Tag Archives: RRResearch

Immune to CRISPR?

I guess if you’re going to use bacteria as part of your gene editing technology (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9) then, you might half expect the body’s immune system may have developed some defenses. A Jan. 9, 2018 article by Sarah Zhang for The Atlantic provides some insight into what the new research suggests (Note: Links have been removed),

2018 is supposed to be the year of CRISPR in humans. The first U.S. and European clinical trials that test the gene-editing tool’s ability to treat diseases—such as sickle-cell anemia, beta thalassemia, and a type of inherited blindness—are slated to begin this year.

But the year has begun on a cautionary note. On Friday [January 5, 2018], Stanford researchers posted a preprint (which has not been peer reviewed) to the website biorXiv highlighting a potential obstacle to using CRISPR in humans: Many of us may already be immune to it. That’s because CRISPR actually comes from bacteria that often live on or infect humans, and we have built up immunity to the proteins from these bacteria over our lives.

Not all CRISPR therapies in humans will be doomed. “We don’t think this is the end of the story. This is the start of the story,” says Porteus [Matthew Porteus, a pediatrician and stem-cell researcher at Stanford]. There are likely ways around the problem of immunity to CRISPR proteins, and many of the early clinical trials appear to be designed around this problem.

Porteus and his colleagues focused on two versions of Cas9, the bacterial protein mostly commonly used in CRISPR gene editing. One comes from Staphylococcus aureus, which often harmlessly lives on skin but can sometimes causes staph infections, and another from Streptococcus pyogenes, which causes strep throat but can also become “flesh-eating bacteria” when it spreads to other parts of the body. So yeah, you want your immune system to be on guard against these bacteria.

The human immune system has a couple different ways of recognizing foreign proteins, and the team tested for both. First, they looked to see if people have molecules in their blood called antibodies that can specifically bind to Cas9. Among 34 people they tested, 79 percent had antibodies against the staph Cas9 and 65 percent against the strep Cas9.

The Stanford team only tested for preexisting immunity against Cas9, but anytime you inject a large bacterial protein into the human body, it can provoke an immune response. After all, that’s how the immune system learns to fight off bacteria it’s never seen before. (Preexisting immunity can make the response faster and more robust, though.)

The danger of the immune system turning on a patient’s body hangs over a lot of research into correcting genes. In the late 1990s and 2000s, research into gene therapy was derailed by the death of 18-year-old Jesse Gelsinger, who died from an immune reaction to the virus used to deliver the corrected gene. This is the worst-case scenario that the CRISPR world hopes to avoid.

Here’s a link to and a citation for the preprint,

Identification of Pre-Existing Adaptive Immunity to Cas9 Proteins in Humans by Carsten Trevor Charlesworth, Priyanka S Deshpande, Daniel P Dever, Beruh Dejene, Natalia Gomez-Ospina, Sruthi Mantri, Mara Pavel-Dinu, Joab Camarena, Kenneth I Weinberg, Matthew H Porteus. bioRxiv posted January 5, 2018 doi: https://doi.org/10.1101/243345

This article is a preprint and has not been peer-reviewed …

This preprint (not yet published paper) is open access and open for feedback.

Meanwhile, the year of CRISPR takes off (from a January 10, 2018 American Chemical Society news release on EurekAlert),

This year could be a defining one for CRISPR, the gene editing technique, which has been hailed as an important breakthrough in laboratory research. That’s because the first company-sponsored clinical studies will be conducted to see if it can help treat diseases in humans, according to an article in Chemical & Engineering News (C&EN), the weekly newsmagazine of the American Chemical Society.

C&EN Assistant Editor Ryan Cross reports that a big push is coming from industry, specifically from three companies that are each partly founded by one of the three inventors of the method. They are zeroing in on the blood diseases called sickle-cell anemia and β-thalassemia, mostly because their precise cause is known. In these diseases, hemoglobin doesn’t function properly, leading to severe health issues in some people. Crispr Therapeutics and Intellia Therapeutics plan to test the technique to boost levels of an alternative version of healthy hemoglobin. Editas Medicine, however, will also use CRISPR to correct mutations in the faulty hemoglobin gene. Labs led by university researchers are also joining the mix, starting or continuing clinical trials with the approach in 2018.

Because CRISPR is being used to cut a cell’s DNA and insert a new sequence, concerns have been raised about the potential for accidents. A cut in the wrong place could mean introducing a new mutation that could be benign — or cancerous. But according to proponents of the method, researchers are conducting extensive computer predictions and in vitro tests to help avoid this outcome.

The January 8, 2018 Chemical and Engineering News (C&EN) open access article by Ryan Cross is here.

Finally, if you are interested in how this affects research as it’s being developed, there’s University of British Columbia researcher Rosie Redfield’s January 16, 2018 posting on RRResearch blog,

Thursday’s [January 11, 2018] post described the hypothesis that bacteria might use gene transfer agent particles to inoculate other cells in the population with fragments of phage DNA, and outlined an experiment to test this.  Now I’m realizing that I need to know a lot more about the kind of immunity I should expect to see if this GTA-as-vaccine hypothesis is correct.

That should give you some idea of what I meant by “research as it’s being developed.” Redfield’s blog is not for the mildly interested.

Redfield is well-known internationally as being one of the first to refute research which suggested the existence of an ‘arsenic bacterium’ (see my Dec. 8, 2010 posting: My apologies for arsenic blooper. She’s first mentioned in the second excerpt, second paragraph.) The affair was known online as #arseniclife. There’s a May 27, 2011 essay by Carl Zimmer on Slate titled: The Discovery of Arsenic-Based Twitter: How #arseniclife changed science.

2012 Canadian science blog roundup and some thoughts on a Canadian science blog network

This is my 3rd annual roundup of Canadian science blogs and the science blogging scene in Canada seems to be getting more lively (see my Dec. 31, 2010 posting and Dec. 29, 2011 posting to compare).

