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Martha Chase, Max Delbruck, and the American Phage Group

Martha Chase is a bit of an enigma. Her career started promisingly enough working in a productive field amongst productive scientists; but following her PhD, her health precipitated setbacks in both her career and her home life from which she did not recover.

She received her bachelor’s degree in 1950 from the College of Wooster. Later that same year, she joined the laboratory of Alfred Hershey in Cold Spring Harbor to work as his lone laboratory assistant asking questions about the mechanisms of life using a viral model system. The virus they used was the bacteriophage T2, a fascinating conglomeration of proteins and DNA that specifically infects bacteria. Through her work with Hershey, she became linked to the remarkable influence of a network of biologists nucleated around the German-American biologist, Max Delbrück, called the ‘American Phage Group.’

Delbrück, himself a Nobel Prizewinner, led a rich intellectual life amongst an elite group of academic luminaries. The Chemist, Karl Friedrich Bonhoeffer, was a close friend and mentor to him during his younger years steering him into the study of physics where he became associated with Wolfgang Pauli and Niels Bohr. It was Bohr’s influence that put him on the path to Biology through its relationship with Physics. Again, not to be on the outside looking in, he became assistant to Lise Meitner who had worked with Nobel Laureate Otto Hahn to discover fission of Uranium (Meitner is often regarded as missing out in the Nobel for anti-Semitic reasons), and with Otto Frisch, who recognized that fission must be accompanied by a massive energy release tying it to both the potential for energy production and a potential massive destructive power. Delbrück initially came to the States to study genetics in drosophila, but made a deeper mark studying viruses, eventually earning a Nobel Prize in 1969 for his work with Salvador Luria and Alfred Hershey, largely thanks to the diligent work of Martha Chase.

Many of the Phage Group’s members are credited with landmark advances in our understanding of molecular biology. Luria, working with Delbrück, demonstrated that mutation of bacteria occurred in a strictly Darwinian sense, i.e. that bacteria could mutate to resist viruses even without the virus being present. This is a fundamental distinction from Lamarck’s notion that evolution was driven by need, rather than by selection of completely random events. It was at this time that he took on and trained his first PhD student, James Watson (who also did something important – I forget what).

In 1949 Renato Dulbecco came to Caltech to join Delbrück’s group with the focus of understanding how some viruses would lead to tumors. Along with David Baltimore and Howard Temin, Dulbecco shared the 1975 Nobel Prize for discovering how these viruses would reverse transcribe their RNA genome into DNA and integrate it into the host’s chromosome.

Matthew Meselson and Franklin Stahl, also working with the phage group, demonstrated that DNA replication is a semi-conservative process retaining one strand from the ‘parent’ DNA and one ‘new’ strand synthesized as a complement to the ‘parent.’ This work did not earn them a Nobel Prize, although it provided early support for Watson and Crick’s DNA structure and remains a landmark experiment in biology that every student is taught.

As evidenced by the sheer number of Nobel Prizes shared by members of this group, the Phage Group and its associates dominated the fields of bacterial genetics and molecular biology. But before those experiments were performed and Prizes collected, the physical molecule carrying genetic material was yet to be discovered.

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Frederick Griffith (see reference 1)

Frederick Griffith was the first to point the way to this molecule by showing bacteria’s mysterious ability to transfer new characteristics (Darwin’s Traits) between organisms. But, tragically, left his work incomplete due to his death in London during WWII. A number of stories exist regarding his whereabouts when he died. Regardless of its veracity, I personally like the one that suggests that he was working late in the lab when it was bombed by the Nazis.

 

Before his death, in the 1920s, Frederick Griffith demonstrated that some element of a bacterium, that is released upon its death, was sufficient to carry genetic information from one strain of bacteria to another. Specifically, he demonstrated that ‘smooth’ pneumococcus, which secreted a glycocalyx, could transfer this trait to ‘rough’ bacteria that lacked the glycocalyx. Clinically, this was very important because the rough type pneumococcus was easily handled by the immune system, while the smooth type colonized the heart and killed the host. He called this element the ‘Transforming Principle,’ but died before he could identify it specifically.2

 

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see reference-2

Experiments showing that the transforming principle was probably DNA were performed by Avery, MacLeod, and McCarty at the Rockefeller Institute in 1944. Despite being both elegant and thorough, many thought these experiments lacked the appeal needed to be convincing.

