Monday, August 31, 2015

What's it like to be a Synthetic Biology Researcher at NASA - Part 3

Ok, this blog post is where things start to become scary. My goal in writing all of this stuff is not so much to call out any individual but more to show people the crazy issues I have experienced at NASA.

People often say to me "Well maybe it is just in your building, or in your group or at NASA Ames." but it's not. I know this because I have reviewed papers for NASA conferences and been to NASA conferences.

In Science when you write a paper about the work you have done, you generally submit it for review by other Scientists so they can give you feedback(this is putting it nicely, more like non-constructive criticism) about your work. Then if your work is of reasonable quality it can be published. At NASA, I have had the "pleasure" of reviewing Scientific papers for conference proceedings, specifically the International Conference on Environmental Systems (ICES). This conferences focuses alot on the ISS and how to keep it up and running so the astronauts stay alive.

The first year I did 3 reviews and rejected two papers outright. The two papers rejected were from NASA and the one accepted was from a company doing work for NASA. And let me tell you, it was leagues above the other two papers in every way.

The main issue with the two papers was that their data had no relevance to their conclusions(such as studying if ghosts exist by looking for orbs in pictures taken, does one really prove the other?). To make it even worse, the papers were written with so many grammatical and spelling errors it was gross (I tried to list them all but gave up because it was taking up lots of time). There were graphs without any labels(seriously? how is anyone supposed to know what they are looking at), basic statistics errors and many more issues.

Despite how bad the papers were I decided to review again in 2015 because even if I was just one person maybe I could make a small impact. Maybe people would stop submitting their shit if they knew someone might reject it. To my absolute amazement I was randomly assigned a paper that wouldn't even pass a high school Science course. I won't post the paper but here is my review.

Review from 2015 ICES Conference
This paper discusses and analyzes the chemical aspects of water used by astronauts aboard ISS 38-41. The paper is well written and provides a lot of data. Would be interested in more information as to the possible sources of the DMSD, is it coming from the ion exchange bed? 

There are some major issues, Background[written] is almost an exact copy of the paper submitted to ICES last year(2014) by the same authors. Table 1 and Figure one are exact copies, Figure 3 is a zoom in of the Figure 3 from last year! The graphs are all almost identical except for 4 additional points on most of them. Not only was Figure 1 reused, it appears to be taken from another paper with no similar authors(!!!!! If this is a common graphic floating around NASA you cannot publish it if YOU did not make it and you CANNOT republish it even if you did make it! This is considered Scientific plagiarism especially with image and data reuse and stealing. This is Scientific misconduct and this paper must be rejected!

I was told that this was not that big of a deal and they weren't going to send my review to the authors....
The authors seriously tried to scam the reviewers by zooming in on picture and cropping it to make it seem like it wasn't the same picture they used from the previous year (Also, putting a picture of an astronaut in your Scientific paper, no matter how cool it may seem, has no Scientific relevance). You would lose your job most places besides NASA if you submitted this paper.

Imagine my frustration. Imagine if people knew that there were lots of researchers at NASA who either A) Didn't know how to do Science and write up a Scientific paper OR B) Plagiarized whole papers.

You are correct, I don't know if this is generally true across NASA.
But I have a number of lines of evidence against real Scientific contribution happening at NASA:

1) The papers I have reviewed(above) from other NASA research centers
2) The work of others I have heard from talks or in passing(I have walked out of at least two research talks because they were so bad)
3) Leaving the American Society for Gravitational and Space Research (ASGSR) conference a day early because the Science was so bad and when I asked specific question in a public forum about experimental issues they were ignored.

What do I consider bad Science? Something that would receive low marks in the first year of graduate school. This means that most of the Scientists seem to have only an undergraduate education's worth of knowledge and skill. However, this is probably true, as a Ph.D. or even a Master's degree, are not required to be a Senior Scientist at NASA.

I don't think most people are being flagrant though. I think that they just don't know how to write a Scientific paper or how to ask reasonable research questions because they weren't trained to be able to do these things.

There is a reason modern Scientists endure 5+ years of graduate school and PostDoctoral training, to make sure the Science produced in the world is of the utmost quality. 