As I did last year, I will start with


Don’t leave Canada appears to be gone as there hasn’t been posting there since May 4, 2011. I’m sorry to see it go as Rob Annan provided thoughtful commentary on science policy on a regular basis for years. Thank you, Rob. (BTW, he’s now the director of policy, research and evaluation at MITACS.)

Cool Science, John McKay’s blog has been shut down as of Oct. 24, 2012,

Hi everyone. This will mark the final post of the CoolScience.ca site and it will be quietly taken offline in November. I will also be closing down the Twitter and Facebook accounts and moving everything over to my professional accounts that are all focused on communicating science, technology, engineering and medicine.

The Dark Matter science blog by Tom Spears, which I reluctantly (as it was a ‘newspaper blog’ from the Ottawa Citizen)included last year  has since disappeared as has NeuroDojo, a blog written by a Canadian scientist in Texas.

Goodbye ish

Marc Leger’s Atoms and Numbers blog’s latest posting is dated Oct. 23, 2012 but the pattern here seems similar to Marie-Claire’s (see the next one) where the posting is erratic but relatively regular (once or twice per month) until October of this year.

Marie-Claire Shanahan is posting less frequently on her Boundary Vision blog with the last posting there on Oct. 9, 2012.

The Bubble Chamber blog from the University of Toronto’s Science Policy Work Group seems to be fading away with only one posting for 2012, Reply to Wayne Myrvold on the Higgs Boson.

Colin Schulz’s CMBR blog hasn’t had a new posting since July 13, 2012’s 11 Things You Didn’t Know About Canada. In any event, it looks like the blog is no longer primarily focused on science.

The Exponential Book blog by Massimo Boninsegni features an Oct. 24, 2012 posting and a similar posting pattern to Marie-Claire & Marc.

exposure/effect which was new last year has gone into a fairly lengthy hiatus as per its last post in January 30, 2012 posting.

Theoretical biologist, Mario Pineda-Krch of Mario’s Entangled Bank blog is also taking a lengthy hiatus as the last posting on that blog was June 11, 2012.

Nicole Arbour’s Canadian science blog for the UK High Commission in Ottawa hasn’t featured a posting since Oct. 15, 2012’s The Power of We: Adapting to climate change.

Gregor Wolbring’s Nano and Nano- Bio, Info, Cogno, Neuro, Synbio, Geo, Chem… features an Aug. 4, 2012 posting which links to one of his nano articles, (Nanoscale Science and Technology and People with Disabilities in Asia: An Ability Expectation Analysis) published elsewhere.

Jeff Sharom’s Science Canada blog highlights links to editorials and articles on Canadian science policy but doesn’t seem to feature original writing by Sharom or anyone else, consequently, it functions more as a reader/aggregator than a blog.

The Black Hole blog which was always more focused on prospect for Canadian science graduates than Canadian science, hence always a bit of a stretch for inclusion here, has moved to the University Affairs website where it focuses more exclusively on the Canadian academic scene with posts such as this, Free journal access for postdocs in between positions  from Dec. 12, 2012.

Returning to the roundup:

John Dupuis’ Confessions of a Science Librarian whose Dec. 26, 2012 posting, Best Science (Fiction) Books 2012: io9 seems timely for anyone taking a break at this time of year and looking for some reading material.

Daniel Lemire’s blog is known simply as Daniel Lemire. He’s a computer scientist in Montréal who writes one of the more technical blogs I’ve come across and his focus seems to be databases although his Dec. 10, 2012 posting covers the topic of how to get things accomplished when you’re already busy.

Dave Ng, a professor with the Michael Smith Laboratories at the University of British Columbia, is a very active science communicator who maintain the Popperfont blog. The latest posting (Dec. 24, 2012) features Sciencegeek Advent Calendar Extravaganza! – Day 24.

Eric Michael Johnson continues with his The Primate Diaries blog on the Scientific American blog network. His Dec. 6, 2012 posting is a reposted article but he has kept up a regular (once per month, more or less) posting schedule,

Author’s Note: The following originally appeared at ScienceBlogs.com and was subsequently a finalist in the 3 Quarks Daily Science Prize judged by Richard Dawkins. Fairness is the basis of the social contract. As citizens we expect that when we contribute our fair share we should receive our just reward. When social benefits are handed out …

Rosie Redfield is keeping with both her blogs, RRTeaching (latest posting, Dec. 6, 2012) and RRResearch (Nov. 17, 2012).

Sci/Why is a science blog being written by Canadian children’s writers who discuss science, words, and the eternal question – why?

Mathematician Nassif Ghoussoub’s Piece of Mind blog continues to feature incisive writing about science, science funding, policy and academe.

Canadian science writer Heather Pringle continues to post on the The Last Word on Nothing, a blog shared collectively by a number of well known science writers. Her next posting is scheduled for Jan. 3, 2013, according to the notice on the blog.

A little off my usual beat but I included these last year as they do write about science albeit medical and/or health science:

Susan Baxter’s blog Curmudgeon’s Corner features her insights into various medical matters, for example there’s her Dec. 1, 2012 posting on stress, the immune system, and the French antipathy towards capitalism.

Peter Janiszewski and Travis Saunders co-own two different blogs, Obesity Panacea, which is part of the PLoS (Public Library of Science) blogs network, and Science of Blogging which features very occasional posting but it’s worth a look for nuggets like this Oct. 12, 2012 (?) posting on social media for scientists.

After posting the 2011 roundup,

I had a number of suggestions for more Canadian science blogs such as these four who are part of the Scientific American SA) blogging network (in common with Eric Michael Johnson),

Dr. Carin Bondar posts on the SA blog, PsiVid, along with Joanne Manaster. There’s more than one Canadian science blogger who co-writes a blog. This one is self-described as, A cross section of science on the cyberscreen.

