Open Science, so what?

In reference to my job at COS, of course people ask me what I do. That is pretty easy to answer: I make websites work better for scientists to use and keep workflow/data. Great. But the question often not asked, maybe because adults left it back in their childhood and it might be considered rude: Why?

Why did I work for telescopes? Why is this current job more than just a pass-time in order to make money to support myself and my family in my old age? Two things, one intrinsically selfish, and another less so, but not completely altruistic: I need motivation in order to do things and I can go for ages without generating any motivation myself, and science needs to be more open.

So I need a bit of motivation. Once given a bit of outside motivation I can often generate enough extra to do a pretty good job at whatever I am focused on. For example summer semester AI course was definitely a motivator, but I liked it enough that I put in the effort to get an ‘A’. I am not certain how much I will like this next course, but proving to myself that I can do A-grade work means that I can convince myself to keep up the work. I will talk more about that course soon.

Anyway, enough preamble, really why am I motivated to do the work?

It comes down to the fact that I believe that we need science. Do I believe that science can solve all of our problems? In short: no. However, it can give us explanations for many questions. Those generally lead to more, or finer focused questions. But it’s the progress that has been made previously that colors my optimism for what may yet be discovered.

The problem is that today’s professional scientist/researcher falls into a system that has the catchy phrase of “publish or perish.” Not a phrase that inspires confidence in those unable to find something publishable. And that is just it, what isn’t published? And why isn’t it published? I am not talking about pseudo-science with obvious flaws and downright false conclusions, but rather negative results.

Negative results come about when a scientist poses a hypothesis, runs experiments, and then gets results that say the hypothesis is wrong. What’s a scientist to do? There are many options, the first of which is the least insidious, but still not good: changing the hypothesis to fit the outcome. But if negative results aren’t published, how can we avoid duplication of effort? Not to say that checking results is a bad thing, in fact being able to reproduce results in another study is great.

Let’s imagine for a moment that there existed a society where parents only told their children positive outcomes, only things (true or false) that could help them. One of the first things you notice is the consistent burn scars on the hands of just about everyone that you meet. The first few people that you meet won’t talk about the scars and the way the react the question seems to be taken as a rude question.

Finally one older guy chuckles and shakes his head when you ask the question again, carefully trying to choose the right words. He replies, “We are a positive society, we don’t tell people about bad outcomes. Everyone has to discover that the stove is hot for themselves, and some are more badly burned than others.”

Or to put it into current day science culture terms: What publisher is going to publish my negative result so others can avoid doing an experiment that will also have a negative result?

Maybe other scientists would be able to move on and try a different angle, or derived questions from the negative result?

But it is more than just publishing negative results: In order for science to pull itself, and its associated parts, out of the decline in popularity it needs to have a vitality and veracity that doesn’t allow otherwise uninterested people to ignore it, or disparage science in general.

Why I like working with and for science is because there is room for improvement. It isn’t just about catering to the masses, but rather discovering things for the masses, and letting them know about discoveries in a transparent way.

There is negative science, but there is also science results that are wrong. When data is falsified or manipulated in such a way that results are completely twisted around, then this is bad science, not just negative results, but false results. If we can help weed these out by making science more reproducible, then we are well on our way to making science trustworthy again.

I am optimistic that I can help in this area by making better tools. That is what motivates me day to day.

Glamour Tug

*Note: This is a final draft by any means, just an excerpt or short story trying to get a slightly different view of my universe.

It wasn’t the most glamorous job, but she made the best of it. She applied retro thrusters, working in concert with the mono-tasked AI, coming to a relatively abrupt halt in relation to the cruiser docking at the base.

She was considered one of the best tug pilots and it showed, the controls had flipped to fine controls, but she knew exactly how much power would give them the centimeters per second relative velocity to contact the warship. What she mostly relied on the AI for was information about the other six tugs and coordinating. Most tug pilots operated the tug in a general sense, but the AI handled most of the fine details.

She blanked out, waiting for the ping that would give her the correct amount of time before all the tugs contacted. Certainly the wash from the tug engines gave the warship a bit of relative velocity, but it was generally negligible. There was no point getting frustrated with the other pilots, she had scars from fights that started from that frustration, in fact because of those fights and a single turned down promotion she was probably going to finish her career as an over-qualified tug pilot, but she would stick it out. (rank?)

