cwhittle's comments

cwhittle | 4 years ago | on: I bought those AR cycling glasses that were on HN last month

Very cool. I can't wait for a more generic data device pairings to these interfaces. I would love them for paragliding, where we have a variometer to track metrics that impact decision making (ascent/descent rate, air/ground speed, altitude, etc) and weight/deck space are a big factor.

cwhittle | 4 years ago | on: How to Work Hard

Someone needs to write a compelling article on "Why to work hard". Just because you should isn't a good enough.

cwhittle | 6 years ago | on: California power outage triggers chaos in science labs

All of these big research universities in CA are on major and active fault lines. My old lab at Cal sat mere hundreds of feet from the Hayward fault that runs through campus. This is a proactive power shutdown when you know it's coming. If they can't an event with advanced warning, what will happen to hundreds of millions of dollars of frozen samples and research instruments when the unexpected earthquake hits any of these universities, not only disrupting power, but also disrupting structures? Incredibly foolish not to have at least reliable power backups and containments irrespective of what PGE is doing.

cwhittle | 12 years ago | on: US intelligence mining data from 9 US Internet companies in broad secret program

I think we all hoped it wouldn't happen but knew it would.

cwhittle | 13 years ago | on: Instacart expands its grocery delivery service to Oakland and Berkeley

Try Monterey Market for produce. Really good quality and generally less expensive than Berkeley Bowl, especially for seasonal stuff. But only buy produce.

cwhittle | 13 years ago | on: Ask HN: Are there any children's websites that teach coding or coding concepts?

Depends on whether she has an innate interest or whether you're trying to spark interest, but I think this is the best/most fun way to start any kid with the basics: http://drtechniko.com/2012/04/09/how-to-train-your-robot/

My six year old just started with Blockly, which is similar to Scratch:

http://blockly-demo.appspot.com/static/apps/turtle/en.html

But we're going to try http://kidsruby.com/ as soon as he's got enough written language under his belt. Probably will work great for a 5th grader though.

cwhittle | 13 years ago | on: Genomics: ENCODE explained

This is the basic science that pays off in the long run. You can't just turn biomedical science projects on and off. It takes time and investment to develop the techniques and technologies to do this work, to gather the samples, and ensure data quality across the project labs. During the time that the ENCODE project was funded, the technology for doing the types of experiments to get this kind of data advanced many times. We are now talking realistically about personal genomics and the $1000 genome; at the project start we were still celebrating the 3-billion-dollar genome sequence.

cwhittle | 13 years ago | on: Genomics: ENCODE explained

Most of the people interviewed in that video are program officers/administrators at the NHGRI (an institute of the NIH) who oversaw the ENCODE project. They weren't researchers who did the work. The mission of the NIH is human health, so anything funded by them has to have a biomedical implication somewhere down the line.

I guarantee that the real impetus for the project in the researchers' eyes is to understand how an identical* instruction manual (ie., genome sequence) in every cell can give rise to a plethora of cells that do very different things to make a functioning dynamic human. In other words, for the most part, it appears that there's the sequence information and then there's how you use it. ENCODE (and modENCODE) are about how you use it.

fyi: I'm a researcher in the modENCODE consortium, a sister project to ENCODE, aimed at characterizing functional regions of DNA in two model organisms, a small worm and the fly. My PhD advisor was funded by ENCODE as well. I obviously find this stuff fascinating and important.

cwhittle | 13 years ago | on: Why women (or men) still can't have it all

I think that she was referring to the idea that, while many aspects of parenting can (and perhaps should) be equalized between the parents, the fact is that current culture places child-related responsibilities more heavily on the mother than the father.

This is to the detriment of fathers as well, because a father who wants to shoulder the responsibilities of raising a child, will also be assumed to have a partner who takes primary care of that.

cwhittle | 13 years ago | on: Lack of sleep increases stroke risk

http://www.regardsstudy.org/

Doesn't appear to be published yet, just presented at the SLEEP2012 conference.

Ruiter M, Howard VJ, Letter AJ, Kleindorfer D. Short sleep predicts stroke symptoms in persons of normal weight. SLEEP 2012; June 11, 2012; Boston, MA. Abstract 0829.

cwhittle | 14 years ago | on: Bored in grad school? Learn Hadoop

While learning Hadoop is a good idea, if you're bored in grad school, you're doing it wrong.

cwhittle | 14 years ago | on: Ask HN: What skills should we teach our kids to prepare them for the future?

self-determination (maybe this falls under your excluded values, character traits, or philosophies), but its a rather important skill in my opinion.

a second language - doesn't matter which one really, but it has clear cognitive and practical benefits. Bonus points for spending time in another culture for a different perspective.

edited to add: Really many of these skills can be learned as needed, but the desire and skills to learn new things are an important skill to have. If you're successful in teaching them the fundamental ones, like critical thinking, then they have the tools to learn what's needed.

cwhittle | 14 years ago | on: Lots of new Coursera classes throughout 2012 posted

The new courses are great, but there's something I don't understand about these course websites. I'm doing probabilistic graphical models, but I just want the content to learn, and I don't really care much about some certificate. I also don't have a lot of time this particular month. I'm guessing that this is true for the majority of people taking the course (I'd be interested to see how many people who signed up actually kept up). What is the point in making time limited offerings for an online, recorded course?

cwhittle | 14 years ago | on: If you want reproducible science, the software needs to be open source

Speaking as a scientist who deals with genomic data, I wholeheartedly agree with many of the comments here. Code and raw data should be available at publication. I shouldn't have to try and figure out what you did from the three lines of text and poorly documented software you mention (that has been updated several times since you used it (no mention of version). Personally, I think pseudo-code would be most useful for reproducibility and for illustrating exactly what your program does.