 

Knowledge of Avery’s work supported the case for DNA as the genetic material, but Protein remained a persistent contender because, with its 20 physiological amino acids, its capacity to carry the information associated with genes seemed more reasonable. DNA, on the other hand, was an arrangement of only four bases, a simplicity that obfuscated its coding potential. One compromise hypothesis suggested that perhaps DNA served as a scaffold for the information-carrying proteins, although Avery’s experiments showing that protein-free DNA preps could transform bacteria strongly argued strongly against this model.

So, the issue remained to be effectively demonstrated denying Avery and his co-workers Nobel. A more satisfying answer, reaffirming Avery’s discovery, was to come from the ever-productive phage group in the hands of Martha Chase.

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Martha Hershey and Alfred Chase (see reference 3)

Working together, as laboratory technician for Alfred Hershey, the two performed their eponymous experiment in 1952 with the purpose of identifying what served as the genetic material in phages.

 

Hershey intended to use the T2 bacteriophage to assess this question, in part because it contained no other molecules such as fats or sugars, making it an exceedingly simple model (See illustration of method, panel A) but also because electron micrographs already hinted of protein ‘ghost’ particles left outside of the cell while new phages were being assembled within. Indeed, by involving only DNA and unglycosylated proteins, it was possible to label the DNA and Protein elements individually using radioactive Phosphorous-32 to mark the DNA and radioactive Sulfur-35 to mark proteins. These isotopes worked well because they were trackable by following the radioactivity, while each was specific to its target due to the natural, exclusive distribution of Sulfur and Phosphorous in Protein and DNA, respectively.

 

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A bacterium with phages attached to its surface and phage capsids assembling within the cell. (attribution unknown)

The basic experiment was simple in theory. T2 bacteriophage was grown in media containing either nucleotides with Phosphorous-32 or amino acids with Sulfur-35. In the first condition, only the phage DNA was radiolabeled. In the second condition, only the protein was labelled (see illustration of method, panel B). Once the phage was prepared, it was allowed to attach to fresh bacteria for a time period known to allow for the passage of genetic material. At this time, the bacterial cultures were moved into a kitchen blender and pulsed to remove the material that did not enter the host cells (the ghosts). Centrifugation permits the separation of the ghosts and any other viruses in the supernatant from the (infected) bacterial cells. The only thing remaining was to check to see where the radioactive elements were: the supernatant fraction that did not enter the cell, or within the cell, where the genetic material was (see illustration of method, panel C). Like most experiments, much of the work invested in the project occurred prior to the actual experimentation in order to optimize each condition.4

 

 

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Illustration of Method for Hershey-Chase Experiment

The answer was clear, Radioactive Sulfur was never found inside of infected cells, only in the supernatant. Radioactive Phosphorus was overwhelmingly found within the cell. With this elegant experiment, the question was answered, and DNA was widely recognized as the genetic material setting up the next, obvious Nobel Prize: what is the structure of DNA? And does this structure reveal any of its properties?

 

At the University of Southern California, Martha continued to study phages under Giuseppe Bertani (Joe to his friends), ultimately following him to the Karolinska Institute in Stockholm, Sweden where she completed her PhD thesis on “Reactivation Of Phage-P2 Damaged By Ultraviolet Light” in 1964.5,6,7 Her obituary, which is one of only a few primary sources of information on Chase, describes life after earning her PhD as plagued with personal troubles arising from short-term memory loss that likely contributed to the end of her scientific career and possibly her marriage.

Despite the fact that this work represented the accomplishment of Hershey in the 1969 Nobel Prize along with Delbruck and Luria, Chase did not share in this honor. As a technician in the lab, it may be that her hands performed many (if not all) of the Hershey laboratory’s experiments, but technicians are rarely (if ever?) included in the Prize on the assumption that it is unlikely that they are major theoretical contributors to the work. Her name, however, will forever be associated with this experiment, serving as a lasting reminder of her contribution to molecular biology.