The soft tone sounded and she pushed forward, contacting the ship on its tug plates at just over three cm/s. Magnetic couplers came online and fastened onto the small steel plates. Another tone sounded telling her that all the tugs were successfully attached. A tone following that told her that there was a little bit of velocity acquired. Tones couldn’t really map well to three dimensional space, but it did tell her the magnitude was well within operational parameters.

Now the part she detested, since she was enlisted and just one of seven tugs they had to be slaved for the final approach, and it was usually done by a lieutenant, sitting a ways down the dock. If she had read the assignments for the day it was a kid just out of pilot school, doing a tour of docking duty because he hadn’t quite made the grade to be assigned to dropships or fighters. Not that many had caused collisions, because the AI generally stepped in to regulate ham-handed pilots, but it rankled her that it was always the ones who hadn’t made the grade.

***

“Johnson,” Someone called her name, but it wasn’t a voice she recognized. If it had been, even an officer, she would have slowed to allow them to catch up, but otherwise continue walking to her destination. No one took it as insubordination from her, though they made sure no one else emulated her. She turned.

The young man approaching her was one of the pilots fresh from pilot school, but he didn’t have the characteristic hang-dog or scared puppy ways about him that most pilots banished to dock duty had.

“Yes sir?” She came to a stop, trying not to regard him in her usual manner, it scared most of the new pilots if they weren’t already afraid of her. She thought she also recognized a fire in his eyes that she generally only saw from ship captains. She straightened a bit.

“I was told you are the best tug pilot around, is that true?” He stopped a meter in front of her and kept his gaze level.

“Probably, sir,” she might snub some officers in subtle ways, but she never forgot ‘sir.’

“Stop being modest. I’ve looked at your AI settings, the only thing it does is coordinate and slave.” She was taken aback, when had he had time to look at her settings? He only just arrived yesterday.

“Yes, sir. I am the best tug pilot I know.” She paused, “Permission to ask a question.”

“Granted.”

“You aren’t a normal pilot fresh from school, are you?”

He smiled, “I am fresh from pilot school, but you are right, I have a mission and an advantage.” Certainly intriguing.

“May I ask what those are, sir?”

“You may, but I can only answer one: I had a very strict upbringing and my father doesn’t like that I am not on track to captain a warship of my own, but rather went for pilot school.”

It didn’t take that long for her to figure out that he must be a son of a high-ranking flag officer, and glancing at his name tag it confirmed her suspicions. He was the son of the Navy’s Joint Chief, one of the three people that ran the entire military. She nodded.

He chuckled, “Quick on your feet and understated, well Johnson, it was nice to meet you.” He held out his hand to shake. It was unusual for salutes to be thrown, except during formal dinners, commissioning ceremonies, or promotions, but it was even odder to shake hands like a civilian. She paused, but then took it and shook it. “I’ll let you know when I can answer that second question. Just know when it comes to that you will be under my command.” He let go, smiled again, and turned waving as he quickly strode away the way he came.

She stood a moment considering that very odd interaction. For all her years she couldn’t think of one time that she had shaken hands while stationed at the starbase.

She turned to continue toward the mess. Also he seemed very cheerful, not just unlike all of the bottom of the bucket pilots, but unlike anybody she interacted with at any point during her assignment.

Boredom

Training in Fusion and Sub-space Generation technologies couldn’t be more different. The fusion training was actually a degree backed by several universities for the military, and took nearly four years to complete. With that he had made Senior Warrant Officer, in charge of an eight-hour duty shift, a junior warrant officer on a short training tour, and five enlisted crewmen. With his graduation most of his family came from a few different worlds to celebrate his achievement. It was a good  five years of routine, and respect.

When he volunteered for the new top-secret power plant testing, he thought it would be along similar lines and that he could use most of his knowledge to command as effectively as he had before. But he was wrong, and very bored for it.

One of the reasons he had volunteered was because of the incentives. The largest incentive was for a post retirement rank of commander, essentially three levels of pay above his current pay rate, with a small pay boost during the first few cruises and a generous bonus at the end of the third cruise. The first thing was a three month training at the end of which nobody could know that he had completed it.

The first assignment after the crash-course was to a refitted cruiser, almost the same exact class as his two previous assignments. Upon arriving he went to the ‘aft power-module’ at least expecting to still see a back-up fusion generator taking up a tenth of the ship’s volume. The surprise at entering the formerly giant space was a shock when it suddenly ended in the back of the officer on duty, the tiny workstation, and the cube.

