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omniscion Why I'm Getting a PhD

[bill lumbergh] I'm gonna have to go ahead and disagree with you on that. [/office space] (My PhD is in behavioral neuroscience, so YMMV)

I've found that if people want to learn, then they will learn. You don't need a PhD for that, and the process of going through a PhD doesn't really teach you anything more than you couldn’t have gotten yourself. Passion drives someone to learn, not getting accepted into a PhD program.

omniscion Ultra-high resolution 3D scan of the entire human brain

Your answer is correct, in order to get any pictures, you typically have to shine light through a sample (unless it is fluorescent, then you can bounce light off of it). Also, in order to stain the sample, it needs to be thin(in this case 20um).Also, for the high mag stuff, you cut the section even thinner (ultra thin sectioning, which is the machine behind the guy under the "path to uploads?" heading). To do this, you need to already work with a thin section. Overall, sectioning brains is a super long, kinda boring process;) Hence why I've watched (listened) to a LOT of netflix.

If you guys are interested in seeing open source brain images, check out http://www.brain-map.org, it's a great resource working on something similar.

omniscion Simple Statistics, a JS library for doing statistics

This may be really helpful :) Thanks a bunch! Keith

omniscion Ask HN: Need for better technical interviewing tools?

Just to bump this, I was at angelhack and saw the demo for streetcodr, it was awesome! I could totally see this being a useful tool for interviewing. Congrats on an awesome app guys Keith @omniscience

omniscion Toxic workplace, what do I do?

"Toxic workplace, what do I do?" quit. F' that noise. It isn't worth the frustration. I did the same thing about a year ago, working for federally funded science. The worst decisions on earth were made, money was wasted AND they complained about budget cuts. It got to the point that someone was like, "you look miserable?" and I was. Toxic is a perfect word, it was literally eating away at me. I quit, had no job lined up, went on vacation while emailing my contacts about jobs, came back with a job. Done and done. Being in a toxic environment does nothing for you with the exception of teaching you how NOT to do things. But, it seems clear the author of this post realizes that, so your lesson is done. Quit. move on, don't look back. Simple as that.

omniscion Ask HN: Doing my first hackathon as a non-developer

Thanks for the feedback. Ended up in the finals and almost took the crown:)

omniscion Who killed the futurist in you? School or you?

Is there an option for "other people?" Speaking with people about the future is difficult when they don't really have a full perspective on what we've accomplished in recent history. If technology continues to move at the rate it's moving (which it won't, it will only move faster), we are in for some really cool shit in the future;) I can't wait to see what the future brings..but I do plan on putting my 2 cents in and making it kick ass.

omniscion How to Attend a Conference

This is a skill that should be taught to everyone. I'm in neuroscience, and our meetings can be super awkward at times. Thank god for booze :) It's a shame that people don't speak about this as much though. We have a huge conference every year (~36k people) and yet many of them have no idea how to deal with a conference. Just an FYI, flying in to give a talk/poster/presentation and then flying out does not = a good conference. Gotta meet people, be persistent, organize your plan of attack, and meet people. Then meet some more people. If you have a hard time not being social awkward, drink. Then meet people:)

omniscion Just 11% of 53 cancer research papers were reproducible

And that is the exact problem with certain researchers. I just had to explain this to my undergrad who's project resulted in negative results (his 1'st study). I congratulated him, as he discovered that the treatment he gave did NOT effect the genes he looked into. He didn't understand, so I had to explain that his study (with the correct controls), provided information that is useful to science. Negative data = data. Data = good :)

omniscion Just 11% of 53 cancer research papers were reproducible

http://news.sciencemag.org/scienceinsider/2013/05/nih-detail...

Already funded grants are getting cut ~20% across the board. There is a ton of cuts going on right now to the NIH budget, google it and take a look. This has been happening for years now, trying to get an RO1 (large research grant) is becoming more and more difficult and it isn't helped by the constant changing in requirements.

Every other point I agree 100% with, the culture change has to happen. Nothing is impossible, and it just takes the right people to make the right things to happen. Everyone recognizes the problem, I can't tell you how many times I hear people complaining about the same problems over and over. The problem is that they aren't taking action, and with no action, nothing is going to take place. While there are many efforts in place (my project being one of them, http://omnisci.org), they need to be implemented properly. The same rule of startups applies to science. The ideas/concept means nothing with proper execution.