Glendon Mellow, a professional science illustrator,  posts on The Flying Trilobite (his own blog) and Symbiartic: the art of science and the science of art, an SA blog he shares with Kalliopi Monoyios.

Larry Moran, a biochemist at the University of Toronto, posts on science and anything else that tickles his fancy on his Sandwalk blog.

Eva Amsen who posts on a number of blogs including the NODE; the community site for developmental biologists  (which she also manages) but the best place to find a listing of her many blogs and interests is at easternblot.net, where she includes this self-description on the About page,

Online Projects

  • Musicians and Scientists – Why are so many people involved in both music and science? I’m on a mission to find out.
  • the NodeMy day job is managing a community site for developmental biologists around the world. The site is used by equal numbers of postdocs, PhD students, and lab heads.
  • SciBarCamp/SciBarCamb – I co-instigated SciBarCamp, an unconference for scientists, in Toronto in 2008. Since then I have co-organized five similar events in three countries, and have advised others on how to run science unconferences.
  • You Learn Something New Every Day – a Tumblr site that automatically aggregates tweets with the hashtag #ylsned, and Flickr photos tagged ylsned, to collect the interesting bits of trivia that people come across on a daily basis.
  • Lab Waste – During my last months in the lab as a PhD student, I made a mini-documentary (using CC-licensed materials) about the excessive amount of disposable plastics used in research labs. It screened in 2009 in the “Quirky Shorts” program of the Imagine Science Film Festival in New York.
  • Expression Patterns – In 2007 I was invited to blog on Nature Network. The complete archives from 2007-2012 are now on this site.
  • easternblot.net – Confusingly, my other science blog was named after this entire domain. It ran from 2005 to 2010, and can be found at science.easternblot.net

I believe Amsen is Canadian and working in the UK but if anyone could confirm, I would be much relieved.

Someone, who according to their About page prefers to remain anonymous but lives in Victoria, BC, and posts (somewhat irregularly, the last posting is dated Nov. 10, 2012) on The Olive Ridley Crawl,

I am an environmental scientist blogging about environmental and development issues that interest me. I prefer to be anonymous(e) because I work with some of the companies I may talk about and I want to avoid conflict of interest issues at work. This gets tricky because I am at the periphery of a lot of events happening in the world of my greatest expertise, persistent organic pollutants, endocrine disrupting compounds, their effects on health and the policy fights around chemicals, their use the controversies! So, I’ve reluctantly moved away from writing about what I know most about, which means this blog suffers severely. I still soldier on, though!

I was born, and grew up in India, so I am interested in all things South Asian and tend to view most all Western government and Western institution actions through a colonialist scratched lens! I am also becoming much more active about my feminism, so who knows what that will do to this blog. I have been meaning to write a monstrous essay about women, the environment and justice, but that’s a task!

I used to live in Chapel Hill, NC with a partner of long vintage (the partnership, that is, not her!) and a crazy cat who thinks he’s a dog. We moved to Victoria, BC in 2008 and I’ve been busy learning about Canadian policy, enjoying this most beautiful town I live in.

Why Olive Ridley? Well, the Olive Ridley sea turtle (Lepidochelys Olivacea) nests on the coasts of Madras, India and I got my start in the wonderful world of conservation working on the Olive Ridley with the Students’ Sea Turtle Conservation Network. So, I do have fond memories for this beautiful creature. And yes, as my dear partner reminds me, I did meet her on the beach when I was doing this work.

Agence Science-Presse (based in Québec and headed by Pascal Lapointe) features three blogs of its own:

Blogue ta science : les billets dédiés aux jeunes.

Discutez avec notre expert : avez-vous suivi notre enquête CSI ?

Autour des Blogues : les actualités de nos blogueurs et de la communauté.

There’s also a regular podcast under the Je vote pour la science banner.

genegeek appears to be Canadian (it has a domain in Canada) but the blog owner doesn’t really identify herself (there’s a photo) on the About page but no name and no biographical details. I did receive a tweet last year about genegeek from C. Anderson who I imagine is the blog owner.

There’s also the Canadian BioTechnologist2.0 blog, which is sponsored by Bio-Rad Canada and is written by an employee.

These next ones were added later in the year:

Chuck Black writes two blogs as he noted in June 2012,

I write two blogs which, while they focus more on space than science, do possess strong science components and overlap with some of the other blogs here.

They are: Commercial Space and Space Conference News.

Andy Park also came to my attention in June 2012. He writes the  It’s the Ecology, Stupid! blog.

Something About Science is a blog I featured in an Aug. 17, 2012 posting and I’m glad to see blogger, Lynn K, is still blogging.

New to the roundup in 2012:

SSChow, Sarah Chow’s blog, focuses on science events in Vancouver (Canada) and science events at the University of British Columbia and miscellaneous matters pertinent to her many science communication efforts.

The Canadian federal government seems to be trying its hand at science blogging with the Science.gc.ca Blogs (http://www.science.gc.ca/Blogs-WSE6EBB690-1_En.htm). An anemic effort given that boasts a total of six (or perhaps it’s five) posting in two or three years.

The Canadian Science Writers Association (CSWA) currently features a blog roll of its members’ blogs. This is a new initiative from the association and one I’m glad to see.  Here’s the list (from the CSWA member blog page),

Anne Steinø (Research Through the Eyes of a Biochemist)
Arielle Duhame-Ross (Salamander Hours)
Bob McDonald (I’m choking on this one since it’s a CBC [Canadian Broadcasting Corporation] blog for its Quirks and Quarks science pr0gram)
Cadell Last (The Ratchet)
Edward Willett
Elizabeth Howell (she seems to be blogging again and the easiest way for me to get to her postings was to click on the Archives link [I clicked on December 2012 to get the latest] after doing that I realized that the images on the page link to postings)
Heather Maughan
Justin Joschko
Kimberly Gerson (Endless Forms Most Beautiful)
Mark Green (a CSWA member, he was born and educated in the US where he lives and works; ordinarily I would not include him, even with his  CSWA membership status,  but he writes a monthly science column for a Cape Breton newspaper, which has made me pause)
Pamela Lincez (For the Love of Science)
Sarah Boon (Watershed Moments)
Susan Eaton (she seems to be reposting articles written [presumably by her] for the AAPG [American Association of Petroleum Geologists] Explorer and other organizations in her blog]

Barry Shell’s site (listed as a CSWA member blog) doesn’t match my admittedly foggy notion of a blog. It seems more of an all round Canadian science resource featuring profiles of Canadian scientists, a regularly updated news archive, and more. Science.ca is extraordinary and I’m thankful to have finally stumbled across it but it doesn’t feature dated posts in common with the other blogs listed here, even the most commercial ones.

