“I’ve seen things you people wouldn’t believe,” the dying replicant Roy says of his off-world experiences in one of the final scenes of BladeRunner. As a structural biologist I often feel I could say the same thing, all the more so now that I have read David Goodsell’s “The Machinery of Life”.
This is a wonderful book that gives fascinating and wide-ranging insights into the molecular components that work together to give us and other organisms the gift of life. The text is clear, accessible and provides a good lay introduction to biology at the molecular level inside and outside the cell. But what makes this book special are the pictures. They are sumptuous.
Wide and close-up views of molecular crowding within a bacterial cell. The blue molecules are protein enzymes. Water molecules (cyan) appear almost triangular. (No place here for homeopathic ‘memory’).
Goodsell, a structural biologist at the Scripps Research Institute in California, has set himself the task of providing a realistic representation of the molecular landscapes within living organisms, a vista that is beneath our everyday sight because of the extremely small size of the components. He has fused his scientific and artistic abilities to generate the stunning images that are generously scattered throughout his book. In every case he has drawn on the latest research (the 2nd edition that I read was published in 2009 and is a significant update of the 1993 original) and endeavoured to render the molecules of life with the appropriate shape, size and number in the various compartments of living organisms — the nuclear and cytoplasmic environments within cells and the blood and tissue fluids that surround them. He has been careful to use the same scale throughout for these intracellular and extracellular panoramas so that the images in the book can be compared.
When it comes to molecular structure, I’m a pro. I spend my days peering at the byzantine architecture of proteins and RNA. I know my amino acids from my nucleic acids, my main-chains from my side-chains and can tell at a glance if molecular interactions are hydrophobic or hydrogen bonded. But my focus is usually mechanistic and tied to one or two molecules at a time. How does this protease work? How does that fatty acid molecule stick to albumin (shown below). But even if my stated ambition is to take a holistic view of biology, the day job too often reduces me to, well, a reductionist.
Human serum albumin (HSA) with a cargo of fatty acid molecules (yellow). The protein colours indicate the three similar domains within the protein. From the crystal structure.
That is no bad thing when you are trying to figure out a mechanism, to pull apart the nuts and the bolts to see how the molecule actually works. But I have to remind myself every now and then to climb out of the tunnels dug into the details of the handful of molecules that my group investigates to have a look around at the wider picture. With Goodsell’s book on my shelf that will now be a lot easier. The views that he offers are beautiful, amazing and mind-bogglingly complex; they offer the best picture we have of the molecular context of the biochemistry of life.
I spent quite some time just poring over the pictures in this book, absorbing the detail. I am glad that Goodsell decided to label his images only very sparsely, so that the view of the crowded cell is not cluttered with artificial words. The variety is wonderful. I gazed at the innards of cell nuclei, the fibres of muscle cells, the synaptic connections between nerve cells, the seemingly innocuous scene of poliovirus penetrating and killing a cell. Strangely, the detail is almost unnerving. I know I biology works, but how can all those molecules possibly manage to find one another and work together in such fantastically complicated environments!?!
Childishly, the experience reminded me of losing myself in the lovingly detailed illustrations in Richard Scarry’s Busytown books. Remember those? I hope that the charm and richly colourful detail of the Goodsell’s pictures might ensnare the non-specialist reader in the wonders of molecular biology.
A human B cell releases a packet (green) of antibody molecules (tan, Y-shaped) into the blood serum on the right of the image. HSA molecules appear as pale green triangles in the serum.
If I were overly artistic in my pretensions I would say that Goodsell is exploring the space between science and the imagination with his illustrations. But I am plainer speaking and contend that there is no space between them–the overlap is too great. Goodsell’s artistic book is simply a wonderful exemplar of the power of scientific imagination.
Though he has worked hard to root his images in established facts, Goodsell is careful to acknowledge their limitations. The structures of many molecules are still only vaguely known and our knowledge of the concentrations and cellular distributions of others is incomplete. So there is some risk in presenting these images since pictures can have a power beyond words. But I am quite happy to live with that and am grateful to Goodsell for his vision and industry.
