Archive | June, 2013

Link Roundup: Bad headlines, social media for academics, women in science, and the 8th Conference of the Science Journalists

28 Jun

I am going to start doing link roundup on this blog – I go through many articles each week, some of which really are worth mentioning but do not quite warrant full blog posts. I will try to do this every 1-2 weeks. Enjoy!

Bad Headlines: As a science communicator, nothing irks me more than terrible headlines.

Social Media for Academics

  • Chris Buddle is an Ecology professor at the McGill University. He recently put together a wonderful presentation on Social media for academics, probably one of the best presentations that I have seen that is tailored for the academics. Chris is very active on twitter, so make sure you follow him @CMBuddle
  • The role of twitter in the life cycle of a scientific publication by Darling, Shiffman, Côté, and Drew came out on ArXiv some time ago, but I finally managed to take a look last week. A very nicely written summary about twitter for academics because it is much more in-depth, and was written specifically for its target audience. I have seen way too many generic twitter summaries written for academics that are just way too light and do not present a strong case on why academics should be using twitter. HT Artem Kaznatcheev for bringing this to my attention.

Women in Science

  • I am working on a review of recent studies on gender bias in science, and came across this. Athene Donald wrote about a paper published this month regarding the under-representation of women as invited speakers at the European Society for Evolutionary Biology Congress. It is more complicated than it seems –  you can check out the paper here. Athene invited comments on her blog post through social media and the comment thread for her post is a good read.

The 8th Conference of the Science Journalists: The conference was held in Helsinki in Finland from June 24 to 28. If you look at the programme, you would notice that there are a many great discussions during the conference! Sad that you missed the conference? Here are a few ways to catch up:

Last but not the least…

The thrill of DIY electronics

23 Jun

Our summer camp program will begin in about two weeks. This is the time we  start looking at empty spots in our schedule and thinking about what we can do with them. One thing that is still missing is an electronics activity for our Grade 8-10 kids.

Now, while I have worked in the Department of Physics & Astronomy for almost 5 years, the last time I took a physics course was in first year undergrad. So the memory of how electronics work is a vague one. This is a pity because we have so many cool things in the department (3D print, water jet cutter, machine shop, you name it) – I just had no time. BUT this is work, right? So I sat down and started working on it.

Originally my coop student came up with a light-sensing electrical fans. “eh…kinda boring,” I said (I know, I was harsh haha). “What about something that moves?” “Like a car? Can these motors do that?” This went on for a while, and I started putting things on the breadboard, occasionally not knowing what the components are doing (“eh, what’s a mosfet?”). But I was pretty determined. I broke a LED and a light sensor in the process (“I smell something burning…”), but luckily my coop student figured it out for me 😉

Anyways, this is what we ended up putting together! It’s a light sensing car: the switches control whether you want it to be in the light sensing mode or not. And when there is no light, it stops running but turns on the LED light.

(I don’t have a video of it running because it was too hard to film that in my office, but it does work really well. Also, it is not a solar-powered car – I don’t think the power input would have been enough, plus the car is too heavy, but maybe we will try that later on)

The circuit is messy at the moment, so he is working on cleaning up the circuit, perhaps changing the switch to something smaller/simpler. Once we finish, we plan to put the instructions up on Instructables. Of course, the camp kids will be able to build these cars during the camp.

But, the really cool thing is that we put this together!! This is so exciting – I guess this is why many people are behind the Maker movement. I also told my coop student that I will brag about it for another few weeks. Haha.

#ILoveMyJob

Taking away basic science funding is not a long-term solution

19 Jun

I came across Scott Findlay’s article in the National Post a few weeks ago. While the Canadian government continues to boast its investment in science, those of us who work closely with basic science research know where the money is really going – into commercialization and application development.

In science, as elsewhere, where money is spent is as important as how much is spent. Most of the $8-billion allocated to R&D has been invested at the top of the scientific research pyramid, in technology development and commercialization. For example, virtually all of the new $454-million R&D expenditures in the 2013 budget target private-public partnerships, mostly in applied or commercialization research. Yet it is basic research that forms the base of the R&D pyramid, the wellspring of the pipeline to technology development and commercialization.

