Diffusion doesn't tell molecules where to go

My latest animation is about the kinetic molecular theory (sounds boring, what does it mean?) and how molecules diffuse, which is one of the core concepts that makes biology possible. There’s a lot of misconceptions around how any why diffusion actually happens, so I took the opportunity to run some computer simulations to visualize what’s going on. I hope you enjoy it and it clarifies some ideas!

On my second channel “Making BIocinematics”, I also uploaded a behind the scenes video explaining a bit how I created the simulations and graphics in the animation. Please subscribe if you’d like to see more!

I’ve decided to present my behind the scenes explanations in video format, rather than on this blog, but I’ll try to post the behind the scenes videos here too, along with references for the videos. Let me know in the YouTube comments what you’d like to see more or less of. This will help me tailor my “making of” videos to the audience that is watching them.

And here are some references for the animation. I’m still pondering better formats. As I’m sure anyone who has done science animation knows, it’s pretty tough to track exactly what references were used, when, and how, but I do think that information is important. More pipeline development required.

References

1. 27.3: The Distribution of Molecular Speeds is Given by the Maxwell-Boltzmann Distribution. Chemistry LibreTexts https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Map%3A_Physical_Chemistry_(McQuarrie_and_Simon)/27%3A_The_Kinetic_Theory_of_Gases/27.3%3A_The_Distribution_of_Molecular_Speeds_is_Given_by_the_Maxwell-Boltzmann_Distribution (2014).

2. Atmosphere of Earth. Wikipedia (2019).

3. Sanger, M. J., Brecheisen, D. M. & Hynek, B. M. Can Computer Animations Affect College Biology Students’ Conceptions about Diffusion & Osmosis? The American Biology Teacher 63, 104–109 (2001).

4. Brown, T. E., LeMay, H. E. & Bursten, B. E. Chemistry: The Central Science. (Pearson, 2005).

5. Earth Fact Sheet. https://nssdc.gsfc.nasa.gov/planetary/factsheet/earthfact.html.

6. David L. Nelson & Michael M. Cox. Lehninger Principles of Biochemistry. (2004).

7. Michell Humidity Calculator. http://www.michell.com/us/calculator/.

8. McKnight, E. J. Student misconceptions of osmosis and diffusion. 103.

9. Edmund A. Marek, Ann M. L. Cavallo & Connie Cruse Cowan. Students’ Misconceptions about Diffusion: How Can They Be Eliminated? The American Biology Teacher 56, 74–77 (1994).

A Summer Move

Hello!

I just wanted to give a brief life update, because I've been awfully quiet on the web this past month. After publishing "The Pinball Machine of Science", I packed up my computer and shipped my family, our stuff, and myself across the country. I'm still in Canada though!

How did all this fit in my last home office?

I was hoping to get back into animation production sooner, but after packing, cleaning the old house, traveling, cleaning the new house, waiting for our boxes to arrive, unpacking, and getting my computer and office reassembled, it's been over a month since leaving.

A good start.

Putting my giant heatsink back in, along with the graphics cards and hard drives (shipped separately).

Oh yeah, and I might have done a very quick side project to wire an old-school SNES retropie to a CRT TV I picked up at the side of the road.

I don’t know very much about electronics, but I had no qualms about sacrificing this old mini-USB cable.

It works!

Despite the "summer break", I have a lot of plans for the next animations and other things I'm excited to share with you. Remember to subscribe to my YouTube channel (http://youtube.com/biocinematics) if you haven't already (it's totally free - $0.00!).

Thanks for reading, and thank you for your patience in waiting for new content to be released.

Stuart

The Pinball Machine of Science

“The Pinball Machine of Science” is the latest Biocinematics video, about how tools of science are used, how science develops over time, and how we can learn about things we can’t even see. I hope you enjoy the video, then read on to get a glimpse behind the scenes and rigorously peruse the references.

Behind the Scenes

Simulating the Pinball Machine

The pinball table was modeled mainly in ZBrush, and brought into Houdini for all the animation and simulation. The difference between animation and simulation is: with animation, the animator (me) specifies the exact position, rotation etc. at different points in time, for example, the metal disk rotation. With simulation, the simulator(?) (also me) sets up some rules for the computer to follow and he sees what happens. Then he tweaks the rules, and tries again and tweaks the rules and tries again until he has a result that he’s happy with. It would have been crazy to animate the pinball ball itself, since it has to bounce convincingly many times for 24 different disk rotations. I thought it would be pretty easy to set up a simulation; I mean, it’s a single ball bouncing in an idealized way with just a single force (gravity) and nothing else going on.