I understand this is not _all_ of NASA. There are still people at NASA that do contribute sound research, I am just beginning to wonder if they are the anomaly?

Saturday, August 29, 2015

Creativity and Science and Art

Two quotes today on creativity:

"The trick to being truly creative, I’ve always maintained, is to be completely unselfconscious. To resist the urge to self-censor. To not-give-a-shit what anybody thinks. That’s why children are so good at it. And why people with Volkswagens, and mortgages, Personal Equity Plans and matching Lois Vutton luggage are not."

"It's not Art unless you can fail miserably."

I am not a big fan of quotes because anyone can say anything and that doesn't make it true. However, lately, I have found myself in many positions where I am looking at the things I do in the context of it being a creative work. I like to view myself as a creative person, which is sometimes more true than others, but I am learning it is a scary place to be. Mostly because, you can fail miserably. That idea that I had, that I spent alot of time on, maybe it is not as interesting to other people as it is to me? Maybe it is really stupid and I am just being really biased?

Failing is really scary in Science. Not failing in that your experiment didn't work type of way but failing in that your ideas are wrong or not completely thought through. Scientists are always asking, "What did I miss?" I have spent years honing my craft and trying to develop my mind into a creative knowledgeable machine and I don't want to be told it is not. BUT I know it is not always going to have the most spectacular and brilliant ideas. I know sometimes those ideas will be wrong or crazy, that's part of Science and part of creativity.

I try and be unselfconscious as much as I can but it is hardwork.

This is the life of an Artist and Scientist though. You should be afraid, have the crazy ideas and have people tell you you're wrong or give you that look(you know that look people give you when they think you are crazy?). You should be challenging yourself everyday and sometimes that means challenging others who also proclaim to be Artists and Scientists. That is how we make each other better, that is how we respect the craft.

If you had a hard time being "creative" lately. Ask yourself how much you really care what other people think.

Thursday, August 20, 2015

What's it like to be a Synthetic Biology Researcher at NASA - Part 2

I work at NASA as a research fellow. A research fellow is an indepent PostDoc that writes a grant proposal for their research. The proposal goes through review, there are about 50 new fellows accepted across the world per year for NASA.

It all started when I met Masood Hadi at the first Gordon Research Conference for Synthetic Biology in 2013. I was wearing a NASA t-shirt that said "I need my Space!". Someone I knew told me that there was a person from NASA at the conference and so I decided to introduce myself. We talked briefly about Science and I showed him my poster. He suggested that I should apply for a fellow position to work with him, only problem was that the application was due in 3 weeks!

I arrived back from the conference and emailed Masood to propose a topic for collaboration. Unfortunately, he didn't email me back till 1 week before the proposal was due(yikes even less time)! I worked my ass off and came up with something.

Here was my proposal: Zayner Proposal

Though it is not one of my best proposals I still think it was pretty cool.

The proposal is titled: Bacterialforming: 3D Light Controlled Sculpting Using Bacteria

The basic idea was to 3D print soil using light. It would work by mixing the soil with an engineered bacterial that would express and secrete enzymes to harden the soil when exposed to light. Shine light on specific parts of the soil and it hardens, in theory. I was using the pDawn system of light activated transcription and using iron reductase genes for soil hardening. Some limited research has shown(or just been suggested) that by changing the oxidation state of iron one can harden soil(very skeptical about it now). Both Lunar and Martian soils contain alot of iron(why Mars is rusty in color) so you can see why I wanted to mess with it.

The lab I was working in was not setup when I arrived at NASA! This meant it was my job to set everything up and test all the equipment. Not a huge deal but definitely set my research back a few months. There also was very little in the way of reagents and chemicals. Fortunately, most of the labs in my building are empty so I could "borrow" chemicals from those labs when needed and "promise" to replace them when we had our own.

