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19 Aug 16:20

Jumpy the amazing super dog

by Jason Kottke
horsepunchkid

Here's the best part as a GIF:
http://i.imgur.com/nD7Zfro.gif

Meet Jumpy the dog. This dog can jump higher than you, skateboard better than you, dive better than you, walk on its front paws better than you, surf better than you, catch a Frisbee better than you, do a backflip better than you, and ride a scooter better than you. Jumpy is better than you.

Ok, this dog is a better skateboarder, but Jumpy is still better than him. Jumpy is better than everyone. (thx, dad)

Tags: video
26 Jul 20:07

On Beating Dead Horses

by noreply@blogger.com (Laurence A. Moran)
horsepunchkid

In a surprise twist, a creationist accuses scientists of argument from authority and trying to hide contradictions with inscrutable jargon. Transubstantial!

I've mentioned this before but it bears repeating. One of my Ph.D. students (Sharon Shtang) wrote her thesis on sequence comparisons and phylogenetic trees. She found a quotation from Emil Zuckerkandl and Linus Pauling in their 1965 review. They were commenting on using amino acid sequences to prove evolution. This seemed at the time to be an example of overkill since evolution was then, and is now, a fact. They said ...
Some beating of dead horses may be ethical, where here and there they display unexpected twitches that look like life.
I was reminded of this while reading Salvador Corova's latest post on Uncommon Descent because he refers to beating dead horses [If not Rupe and Sanford’s presentation (8/6/13), would you believe Wiki? In this case, yes]. I'm not going to make any comments. Read it and weep for the IDiots.
Theme

Mutation
Evolutionists reluctantly admit most evolution is free of selection and therefore non-Darwinian (neutral evolution). When pressed, they’ll say neutral drift is real, but they don’t like it when the dots are connected in a way that demonstrates neutral evolution refutes Darwinism, that there is a contradiction between Dawkins’ vision and neutral evolution! The way Darwinists deal with this violation of the law of non-contradiction is to pretend no contradiction exists. They’ll obfuscate and fog the issue with myriad technical terms and irrelevancies so that the illusion of non-contradiction is protected from public view. Confusion and the illusion of some higher knowledge are their friends, clarity and education of the public are their enemies.

If Dawkins had been faithful to the facts, he wouldn’t have even written The Blind Watchmaker because population genetics precludes his vision of evolution from being reality in anything but his silly Weasel simulations.

There is a simple formula from Wiki that says the rate of new mutations is the rate at which new mutations become features of every member of the population (a process called fixation).

http://en.wikipedia.org/wiki/Fixation_(population_genetics)


The population size is N and the Greek symbol μ (mu) is the mutation rate.

It stands to reason a slightly deleterious mutation is almost neutral, hence, approximately speaking the rate that slightly deleterious mutations become part of every member of the population is on the same order of the slightly deleterious mutation rate. That means if every human is getting 100 dysfunctional mutation per generation, about 100 dysfunctional mutations are getting irreversibly infused into humans every generation (a ratchet so to speak).

But as bad as that is, it’s actually worse in reality. Remember broken bacterial parts in anti-biotic resistance, or blindness in cave fish, or sickle cell anemia? Those are “beneficial” (in the Darwinian sense) mutations, but destructive in the functional sense. So it is actually generous the creationists are modeling the dysfunctional mutations as slightly deleterious (whereas a fair argument might actually model some of the dysfunctional mutations as “beneficial”). So the creationists are cutting Darwinists a lot of slack, and yet, even then the dysfunctional mutations will get fixed (become members of all individuals) in a population! Not to mention, lots of bad may get purged from a population only to get replaced with new generations of bad....

But obvious math is something Darwinism hates dealing with! The above equation should be painful evidence against evolution being some process of increasing complexity from a primordial virus to incredible minds like Newton or Einstein. Darwinist won’t come to terms with it, they won’t come to terms with even a computer simulation based on population genetic models. Oh well! But anyway, Christopher Rupe and John Sanford will be presenting the results of a computer simulation that illustrates the above equation. It’s sort of like beating a dead horse or beating living puppies. It’s not very sporting, but Darwinists keep propping up that dead horse for creationists to keep beating.


Zuckerkandl, E. and Pauling, L. (1965) in EVOLVING GENES AND PROTEINS, V. Bryson and H.J. Vogel eds. Academic Press, New York NY USA
17 Jul 17:34

Differential Interference Contrast Microscopy, or the question I’m never asked

by PZ Myers

Thirty, almost forty, years ago when zebrafish were an up and coming model system and very few labs were working on them, we were used to going to conferences and reciting the zebrafish litany, a list of attributes that justified us working on such an oddball animal: we’d explain, for instance, that it was prolific, fast developing, and optically transparent, so we could see right into the nervous system in the living embryo. And you know, not once have I ever been asked the really simple and obvious question: if it’s transparent, then how do we see anything inside it?

I know. It takes a moment to step outside the assumptions (we say we see stuff, after all) and think about what transparency actually means. Of course, I always have an answer prepared: “With differential interference contrast microscopy, Nomarski optics specifically.” A polysyllabic phrase is always an effective way to shut down the rubes, isn’t it?

