Dr. Jay on incomplete transcription.

If you don’t read the posts by John Timmer (“Dr. Jay”) on Nobel Intent, you should. He has posted some good summaries about the ENCODE project, the anemone genome, and today presents a very interesting discussion of incomplete transcription of inactive genes based on a paper in Cell. (Basically, even inactive genes may experience transcription initiation although this is not followed through to generate full transcripts). If you’re interested in accurate and accessible summaries of newly published findings, and especially if you want some realistic discussion of the significance of new genomics research, this is a good place to start.


How much good can one blog post do?

Readers of this blog will be aware that I am experimenting with blogging as a mechanism of public outreach in science. This time, I want to try a different experiment. Specifically, I want to see how much good can come from a single blog post.

Here is the story. In November, 2006, my father fulfilled a lifelong dream of traveling to Africa to explore the cradle of humanity and to experience first-hand the cultural and zoological diversity to which the continent is home. Amidst the beauty of the landscape and the hospitality of the people, he was struck — as I am sure anyone who visits Africa must be — by the tragedy of poverty and disease (especially malaria and AIDS) juxtaposed with a tangible sense of happiness and hope.

My father has spent most of his life helping others. A social worker by training, he has dedicated much of his career to protecting the rights and dignity of the mentally challenged. This has included efforts to move as many people as possible out of (often horrific) institutions and into dignified group home environments. He has also developed programs to assist individuals with mental difficulties in returning to post-secondary education, and most recently has worked to train a new generation of social work students. In light of this, it comes as little surprise to me that he felt compelled to help the people he befriended in Africa.

My stepmother is equally generous. In her capacity as a gifted singer, musician, and teacher, she has devoted herself over the past decade to creating community choirs for both children and adults in the small town in which they live. The effects that this has had on the confidence and sense of community of the participants is remarkable.

The next phase in their lives will involve the most ambitious endeavour that either has attempted. In six months, they will be selling their house, resigning from their current jobs, and moving to Livingstone, Zambia.


While there, they will work to revamp the local Victoria Hall and to create a musical theatre program showcasing the traditional song and dance of Zambia. This is intended to capitalize on the rapidly growing tourism industry in the Livingstone area (which is less than 10km from Victoria Falls) and will provide a self-sustaining source of income for local performers and tradespeople. It will also be used to inject funds into the Livingstone economy and to improve the desperate conditions of the local hospital and schools.

The Victoria Hall in Livingstone, Zambia.

The mission statement of the project is described as follows:

Mission Statement:

The Livingstone Performing Arts Foundation (LiPAF) mission is to create and perform traditional and original works of music, song and dance which reflect the history, culture, languages and ethnic background of Zambia. Operating as a not for profit organization, LiPAF will enrich the community by providing opportunities for employment, sponsorship of a variety of needy programs and services, and educational programs on topics related to the human condition.

Objectives of the Project:

  1. To operate a not-for-profit Foundation.
  2. To promote the rich cultural diversity existing in Zambia and the Kavango-Zambezi region.
  3. To promote the city of Livingstone, the country of Zambia, and the region of Kavango-Zambezi, as a tourist destination.
  4. To provide employment for local residents.
  5. To raise funds for the sponsorship of various community projects
  6. To assist in the promotion and expansion of the service related industry (restaurants, merchants, etc.).
  7. To cooperate with other community-based groups within the Livingstone district.
  8. To improve and enhance the educational aspect of the city library.
  9. To provide music programs in local schools.
Plans for the redesigned Victoria Hall.



I should emphasize that this is an independent, non-profit project. It is not being carried out with any expectation of personal reward (in this life or any other). It is simply an attempt by two phenomenal people to make a difference by applying their talents to benefit others in need.

So far, they have been hard at work coordinating with local and federal governments in Zambia and generating funds to pay for the project through fund raising events and by making countless presentations to local service clubs and other organizations. They have been tireless in these efforts, but of course they cannot do it alone.

The question I posed as the title of this post is “How much good can one blog post do?”. I am hopeful that the answer will be a resounding “A great deal!”. There are many ways to help.

  • Maybe you run a blog and can draw attention to this post and to the Livingstone Performing Arts Foundation website.
  • Maybe you can inform your colleagues, friends, and family members about this post and the foundation website.
  • Maybe you are a teacher and your school is throwing out old textbooks, dictionaries, or atlases that could be given to the local elementary/high school.
  • Maybe you can help to provide the school with other necessities such as science equipment. I am planning to visit and to teach some basic biology classes, but the school barely has desks, let alone microscopes.
  • Maybe you work in the performing arts industry and can help with the acquisition of sound or lighting equipment.
  • Maybe you’re an artist and could donate some of your work to be used in a fund raising auction.
  • Maybe you work for a charity, shipping company, or other organization that would be interested in assisting the program logistically or financially.
  • And of course, you can make a personal donation in any sum. I have set up a PayPal account for them to receive donations. The donation is not tax-deductible as the foundation is registered as a not-for-profit organization in Zambia, but 100% of it will be put to use in support of the project. See also their 100 from 500 Club, in which there is a chance to win some great prizes donated by artist friends.


