Archive for March, 2012

WoD – Remember Emmet?

Emmet Otter’s Jug Band Christmas.  So so good.

http://www.youtube.com/watch?v=eFJ2jxIe4CQ&feature

Thursday:

ROSHE (RUHsheh)

Evil one, villain

That Darth Maul guy was one bad looking roshe.

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WoD – If you were the POTUS

I saw something the other day that mentioned how the Republican candidates were granted secret service protection, and given their secret service code-name.  In fact, I guess they got to choose the code-name.  Romney chose “Javelin” and Santorum chose “Petrus,” (apparently a biblical reference for St. Peter).  

So, here’s the fun question for today:  if you were the President of the United States and could pick the Secret Service code-name for you, what word would you choose…?  

 

Monday:

Lantzman (LONTSmohn)

Fellow countryman (a homeboy) 

What’s up, Lantzman?  Gimme a bump…   [http://www.youtube.com/watch?v=Rd7dnyNd2Jc&feature=endscreen]

WoD – Why We Sneeze

Why do we sneeze?  Because something itches or irritates the cilia in our nasal passages.  Yes, we know that.  But why do our passages get irritated or tickled?  Sometimes dust gets in there, or pollen, or other things we breathe in.  Makes sense.  

But what about when we have a cold or flu?  (Yep, here we go again into the microscopic world of viruses, germs, and bacteria…)  Why does a cold make us sneeze?  I am going to turn conventional thinking on its ear.  I don’t think it is because of any old wives’ tale reason.  Or because anything gets in there to irritate.  I think it is actually because viruses and bacteria have EVOLVED to MAKE us sneeze (or cough – similar logic, but lung-based instead).  And of course, therefore spread the little buggers.  Wait, don’t judge just yet.  Think about it first…  

Ok.  You with me?  There is NO reason why sneezing has to be correlated or connected with having a cold or flu or illness.  Typically it is one of our body’s defense mechanisms to foreign particles entering our nose or throat.  But when we get sick internally, our nasal linings get irritated and itchy.  I think this is directly due to the evolution of viruses and maybe some bacteria (like strep), which have evolved to cause the bodily reaction that gets our throats and nose irritated.  Which leads us to sneeze.  Which leads the virus to spread.  It is just natural selection and Darwinism at work.  

And as Spock might say, this… is logical.  

Monday:

YEDIE HAKLDIK (yehDEEeh HAHKldihk)

Omniscient 

Sometimes moms are yedie hakldik – it is like they have eyes in the back of their heads!

 

WoD – Remember the Navel Gnome?

Check this out (the comments part):

https://yiddishwod.wordpress.com/2010/01/05/wod-the-navel-gnome/

After over two years of just sitting out there, Paul in the UK came across my light-hearted posting and wrote the two comments below.  What a wacky world it is sometimes.  And Google is amazing, isn’t it…

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2 Responses to “WoD – The Navel Gnome”

Paul Gregson-Allcott, March 8, 2012 at 8:35 pm 

This is proof to me that the World is full of coincidences and the Internet can just about conceive of anything.

This is because…

Me and my fiancee have been discussing the little belly button gnomes for about two years and just for fun, we decided to do a google search to find out if anyone else had thought of this.  Lo and behold, there are a few people who have realised how all the lint is collected.

We think they must mine the fluff/lint and use it to make duvets, cushions, clothes and all manner of linty marvels for all the gnomes of the world.  In fact, we live in a symbiotic relationship with gnomekind, for without male humans, the gnomes of the world would be naked as their lint source dried up.

Who would have thought it, a fellow believer!

Paul, Leeds, United Kingdom.

  1. Reply

Additionally, my fiancee doesn’t get lint in her belly buton either. So to support your earlier hypothesis, it must just be males who get the gnomes.

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Thursday: 

KHOLILE  (khohLEEleh)

God forbid (literally: far be it)

Kholile, you clean up your room.  Someone is going to get hurt in here!

 

WoD – How to use an iPad

Just some light humor today, amidst the iPad and Apple media frenzy.  You don’t even need to speak German…

http://www.youtube.com/watch?feature=player_embedded&v=v0FVm_H_D18

Wednesday:

EPES (EHPihs)

Something, a little

Oy vey!  Eat epes!  You’re too thin as it is.

WoD – Jonathan’s Law Revisited

I just came across a NY Times article about the costs of genome sequencing, which reminded me of the “Jonathan’s Law” WoD (posted yesterday but written 4 years ago.  I can’t believe it has been over 4 years now…!)

