This place in the Bay Area Stochastic Labs(not much information on them) was asking for applications to give $20k to Science, Art, Technology projects. I heard about it with about 24 hours before it was due but decided to write something up because I thought it would be a good exercise and a good way to put some of my thoughts down.
Here it is in all it's glory:
Bio (500 words)
My name is Dr. Josiah Zayner (really Dr.? yeah I know seems pretentious sorry) and I work as a research Scientist at NASA attempting to develop biotechnology for long-term space exploration and colonization. I started in on science and technology in my late teens. At the age of 19 I received a job with Motorola as a Network Engineer and Programmer for their iDEN cell phone network. In the early 2000s I was laid off when the tech bubble burst and I decided to goto college. I ended up with a B.A. in Plant Biology from Southern Illinois University and an M.S. in Cell and Molecular Biology from Appalachian State. For my Ph.D. I studied how light activated proteins function and how to develop them as optogenetic tools. I received my Ph.D. from the Department of Biochemistry and Molecular Biophysics at the University of Chicago in 2013 where I won the Best Thesis Award. I am currently(Till Dec. 2014) an Imagine Science Artist in Residence and a self-taught computer.microcontroller programmer and electrical engineer. I even wrote a slightly useful piece of software for firewall testing and network troubleshooting called IP Sorcery. Definitely, my claim to fame… No, no it was biotech’s first musical instrument, the Chromochord (http://www.scientificamerican.com/article/biotechs-first-musical-instrument-plays-proteins-like-piano-keys-slideshow/). Or even The ILIAD project (http://www.npr.org/blogs/health/2013/12/04/248854769/scientists-turn-to-the-crowd-in-quest-for-new-antibiotics?ft=1&f=1001). or maybe The Kglove?(http://doitourselfscience.blogspot.com/2014/05/the-kglove.html)
What project are you most known for?(500 words)
If I had to choose a single project that I am most well known for it would probably be The Chromochord. The Chromochord is a musical instrument that allows the musician to strum proteins quantum mechanically like they would strum a guitar. The basis of the instrument is s type of protein called Light-Oxygen-Voltage ((LOV) Pronounced Love) domains. These proteins respond to light by undergoing a quantum mechanical energy transition(from a singlet to triplet state) that changes their photo absorption properties. This can be measured spectroscopically. Once in this triplet state this “vibration” decays over time due somewhat to thermal energy. It is very analogous to strumming a guitar string and the kinetics can probably be modeled very similarly. The measured values from these fluctuations in excitation and decay can be used digitally to modulate MIDI notes on a computer. It basically works by the musician interacting with the protein using light by activating LEDs, the excitation of the protein is measured spectroscopically as it is excited or decays and then the computer sonifies this into whatever sound the musician wishes. For The Chromochord I wrote the software and built the hardware and synthetically created and purified the proteins. I have given a number of concerts, talks and demonstrations on The Chromochord.
More Information and media on The Chromochord can be found:
http://www.scientificamerican.com/article/biotechs-first-musical-instrument-plays-proteins-like-piano-keys-slideshow/
http://www.theverge.com/2013/9/5/4694324/biophysicist-uses-proteins-to-create-chromochord
http://en.wikipedia.org/wiki/Chromochord
https://www.youtube.com/watch?v=LJoFazIJ3w4
https://www.youtube.com/watch?v=jlp-k8tqVl0
What project are you most proud of?(500 words)
The project that I am most proud if would probably not be the conventional definition of a “project”. It is my Ph.D. Thesis. I remember the first journal article I wrote that my thesis would stem from (https://drive.google.com/file/d/0B_R75gIJvkFUeVAzZWxsRjJ3R28/edit?usp=sharing). I poured my heart into that article. All the beauty and pain and Science that was me at that point in time is in that article. The figures of the publication were painstakingly crafted to try and portray how much this work meant to me. My Science had become Art and I just wanted others to recognize that. Unfortunately, Science is a very critical and ego driven world. My paper suffered many blows by people who knew little about the Science behind the work. My life changed after that. Science to me was no longer about publishing in well respected journals or being famous or receiving a prestigious professorship and instead became about the beauty in the experiment. My Thesis work became about beauty and creativity, seeing and creating something that I was proud of and something that was beautiful regardless of what others thought of it. My Thesis is the most personal and insightful document into me and my life except instead of a narrative the descriptions are my experiments. Very few people will ever be able to read it and understand me that way because the key to unlock that insight is knowledge and knowledge is not something that can be bought.
My thesis can be found here: https://drive.google.com/file/d/0B_R75gIJvkFUWVAxNWVNTFRmX0E/edit?usp=sharing
Tell Us about your project(1000 Words)
The project I have been working to create is the first living rewritable hard drive. Using light activated gene expression of fluorescent proteins in engineered bacteria I plan to create a computer interface that allows the writing of data to wells of bacteria. The system will be comprised of three major parts: 1) Engineered DNA and Bacteria 2) Camera and Lighting System for Fluorescent Imaging 2) A Computer to Record Data and Interact with the Bacteria.
The Bacterial system will be composed of two plasmids: one will contain a blue light activated gene expression system that creates the Red Fluorescent Protein(RFP) that can be imaged, with a degradation tag, the other plasmid is a green light activated gene expression system that expresses the ClpA, ClpP and ClpX proteins that will degrade the RFP due to the degradation tag. The bacteria will be placed in a 384 well plate, 1 bit per well. When the bacteria express the RFP it will accumulate and will denote a 1. When there is no RFP or the RFP falls below a certain level due to degradation the value will be a 0. This allows 48 bytes of information storage. The camera, lighting and filter system will image the plate for processing on the computer. The computer will read the values and reconstruct the data just as if the data was stored on a hard drive or other media.
By exposing a well to blue light, the bacteria will be “written to” by expressing the RFP protein that can be imaged. By exposing a well to green light, the bacteria will be “erased” as the RFP is degraded.
The blue light system has been mostly created into a plasmid by Ohlendorf et al., only the tag needs to be added to the RFP. All the DNA sequences and primers have been designed and only need to ordered. The parts that need to be accomplished are: the ClpA and ClpX proteins need to deleted out of the bacterial genome, the green light system DNA needs to be ordered and cloned into a plasmid. The hardware and software need to be created. Because the lighting hardware will be very similar to The Chromochord I will base it off that, which should significantly ease the developmental process.
All Engineered Bacteria, Plasmids and DNA will be made available Open and Free to the community of biohackers and anyone else who wants them. All software and hardware schematics created will also be made Open and Free so others can create their own systems.
References
Ohlendorf et al. (2012) From Dusk till Dawn: One-Plasmid Systems forLight-Regulated Gene Expression
https://drive.google.com/file/d/0B_R75gIJvkFUaTVNN0NhVnFTN2s/edit?usp=sharing
Farrell et al. (2005) Cytoplasmic degradation of ssrA-tagged proteins
https://drive.google.com/file/d/0B_R75gIJvkFUUVNuNEpwZEk5M3M/edit?usp=sharing
How is your project Innovative(500 Words)
There has been very limited work done on biological rewritable systems. A publication by Jerome Bonnet in 2012 attempted to use recombination to create a rewritable system in bacteria. However, it suffered from from two major problems: 1) It is extremely noisy and requires precise tuning to achieve the rewritable nature of the system 2) It requires the addition of chemicals to switch the state of the system. This makes the system unusable as a living hard drive. As far as I know, there has not been any other work that attempts biological storing of information and rewriting.
Other working attempts to use DNA to store information is not a viable rewriting solution as we do not know how to manipulate DNA on the level of writing and rewriting yet in a living cell.
How does one define Innovative? Because some people think Yo is Innovative (http://valleywag.gawker.com/the-man-who-gave-yo-200-000-1593328826). I would rather describe this project as unique, interesting, inspiring and perhaps a little beautiful. No one has ever created something like this. People will be able to visualize the inner workings of the device and interact with it by writing to the living drive. Whatever people want to call it, I just think it is damn cool.
References
Bonnet et al. (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality https://drive.google.com/file/d/0B_R75gIJvkFUM21KR1FRVnFmbk0/edit?usp=sharing
How do you plan to reach.build your audience or user base(500 words)
I plan to reach my audience and user base using many different mediums. I write actively for my personal blog about Science, Technology and Art (http://doitourselfscience.blogspot.com/) and would document the process. I am a member and teach classes at Biocurious in Sunnyvale and would do project demonstrations there. I am also an Artist in Residence for Imagine Science films, they would help me document and publicize the work once it is completed. I also currently run the only DIY Science online store(http://www.the-odin.com). The plasmids and bacteria will be available for free on the store from funding provided. I am heavily involved in the DIY Science and Art community online and could find opportunities through people I know to present this work in Chicago and New York city besides the Bay Area.
