A Meditation on the Machinery of Life

Meditation can take many forms, and concentrating on concepts we know to be a little beyond our understanding is as invigorating to the mind as a good workout is for the body.  It brings a feeling of humility about how little we really know, but also enthusiasm about surprises in store one day.

How pleasant it is then to find someone already a great distance off, but willing and capable of showing us what they found up ahead, to lift our sagging morale.  The Machinery of Life by David S Goodsell is just such a find, making us all adventurers in the strange and compelling micro universe within our own selves.

Like cells during the first nine months, most people become specialised in one or another function by adulthood so that they always look at life from one direction, as a laywer,  accountant, or physicist.  Talk to them of anything else and their eyes glaze over.  To an accountant, art is the price of the frame and the cost of shipping, and whether it can be sold on at a profit; to a musician, a mortgage just a bothersome pile of unread letters from the bank.  But some people seem to resemble stem cells in that they retain the flexibility to turn in one direction or another depending on their needs or those of their environment, and Goodsell must be partly of this nature.  To create a visible and coherent molecular world on this scale requires focus, knowledge, and an understanding of graphics; finding these in one person seems a tall order.

In the beginning there was only canvas.  But David Goodsell said, let there be cadmium orange enzymes and cobalt blue ribosomes, and lo, it did come to pass. And on the second day, green was the Golgi apparatus, and the proteosome was finest crimson, and he saw that it was pretty good actually

Goodsell is known for the distinctive style of his popular Molecule of the Month illustrations, but The Machinery of Life is a triumph beyond art, capturing the mind-boggling complexity of complete cellular systems: the tools used, the assembly lines, robotic processes, sentinels, recyclable fuels, the precautions, solutions, messages, postal and sorting systems, dangers, remedies, constructions, motors, fuel, weird delivery creatures, guarded entrances, photon detectors, gated switches, cascading processes, fantastic enzymes and all the other astounding ingenuity of biology we dismiss as a trivial matter beneath our concern: make of this world what you will.

None of it would ordinarily be visible, being smaller than the wavelength of light, so it all must first pass through a human mind and emerge via different understandings working together, not the least of which is imagination.  His illustrations are generally a standard one million magnification, with forays into five million x, to highlight particular aspects.

Goodsell is also an HIV researcher, so the book includes much about bacteria, and their tools for breaking and entering, their various disguises and mechanisms etc.  The author understands the mechanics well enough to explain them simply, and illustrates not with dreary airbrushed ball-and-stick cartoons, but in such a way that the mechanics of our own body seem both awesome and quite beautiful.  If they’d had these books when I was in school, I think I would have wanted to become a molecular biologist; as it was, greenand red splodges and dull schematics made the whole field of biology seem tedious and contrived, even ugly.  How things change!

(Fig 5.2, P73) The image above is a small part of a blood plasma cell, with a cross section highlighted for analysis. The full process of the cell’s production and secretion of antibodies stretches over 8 pages of detailed images and explanations; I have scanned in the images and assembled them in order, somewhat crudely, below.

Keep in mind that each and every coloured, outlined object is a specific, useful component or machine made to a precise specification out of hundreds of amino acids and thousands of atoms, its structure and order of assembly set out within a specific region of the DNA.  The tiny ATP synthase motors in the nucleus of the cell – barely 6mm square here, are colossal atomic engines of 500,000 daltons (one dalton is approximately a single proton or neutron, so that 12 daltons equates to a single carbon atom).

Each component has been perfectly made by the manufacturing equipment inside the cell: your body has around 100 trillion such cells, each a bustling city fulfilling an allotted role, with its components frantically working, building machines, erecting scaffolding, dismantling it again, checking codes, fixing, repairing, disassembling, passing and receiving messages, sensing the environment, building and firing up motors, making fuel, or running hither and yon at a speed which defies the imagination.

To give you an idea how mind-boggling this one single process is, read the text for the 5th and 6th images (p78 and p79):

Fig 5.5 Golgi Apparatus: The transport vesicles carry the new proteins to the Golgi, a set of membrane-bound sacs stacked like plates.  Huge tethering proteins like guantin (A) and GM130 (B) guide the vesicles to the right place.  The Golgi is the processing and sorting plant of the cell.  Sugars and lipids are attached to proteins that need them.

