DIY Guide to Creating a Peptide Immunotherapy Cancer Vaccine

I received an email over a year ago from Lars. His wife Dyanne, a never smoker, had developed Non-Small Cell Lung Cancer. He was reaching out to me to see if CRISPR would be a viable way to try and treat his wife. He lamented at how the medical system and academic scientists he contacted had given up on her to die. Eventually, we decided that CRISPR was probably not the best thing to try and they started down the path of immunotherapy instead. What we found was that a patient could use cutting edge peptide immunotherapy for a few hundred dollars or euros by ordering their own peptides directly from synthesis companies. We started out by helping to coach people through the process of ordering and working with peptides and as the demand increased we decided to do something more.

See the fucked up thing about the world is not the scammers peddling fake cancer treatments, it's the medical doctors peddling infinite wisdom but refusing to do anything, much less everything that they can to help someone who is dying. What lengths would you be willing to goto to save your loved one or partner and does not every human deserve that same dignity and respect? Maybe you say this is irresponsible as if letting someone die without the right to do whatever they want with their body is totally fine.



See, so many people are scared of what might happen if people all over start trying things like this but ya' know what I am scared of? I am scared of people just being left to die because people are to worried about saving their own career and their own paycheck than saving a human life.


So after much thought and deliberation myself, Lars and a few other caregivers and individuals with cancer decided to make a guide based on things people had been trying to some success. Maybe a first of its kind guide(with hopefully many more to come) on how to treat someone who has NSCLC using peptide immunotherapy.
https://goo.gl/omorJA
We are not advertising this as a cure-all or even cure. We are putting this out there as a means of help and hope because one of the saddest things to realize in life is that world doesn't have your back. Sometimes in your hardest moments you need to be your own hope. But you can and that's the amazing thing. It's possible that out there in the scientific literature or through self-experimentation you can help yourself and possibly others.

As I write this there are people dying of cancer and other diseases. Maybe close to home, maybe far away. But if they don't inspire you to learn more, work harder and try harder. What the fuck are we doing Science for?

How to Genetically Engineer a Human in Your Garage - Part III - The first round of experiments

Whenever I start to work on something I have trouble sleeping. The problem is that I am always working on something so I always have trouble sleeping. It's not worry or anxiety, it's hard to describe it without saying that it is just excitement. Not like happy excited but it is an anticipation. When I am working on an experiment, to me it's not even really Science, I am building a world. I am taking this world that exists as a dream in my mind and creating it in the physical world. I stay up at night imagining how to do that.

Starting the experiment to genetically modify myself was scary and daunting. The world I created was so intricate I didn't know if I could possibly share it with anyone or even succeed at creating it.

It is one of the issues I always run into and one thing I have a hard time communicating to journalists. They want access to this sacred part of my life but treat me like a paycheck. They want their sound bite and I try and give it to them but how would I explain my motives? When they were many and complex. To create something beautiful, to test out new technology to try and develop something that others could use, for medical use and on and on The reasons were so arrayed, I had been thinking about it for months. How do you explain a months worth of thoughts to a person who wants to condense it down to one sentence? Even those you are closest to?

And then you start to think about the experiment. How I read countless papers, researched DNA plasmids, viruses and virus serotypes, mammalian expression elements, chemicals to use and try, DNA vaccines, experiments on mice, and you ask me how am I going to do it? Is it safe? How do I explain the reason for every choice, is it possible unless you read the papers I read and thought through everything like I did?

I didn't want to do it alone. I don't want to do it alone. I want to share it but I want to share it without the soundbites.



There are 3 main parts to topical or sub-cutaneous genetic modification
1. Hair removal
2. Skin Stripping
3. DNA application


Hair removal
Not as complicated as it sounds or maybe more complicated than it sounds? First you need some depilatory cream. Yeah, WTF is that shit?I remember sitting there reading this paper on topical DNA transfection in mice and they are talking about depilatory cream and how it can help transfection efficiency and I was wondering how I could get my hands on this stuff. I come to find out that it is Nair, well you could have just said that.

*Sidenote - Though this example is kind of a joke one of my issues with Science is that even a trained a Ph.D.(myself) oftentimes has trouble deciphering papers. The information you really want to know like DNA sequences and techniques is often hidden and obscured in papers. Someone might say "Well those papers are not about the sequence and that is just too much information so whatever". Until recently I was trying to piece together a DNA sequence from a paper about DNA sequences and they weren't in the paper!!!! How does one even publish a paper about new synthetic promoters and not have the exact promoter sequences used in the paper?!!!! I could have pieced it back together from the clues but I figured I would email the author instead and they responded that the sequences were patented and so I would need a license and they didn't give them to me!!!! WTF! Standing on the shoulders on giants? More like standing on the shoulders of patents and paywalls so no one can advance Science!

Nair works as you would expect it. Easy to use on the arm for hair removal.



Skin Stripping

Your actual live skin cells are hidden under layers of dead skin, the stratum corneum.


You can imagine that if you are trying to genetically engineer cells they need to be living and alive so that they can take the DNA you put in them and turn it into protein(jellyfish green fluorescent protein in my case!). What this means is that you need to remove the stratum corneum. Now this next part is no joke. Scientific papers indicate that the best methods are either tape stripping or tooth brush scrubbing and I quote:

"The shaved dorsal skin was then either stripped by applying Blenderm tape (3M Health Care, St. Paul, MN) five times and/or brushed using a tooth brush with rounded firm nylon bristles. The number of brushing strokes varied from 50 to 200."

I still haven't tried the tooth brush method because I just can't find it in my heart to scrub my skin 200 times with a tooth brush. Instead, I have mostly stuck with the tape stripping method. It does hurt. Some tapes work better than others. I usually use duct tape or packaging tape. I usually stop when putting alcohol on it burns.




DNA Application

Now this is a complicated one that I still haven't figured out because there are so many different things to try and so many different variables. Topical application experiments of DNA have been extremely limited as far as I can find. You can use water, or some ions or salt or Tris or DMSO or ...... you get it. Do you cover it or evaporate it or inject it, electroporate it? I think alot of times with experiments it is easy to become caught up in what is the best way to do something instead of just doing it. Obviously, doing this experiment with no knowledge or preparation would be foolish but I have learned that I will never be 100% ready. I don't know what DNA application method is best and over the course of my experiments so far I don't know if I have found out yet either.

Normally, I would just apply it to my skin and then evaporate it using a heat gun of sometype. This seemed to work the best and fastest and wouldn't hurt the integrity of the DNA I imagine. I also tried out just putting tape over the drop so it was just in constant contact with my skin.



I had a plan but I expected that from the beginning things wouldn't goto plan but I adapt well. hahaha.

Visualization

Initially I hoped that I would be able to see the genetic engineering in my skin by looking for fluorescence by exciting the protein and then looking for it using a visual filter. I can say that my first experiments doing this most likely didn't work. They could have worked but it didn't seem like I would ever be able to definitively tell if the cells were making the jellyfish GFP.



The first round of experiments didn't work or were inconclusive so I decided to try new things. I decided to try and use a virus and I decided that I might need to try new analysis methods that would require a skin sample!

