This is dedicated to all the Hackers and the Crackers
To the Hackers and the Crackers
I see in binary, I speak source code
Step on my toes, I'll post a million jpegs if you're in a fag pone
In your digital stance, getting firewalled ho
Cause I'm riding the net in my 6-4
I was a dick with my 56
Now with my cable, I'm able to get that stable
On the out, my name is Ace and I'm a Leo
On the digital highway, my name is Neo and I'm a hero
In a flash, I'll screw you on burning dreamcast
You need some ISO? Let me through my hard drive rifle
Our exchange you could never stifle
In a digital hug, you just caught the love bug
I bootlegged your CD
I caused a fight between Un and Jay-Z
Your CG, it's all gonna be free
Whether we take it by force or we take it nicely
You feel that rattle in your bones
When I tell you we just hacked out Jones
And NASDAQ leaves you flat on your back
Cause I am he who loves to hack and crack
This is dedicated to the hackers and the criminals
Serial phones, source codes, ISO
Hello and welcome to Binary Revolution Radio
Episode number 1414
March 28th, 2006
I'm Strom Carlson
I'm Black Ratchet
And this evening we have with us is Dr. Zygmunt again
Two weeks in a row
Wow, yeah, I guess I'm just a lucky guy
Yeah, you're just really cool and everything
With the whole getting in there
And setting everything up
And not having to answer phone calls
And that kind of stuff
Yeah, you know what I think it really comes down to
Is I kind of live on IRC
So you kind of just constantly exposed to my banter
And you have no choice but to succumb
And invite me onto the show
Exactly, man
I tried to get on the show
And like I was thinking
Man, I can't have Dr. Zygmunt on this week
And then I started going into like twitches
And getting to shoot chills
It was like, oh man
But you're here now
So that's good
Yeah, sure, whatever
I guess you could kind of
We have a subtitle over this episode
This is Episode 141
When Bad Servers Attack
Oh yeah
Yeah, I don't know what happened
It's like the dreaded Voipocalypse came about today
What was that 141 in the old KP style?
Oh yeah
The rooting codes
We'll see
121 was inward
131 is directory
I forget what
I think 141 might be rate and root
Yeah, that sounds right
Hold on
We'll have to actually look this up
Are we going to have that fight again?
KP 141
Let's start
ST
So we start at 2600
Meeeeee
Yep, routing
Ooh, very good, Strom
You get an A-plus this evening
Yay
So it only followed that we'd be having rooting problems tonight, right?
Well it wasn't
I don't know what the hell was going on
Like
Well for example
We suddenly couldn't like
I couldn't
Dial into the bridge on Strom's computer
And we're going
Okay, so
I got on the bridge
And then I was going to conference Zygmunt on
And then all of a sudden
New phone was started acting up
Like
Your phone did ring, Zygmunt, right?
It did, and then I got a dial tone
Yeah
Which was nice
Yeah, and I couldn't actually use one of my alternate providers
Because I just didn't have that set up on my phone correctly
Which is something I'm waiting to have to look into
And
Ugh
It may have to do with the fact that
But we are here
I just recently upgraded my asterisk box to 1.2.5
Although I don't think that would cause any problems
I mean, it is stable after all
This is a big change from the 1.0 series to the 1.2 series
Well yeah, no, but I went from one
Especially in the output on the console
Yeah, but I was running 1.2.4 last week
Oh, that's not a big thing then
Yeah
I've known that you'd be up to date on your asterisk version
Screw you all
I'm still running subversion
They actually fixed the Eek's bug
Just in case anyone's curious
Oh, did they?
Okay, good, I can go back to that then
Yeah
I was running Bleeding Edge for a while
At least I assumed they fixed the Eek's bug
That could be the problem tonight
But
Well, it wouldn't have gotten to stable, would it?
Well, no, no, no
What the weird part is
Like, last night I was actually
I was trying to verify some payphones for Yapple
Yeah
And the, you know, my Eek's trunks kept on, you know, really getting messed up
So I was like, okay, fine
We'll just, you know, redo it right here, right now
And it seemed to be working fine
So I assumed the bug was fixed
But
Who knows?
Maybe it was me again
And all this stuff is causing issues and everything
Might be
Maybe we just got lucky
Or unload
Well, technically we did get lucky
So thank goodness
Yeah
That we actually got on the air
So
What did you guys have to spare?
Like three seconds?
Fifteen, I believe the song started
Um, something like that
I mean, actually what happened was
I saw
Just before I started the music
I saw the
The streaming app that goes from
From my computer out to the
The hack radio server
I saw it drop and then reconnect
Oh, wow
So I was like, whoops
Crap, yeah
I was literally tuning in
And making sure that we were in fact streaming live
So I didn't have to say
Oh, hey, guess what guys?
It's playing last week's episode
Well, you know, whatever
Is it Murphy's Law?
Anything that can go wrong, Will?
Yeah, something like that
Actually, um
Well, since we're talking about Murphy's Law
The Murphy's Law is not
Whatever can go wrong, Will
That's actually Finagle's Law
Oh, sorry
Murphy's Law is
Oh, shoot
I forgot the actual text
It's like
If there's one of two ways
Someone can put
Someone can do something
They'll always do it the wrong way
Oh, really?
Yeah
According to
Murphy's Law
Also known as Finagle's Law
Or Sod's Law
Is a popular adage in Western culture
Which broadly states that
Things will go wrong in any given situation
Well, you can't have a chat about Murphy's Law
Without talking about Occam's Razor
At the same time
That's true
Everybody saw, uh, what was the movie?
Contact?
Yeah, well, the simplest solution
Tends to be the best one
All other things being equal
Yeah, gotta have love for all your laws
Remember, kids
Whatever will go wrong can go wrong
Not just a good idea
It's a law
Exactly
Are you gonna have McGruff say it next?
Only you can take a bite out of
Telephony
Probability statistics
Statistical probabilities
Exact
Bad weight routing statistics
Rawr
Only you can fundamentally restructure
The nature of mathematics
So
It wouldn't be too hard, right?
No?
How many, how many, uh
Oh, let's not get into that
That'll take 20 minutes to get through
The difference between Cartesian and non-Cartesian mathematics
Yeah, so anyway
In housekeeping
Despite all the problems we're having right now
I did go to great lengths to
To set things up, uh, well for our toll-free number
Which now, when you call it during the show
Roots you to, uh, to Zygmunt if he's answering the phones
And if you call it not during the show
It automatically roots you to our voicemail box
So you can now, uh, you can now call us at any time
And it will reach you to the correct place based on the hour of the day
Ooooooo
And also, due to, due to popular demand
And by popular demand, I mean, I heard three people fetching about it
We have a free world dial-up number down as well
Oh, what's our free world dial-up number?
Help to include that in the shoe notes
Um, let me see, I put everything up
There's a post on the, on the bin rev forums actually
Under, uh, I made it a sticky under hacker media
Oh, you mean people actually go to the bin rev forums?
I mean, I don't
Yeah, well you're looking that up
Anyway, our normal, our normal call-in is 888-9-BINREV
Right, and our free world dial-up number is 758-103
Oh, six digits, I thought they were up to like seven now or something
No, no, no, wait
Yeah, six digits starting with seven
Yeah, I have a five-digit, I believe
Yeah, I've got a five-digit too
Oh, aren't you guys classic?
It's like, it's like slash dot user IDs, you know
My user ID is lower than your, therefore my fellows is larger
That sums up slash dot pretty well
Yeah
Um, our UK call-in, which I assume still works, is 0845-646-0102
Yeah, and what I actually will do is sometime between now and soon
I'll get a call-in number that goes directly to our box so I can verify that it works
And I will post that number as well
Well, yeah, well, you just need to talk to the guy, I think he talked about setting it up directly in or something
Okay, or someone else, who cares?
Anyway, do we have any other housekeeping type things going on?
That I think is it, I'm just relieved that we're actually casting live now
You're not the only one
Yeah, and of course this is the week that both, you know, Strom decides to show up ten minutes before the episode
Hey, I didn't decide that
Well, I'm sorry, I'm sorry
L.A. traffic dictated to Strom that he show up ten minutes before the episode
Yeah
And, you know, I was sidelined enough that I had to show up fifteen minutes before the episode
So therefore, like, I couldn't suddenly get on the bridge and I have to pin it on him as soon as he shows up
And I'm like, ah!
