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Johanna Blakley gave a great Ted talk fashion and copyright protection. She would argue that the freedom to copy in fashion creates an environment in which this spork dress (above; screengrab from her presentation) is created (and that's a good thing). I didn't realize how limited intellectual property law is in fashion. Here is her "good enough" picture of the logic of copyright in the US.

Read to share conference info.

Genius iPad stand

Dashing nerd and others say a large part of science is wrong

A genetics professor of mine used to tell his class, "Half of what I'm telling you is wrong, I just don't know which half."

I've heard variations on this sentiment frequently and fully believe them. I think there are many reasons that good research can be wrong, never mind the bad research.

John Ioannidis studies the phenomenon of inaccurate scientific conclusions. He is profiled this month in a readable article in the Atlantic (in which he is called a "dashing nerd"). Here are some excerpts from a scholarly article by John Ioannidis about identifying which science is most likely to be wrong.

The following characteristics predict that the research findings are less likely to be true:

• Smaller studies
• Smaller effect sizes
• For a given set of data, more tests and fewer positive outcomes
  
• Greater flexibility in designs, definitions, outcomes, and analytical modes in a scientific field
• Greater financial and other interests and prejudices
• Hotter scientific fields (with more scientific teams involved)

The article also uses the terrific term "data dredging" to talk about the phenomenon of trying elicit results that were not identified by the initial study design or analysis. Wikipedia calls it "the inappropriate (sometimes deliberately so) use of data mining to uncover misleading relationships in data."

via Derek Lowe

Visual Candy: Chart of Taxonomy of Rap Names

I love the choice of main groups: Wordplay, Physical and Metaphysical Characteristics, Crime, Titles/Honorifics, Alphanumeric, and Animal, Vegetable, Mineral. The subcategories are delightful too: audacious misspellings, similarity to cartoon character. In order to make it legible though, some connections have to be left out. For instance Brand Nubian gets to be connected to the Black and Fresh taxa, but not to Wordplay.

Dog bites and the lunar cycle

If you believe the scientific literature, you'd think that people receive more dogs bites during the full moon if they are in England, but not if they are in Australia. Absent other data, I'd say the best title wins: "Barking mad? Another lunatic hypothesis bites the dust."

3D <-> 2D sewing pattern conversion software

This software can take a pattern in two dimensions and virtually sew the pieces together and show you the result. I'd like to use it with bags, but right now it's clothing oriented, and the three dimensional finished piece is displayed on a custom model. Regions of strain are highlighted. You can also generate a two dimensional pattern from a three dimensional item. Here's an older article about this kind of software, and here's an even older one. Oh, and the price tag? Upwards of $10K. Anyone want to bet when it will come below $200?

Science slogans that are not pithy

from reddit via bytesizebio

Insect visitor

Shiny!

Furniture for my future life

I've been thinking a lot about where I will live next. The chances are extremely high that I will have less room than I do now. Here's a nicely designed piece of space-saving furniture

Ms. Dr. / DRF

Shortly after I officially became Dr. Manduca, I whimsically used "Dr" as my title for an airplane reservation. I was immediately delighted by an unforeseen aspect of the choice: unlike men choices, a woman's choice of title connotes particular politics and identity (coarsely: Miss is conventional, Mrs is conventional and largely limited to heterosexuals, and Ms is feminist). I enjoy the freedoms of Dr, in spite of the implied self-importance. I've used it intermittently since.

Today I read something that dismayed me: Dr. Isis, the author of the wonderful blog "On Becoming a Domestic and Laboratory Goddess" noticed that her travel itinerary referred to her as "DRF. ISIS," which a contact explained is how that particular airline refers to female doctors. If that practice spreads, it will slightly diminish the joy I find in choosing Dr. Not only does choosing Dr free me from the sticky Mrs/Ms/Miss, but I can pretend I don't even have any opinions about Mrs/Ms/Miss. DRF highlights the fact that there are Titles, and Titles for Women To Choose From. I'll choose from the whole list, thank you very much.

Your humble servant,
Magnificent Rector Manduca

Journal of Serendipitous and Unexpected Results

There's a delightful piece at Byte Size Bio about an article in the excellently-named Journal of Serendipitous and Unexpected Results. The piece is called "But did you correct your results using a dead salmon?" and it uses the MRI of a dead salmon to illustrate the fallacious results possible from bad use of statistics. It also has a nice (simplified) explanation of the logic underlying multiple error correction.

