Visit www.microbialart.com!
Here’s just a sample:
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Pyrenaemata by T. Ryan Gregory
A blog dealing with genomics, evolution, and biodiversity.
- Cool! I think Niall Hamilton’s are my fav...
- Negative. Part of their beauty is the tragedy ...
- Love the E. coli images. Somebody’s gotta...
- No problem, just have a look out your window.
- I would like to see your animal facility.
- Oooh. I’ll head over and sign up too. I t...
- Thanks for the heads up on the new blog! IR...
- Ah, thanks. I was trying to clean the informati...
- The collection of bones is musk ox mostly, just...
- Why are there mounds of bones around the sign? ...
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Microbial art is alive!
- Date:
- Sunday, 25 Oct ober 2009
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Evolution and art.
- Date:
- Saturday, 17 Oct ober 2009
From Oct. 9-30, the University of Guelph and Ed Video are hosting a special art exhibit entitled This View of Life: Evolutionary Art for the Year of Darwin. It was organized by professors in four departments: Integrative Biology, Philosophy, History, and English and Theatre Studies, and was curated by Scott McGovern of Ed Video. The exhibit features art by 10 artists, all inspired by the themes of evolution, Darwin, and biodiversity. The Gregory Lab contributed some installations as well, which are shown in this brief clip from just before the opening reception on Oct. 16 (about 200 people attended the event). The first window shows live Daphnia magna (“water fleas”) to depict the concept of overproduction; they also are of interest because they reproduce asexually (the evolution of sexual reproduction being an important question in evolutionary theory). The second window presents images created using live colonies of E. coli bacteria. These last only a few days, so many different images will be displayed throughout the exhibit. The third window shows a projection of a remarkable collection of images of bacterial colonies kindly provided by Dr. Eshel Ben-Jacob.
For more photos of the artwork, see here.
Special thanks to everyone involved in organizing the exhibit, to the artists, and to the following graduate students who are talented artists in their own right: Joao Lima, John Wilson, Tyler Elliott, Paola Pierossi, Nick Jeffery.
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Omnigenomics
- Date:
- Thursday, 01 Oct ober 2009
Sometimes it is helpful to have a catchy word to describe one’s type of research. I think that’s why “omics” words are so popular — they encapsulate a complex combination of approaches (usually something + genomics, or something-more-than-genomics) in a memorable way that immediately conveys the gist of the field. “Metagenomics” is a good example — it’s the study of a larger assemblage of genomes than just one, usually from an environmental sample of microbes. “Proteiomics” is another, or “transcriptomics”. Of course, this can get out of hand (see here). However, I think the study of genome size (which predates molecular genetics, let alone genomics) deserves a catchy moniker. The problem is, I haven’t really come up with one in the past, so I just end up saying “I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and…” — well, you get the idea.
People like me study entire genomes — every component included, be it gene or pseudogene or repeat or transposable element. We also are interested, not in a few model organisms, but in everything (people usually stare blankly when, to the question “which animals do you work on?”, I reply “all of them”). But what to call such a discipline?
Proposed neologism: “Omnigenomics”
Etymology: Latin “omnis” (all or everything) + genomics (study of genomes)
Sample usage: “What do you do?” / “Omnigenomics” / “What’s that?” / “I study the total amount of DNA in different species of animals, which includes genes and all the other sequences, most of which are non-coding and…”
(The alternative Greek version, “pangenomics”, is already being used and sounds way less cool). -
Evolution art exhibit at the University of Guelph - October 9 to 30
- Date:
- Monday, 14 Sep tember 2009
Like many institutions, the University of Guelph is hosting a series of events in celebration of the 200th anniversary of Darwin’s birth and the 150th anniversary of the publication of the Origin of Species. Two of them, a teachers’ workshop and the Yodzis Colloquium, have already run, but there is another coming up that I am pleased to announce.
This View of Life: Evolutionary Art for the Year of Darwin
University of Guelph and Ed Video
Oct. 9 – 30
Reception Oct. 16, 5:00-7:00pm Science Complex Atrium
Admission is free
Click poster for larger view
‘This View of Life’ showcases the melding of artistic and scientific disciplines in this year of celebration for Charles Darwin. This group exhibition presents recent work from contemporary Canadian artists and features several collaborative projects created with scientists from the University of Guelph.
