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Monthly Archives: March 2016

A Genetics Riddle

Along with his brothers, a soldier goes off to war leaving behind his wife and two sons. Six years later he returns to his family after losing both his brothers in action. Something is different though. His wife suspects something, but can’t put her finger on it. She just knows that something is different about her husband. Over the next two years, the family grows by twins (a boy and a girl) and then another girl. Then, in an auto accident, the husband dies and his widow decides that she can now investigate a hunch she has had for some time without upsetting her husband.

That month, she takes all of her children in for their annual checkup and vaccines, and also asks the doctor to check her blood type along with all of the children.

The results, mailed to her (see below) later that week, give her a start as she realizes her hunch was correct.

What was her hunch? How did she arrive at her conclusion?

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Posted by on March 27, 2016 in Uncategorized

 

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One Quarter in

US08395894-20130312-D00000.pngI’ve been working for an intellectual property firm now for three months and I thought it might be time to update my impressions of the field.

When I entered this position (as a technical patent analyst)at the start of the year, I had little background in the area. I have a few patents on work that I’ve done in my various biotech positions which I did work on assembling the data for the attorneys working in our company / the university. However, that didn’t really provide much insight into what a patent is, or what really went into making it work. In fact, one of the only things I learned is that lawyers (or at least some of them) won’t shy away from exploiting your ignorance of their system in order to get what they want. In my case, this was signing over my rights to the company I had worked for after they had laid me off.-That’s a whole other discussion though!

Screen Shot 2016-03-25 at 10.23.32 PM.pngIn the past, my writing had always been of the sort that presented data and built a story around that data in a way that was essentially persuasive in nature. Patent Applications do present data, and they can tell something of a story, but they are not meant to be persuasive documents. No one reads them for the purpose of evaluating the data to see if you’ve missed something, forgotten some important principle, or are making an invalid argument. You simply show what you have, make claims based on both the data and your ideas about it and determine if it’s:

  1. Patentable subject matter
  2. Novel work
  3. Not Obvious

Have you presented enough information such that a representative person skilled in the art can now replicate the invention(i.e. are they enabled)?

Is there an industrial application for this? Not because everything in the world needs to be commercialized, but because it is not worth the time and expense of protecting something that can’t be stolen from you in a way that you have suffered financial harm.

The last question is important because a patent is a deal between the inventor and the society. In general, the US government, at least, does not look kindly on monopolies (e.g. ma Bell). However, what a patent does is give the inventor a period of time when they can legally monopolize their invention. In exchange for this, the inventor supplies all the information one would need to recreate the invention. The public gets something and the inventor gets something. Ideas are shared, but there is still incentive to invent without sinking all your money into research and then having someone copy your work and sell it

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huh?

cheap.

What a patent doesn’t do is try to get you to believe that what someone is claiming as part of their invention is actually a real thing. Of course, it’s easier to get a patent on something that you have in hand, but this is not necessarily required.

Getting back to the point of having patents, this is why your brand name prescription drugs cost so much. For every life-saving medicine, there are hundreds, thousands, millions of other ineffective drugs that had to be tested along the way.That testing costs a lot of money. Moreover, it takes years of research to develop a drug to the point where it is reliably safe and effective to use. Why invest in that, if you can’t pay for the failures with your successes? The monopoly on the invention makes this worth it; it gives you time to recoup your investments and even make a profit.burger-labeled-2.jpg

One thing that has been interesting is learning more about what is, and what is not parentable in the US (point 1 from above). This remains an active question. Can a gene be patented? Can something like a gene be patented?

What if that gene is a naturally occurring thing? What if it is synthetic? What does it mean to be a synthetic gene? You can’t patent something that you didn’t invent. So, the general principle is that a simple DNA sequence, as it occurs in nature, is as unpatentable as is an abstract idea like algebra.