How to Genetically Engineer a Human in Your Garage - Part II - DNA got what I need

Ohhh babbbyyy, you, you got what I need


To embark on an experiment to start genetically modifying myself I needed to obtain DNA and not just any DNA, some that was specifically encoded to work with humans. This is because not all DNA works with every organism. In fact most organism have their own unique codes that allow and don't allow certain DNA to work with them. Kind of like a security system for the cell. Like the CRISPR kits we sell won't work on humans without modification, they only work on bacteria.

The purpose of most DNA used for genetic engineering is to make proteins¹ The targets I wanted to start with were Green Fluorescent Protein(GFP) and Red Fluorescent Protein(RFP). These are genes from Jellyfishes. I figured that in a best case scenario I would be able to actually see my cells glow and fluoresce if they were engineered. Worst case scenario is that I would need to extract the mRNA to look for the presence of these new genes in my cells but they would be easy to find if works because they are not endogenous(natural) to human beings.

Anyways, good thing for me there has been a bunch of work on modifying human cells with fluorescent proteins in petri dishes or cell culture as it is called. What this means is that there is already a bunch of DNA in existence that was made to work with human cells I just needed to find it and obtain it. Which can be more difficult than you think.

I am not going to out any companies specifically in this post because they may or may not want to know they are or have sent their DNA to me for the purpose of human genetic engineering. I am sure you can ask around or do research online and find companies that will sell to you.

I set about obtaining pieces of plasmid DNA^2,3.
And scary but not scary I wanted to obtain a virus⁴ that could put this jellyfish DNA into my cells.

One of the most difficult things about being a Biohacker is that companies sometimes won't sell things to you. Not because there are any laws regarding the sales but because they want to control who is able to do Science. Fuck that shit.


How to Obtain DNA
This is a best practices in how to obtain things that companies try and keep from individuals because they think we are stupid. Some cases may take much less and some cases much more.

1. Start a business. What this basically means is register a domain name and go through the process of setting up an email address so you can send emails from that domain. It legitimizes you 100x more than a gmail.com email address and the whole thing costs like $12 on godaddy.


2. Get a Ph.D. j/k j/k you can always just add Ph.D. after your name in an email. No one checks or can check. There is no database of Ph.D.s


3. Have a FedEx account #. I am pretty sure these are free and giving someone a FedEx account number has gotten me around the "We don't ship to home addresses" a few times.


4. Social Engineer them. It is blatant discrimination that companies won't sell materials because they think us people outside of academia or industry are too incompetent to use them properly or might hurt ourselves. And don't try and tell me it is for safety when I can purchase a gun, knife or car sooo much easier and those can outright kill people. Shit bleach and kitchen cleaner are more hazardous than any chemical in my lab and I can purchase those in a grocery store. Seriously, things like DNA are unduly controlled and we, at The ODIN, hope to do something about it in 2017. 

One of the companies I used is one of the largest suppliers of plasmids. They actually will ship to most anyone and most any address as far as I can tell. They have even encouraged me to lie to them to bypass their own review system. #FunFact


Ok, so what is the difference between using plasmid DNA and a virus?

Current, technology makes using a virus cost and skill prohibitive. Though I could purchase the virus for $500 or so it came in a limited supply. The benefit however is that it should work out of the box. I would not need to do much to make it ready. Plasmids are inexpensive, they don't work as well in terms of human engineering as viruses do but once you have some you can replicate as much as you want indefinitely. You can give it to friends to replicate and use and they are easy to modify for new uses.

I wanted to explore multiple avenues with my goal being to eventually focus on plasmid DNA because I want to work with technology that is cheap and accessible.

At first I began working with plasmid DNA. Though it is somewhat easy to work with it requires that one know how to do bacterial cell culture, plasmid purification and maybe even ethanol precipitation. You need a centrifuge and lab grade pipettes and probably an incubator and shaker. While most of this stuff will only run someone a few hundred dollars it is still a hindrance. However, I started a document on best practices for plasmid purification for human genetic modification. What one can do however is send the plasmid DNA or bacteria with plasmid DNA to a company and have them just purify you up a bunch. Depending on how much you need this can run from $100-$400+
Making and purifying your own viruses while not challenging from a technical or safety sense it is challenging from an equipment and resources sense. One would need to be able to do human or mammalian cell culture and transfection and have materials to purify the virus. Doable but these techniques are far outside the scope of a garage lab at the moment. Maybe not so much in the near future though?

The DNA in the virus came prepackaged and ready to go and despite what people might think, AAV is considered Biosafety containment level 1 by most places(which is the least strict and is on the same level as Sodium Chloride or Agar i.e. it is safe).

Obvi, after I received my DNA it was time for the experiments to begin! 

Genetic engineering in humans usually occurs as intramuscular injections or systemic injections(i.e. into the blood stream. Both of these ways seemed silly as they made it difficult to perform any testing to see if the experiment worked. Muscle biopsy on myself? YIKES! I decided on topical skin and subcutaneous(under the skin) delivery of DNA! The crazy thing is that there hasn't been as much scientific literature and research as I expected on this topic. I did collect a sampling of papers however that I found interesting and you can find them here: https://drive.google.com/open?id=0B_R75gIJvkFUMkhrbUdZRzhscGc


July 5th 2016 was the first day I started experimenting on myself.






Footnotes

1. Proteins are awesome. They are little molecular machines inside cells that let cells do things. Read about them!

2. Plasmid DNA is small circular DNA that is separately from the host cells genomic DNA(compared to genomic DNA. Genomic DNA is the DNA that is transferred from a parent cell. The standard set of genes each cell comes with). Plasmid DNA is circular so that it can be replicated easy by organisms such as bacteria. This allows researchers to grow bacteria and extract the plasmid to use for other purposes.

3. Here is a link to the DNA sequences of the plasmids and virus I used and am using: https://drive.google.com/open?id=0B_R75gIJvkFUMkhrbUdZRzhscGc

4. The virus in question is a non-replicative(it doesn't replicate and reproduce) Adeno Associated Virus(AAV). It has been used a bunch on humans and shown to be super safe. Fortunately, I was actually also able to obtain AAV1 which is efficacious across a number of tissues including keratinocytes(which make skin).

How to Genetically Engineer a Human in Your Garage - Part I

My name is Josiah Paul Zayner. If my name sounds "religious" that's because it is, Josiah was a King of Judah in the Hebrew.Christian Bible, Paul was an apostle of Jesus. I have three brothers Zachariah(older) and Micah and Jedidiah(both younger).

I don't remember a time when my Mom and my Biological father were together. He was severely abusive. We were poor. We lived on a farm. It wasn't a huge farm like people might imagine but a small animal farm in rural Indiana. We collected eggs from our chickens to eat and drank dehydrated milk. I have never met anyone else who drank dehydrated milk. I don't remember much of my childhood because of the trauma from abuse. I only see small flashes like a nightmare one can still feel emotionally but barely recall what exactly happened. This includes the now infamous family story of discharging the the gun my Mom had in the car door for protection. My Mom's second husband was also abusive. I ran away from home twice. Living with computer hacker friends in Oklahoma and Texas after high school.

My Mom is an amazing human. I would not be where I am today without her and her willingness to fight for her family.

