I’m Back. Monday Links

The last few months have been incredibly busy (hopefully, results should start appearing in print over the next few months). I’ll start writing again now.

A few links on recent(ish) anti-science victories in Europe:

  1. Philae went all the way to a comet, then quickly died because Europeans are afraid of “radiation”. The Americans would still be getting data from that probe as it would be nuclear powered (using a very safe type of nuclear fuel).
  2. Another victory from a coalition of environmental groups, including Greenpeace: The European Commission scrapped the position of scientific advisor. The environmentalists called the position of science advisor corporate lobbying!

American bonus: Anti-GMO activists take vitamins out of breakfast cereal.

Why There Won’t Be a Windows 9

John Cook tells this wonderful story about Windows 10:

The version of Windows following 8.1 will be Windows 10, not Windows 9. Apparently this is because Microsoft knows that a lot of software naively looks at the first digit of the version number, concluding that it must be Windows 95 or Windows 98 if it starts with 9.

Many think this is stupid. They say that Microsoft should call the next version Windows 9, and if somebody’s dumb code breaks, it’s their own fault.

People who think that way aren’t billionaires.

Open source has generally been horrible about this type of thing, with the major exception of the Linux kernel, because Linus’ attitude is very different:

> Are you saying that pulseaudio is entering on some weird loop if the
> returned value is not -EINVAL? That seems a bug at pulseaudio.

[redacted]

It's a bug alright - in the kernel. How long have you been a
maintainer? And you *still* haven't learnt the first rule of kernel
maintenance?

If a change results in user programs breaking, it's a bug in the
kernel. We never EVER blame the user programs. How hard can this be to
understand?

Note the very different attitude of the glibc developers, who broke Flash Player for their users and said it was all Adobe’s fault. Technically, yes, Adobe was abusing the system a bit, but it takes a special level of nerdiness to say “well, I will just break people’s youtube because we are technically correct.”

(This is why we need managers: to tell geeks to cut that sort of shit out.)

When will BLAST get its Nobel Prize?

It’s Nobel Prize Season and there is inevitable speculation on who will get one. I have a negative prediction: The Prize will not be award to the creators of BLAST.

However, I think the creators of BLAST should get a Nobel Prize.

In terms of impact in the field, it’s undeniable that BLAST has been huge. These people created a verb! What modern biologist does not know what “blasting a sequence” means? The BLAST paper was, at one point, the most highly cited paper in history. The impact on physiology is undeniable.

Lipman and Gene Myers stand out for their contributions to the computational processing of biological sequences. (See how I phrased that in a Nobel Committee way).

I know, BLAST was built on previous work like FASTA; but (1) so is everything and (2) FASTA is also Lipman’s work so he can claim credit for that.

The other counterargument I’ve heard is that BLAST is mostly a method, but so was GFP (admittedly, a chemistry prize). One may argue that it was very cool that one could have a protein that fluoresced by itself, but the prize was awarded for the impact in the lab (does anybody believe that just the 1962 discovery of a jellyfish protein would have sufficed for a Nobel?)

The statistical and algorithmic ideas behind BLAST and other methods developed by these people are also very cool (the suffix array is one of those “how did it take so long for someone to think of this?” ideas) while solving a hard problem with a large number of applications.

§

Of course, this Prize would bring prestige to the whole field of computational and systems biology, which may seem very self-serving of me (my field gets a prize, so I get to bask in the glow).

On the other hand, I have often heard that systems biology is just physiology with computers. By this definition, eventually, a systems biology prize will have to be awarded or the prize renamed to “Noncomputational Physiology and Medicine”, which sounds weird.

BLAST was definitely one of the most largest advances in the field of physiology in the last few decades. For this reason, David Lipman and Gene Myers should get a Physiology and Medicine Nobel Prize.

SOFTWARE CARPENTRY WORKSHOP @ EMBL

What: A course for life scientists who do data analysis
Where: EMBL (Heidelberg, Germany)
When: 12-14 November 2014
Apply by: 26 September 2014

This course is open to researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will know a little bit of data analysis, but not consider himself an expert. For example, the student might have already written a for loop in some language before or plotted their data, but will not know what git is (or at least not be very comfortable with advanced git usage).

TOPICS

  • Introduction to Python scripting
  • Introduction to the Unix shell and usage of cluster resources
  • Version control with git and github
  • Unit testing

More information:
http://www.embl.de/training/events/2014/SWC14-01/
http://software-carpentry.org/

Tuesday Links

Posting today from the lovely KU Leuven campus (yes, this link points to the actual building where I’m sitting in now!).

  1. From Megan McArdle on why very invasive surgery works better than less invasive surgery:

    Patients may prefer percutaneous coronary intervention — also known as angioplasty — to a coronary bypass because it doesn’t involve cracking your chest open and grafting things onto your heart. But bypass patients seem to have better long-term outcomes, even though both methods increase blood flow to the heart muscle. […]

    A new working paper from the National Bureau of Economic Research suggests a possible answer: Bypass works better precisely because it’s more invasive. The very scale of the treatment makes people more likely to change their post-operative behavior in ways that enhance their long-term chances of survival

The original paper states that

We find that CABG patients are 12 percentage points more likely to quit smoking in the one-year period immediately surrounding their procedure than PCI patients, a result that is robust to numerous alternative specifications

  1. I have in the past criticized nutricional sciences, but this is excellent scientific behaviour

    In one of the best examples of science working, a researcher who provided key evidence of (non-celiac disease) gluten sensitivity recently published follow-up papers that show the opposite.

    […]

    For a follow-up paper, 37 self-identified gluten-sensitive patients were tested […]

    The subjects cycled through high-gluten, low-gluten, and no-gluten (placebo) diets, without knowing which diet plan they were on at any given time. In the end, all of the treatment diets — even the placebo diet — caused pain, bloating, nausea, and gas to a similar degree. It didn’t matter if the diet contained gluten.

One of the most insidious things about some of the health fads is that because of psychological effects, they do “work.”

3. Python San Sebastian will have a keynote talk & tutorial by your truly (it’s not up on the website yet, but it will be).

 

Auto text

This is what I got from running the text predictor on my phone (which has been, at least partially, trained on my texting/email writing):

I am having trouble getting tickets online now from our large stock inventory of the meal and a half years ago and I will be at the moment and I will be at the moment and I will be at the moment and I will be at the moment and I will be at the moment and…

Then it goes into an infinite loop.