Thanksgiving Science!

I’ve got a little formula that predicts how long it will take for our Thanksgiving turkey to cook. It works really well for our temperatures and preparation, but I’d like to make it a little more general so everyone else can use it, regardless of temperature. As a wise man once said, if it’s worth doing, it’s worth overdoing, unless you’re overcooking turkey.

Towards that end, and because this is a science blog, I would like to perform a hypothesis-generating experiment. If you’re willing to further science, please share some details about how you prepared your turkey, and how it turned out. Humanity will thank you. Turkeys will not. I will post the results when I can, and maybe we can try again next year for a full prediction.

Click here to share your turkey data.

How to fix the economy

1. I’m not an economist, so this probably has errors in it.
2. None of these ideas are mine. I’ll hunt down where I got them from as soon as I can. See citations where I put them in.

Businesses aren’t investing in jobs because they have no reason to. They sit on huge piles of cash and continue to make acceptable profits without adding any jobs. Astonishingly, we manage to be in a period when inflation is nil, but prices are still going up. You know what gets people investing in new things? Inflation. Mild-to-moderate inflation drives capital into investments because otherwise the value of that money decreases over time.[1]

How would someone in charge of, say, the Fed, manage to increase inflation? They start by buying debt from banks, which frees up cash in existing banks to make other loans. Home mortgages would be a great start. The Fed can easily start buying up underwater mortgages and forgive the principal above and beyond the current market value. This puts a floor on the housing market and stops the glut of foreclosures, which gives the construction industry something to do again.

I would also start buying up and forgiving student loans of unemployed college grads. This would put them in a position to take greater risks with their careers, either taking jobs that aren’t directly in their fields or giving them room to start up businesses of their own.

This would be hugely controversial, of course, but the Fed chairman is appointed so that he can make these calls. We need something decisive either way, so someone needs to bite the bullet.

But what about everyday prices? Increasing inflation means, in the short term, increases in prices of stuff in general. True, but with the hardest hit people getting loan forgiveness, their overall costs will decrease. Also, investment in new technologies generally decreases real prices even as apparent prices go up. Finally, inflation doesn’t actually impact the poor significantly because they have little savings. In an economy with inflation, wages tend to increase with inflation.

On the fiscal side, there needs to be a resolution to the structural deficit spending. Most of this comes from the Bush tax cuts. Letting them expire takes care of 1/3 of the problem. Another portion of the problem comes from health care costs in medicare and medicaid. These costs can be amortized over a larger population by combining medicare and medicaid into one pool and opening up that pool to everyone. Medicare and Medicaid take care of the most expensive patients in the country, so opening it up to the rest of us would only decrease the overall risk. [2]

Finally, social security can easily be addressed by increasing the witholding limit above 90k. This will put it on sound footing for the next 100 years, based on figures I’ve heard. [2]

1. Krugman, Paul. Why Is Deflation Bad? http://krugman.blogs.nytimes.com/2010/08/02/why-is-deflation-bad/
2. Reich, Robert. What If Everyone Saw This Clip Of Robert Reich Exposing 7 GOP Lies? http://front.moveon.org/what-if-everyone-saw-this-clip-of-robert-reich-exposing-7-gop-lies

Go Out and Vote!

Go vote, if you haven’t already.

Get out the vote. Tell your friends, family, co-workers, fans, enemies, frenemies, random people on the street.

Find out where to vote: http://maps.google.com/vote

Today is the day to make history.

Obama is for Science, We’re for Obama

[Edited to add Obama's positions on NASA and Space Exploration]

Those of you who know me already know that I support Barack Obama for president. I’ve hesitated to post this here, due to the non-political nature of this blog. However, it is long past time for me to make the case for Obama and his policies on science and research. More after the cut on his key positions and why they are important.

