Higher Order Aberrations

Because the world is an interesting place.

s-c-i-guy asked: In Rosalind Franklin's crystallography experiment, how did the DNA strand not get destroyed by the high energy X-rays used?

jtotheizzoe:

I worked with crystallographers for like seven years, and I’m still convinced it’s 95% magic.

In x-ray crystallography experiments, you don’t shine the x-ray beam on one single DNA strand, or protein, or whatever it is you’re looking at. One DNA strand would certainly be obliterated by the beam, but not necessarily the crystal (although, often, the x-ray does annihilate your sample. That’s why you need more than one, which makes it even harder).

Instead of a single molecule, it’s a solid crystal, precipitated out of a complex solution of sometimes more than a dozen chemicals, with each crystal made of bajillions and bajillions of individual molecules arranged in an organized lattice. Different crystal structures, whether they are cubes, or tetrahedrons, or hexagonal pyramidal pentaglobs, will act differently in the beam. You don’t know in advance what you’re gonna get.

The protein crystals we used to look at back in my Ph.D. lab looked a lot like this:

image

Actually, if we’re being honest, they usually didn’t look like that. This is the sort of crystal you dream of. Most things aren’t quite this tidy when they crystallize.

When the x-ray beam is directed at the crystal, it diffracts (bounces off of) any atoms in its way. But x-rays have super-short wavelengths, and molecules are mostly empty space, so only a small fraction of the x-ray waves encounter an atom to bounce off of.

image

It’s the sum of ALL the rare bouncing events, in the entire crystal, organized into its repeating, ordered structure, that creates the x-ray dot pattern. Then the real fun begins, which as any x-ray crystallographer (and I am not one) will tell you, involves lots of math, and a fair bit of magic.

Oh, man. I spent some time as an undergrad trying to crystallize rhodopsin (before I discovered that people had been trying unsuccessfully for decades) and doing SEM measurements. What a nightmarish slog. I would have dreamed of a crystal like that.

Maintaining a laboratory notebook - Colin Purrington

This is a great guide to maintaining a lab notebook, and something to read, even if you’ve been keeping one for years. Because let’s be honest, you and I both know we aren’t keeping as good notebooks as we should, right?

Also, Pigma Micron pens are great.

spytap:

winstonwolfe:

fatmanatee:

singlepatriotsinyourarea:

this is the real first page of a real book by a real Fox News host

duck dynasty guy in a miley cyrus world


Obama’s outchea in these streets taking away people’s bibles and guns and sweet tea. You can take our rainbows, but not my motherfuckin’ sweet tea!

There needs to be a word for “nostalgia for a time that never existed; a made-up ‘time long past’ that as you got older and progressively more angry and less sane, you used to cover for your feelings of increasing irrelevance sparked by the dawning reality of your own fleeting mortality.”
I bet the Germans have a word for that.

spytap:

winstonwolfe:

fatmanatee:

singlepatriotsinyourarea:

this is the real first page of a real book by a real Fox News host

duck dynasty guy in a miley cyrus world
Obama’s outchea in these streets taking away people’s bibles and guns and sweet tea. You can take our rainbows, but not my motherfuckin’ sweet tea!

There needs to be a word for “nostalgia for a time that never existed; a made-up ‘time long past’ that as you got older and progressively more angry and less sane, you used to cover for your feelings of increasing irrelevance sparked by the dawning reality of your own fleeting mortality.”

I bet the Germans have a word for that.

feenomeena asked: So I see your post about Evolution with NDT. But Joe. You have to undrstand, as the devils advocate right now (being me), how do you explain the semantics of this argument. If it is fact, why not call it so. Gravity isnt a theory. It is a law because it is observable. The Law of gravity. The laws of thermodynamics. These arent theories, they are postulates. Why if the scientific community is forthforward about gravity, cant they accept it as fact as with these other observable laws?

jtotheizzoe:

(FYI, we’re talking about this post)

Thanks for being the devil’s advocate. Nobody ever stands up for that guy!

You ask an important question about the difference between a scientific theory, a scientific fact, and a scientific law, and in doing so you may have inadvertently caught a mistake in Cosmos. We’ll get to that, but first, let’s untangle these confusing terms.

A scientific theory begins life as a hypothesis. And a hypothesis is born when an observation comes together with a possible explanation  in the womb of the mind. That hypothesis is fed further observations, and if all remains correct, one day it grows up into a theory. The more a theory can explain, the stronger it is. It can be modified or proven wrong by future observations. What is special about a theory is that it ultimately allows us to predict what will happen and also explain why it is happening. 

A scientific law is fairly similar to a theory, except that it doesn’t explain the why. Let’s take the Law of Gravity as an example. It has been incredibly well supported by observation,and it has been revised over time to adapt to new observations (like spacetime), but nothing about the Law of Gravity explains why gravity does its gravitational things. We usually capitalize them because it makes them look more important.

