Surfing through my site analytics I decided to look at the total number of viewers by their location. Here is what I discovered:
In the 1.5 years that this notebook has been made open, it has spread to almost every country on the planet. I’m not at all surprised that science accessibility could have this kind of influence, but I am in awe that I get to be a part of it.
Hopefully this becomes evidence that open science, science outreach, and science accessibility in general are the keys to the future of the scientific method.
Now that I am done with my Doctoral program, I need to majorly revamp the site:
First, I need to reorganize all of my tags and categories for easier site navigation. I will organize the site by project first:
Shotgun DNA Mapping
Next I will organize each project by organism and then experiment. For instance:
Root Hair Analysis
This will make it much more intuitive to navigate for experiments that are no longer being carried out.
Second, I will also remodel the design of the site so that the design reflects (1) the high quality of science, and (2) reflects the high quality design work that I do. That will just be for fun. With the new redesign, I will also be providing a new weekly column which I’m really excited about. I’m not sure what I’m going to call it yet, but it starts tomorrow and each post will contain real scientific work that reveals exactly how science is aimed to understand the world and better it. Some posts will be very educational, others will be fun and a bit silly but scientific nonetheless, while others will highlight things you didn’t necessarily think about. Regardless, I am quite excited for the series and I hope you are too.
Third, I’ve got a few new projects to unveil. I’m not sure when those will be announced, but two of them I will get to announce this week. I’ll announce the first project tomorrow, and the other project later in the week.
Fourth, my dissertation is 99.9% done and I’m just waiting for my committee to sign the approval cover sheet in order to complete my graduation. Once that is done, I’ll be uploading the document to figshare and will make it available for download. Then after some time, I’ll be uploading a special edition version of my dissertation which will feature some graphic design styling. The special edition is the version that I’ll be getting professionally printed and bound for my advisor, myself, and my parents. I’ll upload that too in case you would rather read the more awesome version.
That is all I have to announce right now. Sorry the site has been kind of dead for the past couple of months. The dissertation work has been beastly, but ONS made it much easier than what I expected the process to be. Now I get to go back to good ole’ fashioned, and fun, science!
This will probably be the last update. I’m going to (1) need to take a break until after I defend, and (2) need to start a new experiment because the plants are running low on media. I did just buy these awesome 1in diameter test tubes which should give the plants all the media and water they could need for a longer period of time. Anyways let’s go to the pictures:
The America Invents Act was initiated in 2011 and institutes some new changes to patent law. The newest inclusion to the law is that now patents are given based on a first-to-file system, whereas previously they were given through a first-to-invent system.
I mention later that public disclosure is called prior art. Under the former system there was a year of protection from the moment of public disclosure prior to filing a patent, as long as you could prove that you are the original inventor. Under the new system there is no longer the first-to-invent policy, so public disclosure could become even more important.
There was the scenario presented with two inventors. Inventor A publicly discloses invention. Inventor B files for patent some time later. Inventor A then files for patent longer than the 1 year grace period for prior art. According to the presenters, neither inventor gets the patent. I didn’t understand why.
According to speakers, the provisional application is low cost ($125 for small entity inventors, such as individuals, $250 for large entities like corporations). The intellectual property is also kept secret during the provisional period until patent. The provisional application provides the inventor with the 1-year grace period that also comes with public disclosure, but you have the ability to maintain the secrecy of your project.
Statement was made about this giving leverage to corporations with lots of money over individuals with lower financial capabilities. This is why provisional application is a decent work around. Also why open notebook science is an even better work around (free).
Foreign patents and foreign public disclosure count in the US as prior art, and fall into the 1-year grace period. Because this places a new burden on the US patent office, patents may be granted in excess (which is already in excess) and patents may not be invalid until there is a conflict dispute. I’m pretty sure that’s how a lot of patent proceedings already occur. This eventually puts the onus on the inventor to find infringements and file suit to argue the point.
This is actually confusing. If you are doing research with a collaborator at another institution/company file a joint research agreement. Neither entity can file a patent first without the other entity. The joint research agreement may/may not act as prior art, I wasn’t sure about that one. But the important point is that joint research agreement helps the process.
