NSERC peer review vs. baseline funding roundup.

Here is at least a partial roundup of posts regarding the must-read paper by Gordon and Poulin (2009). If you have not read it yet, you can obtain a copy by emailing the author: gordonr(at)cc.umanitoba.ca.

Also, if you are not already reading it, have a look at Don’t Leave Canada Behind or sign up for their RSS feed.

Genomicron enters terrible twos.

Well, as if I needed any more evidence that my life has become a time warp of committees, students, grant applications, and manuscripts, it has suddenly been another year of blogging. That’s right, two years ago today was the inaugural post at Genomicron. I think the main trend over the past year has been to enter more into the political realm — out of necessity, really, since this affects much of my research and teaching.

But let’s keep this positive, right? Here’s to another year!!

Update: Happy second birthday to The Evilutionary Biologist too!

Shaking up the theory of evolution.

I was just sent a link to this press release. Is this a parody or something?

Shaking up the theory of evolution

In a year that celebrates the 200th anniversary of the birth of Darwin and the 150th anniversary of the publication of “On the Origin of the Species, Murdoch scientists have made an exciting discovery. Their hypothesis, which argues that DNA junk is essential for evolution, may represent one of the biggest advances in evolutionary theory, since the 1930s.

Murdoch University scientists have developed an improved theory of evolution – a groundbreaking hypothesis which finally reconciles evolutionary theory with the fossil record.

Developed by PhD student Keith Oliver and Program Chair of Biomedical Sciences Dr Wayne Greene, the “Genomic Drive” hypothesis, potentially represents one of the biggest advances in evolutionary theory since the 1930s.

DNA “junk”

In a co-authored report, due to be published in the prestigious BioEssays journal, the researchers argue that transposable elements (TEs) – or what is colloquially termed jumping genes, selfish or junk DNA, have a critical role in ensuring the survival of biological lineages.

Without this DNA junk, a species is effectively frozen and faces eventual extinction.

On the other hand, species with genomes with high TE activity or strong presence of identical TEs possess a greater ability to evolve, diversify and survive.

Take for example humans, rodents and bats.

As primates some 46 per cent of the human genome is comprised of TEs while other mammals such as rodents and bats are known to possess around 40 per cent.

These TE’s are generally suppressed in the ordinary body cells of most species but are allowed to reactivate in reproductive cells for the potential benefit of the next generation.

Their activity can also be triggered when they suddenly hop between species or by stress.

TEs do their survival work by reformatting and rearranging DNA genomes to sometimes create significant adaptive mutations that undergo natural selection.

Current theory doesn’t tally with fossil evidence

Dr Greene, a Senior Lecturer in Molecular Genetics, said current evolutionary theory, which assumed biological lineages evolved by the slow accumulation of adaptive mutations, did not tally with the fossil record.

However, the “Genomic Drive” theory provided a significant explanation for the way new species arose abruptly and periodically.

The theory also fitted with fossil records which showed intermittent and long periods of stasis – where many species stood still or remained the same.

Mr Oliver said the hypothesis argued that significant evolution could not take place without the activity of TEs.

“Although we are standing on the shoulders of others that have worked on TEs, we believe this is the strongest and most comprehensive case ever put forward on the role of TEs in evolution,” Mr Oliver said.

“If our theory proves correct it would be one of the biggest advances in evolution since the 1930s when Darwinism and Mendelism were reconciled in NeoDarwinism.”

Species without junk DNA risked extinction

Dr Greene said species that were devoid of TEs were more at risk of extinction because they simply lacked the capacity to adapt, change and diversify.

“If you don’t have this junk in your genome then you can’t evolve and are stuck, thereby remaining in what is termed evolutionary stasis,” Dr Greene said.

“This would explain why almost all species control their TEs rather than eliminate them.

“And of course having these TEs in a genome doesn’t mean a lineage will necessarily diversify. What it does mean is that it has a much greater potential to do so.”

Mr Oliver said an example of evolutionary stasis occurring in species without TE activity could be seen in the living fossil, the coelacanth, once thought to be extinct for 63 million years.