Zen Neuroscience: Observing Mindfulness

There are specific neural processes that take place when people meditate, which is demonstrated in the PLoS ONE paper “Thinking about Not-Thinking”: Neural Correlates of Conceptual Processing during Zen Meditation:

Recent neuroimaging studies have identified a set of brain regions that are metabolically active during wakeful rest and consistently deactivate in a variety the performance of demanding tasks. This “default network” has been functionally linked to the stream of thoughts occurring automatically in the absence of goal-directed activity and which constitutes an aspect of mental behavior specifically addressed by many meditative practices. Zen meditation, in particular, is traditionally associated with a mental state of full awareness but reduced conceptual content, to be attained via a disciplined regulation of attention and bodily posture. Using fMRI and a simplified meditative condition interspersed with a lexical decision task, we investigated the neural correlates of conceptual processing during meditation in regular Zen practitioners and matched control subjects. While behavioral performance did not differ between groups, Zen practitioners displayed a reduced duration of the neural response linked to conceptual processing in regions of the default network, suggesting that meditative training may foster the ability to control the automatic cascade of semantic associations triggered by a stimulus and, by extension, to voluntarily regulate the flow of spontaneous mentation.

Cross-Reference Visualizations

Bible Cross-References: The bar graph that runs along the bottom represents all of the chapters in the Bible. Books alternate in color between white and light gray. The length of each bar denotes the number of verses in the chapter. Each of the 63,779 cross references found in the Bible is depicted by a single arc - the color corresponds to the distance between the two chapters, creating a rainbow-like effect.

This is a pretty cool visualization of bible cross-references that was developed by Chris Harrison to show bible cross references throughout the length of the bible. I can’t help but think of how interesting this could be for genome visualization: the cross references could be based on genes that are transcription factors for other genes. (activate or deactivate those genes). Chris has lots of other fascinating visualization projects to look at, and is very stimulating to browse it.

Are Genius and Madness Even Closer Than we Think?

“no great genius was without a mixture of insanity”
- Aristotle

“They say madness runs in our family. Some even call me mad! And why? Because I dared to dream …of my own race of atomic monsters! Atomic supermen with octagonal-shaped bodies that suck blood out of…”
-Prof. Hubert Farnsworth

To be clear, by genius I mean the ability for humans to think at the level we do. And by madness, I mean madness. A recent study suggests that we have our big brains at a high price: schizophrenia. It comes down to the massive metabolism needs that our brains have. A team led by evolutionary biologist Philipp Khaitovich of the Shanghai Institutes for Biological Sciences and the Max Planck Institute for Evolutionary Anthropology created an experiment to see how much genes that are involved in schizophrenia have evolved since humans split from chimpanzees.

Searching for Text in Images

We (my lab, http://krauthammerlab.med.yale.edu) recently published on our new image search engine for biomedical images, called YIF, or Yale Image Finder. From our blog post on our web site:

We have recently released a new biomedical image search engine we call YIF. You can access it at:

http://krauthammerlab.med.yale.edu/imagefinder

You can search the actual image content of over 34,000 Open Access articles from PubMed Central. We use OCR with different levels of image correction (article and corpus) for highly accurate image text extraction.

For more details about our algorithms, we have a paper in Bioinformatics titled “Yale Image Finder (YIF): a new search engine for retrieving biomedical images“.

Double Arm Transplant in Germany Considered Success

15 hours and 40 doctors later, a farmer has two new arms. The surgery replaced both limbs of a farmer who lost his arms in an accident in 2002. He lost both arms below the shoulder. From the Guardian article:

Christoph Höhnke, a surgeon on the transplant team, said that the complicated procedure was completed without any unforeseen problems. It involved a team of 40 doctors, nurses and assistants working together, attaching one arm and then the other. “The whole thing went according to script,” he said.

With a surgery as complicated as this, though, many things can go wrong. The patient can reject the transplants, although close matching of blood and other immunological factors can minimize this, along with drugs that can dampen the immune system’s reaction to foreign bodies. The bones may not completely graft together. It’s like recovering from two severely broken arms on top of everything else.

Nerve regeneration has come a long way, however. The man who received a single arm transplant in 2006 was able to write with the transplanted hand within a year.

“nerve regeneration” at Yale Image Finder.

Running Standard Deviations

My friend Dan at Invisible Blocks came up with a great way to compute a long-running mean from the count and mean:

count += 1
mean += (x - mean) / count

I remembered that I had come up with a similar thing for standard deviation back when I was developing clustering algorithms that could use that value. It uses a power sum average, where you track the power sum as an average (divide the power sum by n) in a similar way.