Regular readers will know that molecules are my thing, that my scientific endeavours are devoted to revealing the intricate architecture of proteins — the molecular machines that sustain life.
They will also know that I have at times struggled with the problem of how to write about molecules in a way that might grab the attention of those who rarely think about them. I have tried variously reporting on our own results, or telling stories that link molecules to history or to some of the bizarre claims of alternative medicine.
In each case I have used words and pictures — and, very occasionally, video. But none of my attempts at video come anywhere close to the films made by Drew Berry.
Berry, a legend in the world of animation, has pioneered the use of 3D animation to try to give a real feeling for the molecular action hidden inside ourselves. To get a sense of what he has achieved, please take a look this recent TED talk in which he showcased some of his work.
Inspired by the molecular artistry of David Goodsell (about whom I have written before), Berry has not only added the dimension of time to our view of our cellular machinery, but brought a truly cinematic vision to it as well. Even those of us who are immersed daily in the world of the atom and the molecule struggled to imagine how they all work together. Berry’s work relieves us of that burden and is a compelling revelation.
P.S. For more examples of Berry’s work (and that of other animators), check out MolecularMovies.Org
I am chewing my own fingers off at this point—because for the past two months I have been working with professional animators to create mode of action films… if you happen to go to a rather large oncology conference next summer you’re likely to see a certain major pharmaceutical company displaying our work.
Ooh – I’m not likely to attend any large oncology conferences this year. Any chance this opus might be released on the Internet?
Possibly. Depends on what the client does with it subsequently.
Fabulous. Thanks for showing this, Stephen.
Also – those dyneins are cute. I want one as a pet.
You already have some…
Wow.
Thanks for pointing me in the direction of this awesome seven minutes.
Would evolution have come out the same if Darwin had watched this film first I wonder?
Um, yes?
With the speed of Drew Berry’s delivery and the sheer beauty of the middle section of his film I was too stunned to put any cohesive thoughts into words – pictures are definitely my thing.
But my question really is this:
Darwin thought inheritance was blending. His non particulate gemmules flowed seemlessly in whatever fluid. – In this, he was in analogue mode, and in that there can be no gaps – hence the lines between species in his famous tree doodle.
Drew Berry’s computer presentation is a digital happenning – pixel at a time. – His illustration of the mechanics of cell replication seems equally digital.
When one cell has formed two, there is a gap between them. There seems a bigger gap between my cat and my dog. Somewhere way back down in gentics though, it is surely assumed that an ancestral cell of both contained a shared strand of DNA, and that in some far gone moment of ‘faulty’ cell replication, the ancestors of dogs set of marching down different steps to cats. (Though both my cat and my dog deny that either is faulty.)
My point is this. – Is life, at a molecular level, analogue or digital? – If digital – as two individual cells seem to be – with a gap between them – then the gap formed between two proto quadruped ancestors of cat and dog, in one ancestral cell’s replication, simply got to be a bigger gap. That’s why we have cats and dogs.
If molecular life is digital, then surely we can expect spiecies and speciation to be digital – with gaps.
Darwin’s evolution has no gaps because it has only the one mechanism of natural selection, which dissallows gaps. (Evolution still puts lines to Darwin’s tree.) But the fossil record has gaps – as big now as when Hugh Falconer argued the toss with Darwin way back in the 1860’s.
If life proceeds, at all levels, as digitally as Drew Berry’s dyniens, gaily marching in digital steps, then a second natural mechanism would be handy to both make for and leap the gaps in evolution.
Can we imagine how Darwin or Mendel or Hugo de Vries, living now would feel if they could – as easily as I have done – just click on a mouse button to see in animated beautiful full colour detail what they struggled for decades to imagine and understand.
Would Darwin have come to the same conclusions if the world was as digital then as it is now.
Forty years ago, a chance observation gave me simple second natural mechanism to evolution which science seems to have missed. I have been trying to write the book ever since.
Rpj might be interested to know that I suffer permanent writers block. Though I call it dyslexia. That’s why I’m a plumber – but I am a farmer too and bricklaying and drystone wall laying are in the skills set. – Bricklayers don’t get bricklayer’s block because bricks are boringly consitently the same, the skill is in mindless repetition. – Random drystone walling is a different matter – one minute it flows – the next it comes to full stop – then only a determined feel for the right shaped stone, and the conviction to get on and lay it, sets the job flowing again. Just imagine how boring life would have been if all genes were the same shape like bricks. Random walling is much more fun.
I would be most grateful to Stephen and rpg – and anyone else – if they would put their science to criticising my plumber’s views of evolution.
Frantically busy day — will try to respond later tonight.
Thanks for the comment. OK, I’m most definitely not an evolutionary biologist, but here goes. Though I only have time to pick up on a few points.
First, I don’t think it’s quite right to say that Darwin thought of inheritance as blending. If I remember correctly he realised that a blending mechanism of inheritance would soon lead to uniformity, the loss of the differences that are the very stuff of natural selection.
It’s certainly true that he didn’t have a clear idea of the mechanism of inheritance — his gemmules weren’t so very well defined. But everything we have learned about the molecular basis of inheritance since Darwin — DNA, mutations rates etc — tends to confirm his theory.
Is life analogue or digital? I suspect that’s a false dichotomy. It can certainly be regarded as digital. Perhaps the fundamental ‘bit’ is the nucleotide base of DNA, which can take one of only four values — A, C, G or T. However, that’s a very, very small unit so the ‘abrupt’ changes that one sees upon mutation, such as the alteration of a single base, in most cases have a very mild effect. Looked at this way, one doesn’t need to worry about gaps and the idea of smooth transitions holds up. Biological systems are so complicated that even the loss of a whole protein (e.g. through a mutation that introduces a pre-mature stop codon) may not severely affect the carrier organism because there are sufficient ‘back-up’ systems.