How do you plan to use the 20k grant(500 words)
https://docs.google.com/spreadsheets/d/19uG123bXLtnWZx9XBIl-dBqxOpGelS_SmYp8LC4RNvo/edit#gid=0
Item
Cost
Description
Travel
$300
2 Months Caltrain Pass and.or Gas to Berkeley
Genes and Primers
$3,000
DNA synthesis will be ordered from IDT
Reagents and Enzymes
$2,000
For, PCR, Gibson Cloning, Ligation, Restriction Digests
Computer Controlled Camera and accesories
$800
GoPro HERO3+ or Similar for Fluorescence Imaging
Light Filters
$300
Light Filters for Fluorescent Imaging
Hardware
$400
Microcontrollers, LEDs, Misc. Components
Laptop Computer for Art Installation and Other Displays
$1,100
Inspiron 15(for running Linux) ~$900 + Tax and Shipping
Living Expenses
$500
Food and Red Bull for Working Late Nights and Alcohol for trying to sleep after those late nights
Plasmid and Bacteria Distribution
$300
This would provide enough plasmid and bacteria to distribute it free to ~1000 people
Miscellaneous and Unforeseen Expenses
$1,300
Basic Molecular Biology Class
$1,000
Supplies to teach 3 free basic molecular biology classes
Total
$11,000
What are the greatest challenges to success(500 words)
The project is theoretically sound but still theoretical. The greatest challenges will definitely be in the DNA engineering because the green light system has not been tested yet in living bacteria. If the green light system works, I predict the chances of success being in the 75% or greater range. Even if the green light system does not work a “punch card” like memory storage design could be created from only the blue light system and plates, i.e. only writable once. The hardware and software required is fairly straightforward and will just require some time to sit down and write it.
How do you think your project will benefit from STOCHASTIC community(500 words)
As a Scientist I have not had the chance to develop many of the skills that surround presenting Art. Honestly, I would not know how to even begin to find a place to hold an Art installation or even how to hold one(I guess I could always search the internet). Further, because I enjoy the Science and Engineering part of projects some of them are less than aesthetically pleasing and use copious amounts of duct tape. I think that being around other Artist’s could help me out alot in the many aspects of Art that I have not experienced being primarily a Scientist and Engineer. FInally, groups of intelligent and creativity people often can give you an objective perspective of your work that cannot be reached otherwise.
Rough timeline
Money being deposited in my account being the start of Week 1
Week 1 will be the ordering of DNA and components.
Depending on when DNA arrives(1 - 2 weeks)
Weeks 1,2-4 to clone green light activated system
Weeks 1,2-4 to remove the ClpX and ClpA genes from bacteria
Weeks 4-8 to create hardware and software system
Obvious, this is an accelerated timeline and there are chances that this will likely take 3-4 months to complete.
What building event or service project do you plan to do
I plan to teach 3 Free Molecular Biology classes at either Biocurious, Counter Culture Labs or Berkeley Biolabs(or all three). The class will teach people how to amplify and clone synthetic DNA fragments into bacteria to create a unique organism.
Anything else
I just found out about this grant at ~10PM on July 2nd or the application would be of much higher quality and would not have been submitted so last minute. I thought this would be a great opportunity to work on a dream project I do not currently have the monies to fund.
Links to content
Designed Primers, Genes and DNA sequences for the project:
https://docs.google.com/document/d/1J8bKYXBEL6PBVcbqY5BSJE39OyL147cl_WGgtyidkuo/edit?usp=sharing
Link to answers in one file:
https://docs.google.com/document/d/1d9DqUobiqNxoqzDKEszqrJZQDAa0MDGotcy_Q3uEVIM/edit?usp=sharing
My blog:
http://doitourselfscience.blogspot.com/
Saturday, July 5, 2014
Thursday, May 29, 2014
Who is a Scientist?
i don't know.
To most people I would guess that this seems like a simple question and they would answer "A Scientist is of course, someone who went to graduate school and performs Science as a job." Yeah, sometimes I want to take that stance also. The problem is that I know that it is probably not true.
I grew up in the 90s and early 2000s computer hacking scene(I know I always say this) and if someone were to ask, "What is a computer programmer.developer?" I would have probably answered "Someone who programs in a complex programming language and has written a program or been involved in a project that consisted of thousands of lines of codes." What that means is that everyone can be a developer if they know how to code and do code. That was me. Of course there were lots of things I missed in programming because I never went to school for it and suffer for it now in my coding(why I always encourage people who are really excited about Science to goto Graduate School). Still I could hang with the best of them evidenced by Motorola hiring me. Someone writing a chapter in a book about a program I wrote. &c.
Is this a good analogy for a Scientist though?
One can program without knowing much math or even about how a computer works. It is almost self-contained. Science is NOT! One problem I run into alot with non-trained DIY Science Enthusiasts is that they lack some of the basic knowledge and skills that would allow them to do significant experiments. Sure, I understand DIY Enthusiasts are not all out to do significant experiments. I also understand that I can change this by providing people with knowledge and tutorials on how to do Science and I do (http://www.the-odin.com/tutorials/) Yeah, so this issue can be overcome. (No thanks, to the DIY zine Biocoder who rejected my tutorial on computational protein science? I know, it's my fault, I suck at writing).
So what's the problem? Why does it matter?
I think it matters because the people who are providing Scientific knowledge and training to others, sometimes as mass media, do not have the proper knowledge and skills to evaluate what is good Science and what is not. They sometimes don't even know Science well enough to understand that the statements they make are unScientific. Did you know Bill Nye was never a Scientist or trained as one? He has a Bachelor's Degree in Engineering. That's it. And somehow this man has become the voice for the Scientific world on things like Global Warming... But I am sure he has studied the data thoroughly........... for years....
This is a huge example, so imagine how bad it is as you go down the ladder. People who are considered leaders in the DIY Biology community know little to nothing about actual Science or what is possible (No we can't stick a Monkey's head on a human body, sorry). And they pretend like they can "train" people. And it doesn't seem like trained Scientists really want to be involved. Why not? I guess they don't see the advantage? And they think that DIY Scientists can't really do much (which is kind of true at the moment).
To me I want to be inclusive. Sometimes I want to say, someone who is excited about Science and performs experiments is a Scientist (which is more than I can say for many Graduate Students and Post Docs ROFLMao......) And maybe that is the answer. But because "Scientist" is a title, it denotes some exclusivity. Someone who enjoys playing basketball is not considered a "Basketball Player". Just as someone who transformed bacteria with GFP once is not a Synthetic Biologist...
It is a fight between logic and ego and all those random Science pictures that go around the internet that try and convince people that something amazing is going to come by using a Drosophila eye as a model for the human belly button.
Just because you read Harrison's Principles of Internal Medicine doesn't make you a Medical Doctor(in fact if you called yourself one you could probably be taken to jail?). But anyone who has a slight interest in Science can be considered it's voice...
I am still at the same place where I began.
Who is Scientist?
i don't know. are you one?
To most people I would guess that this seems like a simple question and they would answer "A Scientist is of course, someone who went to graduate school and performs Science as a job." Yeah, sometimes I want to take that stance also. The problem is that I know that it is probably not true.
I grew up in the 90s and early 2000s computer hacking scene(I know I always say this) and if someone were to ask, "What is a computer programmer.developer?" I would have probably answered "Someone who programs in a complex programming language and has written a program or been involved in a project that consisted of thousands of lines of codes." What that means is that everyone can be a developer if they know how to code and do code. That was me. Of course there were lots of things I missed in programming because I never went to school for it and suffer for it now in my coding(why I always encourage people who are really excited about Science to goto Graduate School). Still I could hang with the best of them evidenced by Motorola hiring me. Someone writing a chapter in a book about a program I wrote. &c.
Is this a good analogy for a Scientist though?
One can program without knowing much math or even about how a computer works. It is almost self-contained. Science is NOT! One problem I run into alot with non-trained DIY Science Enthusiasts is that they lack some of the basic knowledge and skills that would allow them to do significant experiments. Sure, I understand DIY Enthusiasts are not all out to do significant experiments. I also understand that I can change this by providing people with knowledge and tutorials on how to do Science and I do (http://www.the-odin.com/tutorials/) Yeah, so this issue can be overcome. (No thanks, to the DIY zine Biocoder who rejected my tutorial on computational protein science? I know, it's my fault, I suck at writing).
So what's the problem? Why does it matter?