Tyler Irving (I had no idea he had his own blog when I mentioned him in my Sept. 25, 2012 posting about Canadian chemists and the Canadian Chemical Institute’s publications) posts at the Scientific Canadian.

I choke again, as I do when mentioning blogs that are corporate media blogs, but in the interest of being as complete as possible Julia Belluz writes the Scien-ish blog about health for MacLean’s magazine.

Genome Alberta hosts a couple of blogs: Genomics and Livestock News & Views.

Occam’s Typewriter is an informal network of science bloggers two of whom are Canadian:

Cath Ennis (VWXYNot?) and Richard Wintle (Adventures in Wonderland). Note: The Guardian Science Blogs network seems to have some sort of relationship with Occam’s Typewriter as you will see postings from the Occam’s network featured as part of Occam’s Corner on the Guardian website.

My last blogger in this posting is James Colliander from the University of  Toronto’s Mathematics Department. He and Nassif (Piece of Mind blog mentioned previously) seem to share a similar interest in science policy and funding issues.

ETA Jan.2.13: This is a social science oriented blog maintained by a SSHRC- (Social Science and Humanities Research Council) funded network cluster called the Situating Science Cluster and the blog’s official name is: Cluster Blog. This is where you go to find out about Science and Technology Studies (STS) and History of Science Studies, etc. and events associated with those studies.

I probably should have started with this definition of a Canadian blogger, from the Wikipedia entry,

A Canadian blogger is the author of a weblog who lives in Canada, has Canadian citizenship, or writes primarily on Canadian subjects. One could also be considered a Canadian blogger if one has a significant Canadian connection, though this is debatable.

Given how lively the Canadian science blogging scene has become, I’m not sure I can continue with these roundups as they take more time each year.  At the very least, I’ll need to define the term Canadian Science blogger, in the hope of reducing the workload,  if I decide to continue after this year.

There’s a rather interesting Nov. 26, 2012 article by Stephanie Taylor for McGill Daily about the Canadian public’s science awareness and a dearth of Canadian science communication,

Much of the science media that Canadians consume and have access to is either American or British: both nations have a robust, highly visible science media sector. While most Canadians wouldn’t look primarily to American journalism for political news and analysis, science doesn’t have the same inherent national boundaries that politics does. While the laws of physics don’t change depending on which side of the Atlantic you’re on, there are scientific endeavours that are important to Canadians but have little importance to other nations. It’s unlikely that a British researcher would investigate the state of the Canadian cod fishery, or that the British press would cover it, but that research is critical to a substantial number of Canadians’ livelihoods.

On the other hand, as Canadian traditional media struggles to consistently cover science news, there’s been an explosion of scientists of all stripes doing a lot of the necessary big picture, broad context, critical analysis on the internet. The lack of space restrictions and accessibility of the internet (it’s much easier to start a blog than try to break in to traditional media) mean that two of the major barriers to complex discussion of science in the media are gone. Blogs struggle to have the same reach as newspapers and traditional media, though, and many of the most successful science blogs are under the online umbrella of mainstream outlets like Scientific American and Discover. Unfortunately and perhaps unsurprisingly, there is currently no Canadian science blog network like this. [emphasis mine]

Yes, let’s create a Canadian science blog network. I having been talking to various individuals about this over the last year (2012) and while there’s interest, someone offered to help and then changed their mind. Plus, I was hoping to persuade the the Canadian Science Writers Association to take it on but I think they were too far advanced in their planning for a member’s network to consider something more generalized (and far more expensive). So, if anyone out there has ideas about how to do this, please do comment and perhaps we can get something launched in 2013.

2011 roundup and thoughts on the Canadian science blogging scene

Last year I found about a dozen of us, Canadians blogging about science, and this year (2011) I count approximately 20 of us. Sadly, one blog has disappeared; Elizabeth Howell has removed her PARS3C blog from her website. Others appear to be in pause mode, Rob Annan at the Researcher Forum: Don’t leave Canada behind (no posts since May 4, 2011), The Bubble Chamber at the University of Toronto (no posts since Aug. 12, 2011), Gregor Wolbring’s  Nano and Nano- Bio, Info, Cogno, Neuro, Synbio, Geo, Chem…  (no new posts since Oct. 2010; I’m about ready to give up on this one) and Je vote pour la science (no posts since May 2011).

I’ve been fairly catholic in my approach to including blogs on this list although I do have a preference for blogs with an individual voice that focuses primarily on science (for example, explaining the science you’re writing about rather than complaining about a professor’s marking of your science paper).

Piece of Mind is Nassif Ghoussoub’s (professor of mathematics at the University of British Columbia) blog which is largely about academe, science, and grants. Nassif does go much further afield in some of his posts, as do we all from time to time. He’s quite outspoken and always interesting.

Cool Science is John McKay’s blog which he describes this way ” This site is about raising a creative rationalist in an age of nonsense. It is about parents getting excited about science, learning and critical thinking. It is about smart parents raising smart kids who can think for themselves, make good decisions and discern the credible from the incredible. ” His posts cover a wide range of topics from the paleontology museum in Alberta to a space shuttle launch to the science of good decisions and more.