How wrong I was. In my first (and second through umpteenth) attempts, the pinball would land on squarely on the launcher and then spontaneously roll around. When it collided with the hidden shape, it would bounce into the air and fly off at crazy angles.

I never did figure out what was going on with this rolling, just tweaked settings until the problem was minimized.

The crucial aspect was that I needed the ball to bounce off the hidden shape at the same angle as it arrived at, and my simulation just wasn’t doing that. The angle of incidence should be the same as the angle of reflection, that’s basic physics, right? Right? I needed this in order to have a convincing data visualization in the video. After a lot of trial and error and head scratching, I decided to assess my assumptions and read up on some physics. Suddenly everything became clear. I was asking the simulation for an impossible situation: I needed idealized physics (assume no friction nor air resistance, perfectly elastic collisions) but I also needed real-world behaviour (friction, drag, and inelastic collisions, otherwise the ball would sail around for far too long). If the ball is spinning and collides with a surface with friction, and loses some energy in the process, it’s not going to be a perfect bounce. But I did recognize that a real pinball machine should be pretty close to an equal incidence/reflection bounce. So instead of assuming there was a magic setting that I couldn’t find, I set out to manually balance idealized physics with real-world properties.

Simple helper geometry shows me where the ball should go, and the numbered path shows where the ball is actually going.

I set up some helper visualization so I could see how close I was to the desired bounce angle, and then I went through and dialed in the friction, bounce, drag, gravity, etc. for the ball, table surface, table walls, and hidden shape individually. Finally I had a convincing simulation that bounced properly. At that point I was confident I would be able to publish the video.

The Island of Human Knowledge

The tropical island was a stylistic experiment. I had a vision of a somewhat cartoony tropical island fully rendered in 3D, with simple 2D stick-figure characters telling the story.

It’s a rock, despite my 2-year-old’s insistent assertions that it is in fact “a poop”.

The island and palm fronds were sculpted in ZBrush, while the ocean was a built-in Houdini tool that I baked into a displacement map for Redshift to apply to a flat plane at render-time, so it’s not a real water simulation. You can tell because the waves don’t really interact with the shore, they just move up and down regardless. I was pretty pleased with the result that I got in a fairly short time, because I had a huge number of frames to render.

A little island in the sun

Right before I submitted my renders to run over the weekend, I noticed a strange artifact. On some frames I was getting black lines around the edge of the water. I tried everything I could think of to fix the problem. Higher trace depth, different index of refraction, single-scattering off, emission, GI, displacement resolution, and more.

A simple case (flat grey shaders) to simplify and isolate the problem - a very useful troubleshooting approach.

But in every case, even with a very simple setup, I still had problematic black lines. Finally some memory was jogged in the back of my mind, and I realized that my ocean grid was hundreds of units away from the origin. So what, you might ask? A precision issue! As objects get farther away from the center of the world, sometimes there can be internal mathematics rounding errors (I guess) that produce artifacts with Redshift, even though the pixels I was rendering were very close to the center of the world. Weird, huh. I adjusted how the grid placement was set up, and the problem was immediately solved! Reading forums can be pretty handy, because the problems that other people have can subconsciously return at opportune times. I submitted my fixed renders just in time for the weekend.

Thanks for reading, and I hope you’ll stay tuned (or whatever the internet equivalent is… oh yeah: subscribed) for the next animated science video!

Stuart

References

1. Allain, R. We Swear There’s a Reason to Model This Ball Bouncing Off a Wall. Wired (2016).

2. Collaboration, T. E. H. T. et al. First M87 Event Horizon Telescope Results. I. The Shadow of the Supermassive Black Hole. ApJL 875, L1 (2019).

3. Gerhard, M. Direct Or Indirect? | Science project | Education.com. Available at: https://www.education.com/science-fair/article/direct-indirect-observation/. (Accessed: 12th March 2019)

4. GRANT, E. HISTORY OF SCIENCE: When Did Modern Science Begin? The American Scholar 66, 105–113 (1997).

5. Kosso, P. Observability and Observation in Physical Science. (Springer Science & Business Media, 2012).

6. Kross, B. Questions and Answers - What is one example of indirect evidence that scientists use to study an atom? Jefferson Lab Available at: https://education.jlab.org/qa/atom_01.html. (Accessed: 12th March 2019)

7. Levi, R. How X-Rays were discovered — by Mistake. Ran Levi (2016).

8. Panchbhai, A. Wilhelm Conrad Röntgen and the discovery of X-rays: Revisited after centennial. Journal of Indian Academy of Oral Medicine and Radiology 27, 90 (2015).