The motto that they have adopted, a quote from Margaret Mead, is “Never doubt that a small group of thoughtful committed citizens can change the world. Indeed, it is the only thing that ever has.”

I will miss my parents when they go, but I can do no other but admire and support their decision to do so.

__________

It took some doing, but I have been able to format the video presentation that they have been giving to local organizations for posting here. It’s meant to be shown on a projection screen, but I think the text is legible even at this size. This really sets the stage for what they are trying to do, and has a very positive message overall with an emphasis on the beauty of Zambia.






Thank you to everyone who has contributed
already — every little bit helps!


To find out more, please visit the Livingstone Performing Arts Foundation website and blog.

___________

A sincere thank you to Pharyngula, ERV, Sex, Genes & Evolution, Aetiology, A Block Around the Clock, Eye on DNA, ScienceRoll, Evolution Space, and BrummellBlog for posting links.


Concept contrasts.

Many science blogs have a regular series on particular subjects. Thus far I have not done anything like that, but I think the “X vs. Y” pieces could make for a useful series. I shall dub it “Concept contrasts”, and present the first three in the following compendium.

I will update this list whenever a new entry in the series is posted.


ASM’s Microblogology.

Over at Aetiology, Tara Smith has posted an excellent video comprised of interviews of science bloggers conducted at the ASM meeting in Toronto. I am not a microbiologist, but Larry Moran did kindly invite me to join the group for dinner during the meeting. Alas, I was in Montreal at the CSZ meeting presenting the Boutilier Lecture and was unable to attend. I also did not make it to the SMBE meeting in Halifax, which has been a source of consternation for RPM. Next time! It’s a very good video, although I felt like Jonathan Badger really phoned it in (ha ha).

(Soundtrack available here).


On framing.

I finally checked out the “framing” presentation by Chris Mooney and Matthew Nisbet which is available with PowerPoint slides here. I am not particularly interested in the debate over this issue, but I thought I would give it a try in light of my hope of improving media coverage and public comprehension of science. This is not my entry into the debate as I think it has garnered more attention that it warrants already; this is simply a set of thoughts on the issue after having spent the time watching the talk.

I will say that I found much to agree with as far as the descriptive components were concerned. That is, I think Mooney and Nisbet make some good arguments with regard to what is and is not working in scientific communication. This is Nisbet’s subject of research, and it was useful to see actual data applied to the question. My sense was that “framing” likely is something that nonspecialists do use when evaluating complex issues, and that this is a problem for scientists who want to convey complicated ideas with societal ramifications to them. However, I think the discussion runs aground in three major areas: 1) How it is presented to scientists, 2) In the failure to distinguish it from “spin” or “marketing”, and 3) When it shifts from description to prescription.

As to the first, Mooney and Nisbet seem to use an only partially appropriate “framing” when speaking to scientists who, both as individual people and as part of a collective, exhibit inherent preferences, biases, and other filters. To wit, scientists in general will be unwilling to compromise certain principles, and there appears to be insufficient appreciation of this fact by framing advocates. For example, scientists will not simplify to the point of eroding accuracy, they will not do anything that could be perceived as lying to the public, and they will never give up on the notion that getting the public to understand science is the primary long-term goal. From what I can gather, Mooney and Nisbet are not asking scientists to compromise on these principles, but this is not stated clearly — following their own advice, this should be presented clearly and repeatedly so as to reassure scientists that they are not being told to betray their scientific ideals. (And if they are asking scientists to do so, then this should be made clear also so that the debate can be put to a swift end).

The question of motives also comes into play as part of the mis-framing of framing. No one can be totally objective, so what scientists are trained to do is to look for biases and associated violations of objectivity so that these can be factored into the evaluation of scientific arguments. Personally, I found myself asking “why do they care what scientists do?”. One obvious explanation is that they are concerned citizens with a particular interest in science and its impacts on society. This is not stated upfront, however, and so questions come up about whether this isn’t an exercise in attention getting (and possibly book promoting) as much as a sincere call to action.

Finally, while I do not read their blogs, I have seen a few links to statements that I have found offensive to my scientific sensibilities. As a case in point, Mooney argues on his blog that science journalists are not the problem (this is also stated in the presentation). It would seem to follow, therefore, that if science is reported inaccurately, sensationalized, overstated in its implications, or otherwise distorted, that is the fault of scientists. Worse, Mooney goes so far as to argue that scientists should just shrug it off and move on if they are misquoted in the media. Again, this ignores the frame that scientists use, in which accuracy is of paramount significance. He also seems to think that simply telling scientists about the difference between a science journalist (well-trained and comprehensive) and a non-science journalist reporting on science (no expertise or experience in dealing with such issues) will make the resentment of the media’s handling of research disappear. It will not.

