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Showing posts from 2012

Science: How does high speed DNA sequencing work?

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Every wonder how something works? With all the talk of personal DNA sequences and other leading edge sequence based research methods, I wondered, how do you do high speed DNA sequencing? In Google searches, I found various text descriptions of how they work but couldn't get my head around what they were saying. Finally, hit a link to a youtube video and voila, it makes sense to me now!



Its amazing!

How it works is a synthesis of multiple technologies:
Molecular biology methods to make the DNA samples and extending the strands
Nanotechnology manufacturing of flow cells with capture sites
Fluorescence chemistry
Digital image capture technology
Computing power to turn the captured images into sequence data

Politics: The Baby Boom Cohort

All the talk about what to do about the fiscal cliff is on the relatively short-term side of the story: tweaks of tax rates, elimination/capping of some deductions and relatively minor changes on spending.

The hard reality not being dealt with is the large size of the Baby Boom Cohort (1946-1964). The leading edge of that cohort started retiring in 2011. If life expectancy holds at 78 years, the trailing edge will pass away in 2042. Thus, there is a 31 year window when this group will be collecting Social Security and Medicare benefits.

Unfortunately, program benefits were promised to this cohort that are now financially unsustainable.

But is anyone really addressing this in DC?

I don't have access to CBO economists to project out how big the changes need to be to prevent the deficits and debts from getting worse than they are now. But I would think the most obvious thing to do on Social Security is to begin trimming back the benefit formula and for Medicare to begin asking partic…

Science: The task of a scientific publication reviewer

One of the professional community service responsibilities of a scientist is to review articles submitted for publication. There aren't any formal classes on the process. Most of us learned to do it by seeing it done by more experienced reviewers.

A recent Google search turned up this article.

I thought it offered a good perspective on the process and summarized into 10 rules.

I suppose their Rule 4: As a Reviewer You Are Part of the Authoring Process has been my main guiding principle.

When someone in our research group writes a paper and circulates it for comments, our task is to look for gaps in the data, unclear explanations to be cleaned up and over-reach/flaws in the conclusions. The goal is improving the paper. And so, as a reviewer, I try to have that mindset.

I also found Rule 3: Write Reviews You Would Be Satisfied with as an Author to be crucial in finding the right tone of voice. Being at the receiving end of sarcastic reviews or reviews that make you wonder if they re…

Life: A Day of Loss at Sandy Hook Elementary School

Despair we fight to keep at bay
As we cry for those lost today
May arms enfold those who sorrow
And love be present when they awake tomorrow
To those near give strength for the sad to borrow
To have hope renewed in the days after tomorrow

Politics: Balancing the federal budget 2% spending, 3% economic and 5% revenue growth scenario

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Okay, let's be more optimistic and say that the economy will grow at 3% per year on average leveling out booms and busts. Using the similar concepts as described previously, we set spending growth to 2% and revenue growth to 5%, we get to balance at 2027 just like in the 1-2-4 scenario. The final balance point is around 21% GDP. See graphs below:


As an FYI, the starting point data I used was obtained from the White House budget history web page. Specifically, I looked at table 1.3 and used the data in "current dollars" and "as percentage of GDP." They offer budget projections to 2017. What is quite striking is that their rate of revenue increase and spending are considerably higher than the rates I've proposed above. Also, they assume economic growth rates of 4 to 6% per year! We have hit 4% and higher only 9 years out of the last 32 years with the last time in 2000 according to World Bank data. In the last 10 years, we have only hit 3% growth on 3 occasion…

Politics: Balancing the budget is as "easy" as 1-2-4

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Balancing the Federal budget is about bringing the revenue line up and the spending line down when measured against the GDP. When measured against absolute dollars amounts, it is about flatting the spending line and getting the revenue line going up a bit faster.

If the economy is growing at 2 to 4% but spending is growing at 5 to 7%, the deficits will continue and debt will pile up which has been occurring for the last decade under both Republican Bush and Democrat Obama administrations.

So fixing the deficit and thus getting the debt under control is as "easy" as 1-2-4.

Cap growth of government to 1% per year. Assume GDP growth at 2% per year. Raise revenue by 4% per year. Do this and the budget balances by 2027.