I was ready, for the record
Yeah, you were ready
Yeah, we'll use that
He wants the most well-prepared
Alright
He gets his bin rev radio preparedness merit badge
I only had to do five shows, nice
I don't know how many shows I've really done, but isn't that how those merit badges work?
You gotta do X number of things?
I think so
Oh, it depends
I'm on a car room with my vast Boy Scout knowledge here
Eagle Scout, baby, yeah!
But anyway
Yeah, well, no, you had, like, a requirement, like, you know, do, like, you know, X amount of things
Or, well, everything had, like, a list of requirements, but some of those requirements were like
Demonstrate five ways you can, you know, do, move someone's spleen in the middle of the woods or something
Just stuff like that
You can do that by rubbing two sticks together, right?
I can start a fire by rubbing two sticks together
What about taking out somebody's spleen?
I can't, I can't do the spleen thing
I didn't get, I didn't get the, uh, spleen removal merit badge there
It's a splenectomy merit badge
A splenectomy
Is that what it is?
A splenectomy?
Well, you can attach ectomy onto anything, and it means taking out of, or excising
Yeah
So, a zigectomy?
It's what it removes even from the episode, the zigectomy
I can just press the button here and perform a zigectomy, but, uh, I wouldn't
I wouldn't
We probably would never be able to get reconnected
Yeah, exactly
Yeah, I know, tell me about it
This, this, this, this, this, this, this, it's like this button on Strom's desk that says
Drop Zygmunt
It has a little post above it saying no
No, it looks like the button, it looks like the button from Wargames
It's like neon red, and it's got yellow and black stripes around it
And the glass case over it, right?
Exactly, the glass case with the key
With the key
Well, that's, that's a very good idea, Joshua
Oh, I mean, I actually, I actually had like this, I, I was, I was dumpster diving
I don't know, we're very veering off topic here tonight
We were, I was dumpster diving, like, back in college
And I found this massive board, and it had all these buttons on it
And it had like, you know, the two keys, and all like the buttons you could push
And the best we could actually tell it was for like, uh, some type of autoclave
Or mechanical sterilization setup, because we actually found it at the biology lab
But it looked very impressive in my dorm room for a while
Had, had like the keys, yeah, had the keys, like the two keys on each, either side
And I didn't know if you had to turn them at the same time or whatever
But it had the, um, it had like, you know, the big red button with the, with the little glass thing over it
That you can't press it accidentally, a little molly guard there
So, uh, you were nice and sterile, unlike every other college student
Yeah
Actually, someone did a, someone did a study on, um, college floors, and they were actually quite clean
The floors in like, college dorm rooms?
Yeah, it was amazing, because they're all usually, uh, because most of the, like the freshman dorms are, uh, tile
Or at least the ones that I've been to
So, like, you know, just can't actually get horrible stuff on them
I wonder if they planned that on purpose
They're like, huh, you know what, it's their first year of college
They're probably gonna be doing a lot of drinking
And it's a lot easier to clean up tile
I'm sure, I'm sure it is
I bet you somebody somewhere has to think of factors like that
Mm-hmm
That'd actually be a kinda cool job
Be like, hmm, what could go on, go wrong in people's first year?
Let's not have any two-story buildings
And, uh, you know, let's not make the windows wide enough so a couch can sit outside
Actually, my freshman dorm was
Your freshman dorm was what?
I guess that's it for
Did we lose a ratchet?
Oh, no
Alright, moving right along
My freshman dorm
Has since been totally demolished and replaced with a nice fancy one
Ah, fancy, fancy
Yeah, mine, uh, I didn't have, I haven't been in the dorms yet, actually
That has not yet been a part of my college experience
You know, that's actually a good thing
We're not allowed to call them dorms at school
They're residence halls
You're actually not allowed to call it a dorm?
No, it's a residence hall
Oh, terrific
They give you one of those dirty school looks
Like, dang, how old are you, five?
Crazy, crazy
Yeah, I don't know, I, uh, I think here's a message from Ratchet
Err, what happened?
What happened?
We lost you
Well, I'll skip ahead and talk about my personal hacking story
Okay, why don't you do that? I'll try and get Ratchet back
That sounds like a good idea
See, we were so lucky to get him so close, you just had to go
Anyway, so my personal hacking story, it is going to carry over again
It is about my currently vaporware version of my search engine
It is getting really, really close
I have the crawler, it's all nice and set up
I'm hoping to release, I can't release the entire crawler because it was work for a company
But I want to release just a package of the way that I parse the robots.txt file
And that's something for them from the robots exclusion protocol
And it's really only relevant to web crawlers and spiders
And it says what they're allowed to crawl and what they're not to
So I'd like to release that as a little library
But the search engine itself is going along
It's been brought online
And a couple of people have given the URL out to
Because they're going to test for some SQL injection
To see if I missed anything
But hopefully next week I'll be able to post in the forums
The actual URL
And we'll give everybody a chance to go in there
And just see if they can't damage it
So, it should be a lot of fun
And I'm looking forward to finishing that project up
It's been definitely a big learning experience
And there's a huge difference in just
When you really think about it, it sounds like it'd be easy
Like, you know what, we'll just throw a bunch of words into a database and search through them
But you have to consider so many other things
Like you can't, normally what you would do if you're going to search through a whole bunch of text for a specific string
In SQL queries, as long as we're talking about that
Specifically for this implementation, I use Postgres
I would have liked to have used Oracle
But, you know, Oracle is expensive and I don't have that
So anyway, normally what you would do is like a likes search
And what that'll do is it'll, it slows anything
And it searches the full text of everything as you're going through
But it's criminally inefficient
So what I'm using is what's called the t-search vectors
And that is a plugin, it's in the contrib directory of the Postgres download
If you download the full source code
But, what's nice about the t-search is it actually stems and stops as it's going through
What that means is, as you're indexing pages
It takes out a's and the's and is
And all those little words that would just make the query take longer
And it stems, meaning if you have, hmm, what are two words?
Well you know you have words that end in ing
That can also end in ed, you know, suffixes, things like that
They all get pulled off and so that you just have a cache of the actual word itself
Now when you do an actual search, you can't just search this special created t-search
Forum or table
It's actually a column, a column in a table
But you can't just search it with a normal like or anything
You also have to use the t-search vectors again
So we go ahead and that's tons of fun
And, you know, the relevance isn't quite perfect, it needs to be tuned a lot more
I think what I'm going to do is put more weight to the value of the text that's actually in the URL or in the title
But I didn't really think about that in advance
And that's why it's always important to make sure you have a really good design out for what you're going to do
But I think that would really help relevance
If anybody else has any good ideas, if anybody's ever, you know, researched or worked like that
Because I'm not really a database programmer, I just like to mess around with everything, I guess
It's a great way to learn everything that's out there, just to try new things
So, that's what's going on with my search engine
Hopefully soon we'll get that out
And hopefully soon we'll get the rest of the crew back on
Oh, is that what we hear them?
Would that be Ratchet?
Boy, the gremlins are out tonight
Alright! Just as I ran out of stuff to say
That's pretty good!
Thank you, Zygmunt, for carrying the show like that
You might have a future in radio
That's what I could do
I'm going to need a shot of liquor or something after all this
Yeah, I know, tell me about it
Well, we've moved on to the more reliable semi-cellphone landline
So, shall we go into the email?
Yeah, let me check to it
Let me see if I can bridge that music in
Hold on
If not, we may just, you know
Should we just start reading email and not tempt the gods at this point?
Let's try it
Try it
Our first email is from Cypress
And he says
I was just sitting in school where my buddy installed Tor
And I was wondering if it would be possible to run a massive man-in-the-middle attack on Tor
Is that possible?
Could you just run FragRouter and or similar programs and just collect user data and passwords using the SSL dump?
Keep up the great work on the show, guys
P.S. I'm the guy that emailed you before about the weird chemistry teacher and that you go
Plus plus Cypress
I actually wonder if it's plus plus Cypress or just pronounced Cypress or
Double cross Cypress
Yeah
It actually sounds great
Double plus or double cross?
Yeah
You answer the email, I'm getting some alcohol
You know, sounds like a good plan to me
That's what I should have done when I got my cell phone
I was right in the kitchen
Ah, what a well
Anyway, I actually was thinking about this for a while
And then I decided, hey, let's go actually consult the TorFact
And the TorFact states
Every Tor server has a public decryption key rotated once a week
When Tor clients establish circuits at each step, they demand the Tor server prove knowledge of its private key
That way the first no in the path can't just move the rest of the path
How do clients know what the servers are and how do they know that they have the right keys for them?
