glimpse of the scale of all the stuff in cells.

[Eric · Rating 4 out of 5]

This book helped me appreciate how cool biology is. In high school I kind of dismissed it as "lots of memorization."[1] I wish I'd read this back then. Here are some things I learned:

--A medium-sized protein inside a cell at room temperature moves at ~ 5 m/s, but a bacterial cell might only be 10^(-6) m long. Random diffusion is really effective for transporting stuff at that scale! It works fast enough that every molecule will run into nearly every other molecule in the cell (including, e.g., the molecule that protein is supposed to interact with) within seconds. The world of the cell is pretty different from ours.
--Our cells have nanotechnology figured out, with proteins performing operations atom-by-atom, electron-by-electron, photon-by-photon.
--E. coli takes about 50 minutes to duplicate its genome, but its cells can divide as fast as every 30 minutes. The bacterium starts the copy^2 of its genome before the copy^1 is even finished.
--Poliovirus and rhinovirus (the common cold) are pretty similar, except the poliovirus's protein shell can survive acidic environments, getting past the stomach and deeper into the body, while the rhinovirus can't and is restricted to the less-acidic throat and nose.
--Bird flu can infect pigs but not humans. Human flu can infect pigs but not birds. But if a pig is infected by both bird and human flu at the same time, the viruses can exchange parts of their RNA. Humans might have no immunity to the new virus (because of the bird virus parts). A new strain occurs this way, the book says, every ~10 years.

Many of the facts in the book also came up in 9th grade biology, but this book's presentation is way more compelling! It has an interesting narrative and good illustrations.

I read this after James Somers mentioned it in https://jsomers.net/i-should-have-lov..., also recommended!

[1] Thanks, Lily, Clarence, and Sherlock, for doing all of the biology memorization for our Science Bowl team!

[Ben · Rating 4 out of 5]

This is how we should teach kids biology.

[Mansour S منصور السدحان · Rating 5 out of 5]

Most molecular biology text books dissect molecular biology into small digestible mouthfuls. That is understandable, indeed one can argue that this is what academic textbooks are meant to do. But that can have a negative side effect; missing the whole picture! A subject as complex and tangled as molecular biology can be an issue. One needs to read most of the 3kg book to get an all round grip on the subject! Enter David Goodsell! The Machinery of Life is a great book for anyone who wants to obtain a general idea of life at the molecular level. But there are many such books, so what makes this one special? Instead of listing the basics, Goodsell takes the reader into a journey inside an eukaryotic and a prokaryotic cell. This is done by an engaging text and what Goodsell is famous for, great Art. Thats right Art with a capital A! Goodsell's art can fit perfectly in a Tate gallery, yet its as technically scientific as it can be! I have never seen such detailed illustration of cells. The illustrations alone are worth getting this book for. Whether you are a veteran biologist, a biology student or just someone who wants to understand life, this book is a must read.

[Atila Iamarino · Rating 5 out of 5]

David Goodsell é autor dos melhores desenhos de moléculas que já vi, incluindo a série de anos "Molecule of de Month" do rcsb.org. E digo desenhos, quando na verdade ele pinta aquarelas usando como base a reconstrução mais realística possível do formato, tamanho e número de moléculas que trata. O melhor exemplo que conheço de como a arte científica pode ser ao mesmo tempo ser acurada e bela. Gostei do livro muito mais pelas pinturas e explicações do que pelo conteúdo em si, e ainda me surpreendi com a descrição do mundo microscópico com uma série de questões e problemas que ocorrem nesta escala e eu nunca havia pensado.

[Tim Verstraete · Rating 5 out of 5]

Awesome book ... I bought this book because of the brilliant drawings on cell mechanics but the text is as good. Well structure, concise, to the point, good explanation ... loved it! Should have bought this earlier.

[Hunan Rostomyan · Rating 5 out of 5]

I wouldn’t mind being stranded on an island with this book. The mechanisms are fascinating, the illustrations are beautiful, the writing is clear. A very engaging book.

[Marco Neumann · Rating 5 out of 5]

Great, condensed insights.

The only annoying thing are the hard-to-spot annotations within the graphics, turning the many of them into picture puzzle.

[John · Rating 4 out of 5]

This book is all about the illustrations, which are remarkable, though the front cover is really the masterpiece, and the rest of them are much more diagrammatic, less beautiful but perhaps providing more insight. With these diagrams, one definitely gets a feeling of density within the cells, the sharp proximity with which the chemical and mechanical machinery of the cell interacts.

