Author Archives: T. Ryan Gregory

Abigail Lustig testimony in Texas.

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I feel very strongly that scientists should know the history of their discipline, as this is of substantial importance in guiding new research and preventing the same tired arguments from continually resurfacing (case in point, the myth that “junk DNA” was dismissed as totally nonfunctional or that epigenetics represents “neo-Lamarckism”). In this sense, the lessons provided by historians and philosophers can be relevant for modern science. Familiarity with the history of science is also critical for effective teaching, so again, historians can play an influential role in improving science education. This is true not only for university-level science courses taught by professional scientists, but also in protecting education standards at the high school level.

Here is an example of that — Dr. Abigail Lustig, a historian at the University of Texas Austin, presenting her testimony before the Texas Board of Education. It is very brief, but eloquently clarifies the crucial distinction between evolution as fact and as theory, and the substantial difference in historical debate and timing of acceptance of Darwin’s ideas on these two issues.

For my take, see Evolution as fact, theory, and path in E:EO.

Research funding in the news

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Two quick bits.

One, tonight the finalists for the prestigious Canada Excellence Research Chairs program will be presented. This program is superficially similar to the kind of big-funding initiatives I argued are needed in Canada and already exist in the US. The difference, as usual, is that these are focused on applied research:

The CERC program invests $28 million a year to attract and retain the world’s most accomplished and promising minds and help Canada build a critical mass of expertise in the priority research areas of environmental sciences and technologies, natural resources and energy, health and related life sciences and technologies, and information and communication technologies.

Two, the Liberal party has released some stats on the actual funding that the government is delivering for research, and it is nothing like what we’re being told is being allotted.

Danish, anybody?

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Sadly, I can’t read Danish and therefore I am not sure quite what this article in Ingeniøren actually says.

Evolutionsteorien er under stadig udvikling

However, I can say that the author, Robin Engelhardt, was not only pleasant but he absolutely had done his homework and grasped the issue (whether the rise of epigenetics constitutes neo-Lamarckism) quite well. I wish more science writers would take this example!

DNA barcodes special issue.

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The journal Molecular Ecology Resources has just published a special issue on DNA barcoding. This is the result of a conference held at the Royal Ontario Museum.

Note the following from the introduction by my friends/colleagues Brian Golding, Bob Hanner, and Paul Hebert:

Despite some popular misconceptions, the goal of DNA barcoding is neither to determine the tree of life nor to carry out phylogenetic studies. The goal of DNA barcoding is also not molecular taxonomy, as it is not intended to replace classical taxonomy. Its purpose is to carry out species identifications so that even non-experts can determine what species might be at hand, and to do so in a rapid and inexpensive manner. This does not mean that barcodes lack phylogenetic information, or that the sequences do not contribute to taxonomic knowledge. Barcodes can provide evidence for cryptic species, and contribute to knowledge of phylogeny and biogeography. Each of these, however, requires corroboration from additional sources of information for robust support of the hypotheses generated by barcoding. For example, no one would attempt to reconstruct the phylogenetic history of the Diptera from 600 bp of mitochondrial sequence.

Central to the DNA barcoding enterprise is a database of previously identified reference specimens and their corresponding COI sequences. This requires taxonomists to apply their knowledge and to provide identifications of specimens that can then be barcoded. They must provide their intimate knowledge of the species ranges and morphologies to direct sampling strategies that would cover the greatest likely range of genetic variation. It is then these couplets of information that can be used to identify an unknown specimen.

Here are the papers, all open access thanks to support from NSERC and Genome Canada (before the cuts):

Molecular Ecology Resources

Volume 9 Issue s1 May 2009

Special Issue on Barcoding Life

Preface (p iv-vi)
G. B. GOLDING, R. HANNER, P. D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02654.x

Abstract | PDF

KEYNOTE ARTICLE

Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity (p 1-26)
DANIEL H. JANZEN, WINNIE HALLWACHS, PATRICK BLANDIN, JOHN M. BURNS, JEAN-MARIE CADIOU, ISIDRO CHACON, TANYA DAPKEY, ANDREW R. DEANS, MARC E. EPSTEIN, BERNARDO ESPINOZA, JOHN G. FRANCLEMONT, WILLIAM A. HABER, MEHRDAD HAJIBABAEI, JASON P. W. HALL, PAUL D. N. HEBERT, IAN D. GAULD, DONALD J. HARVEY, AXEL HAUSMANN, IAN J. KITCHING, DON LAFONTAINE, JEAN-FRANÇOIS LANDRY, CLAUDE LEMAIRE, JACQUELINE Y. MILLER, JAMES S. MILLER, LEE MILLER, SCOTT E MILLER, JOSE MONTERO, EUGENE MUNROE, SUZANNE RAB GREEN, SUJEEVAN RATNASINGHAM, JOHN E. RAWLINS, ROBERT K. ROBBINS, JOSEPHINE J. RODRIGUEZ, RODOLPHE ROUGERIE, MICHAEL J. SHARKEY, M. ALEX SMITH, M. ALMA SOLIS, J. BOLLING SULLIVAN, PAUL THIAUCOURT, DAVID B. WAHL, SUSAN J. WELLER, JAMES B. WHITFIELD, KEITH R. WILLMOTT, D. MONTY WOOD, NORMAN E. WOODLEY, JOHN J. WILSON
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02628.x

