Comments on: The beauty of Molecular, Cell, and Microbiology

The beauty of Molecular, Cell, and Microbiology

Blasdelb — Sat, 25 Sep 2010 16:34:40 -0800

There has been a new discipline developing in molecular biology for some time now, Bioanimation! Projects have ranged in size from WEHI's colossal compilation to Harvard Biovision's magnum opus "Inner Life of the Cell" to commercially produced masterpieces to smaller projects by university PIs and enthusiasts. much

Biomedical Animators Drew Berry and Etsuko Uno are supported by WEHI as they create their marvelous films:

An explanation of the DNA replication complex found in Escherichia coli

An explanation of how DNA is packed into chromosomes

A demonstration of bacterial transcription; showing the initiation, elongation and termination of a novel messenger RNA strand (Yellow)

A demonstration of eukaryotic translation showing a ribosome (Blue/Purple) binding to a messenger RNA strand (Yellow) and producing a protein, in this case globin (Red), using transfer RNA (Green)

A demonstration of how a single amino acid change (Green) can produce sickle cell anemia by causing hemoglobin (Red) to polymerize.

An explanation of the malarial life cycle in the human host (Part 2 in the mosquito host)

An explanation of how Clonal Selection was discovered and is used by the adaptive immune system to fight infection

An explanation of how Colony Stimulating Factor helps to activate the adaptive immune system

A demonstration of restriction enzyme EcoRI binding to plasmid DNA, diffusing along the double helix, and finding its palindromic binding sequence before cutting. A piece of DNA then binds to the plasmid and is ligated

A demonstration of a signaling pathway which leads to apoptosis

An explanation of healthy insulin production and the molecular cause of Type 1 diabetes Previously David Bolinsky and his colleagues at Harvard Biovisions have been working slowly, but producing amazing work:

A new sequel to "The Inner Life of the Cell" looking closely at the mitochondria

A 2d animation detailing Leukocyte extravasation shown in "The Inner Life of the Cell" Previously, Previouslier, Previousliest Hybrid Medical commercially produces its films:

Gorgeous promotional reel

An explanation of the use of folic acid in nucleotide metabolism (sponsored by Eli Lilly)

An explanation of the Pathophysiology of Crohn's disease (sponsored by HUMIRA)

An brief explanation of compliment mediated immunity(sponsored by Biothera)

An explanation of how intestinal micelles contribute to blood cholesterol (Sponsored by Merck & Schering-Plough Pharmaceuticals)

A demonstration of influenza infection

A demonstration of the stages of mitosis

A demonstration of T4 binding

A video demonstrating Streptococcus pneumoniae growth

The beating heart with blood flow Gaël McGill at his company digizyme has also been making beautiful films:

An explanation of Dengue virus entry

An explanation of early events in Reovirus entry

An explanation of HIV entry into the cytoplasm He also curates his own collection of some of the best work out there Previously An explanation of embryonic development and Embryonic differentiation sponsored by HHMI T4 infection process commissioned of Seyet by Michael Rossman Productions by Adrian Elcock's lab at the University of Iowa Finally here are two interpretive dance productions

Protein Synthesis: an epic on the cellular level by Robert Alan Weiss for the Department of Chemistry of Stanford University

Dancing DNA by the OSU Biology program Previously Enjoy!

By: Mister_A

Mister_A — Sat, 25 Sep 2010 16:41:29 -0800

Hybrid is really beautiful, a quantum leap from the old "blobs in space" stuff of ca. 2000.

By: Guy_Inamonkeysuit

Guy_Inamonkeysuit — Sat, 25 Sep 2010 16:49:32 -0800

One of the nice things about working for Merck (I was on contract there for 2 years) was that I occasionally got to play around with animation -- nothing as sophisticated as this stuff, but still fairly high-level. Thanks very much for posting these fantastic links.