I think it matters because the people who are providing Scientific knowledge and training to others, sometimes as mass media, do not have the proper knowledge and skills to evaluate what is good Science and what is not. They sometimes don't even know Science well enough to understand that the statements they make are unScientific. Did you know Bill Nye was never a Scientist or trained as one? He has a Bachelor's Degree in Engineering. That's it. And somehow this man has become the voice for the Scientific world on things like Global Warming... But I am sure he has studied the data thoroughly........... for years....
This is a huge example, so imagine how bad it is as you go down the ladder. People who are considered leaders in the DIY Biology community know little to nothing about actual Science or what is possible (No we can't stick a Monkey's head on a human body, sorry). And they pretend like they can "train" people. And it doesn't seem like trained Scientists really want to be involved. Why not? I guess they don't see the advantage? And they think that DIY Scientists can't really do much (which is kind of true at the moment).
To me I want to be inclusive. Sometimes I want to say, someone who is excited about Science and performs experiments is a Scientist (which is more than I can say for many Graduate Students and Post Docs ROFLMao......) And maybe that is the answer. But because "Scientist" is a title, it denotes some exclusivity. Someone who enjoys playing basketball is not considered a "Basketball Player". Just as someone who transformed bacteria with GFP once is not a Synthetic Biologist...
It is a fight between logic and ego and all those random Science pictures that go around the internet that try and convince people that something amazing is going to come by using a Drosophila eye as a model for the human belly button.
Just because you read Harrison's Principles of Internal Medicine doesn't make you a Medical Doctor(in fact if you called yourself one you could probably be taken to jail?). But anyone who has a slight interest in Science can be considered it's voice...
I am still at the same place where I began.
Who is Scientist?
i don't know. are you one?
Wednesday, May 21, 2014
The KGlove
Lately, I have been coveting lots of cool tech toys, Google Glass and Oculus Rift. I decided I wanted some wearable computing of my own and so like any decent Hacker I decided to build a wearable computer and interface myself.
Before Jumping into the Optical setup I wanted to make sure I had a keyboardless way to type on a computer. Though speech to text is awesome I don't want to be in a bar or room of talking people and not be able to type. So I decided to build the KGlove. Basically, the KGlove is an input interface to a computer that is activated when you bend your fingers. It uses an Arduino and flex sensors. I am going to make it wireless and add in an accelerometer soon for the mouse. I made it so I can type characters using it and also play MIDI, like playing a piano without a piano, see the end of the video.
The way the text typing works is that each finger on the right hand represents a character in alphabetical order and each finger on the left hand goes to the next set of 5 letters.
So Right Thumb is 'a' and Right Index Finger is 'b'.
If I do Left Thumb and Right Thumb that is 'f', the sixth letter or Left Thumb and Right Index that is 'g'. Having the letters in order makes it really easy to learn. This only leaves me with 30 possible characters. However, by combining Left Finger combinations I should be able to achieve 3125 different possible characters(key presses). The hardest part is muscle control. Bend your middle finger, your ring finger wants to bend also. So controlling that movement and calibrating the sensors is important.
Code is all available Here
I am just learning to type with it so in the video sometimes it takes me a second to remember which finger combination is which letter. Also, sometimes I need to backspace. Yeah, I made sure I had backspace, haha.
Oh yeah at the end you can tell I am not a musician or pianist. hahaha.
Before Jumping into the Optical setup I wanted to make sure I had a keyboardless way to type on a computer. Though speech to text is awesome I don't want to be in a bar or room of talking people and not be able to type. So I decided to build the KGlove. Basically, the KGlove is an input interface to a computer that is activated when you bend your fingers. It uses an Arduino and flex sensors. I am going to make it wireless and add in an accelerometer soon for the mouse. I made it so I can type characters using it and also play MIDI, like playing a piano without a piano, see the end of the video.
The way the text typing works is that each finger on the right hand represents a character in alphabetical order and each finger on the left hand goes to the next set of 5 letters.
So Right Thumb is 'a' and Right Index Finger is 'b'.
If I do Left Thumb and Right Thumb that is 'f', the sixth letter or Left Thumb and Right Index that is 'g'. Having the letters in order makes it really easy to learn. This only leaves me with 30 possible characters. However, by combining Left Finger combinations I should be able to achieve 3125 different possible characters(key presses). The hardest part is muscle control. Bend your middle finger, your ring finger wants to bend also. So controlling that movement and calibrating the sensors is important.
Code is all available Here
I am just learning to type with it so in the video sometimes it takes me a second to remember which finger combination is which letter. Also, sometimes I need to backspace. Yeah, I made sure I had backspace, haha.
Oh yeah at the end you can tell I am not a musician or pianist. hahaha.
Wednesday, May 14, 2014
Machine Learning and You
Machine Learning is super cool.
To most people it is just a fancy phrase kind of like Quantum Mechanics.
Working with data most of my life I was happy to finally start to embrace and understand the world of Machine Learning a few years ago. It has really changed my life.
So what is Machine Learning?
Machine Learning is a way to "comprehend" data that humans cannot really understand. Usually because the data is so highly multi-dimensional or has a non-linear association.
So I saw an ad in my Yahoo.com email today(yes I have a yahoo.com email, don't hate. I have had it since 1997 or so and use it when a website asks for website sign-up spam) and there was an ad for a dating site for finding women over 50 years of age. I started thinking.
These ads in your email box usually use some Machine Learning algorithms to take many different factors about you and who you communicate with to determine what ads to feed you. Maybe these ads know me better than I know myself because I can't comprehend all the factors that go into making a good relationship. Maybe I should start dating 50+ year old women because they would be a great fit for me....
This was a very existential few minutes where I attempted to determine if what I knew about myself was actually true or just what I thought to be true.
But then I just refreshed the webpage a few times and found out that the algorithm(if there even is one) to choose which ads to display is most likely not using Machine Learning and just outputs random stupid adverts such as to the Stop the Sugar Addiction I don't have(I actually really dislike sugary foods) or to take out an Extra Loan on the Mortgage I don't have.
Oh well. Let me tell you, that was an intense couple of minutes. At least I am glad I didn't make a extreme life choice because of Yahoo.com's shitty advertisement algorithm. Someday soon this might actually be the case though. Where maybe we should listen to ads on Gmail because they know us better than we know ourselves. Hmmmmmm
To most people it is just a fancy phrase kind of like Quantum Mechanics.
Working with data most of my life I was happy to finally start to embrace and understand the world of Machine Learning a few years ago. It has really changed my life.
So what is Machine Learning?
Machine Learning is a way to "comprehend" data that humans cannot really understand. Usually because the data is so highly multi-dimensional or has a non-linear association.
So I saw an ad in my Yahoo.com email today(yes I have a yahoo.com email, don't hate. I have had it since 1997 or so and use it when a website asks for website sign-up spam) and there was an ad for a dating site for finding women over 50 years of age. I started thinking.
These ads in your email box usually use some Machine Learning algorithms to take many different factors about you and who you communicate with to determine what ads to feed you. Maybe these ads know me better than I know myself because I can't comprehend all the factors that go into making a good relationship. Maybe I should start dating 50+ year old women because they would be a great fit for me....
This was a very existential few minutes where I attempted to determine if what I knew about myself was actually true or just what I thought to be true.
But then I just refreshed the webpage a few times and found out that the algorithm(if there even is one) to choose which ads to display is most likely not using Machine Learning and just outputs random stupid adverts such as to the Stop the Sugar Addiction I don't have(I actually really dislike sugary foods) or to take out an Extra Loan on the Mortgage I don't have.
Oh well. Let me tell you, that was an intense couple of minutes. At least I am glad I didn't make a extreme life choice because of Yahoo.com's shitty advertisement algorithm. Someday soon this might actually be the case though. Where maybe we should listen to ads on Gmail because they know us better than we know ourselves. Hmmmmmm
Friday, May 2, 2014
In Defense of Geniuses Among Us: Against Academic Journal Paywalls
Genius is fueled by Knowledge. Let's say you meet this person, we will call him Joey Joe Joe Junior Shabadu and he is creative and intelligent and has skills in a wide variety of disciplines that makes him capable of solving many problems in Science and Technology. Using Quantum Dots for Solar Cells maybe? Joey Joe Joe is ready to apply his knowledge from patterning biological materials but he can't. Why? Because Joey doesn't know much about Quantum Dot Solar Cells and when he tried to find out he hit academic journal Paywalls. What if Joey had access to this information could he change the energy landscape of the world by developing highly efficient solar cells?