Abstract | PDF

BARCODING METHODOLOGY AND APPLICATIONS

The front-end logistics of DNA barcoding: challenges and prospects (p 27-34)
ALEX V. BORISENKO, JAYME E. SONES, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02629.x

Abstract | PDF

Express barcodes: racing from specimen to identification (p 35-41)
NATALIA V. IVANOVA, ALEX V. BORISENKO, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02630.x

Abstract | PDF

DNA barcoding and the mediocrity of morphology (p 42-50)
LAURENCE PACKER, JASON GIBBS, CORY SHEFFIELD, ROBERT HANNER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02631.x

Abstract | PDF

Biological agent detection technologies (p 51-57)
JOHN P. JAKUPCIAK, RITA R. COLWELL
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02632.x

Abstract | PDF

Efficient algorithms for the discovery of DNA oligonucleotide barcodes from sequence databases (p 58-64)
M. ZAHARIEV, V. DAHL, W. CHEN, C. A. LÉVESQUE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02651.x

Abstract | PDF

BARCODING MICRO- AND MESO-FAUNA

Barcoding diatoms: Is there a good marker? (p 65-74)
MÓNICA B. J. MONIZ, IRENA KACZMARSKA
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02633.x

Abstract | PDF

Development of primers for the mitochondrial cytochrome c oxidase I gene in digenetic trematodes (Platyhelminthes) illustrates the challenge of barcoding parasitic helminths (p 75-82)
ANNA MOSZCZYNSKA, SEAN A. LOCKE, J. DANIEL McLAUGHLIN, DAVID J. MARCOGLIESE, TERESA J. CREASE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02634.x

Abstract | PDF

BARCODING FUNGI

Progress towards DNA barcoding of fungi (p 83-89)
KEITH A. SEIFERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02635.x

Abstract | PDF

Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium (p 90-98)
SCOTT R. GILMORE, TOM GRÄFENHAN, GERRY LOUIS-SEIZE, KEITH A. SEIFERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02636.x

Abstract | PDF

Evaluation of mitochondrial genes as DNA barcode for Basidiomycota (p 99-113)
AGATHE VIALLE, NICOLAS FEAU, MATHIEU ALLAIRE, MARYNA DIDUKH, FRANCIS MARTIN, JEAN-MARC MONCALVO, RICHARD C. HAMELIN
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02637.x

Abstract | PDF

A high density COX1 barcode oligonucleotide array for identification and detection of species of Penicillium subgenus Penicillium (p 114-129)
W. CHEN, K.A. SEIFERT, C.A. LÉVESQUE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02638.x

Abstract | PDF

BARCODING PLANTS

Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? (p 130-139)
ARON J. FAZEKAS, PRASAD R. KESANAKURTI, KEVIN S. BURGESS, DIANA M. PERCY, SEAN W. GRAHAM, SPENCER C. H. BARRETT, STEVEN G. NEWMASTER, MEHRDAD HAJIBABAEI, BRIAN C. HUSBAND
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02652.x

Abstract | PDF

Routine DNA barcoding of Canadian Gracilariales (Rhodophyta) reveals the invasive species Gracilaria vermiculophylla in British Columbia (p 140-150)
GARY W. SAUNDERS
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02639.x

Abstract | PDF

Plant DNA barcodes and species resolution in sedges (Carex, Cyperaceae) (p 151-163)
JULIAN R. STARR, ROBERT F. C. NACZI, BRIANNA N. CHOUINARD
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02640.x

Abstract | PDF

DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India (p 164-171)
SUBRAMANYAM RAGUPATHY, STEVEN G. NEWMASTER, MARUTHAKKUTTI MURUGESAN, VELUSAMY BALASUBRAMANIAM
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02641.x

Abstract | PDF

Testing plant barcoding in a sister species complex of pantropical Acacia (Mimosoideae, Fabaceae) (p 172-180)
STEVEN G. NEWMASTER, RAGUPATHY SUBRAMANYAM
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02642.x

Abstract | PDF

BARCODING ARTHROPODS

DNA barcoding of marine crustaceans from the Estuary and Gulf of St Lawrence: a regional-scale approach (p 181-187)
ADRIANA E. RADULOVICI, BERNARD SAINTE-MARIE, FRANCE DUFRESNE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02643.x