But I can also explain it in simple English, especially if I can flail about on a chalkboard at the same time. So let’s try.

We’ll start with the very minimal basics. Light is a wave, and the properties of that wave are what our eyes see. For instance, one property of a wave is amplitude: in the two light rays below, the lower one has a larger amplitude, so we’d see it as having a greater intensity, or being brighter, than the top one.

amplitude

Another property is wavelength or frequency. Shorter wavelengths (higher frequencies) have have more energy than longer wavelengths (lower frequencies), and we see these differences as color. In the cartoon below, the longer wavelength of light would be seen as red, while the shorter one is blue.

wavelength

Those are the characteristics of light that our eyes can detect, so when I say that zebrafish embryos are transparent, I mean that light passing through them does not exhibit a significant reduction in amplitude or a change in wavelength — it does not get significantly dimmer nor does it change color.

But there are other important properties of light. One is phase. Notice how in the previous picture of the amplitude, the peaks in one line up with the peaks in the other, and the troughs line up with the troughs? We’d say those two rays of light are in phase. They don’t have to be, though. For instance, here are two rays of light that are completely out of phase, with the peaks of one lining up with the troughs of the other.

phase

Here’s the thing, though: our eyes can’t discriminate the phase of light. Both of those beams have the same amplitude and the same wavelength, so they’d look completely identical to us. Which is a shame, because lots of transparent things shift light phases, and especially of interest, lots of biological materials shift the phase. All you need to do is have a material with a different refractive index and you’ll get a phase shift.

For example, most of a cell is water, and it’s surrounded by a membrane that is mostly oil/fats. These have different refractive indices. Shine two beams of light on a transparent cell, one that passes through the center (mostly water) and one that passes tangentially through the membrane (lots of oil), and you end up with two beams of light that now have different phases. Which we can’t see, darn it. My zebrafish embryos are full of membranes in complex arrangements, so while light passes through them with amplitude and wavelength (intensity and color) relatively unaffected, the phases of light are all scrambled and cockeyed in interesting ways full of information. We just have to have a way to detect phase and we could see lots of phenomena in the embryo.

membrane

There is a way to visualize the relative phase of two beams of light, though. If you could just bring them together, combine them, they could interfere with one another. If the two beams are in phase, peaks lining up with peaks, they’d sum up and you’d see a greater amplitude — the combined beam would be brighter. This is called constructive interference. If they’re out of phase, peaks lining up with troughs, they’d cancel each other out, they’d destructively interfere, and you’d get a dimmer beam.

We have this really clever way of combining two beams of light: they’re called prisms and lenses, which bend light. All we have to do is shine parallel beams of light through our specimen, and then use prisms to bend one and bring it into alignment with the other, and we’d get interference patterns that change the intensity of the light, and we’d be able to detect phase changes!

There is a tricky bit to this, though. This is a way of comparing the phase of two rays of light; what are we going to compare? One technique is to illuminate with ring of light, and use light that hasn’t passed through your specimen as a reference beam, and compare that to light perturbed by your specimen, the specimen beam. This is the technique used in standard phase contrast microscopy. It has some drawbacks I won’t get into in any detail; you get halos that reduce the resolution of your image. We don’t like halos. It’s kind of like the lens flares that cheesy sci-fi cinematographers sprinkle into their movies.

Differential interference contrast uses a different method to generate a reference beam. We illuminate with two beams of light that have different polarity and that are offset slightly (by a fraction of a micrometer) from one another. Polarity is another of those properties of light that our eyes can’t really detect; Dr Dryskull has an excellent post on polarity, but simply put, those waves of light aren’t all necessarily vibrating in the same plane — they can be wiggling in all sorts of directions. We use a Wollaston prism, a piece of crystal that splits light by its polarity, so that we have light vibrating in one plane, and another beam vibrating at 90° to the first, both shining through the specimen in parallel. Their phase will be affected in different ways because each will be passing through a very slightly different part of the specimen. Then they are recombined by passing through a second Wollaston prism, allowing them to interfere with one another, to produce interference patterns.

Does this diagram help? Basically you have all kinds of glass in the condenser and above the lens that jigger the heck out of light to split, isolate, and recombine the beams into visible patterns of constructive and destructive interference, allowing you to visualize shifts in phase, which represent changes in the refractive index, of cells and tissues.

dic_diagram

More simply put, this technique compares the phase shift of each point on the specimen to a point 0.2 microns to the right (or whatever; we have knobs that let us shift the relative orientation). If you’re looking at a uniform field, this comparison yields the same intensity everywhere; but at regions in transition, for instance where phase is changing rapidly at a membrane boundary, you get bright and dark edge enhancement. This turns a bland, flat field of cells into a picture of clustered basketballs with a kind of lovely shadowing effect. Like so:

cells

It can also go horribly awry, but I did this to make the difference even more obvious. Here is a field of embryonic cells in a zebrafish imaged without phase optics — we’re just seeing the subtle shifts in intensity of the light as it passes through. (If you’re interested, you’re seeing the margin of the expanding epiblast in a pre-gastrula embryo, with the yolk syncytial layer at the bottom of the field.)

