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Control

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Hash: SHA512

I thought I'd just write a few thoughts down and see where it goes. I'm having trouble writing down my thoughts. Apologies if I go too fast. I'm not in the mood to be patient.

First things first. I write a lot. My mother is a bibliophile. I am a scriptophile, I love to write. But I don't publish most of what I write. My graphic novel Javantea's Fate ground to a halt not long after it started, so I started a blog called "Making of JF" hoping to gain readership by writing keywords and drawing interesting things a few days per week. Years later very few pages of Javantea's Fate were finished, but 378 pages of Making of JF were done. That's a huge amount of writing. It was a very tough part of my life, so I'm glad that I have that corpus of writing to show what my mind was thinking. But I didn't post everything I wrote. The House MD episode "Private Lives" discussed a person who wrote down everything she was going through. I didn't do that back in 2001, but I was spending a few hours three days a week on it. I can't do that now because I signed a confidentiality contract with my previous employer and one of our clients. They went to bat for me and I owe them my current happy status but I also think that the past four years of not quite radio silence (comparatively) has warped my mind. Of course my mind was warped before I went to work in infosec, but the secrets I've kept have gnawed at me. It's the whole issue of doublethink straight from 1984. I am holding two contradicting truths to be true at the same time. Operational security is incredibly important, information should be made free. But information is power and with great power comes great responsibility. I am an irresponsible person. I don't believe in control.

Let's talk about control. There are more than a few theories on the human mind that talk about control and I'm not going to do them any justice explaining them right now. Let's say that my friend, let's call him Descartes for now says that human beings are incapable of moving. He's wrong, but let's say I'm so furious that I want to prove to him that human beings are capable of moving. So I tell him, if I am able to walk from my current position to one foot in front of you, then I can move and your statement is false. He replies, but how do you know you're moving and not changing my mind about what's going on? Occam's razor? Nope. Descartes isn't having it. So I think again. I am unable to reach out and touch you right now. If I am able to reach out and touch you, I must be able to move therefore your theory is wrong. Descartes is too smart for that. You can change my mind, so how do I know if you're actually touching me?

Read more.

New PGP Key

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Hash: SHA512

This is a quick message to those who communicate with me over PGP or who verify my signatures, I am now using a new key and I am retiring (but not yet revoking) the old 1954fed2 key. Many things I have written are still signed with the old key and many software packages I wrote are signed by that key so it will remain secret hopefully for a year or two. The reason I'm changing keys is because the 1954fed2 key is 1024-bit El-Gamal and is 9 years old. How many keys are 9 years old? The longevity of my key probably has to do with my trust in El-Gamal and my distrust of RSA. Over the past few months I have factored a handful of weak RSA keys and I have done a little bit of cryptanalysis. There are many weaknesses in cryptographic keys and many weaknesses in the computer systems that protect them. We hope that we will avoid these and that our random number generators are strong enough to keep the NSA from reading our personal and business conversations that we choose to encrypt with PGP. We also hope that the NSA isn't able to sign malicious software with our keys or the keys of people we rely upon to provide us with software. But in all, we can only do so much and if RSA is broken or SHA-2 is broken, then we just have to deal with the consequences. Until we know better, we have to use the best judgement we have.

So now for the key. It's been signed by 1954fed2. The key id is CBA783EF. As always, only trust fingerprints or keys signed by keys you have checked the fingerprints for.

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Version: GnuPG v2

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=ua9y
- -----END PGP PUBLIC KEY BLOCK-----

For those who are interested in the OpenPGP format. Here is a parsing of the above public key:

Read more.

Protein Tutorial with PyMOL and GROMACS

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You may have been patiently waiting for the first installment of my nanotechnology blog and you're right to expect great things. I have found myself pushing more and more stuff onto my stack and there will be a time for popping all those off the stack. The first one is what I've been working on the past three weeks.

There are plenty of tutorials for GROMACS but because I had a bunch of problems using it, I thought I would write another one. My tutorial is based on this one, so if you want the original, look there.

First, we need a molecule to minimize*. We could use 1OEI, but let's start with a blank slate. Minimizing an already minimized protein is kinda boring.

Read much more.

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