For more information, visit:The investigation of evolutionary theory is not limited to the lab, field or fossil bed. Darwinian theory, after a century and a half, continues to inspire creativity which perpetuates the evolution of these ideas in their own right. Forms of expression can be compared to instruments of observation, magnifying some aspects of evolution while masking or distorting others. Presented by the University of Guelph and Ed Video, these exhibits offer unique perspectives into the nature and scope of biological novelty, organic variation, and evolving life forms.
The reception will feature artwork, biological specimens, and presentations by project participants. Artwork will also be exhibited at the Ed Video Gallery and at various locations on campus for the duration of the show.
Artists:
- Mat Brown
- Jefferson Campbell-Cooper
- Alison Judd
- Christy Langer
- Jean Maddison
- Allyson Mitchell
- Jenn E Norton
- Prof. Burnaby Q. Orbax
- Kelly Richardson
- Stephen Wicks
- College of Arts
- College of Biological Sciences
- Department of Integrative Biology
- Department of History
- Department of Philosophy
- Ed Video
- School of Fine Arts and Music
- School of Environmental Sciences
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The evolution of eyes
- Date:
- Friday, 11 Sep tember 2009
Some of you already will know about the special issue of Evolution: Education and Outreach on the evolution of eyes that I edited last year (see below). There is now another excellent collection of papers on this subject in Philosophical Transactions of the Royal Society B, edited by eye experts Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin.
The evolution of phototransduction and eyes
edited by Trevor D. Lamb, Detlev Arendt, and Shaun P. Collin
Philosophical Transactions of the Royal Society B, vol. 364, issue 1531, Oct. 19, 2009The evolution of phototransduction and eyes
Trevor D. Lamb, Detlev Arendt, and Shaun P. CollinEvolution of phototaxis
Gáspár Jékely
The ‘division of labour’ model of eye evolution
Detlev Arendt, Harald Hausen, and Günter PurschkeEye evolution: common use and independent recruitment of genetic components
Pavel Vopalensky and Zbynek Kozmik
The evolution of eyes and visually guided behaviour
Dan-Eric NilssonThe evolution of irradiance detection: melanopsin and the non-visual opsins
Stuart N. Peirson, Stephanie Halford, and Russell G. Foster
Evolution of vertebrate rod and cone phototransduction genes
Dan Larhammar, Karin Nordström, and Tomas A. LarssonEvolution of opsins and phototransduction
Yoshinori Shichida and Take MatsuyamaEvolution and the origin of the visual retinoid cycle in vertebrates
Takehiro G. Kusakabe, Noriko Takimoto, Minghao Jin, and Motoyuki Tsuda
Evolution of vertebrate retinal photoreception
Trevor D. Lamb
The evolution of early vertebrate photoreceptors
Shaun P. Collin, Wayne L. Davies, Nathan S. Hart, and David M. HuntEvolution and spectral tuning of visual pigments in birds and mammals
David M. Hunt, Livia S. Carvalho, Jill A. Cowing, and Wayne L. Davies
Evolution of colour vision in mammals
Gerald H. Jacobs
The evolution of eyes
edited by T. Ryan Gregory
Evolution: Education and Outreach, vol. 1, issue 4, Oct. 2008
Editorial
351. Editorial by Gregory Eldredge and Niles Eldredge (PDF)352-354. Introduction by T. Ryan Gregory (PDF)
355-357. Casting an Eye on Complexity by Niles Eldredge (PDF)
Original science / evolution reviews
358-389. The Evolution of Complex Organs by T. Ryan Gregory (PDF)
(Blog: Genomicron)390-402. Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey (PDF)
(Blog: Evolutionary Novelties)403-414. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky (PDF)
415-426. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin (PDF)
427-438. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young (PDF)
439-447. Charting Evolution’s Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse (PDF)
448-462. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich (PDF)
463-475. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter (PDF)
476-486. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris (PDF)
487-492. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer (PDF)
(Blog: The Loom)493-497. Suboptimal Optics: Vision Problems as Scars of Evolutionary History by Steven Novella (PDF)
(Blog: NeuroLogica)Curriculum articles
498-504. Bringing Homologies Into Focus by Anastasia Thanukos (PDF)
(Website: Understanding Evolution)505-508. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead (PDF)
(Website: NCSE)509-516. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa (PDF)
Book reviews
548-551. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley (PDF)
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Granting agency beaurocracy jumps the shark
- Date:
- Friday, 11 Sep tember 2009
NSERC has done some weird things in the past. Like running a peer review system that costs more than just giving every qualified researcher the amount of an average grant. Like cutting the MSc scholarship to one year. Like offering other scholarships that are much higher than the average lab’s operating grant. Like being notoriously averse to funding discovery science under the “Discovery Grants” program.But this memo, which I assure you is not a joke, marks the moment when the shark truly was jumped.