The directory servers provide a signed list of all the approved servers and that lists are set as a set of self-signed certificates from each servers
Specifying their keys, locations, exit policies and so on
So unless the adversary can control a directory server and starting in Tor 011x
A threshold of directory servers
He can't trick the Tor client into using other Tor servers
How do clients know what directory servers are?
The list comes with Tor distribution and hardcodes their locations and their public keys
So the only way to trick the user into using a fake Tor network is to give them a specially modified version of the software
So, double-crossed Zypress or whatever your name is, it's about a possible
I would assume that the EFS is kind of sticky on this whole privacy issue thing
So they probably have some of the best and the brightest people working on it
So I would think it would be kind of secure, but you know, who knows
The Tor's only real competition to security is against a global adversary
Yes
And that is an adversary who has large control or the ability to sniff large parts of the network
Because if they can see you going into a traffic node and they can also see traffic coming out from another node
They can't prove that it was you, but if they happen to see a large enough part of the network
And it just so happens that every time something comes in from you, something happens to go out from somewhere else
And they can correlate to times, they can actually sniff your traffic
Because it's going to come out unencrypted
Unless, of course, there's some sort of encryption going on, like you're using SSH or SSL
But Tor has been a pretty damn good product
Especially since it's free
It's free
Free
Yeah, Tor is good
I would think that it would be kind of secure
And they'd probably take into attacks like this
But I think we had an episode on Tor that Zigma was on, now that I think of it
We did
So, I mean, we talked about it there
And if you also want to look at last week's episode
We talked about SSH and public versus private Cree encryption
And that gives you a, it gives you a, sort of a hint of what they're up against
So, either way, yeah
You know, Tor is secure
Well, I wouldn't say Tor is not completely secure
When you start it up, it tells you right there, do not use your strong anonymity
But, you know, I think you're pretty good for normal web browsing
Oh, next email
Alright, our next email, now that I've got some rum in me
Hey, Strom and Black Ratchet
You mentioned polyphasic sleep at the beginning of your show
Actually, this is at the beginning of your show, but whatever
I would not recommend that any of your listeners actually try this
As a way of getting more time in the day off for hacking
It's true that people who are sleep deprived either REM fairly quickly
Or enter REM fairly quickly
However, REM is not the only important phase of sleep
For example, REM is not the only stage of sleep associated with dreaming
And dreaming in all stages of sleep has been found to be extremely important for learning and memory
If you do want to hack your sleep, you might want to try using it to improve your ability to learn new tasks
For example, if you're working on some code and come to a bug that seems unfixable, try taking a nap and then coming back to it
While you're asleep, your brain might come up with a solution you never thought you could think of
The brain is funny like that, works the same for playing video games, doing logic puzzles, studying for tests, etc.
Peace, Mystic
Mystic
Well, Mystic, thanks for your
I'm curious if you actually, whether or not you've actually done polyphasic sleep
And I'm curious as to whether or not we actually have someone who listens and does or has done
Or actually has some experience with polyphasic sleep and what their take on it was as it were
But interesting observation, I wasn't actually completely aware of that
Personally, with your whole and your second thing, you know, going away and taking a nap while trying to munch in a large problem
My experience is that if I walk away from a tough problem, you know, whether I sleep or not
And when I come back to tackle it again, you know, a new solution that I hadn't really thought of usually presents itself
Not all the time, of course, but I think it's less of a matter, at least for me, it could be, you know, different, you know, folks could have different things
But for me, I guess it's less of a matter of taking a rest from the constant non-stop thinking about the problem
Rather than actually just, like, taking a nap
Like, my case in point, I mean, today, you know, for those who don't know, I'm usually on, you know, IRC Monday through Friday 9 to 5
I'm not always on there, but I'm usually logged in and I'm, you know, reading the mail at least
I mean, if you're on there from 9 to 5, you'll often see me, you know, pop in for a bit and then suddenly leave for like a large extended period of time
And, you know, 9 times out of 10, the reason behind this is, you know, I'm taking a break
I'm trying to, you know, stop thinking about the problem
Whatever I'm chewing on at the moment, and then I come back to tackle it
And it usually works
Since we're on the, talking about hacking your sleep and all that stuff
I'm curious that the old stories of, you know, listening to stuff while you sleep
You know, listening to Spanish while you sleep and you'll learn Spanish while you're taking a nap
Are actually true, and I'm actually curious if any listeners have experience with that
See, what's up with you again?
Hmm?
See, he was speaking Spanish when he learned through, uh, through his sleep learning
I think I just said yes, it uses very well
So, obviously, my Spanish is off
Oh, I don't know, I'm on GSM, so it all sounds horrible
Yeah, it sounds horrible on this end, too, anyway
Well, the whole polyphasic thing, you know, the whole polyphasic sleep
Of course, you should never actually, like, do anything that we talk about on the radio show
Because it's really just something that we all kind of get together and do for fun
So, of course, never, you know, I guess, insert disclaimer, you know, speak with your doctor
But, um, I have heard a lot of mixed reviews on the whole polyphasic sleep subject
And one site that has a lot of really good information about it
It's a blog from somebody who actually has successfully made his transition
And he talks about where he had trouble and why he thinks it's better and why he thinks it's not as good
And it doesn't only have his point of view, it has the point of view of his wife as well
And how it's like to live with somebody who's changed their sleep style
The guy's name is, uh, Steve
And I'm going to butcher the last name
It's Pavlina
P-A-V-L-I-N-A
Please accept my apologies for checking it up
Steve Pavlina
I tiny URL'd it
It's tinyurl.com
Slash A-A-L-X-K
Whatever that is in fancy talk
But, uh,
Oh,
Kilowatt
But, uh, it's just something, if you are seriously considering it
You should check out that blog and I'll tell you more about it
So, if somebody wants to be seriously
Go ahead
Go ahead, Zygmunt
Oh, I'm done. Go ahead. I'm sorry
Well, I think Zygmunt actually brought up a very important point
Actually, not never to take the show seriously
And we don't know what the hell we're doing
Yes, ever
Entertainment purposes only
If you ever think you know what we're doing
Or you think we know what we're doing
Pop on the IRC
Talked to a good man
His name is P. Oxby
And asked him what he thinks of the show
So, I mean, he, he, earlier in the IRC
He was, uh, saying that we had a content-ectomy, so
A content what? A content-ectomy?
Yeah, a content-ectomy
But he always complains about our, our apparent lack of content
Yeah
Well, we had some technical difficulties today
So I think that's to be excusable
And we haven't even gotten to the good stuff
Yeah, it was actually before our shoes
So, he's probably like, you know
He probably ran off when I dropped
Anyway, uh, who's our next email from? Magnum IP?
Our next email is, yeah, from Magnum IP
And, uh, let's see, he says
Oh, before we go on, I should probably say that, like, this past week or two
I've been not sleeping, I've been sleeping kind of a few hours in the afternoon
A few hours during the day
It sucks
Major balls
I, I prefer
Yeah, I, I prefer my solid eight hours
From sleeping method
Yeah
So, anyway, Magnum IP writes
Hey guys, I called in on one of your live shows when you were asking people to call in and talk about pretty much anything
I ranted about how the new WRT 54G dot, er, V.5 VX works firmware is horrendous
I also ranted on Verizon installing Fios in my whole neighborhood but my street
Well, after numerous calls to the main office, they admitted to a computer area stating it was reported that the cables were already laid
And everything was ready for Fios service on my street when in fact it wasn't
Verizon is sending engineers out to start the work in a week or two
Can't wait to get my asterisk box finally installed and working with 15 megabit down and 2 megabit up, damn you
I also have a gripe about a certain ISP in my area about their policies on password retrieval
My friend forgot her password to her new email address from her new DSL account she got from a local telco
She never used it because she's still using AOL for her email
Well, as an experiment, I emailed the ISP asking for my password from her AOL email address
After about two days, I sent the password in a reply without confirming any information
Or asking to call the 800 number to talk to a live operator to verify information
In my mind, that's a very big no-no, shame on this local telco
Thanks for your time, Magnum IP
P.S. Strom is my secret love monkey
Strom, I had no idea
Yeah, neither did I
I must do it while you're sleeping for those three hours a day
Yeah, exactly
Well, first off, congratulations on getting your Fiber to the premises
I refuse to call it their little, whatever they call it Fios
Did any of it actually stand for anything?