A moment on this, in academia Professors are called PIs(Principal Investigators) they run labs and are able to use lab space as long as they have money and researchers working with them. At NASA it works differently. A lab is basically a space anyone can use if no one complains but if someone has already "claimed" it, then they will keep that space till they die or leave(I am not even joking. Sadly, there is a person on our floor who must be in his 80s and came into work a bunch when I first started. Word around is that he hurt himself(broke his hip or some such) and now has not been at NASA in at least 6 months. His lab door is locked and the space unused). The people who can claim space are usually Civil Servants and to all common knowledge it is almost impossible to fire a Government Civil Servant because it is a government appointed position. What ends up happening then is there are a bunch of people with no money and no one working in their lab space but lots of unused chemicals and equipment. There are ~7 of ~14 spaces on my floor that are either rarely or never used. Of the spaces used they contain 1-3 researchers at most! (not including when summer interns are around). Average academic labs are 5-10 people minimum. One space was just left until a fridge failed. No one cared that thousands of dollars in enzymes and chemicals were just destroyed, bacteria growing everywhere, it smelled gross, even to me(I have partial or almost complete anosmia). Occasionally, when bored, I would hold my breath and dig around in there to see if I could find anything useful. Recently, as in two weeks ago, a freezer failed and no one knew who's stuff was in it. Inside were animal specimens that had been around for 10 or 20 years and the only reason people knew the freezer failed was the smell the rotting tissue made in the building.

Things started to go downhill a little with my "mentor" Masood Hadi after I setup the lab. He wasn't around much and wanted me to do certain things. Experiments for some of his old papers and create figures and posters for him. At first I obliged, wanting to be a helpful colleague but when it appeared he was doing no work on his own and was just taking advantage of my goodwill, I stopped. Understand, Masood was not my boss. As a fellow, I am supposed to be a independent researcher, independently funded and working on my own independent projects, Masood could not fire me. He was supposed to be my colleague not boss.

He started requesting me to do more and more stuff for him and I started to refuse. This definitely did not help the situation. I'll be honest, and most of you who know me know that I am no diplomat, but I will tell you to your face what I think. Sometimes I can be better than others but I generally don't want to waste your time and mine by trying to convince you something I am doing or you are doing is going to work out well, when it really will not. I have never been described as "nice" or "a people person".

Around this time, I also learned that it would be difficult, if not impossible, to have my experiments sent up to the International Space Station(ISS). This is because the solicitations for proposal don't come out often(once every year or so) and then they take around 1.5-2 years to go up(if the rocket doesn't explode) and another 6 months to 1 year to receive them back. That's if your proposal was one of the few chosen among the 50? - 100? submitted.

Another issue I found out was that the equipment on the ISS is very primitive. Because it costs a shit ton of money to validate equipment, there is very limited equipment and so very limited experiments that one can do on the ISS. What this means is that most of my experiments that I proposed from my fellowship would not be possible to perform on the ISS, even if they could be sent up(testing light activated gene transcription in microgravity). Understand, NASA won't let you send up an arduino with some LEDs. They know how many screws are on their modules in the ISS and they can account for every one of them(I think). You can imagine that if an LED is lost and short-cicuits something, serious damage can occur! So to propose a new ISS experiment would require writing a million dollar grant for hardware validation and development.

Sooooo my research lines started to become less promising and so I decided to look for other research avenues that would interest NASA. Stuff that could be developed on Earth and have a greater impact. This led me to waste recycling.

Alot of Scientists in the sustainable resource field focus on breaking down cellulose and lignin. One day I was staring at the molecular structure of these molecules and I noticed that they were very similar to plastics, long hydrocarbon chains and aromatics. After some research I found that very little research had been done in the field of bacterial or fungal synthetic plastic degradation. I was pretty excited. Imagine if we could engineer a bacteria that could degrade all the plastic waste in landfills.

The way I pitched it at NASA is that the astronauts use about 200 kg of plastic, per person, per year. Imagine if you are taking a trip to Mars with a 4 person crew and it takes about a year to arrive. That means you will have around 800 kg of plastic waste! Throwing it out is not really an option because that far away from Earth, every material is precious, urine is proclaimed the liquid gold (right Elysse?). If you could recycle it into a feedstock for algae or plants or something of that nature it would be awesome! Also, obviously it would be super helpful on Earth, 32 billion kg of plastic waste is generated each year and less than 10% is recycled so each year ~28 million kg of plastic waste is deposited on Earth!

