Feb 17, 2014

"Life At The Speed Of Light" - J. Craig Venter REVIEW

Introduction - Catching Up On Reading

As you see in a lot of regular personal blogs, I've neglected to write for quite some time. I've made New Years Resolutions in the past to update more, but not this year, mostly because I don't find myself reading my friends' blogs as much as I'd admit. Though this last week, I was updating blog posts on my professional site, based on industry-related topics, and forgot how fun it was to simply write out thoughts and then be able to go back on them for reference at a later date. Particularly, I was bummed to find that a lot of the writing I did for previous companies is no longer available online (I'd really love that Googlejuice, to be honest), because it feels like lost months and years. Some I've been able to dig up in my email archive, and was thinking of updating and reposting them somewhere, but until then, I thought it'd be nice to once again write something.

In going back again that I haven't been reading friends' posts as often as I should, I have recently made the decision to severely reduce the amount of regular web articles I read nightly, as I realize at the end of each week that I've spent hours and hours reading, and don't necessarily feel like I've learned anything. Without going too far into the debate of the quality of articles online, it is pretty clear that most are being written for sake of SEO and social shares, and are mostly awful. I'm no better, but I have instead decided to dedicate the time towards books, as I just have an ever-increasing virtual library of books I've been "meaning to read." Although I have been reading pretty regularly for the last few years, they've been mostly referential how-to pieces that aren't really meant to be enjoyed cover-to-cover, or even particularly finished at all. So it was with some surprise that in only six short weeks since the new year, I've completed 3 books, and felt the disappointment of completion that I hadn't felt since college.

So with that, I'll be killing two birds with one stone: reading more, and writing about what I read. This'll be very casual, and probably reveal how little I understand of anything, but it's something to just generally practice and play around with. Again, in the tech world, it's easy to forget how fun doing stuff is.

"Life At The Speed Of Light" by J. Craig Venter

I've always had a long-running, minor interest in genomics, despite my godawful understanding of Biology and Chemistry, and I've been interested in Venter for years. I read A Life Decoded when it was published in 2008, and thought it was a very clear and understandable explanation of the history of molecular biology, at least as far as the 20th century, and Venter gave a taste of where the field was going in the future. Life At The Speed Of Light is more of a published thesis of this future.

In a word, every living thing on this planet has a DNA sequence composed of four nucleotides that describe its common and unique characteristics. Thus, every living organism can be described by its basic coded sequence, which we can infer into a coded sequence that can be read and written like code in a computer. So not only can we define biology like reading the words from a book, but we can actually articulate where in the code we want to find information, and where we want to control information. For example, if we want to find our susceptibility to a hereditary disease, we can examine our own DNA code and see the percentage likelihood of developing the disease, and take proactive measures to fight it, as Sergey Brin is researching and fighting Parkinson's Disease. Or, if we want to generate alternative fuels and combat global warming, we can create an algae that will breathe in carbon dioxide and breathe out methane. Not only is genomic sequencing the next step in understanding our world, but also in building upon it.

Life begins with a short history of molecular biology, and right off the bat we see Venter's notorious character as he blames the lack of basic scientific questioning as "holding us back for 50 years" in research and understanding, when scientists believed proteins were the source of genetic information, not nucleic acids. Forward to modern day, when scientists are now able to decode genomes at an ever-more faster and affordable rate, and are even able to specifically build custom genomes one sequence at a time. The J Craig Venter Institute recently "created life" in the lab this way, by rewriting the phi X 174 virus with a custom-implanted sequence, and it was able to live and grow on its own (I already know that last sentence gave a thousand biologists nose bleeds). The most exciting chapter describes projects undertaken at the International Genetically Engineered Machine (iGEM) program, which has students and experts work projects as fun as, "bacteria that glow in the dark and, in the case of the MIT “Eau d’e coli” project, that smell like wintergreen while they’re glowing and like bananas when they stop."

The final chapter posits the name of the book topic, whereby once an organism's genetic code is sequenced to it's base 4 letters, we can transmit the information faster than the organism is capable of traveling: as data traveling at the speed of light. The closest and most practical current implementation of this is in vaccine generation. Currently, it takes approximately 28 days to develop the recipe for a vaccine, which then have to be manufactured in a lab and either dispersed directly or sent to hospitals. Venter suggests that we can decode a disease within several hours, generate the vaccine within days, and email the information to wherever its needed to be manufactured to a scale much larger than the current process, and in a quarter of the time. In the more abstract implementation of data-transferring genomes, we can send rovers to far-off planets, where they can decode genomes and email the information to us, and we can build and study the alien life here at home.