It's probably like Fiber over or something, I don't know
I don't know yet, I'll look
You know, anyway
I'll get Fiber to the premises from Verizon whenever they remove their asinine filtering policies
And allow me to get a static IP address
Without giving them my firstborn son
Fios, according to Wikipedia, stands for Fiber Optic Services
Trixie Hobbuses
Hell yeah, now we all know
I'm currently using their DSL now
And I'm going to, it's going to, I think the contract is going to expire next January
And I'm going to jump-sip the day after it goes out
I already have like two or three ISPs lined up and me going to call them immediately afterwards
And saying, set it up, do it now
Yeah, I've got six megabit DSL here in California from a company called DSL Extreme
Love them, no restrictions, no filtering whatsoever
Cheap too
Apparently, like, COVID doesn't have my CO
So I'm like, like, what the, it sucks
There's a, there's a small, it looks like there's a small mom and pop on Cape Cod
Which is a, for those of you unfamiliar with Massachusetts, Cape Cod
If you've ever seen a picture of Massachusetts, it's that little hook that sort of goes out onto the eastern part of the state
It's Massachusetts Wang
Yeah
They can't have Florida, that's United States Wang
Or America's Wang, whatever they call it
But anyway, like, you know, there's a small mom and pop ISP called, like, Cape Cod.net
And they actually have rather good service and reasonable prices
So I think I'm going to have to hop over to them
If, uh, Speakeasy or Kovad
Or, it's Kovad who does Speakeasy
And I think they also do their DSL Extreme
Doesn't start on my, uh, CO
So, personally, I just, I can't, in having a filter in place
I, I had Speakeasy before, it was wonderful
They gave me, like, you know, you know, killer speeds
Their, their, their customer support was very cluel
And I have literally, like, little to no complaints about them
Like, maybe, maybe one
But, other than that, it was absolutely fine
Um, so, I, I just can't, I, I've experienced the Rolls-Royce
I've refused to go back to the Pinto
Um, personally, uh, your, your statement of a very big no-no
Is, um, a very, is the understatement of the century
Regarding the password policy
I'm kind of disappointed that you didn't kind of
Drop the name of the ISP
So, you know, people that are looking for ISPs in your areas
Will, can stay the hell away from it
Um, although, I guess, if they kind of handed out passwords
That would be, uh, a smart thing not to drop their name
Because everyone would be like, oh, I need my password
Well, everyone could just jump ship immediately, so
Well, no, because, no, no, well, I mean, all the smart people would
If they actually got out there, but none of the regular people would
Yeah
Um, in my opinion, you really need to contact someone about that
That's, like, you know, very, very dangerous and very, very stupid
Um, you know, find, like, find your ISP security officer
If it's a small ISP, of course, you also used to term ELCO
So, that's a bit annoying, um, it could be actually a telephone company
Which, at which point, you're screwed
Um, at that point, you may want to talk to your local newspaper
Um, that really is a security breach waiting to happen
So, yes, contact somebody, you know, find an adult
Go tell them, at which point, afterwards, when they look at you funny
You know, find the security officer, or find the local outlet
So, yeah, that's about it, you know, just, you need, this issue needs to address
We shouldn't be sending, you shouldn't be sending passwords over the email no matter what
I mean, even, even if you have to verify who it is
I mean, I'm, I'm never a fan of sending out passwords in plain text over emails
So, fix it, this is your job
Go do it, we want a full report
Go take your 15 megabit bandwidth and go do something useful with it
Alright
Um, our next email is from Teoxy
Is it?
Amazing, yes he is
Ah, okay
I actually think he uses his name, but we're not going to actually, we're just going to actually point out, fact out
That he emailed the show
Gas
No wonder we're having technical difficulties tonight
Hell is freezing over
Yeah, amazing
Anyway
The email is, oh, yeah
That's the liquor talking
The book you're thinking of is Firewalls and Internet
Or sorry, the book you're thinking of, Firewalls and Internet
He left as an is
The book you're thinking of is Firewalls and Internet Security by Cheswick and Belevin
The story was a paper Belevin published and isn't the only free material in the book
There's also the paper, There Be Dragons, which discusses a related topic
The paper is available at tinyurl.com slash RomeoLimaMikeEcho4
I also had a question about
What?
Very good, you actually get all right, amazing
Yeah, I'm learning my alphabets
LOL Internet
I also had a question about user mode Linux
If you use raw sockets in user mode Linux
How is that implemented if you aren't running as root?
Can't you use that facility to determine with fair likelihood if you're in UML?
You know, I've done some socket programming
And, you know, if you're not root and you try to open a raw socket
I'm pretty sure you get an error
And the error you get is error, proto, no support
Which is the protocol not supported
And I, you know, I could totally be wrong about this
But I'm pretty sure that that's also the reason why if you try to run nmap and you do certain tests when you're not root
It'll tell you you can't run that test unless you're a super user
And I, that's not something I'm 100% wrong, so don't take that to the bank
But I'm pretty sure that if you try to open that socket as root
Any raw socket as root, you're going to get that error, no prot support error
I actually submitted this question to a couple people that I know
And they were all scratching their heads
So at this point, I am not going to be able to answer this
However, I will get an answer
Teoxi was very kind and actually milled us last week
However, he had the unfortunate mishap of being between two pieces of spam
So, you know, he sort of bled it into the background
But, I need to do some research into this
And I actually want to try this, because this is a very good question
However, if someone actually doesn't know the answer, just feel free to email us at radio at binrub.com
So, congratulations Teoxi, you have stumped BIM Rev Radio
I'm sure you're very giddy about this, and we'll put it on your resume
We should send him a trophy, you've stumped BIM Rev Radio
We'd have to be giving out a lot of trophies
Yeah, I know, tell me about it
Everybody's got us beat on something
Yeah
All right, let's go in the show and tell
Dr. Zygmunt, what have you been working on this week?
You know, I think I believe I've already told this story
Yeah, he's
While you were MIA
Yeah, he pulled it out of nowhere and used wonderful filler while we tried to get you back on the
I earned my mutant ability of the filibuster
The Democrats will want you
I could go run for Senate
Well, what have you been doing then, if Dr. Zygmunt's already blown his load
What have I been doing? Jeez, um
Apart from battling with Asterisk and my machine
That was only like 15 minutes, so what else did you do this week?
Um, nothing major to speak of, I think
Just, uh, yeah
Fun in the sun
Yeah, fun in, well, it should be sun here in Southern California, but it's not
It's rain and rain and more miserable rain
Aw, poor straw
He's scared of his little rain, he doesn't like the cloudiness
Oh, I'm not scared of it, it's just
It made my commute home today
Two hours
Yeah
Personally, you know, at least in Boston when it rains, the commute's always two hours
So, hey, what have I been doing?
Um, what have I been doing?
Let's see, I, I have been, um, I've been data mining for, for work
And you've actually, if you've been an IRC, you can hear me complain about this, uh, software that I've been trying to use
Basically, we've had this software sitting around, um, this highly expensive piece of software
The software quite literally cost about $10,000
Um, and, it's used to data mine two separate databases, and I'm doing this for work
And it's, it's nothing, you know, gray area, illegal, slightly immoral, it's completely fine
It's basically, we're looking at dead people, so, it's a matter of public record and all that wonderful stuff
Either way, I've been seeing dead people
I've been seeing dead people all week, last week as well
So, the, the software package, we'll, we'll just sort of, it's, it's actually owned by IBM now
It's gone through, like, two or three different people, two or three different, uh, company ownerships
So, we've got, it's called, um, Integrity Designer
And, it sucks, don't use it
Of course, no one will actually use it, because it costs $10,000 freaking dollars
And, after banging my head against the software for, oh, I'd say about a week
I finally sat down, and I wrote a bunch of Perl scripts out
That basically replicated exactly what it did
And, I think the only slight advantage that it has is that it's slightly faster
And, I think if I probably actually sat down, worked out some threading into these Perl scripts
It would, I, it would give it a very good run for its money
But, you know, the software to which we've paid, you know, $10,000 to initially buy
And then a, like, you know, three or four year, uh, service contract
That my predecessor recommended at work, um, for, like, $5,000 a year
We, we, we, we've, we've clocked down, like, you know, a good chunk of change about this
And I, I, I've written in about a week, software that basically emulates a good majority of its functions
And, I actually feel kind of proud about that
They should've just given you the $10,000
God, that would be great
That'll be the day
No, it doesn't work that, it doesn't work like that
Hell no
Um, but yeah, that's, that's what I've been doing
And I'm sick and tired of looking at statistics
And I, I, I think I, I set up for a nice little, you know, batch run tonight
And hopefully when I, I stroll in tomorrow morning, I'll be able to wash my hands of
It's gonna fail on the first query
No, no, no, no, no, I actually did a couple of dry runs on it, so I know it was at least working
Okay, okay
We're knock on wood right now, because you brought it up, you, you, you horrible
You know what's, you know what's really surprising? You know what's going on?