References

  1. Photograph of Frederick Griffith, photographer unknown
  2. “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Deoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.” January 1944. Exp. Med., 79: 137-158.
  3. photo: Martha Chase and Alfred Hershey, 1953. Attribution unknown. I found both of these images at https://varietyofrna.wikispaces.com/Hershey+and+Chase
  4. Link to Hershey and Chase’s J. Exp Med paper: http://jgp.rupress.org/content/jgp/36/1/39.full.pdf
  5. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827068/#
  6. http://www.the-scientist.com/?articles.view/articleNo/22403/title/Martha-Chase-dies/
  7. http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll18/id/368326/rec/7
  8. See http://www.nobelprize.org/ for a listing of Nobel Prizes, Biographies, Acceptance Speeches, and even games.
 
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Posted by on October 3, 2016 in Uncategorized

 

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Thinking about thinking.

I’ve often taught Science as a way of thinking critically. That is, science education has (at least) two aspects. First, is the content knowledge. This is necessary because it’s not always necessary to reinvent the wheel. If every person had to start with their own tabula rasa and fill it themselves, without the help of those who came before, progress would be non-existent. Further- and this leads into the second aspect, prior knowledge provides a proving ground for developing critical thinking.

For example, every introductory biology class spends a decent amount of time talking about photosynthesis and cell respiration. Just memorizing the pathways is not enough to actually learn anything. In fact, it’s probably the quickest way to ensure that you don’t learn. Instead, it’s useful to talk about how this pathway was discovered.

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von Helmont

Instead, it’s useful to talk about how this pathway was discovered. What was the question that people sought to answer? What was known /thought / assumed initially? What were the first (apparently unsuccessful) experiments done to address the question?

 

Jan Baptist von Helmont did one of the first good experiments to ask the question: Where does a tree’s mass come from?

He used a willow tree for his experiment and monitored the mass of the tree, the mass of the soil, and the mass of the water he gave it. Because the mass of the soil changed very little, while the mass of the tree grew enormously, he concluded that the tree’s substance came from the water he provided. In his own words, “But I have learned by this handicraft-operation that all Vegetables do immediately, and materially proceed out of the Element of water onely. ”

(It is notable that von Helmont recognized, in other experiments, that carbon dioxide was released from burned wood. He called this ‘gas sylvestre,’ referring to the Latin term for wood / forest, silva. This is important because the majority of a tree’s mass comes from the carbon dioxide in the air. von Helmont didn’t do just one experiment in his lifetime, after all.)

The importance of these historical experiments is that it allows the student to consider, ‘if I were in this person’s position, knowing what he or she did, how would I go about asking such a question?’

It was with this in mind that I came across this video on critical thinking, which I would say is the true value of science.

 

The topics we ask questions about depends on our interests. Perhaps today we are interested in where the mass of a tree comes from and we’ll be biologists. Perhaps most of the time we have a driving interest in the way that molecules interact, so we are primarily chemists. Regardless of the topic, we use the same critical thinking and experimental procedures to answer our questions, so we are really all scientists.

 

 

 

 
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Posted by on September 9, 2016 in Uncategorized

 

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The State of Science Education

Spotting-Bad-Science-v2.pngI’m not sure how I came to be reading this article, especially strange because the byline states that it was published over a year ago in The American Spectator. I expect it was mindlessly following some click-bait on Yahoo that brought me there, but what I found was the tragic remnants of a mind denied a proper education in scientific method, logic, and mathematics.

Emily Zanotti wrote up her impressions of a scientific study she had uncovered in an article titled, “Study Finds John Kerry Worst Secretary of State in the History of Ever. John Hayward wrote a similar piece for Breitbart the same day, as did the Washington Post, under the slightly less scathing headline, “Scholars votes put Kerry last in terms of effectiveness.” So, why focus on this minor publication’s reporting over more mainstream outlets? I don’t have much reason other than the fact that I found the article there first and the visceral nature of the title held my attention best (remember, I found it by following click-bait while trying to find a reasonable source of right wing news).

I really don’t care (at least for the purposes of this discussion) one bit about the actual question, but would rather focus on how these data were interpreted for the popular press (using Ms. Zanotti’s article as my example).

First, the data:

The articles I found pointed to Foreign Policy Magazine as the source, the actual data in the rawest form I could find can be found here.