Some insight into trials that have been getting to this question…

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“Nor do we consider the patentability of DNA in which
the order of the naturally occurring nucleotides has been
altered. Scientific alteration of the genetic code presents a
different inquiry, and we express no opinion about the
application of §101 to such endeavors. We merely hold
that genes and the information they encode are not patent
eligible under §101 simply because they have been isolated
from the surrounding genetic material.
* * *
For the foregoing reasons, the judgment of the Federal
Circuit is affirmed in part and reversed in part.
It is so ordered.”
And, of course there will be dissents…
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Nor are patents the only kind of intellectual property. Trademarks and Copyrights are also protected by the same office. I don’t have to work with those, but there are those around me who do. I just have to admit that I’ve learned nothing about them yet- and may never.
And, as always, I keep asking myself… “is this system really serving the public good?” I definitely think that patent protection is important for there ever to be innovation that requires significant effort and expense. But I am still struggling with the fact that much of what we do is cut the world’s ideas into smaller and smaller pieces assigning each piece’s ownership to one group or another. As such, it is a lawyer’s game, where the rules have been made so byzantine that following them is nearly impossible without great expense.
 
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Posted by on March 25, 2016 in Uncategorized

 

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What’s all the fuss about Zika Virus?

Check out the Cloudy Media Blog for a good discussion about the Zika Virus and it’s Uber transit pal, the Mosquito. Consider why some people are raising the alarm and others are trying to reassure us that it’s not the end of the world if you do contract Zika.

microcephaly-comparison-triple-350px.jpgFor most people Zika is not all that harmful. the symptoms are often described as similar to a mild case of the flu. But, like rubella, the major risk may be to women who contract the disease while pregnant. It has been found that a rise in microcephaly cases in Brazil has coincided with a rise in Zika cases (increasing since April 2015). However, whether there is a causal link between the virus and the birth defect has been more difficult to demonstrate. Correlation is not Causation, otherwise the link between sunburns and the dramatic rise in ice cream sales seen every summer might make us consider shuttering the Dairy Queen to prevent skin cancer.

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So, why think there is a link between Zika and Microcephaly? The immediate reason is the spike in Zika cases just before the spike in microcephaly.

Why doubt the connection? One reason is that Brazil is not the only country seeing a spike in Zika infections. In fact, Columbia has many more confirmed cases of Zika than Brazil (however it is estimated that Brazil may have a larger population of unconfirmed cases) but has not yet seen the spike in microcephaly (or at least I haven’t been able to find good data on it). So, shouldn’t Zika be causing birth defects in children regardless of where they live?

To answer this question, some have decided to look directly at the brains of children born (or fetuses not born) with microcephaly to see if there is any evidence of the virus there. In work performed by the CDC, four of four cases were positive by RT-PCR (a technique looking for virus-specific RNA), and sequence analysis provided further evidence of Zika virus infection, revealing highest identities with Zika virus strains isolated from Brazil during 2015. Workers in San Paulo, Brazil found that the mothers of 23 of 29 infants (79.3%) with microcephaly reported signs of Zika virus infection. The majority of these reported that the symptoms occurred during the first trimester of the pregnancy.

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Now, if you’ll excuse me, I have to get myself into a vector for the airport. Seriously, check out Cloudy Media.

 
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Posted by on March 18, 2016 in Uncategorized

 

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Meet the Guinea Worm

Screen Shot 2016-03-14 at 10.48.20 PM.pngGuinea worm disease is caused by a parasitic worm found in stagnant waters of Africa. It has been known since early recorded history with possible mentions in the Bible and a definite reference (along with a treatment method for removing the worm that is still used today) in the Ebers Papyrus, an ancient scroll written around 1500B.C.
Presently, only four countries, Chad, Ethiopia, Mali and South Sudan have reported cases of the disease. The worm, Dracunculus medinesis infects its (human) host through the drinking of unfiltered water inhabited by the larval forms that have been eaten by “water fleas.” When a person drinks water containing these water fleas, the larva are released from their insect host while in the stomach and burrow through the digestive tract into the body cavity where they grow into adult worms. After fertilization, male worms die in the host, but female worms can grow up to 2-3 feet long.