For sure there are gaps in the fossil record, but the patchiness of this record is something that Darwin addressed head-on in Origin of Species: there are simply too few environments in which fossils are likely to last.
Thank you for thoughtful reply. – Valuing your time, I will not respond to it directly until I have been equally thoughtful as to exactly how – but there are one or two things you say that give me optimism that my thinking is on the right lines.
The following is just brief overview of the way I think..
As evolution seems be the fundamental way life works, and that our future existence may rely entirely on pleasing its dictates, it seems a shame that science treats it in some ways as a poor releative. We build large hadron colliiders, whilst species go extinct at an alarming rate and we can only guess at the outcome, because there are few if any Laws of evolution to tell us what might happen. – At the same time though, atomic structure must have a large part to play in life’s evolutionary workings.
I can study evolution theory, as I have done for the last forty years, in effect by simply thinking, because Evolution is merely a mental construct we overlay on life’s reality, in order to explain its quirks. However, studying atomic structure, with the neccessary technical equipment, as you do, you ‘touch’ the nuts and bolts of practical reality.
If current evolution theory is correct, its overlayed theoretical pattern should absolutely and exacly match the actions of the real nuts and bolts. As to whether it does or not is expessed admirably in your words, ‘tends to confirm his theory,’ – That is about the state of play.
And the theory should surely match reality at all levels – molecular – organism and species. And there are a few more besides.
Drew Berry’s little ‘pets’, marching up and down, beautifully match cats and dogs – or any other. organism – but they are surely digital. – Darwinian evolution’s dogma of continual change is surely analogue.
At present there are 25 or so separate definitions of species – this does not inspire confidence that evoution is done and dusted. (Type ‘species’ into wikipedia if it comes back out of the dark, to see what you think.)
The problem arises because evolution theory sways beteen the digital nature of particulate genetic’s, the digital nature of individual organisms, and the digital nature of individually named ‘species’ – vying with the analogue nature of Cladistics and an evolution theory which has only one mechanism, Natural Selection, which provides analogue speciation in continual ‘joined-up’ change and dissallows gaps. Natura non saltum.
Forty years ago I found a scond mechanism which on rare occasion and in very special circumstance both makes for gaps and allows leaps across gaps but occurs excepionally rarely at species level. – It might be the only mechanimsm at molecular level. (To be honest it might be the only mechanism at any level but that requires a new concept of ‘change’ – we don’t want to go there really but – if all the universe is change – as per Einstein – then how do we identify A change.)
(And brief seems to have gone out of the window – you should not have encouraged me)
So – is my mechanism the only mechanism at molecular level? – My knowledge of genetics is, modestly, somewhat above elementary – but not until seeing Drew Berry’s presentation did I realise just how well well my little pet theory matches what is going on there – and how well the whole thing falls into place when two mechanisms – Darwin’s and mine are working in conjunction. – in the same way that Newtonian physics slots in with quantum theory – along with wave particle duality.
Have a quick look at your hand – now ask yourself how, out of all the atoms in all the universe did these few come to be your hand – and now they are your hand how, and why, do they stay that way just for a while – a relatively short while?. That is the question evolution must answer for science to have a true place in the world.
Sorry for being slow to reply. Busy week. But you’re also losing me, I’m afraid. To address some of the problems I see in you’re response.
I disagree. The LHC has had plenty of headlines in recent years but there has been a ton of work on evolution since Darwin. It is by no means a poor relative.
You can go so far with thought alone but it needs to lead to predictions that can be tested by experiments or directed observations. And again, your distinction between thinking about evolution and studying atomic structure is artificial. No-one has ever ‘touched’ the inside of an atom in the way that you say.
If what you mean is that different fields of science should be consistent with one another, then yes I pretty much agree, though physicists are still having trouble marrying up gravity with other fundamental forces. No-one is claiming that science is complete.
Lots of problems here. Bear in mind that Berry’s video is based on our current understanding of molecular life. But it is still to some degree a work of the imagination. His dynein ‘pets’ (as you put it) are emphatically not like cats or dogs. And neither are they strictly digital (in fact I;m not even sure what you mean by this). They are particulate (i.e. you can count them) and so might seem ‘digital’, but their numbers are large – and hence, due to concentration effects, they can act in concert in an analogue fashion. But I don’t want to get into any further details here since the analogue/digital analogy doesn’t apply in any meaningful sense that I can see.
Did you mean “Natura non facit saltum”? I find it best to stick to English (the title graphic of OT notwithstanding – not my idea, though I did insist on a transition). “Nature makes no leap”. An interesting assertion but I’d rather discuss evidence. Again, I don’t see things in terms of an analgue/digital divide. For sure there are many remaining gaps in the fossil record. But Darwin himself addressed this in ‘On the Origin of Species’ – it is quite hard for many dead trees and animals to be preserved for long periods of time. But the more we look, the narrower those gaps get.
I’d encourage you to publish your ideas so they can be critiqued.
I’d be wary of putting too much weight on an animation. It is a useful tool to try to make a representation of our theories. But images, especially moving ones, are very powerful. Which means that if they are wrong, they can mis-lead.
Evolution has already answered that question as far as I understand.
I am more than grateful for you response.
“But you’re also losing me.” “I’d encourage you to publish your ideas so they can be critiqued.”
The gap between these two is considerable.
I see things clearly in pictures then struggle to put the pictures in to words.
Looking back at my words written on your page I can see clearly why you soon became lost. – Full marks for your stalwart efforts to decipher my ramblings.
Your efforts deserve my most considered reply and that will take a little time.
In the meantime you encouragement might be valued at the end of the pier show.
Thanks so much for your stimulating feedback.
John Somerwill