Let me add to a few points here about the practical obstacles to this.

1) Journals don't support this data (raw data or software).

* You can barely include the directly relevant data in your paper let alone anything additional you might have done. Methods are fairly restricted and there is no format for supplemental data/methods. Unless your paper is about a tool, then they don't want the details, they just want benchmarks. Yes, you can put it on your website, but websites change; there are so many broken links to data/software in even relatively new articles.

* As many people have said, lots of scientific processing is one-off type scripting. I need this value or format or transform, so I write a script to get that.

2) Science turns over fast or faster than the lifetimes of most development projects.

* A postdoc or grad student wrote something to deal with their dataset at the time. Both the person and the data have since moved on. The sequencing data has become higher resolution or changed chemistry and output, so its all obsolete. The publication timeline of the linked article illustrates this. For an just an editorial article it took 8 1/2 months from submission to publication. Now add the time it took to handle the data and write the paper prior to that and you're several years back. The languages and libraries that were used have all been through multiple updates and your program only works with Python 2.6 with some library that is no longer maintained. Even data repositories such as GEO (http://www.ncbi.nlm.nih.gov/geo/) are constantly playing catch-up for the newest datatypes. Even their required descriptions for methodology for data-processing are lacking.

3) Many scientists (and their journals and funding institutions, which drive most changes) don't respect the time or resources it takes to be better coders and release that data/code in a digestible format.

* Why should I make my little program accept dynamic input or properly version with commentary if that work is just seen as a means to an end rather than as an integral part of the conclusions drawn. The current model of science encourages these problems. This last point might be specific to the biology-CS gap.

cwhittle | 15 years ago | on: Ask HN: Why aren't scientific journals free on the web?

Many of these suggestions are being attempted in journals like PLoS One (plosone.org) or through groups like Faculty of 1000 (http://f1000.com/) for commenting/discussion. Many journals now have comment fields on their articles, and you'll notice that most of them go empty. All the discussion happens behind closed doors before publication in anonymous peer review. Nobody wants to stake their reputation on something not polished.

edit: I partially take-back my suggestion of Faculty of 1000. Apparently, they are not open to unaffiliated and require a subscription. I like what they're doing, but it shouldn't be so ivory-toweresque.

cwhittle | 15 years ago | on: Ask HN: Why aren't scientific journals free on the web?

At least for the NIH, they now allow publication costs to be funded in grant applications. Also, many institutions have now set up funds to help offset the open access publication charges.

cwhittle | 15 years ago | on: Ask HN: Why aren't scientific journals free on the web?

For Biomed articles, Pubmed (pubmed.gov) offers free access to articles over a year old as of 2008, and sometimes sooner. Also, I often find it handy to google the full article name or the author, as many times authors may have posted a copy on their webpages.

Some are (PLoS (http://www.plos.org), BioMed Central (http://www.biomedcentral.com/), many small highly specialized journals), but overall many publishers still are similar to magazines.

A few things you may not be aware of in science publishing (at least for my area, biomed):

-The journals argued main role is to peer review research and distribute it. To do so, they engage researchers to act as peer reviewers, who take uncompensated time to do so.

- Journal articles are often noted as "advertisements" because the authors must actually pay for their publication, usually a 1-3K or so. Additional charges for color figures and such. This is not limited to non-profit journals. Some journals have an immediate open access option, which for a higher publication fee, your article can be fully publicly available as soon as its published. Also, NIH grants now allow for some request for publication fees and some universities have programs to aid a research in paying the additional costs of publishing open access immediately.

- With many journals, you must give up your copyright to the material to the journal. So, if you'd like to use a figure you made of your data in another context (grant application, review publication, dissertation, website, book, etc) you have to seek approval from the journal.

- More recently (2008), if you get funding from the NIH, you must deposit a copy of your publication into PubMed Central (http://www.ncbi.nlm.nih.gov/pubmed/) within 12 months of publication. Now, 12 months is a ridiculous amount of time in science really, but at least it's progress.

By the way, although universities generally provide "free" access to many journals, they also pay ridiculous amounts of money to offer access to those journals that are not open access.

Science publishing (at least, biomed) is currently going through the same growing pains in the digital era that many paper-based businesses are going through (newspapers, magazines). Their main business is two-fold really, 1) disseminating research and 2) peer-reviewing research. The internet make #1 largely obsolete. They now act primarily as a filter for "interestingness" and as a prestige-meter. There are many arguments that the current model for #2 is highly outdated, but the funding agencies (eg., government) and scientists as whole are generally a pretty conservative crowd that is resistant to change.