However you slice up the numbers, the growth rate of government MUST be lower than the growth rate of the economy or else we will be forever chasing our own tail. The reality is that the US economy has been growing at about 2% per year on average over the last cou…

Politics: The Good Old Days of President Clinton?

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There is a lot of talk about the fiscal cliff.

One thread in the conversation is that the tax rates will rise from the the Bush era rates back to the Clinton era rates and Democrats state that the Clinton era was an economic boom time. But will the Obama administration and his allies in Congress also lobby for Clinton era spending levels?

Indeed, revenue during the Clinton era ranged from 17-20% of GDP. I'm not an economist so I don't know how much of the rise in revenue was due to the increased tax rates and how much was due to the economy booming.


The spending during that same period ranged from 21-18%. Spending declined as Clinton worked with the GOP Congress to reduce overall spending of which a certain amount was the post-Cold War defense draw down.

Fast forward to where we are now where any deal on the Fiscal Cliff will probably involve an increase in taxes. The current talking point is tax rates should rise to Clinton era levels for those $250,000 and above. As such, u…

World: Hewitt Interview of Author of "Little America"

Another interview spanning the full broadcast was with Rajiv Chandrasekaren who wrote Little America: the war within the war for Afghanistan.

Rajiv covers the good, bad and ugly of the US effort in Afghanistan. No question a lot of good intentions, bravery in the battlefield but sadly there was poor policy choices in the "nation building" project.

One particularly aggravating example was USAID unwillingness to help the Afghans grow cotton because the US wants to protect its cotton industry.

Another was authorization of the surge in Afghanistan but not sending enough troops and then pulling them out so quickly indicating that Washington was half-hearted about the effort.

World: Hugh Hewitt Interview of Jake Tapper Author of "The Outpost"

Hewitt devoted his entire broadcast to hearing the story behind "The Outpost."

The book gives a ground level view of the battle at Combat Outpost Keating in Afghanistan. But beyond the battle itself, Tapper delves into the people there - those who survived and those who didn't - and the people back home who love them. He also went into the history of the base leading up to the fateful battle. A story of incredible valor and infuriating decision making that left those troops in such a precarious location.

Riveting radio.

Here is a video clip from Jake Tapper on his book tour launch explaining how he got started on writing the book.


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Here is another clip from the same book tour launch with remarks from some of the soldiers profiled in the book.


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Business: Twilight for Twinkie & the Auto Bailout

The latest mediation effort has failed and as such a court supervised liquidation appears to be the next step. Companies will probably buy up some of the Hostess brands and facilities. Will be interesting to see what survives and what doesn't and in what form.

Hostess employed 18,500 people.

A handful of years ago, GM and Chrysler was essentially in a similar position: unable to pay its bills, too many unprofitable brands, costly union contracts and excess capacity. But since that industry employed so many more people, the pressure to bail them out was tremendous. The Federal government bailed them out at a cost that is still uncertain despite claims it was a success. Here is a video that explored some of the problems of the bailout beyond taxpayer cost including favoritism to unions, business decisions driven by political considerations instead of economic ones and moral hazard.

One wonders how would things have unfolded if GM and Chrysler had gone through traditional bankruptcy …

Business: Twilight for Twinkies

I have to say I ate them as a kid but not often and haven't had one in decades.

But in any case, Hostess bakery is going out of business and the union blames management and management blames the unions.

If indeed, management was lousy, a company will buy some of the assets of Hostess that are profitable and some of the union jobs will be restored.

But I suspect as more and more Americans are health conscious about eating habits, Hostess successor company will have to change their product line quite a bit.

As for AFL-CIO President Trumka's attack on Hostess, Bain and Mitt Romney: it is emotionalism and disconnected from economic reality. His charges against mis-management of the company probably has some validity but the changing marketplace which the leadership probably failed to respond adequately to and union demands probably pushed the company over the brink.

On a broader question of unions, the one big difference between a union in the private sector and the public sector …

Politics: The press can dig up stuff when it really wants to

Wow, that was fast.

The news broke about the Gen. Petraeus scandal and now a torrent of news stories have come out since.

Meanwhile, over 2 months ago, 4 Americans were killed in Benghazi and the story of what really was going on before, during and after the attack still remains somewhat opaque such that Sen. McCain has called for a Congressional inquiry which probably won't happen because everyone is focused on the Petraeus scandal and the Fiscal Cliff.