By: Rumple

Rumple — Sat, 25 Sep 2010 16:56:42 -0800

great post, Blasdelb. There is a huge Philosophy of Science literature on the use of illustration qua interpretation, this is going to be fun for me to browse around in.

By: stonepharisee

stonepharisee — Sat, 25 Sep 2010 17:03:42 -0800

Oh thank you! What a wonderful post!

By: kchiou

kchiou — Sat, 25 Sep 2010 17:05:04 -0800

Great stuff . . . visualizing our biology down to the cellular or molecular level is hard even for researchers working directly with these topics, which makes projects like these super important.

By: LobsterMitten

LobsterMitten — Sat, 25 Sep 2010 19:02:49 -0800

Thanks for this!

By: Pants!

Pants! — Sat, 25 Sep 2010 19:08:06 -0800

In addition to its other idiocies, the intelligent design movie Expelled ripped off some of the animation in The Inner Life of the Cell.

By: Made of Star Stuff

Made of Star Stuff — Sat, 25 Sep 2010 19:18:11 -0800

I love you so much for posting this. I wonder how much of this stuff is licensed to use with attribution on other scholarly sites. I'll have to dig around and check; so much of this would be so useful for a project I work on.

By: Blasdelb

Blasdelb — Sat, 25 Sep 2010 19:18:23 -0800

Thank you for that link Pants!, that article becomes all the more powerful when one realizes that it is this David Bolinsky who wrote it.

By: tickingclock

tickingclock — Sat, 25 Sep 2010 20:02:20 -0800

Great post, thanks!

By: AElfwine Evenstar

AElfwine Evenstar — Sat, 25 Sep 2010 20:51:35 -0800

Thank you so much; made my night. Now I have something to watch while my Eve toon is shooting pos. :)

By: ubersturm

ubersturm — Sat, 25 Sep 2010 22:24:51 -0800

One of the nice things about these sorts of animations is that they give you a bit of a feel for the role that random motion (e.g. Brownian motion - diffusion of proteins and other molecules through the cytoplasm) plays in biochemistry. It's too easy - looking at textbook pictures - to imagine protein interactions and chemical reactions as nice orderly events everything just sort of falls into place at the right time. For me, it was really sort of revelatory to be able to easily picture everything as mobile molecules, with mechanisms reliant not only on basic chemistry but also on the basic physics of small objects moving through viscous liquids. Of course, there are still challenges that make it really hard to get a truly accurate feel for how these interactions actually play out in the cell. The most basic one is that cells are packed. To use one of the examples above, the EcoRI restriction enzyme and its target plasmid aren't floating alone in a nice black void. Rather, they're being jostled and squished by all the other proteins and DNA and small molecules and whatnot that are surrounding them in the cytoplasm. And there are other challenges: the plasmid may be super-coiled, or there may be other proteins interacting with the plasmid (polymerases and helicases and so on), or the EcoRI enzyme may fall off and rebind to the plasmid several times, or it might move by sort of randomly scooting back and forth in both directions along the plasmid (I don't actually know recall if its movement along DNA is directional), or... Point is, there's a huge amount of stuff going on, but it can be really hard to depict everything while making the main point of the animation (restriction enzyme reactions, in this case) easy to observe and understand. But yeah, these sorts of animations are still awesome.

By: Blazecock Pileon

Blazecock Pileon — Sat, 25 Sep 2010 22:53:26 -0800

I loves me some biology. Thanks, Blasdelb.