9. Tubiana, M. [Wilhelm Conrad Röntgen and the discovery of X-rays]. Bull. Acad. Natl. Med. 180, 97–108 (1996).

10. Ralph Washington Sockman. Wikipedia (2018).

11. Designing an Observation Study. Science Buddies Available at: https://www.sciencebuddies.org/science-fair-projects/references/observation-study-experimental-design. (Accessed: 12th March 2019)

12. How Scientists Captured the First Image of a Black Hole - Teachable Moments. NASA/JPL Edu Available at: https://www.jpl.nasa.gov/edu/news/2019/4/19/how-scientists-captured-the-first-image-of-a-black-hole/. (Accessed: 26th June 2019)

13. Indirect Observations and Inference—Demonstration Kit. Available at: https://www.flinnsci.com/indirect-observations-and-inference---demonstration-kit/ap7425/. (Accessed: 12th March 2019)

14. Observation beyond our eyes. Available at: https://undsci.berkeley.edu/article/howscienceworks_05. (Accessed: 12th March 2019)

15. Ontario Science Centre: Home. Available at: https://www.ontariosciencecentre.ca/. (Accessed: 12th March 2019)

16. RÖNTGEN, Wilhelm Conrad (1845-1923). <I>Ueber eine neue Art von Strahlen (Vorläufige Mittheilung).</I> -- <I>Eine neue Art von Strahlen. II. Mittheilung.</I> Offprints from: <I>Sitzungsberichte der Würzburger Physik.-medic. Gesellschaft,</I> 1895 [no. 9], and 1896, [nos. 1-2]. Würzburg: Verlag und Druck der Stahel’schen k. Hof.-und Universitäts- Buch- und Kunsthandlung, 1895-1896. Available at: https://www.christies.com/lotfinder/lot_details.aspx?intObjectID=5084328. (Accessed: 26th June 2019)

17. Structural Biochemistry/Nucleic Acid/DNA/Franklin’s DNA X-ray Crystallography - Wikibooks, open books for an open world. Available at: https://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/Franklin%27s_DNA_X-ray_Crystallography#Fiber_Diffraction. (Accessed: 12th March 2019)

Are you really a carbon-based life-form?

I recently published the first video in an animated series I'm creating about human biology. It's targeted at as broad of an audience as I could make it, and doesn't make too many assumptions about prior knowledge. If you haven't already watched it, I highly recommend giving it a look.

The purpose of this blog post is to give a little peak behind the curtains to see some "making of" material, and to house the references I used to support the information in the video.

For the animation, I used Houdini almost exclusively, rendered with Redshift, comped in Blackmagic Design Fusion, and edited and mixed in DaVinci Resolve.

Houdini is a very interesting and unique 3D application, in that almost everything is created in a procedural nature, which means that you set up "rules" for how things are created, instead of creating each thing individually. This was very helpful for creating the Periodic Table which featured in the video.

I started by laying out a grid of points that would determine where the elements would end up.

Computers start counting from zero. Adjust accordingly.

Then I imported a spreadsheet of data about the elements, including symbol, name, element number, and atomic radii. Then I mapped that data to the grid of points.

If there are any typos, it’s wikipedia’s fault.

Then, when I had to create animation, for example when pulling out a highlighted element, I was able to set up a "selector" which allowed similar animations to be repeated quite simply.

Oxygen comin’ atcha!

Probably the most involved shot in the video is the "Thinker" being filled with colored atoms pouring in. I was able to find a 3D scan of the sculpture by Rodin, and after some cleanup and retopology, it was ready to fill. Of course things usually don't work out immediately.

I’ve certainly felt like this before.

But eventually I got the spheres filling the statue, albeit with some leakage.

The leaking was a lot worse in other iterations.

Ultimately I set up a rule that if a sphere leaked outside the statue, it was killed from the simulation, so it doesn't show up.

Not quite right.

And rendering is its own challenge. I started using a very basic type of sphere geometry, but it turns out it was designed for very small particles, and so I had to switch to a more complex kind of sphere (skimming over the details here) to avoid artifacts like this where the spheres and glass statue intersect.

I'm pretty pleased with how the final shower of atoms turned out (at 3:17 in the video). Of course I had to search for some "rainstick" sound effects to fit with the visuals.

And now for something completely different. 

You may not know that I've spent quite some time in an academic setting considering how one might present the references that inform different aspects of an illustration, video or animation, from narration to objects, behaviours, and even colors. I contributed to a publication in Nature Methods on the topic: http://rdcu.be/doo5.

Needless to say, dumping references here without linking bidirectionally to specific points in the video is a failure in many respects, but it's better than nothing, and I plan to improve the way in which I present this kind of information as time progresses. Maybe I should re-read my article. Also, almost certainly this is an incomplete list. I’m pretty sure there were lots of wikipedia pages I used at various points and didn’t go through the trouble of tracking down primary references. Lots of room for improvement.

