http://functional-strength.blogspot.com/2010/11/lessons-learned-as-adolescent-and-adult.html

http://functional-strength.blogspot.com/2010/11/lessons-learned-as-adolescent-and-adult.html

funness

things are fun to do every once it a while, but you suck at them

things you do alot, you are good at, but there are no fun.

what a pain.

One time, for real though, I did put 2 Q-tips in my ear at the same time and I took a shit

"One time, for real though, I did put 2 Q-tips in my ear at the same time and I took a shit.  It was the best feeling ever."

-Joe Rogan

Green Jolly Ranchers

Green Jolly Ranchers taste like soap.  I wish they would make a new flavor.

ideas

It is not possible to live in cleanliness 
Having property taxes fund public schools is wrong 
It is not reasonable to expect the best healthcare that money can buy, unless you are willing to pay for it. 
Don't borrow money to buy things that you do not need. 
Long term prison sentences don't make any sense. A sentence of up to a few years is a practical punishment. A life sentence for someone who cannot remain in society makes sense. What is a 30 year sentence supposed to do? 
We should spend as much resources as neccesary to assure that all children are as well educated as is practical. 

Biology

The function of a diploid genome is poorly understood. Intereactions between spefici allele combinations must be prominant, but this generally unappreciated.

Energy

Reusing and repairing things is fundamentally better than making new ones, even if it requires more immediate resource to rebuild or repair.
At 1 kw / square meter solar energy, 10% efficency, 8 hours per day of sunlight, each year a 1 square meter photovoltaic panel will produce the same amount of electric energy as the heat energy content of seven gallons of gasoline.
1 gallon of gasoline contains 41 kw hours of heat energy
1 horsepower is 746 watts
Wireless transmission of eletric energy would be a huge invention
Hydrogen is not an energy source
There are 100 million men in the USA that flush when they urinate. If they pissed in the sink and ran 1 pint of water down the sink instead of using 1 gallon of water in a flush toilet, 1 urinations a day, 365 days a year, it would save 32 billion gallons of water and sewage.
Nuclear power is not sustainable because the problem of radioactive waste has not been solved.

ES cells

Human embryonic stem cells and reprogrammed cells virtually identical CAMBRIDGE, Mass. (August 5, 2010) – Human embryonic stem (ES) cells and adult cells reprogrammed to an embryonic stem cell-like state—so-called induced pluripotent stem or iPS cells—exhibit very few differences in their gene expression signatures and are nearly indistinguishable in their chromatin state, according to Whitehead Institute researchers. Their results are published in the August 6 issue of Cell Stem Cell. iPS cells are made by introducing three key genes into adult cells. These reprogramming factors push the cells from a mature state to a more flexible embryonic stem cell-like state. Like ES cells, iPS cells can then, in theory, be coaxed to mature into almost any type of cell in the body. Unlike ES cells, iPS cells taken from a patient are not likely to be rejected by that patient’s immune system. This difference overcomes a major hurdle in regenerative medicine. "At this stage, we can’t yet prove that they are absolutely identical, but the available technology doesn’t reveal differences," says Whitehead Institute Member Richard Young. "It does mean that iPS cells could be useful as personal ES cells in the future." “Billions of dollars have been invested in the idea that we will use ES cells at some point in the future as therapeutic or regenerative agents, but for ethical and practical issues, this may not be possible,” says Garrett Frampton, a co-first author on the Cell Stem Cell paper and a graduate student in the lab of Whitehead MemberRichard Young. “But if they work out therapies with ES cells, and iPS cells are equivalent to ES cells, then the idea is that those therapies could be used with iPS cells as well. Whereas if iPS cells are different from ES cells, then who knows if you can use iPS cells for therapy?” Since iPS cells were first developed in 2006, the similarities and differences between ES and iPS cells have been hotly debated in the scientific community. Thus far, researchers have gauged the cells’ equivalence by determining whether the cells express the same genes, but such studies have yielded mixed results. In revisiting the question of the cells’ equivalence, Frampton and co-first author Matthew Guenther, who is a scientist in the Young lab, analyzed gene expression patterns and the cells’ chromatin structure. Chromatin is the packaging of DNA around a protein scaffold. Variations in chromatin “packaging” can themselves alter gene expression, yet Guenther and Frampton found that human iPS and ES cells to be almost identical in both gene expression and chromatin structure. “At this stage, we can’t yet prove that they are absolutely identical, but the available technology doesn’t reveal differences,” says Young, who is also a biology professor at MIT. “It does mean that iPS cells could be useful as personal ES cells in the future.” Some earlier studies have indicated that iPS and ES cells are dissimilar enough to be classified as different cell types. To see why the results differed so strikingly from theirs, Guenther and Frampton reanalyzed those studies’ data. They concluded that the differences noted in other studies were not consistent between different laboratories and thus were not likely to be a result of fundamental differences between the cell types. “The key question is, are any of these differences functionally relevant? Do they change how a cell matures or not?” says Whitehead Member Rudolf Jaenisch, whose lab worked closely with Guenther and Frampton. “The earlier documented differences were more noise than anything. But other tests may give you a different answer. So it is still an open question, something that the field will continue to struggle with and have to decide.” Guenther agrees. “Our paper addresses the ground state of iPS and ES cells in a laboratory setting,” he says. “But we don’t know for a fact that they won’t behave differently when they mature into various cell types or tissues. That’s the next step.” This research was supported by donations from Liliana and Hillel Bachrach, Landon Clay, and Susan Whitehead.
	Written by Nicole Giese. * * *  Rudolf Jaenisch's primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology. Richard Young’s primary affiliation is with Whitehead Institute for Biomedical Research, where his laboratory is located and all his research is conducted. He is also a professor of biology at Massachusetts Institute of Technology. * * * Full Citation: “Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells” Cell Stem Cell, August 6, 2010 Matthew G. Guenther (1,3), Garrett M. Frampton (1,2,3), Frank Soldner (1), Dirk Hockemeyer (1), Maya Mitalipova (1), Rudolf Jaenisch (1,2), and Richard A. Young (1, 2). 1. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA 2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA 3. These authors contributed equally. Whitehead Institute for Biomedical Research is a nonprofit, independent research and educational institution. Wholly independent in its governance, finances and research programs, Whitehead shares a close affiliation with Massachusetts Institute of Technology through its faculty, who hold joint MIT appointments.