By: drewb

drewb — Sat, 25 Sep 2010 23:01:33 -0800

Hi folks, I am the guy running the animation production at WEHI. I am delighted you like the animations! I recommend you visit MolecularMovies which is run by Gael McGill at Harvard Medical School. MolecuarMovies is Gael's selection of the best from this field of work. Etsuko Uno will be releasing a new animation in a few weeks (once sound design is complete) on stem cells and breast cancer. In my opinion, it is stunningly beautiful work. Working with Gael McGill, we have a large new set of animations and interactives on mitosis...which I have to say is some of my best work to date as far as accurately representing the science goes. The biomachinery of the kinetochore is awesome. Depending on how we end up publishing this work, it will hopefully be online somewhere soon too. I've been working freelance for the last few years and there are many non-WEHI animations that I have made around the place. For example, check out the Whole Brain Catalog on YouTube, which I am particularly pleased about the musical score Franc Tetaz made for it. There are many other great biologist/artists who are not mentioned in this post yet. The ultimate god of biomolecular art is David Goodsell. He is a molecuar biologist at Scripps and he creates illustrations of the molecular world in our cells that are extraordinarily accurate, beautiful and insightful. We all follow in his wake. His works can be found via his website, his monthly articles for the Protein Data Bank and of course his books which I cannot recommend enough for anyone with an interest in biomolecules, for example his recent "The Machinery of Life" drew

By: ubersturm

ubersturm — Sat, 25 Sep 2010 23:26:41 -0800

Goodsell's stuff is great, and it does a great job of depicting one of the things I mentioned above - namely, how crowded the interior of a cell is. If you're interested in the sort of calculations that guide the some of the details of the animations, there are an increasing number of decent textbooks out there that focus exclusively on the biophysical aspects of interactions and reactions in the cell. Berg's "Random Walks in Biology" or Nelson's "Biological Physics" both do a pretty good job of guiding you through the math behind it all, though there are no doubt other great textbooks I haven't run into.

By: drewb

drewb — Sun, 26 Sep 2010 00:09:35 -0800

@ubersturm I concur with your comments about the EcoR1 animation. When I built that animation back in 2002 I was experimenting with methods of showing a crowded interior with that specific sequence. I still have those busy, confusing-to-look-at tests in one of my archives. Ultimately I stripped all the molecular soup out to make it watchable for students. I have continued to play with different techniques for including the surrounding molecules, with the Apoptosis animation being what I think was my most successful effort (in terms of conveying the molecular world without distracting the audience from the primary storyline). Adrian Elcock's simulations are superb representations of the crowded nature of biomolecules and Graham Johnson is developing some extraordinary tools that will hugely advance the creation of such shots.

By: oonh

oonh — Sun, 26 Sep 2010 05:03:17 -0800

Someone has uploaded TVOntario's cellular respiration!

By: Blasdelb

Blasdelb — Sun, 26 Sep 2010 06:23:55 -0800

uberstrum, Thank you for the links to the textbooks, I've been interested in how phage pregnancy might change the balance of these equations and the implication that may hold for host metabolism shut down. I've got some reading to do. Adrian Elcock's lab at the University of Iowa has published a nice paper on GFP diffusion within the cell with a really pretty supplemental video that would be great for students.

By: Blasdelb

Blasdelb — Sun, 26 Sep 2010 06:49:53 -0800

drewb, Its very exciting to me that you are now working on mitosis and meiosis, and thank you for stopping by and filling in some of the holes I missed! Is there anything else you can think of which is conspicuously absent?

By: ubersturm

ubersturm — Sun, 26 Sep 2010 09:43:53 -0800

drewb: Oh, believe me, that wasn't a criticism. Showing all of the stuff that's surrounding the small molecules and macromolecules would make it hard to see many of the interactions! The molecules-floating-in-space look really is necessary when you're trying to look at a few very specific smaller interactions (this is particularly the case when you're talking about interactions that involve small molecules like nucleotides or whatnot.) It's just nice to have the more general crowded-cell images as well, to counterbalance everything with a reminder of the full complexity of the cell. (The apoptosis video is great, by the way, and does a nice job of balancing the background environment with the actual important interactions.)

By: TungstenChef

TungstenChef — Sun, 26 Sep 2010 13:31:21 -0800

This is awesome, I've got tests this week involving malaria and the circulatory system so this is super useful to me in putting all the information together!