References:

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., & Walter, P. (2002). Molecular Biology of the Cell (4th ed.). Garland Science.

2. Bentley, G., Dodson, E., Dodson, G., Hodgkin, D., & Mercola, D. (1976). Structure of insulin in 4-zinc insulin. Nature, 261, 166–168. https://doi.org/10.2210/pdb1zni/pdb

3. Biomolecule | biology. (n.d.). Retrieved May 8, 2019, from Encyclopedia Britannica website: https://www.britannica.com/science/biomolecule

4. Bruce, A., Andersson, M., Arvidsson, B., & Isaksson, B. (1980). Body composition. Prediction of normal body potassium, body water and body fat in adults on the basis of body height, body weight and age. Scandinavian Journal of Clinical and Laboratory Investigation, 40(5), 461–473. https://doi.org/10.3109/00365518009101869

5. Campbell, N. A., & Reece, J. B. (2001). Biology, 6th Edition (6 edition). San Francisco: Benjamin Cummings.

6. Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: Conformation and dynamics. Proc.Natl.Acad.Sci.USA, 78, 2179–2183. https://doi.org/10.2210/pdb1bna/pdb

7. Emsley. (1998). The Elements. Clarendon Press.

8. Fomon, S. J., & Nelson, S. E. (2002). BODY COMPOSITION OF THE MALE AND FEMALE REFERENCE INFANTS. Annual Review of Nutrition, 22(1), 1–17. https://doi.org/10.1146/annurev.nutr.22.111401.145049

9. Forbes, R. M., Cooper, A. R., & Mitchell, H. H. (n.d.). OF THE ADULT HUMAN BODY AS BY CHEMICAL ANALYSIS. 9.

10. Freitas, R. A. (1998). 3.1 Human Body Chemical Composition. Retrieved May 7, 2019, from Nanomedicine website: https://foresight.org/Nanomedicine/Ch03_1.php

11. Goodsell, D. S. (2005). Visual Methods from Atoms to Cells. Structure, 13(3), 347–354. https://doi.org/10.1016/j.str.2005.01.012

12. Harris, L. J., Larson, S. B., Hasel, K. W., & McPherson, A. (1997). Refined structure of an intact IgG2a monoclonal antibody. Biochemistry, 36, 1581–1597. https://doi.org/10.2210/pdb1igt/pdb

13. International Year Periodic Table 2019 | IYPT 2019. (n.d.). Retrieved May 8, 2019, from The International Year of the Periodic Table website: https://www.iypt2019.org/

14. JMOL Color Table. (n.d.). Retrieved May 8, 2019, from Jmol website: http://jmol.sourceforge.net/jscolors/

15. Koltun, W. L. (1965). Precision space-filling atomic models. Biopolymers, 3(6), 665–679. https://doi.org/10.1002/bip.360030606

16. L, N. D., Lehninger, A. L., Nelson, D. L., Cox, M. M., Cox, U. M. M., & Cox, M. M. (2005). Lehninger Principles of Biochemistry. W. H. Freeman.

17. Natchiar, S. K., Myasnikov, A. G., Kratzat, H., Hazemann, I., & Klaholz, B. P. (2017). Visualization of chemical modifications in the human 80S ribosome structure. Nature, 551, 472–477. https://doi.org/10.2210/pdb6qzp/pdb

18. Otterbein, L. R., Graceffa, P., & Dominguez, R. (2001). The crystal structure of uncomplexed actin in the ADP state. Science, 293, 708–711. https://doi.org/10.2210/pdb1j6z/pdb

19. Pullman, B. (2001). The Atom in the History of Human Thought. Oxford University Press.

20. RCSB Protein Data Bank. (n.d.-a). RCSB PDB - ale Ligand Summary Page L-EPINEPHRINE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/ale

21. RCSB Protein Data Bank. (n.d.-b). RCSB PDB - asc Ligand Summary Page ASCORBIC ACID. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/asc

22. RCSB Protein Data Bank. (n.d.-c). RCSB PDB - atp Ligand Summary Page ADENOSINE-5’-TRIPHOSPHATE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/atp

23. RCSB Protein Data Bank. (n.d.-d). RCSB PDB - cys Ligand Summary Page CYSTEINE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/cys

24. RCSB Protein Data Bank. (n.d.-e). RCSB PDB - glc Ligand Summary Page ALPHA-D-GLUCOSE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/glc

25. RCSB Protein Data Bank. (n.d.-f). RCSB PDB - gly Ligand Summary Page GLYCINE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/gly

26. RCSB Protein Data Bank. (n.d.-g). RCSB PDB - ldp Ligand Summary Page L-DOPAMINE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/ldp

