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Brain time [Jul. 14th, 2009|05:39 pm]
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The origin of temporal illusions - brain dubbing:
But there is a deeper challenge the brain must tackle, without which feature-binding would rarely be possible. This is the problem of temporal binding: the assignment of the correct timing of events in the world. The challenge is that different stimulus features move through different processing streams and are processed at different speeds.

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So if the visual brain wants to get events correct timewise, it may have only one choice: wait for the slowest information to arrive. To accomplish this, it must wait about a tenth of a second. In the early days of television broadcasting, engineers worried about the problem of keeping audio and video signals synchronized. Then they accidentally discovered that they had around a hundred milliseconds of slop: As long as the signals arrived within this window, viewers' brains would automatically resynchronize the signals; outside that tenth- of- a- second window, it suddenly looked like a badly dubbed movie.

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It has been shown that the brain constantly recalibrates its expectations about arrival times. And it does so by starting with a single, simple assumption: if it sends out a motor act (such as a clap of the hands), all the feedback should be assumed to be simultaneous and any delays should be adjusted until simultaneity is perceived. In other words, the best way to predict the expected relative timing of incoming signals is to interact with the world: each time you kick or touch or knock on something, your brain makes the assumption that the sound, sight, and touch are simultaneous.

While this is a normally adaptive mechanism, we have discovered a strange consequence of it: Imagine that every time you press a key, you cause a brief flash of light. Now imagine we sneakily inject a tiny delay (say, two hundred milliseconds) between your key-press and the subsequent flash. You may not even be aware of the small, extra delay. However, if we suddenly remove the delay, you will now believe that the flash occurred before your key-press, an illusory reversal of action and sensation. Your brain tells you this, of course, because it has adjusted to the timing of the delay.
Note to humans: your model of the universe is subtly but consistently broken.
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MONIAC [Jul. 14th, 2009|12:02 pm]
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The Monetary National Income Analogue Computer:
The MONIAC was approximately 2 m high, 1.2 m wide and almost 1 m deep, and consisted of a series of transparent plastic tanks and pipes which were fastened to a wooden board. Each tank represented some aspect of the UK national economy and the flow of money around the economy was illustrated by coloured water. At the top of the board was a large tank called the treasury. Water (representing money) flowed from the treasury to other tanks representing the various ways in which a country could spend its money. For example, there were tanks for health and education. To increase spending on health care a tap could be opened to drain water from the treasury to the tank which represented health spending. Water then ran further down the model to other tanks, representing other interactions in the economy. Water could be pumped back to the treasury from some of the tanks to represent taxation. Changes in tax rates were modeled by increasing or decreasing pumping speeds.
Like a Babbage engine, only messier.
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Graduation party plus balloon animal pro [Jul. 4th, 2009|04:40 pm]
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Organic first [Jul. 2nd, 2009|12:25 pm]
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Organic first: A Biology-friendly Chemistry Curriculum.
Ask your organic chemists, how much of general chemistry is really necessary for students taking organic chemistry? The answer is, not much. The important parts of general chemistry are reviewed in the first chapter of every organic book, and it does not cover much. Lewis structures, bonding, polarity, hybridization (which the students swear they have never seen before and which is always taught in the organic course as if it were brand new), acids and bases, some kinetics, and thermodynamics. That's about the sum total of general chemistry necessary to learn organic. This amount of material could be covered in about five weeks; the rest of general chemistry is useless as far as learning organic is concerned. I suggest, therefore, that our imaginary chemistry department would invent a course that begins with about five weeks of preliminary material and then dives directly into organic chemistry.
What say you, internet? I'm in bioengineering and four semesters of chemistry (2 inorganic, 2 organic) pushes most engineering courses into the junior year, which is too late as far as I'm concerned. Organic first intrigues me; should I subscribe to its newsletter?
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Your tax dollars at work [Jul. 2nd, 2009|12:22 pm]
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How the NIH spent $30 million dollars on a useless (and possibly dangerous) clinical trial involving several known felons.
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Play it less safe [Jun. 30th, 2009|11:10 am]
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Why playing it safe can be a sub-optimal position:
Think of cancer research as a search space, where research advances are moving toward some (perhaps several) peaks. Now, the question is what kind of change will bring you closer to a peak?