My Thoughts

Again, biology and chemistry were never my strongest fields, so I can only trust that the descriptions are sound. Venter's ambition is very well known, so he publishes Life to say, 'this is how we get here, this is where we are now, here's where we should go and how I'm going about doing it.' He did not mention any of the ethical arguments against his research, which would have the opportunity to proactively counter-argue skeptics, but again, his ambition pushes him forward. In Decoded, he describes how his invention of the "shotgun technique" of sequencing was rejected by the science community, and was later adopted as the standard, so I'm not surprised he didn't want to waste his time debating the issue.

Like I mentioned before, the anecdotes of the science teams working on fun, experimental projects were more interesting to me, and I liked to think of the prospective uses of the field. The section on how a genomic lab can improve the time to deliver vaccines, compared to the lousy delivery of H1N1 in recent years, was the most fascinating to me. I would have liked to know more about the fields of genetics and bioinformatics in general- what applications have come in recent years, and what are the challenges currently being faced.

This is by no means Venter's last book, and I haven't read any other on the subject, but like I said, it's a field with an absolute infinite potential both in our current understanding of all life, and what we want to create for ourselves now, so I'll probably check out more in the coming months.

Feb 10, 2014

Jun 7, 2013


My new girl and the special bed I had made to keep her toasty

2007 - Four-Hour Workweek Method
1) Make up a few products with several names, descriptions, and images.
2) Buy Google Adwords on each product and variation.
3) Track which product gets the most clicks, and start selling that item.

2010 - Kickstarter Method
1) Design and manufacture a product, and prepare your business model for producing at scale.
2) Create a Kickstarter campaign to raise money to scale up production, and reward "backers" with lower-priced "pre-orders."
3) Ask all journalists that write blogs on the success of your Kickstarter campaign to link to your store site.

2013 - Reddit Method
1) Build a product.
2) Post a pic to Reddit that either you or "your friend" made it themselves on a weekend for the hell of it.
3) Launch your Etsy store two weeks later.

Dec 28, 2012

The Hobbit: High Frame Rate Is A High Disappointment

Like any other industry, the film industry loves to get into a fury about everything. And it really makes sense, because Hollywood is a multi-billion dollar industry whose impact is felt through businesses and customers all over the world. And when it's stride has been built and standardized for the better part of a century, change is a big deal. Especially when it concerns a blockbuster like The Hobbit, the cinematic sequel to a multi-billion dollar franchise.

Director Peter Jackson already broke some solid ground with everything about the Lord Of The Rings, and came out very successful in the end. After already converting over to working on a purely digital format (The Lovely Bones was his first digitally-acquired feature), he quickly moved onto 3D- a process a lot of great filmmakers quickly adopted. Audiences, however, have been slow to praise 3D because the picture is eye-straining and the premium on ticket prices make it difficult to believe the experience is that much better. But ticket prices be damned, the theory that a higher framerate in projection can reduce the headache. So after countless press from director James Cameron that 48fps would solve all problems, Jackson was the first feature director to stick his neck out to this new paradigm.

My friend Renn Brown wrote a fantastic article on CHUD about how all of the criticisms and debate of the new format are a fallacy- no one has said all features should be shot this way, and in fact Jackson even said this is a "tool" to tell the story (rather, it's only the brush and not the whole "canvas," as Brown puts it). Digital projectors are able to show a wide range of framerates, so it's perfectly possible for a feature to be 24fps, become 48fps for a particular sequence, and then revert back.

So how does the Hobbit come across in 48fps 3D for a full three hours? In my opinion: not great. And I was bummed about that. I absolutely love new, experimental processes, and that the medium is what we make it. I've never minded 3D (over time, I've concluded it isn't worth the additional 50% premium in price for the ticket). I once had a conversation with a director I worked with on a 16mm short film that had a 60p television sequence that we were both getting a little tired of watching 24fps all the time (this comes after the 24p evolution and HDSLR revolution has made nearly all video we see on television and online 24fps). I first saw the film first in 24fps 2D, and loved it. So when I saw it in 48fps 3D, I was heartbroken how disappointing it was.