randomness

Additionally the are two other things that we have learned about ES cells which might end up being general principles. Binding occurs at distal enhancers which physically interact with proximal prometers. Fifth platform for singaling pathways.

One of the major limitations of current biology research is the availability of sufficient quality and quantities of biological material. Cell culture systems are available that recapitulate many important biological processes, but in many ways research is limited by the limitations of these systems. In the future several avenues could be used to overcome current limitations in the biological material for research. The first is the creation of new cell culture systems and the development of new method to collect primary tissue samples. Clearly, this type of advance will give researchers new systems and source of material to study. The second avenue is to improve genomic assays to work on smaller quantities of starting material. This would allow work on highly pure specimens of rare primary cells types that cannot be isolated in sufficient quantities for current methods. Ideally, it would be possible to assay the genome-sequence, histone modification pattern, DNA methylation state, transcription factor occupancy, and RNA content of a single cell. How distal regulatory elements make specific 3 dimensions connections

A new stat for football

( (Percent of distance to 1st down) plus (yards after 1st down / 10) ) per carry

AI

I think the scary part is how the robot hand went from ponderously and kind of clumsily hardly being able to do anything useful a generation ago - skipped straight over being equally as good as a human hand - to being faster, more accurate and more dextrous than a human hand in this video.  Either it can't bounce a ball at all or it can bounce a ball a thousand times a second and you can't even follow it with your puny human eyes.

It's not AI - but you can suddenly see what they are on about with the idea of a singularity - in the same week that AI is able to operate as intelligently as a human mind - they will be 100 times smarter than us.

GWAS

Any gene (allele) that caused disease by itself would be strongly selected against.  A more realistic scenario is an allele that causes a disease when paired with some independent alleles and prevents disease when paired with other independent alleles.  This would not be discovered with current study designs.  An allele that caused disease only when paired with some other alleles (never prevented disease) wouldn't even be found.  The fact that this is not mentioned in this story and not mentioned in much of the gene/disease association study literature makes me angry.  I feel like everyone is stupid or hiding the truth on purpose.

biology ramblings

One of the major limitations of current biology research is the availability of sufficient quality and quantities of biological material.  Cell culture systems are available that recapitulate many important biological processes, but in many ways research is limited by the limitations of these systems.  In the future several avenues could be used to overcome current limitations in the biological material for research.  The first is the creation of new cell culture systems and the development of new method to collect primary tissue samples.  Clearly, this type of advance will give researchers new systems and source of material to study.  The second avenue is to improve genomic assays to work on smaller quantities of starting material.  This would allow work on highly pure specimens of rare primary cells types that cannot be isolated in sufficient quantities for current methods.  Ideally, it would be possible to assay the genome-sequence, histone modification pattern, DNA methylation state, transcription factor occupancy, and RNA content of a single cell.  

Genome Wide Association Studies

Maybe I'm misunderstanding something, but as far I understand it, genome wide association studies look for single polymorphisms that are correlated with disease, and do not currently have much power to detect combinations of polymorphisms.

I predict that combinations of polymorphisms will explain a large part of the link between genotype and health.  New algorithms to do this mike incorporate additional information linking genes and loci to increase power.

Podcasts worth listening to

Here is a list of the podcasts that I listen to.

Savage Love
This American Life
The Moth Podcast
WNYC's Radiolab
Common Sense with Dan Carlin
Dan Carlin's Hardcore History
The New Yorker Fiction Podcast

ChIP-Seq analysis

In ChIP-Seq data analysis the signal behaves nicely when transformed into the ???? space.

A logarithmic transformation does not behave as nicely.

White Squirrel

I saw a white squirrel in my backyard in Somerville, MA. It was eating a piece of toast with jam.

Random Process?

If you have a complex progess comprised of some deteministic processes and a random process, is the complexes process random or deteministic?  What if there are multiple random proecesses in the overall process?

By 'deterministic process' I mean a proces whose current state can be predicted for it's original state.