The second point is the one that has been the primary subject of discussion by some prominent scientist-bloggers, namely that “framing” bears a striking resemblance to “spin”. We all know that “spin” plays a substantial role in politics. To scientists, this is not something to be emulated. I won’t go so far as to say that framing is mere spin, but throughout the presentation I had the strong notion that it was largely indistinguishable from “marketing”. Scientists should care about how their work is presented to and received by the public, and therefore marketing is a legitimate consideration. Indeed, scientists market their work often — to granting agencies, students, journals, and colleagues. Adding some audience-specific adjustments when dealing with the public is perfectly reasonable, but if that’s all “framing” is, then it’s really just repackaged marketing truisms.

The third point, in which Mooney and Nisbet transition from describing the issue to prescribing what scientists should do, was by far the weakest part of the talk. In fact, I found almost nothing in their presentation that actually applied to me as an individual researcher. Almost everything they suggested actually fell under the purview of science writers, press offices, lobby groups, professional societies, or educational organizations. I still do not know what they expect me to do even with information in mind about how the public frames important topics. As a result, much of the talk seems to be about telling scientists what they are doing wrong with no real solutions that individual scientists can or will implement.

If I may, I would also add that Mooney and Nisbet’s discussion is, at heart, not about science or communication, but about American politics. In many other countries, scientific literacy is much higher, issues do occupy the primary stage in election campaigns, and religion and partisanship play a much smaller role in influencing decisions about science. Once again, this suggests that education about science early on is an effective strategy and a viable objective. The question of framing is more geographically and temporally localized than this, and so it is difficult for some scientists who are trained to look beyond such limitations to the larger picture to make framing a primary tool.

In stark contrast to all of this ambiguity and apparent misreading of scientific audiences, I point to the recent book A Scientist’s Guide to Talking with the Media by journalists Richard Hayes and Daniel Grossman, published by the Union of Concerned Scientists. I am only part way through the book, but already I can note that it does a fine job of framing the topic in a manner acceptable to scientists. Hayes and Grossman are very clear that they have the utmost respect for science and scientists, and that they absolutely do not wish to see spin implemented at the expense of accuracy. Theirs is a well articulated set of practical suggestions for dealing with the media. They do not appear to blame scientists but instead point to examples where different strategies could have forestalled problems. They do not let science reporters off the hook, but do try to promote a better understanding among scientists of the challenges of writing for a nonspecialist audience. They do not point out the challenge and leave the solutions unclear, but give point by point suggestions on how to improve the important relationship between scientists and those who report science. As a scientist with some experience with the media, I find a great deal of use in this volume. And I do not hesitate to recommend it as an alternative to the far less helpful argument about framing.


Gene Genie #10 — The Canada Day Ultraspectacular Edition.

Gene Genie was the brainchild of Bertalan Meskó of ScienceRoll. At bi-weekly intervals since February 17, 2007, it has provided a showcase of blogging on the subject of genetics, and has moved well beyond its initial tongue-in-cheek “objective” of covering every gene in the human genome by 2082. In light of its effectiveness in sharing the excitement of discovery in genetics, it is hardly surprising that Gene Genie was mentioned, along with Mendel’s Garden, in a recent issue of the prestigious journal Cell. It was also an easy decision to commit to hosting an issue here at Genomicron when I was asked to do so. It is perhaps fitting (albeit mostly coincidental) that the 10th issue of Gene Genie, which I was invited to host, falls on July 1stCanada‘s 140th birthday. And so, it is with typical Canuck modesty that I am pleased to present the Canada Day Ultraspectacular Edition of Gene Genie.

We begin with a classic in the truest sense of the term. As the June 22nd entry for his weekly series on citation classics, John Dennehy of The Evilutionary Biologist discusses the famous Hershey-Chase “blender experiment” in 1952 that helped to establish the role of DNA in inheritance. The details of the relationship between DNA sequence and phenotype are, of course, still being elucidated 55 years later.

Case in point, discussion continues about the results of the pilot study of the ENCODE (Encyclopedia of DNA Elements) project (for previous links, see here and here). Indeed, it appears that the very definition of “gene” is open to revision. Larry Moran of Sandwalk and adaptivecomplexity of Scientific Blogging discuss a paper by Gerstein et al. in Genome Research that summarizes the history of the gene concept and offers a new definition.