Remember the point about how Moore’s Law, a really significant truism in the IT world, would play a meaningful role in my almost-silly Jonathan’s Law?  Well, check this out  (whole article pasted below if you don’t feel like clicking the link).  http://www.nytimes.com/2012/03/08/technology/cost-of-gene-sequencing-falls-raising-hopes-for-medical-advances.html?_r=1&nl=technology&emc=edit_tu_20120308&pagewanted=all

Genomic testing that costs as much as a blood test!  We can avoid so many illnesses before or just as they are beginning, instead of waiting until our Primary Care Physician feels a golfball-sized lump in our abdomen.  Which, by the way, is exactly NOT the time to find something.  Because if it is that big, it is also that late.

So, maybe we’ll live to 120 after all.  Me?  92 sounds decent enough…

 

Thursday:

GANEYDN (guhNAYdihn)

Paradise

You should see their vacation house in the Caribbean – a regular ganeydn!

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Cost of Gene Sequencing Falls, Raising Hopes for Medical Advances

By JOHN MARKOFF

MOUNTAIN VIEW, Calif. — In Silicon Valley, the line between computing and biology has begun to blur in a way that could have enormous consequences for human longevity.

Bill Banyai, an optical physicist at Complete Genomics, has helped make that happen. When he began developing a gene sequencing machine, he relied heavily on his background at two computer networking start-up companies. His digital expertise was essential in designing a factory that automated and greatly lowered the cost of mapping the three billion base pairs that form the human genome.

The promise is that low-cost gene sequencing will lead to a new era of personalized medicine, yielding new approaches for treating cancers and other serious diseases. The arrival of such cures has been glacial, however, although the human genome was originally sequenced more than a decade ago.

Now that is changing, in large part because of the same semiconductor industry manufacturing trends that opened up consumer devices like the PC and the smartphone: exponential increases in processing power and transistor density are accompanied by costs that fall at an accelerating rate.

As a result, both new understanding and new medicines will arrive at a quickening pace, according to the biologists and computer scientists.

“For all of human history, humans have not had the readout of the software that makes them alive,” said Larry Smarr, director of the California Institute of Telecommunications and Information Technology, a research center that is jointly operated by the University of California, San Diego, and the University of California, Irvine, who is a member of the Complete Genomics scientific advisory board. “Once you make the transition from a data poor to data rich environment, everything changes.”

Complete Genomics, based in Mountain View, is one of more than three dozen firms hastening to push the cost of sequencing an entire human genome below $1,000. The challenge is part biology, part chemistry, part computing, and in Complete Genomics’ case, part computer networking.

Complete Genomics is a classic Silicon Valley start-up story. Even the gene sequencing machines, which are housed in a 4,000-square-foot room bathed in an eerie blue light, appear more like a traditional data center than a biology lab.

In 2005 ,when Clifford Reid, a successful Silicon Valley software entrepreneur, began to assemble his team, he approached Dr. Banyai and asked if he was interested in joining a gene sequencing start-up. Dr. Reid, who was also trained in physics and math, had spent a year as an entrepreneur-in-residence at the Massachusetts Institute of Technology, where he had become a convert to bioinformatics, the application of computer science and information technologies to biology and medicine.

Dr. Banyai had even less experience in biology.

Formerly with the Internet networking start-ups GlimmerGlass and Silicon Light Machines, he in turn began by reading a pioneering 2005 article in the journal Science in which a group of researchers in George Church’s genetics laboratory at Harvard describe a new technique intended to speed gene sequencing.

Today Dr. Banyai is finishing the second generation of a machine that blends robotics, chemistry, optics and computing. It is emblematic of the serendipitous changes that take place when a manufacturing process is transformed: performance increases and cost falls at an accelerating rate.

“Genomes are now being sequenced incredibly cheaply,” said Russ B. Altman, who is a founder of Personalis, a start-up based in Palo Alto, Calif., that is developing software to interpret genomes. “On the discovery and science side we will be able to do clinical trials. We’ll be able to check the entire genome.”

Recently, on the company’s Web site, Dr. Reid predicted that the cost of gene sequencing could eventually be as low as that of a blood test: “I believe that the impact on the medical community of whole human genome sequencing at a cost comparable to a comprehensive blood test will be profound, and it will raise a host of public policy issues (privacy, security, disclosure, reimbursement, interpretation, counseling, etc.), all important topics for future discussions,” he wrote.

Dr. Banyai said he had found that Silicon Valley start-up ideas tracked well. “There is this remarkable thing that happens in start-ups. You make up this plan and then you step off a cliff and magically a little bridge appears,” he noted, as new technologies appear in the nick of time.

In the case of Complete Genomics, the company is riding in part on big advances being made in industrial digital cameras that are capable of capturing the fluorescent molecules that are used to “read” small sequences of DNA.

In the last half-year, a new generation of cameras, more frequently used for factory inspection systems, has made it possible to speed up the Complete Genomics sequencing process tenfold. That, the company has said, will drive its capacity to 100,000 genomes annually from 10,000.