27. RCSB Protein Data Bank. (n.d.-h). RCSB PDB - nad Ligand Summary Page NICOTINAMIDE-ADENINE-DINUCLEOTIDE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/nad

28. RCSB Protein Data Bank. (n.d.-i). RCSB PDB - oli Ligand Summary Page. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/oli

29. RCSB Protein Data Bank. (n.d.-j). RCSB PDB - pyr Ligand Summary Page PYRUVIC ACID. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/pyr

30. RCSB Protein Data Bank. (n.d.-k). RCSB PDB - ser Ligand Summary Page SERINE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/ser

31. RCSB Protein Data Bank. (n.d.-l). RCSB PDB - tes Ligand Summary Page TESTOSTERONE. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/tes

32. RCSB Protein Data Bank. (n.d.-m). RCSB PDB - trp Ligand Summary Page TRYPTOPHAN. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/trp

33. RCSB Protein Data Bank. (n.d.-n). RCSB PDB - viv Ligand Summary Page (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL. Retrieved June 25, 2019, from RCSB PDB website: https://www.rcsb.org/ligand/viv

34. Rutherford, P. E. F. R. S. (1911). LXXIX. The scattering of α and β particles by matter and the structure of the atom. The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, 21(125), 669–688. https://doi.org/10.1080/14786440508637080

35. Slater, J. C. (1964). Atomic Radii in Crystals. The Journal of Chemical Physics, 41(10), 3199–3204. https://doi.org/10.1063/1.1725697

36. Tame, J. R., & Vallone, B. (2000). The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K. Acta Crystallogr.,Sect.D, 56, 805–811. https://doi.org/10.2210/pdb1a3n/pdb

37. Thomson M. A., J. J. (1897). XL. Cathode Rays. The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, 44(269), 293–316. https://doi.org/10.1080/14786449708621070

38. Wieser, M. E., Holden, N., Coplen, T. B., Böhlke, J. K., Berglund, M., Brand, W. A., … Zhu, X.-K. (2013). Atomic weights of the elements 2011 (IUPAC Technical Report). Pure and Applied Chemistry, 85(5), 1047–1078. https://doi.org/10.1351/PAC-REP-13-03-02

Osteocalcin and Bone Mineral

April's Molecule of the Month at the Protein Data Bank features proteins that bind to biominerals. This is osteocalcin binding to calcium ions, a major component of the calcium-phosphate lattice that makes up hydroxyapatite. Hydroxyapatite is essentially "bone mineral", which helps gives bones strength and rigidity.

The glowing spheres are the calcium ions that osteocalcin is currently binding.

This illustration was the first one where I brought molecular data directly into Houdini, the new 3D application that I have been learning over the past few months. Houdini requires very different workflows from other 3D applications, so learning how to manipulate data for this illustration was interesting and insightful, and I believe processes like this will allow me to create some pretty interesting content in the future.

The green balls here are the important calcium ions. It didn’t take too many nodes to generate this, which is nice.

Houdini can natively read PDB data files like the one I downloaded for osteocalcin, however beyond some helpful data organization, it doesn't have any tools for displaying different molecular representations, so everything from space-filling representations (like the one above) to surface meshes to backbones must be created from scratch. Fortunately Houdini is a great tool for building tools, so I'll be spending some time developing an internal toolkit to show molecules in different visual styles.

A single hydroxyapatite unit: Ca in green, PO4 in yellow/red, and OH in red/white

The crystal data for the bone mineral was in a different format (CIF), so I used UCSF Chimera to export a new PDB file and get the measurements that allowed me to expand a single atomic "cell" to the full crystal field of repeated units.

Thanks for reading,

Stuart

Backup Strategies

This Sunday (March 31st, 2019) is World Backup Day! Bet you didn't know that was a thing. Completely independent of that, I thought to share (in the momentary absence of new art) some of my thoughts and strategies for backups. The ideas below are collected from things I have heard and read in conjunction with my own opinions and experiences, and (disclaimer) are not necessarily recommendations for a completely safe and secure system. Implementing any system is never 100% guaranteed; that's unfortunately just an outcome of living in an entropic universe.

Fact: hard drives die. Fact: I am not a data recovery specialist.

What are important features of a complete backup system?