Scientific Blogging has a follow-up on the implications of ENCODE data. Along the same lines, Nick Matzke at Panda’s Thumb has re-posted my “onion test” in the hope of mitigating some of the undue enthusiasm about function for “junk DNA”. (To clarify, the test is neither anthropocentric nor onionocentric — it is just a useful comparison). And speaking of hype about genomes, Jonathan Eisen at The Tree of Life has instituted the “Overselling Genomics Awards“. I suspect that nominees will not be scarce.

Questions about definition aside, several recent blog entries have explored how genes are structured, how they do what they do, and how they evolve. Thus, Larry Moran discusses RNA splicing and the Nobel Prize winners, Richard Roberts and Phillip Sharp, who first identified the intron-exon structure of eukaryotic genes. PZ Myers of Pharyngula gives an overview of pair-rule genes and Evolution Research Blog provides a discussion of genomic imprinting in mammals. RPM at Evolgen examines the causes of variation in the rate of molecular evolution and the genetic underpinnings of smell and taste in Drosophila (which, incidentally, are not fruit flies). Evolution Research News discusses the link between genes and intelligence; environment also matters, of course, especially given new work suggesting that not just birth order but being raised as the eldest affects IQ. Remember: nature versus nurture is a false dichotomy.

Next, VWXYNot? provides a very good overview of the evolutionary explanation for endogenous retroviruses (ERVs), be they functional or not. ERV (the person, not a DNA element) introduces us to the mouse mammary tumor virus (MMTV), which exhibits both endogenous and exogenous viral properties. ERV also discusses her HIV research and Carl Zimmer of The Loom describes one possible reason that humans are susceptible to HIV, having to do with a previously evolved defence against an ERV (a DNA element, not the person). This Week in Evolution also delivers an overview of this interesting trade-off. Meanwhile, Denialism Blog and Aetiology highlight a report in Science about AIDSTruth.org, the electronic antidote to AIDS denialism.

As usual, medical and other applications of genetics featured prominently in the scientific blogosphere in the past two weeks. Notably, Hsien-Hsien Lei at Eye on DNA discusses BRCA genetic testing for women without a family history of breast cancer. Over at Autism Vox there is a report about symptoms of fragile X being reversed in mice. FuturePundit notes how gene therapy may halt Parkinson’s disease. Both Eye on DNA and Dr. Joan Bushwell’s Chimpanzee Refuge weigh in on the association between genetics, the environment, and behaviour, in particular with respect to the monoamine oxidase A (MAOA) gene and susceptibility to alcoholism. Gene Sherpas continues the series on Forbes and Genetics, this time discussing smoking and obesity. And I do some reflecting on my possible ancestry, which could be established with a simple DNA test, in Am I a MacGregor? here at Genomicron.

And finally, under the category of edutainment, Discovering Biology in a Digital World shares a link to some excellent animations of the polymerase chain reaction (PCR) that is now ubiquitous in molecular genetics, The Genetic Genealogist reports on the creation of a bicycle path in Cambridge in honour of the discovery of the BRCA2 gene, mutations of which are implicated in increased risk of breast cancer, and Bertalan Meskó at ScienceRoll interviews the creator of the Genomic Island in the popular online 3D virtual environment of Second Life. He has also posted a more detailed discussion about educational aspects of the online world here.

The next edition of Gene Genie will be hosted at My Biotech Life July 29th. Mendel’s Garden #16 will be hosted at Eye On DNA July 8th.


RSS feeds: not just for blogs.

RSS, or Really Simple Syndication, is a system that allows readers to receive “feeds” of new content from various online sources to their computer without having to visit each site individually. By using an aggregator, one can subscribe to his or her favourite blogs, news feeds, and other sources of syndicated information and receive new articles as soon as they are posted online.

An amusing introduction to aggregators is given in this short video by Commoncraft:

[Hat tip: Retrospectacle via Sandwalk]

Generally speaking, subscribing to a blog or science news site is as simple as clicking on the “RSS”, “XML”, “Atom”, or other “Subscribe” link. For example, you will notice to the right some links that allow you to subscribe to the Feedburner feeds for this blog, either by email or to an aggregator, or through the larger DNA Network feed encompassing the posts of multiple genetics blogs. (The only downside for bloggers is that hits do not register if someone reads a post in a feed reader rather than coming to the blog — but hey, they’re reading the post, which is what counts!)

Aggregators can be used for more than just reading news and blogs. Many journals have their tables of contents available as RSS feeds. In addition, you can have scientific literature databases such as PubMed (which is free) and Web of Science (subscription required) automatically perform regular searches and send the results to your aggregator. This latter application is incredibly useful, but it is more complicated than subscribing to blogs or news feeds. Fortunately, the University of California San Diego has been kind enough to provide an illustrated guideline to setting up RSS feeds for these and other literature databases.

A list of client-based and web-based aggregators is available in Wikipedia. Prominent examples include Google Reader, Bloglines, and Netvibes.

Happy reading.