For instance, the sugare chains that stabilise the base of the Y-shaped antibody are trimmed and perfected in the Golgi.  When the proteins are properly modified and sorted, they are delivered throughout the cell in small transport vesicles.

The protein clathrin (C) provides the molecular leverage needed to pinch off some of these vesicles by forming a geodesic coat on the outside of the membrane.  After the vesicle separates from the Golgi, the clathrin coat falls off and the vesicle is guided to its ultimate destination.  (Magnification: 1,000,000 x )

Note the illustration of the protein clathrin, highlighted in light blue both here and in the larger illustration above: this was the Molecule of the Month in April 2007, written and illustrated by Graham T. Johnson and David Goodsell.

Clathrin illustrates well the purposeful, component-based nature of biology.  It is a versatile part made in several variously specialised forms, one type of which is assembed (above) into one of the smallest possible geodesic domes.  To give an idea of scale, Goodsell shows a hemoglobin molecule (541 amino acid components) which is a marvelous machine in its own right, and one I am still trying to get a company to build a working model of.

Neurotransmitters contained ready for release (top) above a synapse

The staggering complexity of biology and the intelligence required to duplicate its function might be better appreciated if I tell you that a team of molecular modellers advised me that creating a single model of a hemoglobin molecule able to snap between its oxidised and non-oxidised states over the course of this entire year would be too difficult to attempt.  If each hemoglobin in your body was the size of a grain of rice, they would easily blanket the entire planet, two metres deep.  And I only want them to build me one, just one, and they can take all year, and use whatever materials they want!

So in summary, before you pay the rent or heating bill or fill up your jerry cans with petrol, buy this book: but be prepared to read it two or three times to have any chance of full comprehension!

About iain carstairs

I have a great interest in both scientific advances and the beauty of religion, and created www.scienceandreligion.com about 15 years ago with the aim of finding common ground between the scientist and the believer, and to encourage debate between the two sides.
This entry was posted in Antibodies, Authors, Biology, Books, Clathrin, David S Goodsell, Human genome, Plasma cell, The Machinery of Life and tagged , , , , . Bookmark the permalink.

19 Responses to A Meditation on the Machinery of Life

  1. Nandakumar says:

    Wow,It is mind boggling!! am especially intrigued by the shape of the protein and the way the geodesic structure is formed, it’s a spaceframe!…I wonder if the cells within the cells ‘think’ of themselves as individuals.

    • You should see the little motors – up to 100,000 RPM, and they can stop and reverse direction within one revolution. Some of the motors, like the viral DNA packaging motor, has a built in gearbox to avoid breaking the strands of DNA when too much tension builds up. Others pull in hydrogen ions into a revolving set of tubes, like a revolver barrel, which then turns flanges and operates a series of paddles which then weld together fuel molecules. The fuel molecules are so efficient that when used, and broken into the components again, they can be rebuilt with zero wastage.

      Not only that, if there is too much fuel, the rotors work backwards – pulling the fuel molecules into the flanges where they break apart again, rotate the flanges the other way with the released energy, and eject ions out the other side of the pump. There are trillions of these little motors (ATP synthase) working now in your body. And though there’s only about 10g of this fuel (Adenosine TriPhosphate) in your body at one time, each day they recycle your own full bodyweight in it!

      Can you imagine – an atomic scale device of 500,000 Daltons which senses electrical imbalances, and converts that to rotational energy, and then converts that to chemical fuel as stored energy, and works flawlessly backwards as well, converting chemical to rotational to electrical surplus? This is fabulous engineering. We can’t dream of making such devices. How about a car engine which could suck in exhaust fumes and produce petrol out the other end, while travelling backwards!

      The way muscles move is unbelievable – so intricate and so convoluted that if someone proposed it on paper, you could never imagine it actually working. It relies on huge towers of tiny motors all pulling at the same time. You want to get these things working in your cars I think!