Eligible and non-eligible expenses for stationery and office supplies
General Rule
Funding agencies expect institutions to assume the indirect costs and general expenses of the research project. Grant funds are used to cover the direct costs of research, including costs that would not have been incurred if the research project had not been undertaken. Funds cannot be used to pay for general expenses such as costs associated with office accessories normally already provided for institution staff.The funds must be used effectively and economically, and the expenses must be essential to the research supported by the grant.
It may be concluded that an expenditure on supplies is admissible if they are not part of the “basic equipment” of the university’s academic and research mission and if they are not normally provided for institution staff. Moreover, the recipient must explain how those supplies are essential to his/her research activities.
Equipment and Supplies
Expenditures on research equipment and supplies, as well as costs of training staff who will use the specialized instruments or facilities, are eligible.Examples of Eligible Expenses:
- laboratory notebooks
- paper used for laboratory operations in the context of a funded research project (correspondence with clients, printing of results)
- paper used for data collection (questionnaires)
- printing of an equipment user manual for a new researcher or assistant working on the funded research project
- printing of e-journal articles relevant to the research project
- office accessories for laboratory employees, researchers and students (paper clips, pens, file folders, writing pads, ring binders, day planners, wastebaskets)
Costs associated with the dissemination of findings, i.e., through traditional venues as well as videos, CD-ROMs, etc., are eligible, as are costs of preparing a research manuscript for publication.Examples of Eligible Expenses:
- paper and ink cartridges for printing of different manuscript versions
- research-related paper documents, posters and pamphlets distributed to conference, workshop and focus group participants
Costs for the purchase of books or periodicals, specialized office supplies, computing equipment and information services not formally provided by the institution to all academic and research staff are eligible.The funding agencies note that certain miscellaneous education-related expenses, such as costs of thesis preparation, tuition and course fees and costs associated with the preparation of teaching materials, are ineligible.
Examples of Eligible Expenses:
- special paper or writing tools required for the research project
- laboratory notebooks or special binders in which to archive research project data
- paper used by students to print different versions of their dissertation or thesis
- paper used to prepare course notes
- filing cabinets and hanging files
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Self-quoting
- Date:
- Friday, 11 Sep tember 2009
I usually have a rule that it is best to read one’s own work only when it is unavoidable (because one often finds things that could have been done better, etc.). However, I have been working on finishing up my most recent paper for Evolution: Education and Outreach, and I have had to go back through a few of my previous articles in the process. In a few places, I noted a particularly decent line that I thought I would probably quote sometime if it had been written by someone else. It then occurred to me that one can, in blog format at least, quote oneself and not feel too vain about it. So, here are the ones I liked.
From Evolution as fact, theory, and path:
“That evolution is a theory in the proper scientific sense means that there is both a fact of evolution to be explained, and a well-supported mechanistic framework to account for it. To claim that evolution is “just a theory” is to reveal both a profound ignorance of modern biological knowledge and a deep misunderstanding of the basic nature of science.”
“Evolutionary biology has as its purview the entire history and diversity of life, encompassing an unbroken chain of ancestry and descent involving innumerable organisms and spanning billions of years. In light of the tremendous scope and complexity of its subject matter, it should come as no surprise that details regarding the path and mechanisms of evolution are often subject to heated debate. The fact of evolution, however, remains unsinged.”
From The evolution of complex organs:
“As a career, science would hold very little appeal if all it entailed were the confirmation of existing knowledge or the memorization of long lists of well established facts. Science thrives on what is ”font-style: italic;“>not yet known: the more vexing a problem, the more inspiring it is to investigate.”