Nicely done, SoCal Edison

I had the surprising experience of getting a smart automated call today. I called SoCal Edison after the power was out today for about an hour. They told me it was out for some 400 people in my neighborhood. I later received an automated call, asking me to press 1 if my power had been restored. It was a short, efficient script. Brilliant: they followed up with me, and they got a sense of whether their job was done.

Wheeled carry-on backpacks

After traveling to six cities and staying in nine different homes over the course of a month with my bargain bag, I've identified things I want in a travel bag.

• wheels
• backpack straps and hip belt
  
• can be carried on and fits in the overhead bin (typically airlines limit carry-on luggage to 22" x 14" x 9")
• can be checked. This means that I want to be able to cover the backpack shoulder and hip straps.
• as big as possible
• as light as possible
• not hard to look at

Here are my candidates:

• Rick Steves Autobahn 21" Rolling Backpack, $140, 7 lbs , 13 oz. I think it's ugly and the straps don't look very ergonomic.

• Eagle Creek Switchback Max 22, $300, 9lbs, 6 oz, detachable daypack. It’s not horrible looking, reviewers like it, it has Eagle Creek’s fantastic warranty, and I like the daypack option.
  

• Osprey Meridian 22”, $300, 8 lbs. 14 oz. Fantastic looking, technical reviewers love it. Zip-off backpack.
  

Not considered:
Victorinox E-motion 4.0 22" Trek Pack Plus. It's too deep (22" x 14.5" x 10.75").

So the products I like are in the $300 range. That seems like way too much to pay for something I'm not sure I'll like. Maybe I'll find that the combination of backpack straps and wheels takes up too much space to be able to fit my stuff in it. Maybe the combination will be too heavy. I'm considering buying a less expensive one to get a feel for the combination, but even a relatively inexpensive one will be a commitment. Hmm.

Fried green tomato recipes

Ingredients

* 1 cup all-purpose flour
* salt
* pepper
* 1 egg
* 1/4 cup milk
* 4 cups fresh bread crumbs
* Kosher salt and freshly ground black pepper
* 4 large unripe tomatoes, cut into 1/2-inch thick slices, ends removed
* 1/2 cup vegetable oil

Directions

Prepare three dredging bowls. Add flour to one, and add salt and pepper until you can taste it in the flour. Then add more.

Combine milk and egg in the second bowl and mix. Put crumbs in third bowl.

If tomatoes are too wet, the flour will be too thick or fall off--if this happens, you might want to pat them dry with a lint free or paper towel.

With fingers or tongs, dredge tomato through flour, then dip in egg mixture and dredge in bread crumbs. Pat breadcrumbs onto tomatoes, adding more if needed. I left the tomatoes sitting on top of the breadcrumbs until Mass K friend was ready to fry them.

Fry them in a non-stick pan with a few tablespoons of oil over medium-high heat. You'll see the skin on the edges of the tomatoes pucker when the slices are cooked. Drain on paper towels.

I used two recipies as sources.

Maps maps maps

MapMyRun (or Walk, or Bike, or whatever) is generally the best tool for tracking this kind of stuff. However, the web page layout is spectacularly bad. When you view a route, look how much of the (1920 x 1176) page is dedicated to the map:



Also in this morning's map tool criticism category: Google My Maps. I love it, but it's bad when it comes to printing. However, there is a terrific 3rd party tool at taurich.org that prints maps along with the titles and descriptions of places and, here's what's special, the titles and descriptions are keyed by icon to unique places on the map. When you print with google, you can't tell what description belongs where. Also, the taurich tool allows you to print the descriptions in columns, which helps a lot.

Extreme forecast disparity

Weather.com and weatherunderground have some explaining to do.





These are the results for the same zip code. I tried the neighboring zip code same type of difference. Naturally, I hope the cooler forecast is accurate.