Who was polled? (because this is an opinion survey):The poll was sent to International Relations (IR) faculty from colleges and universities around the country. Responses were received from 1,615 IR scholars drawn from 1,375 U.S. institutions.

The question about Secretaries of State was one of many, and was phrased as, “Who was the most effective U.S. Secretary of State in the past 50 years? ” We’re told that the number of responses to this particular question was 655. I think it’s rather strange that only half of the respondents answered this question, especially given that one of the most popular answers was ‘I don’t know’ receiving 18.32% of the vote, or 120 ballots.

The Results were reported as:

Screen Shot 2016-04-17 at 4.19.07 PM.pngIf you count them up, there were 13 distinct answers given –

only 12 are people if we drop out the ‘I don’t know’..
This is interesting because the headline read that Kerry was the worst

I agree that he is last on this list, but depending on how you want to count, the number of people who sat in that office for the past 50 years was either 15 actual Secretaries of State or 28 Secretaries + acting Secretaries.

Either way you slice it, we’re missing some people from this list. A quick look at trusty Wikipedia show us who we’re missing (See below). Where is Will Rogers in the poll? Edmund Muskie? Apparently these poor souls got zero votes, so they don’t show up in a percentage-based calculation.

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At 0.31%, poor John Kerry received only 2 votes as the most effective Secretary of State (SoS) in the past 50 years. But Rogers and Muskie apparently got zero. It’s hard to see that this puts Kerry in last place.

But that’s not all. The question asks, “who was the most effective SoS?” which isn’t the same as asking respondents to “rank the SoSs according to effectiveness.” What would the percentages look like if two Secretaries (say, Bob and Hank) were the clear front-runners and everyone agreed on that point? Moreover, imagine that everyone also agreed that a third Secretary(Sally) clearly came in right behind the two front runners, but couldn’t compare to the undeniable efficacy of the first two. My guess would be that Bob and Hank would split the 655 votes, and no one else would get any. Not even Sally. Everyone else ties for last place.

Ms. Zanotti’s piece continues, “John Kerry is the worst Secretary of State in history according to a survey of professors at the top 25 foreign policy schools conducted by Foreign Policy Magazine, losing out, even, to ‘Don’t Know.'”

bad_science1.jpgBut no one was asked to name the worst SoS. What is true of this survey is that very few people think Kerry is the best. As for ‘Don’t know’, I imagine that these are the people who simply can’t decide between Bob and Hank, from the example above. Those two are just too close to call. Further, since ‘Don’t know’ came in second, it’s hard to say that Kerry was beaten by this answer in any meaningful way.

She continues, “Of the scholars who responded, Kerry earned exactly two votes, and came in after Lawrence Engleberger who was Secretary of State for a whole six weeks at the end of George H. W. Bush’s second term, and spent most of that time keeping the chair warm for the Clinton appointee.Which had me wondering if perhaps one of the best ways to be an effective SoS is to not have much happen, as is the case when someone is in office for only a very short time.

One last statement on the data before going to her conclusion… In reporting the results of the poll, she mentions that, “James Baker — who was actually the most effective secretary in the last 50 years” came in third at 17.7%. Wait – what? Where is this “who was actually the most effective secretary” come from? Was there another measure that we haven’t been provided with? My guess is there was not, but that this is the author’s admission that she has already determined the right answer and that no data applies to this opinion.

Ms. Zanotti then ends her essay with this strange statement, “At any rate, it’s nice to know our collective impression of Kerry’s effectiveness is objectively verified. ”

I guess she knows her audience, so the “our collective impression” probably makes sense saying, but what about the idea that Kerry’s effectiveness has now been objectively verified?

What about an opinion poll could ever result in an objective verification? I suppose she might mean that it is now verified that many people hold some opinion, but it’s hardly objective. To arrive at this conclusion, we have to accept that the sum of many (at least 655) subjective opinions is equal to an objective conclusion.

This is equivalent to saying that a poll of 400 Yahoos objectively verifies that the sum of 2 and 2 is 8. All we have is a group of opinions. They might be the opinions of very smart people who are speaking within their field, but there’s no logical necessity that they are correct.