People are logging into the IRC channel to tell us things
Well, let's say that, people have done that before
Yeah, but like, surprisingly a lot tonight
So, just to answer you guys, yes, we know we're having technical difficulties
And we know there's echo, please stop telling us
But we do appreciate you telling us
Yes, we do appreciate you pointing it out initially, but
Now that we're totally aware of it, uh, thanks, we know
And, uh, to Eggman, who logged in to tell, to say, uh, tell Strom to quit bitching about the rain
It's been raining for 38 days here
I totally sympathize with you
But still, Jesus Christ, rain, no
And actually, it's not me echoing, I believe it's actually Dr. Zegman, but we'll get into that
Because it was echoing before he got on the cell phone
Yeah
I don't know
No, no, no, no
Whatever, who cares
We'll run some digital, technical jiggle
We'll only poke through you over it later
In the archives, so no one ever will be listening to the archives going, I don't hear an echo
God, anyway
I hope I can do that
Shush
Actually, the echo's worse now
Can you, can you drop, Zegman, I'll call you again
Okay
Okay, check
Yeah, it was him, okay
Aha
All these horrible people
Anyway
Our topic tonight is
Bioinformatics
Actually, I think it's bioinformatics
That's how I pronounce it
It could be bioinformatics for all I know
And actually, the reason why we have Zegman on the show tonight
Is because this is what Zegman actually goes to school for
Which is amazing
And it's actually kind of inconvenient because he's not here right now
But, what bioinformatics is
Basically, bioinformatics is a, it's computational biology
And what it does, it involves the use of, you know, applied mathematics, informatics, statistics, and computer science
And they all, you know, tie them together with chewing gum and tape and all that wonderful stuff
And they use it to solve biological problems
Like, we'll go into like what this actual biological problem is because Zegman can actually speak for this a lot better than I can with the actual applications uses
I've just been, I've been kind of fooling around with it because that's actually one of the applications that this data-minded compassion that I have has used for
It's what they kind of pimp it out as
But we won't actually, I don't touch it and I have no clue about it and it won't actually do it
But, computational biology research often overlaps with, you know, systems biology
Major effort, major efforts in the field of, you know, gene sequencing alignments, gene findings, genome essentially
For those of you who don't remember, you know, back in 2000, the genome project where they mapped an entire
Zegman, what is actually the map? They mapped a
The Human Genome Project, where they actually sequenced, they didn't map, but they sequenced the entire genome
They're still sequencing it now, or I'm sorry, they're still mapping it now
And by mapping we mean being able to identify this sequence is for this gene, this sequence is for this gene, and so on and so forth
Okay, so basically I've told everyone that, is it bioinformatics or informatics?
I think that's tomato, tomato
Okay
Well you wrote
I like, in general sounds cool
Who wrote this up wrote definition
Huh?
Whoever wrote this up wrote web definition instead of web definition, so
Hey, okay, yeah, well that's why I'm a biology major
And I'm a social science major, so
Go, go, go, go, go step off to the side there and, you know, go, go hear your spelling Nazi in silence
Boots
Yes
So, okay, you can probably explain, like I was telling everyone, this is what you go for school for, right?
Well, I'm a biology, well I'm actually a triple major, which is biology, computer science, and chemistry
But I do plan to be a doctor, and bioinformatics is something that I was definitely looking in
Because it combines not only excellent job opportunities for somebody who is thinking, maybe what do I want to do with my life
But it also allows you to really do work that's going to make a big difference in people's lives
And really, bioinformatics is becoming such a huge field that daily, we'll talk about some of the databases later
But researchers are using these to save thousands and thousands of hours of sequencing things themselves in the lab
And it's really, just the sheer amount of data that's involved is requiring such advanced programming
That anybody who really wants to take a leap and get into this sort of work can have a really good job for a really long time
And I'm not sure exactly what we said so far, but if you want to start the ball rolling, we'll go from there
I mean, I just talked about what it all involves, it's really computational biology
It involves all mathematics and informatics, statistics and all that stuff
But if you want to take it out from there, you know much more about this than I do
And actually, the first question that I have is, if you become a doctor, are you going to have to change your handle to call you Dr. Zygmunt?
Well, that's why everybody is always saying, oh, are you really a doctor?
Well, that's the idea, so that I'm only going to have to be like, yeah, it really is a doctor
So, that's part of the whole handle, where that comes from
But, I guess if we're going to get back to bioinformatics, probably the first thing that we should talk about
It's not entirely computer related, but the first thing we should talk about is easily, you know, it's just DNA
And one of the major uses for bioinformatics is the major indexes that are maintained of genetic sequences
Probably the largest that's out there goes by the name of GenBank
And that is maintained by the, I believe it's the National Institute of Health
But, ugh, you know, I wish I would have read it down, because I have the URL
I have a tiny URL, but I don't have the actual URL
But, if you want to actually search GenBank, it's free and open to anybody
You can get it at tinyurl.com
Slash YS7FB
And what that basically is, is the search engine of basically the Human Genome Project
The Human Genome Project and other assorted gene sequences
And you as a researcher can input into it a sequence of bases, of nucleotides
And we're going to tell what that is in just a second
And with that, you can get any matching sequences that exist, where they exist, what species they exist
And what's the difference between that specific sequence in various species
So anyway, for anybody who, it's been a while out of high school to talk about DNA
It's a deoxyribonucleic acid
We've all seen the pretty picture of the two spirals going up
With the chain
Yeah, and of course there's the four bases of DNA
Adenine, thymine, guanine, and cytosine
And that's what you see in all these gene banks, A, T, G, and C
That's where it comes from, it's those four bases
And they bind selectively, A to T, and G to C
Of course there's reasons and times when that gets violated
But that's not important for our discussion
And it's the sequence of the bases that form the template for the transcription of the actual sequence of DNA code
Into RNA, which is ribonucleic acid
And what RNA does is that codes actually for protein
The RNA itself is then copied
And amino acids are put together and you're going to have a protein
That protein is now going to be the actual phenotype
So basically the whole mantra we're trying to get to here
Is first DNA, RNA, protein
When you have a change in the DNA, it's going to change the RNA
And it will change the final outcome, the final protein
And what they're doing with a lot of the bioinformatics is they can predict
Okay, if we change this part of a protein, this is going to happen
Some people have seen the, what's the major protein folding that's out there?
Oh, protein folding at home
Folding at home, yeah
Folding at home, and that's not exactly the same thing
But that's kind of, it's in the same realm
It's a little bit more physics related
But you could almost consider that bioinformatics
It's really any use of computers to handle the massive amount of data
That's really affiliated with life
Okay
So just before anyone gets the wrong idea
We're not talking, you know, we're talking about DNA here
But we're not talking that we're suggesting that people re-sequence their own DNA
You know, because we're talking about sleep last week
And people were thinking that we're, you know, endorsing polyphasic sleep here
And I just want to get that out in the open
And make sure no one's going to be doing it
No one's going to be doing it, so
We don't want to have, basically we're going to have like a bunch of like little kids like you
You know, Island of Dr. Moreau
Which is always cool
Yeah
But old Timmy, I re-sequence his DNA and he's now a five-ass monkey
Five-ass
But I'm sure what's really, what it comes down to is what is all this data really used for
Yeah
And really what it comes down to, the perfect example is a researcher
They have a segment of some sort of DNA
It has a specific sequence and they want to know where the sequence appears in the entire sequence
Where it appears in the genetic map
They want to know if their specific sequence is mutated slightly, you know
Like maybe I have a T or I'm supposed to have an A
Something like this can, like GenBank, can look through it
You can feed it a sequence of 50 A's, T's, G's and C's
And it'll find the closest sequence matches to it
You can see maybe you have something that's mutated
Maybe you have something from a different species, et cetera, et cetera
And then you can bring this into a little bit more of the real-world applications
You have something that's called a restriction endonuclease
And that's a really fancy word to say a pair of scissors that cuts DNA
It always cuts it at a specific point, which is a specific sequence
You know, it'll always cut at A, T, G, G, G
A, T, G, G
They're usually paludromic sequences
So I'm trying to remember A, T, G, C
Okay, think of it the same way forwards and backwards, great
But what you end up with is, let's say you're a researcher
And you're going to use this specific restriction endonuclease to cut your sample of DNA
It would probably be helpful to know if that sequence also appears in the middle of your DNA, wouldn't it?