Me(on the right side) and My Brothers circa 1987

Growing up I was never particularly what one would consider smart or gifted. I have just always liked to build and create things. I was mostly an introvert and would often get lost in my head, I still do. In high school I was mostly a jock but navigated through most groups. It was in high school that I found out about computers. I found out that if I wanted to learn something I could just read and teach myself. 

I made a discovery today.  I found a computer.  Wait a second, this is
cool.  It does what I want it to.  If it makes a mistake, it's because I
screwed it up.  Not because it doesn't like me...
                Or feels threatened by me...
                Or thinks I'm a smart ass...
                Or doesn't like teaching and shouldn't be here...
        Damn kid.  All he does is play games.  They're all alike.

The Conscience of a Hacker

My high school teachers made fun of me because I would always be reading in class. "What are you going to be a book reviewer one day?" and then the class would laugh and I would go back to my reading. I was almost expelled from High School twice. The first time I punched a kid a bunch and he ended up in the hospital. They handcuffed me in class. I was arrested and suspended. The second was for writing a program called "HackTheSchool.exe" and putting it on the shared network drive so anyone could access it. The program was a joke, it didn't actually hack the school but teachers back then didn't have enough knowledge to read the code and be able to tell the difference. In lieu of expulsion I was suspended and banned from ever using a computer in the school that was connected to a network or the internet. They had a special computer in my programming class that was unplugged from any network just for me.

Me on the computer at home circa 1999 

I eventually became a "computer hacker" and was a member of Legions of the Undeground(LoU) a hacking group. While that story is long and for another time it is the foundation of why I started my company The ODIN and have invested heavily in Biohackers. During that time in the 1990s and early 2000s I saw kids like me who were awful at school, came from broken homes, who could code circles around and out technical 99% of the world. All of us were self-taught. Little know fact is that you can still find a piece of software I wrote back then on The ODIN website and people still download it. Nowadays all of these people have great jobs at tech companies and most have still never finished college.

When I was 19, I was able to obtain a job at Motorola doing programming and networking. I worked there at the end of the dotcom bubble and then during the burst. I was laid off with tens or hundreds of thousands of other people. The one thing I took away from Motorola came from Dennis Tsai, he told me "People can take away your job but they can never take away what is up here (pointing at his head)." I could have taken another Tech Job but instead decided to goto school and learn. Fill my head with information that no one could ever take away.

Because I did so poorly in high school, I started back at a community college for around 1.5 years before transferring. I ended up majoring in Plant Biology and obtaining a BA from Southern Illinois University and though I did much better than I did in high school I just wasn't good at standardized education. Still there was a minor bit of meritocracy left back then and my Master's Degree at Appalachian(la-chun) State led to being accepted to a Ph.D. program at the University of Chicago.

I owe a huge debt to Ece Karatan, Tobin Sosnick and Tao Pan who taught me in Graduate School. Without them I wouldn't be who and where I am. I also think they owe me an apology because it has taken me years to unteach myself the critical nature I was driven into. I was taught to question everything and be constantly vigilant and critical. While this taught me to be logical and rigorous I think it stole my creativity, it stole my ability to dream and believe. Graduate school was a beautiful and extremely painful experience. It's hard for me to recommend graduate school, I think it really depends on the individual.

After graduate school I was awarded a fellowship working as a Synthetic Biologist at NASA engineering bacteria to break down and recycle materials for long-term space travel or when we colonize other planets. That was an interesting life experience but if you really want to read about that you can check out previous blog posts Here, Here and Here. Let's just say I don't work well in the system. I don't do well with rules that don't make much sense or people who are more interested in improving their position than contributing. Fuck the system.

The two guys named Bob who ran the NASA Fellowship program and Me

My last day at NASA and no one is around because no one is ever around.
Jan. 5th 2016

2015 culminated with me leaving my fellowship at NASA because I was fed up with the system, with everything. Outside I saw so many people hungering to be genetic designers and at NASA people hired to do the same siting on their asses. I began to work at The ODIN full-time. 

My goal at The ODIN has been to give people access to resources and knowledge so that they can Biohack. I have seen what hackers can do and usually because of their different path in life have unique insights into problems and tend to be more creative than trained and pedigreed Scientists. 

If a poor kid like me can end up at NASA and now running their own company but never quite be at the top of their class, never scoring well on tests no matter how much effort I put in, something is wrong with the school system. I can program 3 or 4 languages pretty fluently, can do electronics and basic circuit design and have a Ph.D. in Biophysics but even in graduate school no matter how much I studied I would always end up with lower grades than my peers. The education system is broken. The social system is broken. Or maybe they are all work fine and it is just me who is broken.

That's why I fight.

I fight for access for everyone. But I fight fiercely for the broken among us. Those who need hope.

You deserve better.

In 2016, I began to fight hard. I explored microbiome modification for health and privacy and did a thorough Scientific analysis that you can read Here, Here and Here. I found that it was possible to successfully transplant a gut microbiome and it alleviated alot of suffering in my life. It hurt and was hard.

In Sept. I ran the first conference for Biohackers(http://biohacktheplanet.com), which I worked my ass off for and poured so much into. It was amazing and turned out so much better than I could have ever hoped.

But still there is so much more to be done. The system is fucked up and so many people who hunger for knowledge and the ability to help others can't.

I didn't grow up wanting to be a Scientist or Biohacker or Genetic Designer. I was too poor to dream of that possibility. But, I did grow up wanting to help people and this has lead me to a project that will be a culmination of my life's work so far, Genetically Modifying humans. Genetically modifying myself.

This is me. I am a Genetic Designer.

Sorry, this post wasn't about the actual human genetic engineering experiment but I feel I need to give my background to tell my story.

Let's start at the beginning

I want the world to be like I see it in my head.

In April 2015 I was sitting around thinking. I like to sit around and think. And I began to wonder how genetic engineering technologies would be used in the future. I imagined a world in which people sought out genetic designers on craigslist and made a speculative post there just out of pure curiosity. Well the post was found and ended up going viral.

 

This lead to me studying CRISPR in depth, developing the DIY CRISPR kit(for microogranisms not humans!) and starting to think about how human beings could easily engineer themselves not just for health and medicine but also for "fun".

Around this time, an argument I constantly heard against human genetic engineering is that it would make class divides even greater. The wealthy would be able to afford genetic designers while the poor would not. That is of course if no one ever worked on making it inexpensive and accessible. What if I did? What if the masses have access to genetic modification before the wealthy because we are more clever and actually willing to try it?

So how do we begin?

There are two main ways to genetically modify any cell, including human cells, 1) Edit the genome, which is like the operating system of cell and so as you can imagine this can be dangerous 2) Add in DNA that is separate from the genome and is non-permanent, this also known as plasmid DNA, extra-chromosomal DNA, episomal DNA, transient transfection or a DNA "vaccine".

At first I only thought about (1) because I imagined the project as purely theoretical. I studied and wrote-up a feasible protocol and wanted to post it online for people to see and maybe use. I dug deep and figured out the best place for insertion into the human genome seemed to be this H11 locus and that one could deliver a CRISPR package in two separate viruses(CRISPR system is too big for only one). Use CMV driven SaCas9 and U6 driven guideRNA in an AAV serotype (serotype dependent on the cell type as they have different proclivities) with a viral titer of 10^11 or greater. You can do injections or intravenous infusions.