Silly product names: Nostrilla

Popsicle Progress

After several rounds of faux-creamsicles (made from plain yogurt, orange juice concentrate, and water at 2:1:1), I've ventured into bananas. This is from Martha Stewart's blueberry pop recipe, but I used strawberries instead. And next time, I won't add 3 TBS of sugar. I think it probably doesn't need any sugar at all, actually. And that's using plain yogurt, not the recommended vanilla yogurt (warning: I like tart yogurt).

Beets

I'm nostalgic for these beets my roommate grew last year.

Salt, mostly a failure

MM and I saw Salt Wednesday night. I expected to like Angelina Jolie a little more. I'm not usually much a fan of her acting, but I've enjoyed her in action movies in the past. She's now too fragile-looking to be plausible as an actionista. Also, she doesn't look particularly good in any of it. If I have to stretch my suspension of disbelief to include this waif being an action hero, I think it wouldn't be too much of a risk to pretend that an action hero could also be attractive.

Clockwise from top left: Angelina as Scrawny Salt; Angelina as "lost in my corporate outfit and this weapon is too heavy for me" Salt; an earlier, buffer, Angelina; what a plausible female action hero looks like (and man did I miss Jennifer Garner in this movie); the best costuming in Salt.

Popsicle recipes I'd like to try

Many were found on a list at tip-nut.



Coffee-pops





Martha Stewart Banana Blueberry Swirl Popsicles




Melon popsicles with mint, honey, and yogurt

Homemade Fudgsicles

Grapefruit Lime Cilantro Popsicles

This method for swirling chunks into your popsicles, and a discussion on corn syrup

Here's a pretty result:







Cardamom Rhubarb Creamsicles (a woman after my own heart: "So, I left about 1/4 of the rhubarb sorbet in the ice cream maker & stirred in about 1/2 c of heavy cream."








Martha Stewart's Banana, Berry, and Buttermilk Ice Pops

Watermelon Slice Pops (with chocolate chips as seeds)

And finally, funny pea-ice popsicles I'm not going to make:

No "barefoot and pregnant" in German?

The hipster-chick in line at the bank spoke so loud that I couldn't help but overhear. And soon, I was too repelled and fascinated not to actively listen:

[Speaking emphatically in german]...pregnant. Literally barefoot and pregnant...[More german]... I mean, come on...[Lots more german. Clearly still talking about the same person and not letting a word in edgewise]...Student loan...[More german]...White trash.

Clearly English is better suited for certain descriptions. Ironically, the phrase "barefoot and pregnant" might be ideologically descended from the German phrase "Kinder, Küche, Kirche" ("children, kitchen, church") coined in the 1800s.

Wikipedia's code-switching article seems to be the most relevant linguistic definition of this type of language-switching phenomenon.

Pen love: Uniball Vision Elite Bold

I bought a pack with a range of colors when I was editing my thesis. They write a smooth, sharp, fat (0.8 mm) line smoothly and don't leak in flight. Many people really like the blue-black color. I like it, but it's the other characteristics that send me.

Rattlesnake

The dog and I came across a rattlesnake near the trailhead today. The
dog exhibited curiosity not fear. Time for a snake-aversion refresher?

What are you saying?

I'm somewhat mystified by this illustration titled "no drugs down the
drain." It looks more like a psa about the hazards of childhood pill
addiction.

When text mining goes wrong

Does this gene cause that dreaded decapitation disease?

Ceiling of Union Station in DC

I took more classical pictures on a recent trip.

unwanted period in Latex acronyms list

Using glossaries package, I was getting an undesired period after the definition. I was using this code:

\usepackage[acronym, nonumberlist, toc]{glossaries}
\makeglossaries
\include{acronyms/acronyms}
\printglossaries

(where the acronyms file contains the definitions). The results:

ABA Allen Mouse Brain Atlas.
AMPA α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate.

The fix:

\usepackage[acronym, nonumberlist, toc]{glossaries}

% Define new glossary style
% desired format:
% acronym is bold, no full stop after definition
\newglossarystyle{hbacro}{%
\renewcommand*{\glossaryentryfield}[5]{%
\item[\glstarget{##1}{##2}] ##3\space ##5}
}
\glossarystyle{hbacro}

\makeglossaries
\include{acronyms/acronyms}
\printglossaries

And got

ABA Allen Mouse Brain Atlas
AMPA α-amino-3-hydroxyl-5-methyl-4-isoxazole-propionate

Cobbler v1.0

Used Costo pears (the only canned thing I actively like) and this recipe. Unlike the picture, the cobbler wasn't out of focus.