The media likes to think of itself as the watchdog of those in power and revealers of the truth but here is an example where they go after the stories they like: sex and generals instead of why there are dead diplomats.

Some used to call Reagan the Teflon President but I think these past four years have shown the Obama should have that title.

UPDATE: Heard that President Obama will be holding a press conference. Will be interesting to see how dogged the questioning will be on the various topics.

PS: Of course, the timing of everyt…

Politics: What is the "Fiscal Cliff?"

There is a lot of talk about the "fiscal cliff" and that we should NOT go off it at the beginning of 2013.

As I listen, I've been trying to figure out what this thing we should avoid really is?

From what I gather:
(1) On the revenue side, Bush era tax rates will revert to previous rates resulting in a $500 billion tax increase next year.
(2) On the spending side, the sequester will cut non-defense discretionary spending, around $54.5 billion
(3) On the spending side, the sequester will cut defense spending, around $54.5 billion.

The fear is that going over the cliff will return the USA into a recession.

This item in the WaPo describes what might happen if nothing is done and also describes the political incentives each interest group has in wanting to go over the fiscal cliff.

In brief:
One group thinks taxes are too low and so they want item #1 to happen and will live with item #2 and item #3.
One group wants all spending to be cut  and like items #2 & 3 and will li…

Politics: the Power of Voter Turnout

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I've understood in the abstract that if you can turnout your voters you can win.

From the election day numbers, there was a D+6 turnout and Romney took independents by 5 and President Obama won re-election handily.

Show me the numbers:

Plugging in the numbers described above along with some other bits of information I've heard regarding the exit polls, you get a 3% win.

How much would the turnout need to change in order to tip the balance?

Scenario 2 has D+2.

If you had scenario 1 (D+6), how many independents would you need to win to change the outcome?

That is scenario 3 where Romney would have won if he could win independents by 16%.

Suffice to say, it is probably easier (though not easy) to bring the D+6 down to D+2 than to move independents from +5 to +16!

Now, I can see why they say, it is all about turnout.

Politics: The Day After the Election, Part II

As an observer of the political process, I spent the last week making a series of post about swing state polling and the electoral college.

My three take aways are marked in bold.

In polling, the perspective is "polls are generally right unless they aren't" and last night, they were generally right.

There were reasons, which I went into, as to why the polling might have been mis-reading the public but in the end the state level polling that showed a comfortable lead for the President turned out to be correct and the national level polling that showed a close race plus/minus 1% turned out to be within the margin of error and correct as the President will clear about a 2% popular vote victory.

It was thought that it was unlikely that Obama's turnout would be as strong as 2008 and that Romney's turnout would improve on McCain's. The question was whether the combination of increase on one side and decrease on the other would change the outcome.

In 2008, Obama rece…

Politics: The Day After Election Day, Part I

As a citizen of the USA, I knew, regardless of who would win the election last night, our country faces a number of serious challenges and heavy responsibilities would be upon those elected. As a Romney-Ryan supporter, I was disappointed but not surprised by the outcome. Before I called it a night last night, these were my thoughts:

Congratulations to President Obama on his re-election.

Thank you Gov. Romney for expressing the views of many in our nation.

My prayer for our nation: "Lord, we commend this nation to your merciful care. Guide us that we may dwell in peace. Grant to the President of the United States and to all in authority, wisdom and strength to know and to do justice and love mercy and to serve with humility. Fill them with love of truth and righteousness. Make them ever mindful of their calling to serve the people with reverence to You through Jesus Christ our Lord, amen.

I think the prayer I wrote down would have probably been the same if Mr. Romney had been el…

Politics: Election Day In America

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Got to my polling place 10 minutes before opening at 7AM. By the time, the poll worker announced, "The polls are open," there were 20 in line. I got in and marked my ballot with the ink-a-vote pen and feed it into the reader. My ballot was the second one cast.

All across America, this civic ritual is taking place in fire stations, homes, schools, church gyms and condo/apartment recreation rooms.