The one thing in Academia that there are more of than Ph.D.s are egos. Most every Professor, PostDoc, Graduate Student I have met has a huge ego (graduate students tend to lose it towards the end of their schooling and the beginning of their PostDoc). I guess I am not really excluded in the area of ego. This ego makes people feel as if they are Geniuses and that they have no bad ideas and are the best in their field. Someone said to me today that "It's the Professor's lab they can do what they want." to which I replied, "Without the PostDocs and Students they would not have a lab." What people outside Science don't know is that what most people consider "Actual Scientists", ya' know the people you read about in magazines and such? These people have not done experiments in 10s of years. They are not Scientists they are Managers and they are Tyrants. Science is not a democracy. The best idea doesn't win. This becomes even more pronounced because of the publication system. Papers are thought to be more "Genius" if they are in a publication such as Science or Nature or Cell or &c. If your ideas are so great then why does it matter where they are published?
Who is a Genius? Someone with a Ph.D.? I have meet some Geniuses with Ph.D.s and without(especially growing up in the 90s Hacker scene). I have also met some Ph.D.s that people would be bamboozled by their stupidity. There is this feedback system where Academics want to feel superior to the "common" human. I have heard before when discussing Open Access, "Why would your average human want to read an Academic journal?"(sad) What are these Academians so afraid of? Being found out as frauds? Being required to do actual Science and not just have "ideas"? Being judged by their work and not just what journal you publish in?
So there is Joey Joe Joe and he could change the world if he had access to knowledge and there are maybe thousands of Joey Joe Joes out there. The reason that computer science, programming and engineering have progressed so rapidly over the past 20 years is probably because access to all the knowledge you need to do these things is free and available. That's how I taught myself to program in C and Perl, that's how I taught myself Electronics. Why I was hired by Motorola at 19 to do Network Engineering. Now I can't even read a damn journal article on recent advances in Synthetic Biology that would allow me to progress my research. Neither can a high school kid or someone trying to do DIYScience. I work for NASA to add even more shame to it. The government publishes its work in journals it can't even afford to have subscriptions to!!! How messed up is that? How does the world expect organizations like NASA to be cutting edge when we have extreme difficulty obtaining journal articles from modern literature. Shame on you $cience magazine and Natur€ magazine and El-slime-vier.
I think the worst part, the thing that is most distressing to me is that our world could be so unbelievable. If Science became accessible, who knows the limits of what human beings could do with this? We could have treatments for many diseases, biotechnology that would blow your mind but instead we are held hostage by publishers. How much do you believe in people? How much do you believe that giving people knowledge can completely change the world?
I challenge you as a Scientist and Scholar to never again publish an article that is not made freely available to all. So go on, withhold your knowledge from humanity in hopes that you might be well known in a small circle of Scientists for work you didn't actually do. Because ya' know a 5 point increase in impact factor is worth way more than making sure human knowledge is spread far enough that it can change the world.
The one thing in Academia that there are more of than Ph.D.s are egos. Most every Professor, PostDoc, Graduate Student I have met has a huge ego (graduate students tend to lose it towards the end of their schooling and the beginning of their PostDoc). I guess I am not really excluded in the area of ego. This ego makes people feel as if they are Geniuses and that they have no bad ideas and are the best in their field. Someone said to me today that "It's the Professor's lab they can do what they want." to which I replied, "Without the PostDocs and Students they would not have a lab." What people outside Science don't know is that what most people consider "Actual Scientists", ya' know the people you read about in magazines and such? These people have not done experiments in 10s of years. They are not Scientists they are Managers and they are Tyrants. Science is not a democracy. The best idea doesn't win. This becomes even more pronounced because of the publication system. Papers are thought to be more "Genius" if they are in a publication such as Science or Nature or Cell or &c. If your ideas are so great then why does it matter where they are published?
Who is a Genius? Someone with a Ph.D.? I have meet some Geniuses with Ph.D.s and without(especially growing up in the 90s Hacker scene). I have also met some Ph.D.s that people would be bamboozled by their stupidity. There is this feedback system where Academics want to feel superior to the "common" human. I have heard before when discussing Open Access, "Why would your average human want to read an Academic journal?"(sad) What are these Academians so afraid of? Being found out as frauds? Being required to do actual Science and not just have "ideas"? Being judged by their work and not just what journal you publish in?
So there is Joey Joe Joe and he could change the world if he had access to knowledge and there are maybe thousands of Joey Joe Joes out there. The reason that computer science, programming and engineering have progressed so rapidly over the past 20 years is probably because access to all the knowledge you need to do these things is free and available. That's how I taught myself to program in C and Perl, that's how I taught myself Electronics. Why I was hired by Motorola at 19 to do Network Engineering. Now I can't even read a damn journal article on recent advances in Synthetic Biology that would allow me to progress my research. Neither can a high school kid or someone trying to do DIYScience. I work for NASA to add even more shame to it. The government publishes its work in journals it can't even afford to have subscriptions to!!! How messed up is that? How does the world expect organizations like NASA to be cutting edge when we have extreme difficulty obtaining journal articles from modern literature. Shame on you $cience magazine and Natur€ magazine and El-slime-vier.
I think the worst part, the thing that is most distressing to me is that our world could be so unbelievable. If Science became accessible, who knows the limits of what human beings could do with this? We could have treatments for many diseases, biotechnology that would blow your mind but instead we are held hostage by publishers. How much do you believe in people? How much do you believe that giving people knowledge can completely change the world?
I challenge you as a Scientist and Scholar to never again publish an article that is not made freely available to all. So go on, withhold your knowledge from humanity in hopes that you might be well known in a small circle of Scientists for work you didn't actually do. Because ya' know a 5 point increase in impact factor is worth way more than making sure human knowledge is spread far enough that it can change the world.
Monday, April 28, 2014
How Fight Club defined my generation or maybe just me
Last night I watched Fight Club for the first time in maybe 7 years and it is was interesting to see how much my life aligned with what I imagined it would be 7 years ago. I am trying not to say that Fight Club helped define me but honestly I don't know. Maybe it had a huge impact?
(The Movie, I have never read the book and don't plan on it. Chuck Palahniuk is like a 1990s Kurt Vonnegut and I dislike Vonnegut very much )
Fight Club came out in 1999. I honestly cannot remember the first time I watched it but I have owned a copy of the movie most of my adult life. I have probably seen the movie 50 times but I am obsessive like that. Out of the handful of movies I own I have watched some 100 or more times(Iron Man, Good Will Hunting). Have you ever watched a movie that you haven't seen in 10 years and it blows your mind because your memories of it don't match your current perception because you are such a different person? Watching Fight Club last night was like that because I used to always watch it from the perspective of how I wanted to be instead of the perspective of how I am.
To me the movie Fight Club is about being an individual. The main characters talk about how the current ways that people attempt to be unique do not make them unique at all and instead we should strive for uniqueness by our actions. The movie is also very punk, everything they do is basically to fuck the system. In 1999 I was 18 years old. It is so hard to be young and have so many grandiose ideas. No one listens to you and it is basically a waiting game until you are old enough for people to take you seriously. Coming from a poor family I also lacked resources. I scraped and scrounged and stole to acquire my first computer which changed my life. Now I am somewhat respectable(depending on who you ask), I have a Ph.D. and work at NASA, I have free time and I have money. And I take advantage of all these things.
It is awesome. I can give people the double fuck you. Both middle fingers. Because no one in my life defines me anymore. I define myself. I worked so hard for so many years that I am good at my job and I love my job, Science. People can never take Science away from me. Even if you lock me up in a jail cell I can still do theoretical Science through maths and hypotheses. If I am fired it doesn't matter, I have accumulated a decent lab at my apartment that I play around in all the time. Building stuff, doing experiments, creating art. My life does not revolve around you. You can't control me like you could when I was 18 or 21. You can no longer threaten me with a bad grade or firing me from my job. None of these things matter to me anymore because I have all I need.
This was my generation. The Generation of Computer Hackers and Punk Musicians and Occupy Wallstreet. None of this shitty Anonymous(The hacking collective) stuff either, hacking was for fun or to give some corporate suit a big fuck you, never to seriously threaten people. My generation wrote "The Hacker Manifesto" (http://phrack.org/issues/7/3.html)(Ok well maybe slightly before my generation). My generation has Mark Zuckerbergs who wear hoodies instead of suits. Because we do what we want that's why.
The generation before us were the Suits. And poorly fitting ones at that. Most of them still think things need to be a certain way. Most of them are opposed to change. They don't want to rock the boat or they think by wearing a t-shirt instead of a collared shirt that they are rocking the boat.