While the culture change may be slow, the academic world is having a really hard time keeping up. NIH is also fighting to stay afloat. I have a few friends who work as program officers and they really have a negative outlook on the future of research funding.

omniscion Just 11% of 53 cancer research papers were reproducible

You don't have to do the entire experiment, you can just do a proof of principle and then build on it. For example, a lot of studies in science have 1 big idea, and they show it works using a variety of different methods. Pick 1 method, show consistencies, and then build on it.

One of the serious problems in science is that people state what you said above and will jump in feet first on a huge multi thousand $ study, but never spend the time to validate the model in their own lab. So you waste that money initially, then go back to figure out what went wrong. $$$$ being wasted. (The lack of negative data publications is also a massive problem that contributes to this)

What I'd like to see (and I'm currently working on) is raw data from labs. I do xyz experiment, publish it, and release all the raw images, excel files, raw data outputs etc. Now other scientists can go into those data, ask their questions and try to reproduce it or at lease provide a different perspective. This is what I'm working on at http://omnisci.org and I intend to bring to the scientific community. We need transparency, because this "behind the door" shit (peer review, grant reviews, only positive data etc) isn't working.

omniscion Just 11% of 53 cancer research papers were reproducible

After seeing how much of the research is done, I'd agree with this more.

This is a problem that is getting worse as funding is getting cut more, people feel they have a need to get a paper out, regardless of the results. You get positive results, make a story up about it, then run to publish it before trying to reproduce it or look further into the data. While this doesn't happen in every lab, I'm unhappy to say that I've seen this happen in many "high impact" labs.

omniscion Phdtree: create and discover your academic family history

I found myself, but some of the info was incorrect. I created an account and edited the record. I wasn't sure where the info came from, but I see it pulls from neurotree (which is also incorrect). Nice front end though, much nicer than neurotree :) Keep up the good work

omniscion Y Combinator results

3 views (I had 2 views last time and got rejected, so I'm not sure it matters too much)

omniscion Y Combinator results

because, they did:) Don't think too much into this. If you find out now, or in a few hours that you did/didn't get in, nothing is really going to change. (now, let me get back to refreshing my email every 5 seconds) :) best of luck to everyone!

omniscion Getting into a top graduate school

I'm going to add to this, your letters of recommendation are critically important. Furthermore, getting into grad school is the same thing as any other job. It's not about what you know, it is about WHO you know. People will get you into grad school IF they want you, and they only know if they want you, if they know you. Simple as that. Face time really matters, so if you want to get into grad school but don't have fantastic letters of rec for whatever reason, make an impression on some of the faculty at the school. Go to conferences and attempt to meet professors in the schools that you are interested in.

Also, as stated above, you can always move into a top their school later in the game. For example, I went to a state school for my undergrad and PhD, but I've since moved onto Cornell, Columbia and Rockefeller. The school matters at some level, but you can make stuff happen when you apply yourself. As with anything else, it's not trivial, but it's kind of a fun game:) Best of luck, Keith

omniscion Ask HN: What minor/major would compliment a CS degree?

This is actually quite simple,pick up a minor that interests you. If you like basket weaving, take a basket weaving minor, maybe you can disrupt the whole basket weaving industry in the future...who knows. What you take as a minor has little impact on your job later in life, unless it's something you really enjoy which will give you some direction to apply your CS degree.

omniscion Bioengineers turn mouse brains almost completely transparent

This is a perfect example of taking a simple idea and making it big:) We always clear our brain sections prior to imaging, it's a common practice, but doing this throughout the whole brain is...well...f'in awesome:) Looking forward to seeing how people use these tools.

omniscion Mendeley users revolt against Elsevier takeover

I think it's super awesome that you did all of that! Kudos to you, and I wish more people were doing stuff like that.

My viewpoints are limited to life sciences, where people have no idea what FTP means, let alone GIT. Also, what you did is not typical, people (at least in my field of neurobiology) have no intention of doing something like that in fear of being scooped. The antiquated idea behind publishing is the concept of doing an experiment, filtering out all the negative data, and then submitting their positive data to a journal that they think will publish their data. We've been waiting for 7 months now for a paper to get published in PNAS due to this antiquated process. 7 months to do what you did in a few minutes uploading your data online and making it public.

omniscion Mendeley users revolt against Elsevier takeover

This is exactly what I'm working on. Also, publications by federally funded grants are required to be made public as well (for 1 year). However, even doing that, you are still stuck behind the political pressures, journal bias, and the peer review system which...for a lack of a better term, sucks.