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A section of the Ebers Papyrus

The insidious nature of the beast is the way that it manipulates the host (human) when it is ready to release larvae. At this time, the worm will burrow to the surface of the skin (usually on the foot) where it will cause a blister. When the blister erupts, it causes a painful burning sensation that is somewhat alleviated when immersed in water.

Whenever the blistered area is immersed, the worm will eject a milky liquid containing millions of larvae into the water to repeat the life cycle. During this time, the pain can be disabling and the blisters are easily infected with bacteria.
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As the worm emerges, it can be captured and wound around a twig, etc. Pulling the worm will result in a break that worsens the condition, but if attended to, the worm can be removed a bit at a time as it emerges from the blister over the course of days to weeks.
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Since the 1980s eradication of the Guinea Worm has been aggressively pursued by a number of organizations, most notably the Carter Center, founded by President Jimmy Carter. The Carter Center has coordinated the efforts of the Nation Ministries of Health in affected countries, with the World Health Organization, The US Centers for Disease Control and Prevention, and UNICEF. Together, these organizations provide education to at risk populations, water filters, and pumps to obtain uninfected groundwater.
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These efforts have reduced the number of Guinea Worm Disease cases from 3.5 million in 17 countries in1986 to just 22 in four countries in 2015 (provisional total). Importantly, humans are the principal host of Guinea Worms, therefore, if all cases of infection can be eliminated for just one year, this should lead to complete eradication of the organism.

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Posted by on March 14, 2016 in Uncategorized

 

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OK, let me just say it…

e40c814f113f4d605cef62c3d26f03fa.jpgI would no sooner vote for Donald Trump to be President of the United States than I would the world’s best actor, Keanu Reeves. Sorry, Keanu, you’re just not Presidential material. But I did think you did a good job in Bill and Ted’s Excellent Adventure.

However, tonight, I heard Ted Cruz , in his victory (in Texas) speech, make The Donald sound like a perfectly reasonable candidate. One who pledged to work across the aisle to lead through compromise (by engaging Democrats over appointing Supreme Court Justices), leave the door open to making allies out of long-time enemies (by maintaining the Nuclear Treaty with Iran), who would socialize healthcare in the United States (by making it a single payer system run by the government), and who was just kidding about deporting millions and millions of illegal immigrants (as divulged in a conference with editors of the New York Times).

I was wondering who Cruz was working for. His speech sounded more like an appeal to Democrats to consider voting Republican in order to secure a socially liberal president who was open to negotiation. As the fire began to rage in Teddy’s viscera, he portrayed himself as so far to the right that John Birch might wonder if this guy’s gone too far. He’s socially conservative, religiously conservative, and fiscally conservative. The only thing Ted Cruz doesn’t conserve is fabric in his signature, ‘I’m wearing daddy’s clothes’ fashion statement.

wkxmqf74sxup1efgqjmh.jpgI have to admit that I was shocked when I heard him repeating his oath to put 82,000 government employees out of work ASAP. I’m sure it would save the government money to not have all those extra employees, which might be why he thinks his ‘flat tax’ solution wouldn’t bankrupt the country. Although, I have to wonder if he’s also considering the impact that 1.2 million out of work tax preparers who won’t be paying any personal income tax might have. (IBISWorld estimates a much smaller industry in its report saying that only 290,000 employees work in tax prep). On March 15 of 2015, Cruz suggested that we deport the 82,000 IRS employees to Mexico. Perhaps including the 1.2 million tax preparers might help offset the rise in unemployment and the $10,000,000,000 hole in the GDP.

I didn’t mean to rant about this, but the more I think about what ideas Cruz holds dear, the more I think that he’s an even greater threat to America than The Donald. At least Donald will be creating jobs when his bluster puts the US into open war.

Who am I kidding. The Donald would never take us to war. After all, he was just nominated for the Nobel Peace Prize.

Maybe I can get a job as a riveter.GTY_willow_run_plant_riveter_tk_130731_33x16_1600.jpg

 
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Posted by on March 2, 2016 in Uncategorized

 

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