January 2012
3 posts
A new blog format
It’s 2012, and that means it’s time for another blog format change!
I’ve decided in more recent times to start eschewing cloud services in favor
of remote solutions more directly under my control. Moving this blog to a
new format and off of
Tumblr, is one small step. (The occasional server
problems at Tumblr and my need to tinker with things served to catalyze
this particular...
Carolyn Maloney parroting Elsevier lines →
Michael Eisen shows that Rep. Carolyn Maloney has entire sentences and phrases identical to blog comments written by an Elsevier VP for Global Corporate Relations:
The comments on my blog were clearly Reller – his writing was natural and engaged directly with what other people were saying, so I’m sure he wasn’t just spouting prepared text. There are only two viable explanations for how...
Pre-rigor to Rigor to Post-Rigor
I just read this blog post by Terrence Tao, in which he talks about the three stages of mathematical education — pre-rigor, rigor, and post-rigor:
It is of course vitally important that you know how to think rigorously, as this gives you the discipline to avoid many common errors and purge many misconceptions. Unfortunately, this has the unintended consequence that “fuzzier” or...
December 2011
15 posts
How we think
My mother-in-law was driving our family back from a day trip to Joshua Tree National Park (awesome, by the way, and the night sky view there is spec-tac-ular), when suddenly we heard a “thup-thup-thupping” sound coming from beneath the car. My mother-in-law had blown two tires in the past few months, so her first thought was “oh no, is the tire flat again?”
But wait,...
Reminder: Tis the Season Not to Be an Ass –... →
I dislike militant Christians and atheists alike, and John Scalzi says what I think:
But — but — what about all those horrible atheists taking over holiday displays with crucified Santa skeletons? Surely that’s evidence of a war! Well, no, it’s evidence of some non-believers taking a page out of the PETA playbook, i.e., being dicks to get attention and to make a point. I do strongly suspect...
PSA: Stop everything and go watch →
The trailer for Peter Jackson’s The Hobbit is out on Apple’s site.
Science museums for adults →
The Nature Research Center sounds like a pretty neat idea, part presentation space and part lab science space:
At regular intervals during the day, scientists will present to NRC
visitors using the cutting edge technology and media of the SECU
Daily Planet and its 40×40-foot, high-definition screen.
….
The NRC features research labs where scientists from the Museum,
UNC...
Users Know: STFU About What Women Want →
A good response to the really strange blog post by Penelope Trunk:
When a publication like TechCrunch spews some
nonsense about what women want, it means that the
next time I go into an interview with a male founder
(and they are overwhelmingly male for some reason
that I’m not going to address here, but that Penelope
assures us has nothing to do with bias) who has read
that...
Low Expectations →
Matt Gemmell:
The keyboard, touchpad and screen are the computer, in
terms of what you’re directly interacting with. So every part
you’re going to interface with is notably substandard. Right.
You’d assume that the final rating would duly castigate the
manufacturer, but it’s actually 7.8 (presumably out of ten).
Kind of sad, really.
Selective use of technology — The Endeavour →
In his book The Nine, Jeffrey Toobin gives a few details of
Supreme Court Justice David Souter’s decidedly low-tech
life. Souter has no cell phone or voice mail. He does not
use email. He was given a television once but never turned
it on. He moves his chair around his office throughout the
day so he can read by natural light. Toobin says Souter
lives something like an eighteenth...
Oblivious Supreme Court poised to legalize medical... →
This is crazy:
The case focuses on a patent that covers the concept of adjusting the dosage
of a drug, thiopurine, based on the concentration of a particular chemical
(called a metabolite) in the patient’s blood. The patent does not cover the drug
itself—that patent expired years ago—nor does it cover any specific machine or
procedure for measuring the metabolite level. Rather,...
Five Sci-Fi Children's Books That Should be... →
These ideas are amazing and spot-on, and the cover art is well done.
The Innumeracy of Educators, or Mark Twain Was... →
Chad Orzel has some examples of the types of math questions that Orange County school board member Rick Roach couldn’t answer on a standardized test. It’s crazy how simple those questions are, and that Rick Roach couldn’t get any of them correct without guessing is embarrassing.
Writes Chad:
This is yet another demonstration of a problem I’ve been banging on about for...
Don't be a Free User →
A nice rant against free web services. I particularly like the distinction he makes between free software and free web services:
I love free software and could not have built my site without it. But free web services are not like free software. If your free software project suddenly gets popular, you gain resources: testers, developers and people willing to pitch in. If your free website takes...
Evolution always wins. Always. →
If you don’t pay your respects to natural selection and the population biologists that study it, you’ll get burned:
So a scientific advisory panel urged the Environmental Protection Agency to strengthen the second line of defense against resistance, and demand large refuges on non-Bt corn. They proposed that farmers be allowed to plant Bt corn with this new gene on no more than...