In the past year I have focused on two main avenues in my plastic degradation research: 1) Bioprospecting 2) Genetic Engineering.

I worked fast, came in on the weekends and in a few months time my research began to show promising results. I took my summer interns and we traveled all over the Bay Area, from trash dumps (trying to convince them with my blue mowhawk and government ID that I was a NASA scientist and needed a garbage sample) to having the interns jump out of the car and collect trash on the side of the highway (thanks Tyler and Nathan!).

Why collect plastic waste? The sun has strong UV rays and prolonged exposure to UV mutates a bacterial genome faster than normal. Plastics as a synthetic polymer was first introduced ~108 years ago, if a bacterial generation occurs in 1 hour, that is almost 1 million bacterial generations. We are talking at least 10^25 possible genomes of bacteria engineered naturally, in say, the bay area plastic (understand that the estimated number of human beings to have lived over the whole history of the earth is only 10^7(100 billion)). I figured that some of these mutated bacteria in nature might have evolved a mechanism to interact with and degrade plastics and survived to tell about it (that's natural selection!).

We ran large screens by washing off the plastic waste to remove bacteria and then attempting to grow them in a media that has no carbon source except fresh the plastic we added(polystyrene and polyethylene). Carbon is needed for bacterial survival so without it they die! This means that the bacteria would need to break down the plastics to live and grow. We had a bunch of successes and identified a number of bacterial gen(uses|ii?) through 16s rDNA sequencing. I used an electron microscope to actually see that the bacteria were colonizing the plastic! See the pictures below (that is false coloration to make it look cool).

You can see the bacteria go from initial colonization to forming biofilms, (biofilms are basically just large communities of bacteria).

Despite my successes and promising research, my relationship with Masood became a disaster. He was on the search committee for a job that opened up at NASA and he told everyone else about the job but me (I eventually found out when someone randomly, not in my building or lab, told me about it). One of his only responsibilities as my mentor was to approve my travel paperwork, basically a formality. He refused to do it and many meetings and emails and arbitrations ensued. Finally, he was forced to sign the papers.

At this point my disgust for the NASA working environment was peaking. The first two years of the fellowship are guaranteed but the third year of my fellowship would need to be approved by Masood, the same person who was actively trying to limit (dare I say sabotage? (maybe a little to dramatic)) my career.

So what happened next? Stay tuned for the next episode in this on going series.

Monday, August 10, 2015

What's it like to be a Synthetic Biology Researcher at NASA - Part 1

A question I received quite often besides the obvious questions such as "What can you tell me about the aliens that have been to Earth?" or "What experiments has NASA been doing with time travel?" 


What is it like to be a Scientist at NASA?

I work at NASA Ames in Moffett Field, CA. We are located directly next to Mountain View and Sunnyvale which are considered the heart of Sillycon Valley. Google and many other tech companies have offices nearby. In fact Google recently decided to lease a portion of Moffett Field and during my tenure here I have seen alot of testing of the Google Self-driving car on our research campus.

Yes, that is totally a 1980s pixelated display outside the second guard gate.

The government is pretty strict about security because there is the possibility that NASA Scientists have access to sensitive and classified information(none of us really do). Because of this my laptop hard drive is encrypted and I can only log into my computer using a card reader attached to my laptop that reads my government issued ID card.

Every morning and every time I leave base I need to enter through two guard gates. At the first guard gate they check my State ID and at the second they check my government ID which required a background check and they contacted a bunch of my friends. The guard gates are staffed 24/7.

I work at The Centers for Nanotechnology and Mars Exploration. Besides Aerodynamics studies and some Mars Rover instrumentation and being the back drop for some MythBusters episodes, Ames is known for Astrobiology but fortunately not the Arsenic Bacteria fiasco.

Our building isn't ugly on accident. The exterior is supposed to look like micrometeorite impacts on the Lunar surface. 

Ames is home to NASA's Bioengineering Branch and Synthetic Biology program. There are actually very few of us doing Synthetic Biology here at Ames. Currently, there are 4 Fellows with the occasional intern.