Dave Ng makes me dizzy. A professor with the Michael Smith Laboratories at the University of British Columbia, he’s a very active science communicator who has started blogging again on the Popperfont blog. This looks like a compilation of bits from Twitter, some very brief postings, and bits from other sources. I’m seeing this style of blogging more frequently these days.

The queen of Canadian science blogging, Rosie Redfield, was just acknowledged as a ‘newsmaker of the year’ by Nature magazine. The Dec. 22, 20111 Vancouver Sun article by Margaret Munro had this to say,

A critical thinker in Vancouver has been named one of the top science newsmakers of the year.

“She appeared like a shot out of the blogosphere: a wild-haired Canadian microbiologist with a propensity to say what was on her mind,” the leading research journal Nature says of Rosie Redfield, a professor at the University of B.C.

The journal editors say Redfield is one of 10 individuals who “had an impact, good or bad, on the world of science” in 2011. She was chosen for her “critical” inquiry and “remarkable experiment in open science” that challenged a now-infamous “arsenic life” study funded by NASA.

Rosie has two blogs, RRResearch and RRTeaching. She used to say she wasn’t a blogger but I rather think she’s changed her tune.

Jeff Sharom’s Science Canada blog isn’t, strictly speaking, a blog so much as it is an aggregator of Canadian science policy news and a good one at that. There are also some very useful resources on the site. (I shamelessly plundered Jeff’s list to add more blogs to this posting).

The Black Hole is owned by Beth Swan and David Kent (although they often have guest posters too). Here’s a description from the About page,

I have entered the Post Doctoral Fellow Black Hole… I’ve witnessed a lot and heard about much more and, while this is the time in academic life when you’re meant to be the busiest, I have begun this blog. Just as a black hole is difficult to define, the label Post Doc is bandied about with recklessness by university administrators, professors, and even PDFs themselves. One thing is certain though… once you get sucked in, it appears to be near impossible to get back out.

David, Beth, and their contributors offer extensive discussions about the opportunities and the failings of the post graduate science experience.

Nicole Arbour, a Science and Innovation Officer at the British High Commission Office in Ottawa, Canada, blogs regularly about Canadian science policy and more on the Foreign and Commonwealth Office blogs.

Colin Schultz, a freelance science journalist, blogs at his website CMBR. He focuses largely on climate change, environmental research, space, and science communication.

exposure/effect is a blog about toxicology, chemical exposures, health and more, which is written by a scientist who chooses to use a pseudonym, ashartus.

Mario’s Entangled Bank is written by theoretical biologist, Mario Pineda-Krch at the University of Alberta. One of Pineda-Krch’s most recent postings was about a special section of a recent Science Magazine issue on Reproducible Research.

Boundary Vision is written by Marie-Claire Shanahan, a professor of science education at the University of Alberta. She not only writes a science blog, she also researches the language and the social spaces of science blogs.

Eric Michael Johnson writes The Primate Diaries blog which is now part of the Scientific American blog network. With a master’s degree in evolutionary anthropology, Johnson examines the interplay between evolutionary biology and politics both on his blog and as part of his PhD work (he’s a student at the University of British Columbia).

The Atoms and Numbers blog is written by Marc Leger. From the About Marc page,

I am a scientist who has always been curious and fascinated by how our universe works.  I love discovering the mysteries and surprises of our World.  I want to share this passion with others, and make science accessible to anyone willing to open their minds.

Many people have appreciated my ability to explain complex scientific ideas in simple terms, and this is one motivation behind my website, Atoms and Numbers.  I taught chemistry in universities for several years, and I participated in the Scientists in the Schools program as a graduate student at Dalhousie University, presenting chemistry magic shows to children and teenagers from kindergarten to grade 12.  I’ve also given presentations on chemistry and forensics to high school students.  I’m even acknowledged in a cookbook for providing a few morsels of information about food chemistry.

Massimo Boninsegni writes about science-related topics (some are about the academic side of science; some physics; some personal items) on his Exponential Book blog.

The Last Word on Nothing is a group blog that features Heather Pringle, a well-known Canadian science writer, on some posts. Pringle’s latest posting is, Absinthe and the Corpse Reviver, all about a legendary cure for hangovers. While this isn’t strictly speaking a Canadian science blog, there is a Canadian science blogger in the group and the topics are quite engaging.

Daniel Lemire’s blog is known simply as Daniel Lemire. He’s a computer scientist in Montréal who writes one of the more technical blogs I’ve come across and his focus seems to be databases. He does cover other topics too, notably in this post titled, Where do debt, credit and currencies come from?

Confessions of a Science Librarian by John Dupuis (head of the Steacie Science & Engineering Library at York University) is a blog I missed mentioning last year and I’m very glad I remembered it this year. As you might expect from a librarian, the last few postings have consisted of lists of the best science books of 2011.

Sci/Why is a science blog being written by Canadian children’s writers who discuss science, words, and the eternal question – why?

I have mixed feelings about including this blog, the Dark Matter science blog by Tom Spears, as it is a ‘newspaper blog’ from the Ottawa Citizen.

Similarly, the MaRS blog is a corporate initiative from the Toronto area science and technology business incubator, MaRS Discovery District.

The last three blogs I’m mentioning are from medical and health science writers.

Susan Baxter’s blog Curmudgeon’s Corner features her insights into various medical matters, for example there’s her Dec. 5, 2011 posting on mammograms, along with her opinions on spandex, travel, and politics.

Peter Janiszewski and Travis Saunders co-own two different blogs, Obesity Panacea, which is part of the PLoS (Public Library of Science) blogs network, and Science of Blogging (nothing posted since July 2011 but it’s well worth a look).

I don’t have anything particularly profound to say about the state of Canadian science blogging this year. It does look to be getting more populous online and I hope that trend continues. I do have a wish for the New Year; I think it should be easier to find Canadian science blogs and would like  to see some sort of network or aggregated list.

