Compendium December 2011

So I have been writing for a while now. Early on my writing was a public log of my journey into triathlon. I have been thinking about writing again about my recent revival and injury, but mostly stopped that after a while. The Top few, and a couple that bridge boundaries are repeated so people who only are interested in certain topics can still read them.

My top few:
1) Corporate Venture Capital (2011) - Listed this first out of order. I WANT the right people to read this and consider it!
2) China's Command Economy, Resource Efficiency, and the worlds Geopolitical Future (2009)
3) The Art of Triathlon (2009)
4) Market Based Health Care (2009)
5) Aerobic Training Theory, History, and Methodologies. My take... (2010)
6) The Compton Cookout, and Isadore Hall III: McCarthy's New Age Revival (2010)
7) Climate Prediction Accuracy (2010)
8) Exercise and The Brain. The Body-Mind Connection! (2010)
9) Denialism and FUD (2010)
10) Future Tech: Quantum Redux (2010)
11) Carpe Diem (2010)
12 DNA Replication in silico (2011)
13) Greentech and Alternative Energy (2011)
14) Could we need a revolution any worse? (2011)

Philosophy:
My Departure from Luxtera - Cool note I wrote when I left/got fired a job and how excited  I was.
Wealth Inequality (2008) - Musings from 2008 on Wealth inequality and how USA is actually pretty bad. Seems Media and Public is finally coming around to this.
Denialism and FUD - Thoughts on how we are often bombarded with illogical fallacies disguised as arguments.

Politics:
Signing Statements - One of my criticisms of the Obama administration, along with continued gross abuse of warrantless search and surveillance.
Market Based Health Care - My early musings on how we should implement healthcare reform. I still mostly agree.
Corporate Venture Capital - My thoughts on how we could use the current cash pile to grow our economy's infrastructure and make money!
Being Environmentally Friendly does NOT cost money - Self Explanatory
The Compton Cookout, and Isadore Hall III: McCarthy's New Age Revival - Writings in response to a racist incident at UCSD and a politicians response.
Could we need a revolution any worse? - Comments on my disgust regarding government waste, inefficiency and graft.

Sports/Training (these articles often also involve a good amount of philosophy):
The Art of Triathlon - One of my favorite pieces. Musings on triathlon right as I started Ironman Peak and Taper before IM Cozumel in 2009.
Aerobic Training Theory and History - Good compendium for those looking to maximize training results.
Exercise and The Brain. The Body-Mind Connection! - My views on how activities affect our mind, body, and soul.

Socio-Political Stuff:
China, Resources, and the World in 2009 - China and my view of the world in 2009.
Being Environmentally Friendly does NOT cost money - Self Explanatory
Corporate Venture Capital - My thoughts on how we could use the current cash pile to grow our economy's infrastructure and make money!

Tech:
Weaknesses in modern Data Mining - How not thinking "4th dimensionally" as I like to say affects the way we search data.

Science (often get's philosophical as well):
Lack of Genetic Diversity in key crops - The risks we are inducing by reducing our key feedstocks to a VERY small number of species. Also how natural systems could be more effective than pesticides etc,
The evolution of the online ecosystem - cool musings on the internet
Whole Genome Transcription Paper - Paper I wrote software for and collaborated on.
Climate Prediction Accuracy - My call for predictive accuracy to determine our belief.
Roundup Resistant weeds ATTACK! - More comments on how our attempts to subvert nature are hapless, and a call to return to more natural methods.
Future Tech: Quantum Redux  - Cool things coming out of quantum mechanics science
Future Tech II: Supersolids, Meta Materials, Varying Fine Structure Constant, and Maxwell's Demon! -
Come more cool things coming out of crazy futuristic science
DNA Replication in silico - Cool accidental genetic inheritance in gene chips.
Greentech and Alternative Energy - Defining the concepts.

A couple of instructive postings (read if you wanna learn):
The Vestibular System - Random cool physiology thing
Error Analysis - Basics
Memristors - New basic electronic component, that can sorta behave like a NEURON in silico!
Infrared -vs- Thermal Junction Temperature Sensing Part 1
Infrared -vs- Thermal Junction Temperature Sensing Part 2


And some random Musings.

I left out the stuff that was a bout news events. Hope you enjoy and give feedback on the page as well as the articles!

Green tech and ALTERNATIVE energy

I've actually been saying this for a while. We have NO long term studies showing Solar, Wind, or anything is in any way more sustainable, or sustainable at all. It's JUST another source that could allow us diversified and safer energy supplies, possibly at lower long term cost. It's really just business guys, and it's not more proper in any way. I read this article that got me thinking today about the "myth of renewable energy." Of course no matter how close we get I don't think the wildest machinations contemplated in something like The Singularity is Near will result in endless energy, though we may make it so trivial it's of no consequence.