Abstract | PDF

DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea) (p 188-195)
R. G. FOOTTIT, H. E. L. MAW, N. P. HAVILL, R. G. AHERN, M. E. MONTGOMERY
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02644.x

Abstract | PDF

DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies (p 196-207)
CORY S. SHEFFIELD, PAUL D. N. HEBERT, PETER G. KEVAN, LAURENCE PACKER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02645.x

Abstract | PDF

DNA barcode accumulation curves for understudied taxa and areas (p 208-216)
M. ALEX SMITH, JOSE FERNANDEZ-TRIANA, ROB ROUGHLEY, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02646.x

Abstract | PDF

Combining DNA barcoding and morphological analysis to identify specialist floral parasites (Lepidoptera: Coleophoridae: Momphinae: Mompha) (p 217-223)
VIRGINIA J. EMERY, JEAN-FRANÇOIS LANDRY, CHRISTOPHER G. ECKERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02647.x

Abstract | PDF

Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae) (p 224-236)
JULIO RIVERA, DOUGLAS C CURRIE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02648.x

Abstract | PDF

BARCODING VERTEBRATES

DNA barcoding reveals overlooked marine fishes (p 237-242)
TYLER S. ZEMLAK, ROBERT D. WARD, ALLAN D. CONNELL, BRONWYN H. HOLMES, PAUL D. N. HEBERT
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02649.x

Abstract | PDF

Identifying sharks with DNA barcodes: assessing the utility of a nucleotide diagnostic approach (p 243-256)
EUGENE H.-K. WONG, MAHMOOD S. SHIVJI, ROBERT H. HANNER
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02653.x

Abstract | PDF

Countering criticisms of single mitochondrial DNA gene barcoding in birds (p 257-268)
ALLAN J. BAKER, ERIKA SENDRA TAVARES, REBECCA F. ELBOURNE
Published Online: Apr 21 2009 10:59AM
DOI: 10.1111/j.1755-0998.2009.02650.x

Abstract | PDF

Walking seal.

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Other bloggers and authors have already covered the discovery of Puijila darwini by Rybczynski et al (2009), a transitional fossil (but not a lineal ancestor) between modern pinnipeds (seals and kin) and terrestrial mammals. See, e.g., Not Exactly Rocket Science, Origins, Laelaps, ScienceNOW, Discovery Channel, ScienceNews, Scientific American, and so on…

For lots of information, see the resources provided by the Canadian Museum of Nature.


Like Tiktaalik, this species was discovered in the Canadian Arctic and bears an Inuktitut name.

Etymology. Puijila (Inuktitut): young sea mammal, often referring to a seal; darwini: for Charles Darwin, who wrote with his usual prescience, “A strictly terrestrial animal, by occasionally hunting for food in shallow water, then in streams or lakes, might at last be converted into an animal so thoroughly aquatic as to brave the open ocean”.


Here’s something the other bloggers probably cannot say, though: I have been to Devon Island where it was located!

Bad decisions about scholarships.

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The current administration is making a big deal out of its investment in graduate scholarships. Complaints have already been raised about the ridiculously high scholarships that they have instituted for a small number of awardees ($50K, or about twice the operating grant for many new labs) and the requirement for SSHRC to focus on business-related programs.

The other significant change that I don’t know has been discussed widely is the cut to the MSc graduate scholarship duration by NSERC. It used to be that both the MSc and PhD scholarships were for 2 years (and you could get both, for 4 years of funding overall). No one does a PhD in science in 2 years, so it is good that this has finally been extended to 3 years. However, the MSc scholarship has now been cut to 1 year.

Anyone who does a PhD in Canada either completes an MSc first or transfers from the MSc to the PhD directly. Many students complete the MSc and move on to non-academic careers, so there are far more MSc students than PhD students. In other words, whether they will finish with an MSc or go on to a PhD, all recruitment decisions of graduate students involve admission to an MSc program at some point.

Scholarships are an important supplement to operating grants which, as everyone now knows, are small in Canada and mostly are used to fund students and their research (if you have $30K, $25K may be spent on salaries for 2 MSc students, for example). If a student can obtain a scholarship, he or she is essentially “free” to an advisor because the stipend is then paid. This makes it much more likely that a student will get into a lab of his or her choice, and it also increases the number of students who can be trained. However, if the funding is only available for 1 year, then an advisor has to decide whether he or she can afford the second year.

Cutting the MSc scholarship to 1 year will, I predict, significantly reduce the positive impact that the program has at the MSc level. It may also indirectly affect the PhD level by causing advisors to suggest that students transfer to the PhD even if they are not really qualified.