For an innovation lab our sign is pretty bad, I know, I didn't create it so don't blame me.

Where I work looks the same as most academic labs except that I build my crazy stuff like my artificial evolution system sitting on my lab bench with all the tubing.

As a Fellow at NASA I had to write a proposal that was reviewed and approved by NASA and then they provided me with the resources I need to accomplish my projects (if you have a Ph.D. and want to apply go here: I was chosen as one of ~200 fellows in the whole world, they chose around 50 each year as the old ones rotate out. Fellows apply to work at one of the 10 facilities in the US not just Ames. Despite trying to follow my research proposal, as is Science, my projects change and so I am usually able to follow whatever crazy ideas I may have as long as it follows along with NASA's goals of space exploration. Especially if it involves going to Mars! It is kind of weird writing proposals telling people how you are going to help Astronauts live on Mars!

Because Synthetic Biology is such a new part of NASA things are slow. There is not much overlap between the few projects that are going on and most of us researchers are working alone. 

The mission to Mars is supposed to occur around 2030 so understand that the timeline at NASA is 15 years! That means the whole publish or perish academic game plan is kind of out the door. The goal is to think about the future. This is not easy for myself or most humans to try and build technologies for 15 years in the future but it is possible. 

Though most people are stuck in the past...

~80% of NASA's ~17,000 permanent employee workforce(including students) is over the age of 40 (~70% over 45 and ~54% over 50). This is worsened by the fact that anecdotally I have noticed that very few people retire, creating very few new openings. Numerous stories have been told to me of people dying on the job from old age (YIKES!).

However, most employees at NASA are contractors and not permanent employees. This means that the government hires a company to do some work and once the contract is up for recompete (every few years) a contractor can potentially lose their job, though many manage to stay on and just switch contracts to the new company. Most of the work at NASA is done by contractors and the average age of contractors is higher or just as high as permanent employees! Let me stop and say that there is nothing wrong with people being over 40 years of age in Science, the problem is that when the influx of new ideas and talent is not around, everything stagnates. In my opinion research Scientists need graduate students more than graduate students need research Scientists both because of labor and ideas.

We constantly receive emails telling us how to avoid slipping and hurting ourselves and how we should not believe people when they send us spam email asking for our bank account information. It sometimes feels like I am in a retirement home.

The numbers for total NASA employees including fellows(~200) and contractors(20,000-30,000) is difficult to find but is suggested to be around 50,000-60,000. During the Apollo era the number was around 300,000. I don't know if NASA should still have those same numbers and I think it would be a waste of money. All the bureaucracy at NASA prevents things from moving quick. In synthetic biology NASA still has not even really done recombinant protein expression experiments(a basic experiment) on the International Space Station (ISS) and who knows if it will even happen anytime soon? But we are supposed to create "synthetic biology" for space.... I think NASA does a great job in research and development but I think private industry are the ones who are going to push the boundaries of space exploration. Companies like SpaceX move so much faster and are willing to take more risks than NASA.

I have learned alot at NASA about how to deal with bureaucracy. I always tell people that working in the government is exactly like what they think, no one works, money is wasted and everything moves sooo slow. I think the problems come from a combination of things but mostly it is people just not caring. If you couldn't be fired from your job even if you didn't even come into work, would you go into work? Alot of people don't come into work. My "mentor" Masood Hadi, comes into work about once a month and works a second job...
You can imagine coming from a top tier research university that this was big a culture shock. I worked 7 days a week and so did many people I knew and now most people I know barely work 3 days a week. 
A funny story, after working at NASA for about 6 months, the Vice Chair of our division told me that working in the lab so much presented a safety hazard(I had a higher chance of being injured) and so I needed to not work in the lab at least one day during the work week. I tried to argue but to no avail...

Working at NASA has been interesting. I am fortunate to have had this opportunity and to explore crazy research projects and ideas and I have meet some cool people but I plan to leave if I can find another job that fits me. 

In the next few weeks I will post more articles on the topic of NASA, including more about my research and how and why the Synthetic Biology program at NASA is being ended this year.