1. Ability to recover from:

   A) hardware failure (dead hard drive, fried motherboard, lightning strike)

   B) OS/software failure (can't boot into windows, other colossal mess)

   C) malware (viruses)

   D) ransomware (your files are locked until you pay me $₿$)

   E) theft (I'm physically taking your computer out of your physical house)

   F) natural disasters (fire, floods, earthquakes)

2. Frequent, consistent, verified backups

3. Fast recovery from common failures

4. Prevent access by others

5. Access historical versions (accidentally deleted files, version from last week)

I suppose now is as good a time as any to say, if you don't have any backup at all, please, please do get something. For a "set it and forget it" solution, I recommend Backblaze. It's not perfect or free (it's $6 a month) but probably is one of the best single options to try and fulfill the feature list above. You could instead simply plug in an external drive and copy files to that, but I feel that has three primary weaknesses: (1-CD) a bad ransomware/malware attack could lock up or wipe both, (1-E) it’s easy for someone to steal both your computer and your drive, and (2) it’s easy to be inconsistent and infrequent with a backup schedule. Notice above I said "single option"; a great backup system should have at least two tiers to build redundancy and to fully meet the features listed. You can see how an external drive plus continuous cloud backup (a la Backblaze) starts to strengthen the system because the pros of either part help mitigate the cons of the other. That’s the short version of my thoughts. To dig into the gritty details, read on, brave reader.

What kind of backup system do I use? Before we get there, let's consider the kinds of data I have. First, I have my operating system and programs/software. Yes, I can rebuild from scratch, but that would be a royal pain and a waste of time. I have this data segregated on its own physical drive, the OS drive.

The legendary OS drive

Then I have personal documents, which I don't care to lose, obviously. My photo library is large (30,000+ photos) and is very precious (family photos always are).

Animation projects produce lots of data, easily several gigabytes, while larger projects can produce dozens or hundreds of gigabytes. Some of that is temporary data which can be cleaned out after the project concludes, but while the project is on-going, I do want to keep and protect it.

Finally, there's a lot of ripped media: music and movies (from discs I own, okay?). Fairly easy to recover, so I'm not going to go nuts with the backups, but I don't want to re-rip a ton of CDs and Blu-rays either.

That’s a hefty chunk for one trilogy…

Okay, now I can get to my backup system. My first line of defense is backing up my computer to a two-bay Synology NAS. It's like an external drive that's connected via ethernet instead of USB. And there's two hard drives, so I can fit twice as much stuff, right? Nope: the two hard drives are mirrored (that's called RAID 1), i.e. exact duplicates. This is so if a hard drive fails (it's happened at least twice), all the data is preserved and I just need to stick a new hard drive in to replace the failed one. Side note: RAID is not a backup solution on its own. It doesn't cover scenarios B through F, nor all of A. What and how do I backup to the NAS? I use Macrium Reflect backup software to daily create an image of my OS drive. I have a second daily backup scheduled for all my important data. The NAS isn't huge and I am keeping a few historical backup copies so I can go back in time if needed; this means I have to be a bit selective about the data that's backed up, so some folders (e.g. ripped video) are excluded.

This unit is about 6 years old and has been on almost 100% of that time.

This NAS component does meet several of the features listed. For 1 (recovery), it hits A, B, most of C/D, some of E/F. Number 3 (fast recovery) is a big one. I once had my computer simply not boot. I spent the morning troubleshooting trying to fix the issue. At noon I said forget it and restored an OS drive backup. I was up and running that afternoon. Unfortunately my OS backup was a few months old, which caused more problems than one would think. So now I backup my OS daily. Still, the method works. And for 4 (outside access), no one should be able to gain access to my NAS that wouldn't be able to gain access to my computer. I do wonder how and if I should strengthen that. I don't know quite enough about network security.

Okay, not bad, but we're still screwed in a few scenarios (e.g. fire, massive theft, really bad virus). Also, features 2 (frequent/consistent/verified) and 5 (historical backups) are good here but not great. It's not a perfect "set and forget". Right now it's behaving and verifies all the data, but I've had some hardware/software problems in the past which meant out-of-date or inconsistent backups. Some hands-on maintenance is necessary. And as I said, there's not a ton of space to maintain history. I should get a larger NAS (link to non-existent GoFundMe).

Backblaze working round the clock

So I also use Backblaze, which just backs up mostly everything. This covers my ripped media and adds redundancy for the rarer (#1) scenarios I just mentioned. For 2 (frequent/consistent/verified), it's good*, and for 5 (historical backups), you can roll-back anywhere from today to 30 days prior. By default it doesn't backup OS/software, which would likely be hard to restore anyway with this method. If I had to recover from one of the very bad scenarios, a couple days re-installing wouldn't be my worst problem. For 3, recovery time would be slower since they'd have to ship physical drives to me with the amount of data I have. And 4, do I trust them to protect against outside access? It's a good question, and one that prevented me from using cloud backup systems for a long time. The data is encrypted at rest, and I have a strong password and two-factor authentication, but software vulnerabilities and leaks do occur. I suppose in this case I'm on the side of the benefits outweigh risks. Would I rather lose access to my own data or have someone else access my data? I lean toward the former.