So, to return to my title. I can only assume that this hot mess of an essay comes from a completely science deprived education. Who is the author, Emily Zanotti? I had never heard of her and had her pegged for a one-off writer who wasn’t really involved in the world, but I stand corrected. She’s apparently well known amongst the Right as an outspoken libertarian. Her twitter bio reads, “Writer, blogger, comedian, nerd. Cosplayer. Catholic. Political reporter. Resident geek . Libertarian. Opinions my own but should be yours.” Her R Street bio calls her, “a columnist for the The American Spectator  and an associate fellow of the R Street Institute. She is a ten-year veteran of political communications and online journalism based out of Chicago, where she runs her own digital media firm. Her work has appeared at her former blog, NakedDC, and across the web. She has a law degree from Ave Maria School of Law with a focus in intellectual property and technology law” (Sic).

I’d never heard of the Ave Maria School of law, so I had to look that up too. The Miami New Times  had this to say about the school:

Meanwhile, Ave Maria — founded by Domino’s Pizza magnate Tom Monaghan and relocated in 2009 from Ann Arbor, Michigan — continues to plummet, finishing dead last with a horrific 47.8 percent of students passing the [Florida Bar Exam].

However, this poor performance is apparently relatively new, with  former Ave Maria law professor, Charles Rice, stating in the same article that the school’s performance was good prior to the move. Together, these statements make it difficult to use the school as any proxy assessment of the person’s education. Regardless, her R Street bio suggests that she’s not a fool. Therefore, I’m left wondering… how did this article happen?

 

 
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Posted by on April 17, 2016 in Uncategorized

 

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Science Magazine Undershoots April Fools Joke

Science Magazine posted this article last week for April Fools Day. Unfortunately, I think they missed on this one by not going far enough. Reading it, I was convinced it was just a funny way of writing about a complex computer with a glitch. By the time I got the joke, I was just sort of disappointed that it wasn’t true.

Artificial Intelligence Steals Money from Banking Customers

A breakthrough year for artificial intelligence (AI) research has suddenly turned into a breakdown, as a new automated banking system that runs on AI has been caught embezzling money from customers. The surprising turn of events may set back by years efforts to incorporate AI into everyday technology.

<Read More on the ScienceMag site>

 
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Posted by on April 3, 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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I’ve been away, but now I’m back.

2905f5c4f4fb0354cfc774fa213cd9bf-1Life is funny. If you were to ask me, anytime during my entire life, whether I would ever work in a law firm dealing with details, I would say that you were crazy to even ask that. Details just aren’t my thing.

Not only that, I’ve always been more that a little jaded in my view of the law and those who practice it. On the other hand, I have always thought that the Supreme Court was the most interesting part of our political system and where the more intelligent, thoughtful members of the government find themselves (even if I don’t agree with them — I’m looking at you, Anton!).

But here I am, working at a Patent Firm as a technical analyst. I wish I got to be more of a technical analyst day to day, actually. Unfortunately, that’s only part of the job. The rest is just legal office work, which amounts to a very expensive service industry where you don’t want to make anything shy of the best impression on your clients.

I couldn’t do this job if I didn’t see it as a kind of experiment though. So, if it’s an experiment, what’s the question?

The purpose of Patent Law  comes directly from the Constitution:

Article I, Section 8, Clause 8, of the United States Constitution grants Congress the power “To promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries.”

The idea behind the law is that inventors exchange a detailed description of their inventions in a clearly defined way that would enable one of ordinary skill in their art to repeat the invention for monopoly over the use of the invention for a period of time in order to capture the financial benefit (20 years).

So, my question is, is this what patent law achieves? Is the progress of science promoted? Do inventors receive the benefit the law claims to provide? Does the public benefit from this exchange?

It’s easy to have a feeling for this, but how can one measure it? I’ve got to mull this over and come up with a list of possibilities and then start collecting some data. Ideas?

 
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Posted by on February 10, 2016 in Uncategorized

 

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Back from the Dead

Halloween seems like a good time to resurrect old blog posts that haven’t seen the sunlight for several years. Creeping out of the tomb is my first blog post about Genes, DNA, Memes, and GMO foods. Rather than post it here, I decided to post it over on my Medium site to see if it can catch some new eyes.

Take a look: Linked Memes

 
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Posted by on October 26, 2015 in Uncategorized

 

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