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Drew Berry: Animations of unseeable biology - Comments

Vorlund's Avatar Comment 1 by Vorlund

Astonishing watching the dyneins marching along the microtubules.

Fri, 13 Jan 2012 08:36:29 UTC | #907853

Pete H's Avatar Comment 2 by Pete H

I would like to show my kids the full length feature movie of this.

Why can't the likes of Spielberg and Peter Jackson turn their special 3D effects talents to this project. If they can bring Tintin to life then maybe they could use similar CGI technology to bring life to life.

Fri, 13 Jan 2012 09:43:50 UTC | #907862

Paul42's Avatar Comment 3 by Paul42

Wow, just wow...

That's made my morning.

Thank you!

Love.

Fri, 13 Jan 2012 10:21:53 UTC | #907871

SaganTheCat's Avatar Comment 4 by SaganTheCat

beautiful

Fri, 13 Jan 2012 11:24:33 UTC | #907881

Crazycharlie's Avatar Comment 5 by Crazycharlie

Absolutely amazing! I've often hoped someone would show, in a better way, how the mechanics of the cell work. Wonderful! If scientists want the world to understand their work better, this is the way. Humans are VISUAL, as well as thinking animals.

This video is going in my favorites and staying there.

Fri, 13 Jan 2012 11:39:44 UTC | #907882

PY's Avatar Comment 6 by PY

Outstanding

Fri, 13 Jan 2012 12:27:09 UTC | #907893

peter mayhew's Avatar Comment 7 by peter mayhew

Stunning isn't it? I always imagined proteins etc as little animals, but of course it's much more accurate to think of them as clockwork toys. And I guess that makes animals clockwork toys too.

Fri, 13 Jan 2012 12:32:53 UTC | #907895

SteveN's Avatar Comment 8 by SteveN

As a biologist who also likes to dabble in 3D graphics for presentations, articles etc I am always astounded by both the beauty of (and the effort required by) videos such as these. I do have one little quibble, however. The speaker kept stating that the animations were accurate representations of events at the molecular level. This is not quite true. Although the structures of the molecules are presumably accurate, their movement in the videos is made to look too intentional and purposeful. In reality, the dyneins walking along the microtubicle (for example) almost certainly happens in a 'three steps forward, two steps back' kind of way. Similarly, the molecules homing in like guided missiles to the DNA replication machinery does not really reflect reality. There will actually be thousands of the things all bumping around randomly and if one happens by chance to line up to its target in the right way, then it will bind and initiate an interaction.

I realise that for the sake of clarity it is better to keep things simple, but insisting that the animations are an accurate representation of reality unfortunately plays into the hands of the ID proponents. Ben Stein famously used a rip-off of a similar animation in 'Expelled' to show how complex and 'designed' the molecular machinery of the cell is: therefore God.

Fri, 13 Jan 2012 12:37:30 UTC | #907896

Steve Zara's Avatar Comment 9 by Steve Zara

comment 8 by SteveN

Although the structures of the molecules are presumably accurate, their movement in the videos is made to look too intentional and purposeful.

We should perhaps accept reality, which is that what happens in biology at molecular levels is simply impossible to represent in any realistic way.

The computer software pioneer Alan Kay, who has a history in molecular biology, explained things like this:

If you enlarged a typical protein molecule to the size of a small car, it would be racing around at three times the speed of light.

Any enlargement of molecules to the point where they are visible would mean that a realistic real-time representation is simply impossible. Although individual chemical reactions can be extremely fast, biochemical processes, which involve huge and complex molecules, are usually incredibly slow by comparison. If we scaled things up so that individual chemical reactions took seconds, then something like the building of a protein molecule by a ribosome would be barely noticeable even on a scale of centuries. If we tried to watch a protein being built in an animation, we would see nothing because of the incredible speed of motion and vibration of individual atoms.

What we are seeing in these animations is nothing like reality. Reality is far, far stranger.

Fri, 13 Jan 2012 13:08:12 UTC | #907901

bmaiden12's Avatar Comment 10 by bmaiden12

Absolutely incredible.

Fri, 13 Jan 2012 13:11:53 UTC | #907903

Chris Roberts's Avatar Comment 11 by Chris Roberts

Truly mindblowing.

Biology really is the most interesting thing that humans have ever discovered!