The text is just fine, written with clarity and consistency at an accessible level. The writing definitely has the feel of a textbook, covering what is clearly known without journalistic or scientific straying into the new or speculative. Despite that, it is not too dry, always maintaining an appropriate brevity to keep an engaged pace.

For the most part, the book proceeds hierarchically, starting from the nature of the chemical interactions that allow biological components to do their work, to some of the basic components and processes of every living cell, to the cells of E. Coli (as a representative of bacteria), to the multi-component cells of humans (and other eukaryotes), to the varying architecture of different tissues; but then moving to the molecular boundaries of humans as seen from interactions with viruses and other chemicals.

If the book presents any frustrations, it is that it remains fragmentary, at the level of a tour, rather than really digging in to many of processes step-by-step in a way that reveals their machinery. If a given protein is for cutting, then how does it do the cutting? If a given system can detect and destroy a parasite, how do the components of the system work together to do so? The book proceeds along the lines of: here is an engine cylinder, here is an engine, here is a hydraulic pump, without getting into that step-by-step understand that really reveals how it works. This book is "The Machinery of Life: A Tour" as opposed to "The Machinery of Life: A Step-by-Step Guide to How It Works". This is a fair trade-off: the book covers a lot of ground without much complexity or difficulty.

Overall, this is a nice tour of the machinery of life from chemicals to tissues, giving an illuminating view of the parts, if not the processes, by which it all works.

[Max Krieger · Rating 5 out of 5]

I picked this up for the illustrations, and stayed for the equally lucid writing. I was quite disinterested in high school biology, but this tiny 150-page epic was a page-turner that answered questions I didn't know I had. The illustrations convey the multiscale drama unfolding within us in an explosive colorful way you won't find anywhere else. It gives me vertigo to think about what's going on at that scale, and how it constitutes our experience of life.

Goodsell also paints such a vivid picture of these processes and how diseases occur, that I found myself imagining drug ideas on the spot. I'd love to see a pharmacology sequel in this format; the illustrations seem to beckon an inventive mindset because you can mentally slot new molecules/proteins right on top of the printed image.

I just wish the image letter labels had better contrast!

[Moritz Munzinger · Rating 5 out of 5]

Should be mandatory material for all biology and medicine slides that students get to see in their lectures and books, as Goodsells illustrations are as informative and intuitively graspable as they are beautiful. With this book understanding what goes on in cells has never been easier. I think this is a tenfold improvement to traditional graphics. Save yourself the time and effort and read this instead of other illustrated works whenever you can.

[Becky · Rating 4 out of 5]

So beautiful! I was surprised that the text was written for a general audience, but this makes for a great introduction to the molecular world. Close perusal of the figure captions introduced me to a group of proteins I knew nothing about! I’m thrilled to have something else new for my cell bio class. The illustrations are amazing; I bought this book after buying three full-sized posters for my office.

[Peter · Rating 4 out of 5]

Wow! An amazing look deep inside human cells down to the molecular level. Two things I found amazing: the incredible electro-chemical processes that go on inside our cells; the fact of how much knowledge we have gained on how our bodies work at the deep molecular level. The diagrams are incredible, paintings of cell function magnified 1+ million times.

[Mike Lisanke · Rating 5 out of 5]

Another great biochem book... this one has a lot of great detail on the interaction of biochemicals and pictures which give good insight into the structure of the molecules ... and as we learn, structure equals function in biochemistry. It is Not a biochemistry text book but goes into enough detail to add a lot of background to its understanding.

[Ben Johnson · Rating 5 out of 5]

If you grew up in a young-earth creationist world the way I did, books like this will always delight and amaze. The actual brutish cosmos with its random bumping back-and-forth of elements, molecules, and compounds, is so very much more elegant and magical than the brutish world made by the elegant and magical gods.

[Peter Aronson · Rating 5 out of 5]

A short, concise, readable work about the microscopic machinery that keeps us alive. The 2nd edition's illuminating color diagrams and paintings of the cellular machinery is what pushes this book to five stars.

[Kristina · Rating 5 out of 5]

Beautiful illustrations with complementary writing.

Simple and easy to understand the basic wiring of life.

I would be very proud to have achieved work on a similar level, as a scientific illustrator and researcher.