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 ( 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.

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 email today(yes I have a 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'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 Naturmagazine 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.