alexholehouse

The following week will be; "Oral Treatment Targeting the Unfolded Protein Response Prevents Neurodegeneration and Clinical Disease in Prion-Infected Mice" Moreno et al (Sci Transl Med 9 October 2013: Vol. 5, Issue 206, p. 206ra138

And after that something from Don Cleverland (UCSF)'s lab, as I saw him speak not that long ago and he blew my mind.

That being said, I'd also (probably) take requests!

For the next 52 weeks, I'm gonna try to write a layman's explanation (with some amount of appropriate background) about a paper every week. I suspect these will center around my work, but I also suspect the act of thinking about the kind of stuff I do in a more general sense will be a valuable learning experience, and who knows, maybe someone else will learn something too!

These are the kinds of things which aren't measured when graduate programs are evaluated, but are super important for people who don't plan to plough into academia, and maybe even more so for those who do!

There's a definitely a lot of opportunity to get non academic career path advice and experience here. A grad student in my lab did a couple of internships at Google during his PhD, which clearly is not something every program/supervisor would be cool with.

According to wikipedia (which is in line with how I think about big data) "Big data is the term for a collection of data sets so large and complex that it becomes difficult to process using on-hand database management tools or traditional data processing applications. "

However, as "big data" becomes more mainstream and more tools/services exist to accommodate data at the peta/exobyte scale does that whole definition stop being relevant for kinds of data we're talking about?

Is this based on any kind of information, or just supposition stemming from the problems Boeing had (where, IIRC, Tesla offered to provide engineering assistance).

I use Evernote, but even there often the bullet points get out of sync and you have to manually realign everything. Evernote is fantastic, but there are certain things I don't understand why it lacks (LaTeX support and superscript/subscript would be another).

Often in medicine edge cases provide insight into a more general mechanism or process (e.g. Li Fraumeni and p53/cancer, retinoblastoma and Rb). Part of my work is considering the idea that prion diseases may be very pure examples of a more general process observed in a huge range of neurological diseases, from ALS to Alzheimers to Huntington's to Parkinsons.

While there is some fantastic work going on at the clinical/in vitro side, I hope that a more general understanding of the physical processes governing phenotype will help provide a broader class of treatments.

WRT Eric and Sonia's passion for the research - I've done research in a range of areas, and I've never found a puzzle as fascinating and as engaging as this. I keeps me up at night. I go through flashes of theories and ideas that I have notebooks full with possible hypotheses and associated experiments. The putative overlap in related and unrelated areas of research, from oxidative damage to epigenetic regulation to arguments relating to 3D diffusion within the cellular environment, is extensive and both a source of inspiration and trepidation. Basically, I can entirely relate to that constant feeling of engagement and interest. My work has accidentally become my hobby, and it's awesome.

I believe that the technical term here would be "dick move".

I'm also acutely aware that while staying in academia would be great (despite all the bad things like crazy hours, crazy people, etc.) there is simply a very good chance it's not going to be possible, or if it is it'll be crazy competitive.

The litmus test I always think about is a colleague [postdoc] I worked with years ago. He was disgustingly smart and capable, and applied for over 100 tenure track positions before getting one. He also had an educational pedigree and publication record most of us can only dream of, and was a great guy to boot. If it takes someone like that 100+ applications what chance do the rest of us have!?

Because of this, I've taken on the rather larger responsibility of running the labs computing resources, both hardware/software. It's a lot of work (I'd estimate I spend maybe 20 hours a week doing sysadmin related tasks) but it does also give me a totally inappropriate level of responsibility which I hope will be valuable either inside academia, or in industry. I also really enjoy it, which is a nice bonus.

With it hitting NPR, I suspect this has irreversibly damaged his professional reputation.

I don't mean this is a nasty way, but with a single page which basically says, "can I access your data please?" and no explanation I can't understand who would upvote it?

I've been toying with ideas relating to some kind of text-book killing general publishing platform for a while, but it's not something I'll implement (in the next 5 years anyway). Obviously people are doing this kind of thing already, but this is certainly the closest implementation to the ideas I've been thinking about that I've seen.

Comments which describe the code are much less useful than a commentary regarding the code's objectives, in my opinion.

That said, Outlook 365 is also bloody awful in terms of usability. Say I've sent an email to a list of people, there's no way (as far as I can tell, which is all that matters really) to then copy those email addresses. You have to literally click through each one and get the address individually.

[1] https://news.ycombinator.com/item?id=5908075

I want to agree with you, but how do you know that (I'm making the assumption here that you're not a lawyer, which may be incorrect)? This seems like the main issue - we (as in the common, non lawyery-types) don't necessarily know what things may or may not be incriminating. I'm not trying to instill a sense of fear, and I would always cooperate with law enforcement to the best of my abilities, but not at the risk of doing or saying something which could subsequently implicate me in something which is technically illegal and could get me arrested, convicted or deported.

If the FBI came to my house to ask questions and I said, "Friends, I'd rather not speak with you without a lawyer present - you know how it is", how do I go about getting said lawyer without going bankrupt?

This. A thousand times this.

I'm not talking about technical language - there are often (if not constantly) times when technical language is required to convey a precise meaning within the context of a paper. All I'm talking about here is the use of complexity where it's not required. It's a comment on the quality of writing.

> I'm a PhD student, and never have I read a paper with wording that I would describe as "convoluted."

What field are you in, because I wonder if this makes a difference? I'm in a highly interdisciplinary field, so perhaps that's part of the problem.

Clearly, this is not always the case, and obviously complexity doesn't lend itself to nice 10 word summaries (hat-tip to Jed Bartlet), but equally the choice of language used and the pace of arguments can make a huge difference. There is no need to use "big" words, when simple ones will do just fine. There is no need to use technical language in place of standard vocabulary where it adds nothing to further your ideas. Don't "hit the ground running" but introduce a new idea with an analogy, or a toy example.

Write papers so humans can understand them - often the science being portrayed is complicated enough, there's no need to further complicate your ideas to the point where you leave English speaking audiences trying to decipher the message, let alone what foreign readers must think.

The best papers are the papers you can read abstract-to-conclusion without stopping and asking yourself, "What does that mean?". This is all too rare an occurrence for me. /rant

1) Much more challenging exams

2) The realization that "getting everything right" is not really how any part of the real world works.