The more I read the more I understood how this could actually work and I became more interested in trying to use CRISPR on myself. But that seemed drastic and kind of stupid to try and make permanent genome edits on myself.

What about (2) though? Maybe I could use all the stuff I learned about studying CRISPR and try to transiently and non-permanently modify my own cells. From what I read it would only last a few days or weeks at most. I started to work on this part about a year ago and since then have explored a number of different techniques to express non-human proteins(GFP, RFP and others) in my own cells in my own body. I have been documenting with video recordings that I want to share so that others can learn and experience what it is like to push the cutting edge of Science.

My main goal is to develop methods so that genetic modification of human cells can be done by anyone safe, inexpensively and of course successfully. I plan to release as much information as I can about DNA used, reason for choosing different things. I plan to release the DNA code for the plasmid I have designed and protocols and techniques online(probably mostly on this blog) all to anyone for free.

Because there is alot of footage I plan to release posts on weeklish schedule or so. Which will include data, outcomes, footage and commentary. Going to try and not give spoilers!

For now I created a teaser with some footage from the past year and I hope you go on this journey with me to create something beautiful.

Green Flourescent Protein(GFP) Beer, a short story

Yeast is used in alot of food and drink. It is used to make some of my favorite drinks, beer and whiskey.

I started engineering Yeast about 1.5 years ago. I thought it would be a useful skill to have in general and as I moved more towards running The ODIN fulltime I wanted to be able to have some yeast strains and experiments on the site.

My first ever attempt to genetically engineer yeast was a success(I used the Lithium Acetate method). I don't know how? because I didn't use SS DNA and probably used like 400ng of plasmid.

My 2nd - 10th attempts I think failed, hah.

I eventually figured out how incubation time at 42-43C matters much more than it does in bacteria and many more things and had it working again. YAY! I don't mind yeast much and almost prefer it to bacteria now.


The other part of this story is Nick Moench, who runs Inoculum Ale Works. He sent me some emails(they were loooonnggg) about how he ran his own brewery in Florida and was interested in Engineering yeast to do cool things. At the time it was just me doing ODIN stuff so I didn't have much time or money to do anything and I think we had a few emails. He almost appeared on our now maybe defunct video cast.


I guess I half-hearted thought about making beers and stuff but as I preferred to drink with the least effort possible, i.e. purchase the alcohol. I didn't think much about it. Eventually some other people started helping out with The ODIN and we ran a few preliminary experiments on fermentation using Saccharomyces cereveisiae BY4742. To us non-brewers, we were excited when we could grow GFP yeast in grape juice and still see the fluorescence, days or weeks later.

Nick and I had been chatting on facebook and I brought up how we had grown some genetically engineered labs strains of yeast and that they glow green in grape juice even after weeks. He was interested and excited. He wanted to brew some beer. Unfortunately, as non-brewers we didn't really know what went into brewing beer. We sent Nick the strain and it failed, miserably. I think Nick thought it was his fault, only for us to discover that one of the most abundant sugars in beer(maltose) couldn't be processed by most yeast lab strains(S288C derivatives have knock-outs for enzymes that import(I think) and degrade maltose, this includes BY474(1|2), W303, &c). Also, there are other things that are important like attenuation and flocculation of the yeast that helps make a good beer that brewing strains are selected for.

Sad. But not heart broken. There are plenty of brewers strains of yeast that can process maltose. Problem is that they are not auxotrophic so normal yeast plasmids would be difficult to use and select for.

We tried a bunch of different  engineering methods with a bunch of failures. Nick tried his best to nurse the lab strains in hopes that he could coax them into making a beer, almost. We both run businesses and have many other projects but it was cool having someone who actually wants to DO stuff and not just talk about it.


GFP beer like GFP yogurt is one of those fabled things that Biohackers have been talking about since Biohacking started and you can find many blog posts, writings or articles about people's theorizing about it. It's funny because at UChicago(where I did my Ph.D.), one of the many unofficial mottos is "That's all well and good in practice but how does it work in theory."(Scientists and scholars love to theorize, especially at UChicago). That is an interesting and sometimes fun part of Science but in the end if we all just theorize nothing will actually ever be accomplished. Why I hate business meetings and shit also. Let's stop talking about it and just do it. Show me what you got, I want to see what you got. Even if something is not completely planned out I have learned that sometimes you just need to say "Fuck it!" and try something out and see if it works.

We already knew that the GFP could fluoresce in sedimented yeast cells at low pH for weeks(months maybe) at a time. So I read and read some more and I know more about yeast than I wanted to(my brain-drive is already pretty full).

We manage to engineer yeast and Nick, had us run a bunch of experiments and we started working with the yeast and then he created some beer.

During fermentation you can see the glow of Green Fluorescent Protein (GFP) especially when the yeast flocculates or sediments. It is more difficult but still possible to see in bottled beer but it will require some more testing to make it a more consumer product if we eventually go that route.

People ask what it tastes like. Mostly, it just tastes like whatever you are brewing it to taste like. Nick's Brewery brews sours. So it has had a sours taste to it. We try and have some yeast sediment in there meaning there is a more yeasty taste than normal to it but otherwise there is not much in terms of flavours to discern the GFP! We debuted it at the New Harvest Conference, yesterday(July 13, 2016) and everyone was excited to try it and was excited about it!

I guess GFP yogurt is next.

I transplanted someone else's microbiome in(on)to my body and it was so surreal - Results - Part III

This is a case study of a 35 year old caucasian Male of European ancestry living in the United States, a maternal Haplogroup of H1e1a and a paternal haplogroup of I1*. NOD2 Genotype SNP(rs2066844) CC indicating decreased risk of Crohn’s disease. The subject presented with increased bowel movements(3+ times a day) Bristol type stool 5-7, mainly 6. Blood in stool more than 2 but less than 5 times a month. Experiences nausea, abdominal cramps and pain 2 or more days a week with no correlated inducers besides stress. Diet consists mainly of rice, vegetables and meat protein(chicken or pork). Eats out 1-2 times per week. Average kilocalories consumed per day ~2100. Height 5’9”(1.75 m) weight before experiment 167 lbs (76 kg). Exercises 1-2 days per week. Subject also presents with type II bipolar disorder and takes clonazepam as needed to help sleep. Subject has chronic sinusitis with no clear cause and has been tested for allergies and nasal polyps both coming back negative or inconclusive. Subject has been diagnosed with chronic prostatitis and was treated with ciprofloxacin and then bactrim in Dec. 2013(also last time antibiotics were taken) which did not relieve symptoms. Acute symptoms resolved to mild pain during urination.

The subject attempted a full body microbial transplant from a healthy donor Male caucasian ~30 year of age using fresh stool samples, skin, mouth and nasal swabs. Bacterial swabs were taken from, skin, mouth, nose, poop and environment before and throughout the experiment using sterile swabs and stored in 150mM NaCl and 0.01% Tween.