Goodsell has generously made his illustrations available for anyone wishing to them in personal presentations. Posters and some funky looking models can be purchased here.
I’ve always liked the interface of science and art, and these are indeed beautiful illustrations. A tradition, I suppose, that one can trace back to Leonardo da Vinci. My own artistic pretensions are much more modest, being limited to false-colouring electron micrographs in Photoshop. This may be no more than the elementary colouring in we did as children, but the results can be very gratifying.
Yes Stephen, I guess structural biology and microscopy provide plenty of opportunities to unleash the artist within! When I have the time, I do enjoy preparing images and animations for talks and a papers. What I admire about Goodsell’s work is that he has taken molecular illustration to the next level to set things in context.
This sounds like a book I should read/look at. I’m familiar with some of David Goodsell’s work from the his fantastic “Molecule of the Month” series on the PDB homepage, which I’m sure you’re aware of.
As a follow-up to both the Stephens’ comments – illustrating our work as structural biologists (I’m counting myself in this as an MRes student) would appear to be very important, both in understanding our work and presenting it to others. Yet, my experience of creating figures and diagrams seems to suggest this is a skill that is learned “on the job”, as and when producing a figure is required. It also seems to be one which is quite hard to get “right” regarding colour choices, label placement, sizing and a whole host of other choices.
My question is: to what extent should proficiency in creating and understanding aesthetically pleasing figures be a core part of an education in biochemistry, structural biology and related fields? Or is it in some places, and I’ve just missed out?
James – there is no better place to learn than on the job, especially when it comes to grappling with the intricacies of molecular graphics software such as PyMOL (my package du choix).
But there is a certain about of preparatory work one can do to prepare, such as gaining an appreciation of what works in terms of viewpoint, depth-cueing and colour choices (e.g. what colours complement one another; making sure to use a consistent colour scheme in a talk or paper). Decisions on these may depend on the method of output: paper, computer screen, projector. You will no doubt come across examples of good and bad practice in attending seminars or reading the literature. See what you think works well and make mental notes!
If you’re interested, I have some general and specific pointers here.
Stephen – I agree with you about on the job learning, and I am still in the process of doing the same with molecular graphics software (although USCF Chimera is my current weapon of choice).
The point I was making is that many UG and PG courses include some training on creating and delivering presentations and on writing. These courses give a foundation, because on-the-job training is best. Should figure-making join these perennial favorites, teaching the basics – over-labelling vs. under-labelling, colour choices and technical things such as output resolution, contrast, etc for printing compared to projecting.
Sorry for drifting so far from the original topic. Thanks for the link – bookmarked for future use, and thanks for introducing me to the book – looks like a fitting candidate to spend my poster-prize book vouchers on!
I was given this book by a friend and I love it; I just wish she would now give it back to me!
I think these ‘sumptuous’ artistic representations of biology are fantastic, it’s one of the reasons why I’ve always liked the commitment of the journal ‘Cell’ to scientific artwork (in fact the person who gave me the book was responsible for this lino-cut print that made Cell’s front cover).
oh, and he is ok with people using his pictures ! those are great. thanks Stephen for linking and showing them!
hm, half my comment went away.
What I did say was “oh, and he is ok with people using his pictures! They are great. Thanks Stephen for linking and having them up here (and no _attack ships on fire_ so far…. but maybe if I take a closer look at those outside the cell pictures? 😉 )
James – certainly think for anyone working at PG level, some training in the visual presentation of information would be very useful. Not sure where I stand with regard to UGs — there is an easy temptation to keep adding more to the curriculum, though a skill with figures could be seen as transferable.
Thanks for the link to that Cell cover Jim – that’s a really nice example. Like your friend, Goodsell has the good fortune to be artistically talented (his molecular landscapes are watercolours) as well as scientific.
Did you not see the attack ships, Åsa? 😉 You need to check out Figure 8.2.