As one born in the USA, I've known this opportunity since I was 18. This morning, I think about those new citizens and the excitement they feel the first time they cast a ballot. For some in this world, casting a vote is a charade for dictators to say they have 99% of the support of their people. For some in this world, the possibility doesn't even exist.

Let us take on this responsibility with gratitude and sober mind. And let us offer up a prayer for those elected to govern whether we voted for them or not.


Politics: Electoral College Project November 201

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If the state polling aggregate numbers at RCP are correct:



What if the state polls are under-reporting GOP strength by 1% and undecideds break 2-to-1 for the challenger?

Method:
1. Using the RCP state poll averages for data (O, R)
2. R1 = R*1.01 adjusts for tendency of polls to under-sample Republican voters - this is a debated assumption about systemic error in polling
3. und = O - R1 this is the percent undecided voters
4. O1 = O + (und*0.3333) and R2 = R1 + (und*0.6667) accounts for the debated assumption that undecided voters break 2-to-1 for the challenger
5. O1 + R2 to check to see if the numbers add up to 100%
6. O1 - R2 yields the final vote in that state; a negative value means Gov. Romney wins that state while a positive value means President Obama wins that state
7. EV is the electoral vote value of the state
8. O-EV and R-EV gives the various electoral college totals for the candidates if they hold/lose that state.

Result: President Obama 281 Gov. Romney 257


In order for the …

Non-profit of the Month: November 2012 - Americares

When disaster strikes, and Hurricane Sandy definitely fits the description of a large scale disaster, there are a handful of groups that are large enough and have the experience to get moving quickly. One that I have donated to in times like these is Americares.

Hope you will take a break for all the political news and find a group you can donate to and help our fellow Americans in this time of great need.


Politics: Electoral College Forecast for Nov 2012

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Method:
1. Using the RCP state poll averages for data (O, R)
2. R1 = R*1.01 adjusts for tendency of polls to under-sample Republican voters - this is a debated assumption about systemic error in polling
3. und = O - R1 this is the percent undecided voters
4. O1 = O + (und*0.3333) and R2 = R1 + (und*0.6667) accounts for the debated assumption that undecided voters break 2-to-1 for the challenger
5. O1 + R2 to check to see if the numbers add up to 100%
6. O1 - R2 yields the final vote in that state; a negative value means Gov. Romney wins that state while a positive value means President Obama wins that state
7. EV is the electoral vote value of the state
8. O-EV and R-EV gives the various electoral college totals for the candidates if they hold/lose that state.



Result: President Obama 281 Gov. Romney 257

Poll pros who really do this seriously:
538 (306-232, Obama)
electoral-vote.com (281-206, Obama, 51 too close to call)
electionprojection.com (290-248, Obama)

I'm just a "blogger …

Politics: 2012 Electoral College Projections

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Method:
1. Using the RCP state poll averages for data (O, R)
2. R1 = R*1.01 adjusts for tendency of polls to under-sample Republican voters - this is a debated assumption about systemic error in polling
3. und = O - R1 this is the percent undecided voters
4. O1 = O + (und*0.3333) and R2 = R1 + (und*0.6667) accounts for the debated assumption that undecided voters break 2-to-1 for the challenger
5. O1 + R2 to check to see if the numbers add up to 100%
6. O1 - R2 yields the final vote in that state; a negative value means Gov. Romney wins that state while a positive value means President Obama wins that state
7. EV is the electoral vote value of the state
8. O-EV and R-EV gives the various electoral college totals for the candidates if they hold/lose that state.

Result: President Obama 275 Gov. Romney 263


Poll pros who really do this seriously: 538
electoral-vote.com
electionprojection.com

I'm just a "blogger in pajamas" but why should they have all the fun?

The discussion wit…

Politics: 2012 Electoral College Projections

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Method:
1. Using the RCP state poll averages for data (O, R)
2. R1 = R*1.01 adjusts for tendency of polls to under-sample Republican voters - this is a debated assumption about systemic error in polling
3. und = O - R1 this is the percent undecided voters
4. O1 = O + (und*0.3333) and R2 = R1 + (und*0.6667) accounts for the debated assumption that undecided voters break 2-to-1 for the challenger
5. O1 + R2 to check to see if the numbers add up to 100%
6. O1 - R2 yields the final vote in that state; a negative value means Gov. Romney wins that state while a positive value means President Obama wins that state
7. EV is the electoral vote value of the state
8. O-EV and R-EV gives the various electoral college totals for the candidates if they hold/lose that state.