The Reason Android is Laggy →
I am not an Android developer, so I have no way to verify what this guy is saying. That said, it does sound quite plausible:
It’s not GC pauses. It’s not because Android runs bytecode and iOS
runs native code. It’s because on iOS all UI rendering occurs in a
dedicated UI thread with real-time priority. On the other hand, Android
follows the traditional PC model of rendering occurring on...
Introducing Evernote Clearly: One Click for... →
Looks like Instapaper and Readability are getting even more competition.
(via sophiashares)
November 2011
2 posts
Patient sues dentist over gag order, gets Medical... →
a.k.a. scoundrels get their just deserts:
The filing is a class-action lawsuit, representing Lee and all other Makhnevich patients who have signed Medical Justice-style contracts. It asks the court to declare that forcing patients to sign the contract constitutes a breach of “fiduiary duty and violations of dental ethics.” It also argues that the contract deceives patients by...
Science Experiments for Unimpressed Kids: Surface... →
Awesome:
How to Demonstrate Surface Tension
This easy and fun experiment will be sure to captivate absolutely no one.
via Uncertain Principles.
October 2011
2 posts
More evidence for diseases of protein misfolding →
Scientists are coming to realize that prions or some other sort of misaggregation of proteins may be responsible for more diseases than we thought. Derek Lowe writes:
The authors injected material from human Alzheimer’s patients into the brains
of normal mice, and saw what appears to be the induction of amyloid pathlology.
This didn’t happen in control animals, got worse with...
Stephen Wolfram on Steven Jobs →
Steven P. Jobs, may he rest in peace.
Stephen Wolfram reflects on Steve Jobs’ influence on the development of Mathematica, including the name. Mathematica was bundled on all NeXT computers at the debut, apparently. And this interesting aside:
And as a curious footnote to history (which I learned years later),
one batch of NeXTs bought for the purpose of running Mathematica
went to...
September 2011
1 post
Andy Grove's Idea For Opening Up Clinical Trials →
A good discussion from In the Pipeline about Andy Grove’s proposal for changing how drug development works:
Once safety is proven, patients could access the medicine in question
through qualified physicians. Patients’ responses to a drug would be
stored in a database, along with their medical histories. Patient identity
would be protected by biometric identifiers, and the...
August 2011
4 posts
Bodycount is out now, it's $60, and it's terrible →
I love Ars Technica’s gaming editor Ben Kuchera:
I did not make it far in this game, because one day I will die,
and I refuse to go out thinking I spent one second more than
I had to playing Bodycount.
Doctor Who Definitions, part 203
Wib•bly wob•bly, tim•ey wim•ey
[wib-lee wob-lee tahy-mee wahy-mee]
Indicating resolution of temporal paradoxes with circular logic or causal chains.
Deus ex Moffata.
Comics for Beginners →
Ben Tseng made an excellent list of comics for people just looking to start out.
As I’ve made [no] secret of my love for comic books, a friend of mine who has been enjoying the latest string of comic book movies asked if I had any recommendations for comics/trade paperbacks that a “comic newbie” (i.e. someone who doesn’t know the billion years of backstory that have accumulated over time in...
Pigs Return to Earth: Federal Circuit Reinstates... →
A good summary of the recent Federal Circuit decision on Myriad’s BRCA gene patents.
The Federal Circuit’s long-awaited decision (pdf) in Association for Molecular Pathology v. USPTO (the Myriad gene patent litigation) was issued this past Friday. As we were writing, with the economy having slowed to a barely perceptible crawl and a government default looming more likely by the hour,...
April 2011
1 post
Gauss Facts →
Chuck Norris has nothing on Gauss. “Gauss has an Erdos number of -1.”
Found via Uncertain Principles.
January 2011
1 post
Ars Technica feels Google's stance on H.264 is... →
Peter Bright writes:
If openness is so important that Google is willing to remove features from Chrome, there is no way that the company should be shipping Flash in Chrome.
Other features, too, should be culled. Chrome (currently) supports MP3 and AAC audio when used with HTML5’s <audio> tag. Both of these compression algorithms are patent-encumbered, and neither is...
Is long term solitary confinement torture? →
Atul Gawande says yes, and his argument is pretty convincing.
November 2010
4 posts
Amazon Wins →
Well, it looks like Amazon played hardball with Diapers.com and won.
An Introduction to Modern Chemistry: Experimental... →
This is a pretty awesome text, courtesy of the Google Books project. Hofmann was one of the early great titans of organic chemistry in the 19th century, and this set of lectures is a terrific snapshot of the field of chemistry at one of the most interesting points in its history.
This was published only a few decades after John Dalton hypothesized that atoms existed, but decades before the ideas...
The Burger Lab: Revisiting the Myth of The 12-Year... →
Two conclusions:
Controls are crucial to good science.
Kenji Lopez-Alt is consistently one of the best food writers I’ve seen. See also his articles on making perfect french-fries and replicating In-n-Out burgers.