embryomargin_flat

Now what I’ve done is slipped in the various prisms and polarizers for DIC, and jacked the contrast up to 11. It’s ugly, but you should be able to see the vivid difference you can get by playing with phase; in particular, notice the great big YSL nuclei at the bottom right. The point here is that we can visualize all kinds of transparent objects in the embryo just by adjusting the widgets on the scope.

embryomargin_dic

There are drawbacks. For one, all that glass diminishes the light intensity at every step — you need a good bright light source to start with. It takes some finesse to use properly (see photo above), and increases the complexity of configuring the scope by quite a bit. I’ve tried to train many students to use this stuff, and most of them throw up their hands in horror and get completely confused — too many knobs! Too finicky! It requires esthetic judgment! Good grief, it’s like…art or something.

This is the usual state I find my microscope in. Those of you who know what I’m talking about will see instantly that both the Wollaston prism and analyzer sliders have been pulled out of the light path. I usually feel like I’ve done well if I teach them to adjust the condenser properly. Grumpy aside: have you noticed how often student scopes have no adjustable condenser at all? You don’t know how to use a microscope if you don’t know how to set up Köhler illumination.

leicadmlb

One last picture to show you that DIC can look very pretty. This is the tail bud of a 21 hour embryo; you can see somites with myoblasts, the notochord, mesenchyme, all kinds of cool stuff if you know what you’re looking at. And you can see it all in a transparent embryo.

myotomes

02 Jul 20:46

Recipe: Blue Sunrise Cocktail with Pickled Blueberries

Blue Sunrise Cocktails with Pickled Blueberries

One of the joys of preserving my own food is having delicious, locally grown summer fruits year-round. But as wonderful as traditional fruit preserving methods are, I can only eat so much jam. So I also pickle some of my blueberries, mulberries, cherries, strawberries, peaches, and other summer fruits. Pickling is an incredibly easy, safe, and, it turns out, delicious way to preserve fruit. Plus, in addition to the tasty orbs of fruit, you also create flavorful liquids that are perfect for adding to homemade cocktails or sodas. Everything in the jar has a purpose.

This blueberry pickle recipe uses traditional warming spices and red wine vinegar, which give the fruit and liquid a rich, earthy flavor. The pickled berries and liquid can be used on ice cream, in pancakes and muffins, or with a cheese board. They can also be used to make blue sunrise cocktails, a twist on the classic mimosa. Enjoy as a refreshing drink right now or in the dead of winter as a tasty reminder of summer’s bounty.

Sweet Blueberry Pickle

Yield: About 2 pints
Note: You will need two one-pint jars and some cheesecloth.

  • 2 cups blueberries
  • 1½ cups red wine vinegar
  • 1 cup sugar
  • ¼ teaspoon salt
  • ¼ teaspoon vanilla
  • 1 cinnamon stick
  • ½ teaspoon whole cloves
  • ½ teaspoon whole allspice
  1. Tie cinnamon stick, cloves, and allspice into a piece of cheesecloth.
  2. In a medium saucepan, bring vinegar, sugar, salt, vanilla, and spice bag to a boil, stirring to dissolve sugar. Reduce heat, cover the pan, and simmer for 10 minutes.
  3. Meanwhile, pack one cup of blueberries into each pint jar.
  4. Remove spice bag from pickling liquid and discard. Ladle hot pickling liquid into jars to cover blueberries. (They will float, and that’s okay.)
  5. If canning, process jarred blueberries in a hot water bath for 10 minutes. Otherwise, cover jars with a loose lid and allow to cool before refrigerating. Pickled fruit will keep in the refrigerator for about year.
  6. Blueberries and their liquid will taste best if you can allow them to sit for a day or two before eating.

Blue Sunrise Cocktail

  • 1 oz. blueberry pickle liquid
  • ½ oz. elderflower liqueur
  • 2 oz. orange juice
  • 6 oz. dry champagne
  • Pickled blueberries and candied orange peel for garnish
In a Collins glass, stir blueberry pickle liquid, elderflower liqueur, and orange juice together with ice. Top with champagne. Garnish with pickled blueberries and candied orange peel.

Michaela Hayes will be teaching Fruit Pickling: Sodas and Cocktails and Kimchi: When Fermentation Gets Spicy at BBG later this month.
29 Jun 13:16

Reader is Dead

horsepunchkid

Seems to have failed on my "kept-unread" stream, which is possibly the most important thing missing from the Takeout archive. But it still seems like it's worth running.

Reader is Dead:

A collection of tools to help with the impending Google Reader shutdown

Download a complete archive of your Reader account’s data—including everything Google’s Takeout fails to include—and grab public feed data.

Be quick!

27 Jun 11:09

Wolf in Sheep’s Clothing

by alex
horsepunchkid

It's only fitting that my last share from Google Reader should be my first share from the new The Old Reader.

Wolf in Sheep’s Clothing