Went to see some ducks today and took the new camera along (Nikon D60 with 18-200mm Nikkor lens). Don’t miss the exhibitionist squirrel at the end.
Archive for the ‘Visuals’ Category
Photos: A Bunch of Ducks & A Lady Squirrel
September 21, 2008Photo: Chili Overload
July 5, 2008
Here’s another fascinating update about my Chili plant. I first wrote about it last Autumn, then gave you an update about my hand-pollinated winter Chili crop.
I thought that 7 peppers at once was a pretty good harvest. Boy, was I wrong. Above is a photo I just took of the very same plant. It now lives in my parents’ garden and it looks like it’s about to collapse from the sheer weight of all those chili peppers. Incredible.
Fold It: The Protein Folding Game
May 11, 2008
Fold It is a game developed by the Rosetta@Home team (learn more about distributed computing) under the direction of Dr. David Baker at the University of Washington.
It features a new approach to protein prediction. Instead of using a more or less brute-force approach, with a CPU trying lots and lots of possibilities and calculating which ones give the best results, the game uses the human brain’s pattern recognition abilities (with help from a few automated tools) to try to find the lowest-energy folded state of a protein.
It has the potential to be on the cutting edge of a new generation of scientific games that are fun to play, teach you things, and can actually help researchers.
Words are inadequate to describe it, so please watch the two videos below to get an idea.
Is There a DNA Puzzle in Alberts’ Molecular Biology of the Cell?
April 7, 2008
Last November, I bought Molecular Biology of the Cell by Alberts (5th edition). I’m a few chapters in, and so far it’s an excellent textbook, I recommend it.
But there’s something that has been intriguing me for months: Once every few pages, seemingly at random, there are groups of 4 red letters inside pointy brackets. At first, I thought it was probably formatting meta-data, some kind of printing accident. But the second time the red letter popped up in a weird place, I noticed that the letters were all DNA letters (T,A,G,C).
Could this be a puzzle? Is this some kind of clever biological joke by the authors?
If it is, what do these code for? Some well-known protein?
It’s a mystery so far.
Update: Unless this is a well-known joke among biologists (it’s a common textbook, after all) and someone tells me about it in the comments or via email, I’ll probably compile a sequence of nucleotide letters long enough for it to be unique and then Google it. I had my “duh” moment and realized there’s no need to go through the whole 1000-page book and compile all of red letters…
Big Cruncher
March 27, 2008
I love distributed computing. It’s a great way to help science even if you don’t work in a lab or don’t have lots of money to donate.
The only project I’m crunching for right now is Rosetta@home (I’m waiting for Orbit@home).
I’m excited about it because computational protein/enzyme/RNA design has the potential to move biotech forward a great deal and cure many terrible diseases, help with bioremediation and clean fuel production, and increase our understanding of biology in general.
So I was surprised when I looked at Rosetta@home’s Top Computers list and saw that my new Mac Pro ranks #4. That probably won’t last forever since the project has almost 200,000 users and is still growing at a good pace, so I took a screenshot for posterity (above).
Technology Review recently published a piece about Dr. Baker’s work (the head of Rosetta@home and of the Baker Lab at Washington University) and what they call “a major step forward for computational protein design”. Check it out, and if you aren’t already crunching, I strongly encourage you to join a project.
Idle CPUs are sad little unproductive things, wasting their potential. Give yours something interesting to work on.
Made me Smile
March 9, 2008From the preface of Roger Penrose’s The Road to Reality: A Complete Guide to the Laws of the Universe:
Considering the current state of my math skills, I expect to look like the third drawing most of the time.
Photo: Winter Chili
February 14, 2008
Last November, I posted some pictures of chili peppers I was growing. Here’s a whole new batch: I pollinated the flowers by hand and 7 of them turned into peppers. Some are still green, so they’re harder to see.
Ode to my CPU
January 30, 2008
This is a picture of the CPU that has been in my desktop computer for the past 4 years. It is an AMD Athlon 64 3000+. One “Windsor” 90nm core running at 1.8 GHz, fitting on socket 939 with dual channel memory.