By: drewb

drewb — Sun, 26 Sep 2010 20:45:41 -0800

Blasdelb: Ok, if you're interested, here are some more examples of my work from off the beaten track. EcoR1 is that early experiment I did with trying to show the full molecular environment of the cytoplasm. The colours are ugly because I hadn't tweaked them yet, and I abandoned this experiment because of a looming deadline and it was going to take too much time to make it work visually. Ubersturm: I actually really appreciate criticism/comments as it helps me determine what is important to people and what an audience will look for and pick up on. Small Pox is a brief excerpt of the work I did on the Windfall Films documentary on bioterrorism. Some bugs and microorganisms for EO Wilson's bio-documentary "Lord of the Ants". I was happy with the way the E.coli bacteria in the soil looked, particularly as I only had 1 week to create that shot. The movement of their flagella and general swimming behaviour was based on published papers. Experiments with representing/reconstructing the cytoplasm in a human cell. Founded on tomography data from the lab of Dr Brad Marsh at the University of Queensland. The data I was given by Brad was extraordinary and quite frankly overwhelming in it's richness and depth. I wish I had a couple of years to play with it. And something different: Sperm Whale vs Giant Squid. I created this for the marine exhibition at Melbourne's Museum Victoria. It was based on research on Sperm Whale hunting behaviour that was determined by attaching a probe to a female sperm whale off the coast of Japan. They recorded her depth, velocity and duration for multiple dives. Factoids: Sperm Whales are thought to use the huge spermaciti organ in their nose (that give those whale's their distinctive square head shape) as a floatation/ballast device (by cooling and warming it with blood) to sink one or two kilometers down, then use sonar to hunt the giant squids, with brief, fast chases with longer rest periods in between hunts. Sperm Whales have been detected at more than 2km in depth and can stay under for up to two hours. I recently also worked on a very interesting exhibition in Geneva on DNA and the Genome. I was responsible for the 14m dome projection and my 2003 DNA animations were used on a number of touch screen displays throughout the exhibit. This project was completely awesome to work on. Great, talented people to work with and big ambition by the client, the University of Geneva. And for my 2.3 seconds of fame I created Human/Alien/Hybrid DNA for Keanu Reaves character in the Day the Earth Stood Still. That was a fast fun project (two weeks of production), for which I created about two minutes of shots (client brief: come up with what an alien's 'DNA' would look like, and a human-alien hybrid...). Of the two minutes of footage I created, they used about 1-2 seconds which they played back and forth for some reason, rather than using the dynamic versions I gave them...oh well. And for an additional 1.4 seconds of fame, my scene files from the 2002/3 DNA work were also used in Dr Who, for the episode "The End of The World" where an alien holds up a device to scan the Doctor's DNA or something along those lines.

By: lholladay

lholladay — Mon, 27 Sep 2010 14:34:09 -0800

Oh, this bit? That is awesome! Thanks so much for stopping by the thread.

By: Blasdelb

Blasdelb — Mon, 27 Sep 2010 16:49:38 -0800

Thank you so much for sharing your old films with us, as a teacher every one I can get my hands on is invaluable to me for appealing to students' sense of beauty and inspiring them.

By: drewb

drewb — Tue, 28 Sep 2010 02:57:04 -0800

If you are after these types of animation for education and teaching I recommend you visit HHMI's biointeractive.org and cold spring harbour's dnai.org

By: atrazine

atrazine — Tue, 28 Sep 2010 05:31:51 -0800

Congratulations on your MacArthur Fellowship drewb!

By: sciencegeek

sciencegeek — Tue, 28 Sep 2010 07:07:42 -0800

Congratulations DrewB!

By: Blasdelb

Blasdelb — Tue, 28 Sep 2010 10:45:29 -0800

By: mreleganza

mreleganza — Tue, 28 Sep 2010 19:22:33 -0800

The masses have spoken! They want you to keep going with these! They say, "Drew Barry, more!"