Sick and tired of the ‘social media is changing how science is practiced’ narrative

The whole ‘social media is changing ______’ puzzles me. You can fill in the blank with science/government/social relationships/etc. It’s always the same notion. Somehow social media is engendering changes the like of which we’ve never seen before.

  • The February 2011 overthrow of Mubarak in Egypt was all due to social media, as is the current social unrest in many Middle Eastern Countries.
  • Social relationships are being negatively impacted (nobody talks to anybody else anymore or it’s opening new avenues for relationships)
  • The practice of science is being changed by the use of social media.
  • etc.

Mostly I’m concerned with the one about science since I recently ended up on a panel where the discussion turned on this topic. I think there are a lot of things having an impact on how science is practiced and trying to establish the role social media is playing, if any, is a little premature.

We had Rosie Redfield on the panel. Rosie is a professor at the University of British Columbia who was part of the ‘arsenic life’ story that took the internet by a storm in late November/early December 2010. (Confession: I got caught up in the excitement in my Dec. 6, 2010 posting and recanted in my Dec. 8, 2010 posting.) Recently, there’s been a story about ‘arsenic life’ by Carl Zimmer for Slate magazine titled, How #arseniclife changed science. Here’s Zimmer’s set up (from the Slate article),

On November 29, NASA announced that it would soon hold a press conference to “discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life.” Wild speculation ran amok—perhaps scientists had found living things on one of Saturn’s moons. At the press conference, the scientists did not unveil an actual extraterrestrial, but they did have big news. A new paper had just been published in the journal Science, they said, which described bacteria that seemed able to build their own DNA from arsenic. If that were true, it would be an historic discovery, because no such ability has ever been found among Earth’s life-forms.

The paper was published online in late November and attracted a great deal of discussion and criticism almost immediately on blogs (Rosie Redfield’s RRResearch amongst them) and on twitter via the hash tag topic, #arseniclife. The print version of the paper, along with critical letters, will appear in the June 3, 2011 issue of Science.

Here’s Zimmer’s take on what makes this particular scientific dust-up different,

For those of us who have been tracking #arseniclife since last Thanksgiving, however, today comes as an anticlimax. There’s not much in the letters to Science that we haven’t read before. In the past, scientists might have kept their thoughts to themselves, waiting for journals to decide when and how they could debate the merits of a study. But this time, they started talking right away, airing their criticisms on the Internet. In fact, the true significance of the aliens-that-weren’t will be how it helped change the way scientists do science.

Zimmer goes on to describe this new practice,

Redfield and her colleagues are starting to carry out a new way of doing science, known as post-publication peer review. Rather than leaving the evaluation of new studies to a few anonymous scientists, researchers now debate the merit of papers after they have been published. The collective decision they come to stays open to revision.

Post-publication peer review—and open science in general—is attracting a growing number of followers in the scientific community. But some critics have argued that it’s been more successful in theory than in practice. The #arseniclife affair is one of the first cases in which the scientific community openly vetted a high-profile paper, and influenced how the public at large thought about it.

Post-publication peer review existed before social media as per ‘cold fusion’ (Wikipedia essay). I remember it because I wasn’t particularly interested in science at the time but this was everywhere and it went on for months. There was the initial excitement and enthusiasm (the ‘cold fusion’ scientists were featured on the cover of Times or Newsweek or maybe both in the days when those magazines were powerhouse publications). Then, as the initial enthusiasm died down, the storm of scientific criticism started (those other scientists may not have had social media but they made themselves felt). The story took place over eight to 10 months and achieved public awareness in a way that scientists can only fantasize about these days.  By comparison, the arsenic story blew up and disappeared from public consciousness within roughly two weeks, if that.

Social media may yet change how science is practiced but I wouldn’t use Zimmer’s story about #arsencilife to support that belief, in fact, I think it could support another idea altogether.

The ‘arsenic’ story was, by comparison, with ‘cold fusion’ greatly truncated and most members of the public never really heard about it and, as a consequence, were not exposed to the furious debate and discussion as they were with  ‘cold fusion’.  They did not get exposed to how science ‘really works and therein lies a problem because they did not see the uncertainties, the mistakes, and revised ideas.

As for what factors may be having an impact on scientific practice, I’d suggest reading Identifying good scientists and keeping them honest on The Black Hole blog by David Kent. Here’s an excerpt,

In a February 2011 interview with Lab Times, Cambridge scientist Peter Lawrence1 reflects on his own career and complains that “the heart of research is sick” as he charts the changes in the way in which science is pursued.  Briefly, he cites impact factors and the increased need to assign metrics to scientists (# of publications, H-index, etc) as main drivers of producing low quality research and unfairly squeezing out some good scientists who do not publish simply for the sake of publishing.  Impact factor fever runs deep throughout laboratories but, most damagingly, exists at the funding agency and university administrative level as well.

ETA June 17, 2011: For anyone who’d like to read some updated and contrasting discussion about the #arseniclife aftermath for scientific practice and science education there are two June 16, 2011 guest posts for Scientific American, one from Rosie Redfield and the other from Marie-Claire Shanahan. Plus, if you are interested in more details about the cold fusion story and the role electronic communication played, check out Marie-Claire Shanahan’s post,  Arsenic, cold fusion and the legitimacy of online critique, on the Boundary Vision blog.

The Naked Truth on Friday, May 13, 2011

I’m looking forward to being on the Canadian science blogging panel that’s taking place at the Northern Voice Conference, May 13 – 14, 2011 at the University of British Columbia’s Life Sciences Centre. The presentation panel I’m on is slated for Friday, May 13, 2011, from 1:45 pm to 2:30 pm and it’s called: The Naked Truth: Canadian Science Blogging Scene.