Are we done? Well… we could be. But there's that niggle of doubt. What if I have a huge fire and lose my computer and local backups, and then I realize that Backblaze only has two-thirds of my data? Apparently some people have had issues with Backblaze - I can't say for sure one way or the other, but the fact remains that a third-party service can't be trusted 100%*. So for ultimate backup security, I also periodically transfer all my important data to an encrypted hard drive and store it in a safety deposit box at the bank. And… of course you can't just use one hard drive, because the bank vault is empty while you're backing up to the drive. Gotta have two and swap them out. Yep. That should be pretty secure, and meet the criteria for all of 1 (data recovery) and 4 (outside access), and a reasonable rate for 3 (recovery speed). 5 (historical backups) is also good, depending on what I can fit on a single hard drive. The problem is 2 (frequent/consistent): I aim for once a month, but the reality is more like a few times a year. So it's a terrible primary method, but a great tertiary method.

And that's all! Did I miss anything? Do I have a critical vulnerability? Do you have a good system? Let me know in the comments here or on Twitter or Facebook. Happy World Backup Day!

Thanks for reading,

Stuart

* Backblaze verification: Backblaze does backup continuously, which means there's typically not much time between making a change to a file and that file being backed up to the cloud. However, verification is something that requires a bit of faith. Apparently all files are checksum’d before upload, but there's no great way to verify that Backblaze has all my data intact. I can check online which files are there, and yes, I can download a random selection of files from time to time, but that's still a random selection of < 0.001% of my files. On the other hand, Backblaze is a successful business employing backup experts, so I'm sure they're doing their due diligence (you had ONE job, right?). Still, at the end of the day, I personally don't like to have one company 100% responsible for my backups, so I don't.

Measles Virus Nucleocapsid

In continuing my illustration series following the Molecule of the Month over at the Protein Data Bank (1), this month I created an image showing the nucleocapsid of the measles virus.

Measles Virus Nucleocapsid - March Molecule of the Month

I'm sure you've heard of measles before. In fact, it seems to be a bit of an ongoing newsworthy item now and again. Measles is caused by a virus that is extremely contagious and can be deadly (2). Fortunately, we have a widely available vaccine (typically administered together with protection against mumps, rubella, and sometimes varicella (3)) to prevent the spread of this illness.

This image doesn't show the entire virus, instead it focuses on the genetic material (RNA in red) and the protein coat (grey) that protects the viral genes from our bodies' natural defenses (4) and also plays a role in helping the virus make copies of itself through transcription and RNA replication (5).

Making of

I spent a long time looking at the proteins amazingly illustrated by David Goodsell on the RCSB website, and wondering how I might create an illustration of my own. I liked the idea of the long repetitive pattern of the nucleocapsid. When I did some more research, I realized that a long flexible tail was omitted from the structural data (4) and the close-up illustration of the nucleocapsid. Working with my recent method (explained in this YouTube tutorial) I decided to append the flexible tail to the existing data and create something (hopefully) striking. Although the tail originates toward the hollow space in the center of the complex, there is evidence that the tail feeds itself back toward the outside (there's also space limitations with stuffing it all inside), resulting in an external coat of long flexible fibers (6,7).

PDB 4UFT

Once I had that piece in place, it became clear that I could create something quite menacing, using visual inspiration from the Sentinels in The Matrix (which is 20 years old this month!) (8). This approach did have some technical and visual challenges to work out.

A bunch of simulations all stacked up

Instead of making 2,516 copies (9) of the nucleoprotein and simulating all of them individually, I decided to simulate a lower number of copies and create static meshes that could be randomly scattered along the length of the nucleocapsid. I figured out the correct transformation offsets I would need to spiral the copies correctly, and used MASH to create a single unit of 37 proteins. Side note: Yes, although I'm learning Houdini, I did use Maya for this illustration because I already know the tools well and I have yet to figure out a pipeline for getting molecular data directly into Houdini.

37 proteins and 222 RNA nucleotides

Then I adjusted the random seed to make several more 37-monomer "units", and sent them over to ZBrush for some retoplogy to reduce the mesh density for all the background units. I also made a lower-resolution RNA spiral unit.

Tip: After retopology of thin meshes, use the 3D Gizmo and ctrl+drag the yellow center to inflate the model closer to the original volume.

Turns out the RNA is all cytosine residues… so not perfectly accurate… shhh!

 Finally, I used MASH again to spread the units along a curve, and posed the whole assembly to my liking.

I believe this is approximately the correct full length of the measles genome, and yes it should fit inside a typical measles capsid. Successful assembly!