The database of useful biological numbers

The B10NUMB3R5 website: In its infancy, but a genius idea and a great start in spite of the excessive transliteration of numbers for letters. Wouldn't b10numbers or B1oNumbers have been sufficient?

Nice industrial design

Sure, it's for slicing mouse brains, but there's no reason it can't have good aesthetics too.

Zipper rings from around the web

(clockwise from top left) me, elisaetemadjewellery.co.uk, meganleone at etsy, forever21 (?!), and Doris Viñas.

I've been looking for a new way to make the ring part, but it looks like people mostly use elastic.

YouTube as evidence source for peer reviewed biology research

You can't make this up:

Video Database Analyses

The global database used, www.youtube.com, is a video-sharing website consisting of tens of millions of user contributions from a wide range of people across the globe. Users commonly post animal behavior on YouTube...

fur rubbing behaviour

A happy accident created by my bibliography program assigned a (non-capuchin-related) paper this title: "Resource influence on the form of fur rubbing behaviour in white-faced capuchins." In this paper, they "propose hypotheses on possible proximal causes for these differences." Sigh.

Anniversary of 1989 anti-feminist slaughter

A communique from x_ine posted by Dr. Isis:

December 6th - marks the 20th "anniversary" of what is termed the "Montreal Massacre" - the day where a madman showed up at École Polytechnique, an engineering school at Université de Montréal (University of Montreal) with a rifle and killed 14 women and injured countless others.

His goal was purely sexist in nature, as he declared he hated feminists and felt that women had no place in engineering. In fact, when he entered a classroom with his gun, he separated the men and women. He "let" the men go - and his rampage began.

additional reading:
Canadian Press article
CBC News article
Montreal Gazette article

Beautiful folding bike concept

By Joseph Cadek

Ode to \vref

I'm using LaTeX to write my thesis, and there is this great command: vref. I have a figure called Variability_transcript_abundance. When I'm talking about it in the text, I can create a reference to it. This:

...this approach is illustrated in Figure \ref{Variability_transcript_abundance}...

becomes

...this approach is illustrated in Figure 2.2...

sometimes i want to have a page number too. i use this

...this approach is illustrated in Figure \vref{Variability_transcript_abundance} on page \pageref{Variability_transcript_abundance}...

to get

...this approach is illustrated in Figure 2.2 on page 32...

The genius of vref is this: the same code gets you different types of references, depending on the distance between where your text is and where your figure is. so

...this approach is illustrated in Figure \vref{Variability_transcript_abundance}...

gets you whichever of these:

...this approach is illustrated in Figure 2.2 on the following page...

...this approach is illustrated in Figure 2.2 on page 32...

...this approach is illustrated in Figure 2.2...

applies. when the figure is on the same page, no need to mention the page! of particular joy is that this package was last updated in 1999. such stability. ahhh, LaTeX.

Leading cause of dog injury in flight

picture by Roman Fleysher

OK, these dogs are living the good life. I'm not sure if they're strapped in or not, but that's not the kind of injury I'm thinking about.

Based on the reading I've done, which has not been systematic or exhaustive, the leading cause of dog injury in flight seems to be injuries sustained by pets trying to escape their kennels, and sometimes succeeding. petflight.com emphasizes the importance of zip tying your kennel closed after TSA inspection. I hadn't thought of that, but it sounds like a great idea.

Phone-operated pet feeder

I wouldn't have much use for it, but I love the design.

Sequences were mapped to opossum genome

The title is an addition to my collection of favorite excerpts from scientific publications.

Caveat: this picture is much cuter here than the spitting pig-aliens I usually see.




photo credit

N. R. Saunders, M. Wakefield, J. Ek, S. A. Liddelow1, J. Truettner, B. J. Wheaton, D. Dietrich. Rna-seq analysis of gene expression following transection in immature spinal cord of monodelphis domestica. Program No. 415.5. 2009 Neuroscience Meeting Planner. Chicago, Il: Society For Neuroscience, 2009. Online.

