Posts Tagged ‘academia


Geeks vs Nerds, or “Perhaps an end to this debate once and for all?”

The Difference Between A Geek And A Nerd [Infographic] | Popular Science.

So I have the word “nerd” right in the title of my blog, and that’s always been the term that I’ve preferred for my part of this nifty little subculture I inhabit. But I’ve never objected to be referred to as a geek, either. I just always felt like “nerd” fit me a lot better, and I’m not sure I can rightly tell you why.

The differences between nerds and geeks a topic of relatively frequent debate, and I think PopSci has given us a really good take on the matter (really, who better to trust on this subject than PopSci?). The basic idea is that “nerds” are more interested in ideas and geeks are more interested in tangible stuff. If a a career analogy helps, nerds appear to be more of the scientist/mathematician type, whereas geeks are more the IT/Coder/Computer people. I suppose that fits, as we tend to call people computer geeks more so than computer nerds.

For what it’s worth, I think I really fall easily into both catagories. I’m a published scientist, and actively pursing my PhD. And I like to write and talk about ideas about feminism, queer life, and all kinds of other stuff here on TNF. But I also love my gadgets, which is attested to by the piles of gear in my studio and the multitude of apple devices you’d find in my messenger bag. I still I think I lean a little more to the nerd end, but I suppose this blog could have just as reasonably been TransGeekFeminist (but that just doesn’t sound as good anyway!).

I don’t think this little post from PopSci is going be the final battleground in defining what it is to be a geek vs a nerd,  but it ranks among the best and most sensical ways to give clear identity to each term I’ve heard yet, if you’re into the that kind of thing. But geek or nerd, we’re still all the same community, and I think it’d do us all some good to remember that.


AMP v. Myriad Decision, or “Hey, our genes belong to us again…sort of.”

U.S. Supreme Court Rules On Gene Patents | Popular Science.

I held off on posting a full-length article yesterday, as I knew this decision was being handed down today, and I like being topical!

[Disclosure: I am a member of the Association for Molecular Pathology]

Being a scientist, I can’t NOT talk about one of the most important Supreme Court cases involving my field..well..ever. Today, the AMP v Myriad Genetics ruling was handed down,  and it’s earth-shattering for those of us who work in the areas of genetic and molecular biology. For me, I think there’s a lot of good, but it’s far from what I was hoping for.

I’ll start with some background. I’m not going to teach a whole intro genetics or molecular biology courses here…if you aren’t familiar with the basics of genetics or DNA, you want to spend some time reading through the material here first. Important for this discussion is to understand that genomic DNA or gDNA is the raw, unchanged strands of DNA isolated from cells. cDNA is a form of “synthetic” DNA that does precisely match the sequence in the genome (most frequently it has had the introns cut out, but I’ll get to this in a minute). Years ago, Myriad Genetics discovered the existence of two genes (BRCA1 and BRCA2) that have a significant impact of breast cancer risk. The applied for and were awarded patents covering everything having to do with these genes. From there on out, they required licensing fees from anyone who wanted to do ANYTHING with BRCA1 and BRCA2, from screening tests to research and more. Many other whole-gene patents have been granted since, effectively giving a number of companies exclusive domain to test people for changes in the genes they hold patents for. It’s been a practice fraught with controversy for many years. Some have argued that not allowing patents removes incentives for investment in genetic research, as the patent allows the firm that discovered it to recoup its costs through direct testing sales and/or licensing fees (not unlike the model for the pharmaceutical industry.) Opponents have argued that US law specifically excludes “unaltered products of nature” from being patented, and that allowing these patents to continue restricts research progress and hampers medical advancements. A few years back, a major professional organization in genetics- The Association for Molecular Pathology (AMP)- sued Myriad to challenge the validity of their patents. The case wound its way through the Federal court system, and eventually was taken up by the Supreme Court earlier this year. Today, the SCOTUS handed down their ruling. The very basic interpretation of what the court held is that genes themselves cannot be patented, however cDNA sequences can. Most people who have been following this case for a while expected a ruling along these lines. This invalidates a large portion of Myriad’s patent control of BRCA1 and BRCA2 and seriously weakens the patent positions of a number of companies with important gene patents.