The generation after me doesn't give much of a fuck about anything and even if they did they think an Online Petition is the way to solve problems not going out and fixing it yourself. I was talking to someone in a bar in the Valley who was an undergrad at Stanford(21 or 22 years of age) and they proceeded to tell me that they wanted to be a Project Manager when they graduate. WTF is that? I remember when I was at St. Mark's boarding school talking about NASA and Science. I asked how many of them wanted to be Astronauts when they were younger and maybe 2 in 60 said they did! That blows my mind. Finance they said.
My generation doesn't give up. They are the loudest most annoying assholes you will meet. The ones who post way too much on facebook about their beliefs. But they speak with their actions and money not just their words.
Maybe this post is really all about me and not my generation and of course it is all anecdotal. But I don't give a fuck because I don't care what you think. hahaha.
Anyways, if you have not seen Fight Club in a while watch it and see how much you have changed.
Monday, April 14, 2014
GRC Photosensors
The Photosensory Gordon Conference is over and I am stuck in Italy, oh the horror you say but really I want to be home. Before coming here I was at St. Mark's boarding school to give a talk about technology and the Chromochord it was fun but I have been home 4 of the last 24 days and I really like my own things. I am extensively a creature of habit and really like eating the same foods and seeing the same things and working. I love being able to do Science and work. I am excited to return home.
So the conference was about what I expected except that there was not much on LOV domains, *tear*. It was really great to see everyone again and meet people I have been doing lots of work with, Peter Freddolino(we have been running some enhanced sampling MD simulations). Super computers and remote resources for the win. During, my travels I have had to SSH into these computers from my cell phone to set something up. I enjoy 2014 it is so cool. Hung out a bunch with John Christie from Glasgow and John Kennis my laser lab Amsterdam friend. After my last post it was sad because so many people were telling much how they enjoyed my work and how it had helped them figure stuff out or write grants. In fact someone told me that a preprint I sent them of one of my manuscripts before submission helped them to write a grant that they received! Yay for being open with my work and it helping people, that is exactly the point of Science. Anyways, I think in the end friends and colleagues do make one feel truly appreciated.
The conference has given me so much time to think. So many more ideas. I have so many ideas floating around my head I am having a hard time focusing. It is making me more manic than normal. But because I see this I can start to try and take it under control. Sometimes I wish I could turn my brain off without alcohol and then turn it back on again when I needed more ideas.
Arriving in Pisa today I really wanted a hamburger after eating pasta all week. The one I ate was an interesting attempt at one but probably the most disappointing burger I have had in a while. Oh well. Tomorrow I am off to Heathrow and I stay the night there due to a scheduling mistake. Sunday night I gladly arrive home in Mountain View. I miss you Kirin Chinese restaurant and NASA.
Monday, April 7, 2014
Appreciation
One of the hardest things in graduate school was working so hard and never really having much appreciation. I would slave and slave(I mean this term in no disrespect to people who were actually slaves but graduate school can be very physically, emotionally and psychologically distressing) and have creative ideas(or attempt to) and in the end I would beg for the table scraps of appreciation that people would give to me. Eventually, I just stopped caring and wanted to scream "fuck you" at everyone who told me that something I did was good because they had no idea the sweat and blood and tears that went into it(which reminds me, I really want tattoos that say Blood, Sweat, Tears and Toil). My reaction is a little overboard I know. But that is how I felt and how I still feel a little. I only want people to appreciate my work that I deem their appreciation worthy of my acceptance, hahaha. Yeah, a pretty insane way of thinking. But I came from not much. Parents divorced, grew up poor on a farm, almost failed out of high school, almost failed out of college. School was very difficult for me because I have always been an autodidact and I just don't do well on testing at least not compared to the amount of work I put in. People have just always thought I was stupid(which is a problem with our education system but that is not intended for this post).
Now I work at NASA. Of course I know people now that did not know me 15 or 10 or even 5 years ago so it is somewhat silly but lately I have noticed how much appreciation and can I say "awe" I receive for working at NASA. This is not to say I don't appreciate some of it. I am only human and have an ego also. Sometimes however it is beginning to irk me a little. I know I shouldn't complain but let's be honest isn't that what a blog is for? Say I did not have this job at NASA I would probably be appreciated less even though I have accomplished the same amount. This is silly to complain about though. I guess I wish people were more appreciative of the graduate students and post docs in the world that don't work for NASA. That people were not as revered as much for title or position and more for the work that they _actually_ do. Yes, this is directed to the Investigators who have huge egos but have done not much more than write grants since they received their job.
My motto is kind of like "I am only as good as what I did yesterday."
To me a lifetime of effort is worth much much more than a single breakthrough. In general we can always choose to work harder each day or learn more or develop things. I am sure there is a genetic component to this but maybe there is a very slight fraction that has to do with our willingness to sacrifice i.e. something that was a choice. Maybe we do deserve appreciation? To me most Breakthroughs are usually a happenstance of random chance and who is paying attention. A nature or science publication. In the end people may remember your name but your work will have left nothing indelible in the ether. Your work could have been accomplished by someone else. A puzzle requires the finding and positioning of every piece to solve. There is no shortcut. Each piece must be placed. Me, I would rather be the person who places most of the pieces then the one who only places the last piece to reveal the beautiful picture to much fanfare. I don't want my life to be defined by other people's appreciation but more I want it to be defined by the beauty I saw in it. Am I able to become and create the things I think are beautiful? I think truly admiring your own work is the highest form of appreciation but at least for me sometimes I do still need someone else to give me a high five. Despite how grumpy I act.
Now I work at NASA. Of course I know people now that did not know me 15 or 10 or even 5 years ago so it is somewhat silly but lately I have noticed how much appreciation and can I say "awe" I receive for working at NASA. This is not to say I don't appreciate some of it. I am only human and have an ego also. Sometimes however it is beginning to irk me a little. I know I shouldn't complain but let's be honest isn't that what a blog is for? Say I did not have this job at NASA I would probably be appreciated less even though I have accomplished the same amount. This is silly to complain about though. I guess I wish people were more appreciative of the graduate students and post docs in the world that don't work for NASA. That people were not as revered as much for title or position and more for the work that they _actually_ do. Yes, this is directed to the Investigators who have huge egos but have done not much more than write grants since they received their job.
My motto is kind of like "I am only as good as what I did yesterday."
To me a lifetime of effort is worth much much more than a single breakthrough. In general we can always choose to work harder each day or learn more or develop things. I am sure there is a genetic component to this but maybe there is a very slight fraction that has to do with our willingness to sacrifice i.e. something that was a choice. Maybe we do deserve appreciation? To me most Breakthroughs are usually a happenstance of random chance and who is paying attention. A nature or science publication. In the end people may remember your name but your work will have left nothing indelible in the ether. Your work could have been accomplished by someone else. A puzzle requires the finding and positioning of every piece to solve. There is no shortcut. Each piece must be placed. Me, I would rather be the person who places most of the pieces then the one who only places the last piece to reveal the beautiful picture to much fanfare. I don't want my life to be defined by other people's appreciation but more I want it to be defined by the beauty I saw in it. Am I able to become and create the things I think are beautiful? I think truly admiring your own work is the highest form of appreciation but at least for me sometimes I do still need someone else to give me a high five. Despite how grumpy I act.
Tuesday, April 1, 2014
Peer Review and Frontiers in Chemistry- Don't Publish There
What's the point of Peer Review if it is really faulty?
Peer Review was designed to make sure that Scientist do not become overly bias towards their research and that when someone wants to read a Scientific article they do not have to spend most of their time reading it to determine if the paper is legit or not.
It doesn't seem to be working. There are so many retractions and so many bad papers that are published that the Scientific world is just overwhelmed with much nonsensical stuff.
So when something is broken I generally don't just complain, I attempt to fix it or contribute to a fix. I heard about PeerJ and despite the fact that they are just a business like all other publishers(they just charge less) I decided to Review some papers. I partcipated in the review of a couple of papers but then came upon this one: https://peerj.com/preprints/66v1/ and I made these comments: https://peerj.com/preprints/66v1/#feedback-84 . I thought the comments were very constructive considering the paper has no place in any Scientific journal. The paper basically sounds like it was written by someone with high school or below level of Science knowledge. The author responded with equally nonsensical responses and I was pissed for a little bit but I figured no one would really care because it was a paper on PeerJ, which let's be honest is not exactly a respectable place to publish anything, considering.
Then a few months later I receive an email from PeerJ saying that the paper in question was published in a "more" respectable journal, Frontiers in Chemistry (http://journal.frontiersin.org/Journal/10.3389/fchem.2014.00013/full) I was appalled that a journal that says they do Peer Review published this paper considering it has no Scientific basis and pushes the boundaries of even a high school level lab report. I thought that maybe the paper was just overlooked? So I emailed Frontiers in Chemistry with a detailed Review and asked them how it was published and this was their response:
Peer Review was designed to make sure that Scientist do not become overly bias towards their research and that when someone wants to read a Scientific article they do not have to spend most of their time reading it to determine if the paper is legit or not.