I don't want to call it the "disaster" it feels like everyone is describing it, but the fact is I was conscious about it the whole time. And as an audience member, if I don't get lost in the story and characters and only think about how everything looks sped up and cartoony, that's a big problem. Some sequences in the new framerate I thought were fantastic- contrary to Vincent Laforet (whose long article inspired me to write out my opinion), I thought the whole Gollum scene was beautiful. That was one of the few sequences I thought the 3D looked great and the high framerate was not a problem at all. But that was the very first sequence they shot (so I wonder if the crew worked harder on that sequence during production to get it perfect than they did on the rest of the film), and the movements of the camera and characters weren't as grand as other sequences.

What I'm very curious about is what will happen to the next two films in the series- production has ended and is in the can with this 48fps style. As we see, there can be 24fps 2D and 3D extracted from the material (which, as far as 2D, I think looks great), so will the ratio of HFR releases be reduced to just a handful of theaters? Or, to put it more accurately, just be through a handful of showtimes on the same projectors that screen it the other ways for the rest of the day? Will James Cameron back down on his own loud, public stance that this is the future and we just need to get used to it? I highly doubt it.

What I wonder is could this have been experimented with in a different way? Particularly with 2013's release of Oz: The Great and Powerful. The Wizard of Oz was one of the first full color features, and it aesthetically fit to the story- the real world is two-toned sepia, Oz is beautiful 3-strip technicolor. Could the real world in Great and Powerful be 24fps, and Oz be 48?

Luke Letellier prepared an example of what this looks like by applying a frame blending effect to the Hobbit trailer, making the 24fps version into 48fps. If you can ignore the artifacts of the filter (particularly in quick movements, edges have an odd "stretching" quality), the video is pretty accurate.

Dec 5, 2012

My Digital Shoebox, Pt. 2: Film

Fishing Girl (restored) by Brandon Buck (brandonthebuck)) on 500px.com
Mom fishing, circa 1956.

A few weeks ago, my grandfather passed away, so my family has been working on handling his estate and personal items, which of course includes a lifetime of photographs. For the memorial, my mother handed me a shoebox of some prints and slides she came across that she wanted me to scan and project on the wall during the ceremony. The family thought I did so well with this that they handed me all of the remaining slides they've found, and asked me to scan and share them all.

This is something that's interested me for some time (preservation and restoration are subjects I've covered here before), and it's something I always thought I'd pursue as a long-time hobby- collecting and restoring old photographs. Of course, this is one such service photography stores around the country are continuing to offer, which is excellent for most people, but I wanted to get a good understanding of what exactly it would take to get a good digital file out of these old keepsakes.

I'd want the image to be as high-quality as possible, so I can essentially just archive it safely and store it somewhere without wanting to re-scan the image, as well as be able to treat the scanned file in the same way I treat my digital photos. The way I treat my digital photos, of course, is by saving them all as Adobe Digital Negatives (DNG's), which I can play around with without degrading their quality ("lossless"), which not only includes changing colors, but changing exposure levels and performing lens adjustments after the fact. I know I may not be able to do quite as much modification as my digital stills, but if we spent so many decades making digital photography parallel film, than I should be able to make my film parallel my digital workflow.

I'm still only into the first hundred slides because the process is tedious and my system is buggy, so I have to take care of things one at a time. But I want to say right off the bat that Kodachrome deserves as much praise as it's ever been given- some of these slides are over 60 years old and the color retention is absolutely incredible.

Kids watching TV by Brandon Buck (brandonthebuck)) on 500px.com
Kids watching TV, May 1961. Kodachrome, unrestored

This picture of my aunt and uncles is over 50 years old, and the color representation looks flawless. And I doubt this slide was kept in any better care than the shot below, taken on Ektachrome.

Lunch on the mountain by Brandon Buck (brandonthebuck)) on 500px.com
Lunch on the mountain, circa 1956. Ektachrome, unrestored

The green layer of emulsion is almost completely disintegrated, leaving the red and blue layers behind (I thought blue would be the first to go because it's on the "weaker" end of the visual spectrum), to the point that it's almost beyond restoration.