The subject self treated with 500 mg Tetracycline and 500 mg Ciprofloxacin, four doses over 2.5 days. Subject also performed a complete body scrub with soap and tetracycline, including a nasal rinse. The subject proceeded to stay in a precleaned hotel room using new untouched sheets. The subject did not touch another person during the course of the transplant without the use of nitrile gloves. The subject stayed in the hotel room for 3 days and 3 nights during which he ingest 3-6 grams of donor feces enclosed in gelatin pills. He coated himself with 20-50mL saline solution containing swabs from the donors skin. He also inoculated his mouth and nasal passages no less than 6 times with the donors swabs. Patient returned home and attempted to clean and sterilize ~700 sq ft (65 sq m) apartment and inoculate it with donor skin bacterial cultures.

Within one week of the experiment the subject’s bowel movements were consistently reduced to 1 time per day. Stomach pains and cramps reduced almost completely within 2 weeks. Subjects weight reduce to an average of ~ 160 lbs(73 kg) 2 months after the experiment. Diet has remained very similar(rice, veg, meat) except subject notices more meat(no craving) and a newfound craving for sugary foods. Prostatitis resolved completely. Symptoms from post nasal drip seem reduced but uncertain, symptoms still flare up at least 2-5 times a month. Bipolar disorder not affected.

A total of 77 samples were collected before, during and after experiment. DNA extraction, 16s amplicon library prep using 515f and 806r and Illumina MiSeq 151x151 sequencing was done by Argonne National Lab in Batavia Illinois. Of the 77 samples 73 had counts.

Data Analysis

QIIME 1.9.1 was used for data analysis

Samples 65(storage buffer) and 66(storage buffer and sterile swab) were control samples and used to filter out contamination using standard QIIME workflow. Afterward sample #55 had below 1000 counts and so was removed from the rest of the study.

Beta diversity was calculated for poop samples using a jacknifed subset of 5000 sequences. PCoA plots of weighted UniFrac are displayed below.

Less than two weeks after the transplant the microbiota in the gut of the subject became more closely related to the donors gut microbiota than to the subjects gut microbiota before the experiment.

Observing the different types of bacteria in the samples both on the Class and Family levels, the subjects gut had increased diversity before the transplant (#9 and #11) as compared to after the transplant (50, 51, 52, 53) and had more similar diversity to the donor’s samples (59, 60). Diversity was insinuated by the portion of a sample belonging to species other than those the top 10-15 samples, Shown by "Other".

I transplanted someone else's microbiome in(on)to my body and it was so surreal - Part II

You can follow along Here for my daily questionaire and Here there is a diary near the bottom

Tuesday Feb 16th - Antibiotics Day One, Experiment Day One
The first day I would be taking antibiotics. Didn't sleep much the night before or the night before that. Stress can induce mania in me. It doesn't take much these days to give me the adrenaline of skydiver. The strange thing is I usually have no problem falling asleep, I just end up waking up some hours later and no matter how hard I try can't go back to sleep.

The plan was to take 500mg Tetracycline and 500mg Cirpofloxacin, both broad spectrum antibiotics that target different proteins in bacteria to increase my chances of wiping out as much bacteria as possible. Tetracycline tastes like sour acrid sulfur, pretty awful. If you think the Malort face was bad the Tetracycline face is worse. I weighed out 500mg and mixed it with water and took it as a shot. I had some ciprofloxacin in pill form so it wasn't nearly as bad.

The diarrhea that came after was bad but I had expected as much. As anyone who has taken a significant dose of antibiotics before knows, you get the shits.

My chess rating on chess.com began dropping. Dahhhh, this usually happens when I am preoccupied and have a hard time focusing. It is a pretty good measure of my mental acuity. Also, because my stomach was messed up I wasn't consuming alot of calories which definitely messes with my mental acuity. In fact I only consumed 1000 calories on Feb. 16th!! Yikes. I generally need around 1800 to 2000 calories to perform well on memory tests and chess.



Wednesday Feb 17th - Antibiotics Day Two, Experiment Day Two
My stomach was pretty upset by this time I was also feeling pretty loopy. Unfortunately, it was time to go to the donor's place and pick up the samples for the transplant. I wanted them to be fresh for the transplant tomorrow. I told the donor to try and not eat anything crazy or abnormal the night before.

Fortunately, I had someone to drive me to the donor's place. By this time I was pretty out of it. The donor gave me a pretty hefty fecal sample in a plastic bag fresh from this morning. Then I made him take significant swabs of his arms, legs, mouth and nasal passages that I stored in 150mM NaCl. These would be used to inoculate my arms, legs, mouth and nasal passages. During the experiment I stored all the samples at ~4C in the fridge.

I took two doses of antibiotics today, still had diarrhea and still was having trouble eating much but better than yesterday at 1200 calories, chess score still suffering.

Because I didn't feel tired and hadn't slept much in two days I took 1mg of clonozepam to help me sleep and I accomplished an amazing 6 hours.... Usually, if I can get at least some sleep it keeps me from being manic. Mania for me is compounding, the less I sleep the more manic I become and the less I sleep. To help abate the cycle I take medication that helps me sleep. Sometimes this doesn't work and is insanely annoying

Thursday Feb 18th - Antibiotics End, Hotel Room Day One, Experiment Day Three
Still on the antibiotics but moved to the hotel room on Thursday, with my chess rating still suffering, down from 1425 before to 1393 today. The experiment has already started to become surreal but today it took it to a whole new level.

Once in the hotel room, I strip down to my boxers and put on booties, gloves and gown and start cleaning. I use disinfectant wipes and spray to clean most areas of the hotel room I would feasibly touch. I took bed sheets I purchased from amazon, still in packing and placed them over the hotel bed sheets and used pillow cases from amazon over the hotels. Anyone who entered the hotel room had to wear booties and if they planned on touching stuff, gloves. There was also a separate bed in the room that I never touched that they could sit on or lay on.

Then it was time. I went in the shower and cleaned myself and then started scrubbing myself using a sponge and antibiotics. My goal to wipe my microbiome completely off and out of my body before the transplant. For about 1 to 1.5 hours I scrubbed ever crevice and part of my body. Alot of people suggest it is impossible to remove all microbes from your body or that you would die if you did or any other number of insane hypotheses. It's possible but I didn't think likely. And though I didn't imagine I could remove every microbe I really wanted to try. Sadly, I only remembered to take microbiome samples before the cleaning and didn't really take any at all on the 19th because I was feeling so strange and out of it and just forgot.

At 1730 I took my first FMT pills and performed by first skin, mouth and nasal inoculations.

I did it again a few hours later.

I wanted the end of my antibiotics to overlap with the start of transplant so that the new bacteria had overwhelming numbers on and in my body.

I put on a white t-shirt I purchased from amazon. I put on underwear from amazon and a pair of laundered jeans while people were around. The Verge mention the laundered jeans as strange instead of just having purchased some new ones from amazon. How much different would the bacteria be on a new pair of jeans versus an old laundered pair of jeans? I don't know, maybe there would be a significant difference but I imagined not so. I also imagined not wearing pants much(I only really wore them when people came to my room).

I think in probabilities and some people think in exactitudes. What would the probability be that an old laundered pair of pants would effect the outcome versus a new pair of pants. In my opinion it was very small to none. I call it reason.