There is another effect that will surely arise. In addition to the NSERC scholarship program, students in Ontario can seek funding from the Ontario Graduate Scholarships (OGS) program. Most students apply to both. Generally speaking, if a student receives an NSERC they also get an OGS, as the latter is slightly less competitive. However, a student can only accept one, which means that NSERC and OGS fund different students and therefore increase the total number with support. Now that NSERC is 1 year, scholarship holders will no doubt be applying for OGS for the second year. This means that the pool of applicants will soon include former NSERC winners along with new applicants for OGS. Unless OGS greatly increases the number of awards, this means fewer scholarship students and thus fewer graduate students trained.

What’s driving cuts to basic science?

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As you no doubt are aware from reading this blog and others (CanadaResearchFunding.org and Don’t Leave Canada Behind), NSERC, CIHR, and SSHRC are having their budgets cut by around $148 million over the next three years. They also cut $30 million from the National Research Council.

Surely unrelated, Minister Clement Acts to Advance Automotive Research in Canada. At the bottom of the story, we find:

Automotive Partnership Canada (APC) is a five-year (2009–2014), $145-million initiative to support significant, collaborative, industry-driven research and development (R&D) that benefits the Canadian automotive industry.

APC involves funding from the following agencies:

  • Natural Sciences and Engineering Research Council of Canada (NSERC): $85 million;
  • National Research Council Canada (NRC): $30 million;
  • Canada Foundation for Innovation (CFI): $15 million;
  • Social Sciences and Humanities Research Council of Canada (SSHRC): $5 million; and
  • Canada Excellence Research Chairs program (CERC): $10 million.

Proposals funded under this initiative will be led and submitted by university or government (NRC) researchers, but they must be clearly driven by industry needs.

Protect Science Funding in Canada (Facebook group).

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The Don’t Leave Canada Behind letter has been signed by more than 2,000 scientists. But what about the other individuals who are just as affected, namely graduate students and postdocs? Given that most of the small amount of funding provided by NSERC goes directly to paying student stipends, they are stakeholders in this as much as anyone else. There is now a way for them to express their support for research in Canada and to send a message that the cuts are unacceptable.

Join Protect Science Funding in Canada at Facebook!

Hat tip: CanadaResearchFunding.org

Another Earth Day, Canadian scientists concerned.

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From the Quirks and Quarks blog by Bob McDonald, beloved host of the CBC program of the same name.

Another Earth Day, Canadian scientists concerned

While people around the globe celebrate the beauty of our planet on Earth Day, April 22nd, scientists in Canada are concerned that government funding is heading in the wrong direction to provide sensible solutions to environmental problems. More than 2000 scientists from across the country have signed an open letter to Prime Minister Harper and the Leader of the Opposition, expressing concerns over cuts to basic science research. It’s basic science that takes the pulse of the planet.

The scientists are concerned that government money is overlooking vital areas. For example, the current Conservative budget allocates $2 billion for university infrastructure – in other words, renovations to aging buildings. But those funds come with a catch. They must be matched with private funding, something everyone is having trouble finding during these tough economic times. Keeping roofs on buildings is important, but if there are no scientists to work in them, what’s the point?

The Canada Foundation for Innovation, a major source of science funding, did receive $740 million, but it also comes with that match-funding hook. The other funding agencies, the Natural Sciences and Engineering Research Council and the Canadian Institutes of Health Research, have had their budgets cut back, while Genome Canada was essentially ignored.

The rest of the government’s support for science is going towards the automotive industry, carbon sequestration, biofuels and scholarships for business students. In other words, applied science is taking precedent over basic science.

While we do need both, when it comes to the environment, the two types of science are often at loggerheads.

Politicians like to support applied science because it leads to jobs and products, such as more efficient cars or new wireless devices. Basic science, on the other hand, can’t promise an immediate economic return because it simply looks at nature to understand how things work – and more importantly these days, how things are changing. As we’ve seen with climate change, basic scientists have been out in the field watching ice caps disappear before their eyes, carbon dioxide levels rise and climate patterns shift. At the same time, those dealing with the technology at the heart of the problem resist the basic science to keep the current systems in place.

The beauty of Earth Day is how we come together for a short time to appreciate the complexity and unity of our planet. Basic science describes the many spheres we live on and within. There’s only one atmosphere, one hydrosphere, one biosphere, one cryosphere, one geosphere, and they all interact with each other in ways we’re just beginning to understand.

We need those scientific eyes to keep track of this dynamic Earth. We also need to see how our technology is impacting every one of those spheres.

Applied science and the technology it provides have made us who we are, but it needs to be guided. An airliner can fly itself but it still needs the eyes of a pilot to see the destination. Basic science is our eye to the future destination of our spaceship called Planet Earth.