It doesn't seem to be working. There are so many retractions and so many bad papers that are published that the Scientific world is just overwhelmed with much nonsensical stuff.
So when something is broken I generally don't just complain, I attempt to fix it or contribute to a fix. I heard about PeerJ and despite the fact that they are just a business like all other publishers(they just charge less) I decided to Review some papers. I partcipated in the review of a couple of papers but then came upon this one: https://peerj.com/preprints/66v1/ and I made these comments: https://peerj.com/preprints/66v1/#feedback-84 . I thought the comments were very constructive considering the paper has no place in any Scientific journal. The paper basically sounds like it was written by someone with high school or below level of Science knowledge. The author responded with equally nonsensical responses and I was pissed for a little bit but I figured no one would really care because it was a paper on PeerJ, which let's be honest is not exactly a respectable place to publish anything, considering.
Then a few months later I receive an email from PeerJ saying that the paper in question was published in a "more" respectable journal, Frontiers in Chemistry (http://journal.frontiersin.org/Journal/10.3389/fchem.2014.00013/full) I was appalled that a journal that says they do Peer Review published this paper considering it has no Scientific basis and pushes the boundaries of even a high school level lab report. I thought that maybe the paper was just overlooked? So I emailed Frontiers in Chemistry with a detailed Review and asked them how it was published and this was their response:
Dear Dr Zayner,
We thank you for your message and for taking the time to send us
your comments on the article by Dr Moustafa that was recently published
at Frontiers in Chemistry.
I would like to kindly clarify that this manuscript underwent
thorough peer-review before being accepted for publication at Frontiers.
We received reports from three independent reviewers and two of them
supported and endorsed the publication of the manuscript.
The final decision was taken by the Associate editor after taking into
account all of the reviewers' recommendations.
As you pointed out, any published article should be supported by
evidence, and it was decided by two reviewers and the associate editor
that this particular article included enough evidence to warrant its
publication.
I would also like to point out that this manuscript is an Opinion
article. These Frontiers article types allow researchers maximum freedom
of expression to publish viewpoints on the interpretation of facts,
weaknesses and strengths of any scientific theory
or on any topic relevant to the field of research.
We certainly understand that this is an area of controversy and
that there are various opinions on this point. We would encourage you to
enter in a constructive discussion by submitting either an Opinion
article of your own or a General commentary on this
article (http://www.frontiersin.org/Chemistry/articletype), which would be
linked to the first article and provide an alternate viewpoint of the situation and continue the debate in a constructive way.
Kind regards,
Marie Soulière, Ph.D.
Journal Manager
Frontiers | Chemistry Editorial Office
www.frontiersin.org | twitter.com/FrontiersIn
EPFL - Innovation Square, building I
Lausanne, Switzerland | T +41(0)21 510 17 11
Journal Manager
Frontiers | Chemistry Editorial Office
www.frontiersin.org | twitter.com/FrontiersIn
EPFL - Innovation Square, building I
Lausanne, Switzerland | T +41(0)21 510 17 11
WHAT! I AM APPALLED THAT DESPITE EVIDENCE TO THE CONTRARY THEY REFUSE TO ADMIT A SHODY JOB WAS DONE ON PEER REVIEW!
(If you goto the Frontiers article you can actually see who Peer Reviewed this paper... I feel bad for these people)
That is why I am writing the post. Open Publishing and Open Access and even Peer Review are not all that they are made up to be, which we have heard again and again and again.
So what now? If a paper in a High Impact journal has a higher than normal chance of being retracted and a paper in low impact journal has a higher then normal chance of being awful.
I really enjoy working at NASA and the freedom they give me but if I have a say NASA will probably be the last normal Scientific post I have(either because I stay here or leave). Science and publishing are just so messed up at the moment and I can do so many more cool things if I don't need to stay within those boundaries.
Monday, March 31, 2014
Sending and Receiving Data from an Arduino Through a Webpage
I thought it would be kind of cool to be able to control an Arduino remotely so I hacked up a bunch of code that allows me to do this. The website can control multiple Arduino's at one time and recognizes them by their unique IDs that they send.
Basically, what you need is:
A computer running Linux
A webserver, Apache is nice with ability to run Javascript and Perl
Perl
An Arduino
How it works is like this:
1. Arduino sends data to the Serial port that is polled by computer_interface.pl and written to a file that is plotted using gnuplot to display on the webpage
3. Webpage uses web_interface.cgi to write data to a file that is read by computer_interface.pl and sent to Arudino
2. Arduino is polling Serial port to receive data and uses the data to modify variables that can change how the Arduino operates.
What this code was written for was having an Arduino controller multiple pieces of equipment in a Scientific lab but it can be ported to use for many other things.
Here is the Arduino Code: http://pastebin.com/f8eBJc7R
Here is the computer_interface.pl: http://pastebin.com/yGNMCH54
Here is the webinterface.cgi: http://pastebin.com/qpUZ5n9A
Here is the gnoplot formatting file should be in the same directory as computer_interface.pl: http://pastebin.com/1BWNaAc4
HTML file: http://pastebin.com/e2Fpkrfi
HTML CSS: http://pastebin.com/1YUnWS0Q
HTML Javascript: http://pastebin.com/kNvEVa0d
1. Install gnuplot: apt-get install gnuplot or yum install gnuplot
2. Put the HTML files in /var/www/html
3. Setup Perl execution on your webserver (http://stackoverflow.com/questions/560749/how-do-i-configure-apache2-to-run-perl-cgi-scripts)
4. Make sure you Arduino has code loaded and is plugged in.
5. Run computer_interface.pl in background and make sure the gnuplot file is in the same directory
6. Use!
The webpage refreshes every 30 seconds you can change this in example.html.
The Javascript is just for giving the webpage a tabbed format to run multiple devices. This can easily be removed and changed so that you don't need the CSS or Javascript files.
Basically, what you need is:
A computer running Linux
A webserver, Apache is nice with ability to run Javascript and Perl
Perl
An Arduino
How it works is like this:
1. Arduino sends data to the Serial port that is polled by computer_interface.pl and written to a file that is plotted using gnuplot to display on the webpage
3. Webpage uses web_interface.cgi to write data to a file that is read by computer_interface.pl and sent to Arudino
2. Arduino is polling Serial port to receive data and uses the data to modify variables that can change how the Arduino operates.
What this code was written for was having an Arduino controller multiple pieces of equipment in a Scientific lab but it can be ported to use for many other things.
Here is the Arduino Code: http://pastebin.com/f8eBJc7R
Here is the computer_interface.pl: http://pastebin.com/yGNMCH54
Here is the webinterface.cgi: http://pastebin.com/qpUZ5n9A
Here is the gnoplot formatting file should be in the same directory as computer_interface.pl: http://pastebin.com/1BWNaAc4
HTML file: http://pastebin.com/e2Fpkrfi
HTML CSS: http://pastebin.com/1YUnWS0Q
HTML Javascript: http://pastebin.com/kNvEVa0d
1. Install gnuplot: apt-get install gnuplot or yum install gnuplot
2. Put the HTML files in /var/www/html
3. Setup Perl execution on your webserver (http://stackoverflow.com/questions/560749/how-do-i-configure-apache2-to-run-perl-cgi-scripts)
4. Make sure you Arduino has code loaded and is plugged in.
5. Run computer_interface.pl in background and make sure the gnuplot file is in the same directory
6. Use!
The webpage refreshes every 30 seconds you can change this in example.html.
The Javascript is just for giving the webpage a tabbed format to run multiple devices. This can easily be removed and changed so that you don't need the CSS or Javascript files.
Sunday, March 30, 2014
SXSW
This post is about a month old but I have been so busy I am just finishing it up.
So for some reason I was fortunate enough to be invited to South by Southwest(SXSW) from the wonderful Karen Ingram and Shawn O'Keefe. At first I didn't know if I would go. Plane tickets were kind of expensive and I am currently in what will probably be the most busiest time of my year (Conferences, Science, Talks, &c.). Also, I am not a spontaneous person and don't like random people. I had never met Karen or Shawn in person and didn't know anyone in person who would be going to SXSW. I can be introverted at times. Well considering I spend most of my non-sleeping life in lab I guess I would be considered significantly introverted, yeah, I mean I just don't usually like people, at least when I am sober. Anyways.... I decided to go because I felt like the opportunity was so good I could not pass it up and because I only had a few days to spare even if it didn't turn out well I wouldn't lose much besides money.