Result: President Obama 275 Gov. Romney 263

Poll pros who really do this seriously:
538
electoral-vote.com
electionprojection.com

I'm just a "blogger in pajamas" but why should they have all the fun?

If one takes the s…

Politics: Nov 2012 for Culver City Voters Measure Y

Had the chance to hear the mayor of Culver City (Weissman) and one of the council members (Clarke) talk about Measure Y, a sales tax increase that will help help get the city budget in balance.

The two speakers pointed out that cuts have been made in the city workforce and pension commitments renegotiated but that the hole in the budget from the end of redevelopment agency funds and economic downturn was still eating into the city's reserves because of a structural deficit.

Here it an op-ed from the vice-mayor Cooper.

Culver City is a relatively small city of 40,000 and much of the budget goes to basic services like police, fire, sanitation, transportation and parks. The rise in sale tax will leave Culver City with rates comparable to neighboring cities. Additionally, the sale tax has a sunset provision (10 years) and could be rescinded by a vote of the city council.

The measure received support from the Culver City Chamber of Commerce.

I'll be voting Yes on Y.

UPDATE: The LAT…

Politics: Nov 2012 LA County - Measure J?

Measure R passed a few years back raising sales tax for 30 years to fund transportation projects.

Measure J on the Nov 2012 ballot for LA County voters will extend that sales tax for an additional 30 years. This extension will permit the County to borrow money in the next decade and use the future revenues to help pay off the debts.

LA Weekly has a good summary of the pros and cons.

I'm leaning toward a NO vote on this item.

Politics: Taking a guess at the 2012 electoral college outcome

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Method:
1. Using the RCP state poll averages for data (O, R)
2. R1 = R*1.01 adjusts for tendency of polls to under-sample Republican voters - this is a debated assumption about systemic error in polling
3. und = O - R1 this is the percent undecided voters
4. O1 = O + (und*0.3333) and R2 = R1 + (und*0.6667) accounts for the debated assumption that undecided voters break 2-to-1 for the challenger
5. O1 + R2 to check to see if the numbers add up to 100%
6. O1 - R2 yields the final vote in that state; a negative value means Gov. Romney wins that state while a positive value means President Obama wins that state
7. EV is the electoral vote value of the state
8. O-EV and R-EV gives the various electoral college totals for the candidates if they hold/lose that state.

Result: President Obama 271 Gov. Romney 267


Poll pros who really do this seriously:
538
electoral-vote.com
electionprojection.com

I'm just a "blogger in pajamas" but why should they have all the fun?

Politics: States to Watch on Election Night

If Obama wins the same states as in 2008 = 358 electoral votes.

I list the states Obama might lose with the top ones most likely and the bottom ones least likely.
Lose Indiana (11) = 347
Lose North Carolina (15) = 332
Lose Florida (29) = 303
Lose Virginia (13) = 290
Lose Colorado (9) = 281
Lose New Hampshire (4) = 277
Lose Iowa (6) = 271
Lose Ohio (18) = 253
Lose Nevada (6) = 247
Lose Wisconsin (10) = 237
Lose Pennsylvania (20) = 217
Lose Michigan (16) = 201

Remember, 270+ out of 528 electoral votes are needed win the Presidency.

Be sure to watch the key Atlantic states: Virginia, North Carolina and Florida. There is no realistic scenario where the President loses re-election if he holds onto any of these three.

The President's mid-west firewall: Wisconsin, Pennsylvania and Michigan. If Romney wins any of those three, the undecideds have clearly broken strongly to him.

If the President's mid-west firewall holds up and Romney sweeps the three Atlantic states, then Ohio will put …

Politics: What happens if the late deciders decide for the challenger?

The polls are close.

Some have Romney ahead and some have President Obama ahead.

The "conventional wisdom" is that if a voter is undecided they are more likely to vote for the challenger. Thus, let's assume for the purpose of discussion that 6 of 10 voters will vote for the challenger if they decide in the final weekend before the vote.