  2. Nandakumar says:

    I agree Iain, the human body is the very definition of unity, and I think that we only have a surface understanding of what it is really capable of. I’ve always looked to nature for inspiration in my work, & have actually incorporated a lot of such ratios and numbers into my designs. Because I work in development (ie fixing design screw ups) I’ve seen first hand, what happens when you stray from or ignore fundamentals, which are actually expansions of nature’s guidelines.
    Since u mentioned cars, I’m actually working on a radically new peoples car right now, hopefully it’ll see the light of day soon 😦

  3. Nandakumar says:

    I do apologise for turning the topic away from biology,
    But it won’t be petrol but energy – it’s called Regenerative Braking. I’m trying to form a cluster of other component manufacturers to help me.The plan is for the car to be manufactured without the megabucks required for a current manufacturing plant.
    One of the other reasons I’m in Holland right now. Problem is it’s all so political and it feels like the steps I’m making are too small..I’m working on a proof of concept prototype at home.

  4. Hey, good luck – new things take time, don’t quit before you get it done

  5. Nandakumar says:

    Thanks, I love the new introduction, brilliant.

  6. Nandakumar says:

    I agree, much to the chagrin of my co-contractors, Have you thought about visiting Holland over the weekend?

  7. Nandakumar says:

    Sounds Interesting, I’m leaving on the 15th, I guess we’ll meet another time then.

    • For sure we will, and remember it’s a small planet. I thought of organising a Science and Religion conference and seeing who turns up. It would be a good chance to listen to all the people involved in writing, teaching, researching, or whatever, and let people mix and meet. I’d definitely want the atheists represented, because people need to understand all the kinds of personalities involved, and there’s a lot to learn. We could have a religious forum where different religions see what they agree on. We could invite the Dalai Lama, David Goodsell, Rupert Sheldrake, even Richard Dawkins. We could invite anyone who has something to say, and just see what happens.

      This year it’s our book “Natural Intelligence”, the painting exhibition “Oil and Water” for 3rd world water charities, the database on mystical experience, the blog of course, and getting a hemoglobin molecule built. If there’s any interest, let’s start thinking about this for 2013. We could call it “Celebrating the Failure of the Aztec Calendar” or something. I’d like to hold it in London, as it would be easier for me to organise and check out the venue etc, and perhaps we could get a special deal on hotels and so on. We could do a tshirt along the lines of the 2012 Olympic logo. They’re bound to have loads left over!

      Actually I saw them prepping the Horseguards Parade last weekend, for the Beach Volleyball tournament. I don’t think they’ll bother with a scoreboard

      • Nandakumar says:

        I just saw a pic that said ” If the Spanish hadn’t wiped out the Mayans, they might’ve finished the calendar” well something like that anyway.
        Yes it’s a small planet and it gets smaller everyday. The conference is a great idea, we could get the ICR involved and lots of other people too. 2012 is going to be a busy year with lots to do but we should definitely work towards it…

  8. Thank you for a great review and post! This is actually one of the points that I try to impress upon my students. Whenever they se a diagram in a biology book, it is a safe bet that is is VERY simplified… I now want to get the book!!!!! (:-)…..

    • Funnily enough, a couple of weeks ago I was at a parent-teacher evening with my 14 year old daughter, and when talking to her biology teacher I started enthusing about this book. He reacted with excitement and before long we were swapping “incredible molecule facts” the way kids might rave over rock bands. Olivia was shaking her head in despair, as if we were beyond salvation! He and I just looked at each other and sighed.

      David Goodsell proved to be very helpful as well; I have been trying to interest someone in making a working hemoglobin molecule but nobody wants to take on the task, even though the design is alredy known; it is thought that assembling it would be too difficult. David kindly recommended a colleague of his who turned out to be very switched on and competent. So it seems if you want to get something done, ask a busy person!

  9. I’ve had Goodsell’s “Machinery of Life” on my wishlist ever since reading this post, and it just arrived today. What a beautiful book! Looking forward to diving in.

    • “..For he will surely find, worlds within worlds!”

      • About 3/4 the way through Machinery of Life. Wow! Many of the things here are in my undergrad Biology textbook, but Goodsell’s explanations and brilliant illustrations (down to the atomic “shapes”) take it to a whole new level. Also, the part about ubiquitin ‘marking’ proteins for destruction gave me an idea for solving a problem in a fiction story. Great recommendation, Iain.

      • That book is a real groundbreaker! Actually David Goodsell is a great artist to work with as well. He agreed to do a painting of some hematology related imagery for me some years back for a laboratory named after my late father, in Toronto, and it was a joy working with him. The result was spectacular and I only wish I had a regular stream of such projects!

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