Friday Feb 19th - Hotel Room Day Two, Experiment Day Three
I ordered some take-out and chilled. I had heartburn all day but was refraining from taking an antacids because I didn't want them to mess with my gut. I actually was starting to relax and regain some of my normalcy as can be seen by my chess rating increasing and my calorie intake was also up. I enjoy staying in hotels because I don't have cable or network TV at home and it is great to watch old movies.

Saturday Feb 20th - Hotel Room Day Three, Experiment Day Four
I haven't taken a shower since he transplant started and I have been rubbing bacteria all over my body. Heartburn was getting to me and sitting in the same bed and not really leaving the hotel room was really getting to me. I was mentally and physically exhausted.


Sunday Feb 21st - Hotel Room Day Four, Experiment Day Five
I finally get to go home. When I arrived home I cleaned the apartment and put new sheets on the bed and the coverings on the couch were laundered. I rubbed my skin all over the bed and the couch to try and populate them with my new microbiome and then I took a shower.

I transplanted someone else's microbiome in(on)to my body and it was so surreal - Part I

This is the story of a Speculative Science experiment. The data and results are meant to be a guide and not meant to withstand rigorous peer review (though I did my best to be as rigorous as possible). The experiment has an 'N' of 1, as Scientists say, meaning it was only done once on one person and therefore the results cannot be statistically generalized.

This is a story of how I challenged myself mentally, physically and intellectually to push the boundaries of what I think human beings are capable of in terms of Science exploration.
 
And this is story of me, about my need for self-reliance after all the shit I have been through in my life, my hope to inspire others and my reckless pursuit of Science Fiction.

This is a long story.


And it starts with medical issues.

I have suffered from gastrointenstinal problems, so do other members of my family. In college I began to have serious GI issues and an MD told me that it might be IBS. This was around 2004 there was no test for IBS. Ever since then when I talk to a GP I have received the generic MD advice, "Don't be stressed, eat healthy, exercise." all to no avail. I pooped alot or felt like I had to, maybe 3+ times a day on a normal day. I always thought it was just something I needed to deal with until it became much worse in the past few years. I was ovo-vegan for a year, vegetarian for the preceding year. My diet in the past 15 years has fluctuated between mostly chicken nuggets (first year of graduate school) to mostly vegetarian (near the end of graduate school). My diet now consists mostly of chicken, rice and vegetables.


Post-nasal drip is brutal. I have had it for about 5 years. I finally went and was tested for allergies and such 6 months ago and the tests came back negative. Spent thousands of dollars in deductibles, tried a bunch of different medication anyway that the MD was prescribing. They kept giving me stronger and stronger nasal sprays, none worked (LOL). Then I had a CT scan for polyps but the MDs responses were not clear on the results, really vague about maybe something. 

You may not know or maybe you do but I suffer from Bipolar Disorder. It's actually not much like what you see in the movies or TV much more boring and painful. Days or even a week without sleep, depression, anxiety and a hint of crazy. Medication with rough side effects(I didn't even know akathisia was a thing or how painful it could be, until I took seroquel). MDs who want to charge you $200+ per session and all seem disinterested in really helping you. A therapist who would fall asleep during our early morning sessions, a therapist who would answer emails during our sessions, a therapists who thought I was his rival and would try and get the group against me during sessions (super fucked up). Mental illnesses are diseases that giving hugs or being loving doesn't fix.

Great Odin, I sound like a mess.

Besides these things I would probably be considered by many to be healthy. Resting pulse rate of ~60 bpm, very little sugar with small amounts of fat in my diet. Weight around 170 lbs at the time of the experiment. My exercising has fluctuated, in the past 15 years but I have probably averaged 1-2 days a week of rock climbing or soccer(some weeks 5, some weeks none).  



Gastrointenstinal issues, obesity and many other things have been linked or suggested to be linked to each individuals microbiome. There have even been suggestions that your microbiome can influence your mood or play a role in mental illness(don't know enough to agree and to link any of those papers) Interestingly, the Fecal Microbiota Transplant(FMT) company(organization?) Open Biome screens for mental health issues in potential donors!

So it began with the question, Could a microbiome transplant cure me of some or all the things that ail me?

In May 2015, I wrote an article titled The Future of Microbiome Forensics tldr; it discussed recent advances in using the human microbiome as a tool to identify individuals. Being a hacker it started me thinking about how one could obfuscate the microbiome or maybe even replace their own microbiome with someone else's to circumvent the ability of people to use the microbiome for surveillance.

I applied for an Art grant to explore these things because no one would fund a Science grant to do this stuff. Check the Video part of the application out here I didn't, however, receive the grant.

I wanted to replace my whole microbiome. Replace my mouth and nasal bacteria with a healthy donors and maybe cure my post nasal drip. Replace my GI bacteria and maybe cure my GI illness, and replace my skin bacteria because we are a whole ecosystem and and maybe all the bacteria contribute to mental health and maybe I would reinfect myself with my old bacteria.

I had to two reason to perform this experiment

1. Health
2. Is it possible to replace my whole microbiome

So the next question was, How to do it?

Obviously, I didn't just want to do the experiment and be like "Hmmm, I feel better, #WINNER!". So, I needed a way to track how my body and mind function on a daily basis to help me better understand how I am functioning. I created a questionaire that tracked the things I thought would be effected by the experiment, everything from working out to sexual libido to caffeine and alcohol consumption. Check out daily data here. 

I also wanted to take samples that could have the bacteria in them sequenced eventually using 16s metagenomic sequencing. List of samples taken over the course of the experiment here

Then I needed to figure out how this thing worked. How do I store donor samples? How do I inoculate myself with poop samples, from above or below? What about skin inoculation, nasal inoculation, mouth?

I read up on some stuff and decided to create a short protocol.This document also has a more detailed diary from during the experiment (but don't cheat and read ahead).


Well, (un?)fortunately this was something that had been in my mind for a long time and it was going to happen. I decided that I needed to set some dates. I knew March 2016 and April 2016 would be busy months with traveling and such so I figured February would be a great time.

The weird thing about this experiment is that many people I talked with thought it was super cool, scary, but cool. Pain, C. diff, hospital, all awaited me many warned.

Scary. I mean the experiment came with risks but as it became closer to the date of the experiment it seemed that others were more scared for my safety than myself. So much so that it scared me alot. Was I being completely reckless, so much so that I would regret it? I would be sitting contemplating the experiment and see myself 10 years in the future completely regretting my decision to not plan better or chose a better donor.

I wish I could I say I had a rigorous process of choosing a donor but instead very few people were actually willing to participate. Maybe it was the thought that if something went wrong they would feel responsible. I don't really know, I never really asked. It is a weird conversation to have to begin with. Imagine receiving a text from your friend that says "Hey I was wondering if you have any illnesses that can be transferred by blood or poop or if you have any history of gastrointestinal problems, post-nasal drip or allergies or mental illness." HAH. Then being like "Well why don't you want to help?"

It took me a while but I finally found someone within driving distance(I wanted fresh samples) that was a healthy, male. Someone I have trusted with my life before, we have Rock Climbed alot together, so I figured I could trust him with my life again. People have asked me if I was against having someone who was female donate, I wasn't against it if needed, in fact when I was having trouble finding a healthy male donor I seriously considered it. My goal, however, was to reduce the variables that would lead to a negative health outcome. Some studies have shown sex differences in the microbiota of individuals.