The coelacanth, which had been found off the coast of South Africa and Indonesia, had inactive or low levels of TEs and had been in stasis for 400 million years.

In another example he referred to the tuatara, where just two species had been found off the coast of New Zealand.

Like the coelacanth, the tuatara was characterised by very few jumping genes and has been unchanged for 220 million years.

An explanation for many unanswered questions

Dr Greene said Genomic Drive theory provided an explanation for many unanswered questions such as why species suddenly appeared in the fossil record, why some groups of organisms were species rich and others species poor and why some species changed little over millions of years.

Successive waves of TE activity in a lineage potentially explained alternations of rapid evolution and stasis.

He said some species – such as bats which “came out of nowhere” in the Eocene Period – suddenly appeared in the fossil record.

This was in keeping with evidence that TE or jumping gene activity occurred in sudden episodic bursts.

Improving the ability to diversify, adapt and survive

Dr Greene said an example of how TE activity affected the richness of a lineage was seen in rodents and bats.

These were species-rich orders of mammals and, unusually for modern mammals, both harboured highly active TEs.

Although there wasn’t enough data yet, the presence of TEs could also help to explain why one order of birds, commonly known as the Songbirds, (the Passeriformes) accounted for over half of all bird species and why the Perciformes accounted for 40 per cent of fish species.

While jumping gene activity in the 235 species of primates had quietened down a lot since its peak about 40 million years ago, the high presence of identical TEs in the primate genome pointed to an improved ability to diversify, adapt and survive.

By comparison a cousin of the primate, the Flying Lemur, lacked a key TE that primates had in abundance and only two species of it remained.

Supporting transformative research: we need this in Canada, too.

Here is the kind of thing we need more of in Canada. We do have things like Canada Research Chairs, Steacie Fellowships, and so on (though mostly these just free one from teaching), but most of the time it is a fight for very small grants that strongly focus efforts on safe, hypothesis-driven, incremental discoveries.

One from private sources:

HHMI Gives 50 Early Career Scientists a Jump on Their Next Big Idea

Fifty of the nation’s best early career science faculty will have more time and resources to focus on their boldest—and potentially transformative—research ideas with support from a new initiative from the Howard Hughes Medical Institute.

(See Nature)

And another one:

25 New MacArthur Fellows Announced

MacArthur Fellowships offer the opportunity for Fellows to accelerate their current activities or take their work in new directions. The unusual level of independence afforded to Fellows underscores the spirit of freedom intrinsic to creative endeavors. The extraordinary creativity of MacArthur Fellows knows neither boundaries nor the constraints of age, place, and endeavor.

One from public sources:

NIH Director’s Pioneer Award

The NIH Director’s Pioneer Award Program is a unique aspect of the NIH Roadmap for Medical Research, a high-risk research initiative of Research Teams of the Future. Pioneer Awards are designed to support individual scientists of exceptional creativity who propose pioneering – and possibly transforming approaches – to major challenges in biomedical and behavioral research. The term “pioneering” is used to describe highly innovative approaches that have the potential to produce an unusually high impact on a broad area of biomedical or behavioral research, and the term “award” is used to mean a grant for conducting research, rather than a reward for past achievements. To be considered pioneering, the proposed research must reflect ideas substantially different from those already being pursued in the investigator’s laboratory or elsewhere. Biomedical and behavioral research is defined broadly in this announcement as encompassing scientific investigations in the biological, behavioral, clinical, social, physical, chemical, computational, engineering, and mathematical sciences.

(See Science)

And another:

American Recovery and Reinvestment Act (Recovery Act) Frequently Asked Questions

  1. Are there special priorities for awards that will be made via the Recovery Act?

Funding of new Principal Investigators and high-risk, high-return research will be top priorities. With the exception of the Academic Research Infrastructure Program, the Science Masters Program, and the Major Research Instrumentation Program, the majority of proposals eligible for Recovery Act funding include those that are already in-house and will be reviewed and/or awarded prior to September 30, 2009. NSF also will consider proposals declined on or after October 1, 2008. The process for reversal of the decline decision is outlined in this FAQ document.