The cube measured one meter by one meter, massing just over two tonnes. It had four connections, the negative node, two coolant lines, and the output power. The theory behind the cube was simple: It harvested energy from subspace by using the difference in physical laws between our universe and subspace.

The way it did it was a carefully controlled bubble of subspace-time generated within the generator. Two atoms were ionized, stripping all electrons, and then shot through the bubble at converging angles. The collision released quite a bit of energy that exited the bubble. When the new atoms exited bubble they also had an energy higher than they had gone in with, and a few more translated particles. This exit was also accompanied by the reuniting the atoms with electrons, the potential energy of which was huge, but about 90% of the produced energy went to prepare the next atoms. Though only 10% efficient it was essentially free energy.

A single generator measured 1x1x10 micrometers and produced approximately 1 Watt. In the cubic meter the volume just for generators came to about 30%, the rest was cooling and fuel and exhaust handling. Theoretically this would mean that the power output could be 30 Petawatts, but with control for safety and inefficiencies the actual power output can be about 5 Terawatts.

With such power in such a small package it was a bit of a surprise during the engineering briefing that followed that day that they had four of these broom-bot sized closets carefully tucked around the ship.

His fellow Power Controller beside him chuckled. “Only twelve of us they have to replace when we go mad.” He chuckled at her joke, as close as it was to the truth, and looked around the room. A ship’s engineering complement usually had a majority of power engineering, with the lightning bolt clearly visible on both shoulders no matter what rank. But he only quickly counted about twenty people in the room with just the lightning bolt. The majority was now the lightening bolt with a wrench across it, the repair crew, maintaining the many electrical systems that made the ship run.

The briefing continued into emergency operations: Normal duty would only have one person on duty at any time, but during General Quarters a second would rush to the each power plant to be a second. But really if something went wrong, it was unlikely the second wouldn’t experience the same issues, rather it was a tradition. Even during GQ only one of the four power plants really needed to operate at increased power at any time, but during normal operations and maneuvers (including transitions to sub-space) all four would run at approximately one tenth power.

After his first shift he was missing the fusion power plants. Eight hours essentially babysitting a system that really only needed a person there to do an emergency disconnect. In fact his only real duty was reporting the current capacity to the Lieutenant who then attended meetings to tell the Captain that a certain percentage of the micro-generators were working.

It was an affront to the traditions of Engineers everywhere, he suspected that soon it wouldn’t even require an officer when the generators went into service across the Navy. A petty officer wouldn’t even deign the long hours of drudgery, and it would probably be assigned to several more E-3s that would be paid less and be assigned to different areas on a rotation. But now due to its sensitive nature it required a person with more supposed integrity, if he didn’t lose that with all of the boredom he was going to endure over the next few months.

Buyer's Remorse

To assuage his buyer’s remorse he stood in the hold of his cargo ship and looked at the lines of the craft he had purchased. It wasn’t alien in design, there being no confirmed contact with aliens that could design anything beyond rock tools, but it was a human attempt to make the craft look alien. The design really didn’t work that well, there were a many awkward intersections of otherwise smooth flowing curves. But he hadn’t bought it for the looks, he had bought it for its new power plant design.

The new power plant, supposedly technology stolen from the Terra Faction, allowed a cube less than a cubic meter to supply the twenty-five meter craft with enough power to supply a navy space cruiser, generally rated at 4 times the length and not quite 64 times the mass, with power to spare. That meant the small ship could mount engines and sub-space generators that were well over powered for a ship its size. The gravitic technologies could be strained to a point where they might theoretically give out under massive acceleration. Although it was a theoretical failure point of around 15,000 m/s2, he wasn’t going to get that close to test the theory. He had figured out that his acceleration could probably be pushed up to a point where 0.3c would likely be twenty seconds, give or take five seconds.

Usually a craft half this capable was first of all twice as massive, with about a third of the mass going toward the power plant and another third going to engines. As it was the engines still took up a third of the mass of the ship, but that was it, the cube was a tiny percentage and the rest was free space, if someone hadn’t designed the cabin space as awkwardly as they had the outside intersections of curves.

He shook his head, when he got through customs he would probably have to just build a new one, he had really bought it for the powerful new power plant. At least it wouldn’t be too much a pain to install in a new craft, a cube was a cube, not built for a specific ship like most power plants.

Subjected to...

Why would anybody want to subject another to targeted advertising?