It was a great time. I met Dan Grushkin which was pretty sweet and we achieved the high score on Marvel vs Capcom at a bar and became pretty drunk in the process. Austin basically turns into New Orleans and 4th st. into Bourbon st. I am pretty excited to go again next year and I hope to have some cool Science.Technology to show-off and impress people. Well at least impress myself.
I went to see the movie The Immortalists at SXSW because Jason Sussberg came to the Biohacker meetup and convinced me to go. You should check out the link and trailer and if ever have the chance to see it you should. I really love documentaries and wish people would make more of them. It is just so cool to experience someone else's life that is different from my own or learn about something new. Seriously, I wish I could watch a documentary on everyone I know. I guess that is kind of creepy?
Anyways, there were so many interesting and cool people that I met there. I hope I actually can spend time with them in the future.
I am learning to go a little bit outside my comfort zone more and attempt to experience new things even though I would rather just sit in my apartment and build stuff. Also, I am beginning to see that I don't hate people as much as I say I do. Hah, I think I just don't enjoy people who are boring and.or stuck-up.
So for some reason I was fortunate enough to be invited to South by Southwest(SXSW) from the wonderful Karen Ingram and Shawn O'Keefe. At first I didn't know if I would go. Plane tickets were kind of expensive and I am currently in what will probably be the most busiest time of my year (Conferences, Science, Talks, &c.). Also, I am not a spontaneous person and don't like random people. I had never met Karen or Shawn in person and didn't know anyone in person who would be going to SXSW. I can be introverted at times. Well considering I spend most of my non-sleeping life in lab I guess I would be considered significantly introverted, yeah, I mean I just don't usually like people, at least when I am sober. Anyways.... I decided to go because I felt like the opportunity was so good I could not pass it up and because I only had a few days to spare even if it didn't turn out well I wouldn't lose much besides money.
It was a great time. I met Dan Grushkin which was pretty sweet and we achieved the high score on Marvel vs Capcom at a bar and became pretty drunk in the process. Austin basically turns into New Orleans and 4th st. into Bourbon st. I am pretty excited to go again next year and I hope to have some cool Science.Technology to show-off and impress people. Well at least impress myself.
I went to see the movie The Immortalists at SXSW because Jason Sussberg came to the Biohacker meetup and convinced me to go. You should check out the link and trailer and if ever have the chance to see it you should. I really love documentaries and wish people would make more of them. It is just so cool to experience someone else's life that is different from my own or learn about something new. Seriously, I wish I could watch a documentary on everyone I know. I guess that is kind of creepy?
Anyways, there were so many interesting and cool people that I met there. I hope I actually can spend time with them in the future.
I am learning to go a little bit outside my comfort zone more and attempt to experience new things even though I would rather just sit in my apartment and build stuff. Also, I am beginning to see that I don't hate people as much as I say I do. Hah, I think I just don't enjoy people who are boring and.or stuck-up.
Friday, March 21, 2014
Magic
The summary is I think people should play more than 60 cards in their magic deck if they think the card is beneficial. Argue away tell me I am wrong. I don't mind. I was just bored.
So why do people play with 60 card decks? I have often asked this question and the only clear answer people say is that you have a higher probability of drawing a single card. Indicating that in the case of top decking a 60 card deck is better.
I think there is lots of misinformation: http://www.starcitygames.com/
Chapin saying that 0.7% is alot of changing by adding one card to your deck because that is 1 extra loss every 250 games. What he fails to mention is that it is only a loss if the card doesn't help you win or prevents you from winning. Say the card helps in 50% of your matches and 50% it is dead. That means that any possible bad effect is ngated by the good effect. You would lose 50% of that 0.7% but you would win 50% of that 0.7%. If the card is actually beneficial alot like lightning bolt in an aggro deck then he is completely wrong. Saying 61 cards is bad because it reduces your chance of drawing a winning card by 0.7% is ridiculous.
He also claims that Battle of Wits sucks because the mean power level of the cards in the deck is not that strong and so one should not add cards. What he fails to mention is that in a 200+ card deck you are virtually turning all card draw percentages into 1/4 what they originally were and obviously there are only so many cards with specific effects (i.e. even if I have 4 Ponder, 4 Preordain and 4 Brainstorm the probability that I will draw one of those in Bwits is still less than if I just have 4 Brainstorm in a 60 card deck).
Olivier Ruel says to never play with 62: http://www.starcitygames.com/
Because it screws up your manabase.
Say you need to have 3 lands by turn 3:
70 card deck: 67%
64 card deck: 75%
63 card deck: 76%
62 card deck: 78%
60 card deck: 79%
So we have a 3% less chance of making our 3rd land drop by turn 3 in a 63 card deck!! A drop of 79% to 76% means you are 96% as likely to have the same thing happen! Are you telling me you wouldn't bet on those odds?
Chingsung Chang had a nice article about why 61 cards is ok (http://www.gatheringmagic.
So let me ask you this, say I have 4 Karn Liberated in my deck and 60 cards what is the chance I draw a Karn in my first 7 in a 60 card deck as opposed to a 80 card deck?
Using a my simulator:
60 cards: ~39%
70 cards: ~35%
80 cards: ~31%
As turns go on we should see less of a separation. All these simulations assume you are on the play. 10,000 simulations per value. The numbers are not exact because we are simulating so there is obviously a margin of error.
What this graph shows is not the percentage you have the card in your hand but rather "How likely are you to have the card in your hand compared to a 60 card deck?" Am I 90% as likely? We see that in a 70 card deck we are still ~90% as likely to see the card as we are in a 60 card deck. In a 64 card deck we are 95% as likely and in a 61 card deck there is almost no change!!!
So I looked at my Modern elf deck (http://www.mtgdeckbuilder.
As you increase in number of turns you become exponentially more similar to a 60 card deck and more likely to draw the card. As the number of the card increases in the deck you become exponentially less likely to have the same draw percentage between a 60 and 70 card deck. Of course you become more likely as you approach the limit of 99%, which starts near 18 cards in a deck.
It seems that changing your deck size from 60 to 70 cards doesn't have as much effect on 1-4 cards as I would expect. So when we have 4 cards in a deck our percentage of having the card in our opening hand is only 4% different in a 70 card deck as a 60 card deck.
With card draw and scry and searching these numbers probably drop even more. To the point that if you have a bunch of card draw there really is no point in not having more cards in your deck if you think they will be useful. If you are playing a pod deck or toolbox the only cards you are really really want to draw are Birthing Pod or Chord of Calling. So adding say a Fulminator Mage because you expect a bunch of Tron decks in the meta will almost have a non-existent effect on drawing your other cards and will provide you with a card that can have uses even if not playing Tron and you draw it.
So why do people play 60 card decks then? One reason seems to be self censorship. I wouldn't want 6 Karn's in the deck even if I could because I don't want my opening hand to have more than one Karn in it. Ok so what is my percentage of having two or more Karns in my opening hand with 3 versus 4 cards in the deck. It is 4% versus 6%. However, my chances of having the card at all in my opening hand changes from ~31% vs 40%!!! If we subtract that's 27% vs 34%. That's a 7% increase for only a 2% chance more likely to have doubles in your opening hand. Maybe I would want more Karn?
Anyways, situations where I think having more cards that are useful.
#1. Relic of progenitus or a card versus the metagame
If there is alot of Jund and alot of snapcasters and floating around it never hurts to have a 1 costing artifact that you can cantrip if it is useless. Obviously if you are running deathrite and friends there probably is no need but any midrange or control deck should run some even if it bring you over 60 the card draw basically negates any effect of having the extra card. (obviously there are drawbacks to this strategy if you are combo or burn? maybe?)
#2. Combo
Yes it sucks to have 2 kiki jikis and 2 splinter twins in your opening hand but you know what is worse not being able to find the cards. I see Twin decks often running less than 8 exarch/pestermite and less than 8 kiki/twin, maybe for fear of going over 60 cards. When has a twin player not wanted 2 twins and 2 exarchs in their hand?
#3 Control
In a control deck many of the cards are very similar. You have deck manipulation, wrath/creature destruction effects and control cards(counter spells and bounces). Playing a 61st or 62nd card main deck to help against half the field or more will probably have little to no effect due to the deck manipulation alone. Further, control decks usually go 10+ turns meaning that any effect that adding extra cards would have will be cancelled out the more you draw.
How often am I going to draw a 1 or "2 of" card in a deck when it will be useful versus when it will just be a blank. In a 70 card deck your chances of drawing a "1 of" by turn 6 is 17%. With deck manipulation, slightly more or less as you desire. In your opening hand it is 10%. If the card is say Serum Visions, I can't statistically see how it would be bad to have that card.