Fri, 13 Jan 2012 14:32:45 UTC | #907914

Red Dog's Avatar Comment 12 by Red Dog

That really was amazing. Its funny because my daughter is studying this in class right now and just yesterday was telling me how interesting she finds it, I'll share this with her.

In reply to:

Comment 8 by SteveN :

I realise that for the sake of clarity it is better to keep things simple, but insisting that the animations are an accurate representation of reality unfortunately plays into the hands of the ID proponents. Ben Stein famously used a rip-off of a similar animation in 'Expelled' to show how complex and 'designed' the molecular machinery of the cell is: therefore God.

IMO, we can't start playing those games. Ignorant people are going to distort science no matter what, its a waste of time to worry "if I present it this way then X will distort it like this..." Go for the most accurate representation and understanding and don't waste energy worrying about how people may mis-use it.

Fri, 13 Jan 2012 15:51:04 UTC | #907932

Neodarwinian's Avatar Comment 13 by Neodarwinian

I had good animations at an associated web site when I took first semester biology and it is a great help in conceptualizing and actually " being " part of the process. Sometimes I am told, " biology is all memorization " and this could not be further from the truth, especially in molecular cell biology. You have to see it and be it to learn it because you can not memorize these complex processes very well.

Fri, 13 Jan 2012 22:20:10 UTC | #908038

SteveN's Avatar Comment 14 by SteveN

Comment 12 by Red Dog :

IMO, we can't start playing those games. Ignorant people are going to distort science no matter what, its a waste of time to worry "if I present it this way then X will distort it like this..." Go for the most accurate representation and understanding and don't waste energy worrying about how people may mis-use it.

It's not the animation that I have a problem with. It was the speaker's repeated insistence that it was a true representation of reality. As Steve Zara pointed out, what we are seeing in the animations is nothing close to reality. They are extremely useful for education and for inducing awe in biological processes (which are awesome, of course), but I would personally prefer to see a little more objectivity from the speaker.

Fri, 13 Jan 2012 22:39:50 UTC | #908042

QuestioningKat's Avatar Comment 15 by QuestioningKat

A M A Z I N G !

I want to see more. I can see these being turned into stories for kids.

Sat, 14 Jan 2012 01:10:14 UTC | #908080

huzonfurst's Avatar Comment 16 by huzonfurst

Incredible work! I had no idea this kind of thing was out there. 3D is the next step!

Sat, 14 Jan 2012 03:35:05 UTC | #908110

Quine's Avatar Comment 17 by Quine

The value I see in these is that they can communicate decades of research results in just a few minutes. That is a big speed up for the education process. Yes, you then have to go in and spend time explaining how the simplification is not quite what is going on, but that is still faster, and lets you decide what level of zoom-in is appropriate for the given context. You have to explain that the inside of a cell is not full of air or empty space, but full of water and ions and a vast array of small to medium molecules that are not shown because that would hide the large molecules you want to watch. Then you have to explain that all these not shown molecules are in very rapid (at body temp.) Brownian motion that cause them to continually crash into the molecules that you are watching, and imparting random motion to them. Molecules don't just jip over to a hole in the membrane they are "supposed" to go through, they have to bounce around until they happen to bang through (known as the narrow escape problem).

Likewise, kinesin molecules don't have knees or leg muscles and don't really "walk" using gravity (as much as the Intelligent Design idiots will try to describe it that way). However, in a system where every lose molecule is flying all over in Brownian motion, you can get simple directional transport if you have any means that makes it harder to move backward, because then forward is for free. You don't get that from an animation that leaves out all the jiggling (beloved of Feynman), but if you could see that jiggling, you would understand how much, much, simpler (but slower and less efficient) means could have been there doing the job long ago in Evolution, i.e. no Irrefutable Perplexity.

Sat, 14 Jan 2012 08:56:52 UTC | #908139

SteveN's Avatar Comment 18 by SteveN

Comment 17 by Quine :

Likewise, kinesin molecules don't have knees or leg muscles and don't really "walk" using gravity (as much as the Intelligent Design idiots will try to describe it that way). However, in a system where every lose molecule is flying all over in Brownian motion, you can get simple directional transport if you have any means that makes it harder to move backward, because then forward is for free. You don't get that from an animation that leaves out all the jiggling (beloved of Feynman), but if you could see that jiggling, you would understand how much, much, simpler (but slower and less efficient) means could have been there doing the job long ago in Evolution, i.e. no Irrefutable Perplexity.