The other panelists include:

Beth Snow of The Black Hole. In one of her most recent postings, she tackles a topic most of us don’t think about when we’re talking about careers in science, Academic Couples. Excerpted from the post,

I can think of a few people right now who are in some stage of dealing with this issue [both partners are academics]. In addition to the friend I mentioned above, I know a dual-academic couple who both work at the same university, I know a couple where both partners are former-academics (they did their PhDs at the UBC, found their first postdocs together in another city, came back to UBC for second postdocs each and then both left academics for non-academic jobs) and I know a couple where the academic partner is seriously considering leaving academics because of a variety of reasons, with family being one of the big ones.

Eric Michael Johnson of The Primate Diaries in Exile recently blogged this intriguing piece, The Allure of Gay Cavemen, which was cross posted on the Wired magazine website,

In 1993 the reputable German weekly Der Spiegel reported a rumor that Otzi, the 5,300-year-old frozen mummy discovered in the Otztal Alps two years earlier, contained evidence of the world’s earliest known homosexual act. “In Otzi’s Hintern,” wrote the editors, referring to the Iceman’s hinterland, “Spermien gefunden worden.” (If you require a translation, chances are you didn’t want to know anyway.) The rumor quickly spread on computer bulletin boards as the recently unveiled World Wide Web inaugurated a new age in the free flow of misinformation. The origin of the rumor, as Cecil Adams discovered, turns out to have been an April Fool’s prank published in the Austrian gay magazine Lambda Nachrichten. The joke about our ancient uncle being penetrated deep in the Alps was then picked up by other periodicals, but with a straight face.

Twenty years later it appears that little has changed.

Rosie Redfileld of RRResearch talks about mutant cells amongst other things in My experiments: might I have a plan?

Classes have been over for a month and I have yet to do an experiment! For shame. But after going over everyone else’s projects I think I have a clear idea of what I should be doing.

1. Measure starvation-induced competence for each of the competence-gene knockouts: This will be replicating measurements done by an undergraduate over the past 6 months. I’ll just do each strain once, provided my results agree with hers. I’ll also freeze some of the competent cells.

2. Assay phage recombination in the competent and non-competent mutant cells: Old experiments using temperature-sensitive mutants of the H. influenzae temperate phage HP1 showed that recombination between the ts loci is more frequent in competent cells and completely dependent on the host RecA pathway (undetectable in a rec1 mutant). Phage recombination is much more efficient in competent cells than in log-phase cells; this is true both when competence is induced by starvation of wildtype cells (in MIV medium) and when it is induced by the presence of the sxy1 hypercompetence mutation (in rich medium).

The panel moderator, Lisa Johnson is a CBC journalist specializing in science and environment stories. She also has her own blog where her Oct. 14, 2009 posting, Squid surveillance, in several ways proves sadly timeless,

I find squid pretty inherently interesting. They’re believed to be smart, and I’d call them beautiful, but they’re also so alien to our terrestrial, vertebrate selves.

Even more interesting, or perhaps alarming, is what’s happening with the Humboldt squid in B.C. waters.

First, why are they here? They’re native to northern Mexico, but in the past ten years have spread northward, first to California, and now all the way to southeast Alaska. That is a big change in such a short time.

Secondly, they’re washing up dead on beaches in large numbers.

Then, there’s me. Maryse de la Giroday, FrogHeart. If you keep scrolling down this page, you’ll probably find something of interest.

We will all be there on Friday and we look forward to discussing science and science blogging in Canada. See ya there.

FrogHeart on science blogging panel at Northern Voice 2011 Conference

Friday, May 13, 2011 is the date for what I believe is a first anywhere: a panel about Canadian science blogging. It’s going to be held at the 2011 Northern Voice Personal Blogging and Social Media Conference (May 13 – 14, 2011) at the University of British Columbia’s Life Sciences Centre.

FrogHeart (aka Maryse de la Giroday) will be on the panel titled: The Naked Truth: Canadian Science Blogging Scene. My fellow panelists will be:

Rosie Redfield of RRResearch and author of the post that raised a storm of interest in the science blogosphere by bringing into question some research published by NASA (US National Aeronautics and Space Administration) scientists in Science magazine;

Beth Snow of The Black Hole (co-written with David Kent) where she writes about what happens after you get your graduate science degree and other issues of interest to science trainees; and

Eric Michael Johnson, The Primate Diaries in Exile, who writes about evolutionary biology and its relationship to politics;

and moi.

Our moderator is Lisa Johnson, a CBC (Canadian Broadcasting Coroporation) reporter who specializes in science and environmental issues.

Here’s the description for the session:

Bloggers are changing what was the tightly controlled world of science communications — dominated by peer-reviewed journals and mainstream media — into a two-way street.

Join four popular science bloggers to hear how social media lets them tell their stories without compromise. The panelists will tell you about political science and apes during the 2011 federal Canadian election; about what you do after you get your graduate science degrees and start developing your post-school career; about running a science lab and writing one of the most incendiary science blog posts of 2010; about the very well kept secret that is the Canadian nanotechnology community. We anticipate a lively (rowdy) interactive session with lots of questions from the audience to the panel and from the panel to the audience.

The panel will be on from 1:45 pm to 2:30 pm.

Thoughts on the Canadian science blogging scene and on the FrogHeart blog

I thought the timing was right for a review of the Canadian science blogging scene. At this point there seems to be about 12 of us. I found 4 new (to me) blogs this year:

  • The Bubble Chamber which is maintained by the History of Science programme students at the University of Toronto. As you might expect, it’s very academic at times. You might find a recent posting, How to pursue science from the humanities, an interesting read.
  • CMBR is maintained by Colin Schultz. He’s a science journalist. I haven’t read it often enough to be able to comment on it although I am intrigued by an item he has about science and the movies.
  • PARS3C is maintained by Elizabeth Lowell, a science journalist and editor. She focuses on space exploration (not a very strong interest of mine). Here’s her profile of Rocket Scientista, a PhD student in astrophysics who discusses, amongst other things,  why she thinks science blogging is important.
  • Nicole Arbour, a science and innovation officer in the UK’s Foreign Office in Ottawa, blogs about the science in Ottawa and in Canada regularly on a site maintained by the UK Foreign & Commonwealth Office. One of her latest is titled, Science Policy in Canada, and features a video of Mehrdad Hariri, Chair of the Canada Science Policy Conference, talking about plans to create a science policy centre in Canada.