It is not to say that putting money into applications isn’t a great thing. It is – but you still want to have a strong foundation of basic science research, serving as the backbone. With the heavy emphasis on application development these days (because that’s where the money is – many new grants require a industrial collaboration component), what we will end up doing is to “guess” which basic science project will be more useful in the future, when the future isn’t here yet. This is like drafting major league players for 2033 when they are still playing t-ball, or finding the next Wayne Gretzky and Sidney Crosby by looking at baby photos.

We might not see the immediate financial return of investing in basic science research, but we will benefit from it 10-20 years later. Without this investment, there will be a gap in the future of application development, and soon we will start falling behind other countries. Of course, the current government does not need to care about this much. It is the problem of the future elected government, isn’t it? But we should all care about it, because this future is ours.

What Scott Findlay said inspired me to draw the following.

Commercialization is not a long term solution sm
Can we strike a balance between investing in basic science research, and encouraging commercialization and development of applications? Hopefully. But cutting basic science funding is not the answer for our future.

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Note: By the way, I really like this comment by ChadEnglish for the article. According to the comment, he’s an engineer so he is most likely to benefit from this shift to application development and commercialization.

Without a growing science base to build from the only thing we engineers can do is repackage the old technologies into new boxes. Engineering is also known as applied science. Without good science, and without good access to it, there is nothing to apply.

Notes from the Northern Voice #nv13, a blogging & social media conference

17 Jun

(If you want to go straight to the notes, they are here – Storify: Social media & blogging tips from the Northern Voice 2013 #nv13)

This past weekend, I finally had the opportunity to attend the Northern Voice, a blogging/social media conference here at Vancouver. It’s funny to think that a year ago, I owned neither a blog, nor a twitter account. This is the first time that I feel I am “qualified” enough to attend – imagine my excitement!

But the excitement comes with some timidness. This conference is quite different from the science conferences that I am familiar with. The Northern Voice is not about a specific subject or topic, but about the desire to share and communicate thoughts, ideas, and experiences through online publishing; this means that we came from all walks of life – from mommy bloggers, PR managers, archivists, technology enthusiasts, to photographers and (obviously) science communicators. Some of these people have tens and hundreds of thousands of readers! I have only just started blogging not long ago, so obviously don’t want to act like an idiot (or too much of a science nerd :P).

Luckily, my experience at the Northern Voice was wonderful. I met many who are also passionate about sharing their stories, some of whom I think I will be friends with for years to come. I also was able to tweet throughout the conference without any guilt (Come on, it is a social media conference – it was almost expected that everyone would pull out their smart phone/laptop/tablet and start tweeting away. Like what Mark Blevis said before his keynote, “if it wasn’t tweeted, it didn’t happen”)

Anyways, for novice bloggers out there, or for those who are interested in starting a blog but haven’t done so, here are some notes I took during the conference. It is in the Sorify format because, well, I took the notes using twitter.  Hope that this will be helpful for you.

Storify: Social media & blogging tips from the Northern Voice 2013 #nv13

If you have any other tips, please feel free to share them by commenting below!

Your genes cannot be patented, but it is too early to celebrate

14 Jun

The US Supreme Court came down with its ruling on the Myriad case. Maybe somewhat expected, the Supreme Court ruled that as genes are considered “naturally occurring,” they are not patent eligible. This is not surprising, although quite a relief at least (a good thing). The idea of a company being able to patent genes in us is simply quite disturbing.

However, I think it is too early to celebrate. The judge, interestingly, stated that as complementary DNA (cDNA) are not naturally occurring, they will be patent eligible. According to Justice Thomas in the opinion of the court:

cDNA is not a “product of nature,” so it is patent eligible under §101. cDNA does not present the same obstacles to patentability as naturally occurring, isolated DNA segments. Its creation results in an exons-only molecule, which is not naturally occurring. Its order of the exons may be dictated by nature, but the lab technician unquestionably creates something new when introns are removed from a DNA sequence to make cDNA.

