Science: How does high speed DNA sequencing work?

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 participants to bear a greater cost of the program. Of course, politically, people will say, you want to throw grandma under the bus and push grandpa off the curb. But if nothing is done, the cost of these programs is going to crush the next generation in taxes and debts.

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 read the paper is very frustrating. Even though the vast majority of journals use blinded reviews, I think a good attitude to take is to write the review as if the authors of the submission would find out who you are.

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

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 occasions. Of course, with a realistic road map to a bring the deficits and debt under control, the economy may perform better thus reaching the balance point sooner.

Below is a graph generated from a CBO report of budget estimates for 2011 to 2021. As you can see the growth of the two lines is much steeper and yet the two lines do not meet. I was not able to figure out what their economic growth assumptions were. I'm sure it is in there somewhere but I didn't find it in a quick scan of the data table.


Suffice to say, I'd like to see the types of charts I'm generating here rather X number of dollar of tax increases and Y number of dollars in spending cuts reported in fiscal cliff negotiations. The cited numbers are always relative to some unstated "baseline." Instead, they ought to show absolute dollar charts like what I have here. Also, the fiscal cliff negotiators probably have unstated economic growth projections that are unrealistic. I just wish the politicians would just tell the truth about the numbers!

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

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 couple of decades. Clinton era boom times hit around 4% for a few years. Assume inevitable booms and busts average out to 2% growth per year. Thus, growth in government spending must be LOWER than growth rate in the economy. We also should aim for 4% growth in the taxation side per year to speed up reaching balance.

1% growth in spending, 2% growth in the economy and 4% growth in taxation, you get to balance by 2027.

The math is easy. It is just plugging in numbers and you get to balance. You can tweak the exact combination of numbers but the spending growth rate has to be LESS than economic growth rate and the rise in taxation should be a gentle one since sudden increases cause panics. If the economy grows faster than 2% you get to balance sooner. If the economy grows slower than 2% but above 1% growth in spending you eventually get to balance, it just takes a few more years.

The problem is the political will to cap spending growth to 1% per year given that we have routinely been spending 5-7% more per year.

All the angst and sackcloth over the fiscal cliff is political gamesmanship. The mathematical road map to balance is actually rather straightforward.

The graphs that illustrate the 1-2-4 plan are below. First, in absolute dollars.



Second, in percent GDP.




P.S. Another way to look at it is to look at THREE key numbers:
(1) what % GDP we want government spending to be
(2) the year we want to reach that target
(3) assumption about economic growth.

In the above graphs, the target is 21% GDP by 2027 assuming 2% economic growth.

There are of course other possible scenarios, for example 20% GDP by 2030. The slope of the lines in that scenario would be a little different. One could aim for 19% GDP by 2020 and the slopes in those lines would be also a bit different.

The $16,000,000,000,000 question: if the White House had to pick a GDP number and a year, what would they pick? What numbers would the House Republican's pick? Of course, they would probably pick very different numbers! Would they split the difference?

The thing they probably would agree upon is overly optimistic economic growth assumptions which makes the effort pointless. Sigh.

P.P.S. I do like to read Dan Mitchell's stuff. I posted the above item before I saw this item over at Cato he wrote recently. In sum, Mitchell declares, Simply stated, even huge tax hikes won't stem the flow of red ink in the long run if government keeps growing faster than the private economy. This is the fiscal problem that demands attention. Alas, unfortunately, it would appear that the wisdom of a non-economist blogger in pajamas and a seasoned pro like Mitchell will get ignored just the same by the powers that be in the White House and the Hill.

Aging Parents - Random things from this season of life, part I

A handful of years ago, I entered the phase of life of helping out in looking after aging parents.  At this moment in 2024, my dad passed on...