I think it's important that people differentiate between alternative energy, and green technology, as I believe there is no way of creating energy that will not have good and bad side effects. I've personally always wondered what effects large numbers of wind turbines for example would do to wind patterns, and could they have effects like El Nino or something else? That being said what we CAN do is persevere through constant innovation to reduce our NEEDS of energy, land, and natural resources through innovative technology. THAT is what green tech is!

If you haven't read Natural Capitalism it's available free online ( I LOVE Somebody who believes in something so much they give away content for free! ) at natcap.org. Reading this book really changed my life. Green Tech = Tech for reducing our foot print like smart meters, more efficient energy production of any type (more efficient solar cells, less wasteful coal plants etc.), motion sensor lights, or even compact fluorescent bulbs.

ALTERNATIVE ENERGY is just another way of generating energy. Geothermal (cool for places like nordic region, who I'm guessing are also not ripe for solar), Dams (do affect ecosystems, maybe reducing floods for people but destroying ecosystems based on their sediment, as well as disrupting breeding), Solar, Wind etc. It's VERY likely that in the long term some of these things will be more sustainable, and cheaper than others. It's also the case that some places don't have oil, or natural gas, or have used most or all of it up. For the US for example reducing oil needs would reduce money that mostly goes to significantly more corrupt (Knowing that our politics is just LESS corrupt) regimes which are often politically opposed to us on global policy.

That makes me wonder the impact we'll see from the revolutions in the middle east on the impetus for alternative energy. I always say that it's silly for any entity to not be self serving for some degree, so I don't think democracy will change their policies on oil (like China recently putting a crimp on exports of rare earth metals), though perhaps joining the WTO would make them have to leave OPEC (can anyone comment on that?). But these musings I'll save for another time.

Could we need a revolution any worse?

So not to long ago I saw an article about a drug that for the cost of $93,000 would extend the life of patients with terminal prostate cancer and average of 4 months. This just disgusted me and was a HUGE symptom of our disgustingly bloated government beauracracy.

This morning I read in the weekend Wall Street Journal that the FDA has pulled Avastin from the market for the treatment of Breast Cancer. Of course we all know the conundrum of prescribing off label, but another reference article also quotes and notes:

“Medicare will continue to cover Avastin,’’ said Brian Cook, spokesman for the Centers for Medicare & Medicaid Services. The agency “will monitor the issue and evaluate coverage options as a result of action by the FDA but has no immediate plans to change coverage policies.’’ Including infusion fees, a year’s treatment with Avastin can reach $100,000.

The middle east is not the only place where it's time for an uprising that has been long coming. The government of the United States of America is so corrupt and convoluted it is time for a change. The occupy movement probably has it right. When payoffs and lobbying result in a medicare system with problems like those mentioned above even as we are teetering on the brink of insolvency the government is NOT WORKING!

Having recently read The Tipping Point by Malcom Gladwell and reading about the Broken Windows Theory I believe this is translating into our monetary and philosophical ethos in the United States. We are BROKE And are spending BILLIONS we don't have on WAR, unaffordable drugs and treatments, and lining our legislators pockets.

Why should anyone pay their mortgage? Why should anyone work and be a productive part of society? Why should anyone live within their means and try to get along with people who disagree with them? Despot's in the middle east, along with our politicians do NONE OF THESE THINGS! I'm starting to feel the occupy movement represents the people saying "We can clearly see everything is broken!"

It's time for a flat tax. No loopholes, and no budget for an IRS we don't need! No more insider trading on the part of our congress men and women. No more entitlements. Everyone get's the same medical care INCLUDING our government representatives. Sorry but the retirement age has to rise! Sorry medicine is NOT free and we can't give everything to everyone!

 Where do we start? How do we start? The time is clearly now!

Corporate Venture Capital

Right now we are sitting on PILES of $$ at big US multinational firms. I've been hearing commentary for example Berkshire Hathaway authorizing share repurchase at Buffett's discretion. I found a quick article indicating there's almost 1 trillion of CASH on corporate balance sheets. Most of this money is probably paying VERY low yields and doing NOTHING for their core business or the USA.

Then I read this article on a mountain with literally tonnes of rare earth metals inside, and very little is being done to get at these minerals while China has a monopoly and is constraining exports. Why are these guys going to the government? Many of our biggest and most successful companies depend on things like rare earth metals, infrastructure like transportation, and other things that our government seems unable to break out of gridlock and do much about.

How about a STRATEGIC fund pooled among our top 500 companies. Proportional voting based on contributions. A sort of endowment for US industry. Perhaps it could even be run as a charity. What is important is that this fund looks at things that will make the US succeed in the long term. If public school education stinks, make private schools. If the government isn't handing out enough money for mining, fund it. Need some pipelines and roads. Government is broke, but BUSINESS has money, so we'll fund it.

What would the results be? Certainly all this construction and investment will fuel jobs, and production. Not only will our biggest companies be getting the things they need, but their customer base (the US population) will be growing it's earnings and spending power. Obviously this ecosystem will also facilitate the success of small businesses which are the bread and butter of the United States, not to mention a big customer for those top 500 companies as well.