Precisely.

Sat, 14 Jan 2012 09:04:40 UTC | #908143

PERSON's Avatar Comment 19 by PERSON

For those with broadband, there's what looks like a higher resolution version (61MB) at the TED page.

Sat, 14 Jan 2012 18:09:50 UTC | #908272

drew_berry's Avatar Comment 20 by drew_berry

Hi, I am drew berry, the presenter and animator. Thanks for all your feedback and comments. Really appreciated.

I did want to respond (and actually concur with) SteveN's comments about the 'accuracy' of my visualizations. Yes, I should avoid overstating how accurately I have depicted the reality of the molecular world. It is vastly messier, random and crowded, and it's physical nature is unimaginably alien to our normal perception of the world around us. That said, my work is not intended to be a lab-bench-calculated model for research use, it is an impressionistic, artist-generated crude sketch of phenomena and structures science is measuring and discovering at the molecular scale (which is why I begin with Galileo's water colours and Darwin's notebook sketch as reference points). Now that I have put my work in it's place, I would then assert that the animations are firmly founded on real data and are as accurate as I can possibly make them, while making them watchable and interpretable to a human audience. By far the largest portion of my time is spent conducting broad ranging literature reviews of the topic I am working on, gathering the fragments of data scattered throughout the journals, and holistically reconstructing what we currently know and do not know. Wherever data and models are available, I incorporate them directly into the construction of the animation, including molecular structures, dynamics simulations, speed measurements, and so on. My work is most akin to 'review' paper in the literature, presented in visual form.

The goal of my work is to show non-experts – the general public aged 4 to 99, students of biology, journalists and politicians, and so on – what is being discovered in biology, in a format that is accessible, meaningful, and engaging. I hope that my work provides some sense of what biologists and medical researchers are discovering and thinking about, to provide the public with a framework of understanding to discuss these important new discoveries and the impact it will have on us as a society as we head into the future.

In regard to Dynein's walking, it actually is quite directional. They can only walk in one direction along the microtubule (which have a polarity in their physical structure). Dynein can take 8nm, 16nm and 32nm steps, which is where it locks its 'feet' onto the microtubule. The critique I would level at my representation of Dynein is that the legs flail around much more and that the 'steps' are not so regularly timed. It is also much quicker in it's directional movement along the microtubule... I could go on if that is of interest to you. I could also discuss Kinesin (the yellow-orange guys heading the other way) and the kinesin-14 (the long light blue kinesins cross-linking the microtubules). This is all from my vague recollection of the literature review I did mid-2010 for that piece.

The DNA replisome (the replication machine) is one I am particularly proud of as it brought together very fragmentary data and 'accurately' represented our level of understanding mid-2002 when it was created. I deliberately left many out proteins that we knew about and opened-up the whole structure so that students would be able to examine the mechanisms in action.

I know the dozen or so people who are at the top of the game at creating biomedical animations (most have a PhD scientific background) and we all struggle with the problem of having a molecule arrive at a particular location from the thick molecular soup of the cytoplasm and not look directed. Part of the problem is that we strip away most of the surrounding molecules to make this stuff visible. I can make the molecule wander around in a brownian type manner, but for story telling and visual explanations, I need it to get to a certain point and do it's thing at a certain time to move the story along. This can make it look determined and directed. This is a problem I work on and try new approaches to solve with every new piece. I think we will develop/find a resolution or technique that will solve this problem that is acceptable to most at some point. Just one of the many fun challenges of doing this work.

Sun, 15 Jan 2012 01:31:03 UTC | #908389

Quine's Avatar Comment 21 by Quine

Re Comment 20 by drew_berry,

Thanks for your clarification, Drew. I recommended this piece for discussion here, because it really does have so much value in spite of the unavoidable simplifications. I hope you understood that my comments were not criticisms, but more in line with what can be explained further from here.

Again, truly great work!

P.S. Also remember we have had the animations from Harvard misused by the Intelligent Design idiots, so there is some residual sensitivity.

Sun, 15 Jan 2012 01:52:39 UTC | #908392

phil rimmer's Avatar Comment 22 by phil rimmer

Good work, Drew. I found it quite enthralling.