Yes, these support only a small number of individuals, but they also give hope that the nation’s agencies and foundations care about funding risky yet possibly transformative research.

Bad argument against baseline funding.

Over at Sandwalk, the following comment was posted by Rosie Redfield in response to the idea of 100% baseline funding for qualified researchers.

I think that’s a terrible idea. Everyone gripes about preparing grant proposals, but that’s the one time we’re forced to think rigorously about our research BEFORE we do it. If I didn’t have to justify what I want to do in order to get the funding, I’d waste a lot of the taxpayers’ money doing what I would only later realize to be useless experiments.

I don’t know Dr. Redfield, but I have generally agreed with her comments on Larry’s posts. This is not one of those times, however. Where to start?

First, if this is true, it is an astonishing admission. Your research is still going to be evaluated during peer review before publication, your productivity will be evaluated by your institution, and, presumably, you do not want to waste your time and funds. Who doesn’t think about an experiment beforehand?

Second, most research is done by graduate students. In my department, graduate students take a mandatory course in scientific communication, a component of which is writing, presenting, and justifying their proposed research. This proposal is further edited by their advisor, and then presented to and defended in front of their advisory committee. A standard NSERC proposal must explain the work for 5 years in 5 pages. Each student’s proposal, which is evaluated by peers as well as several faculty, may be 30 pages or more of literature review, justification, study design, and research timelines. That is, the research will still be subject to considerable evaluation.

Third, money is already being wasted.

Fourth, the current system is totally focussed on small hypothesis testing. As the authors of the paper in question pointed out, a stable baseline would allow higher risk projects to get going.

Finally, the authors suggest a mixed approach, with this being only the baseline. Increases could be based on performance, and if you need more money, you have to apply and justify why.

Attention biology teachers from Ontario!

On May 19, the University of Guelph is holding a workshop on evolution education open to teachers from southern Ontario (and elsewhere if you’re willing to travel).

Evolution Education Workshop
May 19, University of Guelph

Speakers:

  • Brian Alters Evolution educator and researcher, McGill University
  • David Campbell Florida high school biology teacher making news on his approach to teaching evolution in US classrooms
  • Eugenie Scott Director, National Center for Science Education, USA
  • David S. Wilson Biologist, author of Evolution for Everyone

There will be interactive question periods as well as the talks. Teachers who present a poster on the teaching of evolution will have their registration refunded, and some programs are in place to help cover leave time to attend this workshop.

Download poster for more details.

Frontiers in Evolution.

These two meetings are coming up in May, one at the University of Guelph and one at McMaster University. If you are in the area, you are welcome and encouraged to register and attend!

The Peter Yodzis Colloquium 2009 – Frontiers in Evolution
May 20-21, University of Guelph

Speakers:

  • David Sloan Wilson (levels of selection)
  • Richard Lenski (experimental evolution)
  • Hans Thewissen (paleontology)
  • Belinda Chang (molecular evolution)
  • Ryan Gregory (genome evolution)
  • Craig Albertson (developmental evolution)

The talks are spread over two days, and on the second day will be a panel discussion. No concurrent talks, only invited speakers, plus a contributed poster session.

Download poster for more details.

Darwin’s Legacy
May 25-29, Origins Institute, McMaster University

Speakers:

  • Mark Rausher (selection)
  • James Valentine (paleontology)
  • Brian Hall (diversity)
  • Christof Koch (cognition)
  • Hopi Hoekstra (speciation and adaptation)
  • Steve Benner (molecular evolution)
  • David Deamer (origins of life)

There will also be other invited and submitted talks as well as a poster session.

NSERC peer review costs more than funding scientists.

Depressing or infuriating, you decide.

Gordon, R. and Poulin, B.J. (2009). Cost of the NSERC science grant peer review system exceeds the cost of giving every qualified researcher a baseline grant. Accountability in Research 16: 13-40.