A scientific fact, the way I interpret it (its philosophical definition has been debated many times), is an observation that no one has been able to disprove and that we expect two people would observe in exactly the same way regardless of when or where or how they observed it. For instance, it is a scientific fact that the jellyfish green fluorescent protein emits light at a wavelength of 509 nm when it is excited by 395 nm light. This is just a thing that happens. It is an observation that can then be applied to a more general theory of fluorescence. Got it? Good.

So what is evolution? It’s a scientific theory. It is a thing that we can see happening (yes, I mean actually observe it happening) and it also allows us to explain why it is happening. The theory of evolution encompasses all the chemistry of DNA, the random action of mutations, and the mathematics of selection. It’s a what and a why

What about gravity? Why did Neil call it a “theory”? Here’s the mistake in Cosmos that I think you’ve identified. He shouldn’t have called gravity a theory. It’s a law. We know a lot about the what of gravity, from how mass interacts at a distance to curvatures in the fabric of spacetime, but we don’t know why gravity gravities. So you’re right that gravity is a law. Neil was wrong, at least on this week’s show.

By this time you’re all probably thinking “Joe, this is a load of semantic bulls**t!!" You are absolutely right. It is a load of semantic bulls**t. It’s actually the very definition of semantics, the study of meaning. I’d forgive some of you for thinking this is all a worthless waste of verbal and cognitive energy, because what’s wrong with just saying something is or isn’t

Well, that all depends on what your definition of “is” is.

Neil Young is a 68 year old man with decades of eardrum abuse under his belt. He's undeniably great, but he's dead wrong about "audiophile" sound.

'Actual professional digital audio engineers who say it makes no sense present a problem for the Pono believers. Heck, it's actually perfectly possible for ultrasonic intermodulation to make high-sample-rate music sound worse.

Pono is not actually a whole new audio standard, either; it’s your standard 192-kilobit-per-second-sample-rate, 24-bit-sample-depth audio, as seen not only in production studios but also in DVD-Audio, which has been around since the turn of the century but notably failed to set the world on fire.

And then there’s Super Audio CD (SACD), which came out a year before DVD-A. It’s a bitstream format that can effortlessly provide waveform accuracy far beyond that of CD audio, in six-channel surround if necessary… and which also failed to get traction, not least because it only sounds better, particularly for ordinary music reproduction, when you know you’re listening to it. (And it helps to be young, because of the inevitable loss of high-frequency hearing with age, even if you aren’t a rock musician who’s abused his ears for decades.)

Pono recordings promise to truly sound different from the same albums on CD because music is promised to be re-mastered for Pono. There’s no evidence that these improved recordings wouldn’t sound just as good on CD as in high-bit-rate Pono, but it may be easy to check - there’s been a suggestion that you’ll be able to listen to Pono recordings on standard CD-quality equipment for free. Which would certainly show confidence.

Pono audio files and their special player still aren’t available yet, so nobody’s done any tests of it yet. But people who’ve gone to considerable lengths to do a well-designed blinded test of other high-bit-rate audio versus CD quality can’t hear the difference.

"Audiophiles" who don’t even seem to be aware of the existence of blinded tests, in contrast, hear the difference all the time.

This pattern holds perfectly for every level of contrary-to-physics audiophile enthusiasm. At base there’s bit-rate and bit-depth stuff like this, where science agrees there could indeed be a difference with good enough equipment, but humans would not be able to perceive it. In the middle there’s entertaining silliness like the notion that bits coming from an uncompressed PCM WAV file sound better than the same bits coming from a losslessly compressed FLAC file, or that there is such a thing as an “audiophile SATA cable”. And, of course, the pattern also holds all the way up to the most preposterous quantum flapdoodle and magic rocks.’

The tyranny of math and science!

(Source: ericmortensen)

scienceisbeauty:

Detected primordial gravitational waves! See how looks the excitement of a big discovery in scientists, or more precisely, the emotion after experimental evidences about a theory, inflation theory, over one of the fathers of it. Assistant Professor Chao-Lin Kuo surprises Professor Andrei Linde with evidence that supports cosmic inflation theory.

Some links:

A Scientific Breakthrough Lets Us See to the Beginning of Time

At rare moments in scientific history, a new window on the universe opens up that changes everything. Today was quite possibly such a day. At a press conference on Monday morning at the Harvard-Smithsonian Center for Astrophysics, a team of scientists operating a sensitive microwave telescope at the South Pole announced the discovery of polarization distortions in the Cosmic Microwave Background Radiation, which is the observable afterglow of the Big Bang. The distortions appear to be due to the presence of gravitational waves, which would date back to almost the beginning of time.