The Politico 10/22-10/25 poll has: Obama at 49 and Romney at 48.
Thus, there are 3% undecided.
If the 60/40 rule holds, then Obama will add 1.2% to his totals and Romney will get 1.8% more.
Final result: Obama 50.2% Romney 48.8%.

This scenario would probably mean a very long election night and possibly many days of counting absentee ballots and perhaps recounts in some swing states.

In the IBD 10/22-10/27 poll, Obama has 45 and Romney at 44.
Thus, 11% undecided.
If the 60/40 rule holds, then Obama adds 4.4% and Romney 6.6%.
Final result: Romney 50.6% Obama 49.4%.
Again, likely a very long night with a possible Romney popular vote win but …

Non-profit of the month: October 2012 - Los Angeles Philharmonic

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I'm a patron of the arts!

Okay, not a million dollar donor type of patron who gets a name stenciled on something in the building or printed in the program books. But, as a subscriber to the LA Phil since 1999, I've attend usually 4 concerts a year with them. And as a result, I've come to enjoy what they do and am happy to know the organization has a footprint in bringing music to youth and the community beyond the iconic Walt Disney Concert Hall venue.




Politics: Cal Ballot Propositions for November 2012

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Propositions 30 to 40 is a lot to sift through and below are some preliminary thoughts on how I'm leaning on the ballot measures. I welcome input as I reserve the right to change my mind right up to election day when I finally mark my ballot.

Let's take the easy one first ...

Prop 40 is the easiest with a YES vote.

Prop 40 is a yes/no vote on the new state senate district lines drawn up as a result of the 2010 census. There is no opposition to Prop 40 in any newspaper editorial board or major political party.

The rest are a bit more complicated and as I read through them and form a view, I'll post them below.

Vote NO on Prop 37.

This ballot calls for labeling of some food items to let the consumer know it contains genetically modified ingredients. This Freakonomics.com item highlights some of the problems with the labeling plan. Problem number one is that numerous scientific organizations have gone on record as saying that genetically modified food items are safe. Problem nu…

Politics: The Sequestor

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Image source: http://upload.wikimedia.org/wikipedia/en/2/2b/U.S._Federal_Spending_-_FY_2011.png

The sequestor says that over ten-years, $600 billion needs to be cut in discretionary spending and $600 billion needs to be cut in defense spending. Thus, the target would be $60 billion in each of the two items per year.

Of course, looking at the chart, that leaves 63% of the budget untouched. The 6% that is interest payments is untouchable in the sense not paying it would be defaulting. As a political matter (and perhaps as a legal one as well), the other mandatory, Social Security and Medicare & Medicaid is virtually untouchable.

And that is really the problem: it is hard to balance a budget when 57% of the budget essentially isn't on the table for cuts.

Imagine if we could get at all segments of the pie except interest payments?

How about cutting $24 billion from each of the five pie segments?

Or how about slicing $20 billion from each of the five portions and close loophol…

Politics: Rasmussen and Gallup Diverge On 2012

Rasmussen and Gallup Diverge On 2012 ... at the moment, as of this Friday morning, as I look at the RCP numbers. Gallup is saying Romney by 7% and Rasmussen has it tied. Rasmussen claims an MoE of 3%, so the tie could really be a 6 point lead for either side. Gallup cites an MoE of 2%, so Romney's lead could be as big as 11 and as small as 3.

Why are the two polls so divergent?

The likely voter screens they apply are different. But I wonder what aspect of their screens is leading to such different results? Any polling experts out there who can offer a hypothesis as to why the 2 big name polls are so different at this moment?

We shall see if the divergence continues.

At the moment, on RCP, Gallup is the "outlier" data point with the race being much closer if one aggregates the polls.

UPDATE: Jay Cost of the Weekly Standard was on the Hugh Hewitt radio show and suggested that Gallup's use of a tight likely voter screen ironically makes it more volatile to momentum shif…

Politics: Nov 2012 California Ballot Measures as Viewed by Newspapers

Proposition San Francisco Chronicle Sacramento Bee San Jose Mercury News Los Angeles Times Orange County Register San Diego Union Tribune 30 Endorse Endorse Endorse Endorse Oppose Oppose 31 Endorse Oppose Endorse Oppose Oppose Endorse 32 Oppose Oppose Oppose Oppose Endorse Endorse 33 Oppose