Lunch on the mountain (restored) by Brandon Buck (brandonthebuck)) on 500px.com
Lunch on the mountain, circa 1956. Ektachrome, restored

This was a quick pass at just modifying the colors in the scanned sample, beyond this point I'd have to add color into the picture to bring it back to normal.

From what I see as far as the equipment goes, there's not much available that's affordable and easy. I'm using a flatbed scanner with a light adapter built in (a Epson Perfection 4490 that was previously my other grandfather's, no doubt top-of-the-line at the time he purchased it for the exact same endeavor). You could buy this unit for a couple of hundred bucks, but a dedicated film/slide scanner runs in the thousands. Fundamentally I'm not quite sure what would be the difference- controlled light blasts through the film onto the sensor. The difference with the flatbed is you've got a giant pane of glass that can't possibly be in good condition if you use it to regularly scan papers or solid objects- any scratch in the glass reveals itself in your scanned image. Additionally, placing a cardboard-bound slide introduces spacial distance between the film and the glass surface to be scanned, so there's doubt whether the scanner is properly "focused" on the slide. And there's only one light source that I can't figure out how to calibrate, nor do I even know if it's truly "white" light and I'm getting a good representation of all three color channels.

On the plus side, the scanner does include an infrared light in addition to the regular light. Infrared light completely passes through film emulsion, meaning if dust or specs are on the filmstrip, they will be "seen" by the infrared light, and the emulsion will pass through- this allows us to know the difference between grain or specs that are supposed to be a part of the image.

Now in terms of the actual files being created, I was disappointed to find that although I can directly scan straight into Photoshop, I'm not able to control the settings of the scan as much as I'd like- I'd have to bring it in as a jpeg, tiff, or pdf file. However, I'm not alone in this disappointment, and some people have created third-party software that allows you more control of your scanner. With Vuescan, I'm able to
1) Create a DNG file (technically a DNG wrapper to a TIFF file),
2) Utilize the infrared channel.
Additionally, Vuescan is able to do multiple scans of your pictures at varying exposures, so you'd be able to create an image with HDR-like range- change the exposure after the fact, or at least retain the image detail that's lost in the highlights or shadows. Unfortunately this feature doesn't come without a bug, which I'm not sure where the error lies, in that the multiple exposures aren't perfectly aligned, so the entire picture comes out blurry.

Girl on carnival horse by Brandon Buck (brandonthebuck)) on 500px.com
Girl on carnival horse, circa 1956. Kodachrome, unrestored

Researching the matter further, scanning via flatbed or dedicated film scanner is also not ideal. True experts perform a process called "wet-gate scanning," which is soaking the film in a chemical solution as the film is scanned. This utilizes light refraction to fill-in small scratches to the plastic, as well as makes the scan appear sharper and more vibrant. This is standard for medium-format photography and feature-film restoration, but no machine is available in the consumer or even pro-sumer level that does this. And it's not even possible for cardboard-bound slides- you'd have to remove the cardboard casing around each picture, and then after the scan you'd be left with an individual frame that you'd either have to re-case or store loosely in a slide holder.

I did come across one process a lot of hobbyists have done to handle the bulk of limitations of scanning, and that's by creating a special casing in front of their DSLR camera lens to hold the slide or negative and take a digital still shot of the film. This way they'll have a camera raw file of the picture at a low file size (each of my scans are coming in at around 250MB a piece, as opposed to the 20MB my Canon Rebel T3i creates), and be able to go through pics much faster than the flatbed process (and much, much, MUCH cheaper).

As you can see, I'm not the only one with this problem, and the solution is a lot more complex, in my opinion, than what's being offered on the market. Truth be told, I haven't checked in with my local camera shop to see if they're offering solutions that affordably meet the challenges I'm facing. Maybe the tech is sure to evolve to this point, and there's simply been a lack of market demand. I'm sure this is going to turn around very quickly as most of the world will start finding themselves coming across this exact problem- billions of photographs that aren't as accessible or secure as the rest of our library. Especially as the last generation of film-shooters are going to leave behind lifetimes of memories for the next generation to sort through.

Gunning Grandpa by Brandon Buck (brandonthebuck)) on 500px.com
Gunning Grandpa, circa 1951. Kodachrome, unrestored

Buckshot Creative

Finished off a new portfolio reel for what'll be the official title for the videos I produce ("Who shot that? Buck shot that.") This coming year should be fun.