What could we do with $200 billion to $300 billion dollars INVESTED into our national economy? Nevermind that the big companies funding all of this will make $$ of their investments as well as their core business. Which corporate titans are willing to make this happen? I don't think it will take many to get the ball rolling. Let's not wait for our government. We have a LOT of really smart capable people at the top of corporate America. Let's get it done!

DNA Replication In Silico

"Did you get that new Anti Virus Software?"
"For my computer?"
"No for your gene sequencer!"

So I read an interesting post on an MIT blog about Mycoplasma contaminating "the human genome." I think its a bit of a stretch, but in fact it looks like bacterial DNA has corrupted what we call the "human genome." Literally bacterial DNA has slipped in via contaminated cell cultures. Now when we test gene expression from a human sample, it appears we are also frequently checking for mycoplasma genes as well.

How does this happen? The article mentions another study that indicates a large amount of human cell contamination in samples from other species that we have sequenced. This is no surprise as biologists ARE human (right?). But this means we are slowly corrupting the data that we use to compare other species for similarity using tools like BLAST and other methodologies. On the flip side viruses and mycoplasma which are VERY small, hard to detect, and hard to filter are all over the place, and easily contaminate and multiply with laboratory samples.

So in a sense there is "replicating" DNA propagating through gene chips, sequencing tools, and our knowledge, though it doesn't QUITE meet our definition of a living organism, much like viruses and prions they are replicating simply one way or another. What's really scary is that once we start working gene therapy by for example splicing DNA into a retrovirus, which then starts re-writing our DNA with synthesized strings we could complete the loop.

This will be just another example of horizontal gene transfer. For all eternity we have had ways of exchanging DNA without literally being related, or through a myriad of epigenetic ways, by viruses which infect us by splicing their genetic material into OUR DNA and using the cellular apparatus to reproduce, occasionally leaving pieces behind, or taking a piece of our code along to the next host. This has occurred NOT just between humans, but humans and animals, plants, and other organisms some as close as the bacteria that live symbiotically in our gut.

Soon the list of things we exchange genetic code with will not just contain carbon based plants, animals, bacteria, and fungi, but carbon based silicon chips and information networks. We could have a bit error in an encoded DNA strand, or a virus that re-writes a character. Imagine a future where machines can directly affect our bodies through a myriad of ways.

Armageddon. OK, not really, but Nature is kicking our ass!

Personally I have lived about half my life in San Diego or One of it's Suburbs... I did brief stints as a wee one in LA and NYC before moving to Poway when I was about 4 where I lived until I moved to Austin when I was 14.  Now as a child, rain was VERY rare indeed. Poway was naturally dry and hot, which is not really odd since southern California is mostly a freakin' desert anyway. Those ten years in Poway I basically NEVER saw rain. I do recall it was a drought, and there were all kinds of water rationing and fire warnings. I guess officially my recollection is likely based on the period from 1987-1992.

Then I moved to Austin Texas in 1994. WHAT A CHANGE!!! In Poway even 100 was not really that bad. I remember getting off to the plain and feeling unable to breath from the Humidity in the air! I LOVE Austin but frankly summer's there suck. Month long periods of dense humidity where it's still often 80 degrees when the sun is about to COME UP!

Where am I going with this? Well nature is a fickle friend. I noticed when I went to Austin for a couple weddings (avoiding parking garages at all costs....) and while I LOVED the weather, apparently that dryness was the result of massive drought. My friend Ginni's wedding was actually on the Lake and you could see how low the water level was. Apparently it is the driest 7 months on record!

Here in California we've been complaining of wet weather all winter, and we have been getting HAMMERED with snow in the Sierra Nevada range and other mountains. I read in the LA Times that too much snow has resulted in a 12% DECLINE in skiers because people couldn't get to the slopes, or felt unsafe.

Nature has been showing it's teeth in even louder ways so far this year. We have recently had a rash of tornadoes in the South that easily qualifies for the biggest natural disaster since Hurricane Katrina in 2005, which took the lives of 1800 people and destroyed New Orleans along with tons of other negative effects. So far 481 Americans have been killed by tornados this spring! News reports indicate 116 or 117 people have been killed in a recent tornado in Joplin! While researching sources for this article, I found a post that was making a similar observation of recent natural phenomenon's excesses. 

Earlier this year a massive 9.0 earthquake hit Japan, along with a massive Tsunami which caused enough trouble on it's own. THEN came problems with radioactive contamination, and resulting collateral problems to energy security for Japan. Currently in the United States after bad Hurricanes, and the BP spill in the Gulf of Mexico, Louisiana is currently under historical flooding problems, and the Army Corps of Engineers is working hard to save two major cities, New Orleans and Baton Rouge from flooding at the cost of flooding mammoth swatch of countryside and farms.

What's coming next I wonder? 2011 promised to be an interesting year in many ways, but I'll be keeping a close eye on nature!