“…the evolution of complex organs does not involve re-design from scratch at each stage; whether by direct adaptation or shifts in function, the process builds upon and modifies what is already present. "
“By definition, natural selection is the ”font-style: italic;“>non-random differential success of individuals on the basis of heritable variation and therefore the cumulative outcome of this process – adaptation – is the ”font-style: italic;“>opposite of random chance.”
“Because organs are built by tinkering rather than design, their features are impacted by historical contingency and inevitably reflect holdovers of past states. The net result is that all complex organs represent a mixture of optimizations and imperfections, both of which are accounted for by their evolutionary history.”
“Following in the tradition of Paley (1802) from two centuries ago, it is sometimes asserted that if a natural explanation is unavailable to account for an observation, then the only alternative is to assume a supernatural one. Such an assumption misses the obvious third option, and the one that drives scientific inquiry: that there is a natural explanation that is not yet known.”
From Artificial selection and domestication: modern lessons from Darwin’s enduring analogy:
“No reliable observation has yet been made to refute the notion that livestock, pets, and crops evolved from wild predecessors. On the contrary, the details of when, where, and how this occurred are becoming increasingly clear. Where there is disagreement, it relates not to the fact of evolutionary descent but to specific points about the mechanisms, locations, or timing of change. All of these considerations apply in the study of evolution by natural selection as well.”
From Understanding natural selection: essential concepts and common misconceptions:
“The occurrence of any particular beneficial mutation may be very improbable, but natural selection is very effective at causing these individually unlikely improvements to accumulate. Natural selection is an improbability concentrator.”
“The process of adaptation by natural selection is not forward-looking, and it cannot produce features on the grounds that they might become beneficial sometime in the future. In fact, adaptations are always to the conditions experienced by generations in the past.”
“Intuitive interpretations of the world, though sufficient for navigating daily life, are usually fundamentally at odds with scientific principles. If common sense were more than superficially accurate, scientific explanations would be less counterintuitive, but they also would be largely unnecessary.”
“…it is abundantly clear that teaching and learning natural selection must include efforts to identify, confront, and supplant misconceptions. Most of these derive from deeply held conceptual biases that may have been present since childhood. Natural selection, like most complex scientific theories, runs counter to common experience and therefore competes – usually unsuccessfully – with intuitive ideas about inheritance, variation, function, intentionality, and probability. The tendency, both outside and within academic settings, to use inaccurate language to describe evolutionary phenomena probably serves to reinforce these problems.”
“Natural selection is a central component of modern evolutionary theory, which in turn is the unifying theme of all biology. Without a grasp of this process and its consequences, it is simply impossible to understand, even in basic terms, how and why life has become so marvelously diverse.”
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Journal websites
- Date:
- Friday, 11 Sep tember 2009
Some time ago, I put together a list of websites for the journals I am most interested in. It occurred to me that this could be useful for others. (I am also planning to post some information on how to aggregate journal tables of contents, automatic index searches, and science news).
General
Evolution
Genome biology and evolution
Zoology
Education
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Breaking news: evidence for evolution found!
- Date:
- Friday, 11 Sep tember 2009
One of Doug Futuyma’s great quotes is this one:
“…no biologist today would think of publishing a paper on ‘new evidence for evolution’… it simply hasn’t been an issue in scientific circles for more than a century.”
Press officers are a different story. Here’s one from the University of California, Riverside:
– Futuyma, 1998 Evolution Biology, 3rd edition
Molecular decay of enamel-specific gene in toothless mammals supports theory of evolution
It’s a cool study, linking fossil and genomic data. But it’s not cool because it provides “fresh support for Charles Darwin’s theory of evolution”. This is about the historical path and genetic mechanisms of evolution — the fact has been well established for 150 years.Biologists at the University of California, Riverside report new evidence for evolutionary change recorded in both the fossil record and the genomes (or genetic blueprints) of living organisms, providing fresh support for Charles Darwin’s theory of evolution. Read more
Here’s the actual abstract and author summary:
Abstract
I can see why the reporter got somewhat confused. But note what they say, as there is a subtle but important distinction: this provides evidence for the predictive power of evolutionary theory. This is news, because it is sometimes argued that evolutionary research is purely descriptive. Examples like this and the discovery of Tiktaalik in the type and age of rocks where an intermediate fossil was predicted to occur show just how strong modern evolutionary ideas are.
Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of “molecular fossils” of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the “molecular fossil” hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin’s theory.Author summary
Enamel is the hardest substance in the vertebrate body. One of the key proteins involved in enamel formation is enamelin. Most placental mammals have teeth that are capped with enamel, but there are also lineages without teeth (anteaters, pangolins, baleen whales) or with enamelless teeth (armadillos, sloths, aardvarks, pygmy and dwarf sperm whales). All toothless and enamelless mammals are descended from ancestral forms that possessed teeth with enamel. Given this ancestry, we predicted that mammalian species without teeth or with teeth that lack enamel would have copies of the gene that codes for the enamelin protein, but that the enamelin gene in these species would contain mutations that render it a nonfunctional pseudogene. To test this hypothesis, we sequenced most of the protein-coding region of the enamelin gene in all groups of placental mammals that lack teeth or have enamelless teeth. In every case, we discovered mutations in the enamelin gene that disrupt the proper reading frame that codes for the enamelin protein. Our results link evolutionary change at the molecular level to morphological change in the fossil record and also provide evidence for the enormous predictive power of Charles Darwin’s theory of descent with modification.As evidence for the fact of evolution, though… yawn … just put it on the pile with all the rest.
Reference
Meredith, R.W., Gatesy, J., Murphy, W.J., Ryder, O.A., and Springer, M.S. 2009. Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals. PLoS Genetics 5(9): e1000634.
For descriptions of the study, see Ed Yong and Carl Zimmer (both among my top science writers list).
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Mendeley (and other free software)
- Date:
- Friday, 11 Sep tember 2009
Some time ago, I posted about my search for a new reference management program for Windows that would be the rough equivalent of Papers for Mac (which is the rough equivalent of iTunes for PDFs).
I played around with Zotero, but I prefer something standalone rather than embedded within a browser. You may like it, though, so feel free to check it out.
Instead, I have decided to make the switch to Mendeley, a desktop application with an optional online sync function. It is still in beta, but is coming along nicely and soon should be able to do all the things I want. Specifically, allowing PDFs to be linked with records and read within the program, searching within PDFs, creating “playlists” rather than separate files for each paper I am working on, and automatic organization and renaming of PDFs in a single folder.
The program is not quite there yet, but I am now very optimistic. For now, the automatic metadata extraction mostly only works if you sign in to a Mendeley account and use new papers followed by “search by title”, but then again I currently have to enter everything manually anyway with my existing program. In this case, you can have the PDF open in the same screen as the record update window. This alone is much easier than flipping back and forth or printing every reference.
Another issue is that it is dreadfully slow when loading if you have a lot of PDFs. Apparently this only happens when you first input a bunch of new papers, but we’ll see. I have thousands of papers that will need to be entered, so if it can’t handle it, then it’s not going to work. Also, it has a tendency to crash when inputting a lot of papers.
In short, the program looks like it will be great once the bugs are worked out and some other missing features are incorporated.
This raises a larger point, which is that free, community-driven projects are getting to be my preferred kind of software. This is because the programmers are usually very responsive to user feedback, and in many cases users themselves can create add-ons for specific functions that make the software even more useful. Here are some additional examples:
Firefox — A great browser, with an unbelievable collection of user-provided plugins.
Google Earth — Simply awesome.
iGoogle and Google Reader — Also awesome. (Google Desktop looks good too, but I haven’t used it).
IrfanView — A nice image viewing program.
Mesquite — Phylogenetic analysis software (there are many others, but I am partial to this one).
OpenGoo — A free lab management program that lets students and advisors keep track of projects, share files, and set schedules.
OpenOffice.org — A free office suite with counterparts to Word, Excel, and PowerPoint.
R — My statistician colleagues swear by this open source stats program, but I haven’t really tried to figure it out yet.
Skype — Free online video chat and inexpensive long-distance to land lines. Extremely useful for keeping in touch with friends and family.
Thunderbird — If you don’t have Outlook, try this free email software.
WinTidy — Simple little application that restores your icon positions on the Windows XP desktop if they get moved around (e.g., following a crash).
Wordpress — Not just for blogs. Entire websites can be created using it (e.g., Evolver Zone), and there are lots of user-created themes and add-ons available.
Xobni — A plugin for Outlook that indexes email and makes searches vastly easier.
Zone Alarm — A free firewall program.
If you have other suggestions, leave a comment and I may add them to this list.