Using Natural Science and Engineering Research Council Canada (NSERC) statistics, we show that the $40,000 (Canadian) cost of preparation for a grant application and rejection by peer review in 2007 exceeded that of giving every qualified investigator a direct baseline discovery grant of $30,000 (average grant). This means the Canadian Federal Government could institute direct grants for 100% of qualified applicants for the same money. We anticipate that the net result would be more and better research since more research would be conducted at the critical idea or discovery stage. Control of quality is assured through university hiring, promotion and tenure proceedings, journal reviews of submitted work, and the patent process, whose collective scrutiny far exceeds that of grant peer review. The greater efficiency in use of grant funds and increased innovation with baseline funding would provide a means of achieving the goals of the recent Canadian Value for Money and Accountability Review. We suggest that developing countries could leapfrog ahead by adopting from the start science grant systems that encourage innovation.

Hat tip: Sandwalk, Blog Around the Clock

"Evolution-proof"?

A while ago I posted about some claims that a snake species had evolved an “unbeatable” predation tactic.

Orgel’s Second Rule and “unbeatable” predation tactics

I also posted about a claim that an antibiotic had been invented to which bacteria could not evolve resistance.

“Everlasting antibiotics”, wanna bet?

Here is the most recent in this series of “I can’t imagine how evolution could occur in this circumstance” silliness.

How to Make Evolution-Proof Insecticides for Malaria Control

Insecticides are one of the cheapest, most effective, and best proven methods of controlling malaria, but mosquitoes can rapidly evolve resistance. Such evolution, first seen in the 1950s in areas of widespread DDT use, is a major challenge because attempts to comprehensively control and even eliminate malaria rely heavily on indoor house spraying and insecticide-treated bed nets. Current strategies for dealing with resistance evolution are expensive and open ended, and their sustainability has yet to be demonstrated. Here we show that if insecticides targeted old mosquitoes, and ideally old malaria-infected mosquitoes, they could provide effective malaria control while only weakly selecting for resistance. This alone would greatly enhance the useful life span of an insecticide. However, such weak selection for resistance can easily be overwhelmed if resistance is associated with fitness costs. In that case, late-life–acting insecticides would never be undermined by mosquito evolution. We discuss a number of practical ways to achieve this, including different use of existing chemical insecticides, biopesticides, and novel chemistry. Done right, a one-off investment in a single insecticide would solve the problem of mosquito resistance forever.

Ok readers, go see their paper, then post ideas regarding how evolution might still occur either in the mosquitoes or Plasmodium to make this not so very “evolution-proof” after all.

Hint: Note the following specifics:

The population genetics model makes the following assumptions:

1. Adult mosquito population size is constant.
2. Mosquitoes do not complete more than ten gonotrophic cycles.
3. The genetic make-up of mating males in any cycle is the same as that calculated for newly hatched mosquitoes in that cycle.
4. Males of all resistant/susceptibility genotypes are equally likely to mate successfully.
5. Females mate once only, in their first cycle, as is the norm.
6. Number of eggs produced per laying female is unaffected by egg paternal genotype.
7. Genotypes of emerging adults joining the population are in the same proportions as the genotypes of the generation of eggs from which they hatch.
8. Resistance is dominant, as can be the case.
9. Costs of resistance are dominant.
10. The proportion of infectious humans is constant.

The feeding cycle model makes the following assumptions.

1. Mosquitoes bite humans randomly and uniformly.
2. Malaria-infected mosquitoes never become uninfected.
3. The proportion of humans who are infectious is constant.
4. A variety of parameters do not change over successive gonotrophic cycles: (i) the background mosquito mortality rate (what Smith and McKenzie call “force of mortality”), which is considered as a constant per-capita daily death rate (i.e. there is no senescence), (ii) the probability of taking a blood meal and (iii) the probability of feeding on a human.
5. Conventional insecticides are instant kill.

I’ll point out again what Orgel’s second rule says: Evolution is cleverer than you are.