I feel like the RNA is the most central and dangerous aspect of this virus, so I wanted all of the color in the image to come from that and have it draw the eye. Because of how the protein binds to the RNA, I didn't get as clean a view of the RNA helix as I was hoping, but I think overall the image works as intended. I hope you like it.

No connection to the Xbox Red Ring of Death

Thanks for reading,

Stuart

References (fancy!):

1.  PDB101: Molecule of the Month: Measles Virus Proteins. RCSB: PDB-101 Available at: http://pdb101.rcsb.org/motm/231. (Accessed: 12th March 2019)

2. Measles. World Health Organization (2018). Available at: https://www.who.int/news-room/fact-sheets/detail/measles. (Accessed: 15th March 2019)

3. MMR Vaccination | What You Should Know | Measles, Mumps, Rubella | CDC. Centers for Disease Control and Prevention (2018). Available at: https://www.cdc.gov/vaccines/vpd/mmr/public/index.html. (Accessed: 15th March 2019)

4. Gutsche, I. et al. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Science 348, 704–707 (2015).

5. Jiang, Y., Qin, Y. & Chen, M. Host–Pathogen Interactions in Measles Virus Replication and Anti-Viral Immunity. Viruses 8, (2016).

6. Jensen, M. R. et al. Intrinsic disorder in measles virus nucleocapsids. Proc. Natl. Acad. Sci. U. S. A. 108, 9839–9844 (2011).

7. Desfosses, A., Goret, G., Farias Estrozi, L., Ruigrok, R. W. H. & Gutsche, I. Nucleoprotein-RNA Orientation in the Measles Virus Nucleocapsid by Three-Dimensional Electron Microscopy. J. Virol. 85, 1391–1395 (2011).

8. The Wachowski Brothers. The Matrix. (1999).

9. Lund, G. A., Tyrrell, D. L., Bradley, R. D. & Scraba, D. G. The molecular length of measles virus RNA and the structural organization of measles nucleocapsids. J. Gen. Virol. 65 ( Pt 9), 1535–1542 (1984).

Maya Tutorial - Making of: eIF4E

Today I released a tutorial about how to use Molecular Maya’s Modeling Kit to fill in a missing region from protein data, based on the illustration I shared in my previous post. You can learn more about Molecular Maya and the modeling add-on kit here (https://clarafi.com/tools/mmaya/), but even if you don’t have the kit, there’s still a number of points about structural data and how to understand PDB reports that may be helpful.

The protein up for demonstration here is a eukaryotic translation initiation factor (English: It helps get messenger RNA to the ribosome so proteins can be made). The challenging thing about this protein is it has a long flexible “disordered” tail that is not included in the x-ray crystallography data, because flexible poorly-structured regions just don’t crystallize well, so this is a very typical scenario when trying to use Protein Data Bank (PDB) files.

Fortunately, we do know the amino acid sequence of this tail, and we can use features of the mMaya modeling kit to synthesize and simulate the missing region, allowing us to complete our protein model.

I hope this tutorial is interesting and useful. If you have questions or if you’d like to see a tutorial on another aspect of building molecular models, you can ask me in the YouTube comments, or DM me on Twitter, or any number of ways!

Thanks for reading (and watching)!

Stuart

A Fresh Start

If you've been following my work for any length of time, you're probably aware that I've kept a blog over at biocinematics.blogspot.com. This week I reached the 10th anniversary of that blog and decided it was a good time to "reboot" the blog fresh and new on this site.

 So here we are!

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Blank Page Syndrome!

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Oh, I'll share the first image from a series of a molecular illustrations I started which is inspired by the Molecule of the Month series created by David Goodsell at the RCSB Protein Data Bank.

The February Molecule of the Month is the eukaryotic initiation factor eIF4E. By binding to the 5' cap of mRNA (seen in the lower part of the image), eIF4E helps bring mRNA and the ribosome together to start protein synthesis. eIF4E also features a disordered flexible "tail" (in the upper left) which is involved in binding other parts of the initiation complex.

If you are on Instagram, I suggest following me @biocinematics to see more of this series as I create more molecular portraits.

On a related note, if you haven't yet seen anything on my "Blog 1.0", and you want to catch up a bit on recent news, I'd encourage you to have a peek at these posts:

10th Anniversary: The end of one blog and the beginning of another (and my demo reel!)

Knots and Robots: Recent client work

And now for something (almost) completely different: Job changes and new beginnings

If you want to read some humorous off-topic stuff, I'd recommend these:

Changing a Hard Drive

Bad auto transcription

One thing I would strongly caution against is going right back to 2009 to see the ugly beginnings of learning difficult software. Or… /shrug I can't stop you.

Thanks for reading!

Stuart