So that you don't end up cutting what you want to study in half
That would kind of suck
Totally
So what you can do is you can turn to GenBank and say, hey, in this sequence
I'm trying to determine what gene this is
I think this might be BRCA1, which is breast cancer gene 1
I want to study that
So what's the exact sequence for that?
It'll pop up, you know
What do they call it? BRCA1?
Oh, BRCA1
Yeah, BRCA1
And that's one of the genes that's linked to breast cancer
But you know
I mean, this just
This always confuses me
Like from the beginning when they're talking about
Like, oh, we mapped everything
I mean, they mapped all of the genes
Now, what actually does that mean?
Well, they haven't actually mapped all the genes
And they don't know the function of every gene and every protein
Okay, like for
They took somebody's DNA and they mapped all the genes on it, right?
They took the sequence and they were able to break down the sequence into its collections of A's, T's, G's, and C's
Okay, but also at the same point, I mean, my collection of DNA is unique
And it's not going to be, say, for example, you know, exactly matching their collection of DNA
So what use does this actually serve?
It's not that you're
The genetic difference between two humans is really
In the grand scheme of things, it's minuscule
Okay
The genetic difference between a human and a primate, a monkey, is only
There's a 99% correlation
You know, 99% of the sequences are pretty much exactly the same
So there is going to be difference between human to human
And they actually did have a paper
I wish I could recall exactly where they got the DNA for the human genome project
But it's such a small, like the only difference that you're going to have is you have boy or girl
Of course you're going to have an X or a Y, you're going to have that extra
You know, there are subtle differences, of course
You know, eye color and everything that makes everybody look slightly different
It's going to be a result of their genetic code, the phenotypes, the proteins that are produced
But a lot of that, with bioinformatics, they're starting to catalog those differences
Why is it that you have brown eyes versus green?
You know, what is the exact change in the genetic code that's causing that?
And something like that is very useful for, let's say, that there's also a degenerative ocular disorder
That's causing cancer
Now we can look at that exact gene sequence and say, hey, you know what?
We see this correlation between people who have blue eyes and higher incidence of cancer, for instance
Maybe there's something to do with the genetic sequence
So they can look up that genetic sequence and they can see what's different
They can experiment that on the lab
And they have the ability to access this exact sequence
When 20 years ago, if they wanted to do any sort of research like this
It was millions of dollars to be able to build the libraries of genes
And, you know, you'd have to try different restriction endonucleases to try to get the right sequence
But with this, you can look it up
It's at a couple of clicks
Oh, oh, wait, there's a T here instead of a G
I wonder what a difference that makes
Let's see how that folds as a protein
They can put that into a computer
Granted, they have to be rather complicated computers, really sophisticated
But that's why this is such an emerging market
Right, yeah, you're not going to be running those on your, you know, 386 laptop from 1992
This is going to require something pretty beefy
Yeah, but you know, even those little computers help
Just like a protein, or the folding at home
They're just breaking it up into a little work unit
Oh, yeah
It's all very fascinating stuff
Wide area distributed computing is just cool anywhere
Mm-hmm
Now, a question I have for you, Zygmunt
And I don't know if I missed it
Because I was busy trying to get the stream working correctly
And I guess it's not really working
But my question for you is
Like, of the actual
I mean, I know they've got the thing mapped out
As far as the actual sequencing goes
No, sorry, they've got a sequence
But how many of the genes do they actually have, like, really mapped out now?
And how many do they still have left to go?
You know, I really, I can't quote a specific number
Well, roughly
I wish I could
You know, I really, I can't even make an educated guess
As to the number that has been sequenced
I know if you talk about different species
Like, if you look, one of the most used animals for genetic research
Is Drosophila
Yeah, is the fruit fly
And that entire, it's only four chromosomes
Every gene has been sequenced
They know exactly what every single gene does
They know where it is on the chromosome
And they know if it's altered like this, this will happen
If it's altered like that, that'll happen
They could talk about the inheritance and all that
But, you know, I can't give that exact number for the Human Genome Project
I know they're definitely making leaps and strides
And it's a huge area of research
Because it really is, you get into the future of what's going to be medicine
And you're going to start coming away from all these, all the different drugs and the different substances
Where there's so many, so many bacteria that are resistant to antibiotics
There are so many disorders that are genetic in nature
It's going to start getting to a point where we're going to be using genetic engineering to cure disease on the fly
You know, we're not quite there yet
And we're looking at a lot of bunch of, a lot of immunological cures for different disorders
A main one, because I hate to keep bringing it up and harping on it, but really cancer
Cancer is going to be so difficult to treat
Because it's different in every person
And actually, and now as we're doing it real quick
The reason that cancers are different is because they result from mutations
You have to have at least five mutations in five different genes
In order for a cell to revert to a cancerous state
So it's going to grow uncontrollably
You know, and that's why when you hear about people saying
Oh, he has a, he has an increased risk of breast cancer
Or not he
Some men can get breast cancer as well
I seem to recall that
They do
Well, it's not, it's not truly breast cancer
It's cancer that's in the breast area, but it's some other form of cancer
Breast cancer
I actually had a job that used to deal with this
And breast cancer can only be occurring in women
Because it's, it's, it's, because I actually had to format all of these reports and everything
And, like, you know, when you were talking about breast cancer
You didn't want to put a, you didn't want to try to calculate out the male
Because there was no data on that, so
Take that, Susan G. Cummins
Yeah
Just like, just one of the lines of you didn't want to calculate out testicle cancer for the females
Because there was going to be no data
I, I don't recall that it'd be actually zero
I thought it was a very, very small percentage
But you could, I mean, I'll yield to you on this one
Well, I, I don't, I, I, if I, if I remember correctly
It's not, you, you, you, I mean, a man getting a cancer in his breast area
But it's actually not breast cancer as the actual terminology goes
In the same tissues, I'm sure
I mean, yeah, yeah, because I believe breast cancer, breast cancer has to be within the mammary tissue of the female
And we're completely drifting off topic here, so, yeah
Back to bioinformatics
Yeah
But, really, the whole, the, the crux of the argument for bioinformatics is that it's, it's such a lot
There's so much data to be processed
You look at the, the human genome, it's absolutely gigantic
You're talking about between 20 to 30,000 genes
And each gene can be anywhere from, you know, a hundred bases up to a hundred thousand plus bases
Tell me, how much, how much storage are we talking about?
Well, GenBank, for one, has, has cataloged one, one gigabase of data
Which is, think a gigabyte, and now you have gigabase, you know
And it's really, it's gotten to the matter, and that's just on genetic sequences
We could be talking about any other
Are, all their bases are belong to them?
All their bases are belong to them
Oh, God, there's a t-shirt, right?
There's a, do a, do like a DNA strand or something
And then have, all your bases are belong to me
That's a new shirt that you guys should come up with
Yeah
It'll be up with all the biology majors
Yes
You can have Watson and Crick on the shirt saying, all your bases are belong to me
That's it, that's the shirt, right?
Okay, so, I mean, so a gigabase, so that means like
A billion bases, right?
Yeah
If that's what that, I guess
Yeah, a billion base pairs
I can't remember how much it was
And that's just one database
But I mean, GenBank does, it does take its data from several different locations
A couple of them being the DNA Data Bank of Japan
The European Molecular Biology Laboratory
And GenBank at the National Center for Biotechnology Information
So they're definitely, there's more than one database out there
And GenBank just happens to be a search engine that will crawl through all these different ones
And GenBank stands out because that's the one they really educate students about
It's really the easiest to use
And you can still get a whole lot of information
And it's the same thing that researchers are using
We're talking people who have their PhDs
And beyond, people who are working on their Nobel Prizes
When are you going to get your Nobel Prize?
That's exactly what I want to know
When am I going to get my Nobel Prize?