One of the toughest decisions I had to make was whether to test the donor for diseases that could be transmitted. It was a really interested conundrum and had me thinking alot about how much we really trust each other in life but we really don't. Do you trust someone enough to be your friend but not enough to take their word that they don't have any health issues because you are going to ingest their poop? How does this relate to the Hacker mentality? If someone wants to replicate this study should they feel the need to to test their donor? Am I being reckless and.or promoting reckless behaviour?

Most of the illnesses that are tested for and possible to transmit through poop are obvious. No one walks around with a pathogenic E. coli infection and doesn't know it(though maybe some might argue). The main issues is hepatitis, especially because it is suggested that viral hepatitis can lie dormant for 10 years. There are many types of Viral Hepatitis but A, B and C are the most common. From what I have read acute infections of Viral Hepatitis can clear on their own for A, B and C. Even so A is usually cleared by the body on it's own and for C there is medication that can cure you. Generally, poop is also tested for HIV.

What is my goal? That was my question. My goal was to create something that was accessible. I believe that the more difficult a technology is to access the less impact it can have. Getting tested for Hepatitis can only be done through a medical professionals orders as with most blood tests, which makes the process even more complicated and expensive.

I constantly have a battle within myself.

I grew up poor on a farm in the middle of nowhere in Valparaiso, Indiana and my single mother worked as a babysitter and bookkeeper to pay the bills. Both my Mom's first and second husbands were physically abusive and we always struggled through poverty. Evictions, repossessions and writing checks at the grocery store that my parents knew were going to bounce. We regularly had utilities shut off, electricity and phone disconnected. This was no fault of my mother's as she worked as hard as she could, ended up obtaining her college degree in accounting after 40 and sacrificed to give me and my brothers many opportunities.

Now I am not poor. I went to the University of Chicago for graduate school, a private school and generally considered one of the top ten in the world. Most people I interact with would be considered upper-middle class. I worked at NASA for two years under a prestigious fellowship.

I left NASA because I was tired of how fucked up Science had become, how it was classist and wasteful. I paid around $4,500 to sequence samples for this project out of pocket so the results wouldn't be dismissed. I teach Science classes for free at local BioHackerspaces and I teach Science classes for Money at local BioHackerspaces. I run a company that is trying to make Science inexpensive and accessible but I also run a _company_ that is trying to make Science inexpensive and accessible.

I just want people to be able to be free. Free to explore this reality. I think all other freedoms come from this one. Freedom to have access to information and tools and resources. It is hard to oppress people without controlling what information they possess.

If knowledge is outlawed then I will have and disseminate knowledge.

This is the thesis of this experiment. A fuck you to everyone who puts journal articles behind paywalls, who has rules so we can't explore, who tells us what is and isn't worthy of being published and who charge outrageous prices for everything Science because they are profiteering gluttons. I want to give back for the opportunities I have had and I want to show that even though you might be poor financial there is so much you can contribute through Science.

Ok back to the experiment.


It's December 2015 and I decide that I am going to reserve a hotel room in February 2016. Our homes are covered in our microbiomes. Papers have shown that within a few days of moving into a new place we colonize it with our bacteria. This would make it difficult to transplant a completely new microbiome onto my full-body so I thought that I should stay in a hotel room for a few days. I would clean and sterilize the room as best I could.

My GI had been bothering me a shit ton in Jan. I was co-chairing the GRS Photosensory conference and spent half the time in my hotel room trying not to poop in the bathroom. It was the worst. Probably one of the worst attacks I have had.

I couldn't wait for the experiment to start. I actually wanted to start it early I was suffering so much. But I knew other people were invested in documenting it. So I waited.

I decided to take antibiotics for this experiment. It was rough. If I had to do this again solely for health reasons I would probably forgo the antibiotics.

Understand, most all studies of FMTs are in relation to C. diff infections of which I did not have nor was I trying to cure. Could I have used the exact same protocol for a C. diff infection? Maybe, but instead of attempting a maybe I wanted to do my best to make sure this experiment was successful.

This experiment was more than just an FMT.

Normally, FMTs are done without antibiotics but I figured since I was trying to do a transplant across my whole body it might be required. Also, I wanted to have a complete replacement and not just a few species. My work at NASA was around microbial communities and plastic degradation and my Master's degree from Appalachian State was in studying microbial biofilms and signaling. In ecosystems, microorganisms don't function alone, through quorom sensing and many other methods they communicate and share resources and space. I wanted a new community not just a few new species and to accomplish that I thought the best way was by using antibiotics. In theory populating a community with a few species of bacteria is done much easier than replacing the whole community due to competition and the reason that the old bacteria might not have a reason to go away. Antibiotics I imagined would help so that the new bacteria had much less to compete against and many of the old bacteria were gone.

There have been many studies to show that FMTs work well with glycerol treated frozen feces but again these studies are usually all in relation to treatment outcomes of C. diff infections. I wanted my samples to be fresh. I did not want to risk the bacterial communities in the samples being disturbed from the original donor communities.

One of the reasons FMTs are difficult to replicate with a designer community(i.e. a human putting quantities of bacteria in a designer pill) is that we don't know how much or how little importance each species plays in the process. I had no reason to risk using frozen poop.

There was also the choice of inoculation orally or through enema or both. Most(all?) FMTs are done using a gelatin capsule inside an "acid resistant" capsules as it should help the bacteria survive the traverse through the stomach acids. I used only gelatin capsules. There are no papers that I can find that use solely gelatin capsules, so this isn't to say that it shouldn't have worked just that I was probably better off using the acid resistant capsules. The original plan was also to do both enema and oral but I read research that oral dosages are just as efficient so I went with just that. This could have compromised the experiment but in the end it worked out. Why did it work out? It could be a couple of reasons, I ended up not diluting down the samples or adulterating them in anyway(removing particulates adding saline, glycerol or freezing) and I took antibiotics. It could just be that the acid in the stomach is not as big a worry as suggested but these are just hypotheses with not much evidence to back them up.

Feb 16th 2016, the first real day of the experiment and the first day I would start taking antibiotics.

Science Hack Day SF 2015 - Amino Acid Dependence of alpha Helix Length

Last year at Science Hack Day SF I led and ardent band of marauders into battle in an attempt to create a simple method to sequence DNA. Though we accomplished some stuff it was alot of work! This year I just wanted to hangout and relax and code for 8 or 10 hours straight.


The project I decided to work on was the amino acid dependence of secondary structure lengths in proteins. Proteins as we all know and love, are little nanomachines. In order to better engineer and create proteins from scratch we need to understand how they have evolved and why. The smaller parts that make up proteins (i.e. alpha helices, beta sheets, &c.) are made up of specific amino acids with specific properties. I wanted to take that one step further as I have never seen a paper or heard much about the amino acid dependence based on the size of a secondary structure element. One could imagine that a smaller helix might have a propensity against certain amino acids that are less helical as opposed to a longer helix. 