I have long argued against the idea of gene patenting. Like many other in my field, I have never been comfortable with a number of the implications, the largest being the idea that a company someone holds control over my ability to learn information about the one of the most basic parts of my body, my genome. Please don’t misunderstand, as a scientist, I full understand the importance of intellectual property protections. However, my DNA belongs to me, and I hold strongly that I’m the one who should have ultimate control over its analysis. Furthermore, I feel that gene patents fail another crucial test: you cannot invent “around” them. A hallmark of the concept of the patent is the idea that whatever is patented can still be improved upon. If you’re intelligent enough to design a way to get to the same endpoint by different methods, then you’re in the clear (and can even be granted a patent of your own). However, granting complete patent control over the gene itself removes that “invent around” possibility, which (to me) is a violation of the basic tenants of patent law and patentability.

The decision has some pretty important implications as genetic and genomic technology race forward. So called next-generation sequencing technology is rapidly bringing down the costs of large scale sequencing of the human genome (as well as exome and transcriptome, which again, we’ll cover shortly), and whole gene sequencing is staged to move from an extremely complex, expensive, and time-consuming test to something relatively routine within just the next year or so. This technology will allow us to sequence entire genes (and soon entire genomes) of large numbers of individuals and give us insights into genetic function and variability beyond out wildest dreams, as well as significant advancements in personalized medicine. If gene patents had been allowed to stand, it would have created a nightmare of licensing complications for interpreting complete genome sequences. Companies wishing to offer complete genome testing would have been required to negotiate licenses (and fees) with every single holder of a patent on a human gene. Not only would this have been an administrative nightmare and a constant risk of litigation, it would have almost certainly made this kind of testing prohibitively expensive to all but the richest of patients, turning a potentially paradigm-shifting medical advancement into a niche sector.

The decision isn’t perfect however. The upholding of cDNA patents leaves a number of complex issues in place. The largest among these (at least from my reading of the case law) is transcriptome research. One of the most common places where cDNA is made is from messenger RNA (mRNA). mRNA’s function within the cell is to provide instructions to produce proteins. mRNA is isolated from cells to study the changes in these signals (generally known as gene expression). The sum of all these mRNAs from a cell is known as the transcriptome. Current technology allows us to examine large portions of the transcriptome to monitor gene expression in cells, tissue, and ultimately organisms, and it has wide-ranging applications in medical research, particularly in complex situations like heart disease, diabetes, and cancer.  Again, as the technology in molecular biology advances, we are able to examine much larger portions of the transcriptome and gain a much deeper understanding of the mechanisms at place in many processes, both cellular and throughout an organism and the potential for major advancements in human health is huge. However, if the cDNA made from the mRNA of a particular gene remains under patent, we again run into the issues of licensing for this kind of work. It seems to me that it’s more the wording of explanation of what cDNA is that skirts the “natural products” restriction, not any significant difference in fact. cDNA is essentially a copy of a natural product (mRNA); it just so happens that the particular method in which nucleic acids replicate (through complimentary sequences) gives it appearance of something novel. It’s still essentially a patent on something innate to my body (the genes it’s expressing, rather than the basic instruction set). It still fails at the “invent around” test, and I believe these patents should have (at least as they apply to mRNA) been overturned as well. I believe the repercussions of allowing these patents to remain will significantly stifle research in gene expression and the transcriptome for years to come.

I think the AMP v Myriad ruling is an important step forward, and a correction to a major standing error in US intellectual property law. I believe it will open to door for major advances in many areas of medicine and basic science, and it maintains an individual’s absolute control over the content of their genetic code. However, the upholding of cDNA patents is a sticking point for me, and I’m anxious to see how this plays out in research community and in IP litigation.


New Academic Journal about Trans Issues, or “We’re not just a medical curiousity anymore.”

DU Press to publish transgender quarterly | The Chronicle.

I can’t say enough good things about this. Having an academic journal that specifically publishes non-medical academic material about the transgender community means a chance to both encourage greater study, and to give us better visibility in the academic community. There are so many social, cultural, and political issues that are incredibly specific to the trans community, and perhaps this will shed light on some of them. My hat is off to the Drs Stryker and Currah for undertaking such a momentous project.

A blog about nerdy things, feminist thoughts, and queer/trans life. It's full of rants, opinions, and personal stories. I don't claim to speak for absolutely anyone but myself. Read at your own risk.

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