There’s no problem with it. It’s still working, and has always been dependable, running cooly even when I pushed it to 100% usage with distributed computing projects. But I’ve replaced it with an Athlon 64 X2 3600+ (2 cores running at 2 GHz). These are so cheap now, and I figured it would be a good way to do more data crunching inexpensively. I know that my computer will keep being used for a few years - if not by me, but my parents or someone else - so more than doubling the amount of scientific work it can do makes a difference.
I don’t get sentimental about objects. I don’t collect stuff. But holding that CPU in my hand made me realize how fantastic our technology is, and how many great things it allows us to do. Had I been born in a non-networked world without inexpensive computers, there is so much things I wouldn’t know, so many people I never would have connected with, so many books unread, so much music unheard. I wouldn’t have the job I have now, and you wouldn’t be reading this.
I certainly wouldn’t be the same person…
So this is my homage to my CPU.
In the Mail: A.I. & Neuroscience Books
January 14, 2008
Photos: Trip to New York City
December 24, 2007I went to NYC for business between December 11th and 14th. Here are some photos. More on my Flickr account here.
Me looking out the window.
Here’s what I was looking at. They were removing snow from the plane.
Now it’s our turn. First orange stuff…
…then green stuff.
Mark Bittman’s Pasta Sauce
December 8, 2007After watching this video of New York Times food columnist Mark Bittman, I decided to try his pasta sauce myself. The video isn’t really about the sauce, rather it’s about the concept of changing the pasta/sauce ratio, something that I think makes lots of sense. But the sauce looked really good and easy to do…
Here are the results (high resolution pics here):
It was delicious!
In the Mail: Macbook
December 6, 2007For someone that spends his days and many of his evenings on a computer, I’ve had relatively few computers. I tend to keep my PCs for a very long time, all the while obsessing about potential upgrades (and never actually pulling the trigger — there’s always something better coming soon).
Well, I finally did it. I’ve wanted a Mac for 4-5 years, and now it’s here:
In the Mail: Molecular Biology of the Cell
November 26, 2007By Alberts & al. 5th edition. According to Amazon, it’s supposed to come out on December 31st, but here it is in all its glory:
Related:
Photos: From Autumn to Winter
November 22, 2007
In the Mail: DNA Crystal
November 19, 2007
The photo doesn’t do it justice. It’s beautiful.
See this post for more details about Bathsheba Grossman’s Art.
Photos: Autumn Part 2
November 19, 2007This is a follow up to this post. You can see high resolution versions of all my Autumn-themed photos here.
I’m not sure what this plant is, but I’ve noticed that each year during autumn it creates this little red heart-shaped thing. I think it’s beautiful.
Update: I think I know what that plant is. Physalis alkekengi, a.k.a. Chinese Lantern.
Bathsheba Grossman’s Art
November 14, 2007
Antichron
I just discovered Bathsheba Grossman’s art, and I’m hooked.
I spent a long time looking at each sculpture and crystal laser etching on her site and ended up ordering the Mega DNA crystal along with the White light LED stand. I’m pretty sure I’m going to get more at some point in the future.
About the laser crystal technique:
The points are tiny (.1mm) fractures created by a focused laser beam. The conical beam, with a focal length of about 3″, shines into the glass without damaging it except at the focal point. At that one point, concentrated energy heats the glass to the cracking point, causing a microfracture.
To draw more points, the laser is pulsed on and off. To make the beam move between points, it’s reflected from a mirror that is repositioned between pulses. The mirror is moved by computer-controlled motors, so many points can be drawn with great speed and accuracy. A typical design might use several hundred thousand points, or half a million isn’t unusual in a large block, each placed with .001″ accuracy.
Here are some other cool crystals:
DNA Polymerase
Our Neighborhood, 10 Lightyears to the Inch
A Cross-Section of the Calabi-Yau Quintic
Enough crystals for now. Check out these sculptures:
Soliton
Photos: Autumn
November 13, 2007It’s a nice day so I decided to take a walk and snap some photos around the neighborhood. It’s finally starting to look like autumn even though it’s still warmer than historical averages. It isn’t rare to see snow this time of year, but last year we had to wait until late December.