Science needs to be transparent and made available in real time. This is the whole purpose of science, to freely distribute knowledge for the well being of humanity. I honestly believe that and I'm working to bring that transparency to science as we speak.

omniscion Mendeley users revolt against Elsevier takeover

One of the many problems with academic publishing is that it's holding on to an antiquated idea behind publishing and not progressing with the way communications are moving now. In a sense, publications are moving at 1970s speed and this hurts science. Hence the technical need to bring it to current times.

Is it a "technical issue"? No, but neither is booking your flight via phone, that worked just fine. Could it be made much better, more accessible, cheaper, and overall better via technology. Yes.

omniscion Mendeley users revolt against Elsevier takeover

Yes, I actually do:) Me: Neuroscience PhD at Columbia w/ some a technical background but not a coder.I'm working on going up against academic publishing right now. I have a YC application that is currently being reviewed and I'm in need of a technical cofounder.

Project: Very briefly, I'm working on collecting raw data (positive AND negative), indexing it, and making relationships between datasets. For example, my neuroscience study has relationships to cancer biology, so the data presented to the user would include results from both.

Re: Publishing, I'm going to provide raw data to scientists and create a venue for them to "blog" about these datasets. I think science needs to move incrementally (at internet speed) and get away from taking 3 years to produce a study and publishing a big paper of only positive data. Also, I'd like for the "peer review" portion to be more transparent, so that we can avoid the insane bias that goes into peer review.

Goal 2: Create "big data" by combining small academic science results into a big ass database. Meta data could be the new preliminary data for academic grants.

So yeah, if anyone is interested in playing with this, let me know. klg2142 @t columbia.edu

omniscion Does Startup Life Have To Be A 24/7 Grind?

Thank you! I hear this all the time and it drives me nuts! "Omg, I'm sooooOoOooO busy.... I've been working (on my facebook profile) for 10 hours today :sadpandaface:"

I have no problem with posting cat videos to facebook, more power to you, but don't claim that you're busy when your not. My fav is the "I didn't have the time (enter any task here)" forgetting that the two of your are friends on facebook and you can see the 189321983729 icanhascheezburger photos that were shared during the "busy" time.

omniscion Thesis Hatement

Uhh, I may get hated on for this one and it doesn’t help that I just got out of a meeting with a bunch of academics, so I’m kind of annoyed right now, BUT, take note that I'm a PhD working in an academic environment.

[angry bold]Stop whining and start working. [/]

This article is one of the many articles, blogs, etc I’ve read from academics complaining that there are no jobs and how it's so hard, and OMG the hours are long, and why is this happening to me, and waaaaaaaaaa, I'm a victim. I literally have 2 of them talking about this right now across from me as I’m typing this. You know what they aren’t doing? Working (says the guy who is typing on hacker news:) ). Stop complaining and start being the best. Every academic that I have a lot of respect for was able to get a job. They are also the ones that work their asses off, networked, give talks, and play the game correctly. Being “smart” doesn’t get you a job, regurgitating papers isn’t what makes a good faculty member and thinking that you deserve a job because you have PhD does NOT quality for a job. Simple as that.

Yes, there are very few jobs and way to many PhDs. But, I’d bet that statistic would look much different if you looked at people who actually work smart ,play the game and have some business sense. When you have no business experience at all, and only have been through school with your parents paying your way , well..yeah, it’s an eye opening experience that working is hard. Deal with it, stop complaining and go work harder/better than anyone in your field or work at starbucks.

omniscion Stop working so hard

My boss (Academic scientist) told us that we had to work a 70-90 hour work week to be successful in this business. I found that funny as I don't count my productivity in hours work, but in the amount of "product" I produce. "Working hard" shouldn't be a function of time, and I think more people need to appreciate that. This tends to be a little more difficult for people to do however, as it typically requires a lot of hard work up front. For example, it took me a month to figure out how I could make a 45 minute procedure turn into a 7 minute procedure while still maintaining the same quality. But I got it working and I can do 6 times the amount of work in the same amount of time.My free time can now be spent doing other things, such as working on a startup:) People just don’t do this for some reason. Put the initial investment into what your working on, make it as efficient as possible, and then reap the benefits while being productive AND having enough time to post cat videos on facebook:)

omniscion Crowd-funding Preventive Treatment for Breast Cancer

I'd like to help with this process. I've been funded by both NIH and NSF and have been through the process. I've also reviewed grants as have my friends/colleagues. I emailed you a few days ago (irollboozers), so you have my email address.