Colleagues that have stimulated my thinking and opened new vistas include,

  • Rob Annan on a blog that seems to have changed its name recently (glory halleluiah!) to Researcher Forum. (Rob, I will change my blog roll soon.) It was a blog developed as a consequence of a protest letter written to Stephen Harper’s Conservative government a few years back when science budgets were affected. Months after its inception, Rob Annan was asked to take on the job of blogging regularly. His writing on Canadian science policy is always thoughtful and thought-provoking. Here’s his latest one on innovation in Canada and some of the problems. And, here’s one of my favourites from June 29, 2010, Public has a right to influence research policy. It’s about multiple sclerosis and the ‘surgery cure’ that has excited an enormous amount of interest.
  • The Black Hole is a blog about what happens once you graduate from university. It’s mostly aimed at those who have PhDs or Masters degrees although I think anyone could benefit from the insights that Beth Snow and David Kent provide. They certainly opened my eyes up to some of the issues in ways I couldn’t have anticipated. There’s a very interesting and humourous response to a current discussion taking place about whether or not there are too many people getting doctoral degrees, Professionals in High Demand. They ran a series during the summer about work that graduate students can aspire to and that doesn’t involve becoming a professor at a university.
  • Gregor Wolbring, a professor at the University of Calgary, maintains probably one of the longest-running and well-known Canadian science blogs, Nano and Nano- Bio, Info, Cogno, Neuro, Synbio, Geo, Chem…. He doesn’t blog that frequently these days; his site biography indicates that he must be screamingly busy. It’s worth taking a look at his blog as he often features material that no one else does.

Strictly speaking these aren’t science blogs as I think of them but this is a review of the ‘scene’ as much as anything else and these blogs definitely contribute,

  • Jeff Sharom maintains the Science Canada blog whose goal “is to highlight science policy issues in Canada’s political arena and media.” He doesn’t offer any commentary so this site functions more as an aggregator or reader but he picks up just about everything on Canadian science policy and it’s definitely worth a look if you want to know about the latest news.
  • RRResearch is maintained by Rosie Redfield at the University of British Columbia. As she notes, “This is a research blog, not a conventional science blog. Most posts are not about published research or science in the public domain, but about my lab’s day-to-day research into the mechanism, function and evolution of DNA uptake by Haemophilus influenzae and other bacteria.” She’s probably best known for her response to a recent science controversy over arsenic and bacteria.

The rest of these are blogs that haven’t been updated for a few months or more or don’t fit easily into the notion of being a Canadian science blog.

  • Je vote pour la science has been maintained by Pascal Lapointe and his colleague, Josée Nadia Drouin. There hasn’t been a new podcast (yes, a Canadian science podcast blog) since May 2010. These are expensive and time-consuming and both Pascal and his colleague work for Agence Science-Presse (which is being kept current). If you do have the French language skills I do encourage you to check out both sites.
  • David Ng is a professor at the University of British Columbia and he is a member of a group blog (his two partners are both from the US).  One of Dr. Ng’s most recent postings at The World’s Fair was titled, Crickets chirping and Collider Whales. There’s more about Dr. Ng and his various projects here.
  • Jay Ingram, co-host of Discovery Planet, maintained a blog , which featured podcasts, until Oct. 2008. I wonder if he will start it up again now that he’s retiring from Discovery Planet.

As for FrogHeart, I had a banner year bloggingwise. January 2010 statistics (AW stats. package) show the site as have 4225 visits in total and this month the site has clocked over 25,000 visits.That’s an increase of over 600%. In fact, FrogHeart consistently showed over 20,000 visits per month in the last quarter.  Based on this data, I’m going to make the claim that as far as I know,  FrogHeart is the largest, independent Canadian science blog.

Nanocrystalline cellulose is the most searched topic on my blog this year. It may not be the top search in every month but it’s consistently in my top 10. I want to thank Peter Julian, Rainer Becker, Charles McGovern, Richard Berry, Forrest H Bennett III, Leon Chua, Blaise Mouttet, Fern Wickson, Betty J. Morris, and Teri W. Odom who kindly provided answers to my questions (some were full length interviews while others were quick e-mail questions).

Please do contact me if I’ve missed something or someone or got something wrong.

I think 2010 was a better year for Canadian science blogging if you consider the addition of a couple new blogs as evidence (and I do). Many of the bloggers are independent, i.e., they self-fund their blogs and that suggests a big commitment.

I think at this point I’d like to highlight a December 28, 2010 article from the Calgary Herald on  how to pour champagne by Tom Spears (from the article),

It took six French scientists and a lot of free samples to prove this, but the official word says you should pour Champagne down the side of a tall glass to preserve the fizz and the flavour.

Bubbles also last longer when your Champagne is really cold — about 4 C.

I wish a great 2011 for everyone and an even more active year for Canadian science blogging.

ETA Jan.19.11: I found another Canadian science blogger: Nassif Ghoussou, a professor of mathematics at the University of British Columbia. His blog is called Piece of Mind. Thanks to Rob Annan’s blog, Researcher Forum, for this find.

ETA Jan. 24.11: This is great. I found Cool Science today. The blogger, a science communicator and parent located in Ontario,  focuses on something called ‘science parenting.  From the blog’s About page,

This site is about raising a creative rationalist in an age of nonsense. It is about parents getting excited about science, learning and critical thinking. It is about smart parents raising smart kids who can think for themselves, make good decisions and discern the credible from the incredible.

Are there any other Canadian science bloggers I can add to this list? Please, do let me know.