The parallels between the evolution of the nascent gene sequencing industry and the Valley’s chip makers are striking. By placing more circuits on a silicon wafer at an exponentially increasing pace since the early 1960s, the semiconductor industry transformed the cost of computing. As a result, today the world’s most powerful supercomputer from the 1980s nestles comfortably in your hand and costs several hundred dollars.

Complete Genomics’ competitors are also exploiting designs to drive costs down. For example, Life Technologies, based in Carlsbad, Calif. uses a direct approach to read the bases in the genome from an array of sensors on the surface of a semiconductor chip. As more sensors are packed onto each successive generation of technology, the cost of sequencing will also fall sharply.

Last month, Oxford Nanopore Technologies created an industry sensation when it introduced a machine that sequenced genes using an alternative approach called nanopore sequencing, in which a strand of DNA is read as it is pulled through a microscopic hole.

The system is scheduled to be available later this year. However, it has an error rate much higher than that of the Complete Genomics system, which has independently been given high marks for accuracy.

Because there is no clear winner yet, all of the companies are pushing hard to get down the cost curve as fast as possible

In 2011, Complete Genomics became one of the market leaders. This year, it has produced more than 3,000 sequences at a cost of about $5,000 each. Dr. Banyai’s higher capacity second generation system is now being installed and will begin production during the first half of this year. A third generation design has been completed.

What initially set Complete Genomics apart from the field was its strategy of offering gene sequencing as a service, rather than selling a machine to laboratories. More recently, Illumina, one of its crucial competitors, has also begun offering sequencing as a service, in addition to selling its machines.

“Our competitors have to supply kits that can be executed by a graduate student rolling out of bed with a hangover,” said Dr. Reid. “We don’t live with that standard, and that can be tremendously liberating. Ours can be horrifically complex as long as it can be executed by a robot.”

The company also began with the business intent of sequencing only the human genome, rather than those of other species, too — a strategy that was heresy in 2005, when the founders set out to raise money. At that time, only two human genomes had been sequenced. However, Complete Genomics founders argue that focusing just on the human genome has given them a leg up.

“You make a whole bunch of decisions that don’t work well for corn or bacteria, but they work very well for humans,” Dr. Reid said.

WoD – Jonathan’s Law

(This was actually written back in 2007 but never posted until now.)

I’ve been thinking a lot about medicine and healthcare, and had a thought.  It’s in the same construct as the infamous Moore’s Law, which you all probably know or ought to know (http://en.wikipedia.org/wiki/Moore%27s_law), namely that the number of transistors that can be placed on an integrated circuit is increasing exponentially, doubling approximately every two years.  For those anywhere near the IT world (me), this is such a huge and fundamental and powerful Law — Moore’s Law is at the heart of all of the amazing technological advances we see and feel each day.

This is nothing like Moore’s Law, sorry about the hyped-up lead-in.  But I still think I am going to call it a Law.  Jonathan’s Law.  Ok here goes:

Like Moore’s Law, I think the average life expectancy of a human is elongating by approximately 3 months per year, every year.  Or, one year every four years.  (Maybe even faster than this.) 

This has been the case (probably even on an accelerating curve) for almost the last 100 years*.  I think we all think there’s no way this can possibly continue and inevitably our bodies will “hit a wall,” right?  After all we were not made to live to 120 years old.  Think about it right now – do you really believe that you can live to be 120 or 130?? (Not everyone of course, but some people.)  Won’t our bones or our heart or liver, kidney, or lungs just give out?  Could age 60 or 70 really only be half of our living years?

Well today, right here right now, I challenge this notion.  With advances in medicine like we have seen over the past ~50 years, and will invariably see over the next 50 (and by the way, Moore’s Law has played and will continue to play a HUGE role in these advances), I believe that we can, in fact, extend our life expectancy at this same pace going forward indefinitely.  (Thus the Law part of it.)  There.  I said it.

So what does this mean in numbers?  Average life expectancy in the U.S. in 1998 was 77.  Per this Law (ok ok, I admit I am using the “Jonathan’s Law” thing in this email for effect), this extrapolates to mean that by 2058, the average life expectancy in the U.S. would be 92.   92!   And this is just the statistical mean – the highest could be more like 120 or so!  (Remember, you heard it here first…)  So go ahead, eat that big juicy steak, smoke a few packs a day, and stay out all night partying.  Who cares… we’re all living until we’re 92!

(*  Yes, I dug up the data behind this for anyone more interested in the statistical nuances.  And in fact, there is one pretty big reason or driver that has led to the average life expectancy increasing from 47 in 1900 to 77 by 1998.  A big prize for any of you data hounds that can guess the underlying cause/reason for average life expectancy growth this past century…)

Wednesday:

TSEDREYT (tsehDRAYT)

Nutty, crazy

Those tsedreyt kids tried to rob a bank, but got their getaway car towed!



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