As for incorporating the NIH scores, I'd actually like to see the opposite. It's funny how people think that the NIH/NSF scores are actually representative of a proper review. They really aren't. They are assigned by people, typically people who don't even really read the grant well because they have 20 to read and leave them to the last minute because they are doing 100 other things. As such, many times grants (actually, any of the peer review items) are not really evaluated properly. Any federal funded scientist who has been through the review process will tell you how faulted the system is.

This isn't the place to rant/rave about this, but I'm happy that we are starting to evolve this system and change it. My YC application will be working on something similar, with the goals of getting around the stupidity behind the current system. What we need is to revolutionize the way science is performed, from the ground up.

Also, in terms of the "snake oil" statement, when you dig deep enough, you see that the entire peer review system is not immune from snake oil. Buzz words get grants funded, papers published in high tier journals, and careers sky rocketing. Doesn't even have to be good work, it just needs to include the buzz word and its getting published like crazy.

The fact is, science is broken and it's a great time to fix it with the technology, transparency, and forward thinking groups that are breaking the mold.

omniscion Academia Is Eating Its Young

Wow, this is an interesting article and I agree with much of it. I've had my PhD for about 2 years now (neurobiology) and I agree that academia is eating..itself. The inefficiency, politics, hostility are some of the things, but much like any other governmental thing, it's just run poorly...and that trickles down to the PIs, students, departments etc. [edit] this got really long, I'm going to create a blog post on this instead and host it at another time [/edit]

Here is an example:I applied to a training grant (t32) that will pay my salary and help me through my PhD. It was not funded initially because my PI's funding was running out in a year. <angry bold>I was applying for funds to continue my education so my PI wouldn't have to pay me (so we could use that money for my research), but they wouldn't fund me because my PI was running out of funds...to fund me. </>

I resubmitted the exact same grant, with zero changes, but I included a letter staying that I'd be covered if my PI ran out of money. Then I got funded. Total time? 1 Year! It took a year for a paragraph to propagate through the granting agency, as I had to resubmit the grant again and wait 6 months to get a vague answer (priority score).

This is one of many examples I have that are consistent with the OPs article, the system is broken. And this is a wide spread problem that is going to require all of science to really make a change happen. I'm intending on doing so with my startup (just applied to YC) to bring transparency, efficiency, and opportunity to scientists. My goal is to bring the semantic web to academic science to start linking data sets between fields. Positive, negative and pilot data all available in one spot so I can run meta analysis on these data and create preliminary data for a grant or future studies. (there is more to it, but this isn't the place to plug my site)

What I'm most concerned about isn't the technology, it's the people using the technology. I recently got this comment, "Wow, that is a brilliant idea....but good luck getting scientists to use it." The dinosaurs are scared of change, and their fear(ignorance?) is by far the hardest thing I'm going up against. It's also one of the biggest problems we are going to have in science.

Still gotta try though:)

omniscion The illustrated guide to a Ph.D.

Sure, I'm working on a process to bring linked open data model to scientific raw data sets. While this has been done before, it hasn't been across related research fields. I'm looking to link environmental science with neurogenetics and everything in between.This will allow from the tiny "PhD" portion of the graph in the OP with the rest of the circle:)

omniscion The illustrated guide to a Ph.D.

My YC application is specifically to get around this issue. I've been in science for 8 years now and this article is absolutely correct. Our whole system isn't helping this process either. From funding agencies to the "peer review" system, scientists are almost forced into this situation. Also, we are so separated from one another (via specialized publications, jargon, lack of consistency between fields etc) that it's going to continue to happen until someone tries to break that system. That's my goal:) One of my major goals is to use technology to bring the larger perspective back into science so we can focus on our little parts, but continue to see the big picture.

omniscion Obama Seeking to Boost Study of Human Brain

It's clear that the software that we are using is not sufficient, and a lot of it seems to be a lack of quality control. I've been in science now for close to 10 years and the software that we use looks like it was built in 1995.

This is a serious problem with science software. The features are there (for the most part), but it seems clear that much of the software engineers are not working with the users. There is a severe lack of thought when it comes to UI and as such the learning curve is pretty steep.

With that said, my first YC application was to build software (web based) to tackle some of these issues. I'm actually looking for coders to help build this product, so if you have any interest in jumping into this field, send me an email (in profile). I intend on applying to YC this summer and would love to work with a few programmers to give this project a real shot.