(h/t Bill Jusino)
Quintiles’ Dennis Gillings Profiled in Forbes →
Quintiles, a clinical research organization (i.e. a for-profit company that runs clinical trials/analysis, ostensibly as an impartial, independent entity), has started to invest in drug development themselves. David Kroll points out that there’s an troubling conflict of interest there, but I’d say that this isn’t a new problem, since we’ve always been scrutinizing trials...
October 2010
1 post
Firefighters allow a man's house to burn because... →
The firefighters (from another jurisdiction) stood by and allowed a house to burn because the man hadn’t paid a $75 annual firefighting fee. There was no local (and hence tax-funded) firefighting unit. This is bad, because the firefighters weren’t doing their job.
I think the homeowner was completely irresponsible; what’s $75 a year for fire protection? Far less than his...
August 2010
1 post
Dr James L. Sherley et al. v. Kathleen Sebelius et... →
Judge Royce Lamberth writes:
This prohibition encompasses all “research in which” an embryo is destroyed, not just the “piece of research” in which the embryo is destroyed. Had Congress intended to limit the Dickey- Wicker to only those discrete acts that result in the destruction of an embryo, like the derivation of ESCs, or to research on the embryo itself, Congress could have written the...
May 2010
4 posts
An Apple ][+ music video →
Cute ASCII art.
Square-ing money →
I love Square’s product concept and their design. The marketing material starring Adam Lisagor, of course, is also pure delight. Here’s a great quote from their CEO:
Paying someone is just another form of communication, an exchange of value
that deserves to have the same design and product considerations that every
social service prides itself on maintaining.
What a wonderful...
A Dicer-Independent miRNA Biogenesis Pathway →
Yet another twist to the microRNA story. We still have a long way to go before we understand how microRNAs are formed and how they work. RNA biology is a wide-open field of research right now.
Lunch with a Michelin guide inspector →
John Colapinto dines with and interviews the mysterious inspector “M”, who works for the historically very secretive Michelin guide. One bit of the interview really troubled me, in which they discuss reasons for denying a restaurant a third star:
“But it wasn’t there.”
“In terms of consistency?” I asked.
“Consistency—and accuracy,” she said. “It’s just technical. I mean,...
April 2010
4 posts
Nature News article on the growing problems of... →
Plasticizers from plastic containers leeching into the contents isn’t just a problem for foods.
Lately, people around me have started to switch from spectrophotometric-based instruments to fluorescence-based DNA and RNA quantification. Fluorometry tend to be more specific–it doesn’t suffer as much from non-specific contamination–and its also more sensitive–fluorescence is often...
A bug hunt →
Daniel Jalkut writes a short, great story about one bug in one of his programs. Every programmer has probably experienced both the frustration as well as the satisfaction of finding and squashing such a subtle bug.
The best iPad review so far →
The battery lasts long enough to escape worry.
I don’t need stats or numbers, because I don’t have a reference point to judge those numbers, like I do with a computer. Instead, I need insights like this, things that actually help me figure out how it will fit into my life:
I stay up until 4am the night before the first day it’s on sale, searching for iPad specific apps. I find...
Well, are plants like humans or not?
According to this research highlight in Nature Reviews Genetics, no: “Complex traits: Plants are not humans.” Ok, thanks, that title enlightens so much.
Then there is this pretty neat paper, called “Systematic discovery of nonobvious human disease models through orthologous phenotypes”. The abstract’s own words are intruiging:
Our method suggests a yeast model for...
Pogue's take on the iPad →
His conclusion: it’s slick, like a 9.7 inch pane of glass.
Genomics Law Report summarizes the Myriad decision →
The more I think about the Myriad decision, the less I like it. I agree with the decision itself (i.e the holding), but not the logic. A key section from Genomics Law Report:
In his search for “markedly different characteristics,” Judge Sweet focused—and this is the most radical part of the opinion—on the critical functional property of a gene, whether in the body or in isolation: its ability to...
March 2010
4 posts
Genome-wide siRNA timelapse screen for mitosis →
Pretty amazing set of data. This is a whole-genome-wide siRNA screen in HeLa cells for genes essential for mitosis, but with a twist: each siRNA’s effects on mitosis was monitored by timelapse microscopy, and you can watch any one you want! (via @dgmacarthur)
Myriad's BRCA1/2 diagnostic patents are down for... →
On a gut level, I agree with the direction of the decision, but the finer legal parsing for this patent ruling might not hold up on appeal. The essential problem at stake in this ruling is how to interpret the patentability criteria to allow for patenting things like natural product drugs without allowing for patents on simple restriction fragments or PCR products of DNA and DNA sequences.
...
November 2009
1 post
Looking at the (microRNA) Stars
Several papers this week on the mechanisms of loading microRNA star sequences (miR*) into RISC complexes, two of them back-to-back in Molecular Cell:
Kawamata et al. (2009) Nat Struct Mol Biol 15(9), 953-60.
Okamura et al. (2009) Mol Cell 36(3), 431-44.
Czech et al. (2009) Mol Cell 36(3), 445-56.