Good question. Why are you reading this blog? Friends of mine? Similar interests? Family? Well the first two mean that maybe *some* of the advertising will actually of interest. It is actually along the lines of my links page that I am doing a major overhaul on: I want the links to be a reflection of what I find important or useful. The advertising should be of use to someone, especially when I am writing about interesting things. Sorry family, maybe you like some of the things I do.

So why would I want to start making an infinitesimal amount of money from advertising on my blog? Here is an article on side hustle. Do I really want to write for a living? I already do. Coding.

But what this is is a small way to write a bit and get a bit of money. I am not expecting thousands of dollars, but I do need just a bit more motivation for some of my writing ideas.

Really though I have a much more lucrative side hustle already, reviewing code for Udacity. Depending on the projects and complexity of the rubric it can pay quite well, but guess what I am doing in that situation: writing. I write comments on specific parts of the code and write broader reviews for the rubric. It has really given me an opportunity to see some pretty good code as well as help those that need a bit of support to make their code work well. The only real issue is that there are waves of activity and I am usually busy with something else when they need tons of reviews done.

Why am I busy? Work, school, life.  And two of those are writing intensive. I want to work more on my universe building, or really extending our universe. I certainly know that not everything is working together right now. I have actually been doing some research on some of the tougher physics ideas, but I really have a hard time concentrating on things like that. I have also read a ton of sci-fi over the last year, choosing it over fantasy in order to just fill my mind with concepts, what works, what is wonky, what could be done better. I really want to have something believable to base a story on, I just get caught up in the world building idea.

One thing I worry about is character development. I know about it in theory, and experienced it in “the story of my life,” but there is still something that just scares me about it. I don’t want to just focus on one character’s major development, but I also don’t want to have flat characters. So how will I balance plot, characters, and the ever so essential technology? Well the technology will have posts here, but might also have some of its own material, only appearing in the story with enough context that you don’t need to go look it up, but hopefully for all those that want to they can find it.

Completely Different

Not speaking of work or side hustles, there is a group that I have tried twice that I enjoy to some extent: http://www.meetup.com/Cville-Dagorhir/. Hit one another with foam weapons… what could be more fun? It is great since you don’t need anything except a foam weapon, no armor, and if the people aren’t strict, no medieval costume necessary. The C-ville club has a few loaner swords, so it isn’t necessary to build your own right away. One issue that I have with the concept is that the head is verboten, only archers and rock-throwers can hit the head. That really messes with quickly choosing targets if you have been practicing longsword in your garage, like I have. Jessie and I will be practicing with fencing helmets and a few other pieces of protection, but much more in the Germanic tradition. But anyway, the people are nice and it is a fun form of exercise!

Contrasting Old and New

What’s the best thing about living on the mainland after seven years of living on Hawaii? Flights aren’t working out in my favor as far as schedule and cost, nor is it cheap to send furniture from my parents’. In Hawaii? Suck it up, the only way you are getting off this island is to fly or get really good at sailing. Also freight is going to cost you 1400 bucks to ship an end table… okay maybe not that much. Mainland? Okay, we will drive 3200 miles round trip for about 500 bucks, be able to take all the luggage we want, and then turn around and bring home the furniture. The bad news? We are looking at doing that in December and January. Oh seasons.

Whatever plans we have though, I think both of can be pretty flexible and be able to go before any large storms are going to occur. Then we won’t need to be as regimented to catch flights. And if we really need to we can go south. Add a few hours or more, but still make it in our own time. Also, if the weather is bad on the days we have plane tickets, the changing of plans or waiting would be frustrating to say the least.

What car are we going to drive there and pick up furniture with? Ah, but we have a direct line on a Subaru Forester, buying it Saturday. It might be the car’s first real trip period, but we are really excited to get it.

Furniture, but not really -

Due to office remodeling I also got cabinets with a countertop,  going to install that in the garage for a workbench. Might be modifications throughout the years to make it more useful, but I think it will be quite a bit easier than trying to build my own with basically no tools currently.

Short observations on work

One of the best things about working for a startup is the fact that there is huge right of way for creativity, in order for an idea to be really crazy it has to be at least one more level of crazy than normal. To put it into perspective, we have 30+ interns working for us this summer, about half the company. That is nuts in my mind, but the amount of work they are doing is actually amazing, in fact swamping our normal processes. But speaking of processes, still a large amount of room for growth or massive change.

Compared to the Joint Astronomy Centre the Center for Open Science is a massively younger, more flexible place. This is both a blessing, but it also means that we aren’t playing with 120 ton telescopes that can look at a gas cloud being eating by a black hole in the middle of our galaxy, trade-offs.