I think you can animate the problems of seeing what is going on just as you have described them here. Animate the clearing away of the obscuring molecules, identifying them in turn, to finally reveal the thing you want to show, then put them back afterwards as a reminder. Show a blur of brownian movement, then slow it down to a visible randomness then remove the random component to reveal the net effect. The Dynein walking can likewise can be shown erratically moving and net effect moving subsequently.

Reminders of these still non too visible realities may hover around as a smear of ghosting around the very solid "net effect" images for some of the time until the idea is grasped.

What you've just explained here about the basic realities of these molecular processes is just as interesting in its way to the novice as the more recent discoveries you focus on. Finding a visual (cinematic!) language for these unviewable things is the key and what you have made great progress in already.

Sun, 15 Jan 2012 02:10:18 UTC | #908397

SteveN's Avatar Comment 23 by SteveN

Thanks for the clarification, Drew. I realise that "showing it like it really is" would just make it a big confusing mess and would defeat the whole point of the animation. It was just your statements about realism that set off some alarm bells for me.

I would also like to say that I am a huge admirer of your work and the similar works of others. I mentioned earlier that I dabble in 3D modelling of biological systems (using Blender) and have even had a picture (a 3D representation of HIV) used on a book cover. Having some hint of an idea of how difficult this is, I am therefore completely gobsmacked by the beauty, ingenuity and quality of works such as yours. As others have pointed out, their value in the education arena is probably enormous. I can imagine that seeing your animations during a high school biology class would inspire many to consider a career in the field. I look forward to seeing more of your work in the future.

Sun, 15 Jan 2012 08:04:15 UTC | #908469

drew_berry's Avatar Comment 24 by drew_berry

Thanks again for the critiques and comments. All of what you have raised are valid concerns and ongoing challenges.

There is one project that I did solve the problem of creating random, brownian motion not look directed: My Apoptosis and Signal Transduction.

YouTube video:

http://tinyurl.com/apopSignal

This was an exploration of what a signal transduction would 'look like' if you were to follow the chain of molecular events along a pathway. I published that animation in Science Journal's STKE ( (Molecular Animation of Cell Death Mediated by the Fas Pathway, Sci. STKE 2007 (380).

The technique I used to make it work was difficult and very slow to pull off. The whole 4 min sequence took me around 12 months to research, construct and generate the imagery. I think visually it is my most successful piece at showing the mechanisms that emerge from randomly wandering, cytoplasmic molecules and membrane bound receptors.

Mon, 16 Jan 2012 01:59:46 UTC | #908735

Quine's Avatar Comment 25 by Quine

Wow! That, Drew, was beautiful!

Mon, 16 Jan 2012 02:08:08 UTC | #908737

Steve Zara's Avatar Comment 26 by Steve Zara

Comment 24 by drew_berry

There is one project that I did solve the problem of creating random, brownian motion not look directed: My Apoptosis and Signal Transduction.

That is simply stunning.

It does show quite an amazing perspective on the nature of life on Earth. From that perspective, we multi-cellular organisms are nothing much compared to the phenomenal complexity inside the cell.

Mon, 16 Jan 2012 02:17:42 UTC | #908739

Steve Zara's Avatar Comment 27 by Steve Zara

I wonder if the moderators would add Drew Berry's Apoptosis video to the News list? It certainly deserves promotion equal to that given to the video in article above this thread.

Mon, 16 Jan 2012 02:58:08 UTC | #908742

Sample's Avatar Comment 28 by Sample

Rewatched and shared the apoptosis animation. Very, very nice. Congratulations and thank you!

Mike

Mon, 16 Jan 2012 03:16:21 UTC | #908747

SteveN's Avatar Comment 29 by SteveN

Comment 24 by drew_berry :

There is one project that I did solve the problem of creating random, brownian motion not look directed: My Apoptosis and Signal Transduction.

Words fail me. That was simply superb. The major thrust of my lab happens to be the induction of virus-specific cytotoxic T-cells, and I will never again look at the apparently static assay plates without visualising the franctic activity actually going on in there at the molecular level. Thank you.

Mon, 16 Jan 2012 06:38:36 UTC | #908778

phil rimmer's Avatar Comment 30 by phil rimmer

"Apoptosis" is indeed quite superb and I second Steve Zara's suggestion to have it in the News list.

The representation of Brownian motion was nicely judged, balancing realism of effect with readability. The imaginative sound helped enormously as a process label and came into its own with the different scales.

Mon, 16 Jan 2012 09:28:44 UTC | #908796