Well, it depends how close to the peak you already are. If you're already close to a peak, a very large change can do nothing but take you further from it. An incremental change will be roughly halfway likely to take you up a small amount; halfway likely to take you down. So if you think you're already very close to an acceptable cure rate for cancer, you should focus on the very small incremental improvements.

On the other hand, if you're far from a peak, a large change is not unlikely to take you closer to the top, and it will certainly get you there a lot faster.

But worse, what if you're climbing some low peak, where the outcome -- even if you do everything entirely right -- is poor? A small incremental change will never do any better than the short peak you're on. But a large change has some chance of finding some other peak -- a radical shift in treatment that would bring much better outcomes. The likelihood of that for any particular change may be very low. But your coverage of the search space would be vastly larger -- making progress much faster.
It's a useful analogy to consider, and not only for cancer research funding. Knowing when to shift into incrementalism is just as important - a failure to do so makes the perfect the enemy of the good.
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Activating neurons with light [Jun. 30th, 2009|11:00 am]
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Also, moderate exercise increases the number of stem cells in the brains of aging mice.
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There are many copies. (Very few plans, however.) [Jun. 22nd, 2009|11:08 pm]
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Which (art) student are you?

I could only come up with 12 Types of Engineers.

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What happens when you drop 50 pounds of Silly Putty from a 10-story building? [Jun. 19th, 2009|04:08 pm]
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Here's a hint - it's highly non-Newtonian.
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Hyalinobatrachium pellucidum (glass frog) [Jun. 19th, 2009|04:06 pm]
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Ants and spiders [Jun. 19th, 2009|04:05 pm]
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Some species of ants may use compasses:
"The incorporation of minerals probably starts as soon as ants start getting in touch with soil," she added, explaining to Discovery News that her team found ultra fine-grained crystals of magnetic magnetite, maghemite, hematite, goethite, and aluminum silicates in ant antennae. These particles could make a "biological compass needle" that drives ant GPS.
If only they had a spider-detector as well:



More here.
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Biotech roundup [Jun. 18th, 2009|05:27 pm]
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Did aging evolve to prevent epidemics?

Using evolution to develop adaptive chemotherapy.

Simple Stem Cell Therapy Shows Promise in Treating Corneal Damage.

Gene Defect Corrected in Human Stem Cells.

Researchers engineer metabolic pathway in mice to prevent diet-induced obesity.
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Scottish Dalek [Jun. 12th, 2009|01:14 pm]
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Pokemon explained [Jun. 4th, 2009|11:37 am]
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Sex roundup [May. 29th, 2009|05:00 pm]
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Ten things you don't know about orgasm. Includes the phrase "in utero masturbation".

Number eleven: higher emotional intelligence correlated with more orgasms.
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Looking for an illustrator [May. 29th, 2009|12:34 pm]
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If you or anyone you know would be interested in creating several illustrations (probably but not definitely black and white) for an upcoming book of staggering genius, please leave a comment pointing me at an online portfolio. The book will be a humorous look at biotechnology - think How to Defeat a Robot Army with test tubes.

Please note: these will be passed along to people who know one hell of a lot more about publishing than I. I will not comment on the selection process - the best I can do is thank you in advance for your interest.
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Biotech roundup [May. 28th, 2009|05:55 pm]
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Stem cells delivered by contact lens for corneal disease.

A mouse model for exploring a medically relevant mutation:
This story begins with a family in London who had trouble with language. Some members of the family had trouble speaking and understanding grammar. They turned out to have an inherited language disorder, and scientists were able to use the family’s genealogy to pinpoint the gene involved, which they dubbed Foxp2.

...

To get a sense of how this new version of Foxp2 might have changed the brains of our ancestors, Enard and his colleagues have now tweaked Foxp2 in mice into a human form. Because Foxp2 has changed very little in mammal evolution (except in humans), a mouse version of Foxp2 is a fairly good model for what the gene looked like in our own ancestors. And so this experiment can, in very rough form, replay the transition from the old Foxp2 to the new.

As the scientists report in Cell tomorrow, the mice are generally healthy, but their behavior has changed. Their squeaks are lower in frequency. They explore less. They have less dopamine in the brain, a neurotransmitter that we need to control our bodies and to pursue rewarding things like food. Dopamine is produced in the base of the brain by a clump of neurons called the basal ganglia.
Genetically engineered glowing monkeys pass the glowy genes to their glowy offspring.