I don't even want the money, I just want the prize
So I can be like, my friends are going to come over
And say, oh yes, this is my kitchen, this is my dining room, my Nobel Prize
I mean, you've got to get chicks if you have a Nobel Prize
Oh yeah
Hey, do you want to check out my medal?
They'll be like, ooh
But there's also some information on the hardware that's used
Or actually, rather, before the hardware
I know they're using a lot of different scripting languages for stuff like that
What's going on with that?
Well, I mean, I was looking into this
And apparently there's a fair share of, like, you know, regular languages that are actually being used to this
Like, I mean, I actually knew that Perl was, you know, was actually used a lot in, like, you know, gene sequences
But I actually had no clue what actually it is
But what really shocked me is actually, well, two-fold, because A, because people actually use Python
But what shocked me more was people were actually using Python for this type of stuff
Which was, I mean, Perl and Python, yes, can do a lot of things
But I did not expect it to actually get involved with gene sequencing and various other forms of, you know, biology type stuff
I mean, I just use it as a data-munching language
But I guess when you're dealing with, you know, gobs and gobs and gobs of data, it's a good thing
But, like, you know, Perl, Python, they're often used to, you know, interface with the actual databases and parse output from the various programs
However, it's actually interesting because Linux is actually used and open-source software is used a lot in this stuff
Like, you know, communities of, you know, bioinformatics programmers have set up projects
Like, you know, a couple of them that I just, you know, quickly want to rattle off here
Mboss, M-B-M-B-O-S-S, Bioconductor, BioPearl, BioLinux, BioPython, BioRuby, and BioJava
Hmm, I wonder where they get these names from, I don't know
And what they do is they distribute shared programming tools and objects and file libraries
That try to make bioinformatics easier
And I actually found this cool article on O'Reilly about Perl and bioinformatics
And it's HTTP colon slash tinyurl.com slash November Quebec Juliet
Sorry, I've got a stuffy nose all of a sudden
November Quebec Juliet 2 Echo
Now, I knew in a while we actually had a bunker of an episode
But I guess all good things must come to an end
Actually, what really found cool is that I found an integrated software workbench
And it actually has a lot of these tools described already
And it's called, I'm not going to be able to pronounce it
VigyanCD, V-I-G-Y-A-N-N-C-D
It has all these tools
And in itself it's open source bioinformatics workers
And it's, apparently, it's quite complete
I mean, I looked at it and I saw a nice like uh-huh-hah-huh-hah-huh-huh-hah-huh
But, apparently, people are raving about it
you actually do some Google in it,
and it's available at vigyancd.org, two A's.
They do also have, they have full Linux live CDs
that are being used for this exact purpose,
and something that's built into a lot of them
is the ability to do distributed computing.
Well, yeah, that's what part it is,
and this program is actually part of a grid package
so you can do your own little miniature grid computing.
And it's cool, but I'm looking at it and going,
I have no clue what the hell all this stuff is.
I guess it's more along the lines of
if you know exactly how to use the tools,
this is actually good,
but I'm just kind of going at it and saying,
well, this looks impressive,
but I actually have no idea actually how to use it.
You can sequence DNA in the comfort of your own home.
Woo-hoo!
Yeah, I know.
You can make all the searches on,
especially GemBank.
GemBank's really heavily used.
You can, you know, just for kicks,
you can throw in a couple of sequences
and see what, it'll actually tell you the difference
between, like, the relevance,
you know, like, percent match.
You see if maybe two proteins
are going to interfere with each other.
Well, actually, I did a search on that URL that you gave,
and I did a search for boobies,
and I was like, you know, 25 hits came up, so.
Hey.
Hey, I was like, all right, good for them.
Hey, even biology majors need to have a daily dose.
Apparently so.
All right, so,
since we already talked about software,
you know, like,
this is good for my own little home PC,
but I assume that these diet pieces
that are trying to, you know,
sequence the entire human genome
have slightly better hardware
than my, you know,
Athlon 1.7 gigahertz computer,
at least I would hope,
even if it's why it's taking so long.
They do have some serious computers.
One of them,
they have a couple of nicknames.
One of them that is used heavily,
it's called Big Ben.
It's a crazy XT3 MPP system.
Oh, great.
With a peak,
yeah, with a peak,
a peak teraflops,
a 10 teraflops,
which is a lot of calculation.
And you just, I mean,
we can ramble on.
Another thing,
they have an HP Alpha cluster
that's being used.
It's a cluster of more than 3,000 processors.
And it has a peak speed
of six teraflops.
You actually see a lot of it
is, because remember,
there's a lot of universities
and government agencies.
Rather than buying
a whole bunch of new hardware
or buying a brand new supercomputer,
they're just taking a bunch of,
you know, normal computers
and putting them in clusters.
It makes my money very cheaper.
Yeah, that was the entire point
of the, what was it,
the Virginia Tech XServe cluster
when they actually came out
with all new G,
was it G4s or G5s?
I forget now.
I think it was G4s.
I think it was like pre-G5.
But when they came out
with all that stuff,
they just made,
they tossed them all together
and made a giant
supercomputer cluster out of it.
And actually,
it looks very, very cool.
It's like it's hot.
Yeah, I'm sure it does.
I mean,
the clusters in itself
are just incredibly easy
to set up.
I mean,
I remember when
I, you know,
stumbled right upon
the Beowulf clusters
back in the day,
like 2000.
We had like a bunch
of old 486s
sitting there
gathering dust
waiting to be
thrown out at work.
So I wired them all up
from underneath
that hub,
you know,
installed all the
Beowulf patches on there
and they purred like kittens.
And I was able to
crack RC5 keys on them
at amazingly fast rates.
But yes,
clusters are like
very powerful
and very easy to set up.
And it's perfect.
You know,
a lot of the people
in this field,
they do have the money
to buy the crazy computers.
You know,
the true supercomputers
where,
you know,
it's got all the bells
and whistles
and it's,
you know,
half a million dollars
or more.
But I mean,
a lot of it,
a lot of the research
it's all research.
It's a lot of it
is all being done
from universities
where,
you know,
if you're going to get
that big grant,
you don't want to spend
it all on computers.
Well,
that we all know
that biologists
are very cheap.
I wasn't aware
of that stereotype.
Oh,
yeah,
I knew that.
You see,
because biologists
don't want to admit it,
but we know.
We know that biologists
are cheap.
Meanwhile,
I mean,
how many biologists
do you know
that are driving
Rolls Royces?
I don't know
if that's them
being cheap.
It's just them
being underpaid.
Anyway.
So,
yeah,
this was turning
into a clunker
of an episode.
You want to just
cut it here?
No,
not really.
I think we're doing
actually pretty well.
So,
okay,
so we talked
about Big Ben
and,
I mean,
like,
what all these
computers just do
is they just
try to redo
all these
gene sequences
and gene mapping
and basically
they've been doing
this for five years
and they're still
not done yet?
Well,
actually,
it could take,
what a lot of the
computers are doing,
it's not that
they're sequencing,
the actual computers
are doing all
this sequencing.
They do actually
have machines
that are used
in order to
sequence DNA.
They have special
machines for it.
we can get into
the whole process
of the polymerase
chain's reaction
for duplicating DNA.
It's not really
necessary.
But what most
of these actual
computers are doing
is they're handling
just the load
of people searching
the database.
Because you think
about all the load
that's going to go
in,
because you have
this one gigabit
database that people
are doing,
you know,
more or less
like searches
through the entire
thing.
And you have
the entire research
community doing
these queries.
You know,
actually,
the way GenBank
works is it
actually doesn't do
your query
as soon as
you make it.
It puts it
in line.
And it'll reload
when your turn
in line has come
up.
And that's one
of the ways
that they do
their load
balancing.
You know,
because it's a lot
of information
to process.
Of course,
there are some
things that you
can do entirely
in the computer
world,
such as,
you know,
some of the
protein folding.
But that has
to be validated
and, you know,
all the theories
of how the
computer program
is working
has to be proven
to be the way
things exist
in the real world.
Because we all
know,
you know,
academic and
theory versus,
you know,
actuality is never
a hand-to-hand
or an exact
same transition.
So,
so wait,
you kind of
mentioned this
in passing,
but like,
for example,
when I'm doing
something like
protein folding
or I'm doing
like something
of folding at
home,
I'm doing it
but someone
actually has to
re-verify my work?
They don't have
to re-verify
every single
calculation that
you do,
but as a good
researcher,
you can't just
blindly accept
data.