The speakers gave an example, but the details are fuzzy. They said they would post the slides, so when that happens, I’ll share them and refer to the timeline.
Based on the presentation and the discussion afterward, open notebook science can actually be beneficial for patent filings. JC Bradley highlights this below, and even with the law change it seems to be even more useful since first-to-file is the crucial step now.
That was all I had for the presentation. I spoke with the speakers after the presentation, and asked them about the relevance of ONS to this topic. As I mentioned above, the change from first-to-invent to first-to-file makes it a race to patent. The argument is that entities with a lot of money would benefit since they could just patent every idea. The law is made more accessible because first-to-file can be attributed via a provisional application or public disclosure. From that point on, the applicant has 1 year to file a patent.
To me, open notebook science can be a major benefit to the new patent process. Since it does cost money to file a provisional application, ONS (or other web disclosure) would provide a free alternative to the provisional application. The only difference between the two routes is that through ONS, the patent is immediately public information, while the provisional application keeps the idea in secret. Because the patent will eventually be public domain, the incentive to innovate is delayed a bit.
It should be noted that even though ONS makes your idea open, and encourages potential modification it does not encourage stealing of the idea. You are still protected from patent infringement. But if a competitor sees your idea and makes non-trivial (non-obvious) changes to your idea, then they can be granted a new patent. That is no different from how the patent process works anyways.
But to me, filing a provision for every idea you ever come up with and paying $125 every time is a waste of money since you aren’t likely to follow through with every idea. It also gives the US patent office a lot of unnecessary paper work, and could actually stifle innovation and creativity. ONS would in turn allow some one to share their ideas and protect the best ones for the original creator (since you have one year from first disclosure). You could use your resources to fight for the ones you want to keep and allow others to cultivate the ideas that you won’t ever get to work towards.
It was interesting that when I asked the speaker about ONS and patents, while he didn’t say the conflicted (cause they don’t), he did say that it didn’t make sense to pursue both paths. His reasoning was basically what I outlined above, but it also felt like there was a money undertone to it. You can’t make money if you share your ideas. To that I disagree, but that’s an entirely different story altogether. One that I hope to address in April.
A friend of mine, sent me to a link for Gizoogle.net, which customizes a Google Search to make it a bit more hip-hop cultured (my favorite type of culture!). A search for me brings you here. And a click on my notebook reveals this:
Take note of the Water Type Effects on Organism Growth category. Also my favorite quote: “Boy was I stupid. Ya’ll know dat shit, muthafucka!” which actually just reads, “Boy was I stupid.” Ahahahaha. I encourage you to read all my articles Gizoogled! Naaahhhmean?!
This morning while setting up for a time trial experiment, I noticed the 20% yeast sample didn’t smell like yeast anymore. It smelled like a mixture of yeast and something else. So I setup the experiment, took initial measurements, and then analyzed the sample in the microscope. This is what I saw:
Surrounding my slightly modified yeast are these tiny things, that look like super small e. coli so they are probably some bacteria or perhaps they are some kind of spore. Regardless that was not at all in the sample from yesterday (see above), and looks nothing like the e. coli that I temporarily believed was adapted yeast.
So I began a mission to decontaminate the lab. After the cleaning I just did, nothing is alive! Not even myself! In fact I’m not even writing this… (Note to dead future self: Sorry :-\)
Anyways, I began by bleaching the fuck out of everything. The incubator got it the worst as I basically drowned it in bleach. I scrubbed real hard with this super awesome huge bristle brush. I let the bleach sit for about 10 minutes and then wiped it down with clean rags.
Next I used the Activeion Ionator EXP, which was loaned to me by the custodial staff here at CHTM. It’s a spray that ionizes water to clean and disinfect, and supposedly can kill viruses and bacteria. After the bleach treatment on the incubator, I Ionated it and wiped it down and allowed it to air dry.
Then I used the Ionator EXP to clean all the bench tops and all my lab equipment (pipetters, racks, scales, hot plate, etc). I finished by emptying my current supply of YPD and made new stocks for use tomorrow. I feel sad that I had to throw about $80 worth of D2O down the drain, but I gotta be careful in the lab and so it had to go.
Tomorrow I will start the D2O adaptation experiment again (Round 3!) and let’s hope the contamination issues are behind me.