Cost of "whole" genome sequencing falls to $24,500.
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Rumors of my lack of attention have been greatly underestimated [May. 27th, 2009|01:08 pm]
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The past few weeks have been a maelstrom of final exams, family emergencies, and serial exhaustion. In the past week I've slept perhaps 70 hours, and I think I'm just now caught up.

I am also mere days from having a complete book with an editor's stamp of approval. From there, to the copy editor. Step n: profit!
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Lady Ace Hardware of Fillmore [May. 23rd, 2009|05:32 pm]
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Eye-catching biology [May. 20th, 2009|04:46 pm]
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DIY [May. 20th, 2009|01:24 pm]
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From kitchen chromatography to stone-age glue.
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Either awesomely terrible or terribly awesome [May. 19th, 2009|10:23 am]
Robert Downey Jr. as Sherlock Holmes, Jude Law as Dr. Watson.

Hilarity ensues.
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The awful truth [May. 16th, 2009|10:40 am]
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Pregnant women are smug [May. 7th, 2009|10:53 am]
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Pregnant Women are Smug -- powered by Cracked.com
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Impact factors aren't usually measured in dollars [May. 5th, 2009|04:03 pm]
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Merck publishes advertising meant to look like a scientific journal:
It's a safe guess that somewhere at Merck today someone is going through the meeting minutes of the day that the hair-brained scheme for the Australasian Journal of Bone and Joint Medicine was launched, and that everyone who was in the room is now going to be fired.

The Scientist has reported that, yes, it's true, Merck cooked up a phony, but real sounding, peer reviewed journal and published favorably looking data for its products in them. Merck paid Elsevier to publish such a tome, which neither appears in MEDLINE or has a website, according to The Scientist.
You stay classy, Merck.
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Ouch [May. 5th, 2009|12:01 pm]
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"Graduate education is the Detroit of higher learning."

Via [info]nyuanshin. No disagreement with the general premise laid out in the first page, though many of the specific suggestions that follow aren't that impressive. (3-6 aren't bad.)

1. Restructure the curriculum, beginning with graduate programs and proceeding as quickly as possible to undergraduate programs.

Basically, this boils down to "teach everyone everything". As someone who's been working on a curriculum for the past decade, this sounds great but implements terribly. What I want my students to get out of basic chem differs in many ways from what the chemistry and chemical engineering departments (or med schools) want. Too much cross-disciplinary coursework leads to a curriculum by ever-expanding committee. Everyone in the room is convinced that the core of their own discipline is "what every student needs to know", and few are inclined to kill their academic darlings.

2. Abolish permanent departments, even for undergraduate education, and create problem-focused programs.

A separate power structure with attached bureaucracy for every problem? That sounds fun.
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(no subject) [May. 1st, 2009|01:30 pm]

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Newborn neurons crawl along a blood vessel searching for a home [May. 1st, 2009|01:29 pm]
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Break it to make it stronger [Apr. 28th, 2009|04:39 pm]
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Cracks in teeth make them stronger:
As the pressure increases, the occasional tuft gets much larger and breaks away from its neighbours. But for the most part, they grow very slightly and in unison, shielding each other from the full force of the stress. This shielding explains why it's easy to start a crack in a tooth, but difficult to finish it.

Chai also suggests that the tufts help to bridge the physical differences between the hard, brittle enamel and the softer, more flexible dentin lying underneath it. That protects the dentin, by providing a smoother gradient between the otherwise starkly different properties of the two materials.

Other microscopic feature make it harder for individual cracks to get larger. Enamel consists of thousands of cylinders called "prisms" or "rods", each consisting of aligned mineral crystals. The prisms are arranged in rows, which can often cross over one another like a basket weave. On a cross-section of a tooth, you can see this weaved pattern as alternating dark and light lines.

By regularly switching their direction, the prisms make it harder for cracks to grow in any particular one.
Sweet.
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Biotech roundup [Apr. 28th, 2009|02:53 pm]
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The personal genomic project is looking for volunteers to get their genomes sequenced.

Autism linked to a between-gene DNA variant that may change the expression of cadherin genes (which are involved in contacts between neurons).

Extremely enhanced bioengineered corn: "The resulting plants had double the usual amount of folate, sixfold levels of ascorbate and 169 times more beta carotene. At that level of expression, a single serving of corn can provide a recommended daily beta carotene intake."

Fluorescent puppies - latest in a long line of glowy transgenic animals.
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