Protein Model of Lysozyme, alpha helices are in teal,
beta sheets are in red, loops are in purple

I downloaded the amino acid sequence and secondary structure of each protein in the PDB(http://www.rcsb.org) and then wrote code(code is here) to parse and quantify the data. In the end I was a little dissapointed. It doesn't seem like many or any amino acids really have a dependence on secondary structure length.

Here is a graph of the ones that seem to change the most.

Alanine(A) might have some dependence and same with Proline(P) though I think Proline is an artifact(helices tend to end with prolines as a helix breaker, if this helix breaking residue is included in the count it can skew the percentages for shorter helices).

Anyways, want to look at beta sheets next and then maybe the protein size dependence of the amino acid dependence of secondary structure length. Or even secondary structure length dependence of protein size dependence.

And the Nobel Prize goes to a Biohacker

I heard something said by a collaborator, Vidhi Mehta, which moved me.
"Will the next Nobel Prize be given to a citizen scientist?"

I sat back and I imagined. What if this week a phone call was made to a Biohacker that I know, instead of the usual academic Scientist? Wouldn't that be something?

Thinking about my life and my career, I see how important this is to society and I want to be a part of that. I want to make Science available to everyone so they can contribute to the benefits of society.

This could be you but it probably won't be easy. It will probably take hours and years of dedication and work and perseverance but I think there is a chance that in the next 10 to 20 years, you can pull it off.

I think education is key. I always try and impress on the Ph.D. Scientists that I know how much they need to teach and lead and show others how to do Science. How they can give knowledge to change the world they live in.

One thing I have found by working at NASA is how little work a single person is capable of on their own. This is also sad because Nobel prizes are given to the Principal Investigator who didn't do the experiment and who might not even have come up with the experimental procedure. I guess the prize needs to goto someone but it seems the whole, limiting it to individuals, in the majority of cases is wrong. I think this is important because many Biohackers still work on projects in isolation in the majority of cases.

Biohackers need to start coming together and combining their powers. Maybe then the Nobel Prize will be within reach.

Is this Scientific paper on Genetic Encryption publishable?

The paper in question:
How to Protect your Genetic Assets Through Obfuscation and Encryption
In software based systems, obfuscation and encryption are techniques used to prevent reverse engineering and access to information. As society progresses towards using more Genetically Modified Organisms(GMO) and DNA sequencing becomes more inexpensive, a company’s genetic intellectual property can be reverse engineered and stolen by simply analyzing the DNA sequence. To prevent theft, techniques will need to be used that obfuscate and encrypt what changes are being made in the genome. This paper provides different methods that allow the safeguarding of years of research and development and millions or billions of dollars in monetary investments.
 
For the past few months I have been working on the fairly novel idea of genetic encryption. You can find a few sparse mentions of it on the internet but as we like to say in Science, to my knowledge this idea has never really been explored in depth.

I began by thinking in the context of how a company could protect a genetic asset(GMO) that is worth alot of money due to its genetic traits. I am usually on the other side, trying to break the protections but there needs to be something to break before one can break it. So I decided to try and build it.

I ended up writing a paper that runs through examples and ideas on how someone could institute Genetic Encryption and Obfuscation. Though I wouldn't consider the paper my finest work, it definitely has its merits, foremost because it is a prediction of our biological future.

Originally, my acknowledgments included:
"To everyone who is doing good Science for shit pay because someone tells you there is price for doing what you love. And to everyone who wants to fuck the system because it really needs it."

After consideration I took out the second  sentence about fucking the system because I thought maybe it was going too far. I was wrong.

I heard about bioRxiv and thought it would be a great place to submit the work as it is a free publishing server that promotes openness in Science. I knew my paper was more Biological theory and so might suffer some prejudices but I didn't know it would be this bad.  Usually these pre-print servers do not reject any papers unless they are ridiculous. My paper was rejected... The moderator said it was because the paper not experimentally based! I guess I understand that maybe bioRxiv only wants experimentally based papers but why?

Arggghh. Fuck the system, I put that line back in the paper.


Ok, well, maybe I can submit it to aRxiv another Scientific publishing server that focuses more on math and theory. I have submitted a single author paper there before and it was published without any issues. Genetic Encryption seems to fall under math and theory so it seems like a good fit. I submitted it to the Quantitative Genomics section(Genetics and Encryption seems to fit there) and thought nothing of it and then I received an email this morning that the paper was rejected.

The email:

The moderators determined that your submission was in need of significant review and revision before it would be considered publishable by a conventional journal.  Please note that arXiv moderators are not referees and provide no feedback nor detailed reviews with the removal of submissions.

WTF? What revision does the paper need? I am sure there are some small issues with it but significant revision? I guess it is partially my fault. I know some of the people in the Genomics pre-print community and they are pretty militant and dear I say stuck up assholes?

Where to next? I don't want to pay to have a Scientific paper published because that is the totally opposite point of Science but I want people to see this paper. I think it is interesting(maybe I am wrong) and I think it could spur some interesting innovations and discussions.

In the end what this all really tells me is just FUCK THE SYSTEM.

When someone can do serious Science but can't put it out there for people to see how is this system supposed to work?

Are we really doing Science anymore?

Wildtype vs Mutant

    I have been feeling a little angry lately because it seems like the ability for DIY Scientists to accomplish things is still difficult. This is noticeably seen through a lack of Scientific publications or data generated by us.

People in DIY Bio seem to be working towards something that doesn't seem possible because of the lack of resources, knowledge and tools.
Papers, plasmids and strains that would be dirt cheap if the whole system wasn't run by profiteering gluttons($65 for a plasmid, seriously addgene? $200 for a strain at atcc).
Academic scientists sit by and use the phrase "open science" as a motto of apathy. How long would publishers survive if scientists stopped citing and publishing in their journals? Or refused to pay publishing fees? And just posted data to their website instead? And DIYers remain with no access.

At The ODIN(http://the-odin.com), I have been trying to provide cheap prices and single researcher size quantities to DIY Scientists to allow them to do experiments. After lots of contemplation, I want to move away from my job as a Scientist at NASA because I think big things can happen in DIY just like what came of the computer hackers in the 90s. I want to help that stuff happen by creating more resources and tutorials for people.

This is where I need your help.

In the next few months at The ODIN, we have plans to release a Codex of plasmids and bacterial strains(yeast maybe?) for cheap. We want people to have the resources they need. Sign-Up at http://wildtypevsmutant.com and let me know what you are looking for or need.

We are also planning a crowdfunding campaign to take cutting edge genetic engineering tools like CRISPR and make them accessible physically, intellectually and financially. We might be looking for some beta-testers soon. Again, Sign-Up at http://wildtypevsmutant.com to keep updated. (Also, let me know what you think of the video)

I think that until genetic engineering arrives in many homes, what we do will just be scary and misunderstood. At The ODIN, we want to create a conversation around "Why do people think mutants are bad when they are here to save us?", i.e. Wildtype vs Mutant.

I appreciate all the support people have given The ODIN so far and I hope to continue to provide to the community through biting commentary and ad hoc Science.

Finally, to make DIY more successful get involved if you aren't already. Teach classes at your local hackerspace, if you can't, then write tutorials online(I would be glad to host them on The ODIN), mentor other DIYers or if you need a mentor contact me!

There is a little ways to go before DIYers can accomplish cutting edge Science so let's make this thing work, together.