So why do people play with 60 card decks? I have often asked this question and the only clear answer people say is that you have a higher probability of drawing a single card. Indicating that in the case of top decking a 60 card deck is better.
I think there is lots of misinformation: http://www.starcitygames.com/
Chapin saying that 0.7% is alot of changing by adding one card to your deck because that is 1 extra loss every 250 games. What he fails to mention is that it is only a loss if the card doesn't help you win or prevents you from winning. Say the card helps in 50% of your matches and 50% it is dead. That means that any possible bad effect is ngated by the good effect. You would lose 50% of that 0.7% but you would win 50% of that 0.7%. If the card is actually beneficial alot like lightning bolt in an aggro deck then he is completely wrong. Saying 61 cards is bad because it reduces your chance of drawing a winning card by 0.7% is ridiculous.
He also claims that Battle of Wits sucks because the mean power level of the cards in the deck is not that strong and so one should not add cards. What he fails to mention is that in a 200+ card deck you are virtually turning all card draw percentages into 1/4 what they originally were and obviously there are only so many cards with specific effects (i.e. even if I have 4 Ponder, 4 Preordain and 4 Brainstorm the probability that I will draw one of those in Bwits is still less than if I just have 4 Brainstorm in a 60 card deck).
Olivier Ruel says to never play with 62: http://www.starcitygames.com/
Because it screws up your manabase.
Say you need to have 3 lands by turn 3:
70 card deck: 67%
64 card deck: 75%
63 card deck: 76%
62 card deck: 78%
60 card deck: 79%
So we have a 3% less chance of making our 3rd land drop by turn 3 in a 63 card deck!! A drop of 79% to 76% means you are 96% as likely to have the same thing happen! Are you telling me you wouldn't bet on those odds?
Chingsung Chang had a nice article about why 61 cards is ok (http://www.gatheringmagic.
So let me ask you this, say I have 4 Karn Liberated in my deck and 60 cards what is the chance I draw a Karn in my first 7 in a 60 card deck as opposed to a 80 card deck?
Using a my simulator:
60 cards: ~39%
70 cards: ~35%
80 cards: ~31%
As turns go on we should see less of a separation. All these simulations assume you are on the play. 10,000 simulations per value. The numbers are not exact because we are simulating so there is obviously a margin of error.
What this graph shows is not the percentage you have the card in your hand but rather "How likely are you to have the card in your hand compared to a 60 card deck?" Am I 90% as likely? We see that in a 70 card deck we are still ~90% as likely to see the card as we are in a 60 card deck. In a 64 card deck we are 95% as likely and in a 61 card deck there is almost no change!!!
It seems that changing your deck size from 60 to 70 cards doesn't have as much effect on 1-4 cards as I would expect. So when we have 4 cards in a deck our percentage of having the card in our opening hand is only 4% different in a 70 card deck as a 60 card deck.
With card draw and scry and searching these numbers probably drop even more. To the point that if you have a bunch of card draw there really is no point in not having more cards in your deck if you think they will be useful. If you are playing a pod deck or toolbox the only cards you are really really want to draw are Birthing Pod or Chord of Calling. So adding say a Fulminator Mage because you expect a bunch of Tron decks in the meta will almost have a non-existent effect on drawing your other cards and will provide you with a card that can have uses even if not playing Tron and you draw it.
So why do people play 60 card decks then? One reason seems to be self censorship. I wouldn't want 6 Karn's in the deck even if I could because I don't want my opening hand to have more than one Karn in it. Ok so what is my percentage of having two or more Karns in my opening hand with 3 versus 4 cards in the deck. It is 4% versus 6%. However, my chances of having the card at all in my opening hand changes from ~31% vs 40%!!! If we subtract that's 27% vs 34%. That's a 7% increase for only a 2% chance more likely to have doubles in your opening hand. Maybe I would want more Karn?
Anyways, situations where I think having more cards that are useful.
#1. Relic of progenitus or a card versus the metagame
If there is alot of Jund and alot of snapcasters and floating around it never hurts to have a 1 costing artifact that you can cantrip if it is useless. Obviously if you are running deathrite and friends there probably is no need but any midrange or control deck should run some even if it bring you over 60 the card draw basically negates any effect of having the extra card. (obviously there are drawbacks to this strategy if you are combo or burn? maybe?)
#2. Combo
Yes it sucks to have 2 kiki jikis and 2 splinter twins in your opening hand but you know what is worse not being able to find the cards. I see Twin decks often running less than 8 exarch/pestermite and less than 8 kiki/twin, maybe for fear of going over 60 cards. When has a twin player not wanted 2 twins and 2 exarchs in their hand?
#3 Control
In a control deck many of the cards are very similar. You have deck manipulation, wrath/creature destruction effects and control cards(counter spells and bounces). Playing a 61st or 62nd card main deck to help against half the field or more will probably have little to no effect due to the deck manipulation alone. Further, control decks usually go 10+ turns meaning that any effect that adding extra cards would have will be cancelled out the more you draw.
How often am I going to draw a 1 or "2 of" card in a deck when it will be useful versus when it will just be a blank. In a 70 card deck your chances of drawing a "1 of" by turn 6 is 17%. With deck manipulation, slightly more or less as you desire. In your opening hand it is 10%. If the card is say Serum Visions, I can't statistically see how it would be bad to have that card.
Sunday, March 2, 2014
Passion
I love Science.
Some people do Science and some people enjoy Science but I love Science. I _LOVE_ it.
I am not the best Scientist. I have whacky ideas and spend lots of my time trying to do crazy stuff when I could be actually accomplishing something. It sucks. I wish I was better. I really do. Because. Science is my heart. It is my soul. It is my Passion.
Maybe you are Passionate about Science. Well let's show it.
Watch this video:
http://vimeo.com/18166037
Maybe you are not a football fan. But I am sure you can see the Passion of these footballers. Why is Science different? Why can't we show our Passion and be so Passionate about our work that we cry, scream, hate, love?
Does going to Scientific talks inspire you? Or does it put you to sleep? They usually always put me to sleep. Science is so much a job now. Which is cool. It is cool. Everyone who does Science can't be passionate about it. Do people even have Science heroes anymore though?
Oh you love Neil deGrasse Tyson or Bill Nye, great people who don't even do Science anymore. Bill Nye is not even a Scientist. These people are not the worst, they do attempt to inspire people to do Science. But ya' know what is more inspiring? Someone who is actually in the game, sweating the blood and tears. Toiling to make something. Is that you? Why do you hide it? Are you afraid that showing emotion and Passion might ostracize you in the Scientific world?
Ya' know what I don't want? A science or nature paper. Ya' know what I do want? To maybe hopefully possibly do something that is so intricate and beautiful and someone else sees that and is inspired by it.
I will never be as intelligent as some of the people I know and have worked with. I probably will never rock the Scientific world. But I will always try hard and I will always keep going because Science is too amazing and beautiful to ever give up on.
As ODB said "Science[Wu Tang] is for the children."
Some people do Science and some people enjoy Science but I love Science. I _LOVE_ it.
I am not the best Scientist. I have whacky ideas and spend lots of my time trying to do crazy stuff when I could be actually accomplishing something. It sucks. I wish I was better. I really do. Because. Science is my heart. It is my soul. It is my Passion.
Maybe you are Passionate about Science. Well let's show it.
Watch this video:
http://vimeo.com/18166037
Maybe you are not a football fan. But I am sure you can see the Passion of these footballers. Why is Science different? Why can't we show our Passion and be so Passionate about our work that we cry, scream, hate, love?
Does going to Scientific talks inspire you? Or does it put you to sleep? They usually always put me to sleep. Science is so much a job now. Which is cool. It is cool. Everyone who does Science can't be passionate about it. Do people even have Science heroes anymore though?
Oh you love Neil deGrasse Tyson or Bill Nye, great people who don't even do Science anymore. Bill Nye is not even a Scientist. These people are not the worst, they do attempt to inspire people to do Science. But ya' know what is more inspiring? Someone who is actually in the game, sweating the blood and tears. Toiling to make something. Is that you? Why do you hide it? Are you afraid that showing emotion and Passion might ostracize you in the Scientific world?
Ya' know what I don't want? A science or nature paper. Ya' know what I do want? To maybe hopefully possibly do something that is so intricate and beautiful and someone else sees that and is inspired by it.
I will never be as intelligent as some of the people I know and have worked with. I probably will never rock the Scientific world. But I will always try hard and I will always keep going because Science is too amazing and beautiful to ever give up on.
As ODB said "Science[Wu Tang] is for the children."
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