A study of electrically exploded wires

A Caltech thesis title from 1924. It produced not only that wonderful title, but this image:

Grammar check

Grammar and word usage are two things that web references can't really resolve. Looking up a definition in the dictionary isn't adequate to explain correct usage. I've started using site-specific searches of sites with high-quality, copy-edited writing to check usage. For example, the spelling of the phrase "doling out" looked strange enough to make me uncertain. Spell-check liked it, but it could have been the correct spelling of a different word. I ran this google search:

site:nytimes.com doling out

And got these results:

Bureau of the Public Debt, Doling Out America's I.O.U.'s
N.E.A. Faces Tough Task of Doling Out Limited Stimulus Funds
U.S. starts doling out funds to banks

Resolved.

Nominations open: worst immunoblot ever published

He's hot! He's on Fi-ah!

My dog loves to be in the car. He'd rather be in the car than be at home alone. So I indulge him, but I worry about him overheating. I obsessively park in the lowest levels of underground garages and reset my digital recording thermometer so I'll know the maximum and minimum temperatures in the car while I'm gone.

A few minutes ago the dog came staggering in the open door to the porch. He came over to greet me, and when I felt his coat, it was so hot I couldn't keep my hand on it for long. Who is this sun lizard, and why does he have a long black coat? Choosing to lie in the heat as long as he can stand it is certainly different than being trapped in a car that's too warm, but maybe my dog is tougher than I am when it comes to heat. In truth, that's not hard.

Scientific advance: bang mouse on head

Nature Protocols is a prestigous journal that publishes what they judge to be important advances in scientific techniques. There's an article annouced today called "Mouse closed head injury model induced by a weight-drop device." Maybe somebody made the better mousetrap, but they're underselling it with that title.

QuickLook CSV Plugin

I never thought I could be a fan of a QuickLook plugin, but I am. Here's the link.

Boars, Barrows and Gilts

I just came across the article, Genetic Correlation Between Boars, Barrows and Gilts for Various Carcass Traits, from the Journal of Animal Science.

1. "Boars, Barrows and Gilts" - it rolls off the tongue. What a lovely phrase.
2. Carcass traits. Ick.

Mirriam Webster defines "gilt" alternately as "superficial brilliance" and "a young female swine." Equally evocatively, it defines "barrow" as "a large mound of earth or stones over the remains of the dead: tumulus" or "a male hog castrated before sexual maturity."

JetBlue All-You-Can-Fly pass

There are publicized restrictions, but I figured there must be more of a catch. But: "No blackout dates apply to Pass travel, and Pass travel is not capacity controlled" (from their terms available here).

Good-bye, Clarifi

I wanted to see if I still needed the Griffin Clarifi, the iPhone case that allowed me to take good pictures of receipts with my iPhone 3G. The 3G S is said to have a shorter focal length. I included pictures with my Nikon D-70 as a reference standard.

Unique file IDs

I write code to generate graphics. When I have a graphic I like, I save the image I've generated. In order to know exactly what code created that image, I like to save the code with the same name. As I gradually improve the code, the names evolve, with an addition of a descriptive word or with a version number. This all requires a kind of foresight (to know what description will be useful to my future self) and systematicness that I don't want to spend the time on. For now I've contented myself with a script that generates a unique time-based ID that I paste onto the end of the file names for the graphic and the code. The script copies the ID to my clipboard (requires OSX). Now all I need is a quicksilver trigger, and I can be more brainless than usual.

the code:

echo `date "+%Y%m%d_%H%M%S"` | pbcopy ; echo `pbpaste`

E-mail closings

From a WaPo article linked at Lifehacker:

Favorite:
Love and Bacon (Spike Mendelsohn)

Occasionally fun:
Seacrest out
Off like a prom dress

Meh:
Warmly
XOXO (meh when i wouldn't XOXO in person)

Does "Cordially" ever mean anything other than "My hostility is only thinly veiled"?
(Ruth McCann, WaPo)

The terseness of these is appealing:
Navy and the Air Force: "V/R" ("Very respectfully")
Marines: "S/F" (Semper Fi)
Army Rangers: "RLTW" ("Rangers Lead the Way")

Sadly, my favorites are probably not fit for public consumption. For example, I'd love to regularly close communications with "I have the honor to remain your obedient servant" but I think it might just make things awkward. I'll be sticking with my stand-by, "Best," unless "Thanks" is relevant.