This, to me, feels like a very awkward decision based on my understanding of biochemistry (I do have a biochemistry degree after all!). In your cell, many processes are involved in going from the genetic code in your genome to a final protein product that will be made. This process is known as the central dogma. The DNA code is first transcribed into mRNA (“transcription”), the mRNA goes through a few additional steps (adding the 5′ cap and the poly-A tail, and “splicing” – during which parts of the mRNA called “introns” are removed), and then based on this mRNA sequence, an amino acid chain is made (“translation”). This amino acid chain goes through more modifications and eventually becomes a protein. Here is a quick video about the splicing process (please watch it before reading on if you are not familiar with the central dogma):

To generate a cDNA,  an enzyme called the reverse transcriptase is used to produce the cDNA based on the sequence of the spliced mRNA (here is an infographic on making a cDNA library). This means that the cDNA contains the genetic code in your genome, except with the introns already removed (this is likely a simplification of the process, because I am sure there are exceptions, but for majority of the time this is the case).

So let’s come back to this “cDNA being patent eligible” business. Because I am not an expert in the different types of patents, I am hoping to cover the different situations I can think of – none of which sit well with me.

Situation 1: cDNA essentially contains your genetic code (well, sort of, then we probably need to define what your “gene” really means – with the introns? without the introns? complementary to the mRNA sequence?). So to allow patents for the information on cDNA doesn’t seem too different from allowing patents for your gene…at least in my opinion.

Situation 2: A few have mentioned that the judge was pointing to a “method patent,” which also seems weird to me. The technique used to generate cDNA has been around for a few decades (HT Mark Hoofnagle for mentioning this in his blog post). So, the technique itself is definitely not novel.

Situation 3: If the judge was suggesting a “method patent” for the act of technicians from Myriad generating cDNA of BRCA1 and BRCA2, then does this mean that any of us with enough knowledge of how to use reverse transcriptase, with access to equipment, and a source of mRNA, can walk into a biochemistry lab to generate cDNA and patent the “method”? (if so, we probably all should start doing this…)

Situation 4: Research labs often isolate cDNAs for many purposes, or prepare cDNA libraries. If a specific cDNA is patented, does it mean that researchers will then need to pay the company a licensing fee in order to continue isolating the said cDNA or cDNA libraries? Will it be considered that they infringed on the patent?

It was, however, noted in the court opinion that:

This case, it is important to note, does not involve method claims, patents on new applications of knowledge about the BRCA1 and BRCA2 genes, or the patentability of DNA in which the order of the naturally occurring nucleotides has been altered.

This means there was no actual ruling about whether cDNA should be patented (yet). This case, therefore, is not the end of the patent discussion for genes – companies are already moving toward working with cDNA and there will likely be more discussions and court cases about cDNA down the road.

According to the Daily Beast:

…a cDNA patent would still have to show that its invention is “non-obvious,” says Matthew Dowd, the lawyer who filed an amicus brief on behalf of James Watson, who won a Nobel Prize for his co-discovery of the structure of DNA. “If you have human genes you almost necessarily have cDNA,” says Dowd. “Down road will be battles over whether cDNA is non-obvious.”

This brings up another issue that is burning to be discussed – how do we provide companies with enough financial incentives for investment in innovation, without prohibiting others from accessing the innovation? From this case, to the patent wars between Apple, Google, and Samsung, to the lack of drug development for rare diseases (mostly as a result of the lack of financial incentives), a bigger discussion will probably need to happen as to how we can create win-win situations. Otherwise, we will continue chase the patent tail, and fill up the pockets of corporate lawyers.

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Note: I would like to thank Joyce and Jone for our discussions on this topic. I am really just brushing the surface here – Joyce provided me with a much more extensive reading list (which I unfortunately didn’t finish – sorry Joyce!)

(updated June 14 at 4pm) Joyce also wrote about this for her first blog post – if you enjoy some additional technical/legal details you will likely enjoy it.

Note 2: I met Andrea, a graduate student in Biology (Genetics), on twitter. She is collecting links about this ruling on her blog “Appetite for Awesome.” Go check it out!

Note 3: This whole patent discussion reminds me of Kevin O’Leary! If you watch Dragon’s Den or Shark Tank, you would know what I am talking about 😛 Apparently he also had some opinions about this (and I’m absolutely not surprised by his standpoint):

Note 4: No, I am not an american citizen, but at the same time rulings like this set precedence…so of course I am gonna write about it 😛

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