Yeah,
I guess it
kind of makes
sense in the
actual long run,
but that does
kind of hurt my
feelings,
like they don't
trust me.
I'm honest,
I'm a boy scout.
It's not all,
like,
they're not going
to have to
re-go,
go ahead and
re-check the
way that the
protein is folding
and check the
chaperone molecules
and et cetera,
et cetera.
You know,
they're just going
to test the
interactions and
make sure that
things are behaving
the way they
should.
There's such
thing called
chaperone molecules?
Oh,
chaperone proteins?
They help
proteins fold.
They're also
called heat
shock proteins,
which is another
emerging technology
in cancer
treatments.
Hot damn,
I always liked
biology back in
high school,
but I never
actually got into
it,
and I really
kind of miss
that now.
And actually,
the entire world
has kind of
blown me by
from high school
biology,
and we're
talking about
highly advanced
stuff here.
But anyway,
so we also
have a note of
some other
database on here
called ChemFinder.
What ChemFinder
is,
it's not
truly bioinformatics,
it's a lot
more of just
a great database
that's being
used a lot
in the field
of chemistry.
What it is,
is it's basically
a huge depository,
ooh,
depository,
what?
A huge depository,
a huge depository
for information
about various
chemicals,
various substances,
you know,
it includes a lot
of the vital
statistics,
like boiling
point,
melting point,
vapor pressure,
et cetera,
et cetera.
But that's done
by Cambridge Soft,
and what's nice
about them is
they actually give
you,
you can do five
free searches
without registering,
and then you have
to register,
but you can keep
doing searches.
And for anybody
who's listening
and is in school
and has a chemistry
class where you
have to do lab
write-ups,
and et cetera,
et cetera,
this is an excellent
resource for that
sort of thing.
The internet's making
the kids see it
be soft.
I mean,
I remember having
to do all this
shit in books,
looking up like,
oh,
look at that,
the specific
gravity of this
material is a
whole lot bigger.
Well,
that would be
all the answers.
Why don't you
just go to
ChemFinder and
find all this
crazy shit?
Online,
automatically.
Back in my day,
when I was your age,
uphill both ways,
uphill both ways
in the snow,
in the middle
of the summer,
had to slaughter
an animal on my
way to school
to have lunch
without shoes.
Yes.
Shoes?
I didn't even
have feet.
All the way
on a road
made entirely
of razor blades.
Yes,
and I enjoyed it.
And then afterwards
walked through
the rubbing
alcohol river.
All right.
So,
I mean,
we kind of
like really
basically glossed
over a lot of
stuff here.
I mean,
this is a very
intense field
and,
I mean,
we're not going
to be able
to cover all
the stuff
on one night,
but I think
we did kind
of cover a lot
of the basics
and what
bioinformatics is
and how you
can actually use
all this stuff
and why it
actually be
interesting to
some people.
And I'm sure
there's a lot
of people out
there when we're
talking about
shaperone proteins
and specific
densities,
sorry,
specific gravity
and all that
kind of stuff
and RNA,
DNA,
and I'm sure
there are a lot
of people just
sleeping right now,
but hey,
screw you all.
It's a nice thing
to think about
for a career.
You know,
if you're somebody
who's really
interested in computers
and you're also
really interested
in biology,
it's something
to consider
because you get
a chance to work
with medicine,
you get to help
people with what
you're doing,
and you get to
handle some
really,
really nice
computers and
do a lot
of data crunching.
If you like
data crunching,
this seems to be
the field for you.
And actually,
before I left
work today,
I actually set up
to download
that bootable CD
and I am going
to try and play
with it and see
what the hell
I can do with it.
It's interesting
and it just seems
to be like
massive data.
I do enjoy
just crunching
massive databases
for some reason.
I'm a sick,
sad person like that.
I mean,
look at me.
I keep a database
of payphones.
But it's fun
to crunch numbers
in my opinion.
If you do enjoy
this sort of thing,
I think this is
going to be
a very interesting
way of interesting
things for you
to do.
And I didn't mean
screw you all.
Please,
you know,
tune in next week.
We love you,
listeners,
all that stuff.
Look at that.
I'm Strom dropping
off on me.
I'm insulting
all of our
listener bands.
Yeah.
Anyway,
announcements.
Strom,
do you have
announcements?
Layer 1.
Two and a half
weeks from now.
Layer1.info.
Oh, really?
Yes.
I'm talking.
Come see my
awesome talk.
What weekend
is that?
That's Tax
Day weekend,
April 15th and
16th.
Tax Day weekend?
Okay, so
in the weekend
before that,
if you want to
head over to
Ohio,
Nauticon is
coming,
and that's in
Cleveland.
You see beautiful
downtown Cleveland.
Droops is
presenting.
I think Droops is
presenting,
isn't he?
Yeah.
I think he's
been also with
Ponyboy.
Yeah,
Droops,
Ponyboy,
Nightlord,
a lot of the
Infonomicon crew
over there on
PoundInfonomicon
on irc.freeno.net.
So head on over
there,
show your support,
and it seems to
be a very
interesting thing.
It's not
specifically a
hacker convention
from what I
can tell.
There's far too
many girls in
the pictures.
Other than that,
it seems pretty
cool.
They actually have
something,
one of the
contests they
had was transmit
data over
anything you
can.
I don't know
what the exact
title is,
but use your
most interesting
creation to
transmit data and
you get points.
because,
you know,
Ethernet isn't
everything.
I think there's
your tagline.
Bring back the
string and
can.
They actually
do that.
If you do
something with
a string and
can,
you get 10
points.
I wonder if
you could do
that.
See,
now I have to
go just so I
can do that.
It'd be
really interesting.
I actually
think it'd be
cool to set up
some type of
flashlight Morse
code system.
That'd be
pretty sweet.
It wouldn't
be hard.
I'm sure it
wouldn't be.
I guess
we're going
to shout
shouts.
Who has
shouts?
Shouts to
everybody.
Shouts to
everybody in
IRC and
everybody who's
always helping
me with all
my code
rage,
especially
Ali,
A-A-L-I,
in IRC.
He's been a
big help with
a lot of the
code that's
been going
through.
So a
special thank
you to
that fine
gentleman.
Yes,
Ali is a
nice person
and he always
seems to be
very helpful
for Dr.
Zygmunt and
his rams
and raves.
I'll send
shouts out.
Oh,
you know,
another
announcement,
I guess.
We're kind
of going
back to
Linux World
is coming
up in
Boston.
I believe
you can
actually still
get in
free if
you sign
up now.
However,
the clock
is ticking
and I
believe it
will end
this week
as the
free sign
up.
I'll be
there.
Various
people from
Boston
2600 will
be there.
Just stop
on by.
If you're
going to be
in the
area,
just give
me a
ring or
something.
Email me
actually because
all my
phone is
messed up
because
asterisk is
sucking.
I don't
shout out to
Dr.
for coming
up on
this topic
with short
notice.
When you're
getting married,
your weekends
really start
going downhill
very,
very quick.
Side of
the week.
Kyle L.
posted this
in IRC
today.
I was
morbidly
fascinated by
it.
It's
called
www.mydeathspace.com
and it's
people who
have died
in their
MySpaces.
www.mydeathspace.com
It's a lot
like a car
wreck.
You're
looking at
it and
you're kind
of disgusted
by it but
you just
can't look
away.
It's weird.
It really
is.
It's kind
of eerie.
Email us
at
www.radioatbinrev.com
or voicemail
us at
www.lake9binrev.com
Yeah,
www.lake9binrev.com
So leave us a
voicemail.
Give us a call.
We actually did
have a voicemail
botched for a
while and I
think one
person used
it but hey
you know if
you're too
lazy or you
it's 2am
you're not
wearing any
pants and
you're thinking
of us hey
just give us
a call and
leave us a
voicemail.
We have
closed music
tonight.
Our closed
music tonight
is the
Zelda 64
Orkiana
I can't
pronounce this
Orkina
Ocarina
Hey
Ocarina
I think I
made that
joke last
time.
Ocarina of
Time
Prayer.
The Ocarina
of Time
what?
Prayer.
Ah,
okay.
It had a
nice beat.
I kind of
liked it.
It sounded
nice.
You should get
the Boolean of
Fire next time.
Yeah.
So,
next week
hopefully we
don't have all
these issues and
we'll actually
have an episode
that doesn't
suck as bad.
We'll see you
next week.
Same Hack
time.
Especially
time.
Bye.
Thank you.