Hour by hour temperature predictions

This is one of the hardest things for me to predict, and something I most like to know about the weather when I travel somewhere unfamiliar. I like pages like this.

scheduled ringer un-silencing: the killer mobile phone feature

How many people have forgotten that they muted their mobile phone ringer? I can go for days before I figure it out.

The solution has been around for years in the land of windows mobile. It's a feature in the third party program called "SPB Phone Suite" which I last used several years ago. It configures different groups of ringer-related settings. You might have one with a quiet, respectable ringer that you use when you're at work and a bunch of goofy loud personalized ones you use on your own time. But my favorite feature uses the one of the default profiles, the one called "Silent." You can set a category of appointments to trigger that profile automatically. Then every time you have an appointment scheduled, your phone will automatically not ring during that time. More importantly, it will switch back to your usual profile again after your appointment.

Only minorities have identity-based opinions?

There is a despicable implication in many questions Sonia Sotomayor's confirmation hearings: only minorities are biased by their identities. Has no one mentioned that we all have identities that influence our perceptions?


-- Mobile post

The hot cash market for 3G iphone...

I posted my 3G iphone on EBay yesterday. I've gotten two messages asking whether I would be willing to sell it for cash in person. I wonder what that's about.

The two messages were very similar, but from different EBay ids. They have some indistinct similarity to brief replies I've gotten when selling things and offering apartments for rent on craigslist, replies that are vague and suggest the person is replying to a great number of ads.

Are these phones going overseas? Being superficially altered and resold as 3G S? Simply being sold to people who don't want contracts?

Billed as "Retro Future"

I don't even know what to make of it.

word of the day: artifactual

dismissive. in biology, it means a result that is unintentionally caused by the process of asking the question (e. g. pressure on a sample when you put a coverslip on a microscope slide). a result that is not relevant to the general biological truth.

Science should be FUN

like this:

Five competition polo ponies were ridden by a professional rider to perform five maximal accelerations and five maximal decelerations in an all-weather polo arena...Stride timings were derived from hoof-mounted 50 g accelerometers logged into MP3 recorders.

From the article "Pitch then Power" in the Biology Letters journal.

As an aside, I think it's interesting that they choose to compare greyhounds with polo ponies. Racing greyhounds accelerate in a linear context. Winning races does not depend on deceleration. Polo ponies, on the other hand, work in a multi-directional environment responding to other players on different paths. Mostly they're turning on a dime, negotiating melees, suddenly starting or stopping, and changing stride to adjust to changing conditions. The study seems to find equivalence between the two groups, but it would be hard to know if any differences were the result of one variable (species) or the other (competion conditions). A hard-core reductionist could instead compare race horses with greyhounds or herding dogs with polo ponies.

Recursive dog

Roomate: Good-night little dog, little dog with a little dog in his mouth
me: He's recursive dog
Roommate: Yes, you need to sew a smaller dog in the little dog's mouth.

Caltech PhDs awarded in 2009 by division and date of undergrad degree

A back-of-the-program sketch.

Worst phone I've ever had: iPhone

Sure, it's also the best piece of electronics I've ever had, and that's why I keep it. But for making calls, it continues to be the worst phone I've ever had, including my first cell phone, that creaky Kyocera.

Best: interface, content, features. Maps, web, games. There are lots of improvements I'd like to see, but it's the best thing going for a mobile device. One of the reasons I like it is because it reduces the amount of stuff I need to carry. But what I really need to add to my purse is a phone that works.

Still: Women underrepresented in applicant pool for science faculty positions

This is the same result I remember from the last report. Basically, even when women are present in equal numbers in graduate programs, they are less likely than men to apply for faculty positions in their field. However, women who do have faculty positions are generally compensated as well as men. The bottleneck is in the applicant pool.

Why? Here's what I think: women are motivated to pursue science. Once they have reached the point of considering whether to apply for a faculty position, they have become intimately acquainted with work conditions in academia. They've seen that successful faculty forsake all other interests. Many women are not willing to do that, especially if it means forsaking family. So if they have a choice, they don't pursue an academic faculty position.