Probably my biggest issue is that there is so much going on that it is hard to keep track of who is working on similar or potentially conflicting things. I have to say that one of my merges of code essentially wiped out an entire commit by an intern, not because they did anything wrong, but because I started using schema validation rather than writing out a dataset line by line. Also there have been a couple cases where interns figure out that an issue already has a PR that just isn’t merged yet, after they code a solution. Even with all of that and the semi-chaotic nature of interactions I have to say I enjoy it nine out ten or fifteen days which is a bit better than some spans of time at the JAC.

And I have certainly learned a huge amount. That is not all that different from the JAC, but the pace is much faster, and the tools are so much newer in general at COS that sometimes you have to fix them and send in a PR to a stand alone tool. But that leads to other things: Open source! Oh man, so glad to still be working for science and for the greater good. I am not sure if I could work for a “business” company, even if I’ve dreamed of starting my own sometimes.

Anyway, on to solving the world’s problems by facilitating a better website for scientists to do better, more transparent work.

Done! For Now...

Sometimes progress is hard to come by. Right now, for instance, I am trying to learn something new, specifically a Python web module known as flask but running it on a ipython notebook which is probably complicating matters. Maybe I should just make another sandbox to test these things with…

Anyway, on to other more interesting things while I wait for the program to complete or fail: I turned in my final for Knowledge Based AI for Georgia Tech’s Online Master's in Computer Science. It was actually quite an interesting class. We had three projects over the course of 3 weeks looking to solve visual IQ tests using cognitive techniques.

I certainly wasn’t the best in the class by a long shot, but I know I got a pretty solid B in the course and am hoping that I somehow squeaked an A, though if I don’t get one I will be close. I really enjoyed the challenge of the class and most of the time I enjoyed writing the papers too. An interesting tool the course used was a peer feedback system for the papers. Some feedback was less than useful, but there was certainly quite a bit of it that was useful.

The topics looked into how we could model AI off of human intelligence, rather than just building a logical and/or super fast machine, think Deep Blue: brute force chess playing works, but it really isn’t the way most people would approach chess, not even the masters. No one can consider the next million possible moves in a few seconds.But even if there are approaches to how to do something that make a computer behave a bit more like a human, it still isn’t the generalists that we are. Even the most strictly uni-tasked human can generally figure out how to do something new, and we are only beginning to delve into those depths of general learning. And hopefully Empathy, but I will leave it at that.

I didn’t feel as though I got my agent to be an AI much. There was quite a bit more image processing going on than trying to follow all of the different concepts we were introduced to. It might be interesting if each of those topics had a more in-depth set of materials to mess around with and code a small agent using all of those materials. That does sound like a possible project, to make mini-agents that incorporate each concept separately and only include other concepts that are needed to facilitate the actual workings of the agent. Of course that is possibly a great undertaking… and I am mostly just full of good ideas and distractions.

For instance, I was introduced to an interesting thought just now: http://nytlabs.com/projects/editor.html that could have huge effects on the osf.io wiki, by connecting it to SHARE, allowing the piecemeal typing to be sent to an agent that would use previously learned references and list them to the side of the wiki editor, so that the person writing a wiki page might see similar published items. These could also be split, sort of as the article describes, into smaller agents.

However, my agents might be grouped into science categories so that a chemist gets chemical references, and not psychological references. That could lead to boxing results a bit too closely, so there might be agents that cross disciplines so that discoveries in other disciplines might be helpful to the current project. But of course this “distraction” would have a dedicated “9-to-5” time to work on it.

Another problem with free time projects is that we just moved into our new house. It is huge, at least compared to the last, well, long while. Unpacking is nearly done and mostly waiting on Jessie to get back, but there are plenty of things to do.

One of the more fun things will be making an archery target. With all the empty boxes I have started doing triage to find the worst of them and cut them up to make the target. We also have way too much packing paper and grocery bags. Moving from Hawaii, where they were banned, to Virginia was quite a shock as to how many we accumulated over 6 months. The bags will make pretty decent fill though.

Also I have been working pretty much eight to sixteen hours extra a week on the class, no real down-time. Some projects, especially on my own will have to far away from code so I can mentally refresh and prepare for the Machine Learning class that starts at the end of August! Oof.

Maybe I should just keep the nose to the grindstone in order not to miss the fleeting down-time.