Do you know what this is?

 
If you can't identify the organism in the photograph then read The Beautiful Angel of Death on Catalogue of Organisms.

Life is stranger than most of us realize.

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Buy a Dinosaur

 
Today's the day you can buy a dinosaur fossil. Maynards, in Vancouver, is auctioning off the complete collection of dinosaur fossils from the Seibu Museum in Tokyo, Japan [Auction Details: Dinosaurs].

The collection includes ...

* Eusthenopteron foordi
* Bothriolepis
* Aspidorhynchus
* Araripichthys castilhoi
* Crinoids
* Tyrannosaurus rex
* Ankylosaur
* Dinosaur eggs
* Stegosaurus
* Edmontosaurus annectens
* Triceratops
* Whiteia
* Platecarpus
* Araucarites mirabilis
* Alethopteris
* ...and More

Haven't you always wanted a Stegosaurus in your living room? I think I'll bid on the T. rex. It would look great in my office. Do you think my students might be intimidated?

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Get a Job in Newfoundland

 
Memorial University: Departments of Computer Science and Biology

MEMORIAL UNIVERSITY
Tenure-Track Faculty Position in Bioinformatics

The Departments of Computer Science and Biology at Memorial University have each embarked on multi-year renewal programs. Each department currently has more than 20 tenure-stream faculty members, and supports M.Sc., Ph.D. and collaborative graduate programs. For more details, see http://www.mun.ca/biology/Home/ and http://www.mun.ca/computerscience/. Both departments invite applications for a tenure-track position in Bioinformatics, starting no later than September 1, 2009. This will be a joint appointment between the departments. The appointment will be made at the level of Assistant Professor, with the primary appointment in Computer Science, and equal responsibility in both departments, in accordance with the terms of Memorial’s Collective Agreement.

A Ph.D. in Computer Science, Computational Science, Biology, or related fields is required and postdoctoral or equivalent experience is desirable. Applicants should have experience in Bioinformatics, and be keen to do interdisciplinary work between the departments. Applicants should possess a strong research record with outstanding promise for future research, and be able to demonstrate the potential for excellent undergraduate and graduate teaching in Bioinformatics.

Applicants should submit a Curriculum Vitae, statements of research interests, teaching interests and philosophy, and up to three reprints of publications. The application should be accompanied by names of at least three referees of international standing, who are willing to provide letters of recommendation (include details on affiliations, plus phone numbers and email addresses). All material must be received by January 15, 2009; refer to position VPA-COSC-2007-001 in all correspondence, and submit materials to:

Dr. Wolfgang Banzhaf, Head
Department of Computer Science
Memorial University
St. John’s, NL, Canada, A1B 3X5
Email: chair@cs.mun.ca

Memorial University is the largest university in Atlantic Canada. As the Province’s only university, Memorial plays an integral role in the educational and cultural life of the Province of Newfoundland and Labrador. Offering diverse undergraduate and graduate programs to almost 18,000 students, Memorial provides a distinctive and stimulating environment for learning. St. John’s is a very safe and friendly city with great historic charm, a vibrant cultural life, and easy access to a wide range of outdoor activities.

Memorial University is committed to employment equity and encourages applications from qualified women and men, visible minorities, aboriginal people and persons with disabilities. All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority. Partners of candidates for positions are invited to include their resumes for possible matching with other job opportunities.

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Get Several Jobs in British Columbia

 
University of British Columbia: Departments of Botany and Zoology

Tenure track biology instructor positions
Closing date: January 15, 2009 at 5pm

The Departments of Botany and Zoology at the University of British Columbia (Vancouver, Canada) are seeking candidates to fill at least four tenure-track Instructor positions to teach in the Biology Undergraduate Program. At least two positions will be in cellular and molecular biology, with the remaining positions open to biologists in any area. Candidates must hold a PhD in Biology, have a broadly integrative perspective on the biological sciences, and be committed to the improvement of biology undergraduate teaching. Postdoctoral teaching and/or research experience is preferred.

Successful candidates will demonstrate 1) evidence of outstanding teaching, and 2) the ability to contribute to ongoing curriculum and course redevelopment.

Duties of the positions vary, but may include lecturing in introductory and advanced courses, teaching and administration of a large third-year undergraduate laboratory course in the area of specialty, participation in course and curriculum development, and the training and supervision of graduate student teaching assistants. There are also opportunities to work in collaboration with the Carl Wieman Science Education Initiative (www.cwsei.ubc.ca).

Interested candidates should submit a letter of application, a curriculum vitae, a statement of teaching philosophy, an outline of teaching interests, evidence of teaching effectiveness, and the names and contact information for at least three individuals who would be willing to provide letters of references to jobs@zoology.ubc.ca. Candidates are particularly encouraged to highlight previous experience in fostering the education of students from diverse backgrounds.

Review of applications will begin January 15, 2009 and continue until the positions are filled, with appointments anticipated to begin by July 1, 2009.

The University of British Columbia hires on the basis of merit and is committed to employment equity. All qualified persons are encouraged to apply; however, priority will be given to Canadian citizens and permanent residents of Canada.

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Get a Job in Ontario

 
University of Western Ontario: Department of Biology

The University of Western Ontario
Faculty of Science
Department of Biology
Applications are invited for a 3-year Limited Term position in Biology commencing July 1, 2009. As a minimum, the preferred applicant will have a Ph.D. in Biology or a related field, and appropriate training in University level teaching. The successful applicant will be expected to contribute to the department’s commitment to excellence in teaching and provide evidence of his/her ability to teach at the undergraduate level. The successful candidate will be responsible for participating in the teaching of courses in cell and developmental biology as well as general biology.

Applications, including a curriculum vitae and names and addresses of three referees whom we may contact, should be submitted to:

Dr. M. Brock Fenton, Acting Chair
Department of Biology
The University of Western Ontario
London, Ontario
N6A 5B7

Applications for this position will be accepted until January 31, 2009 or until a suitable candidate is found.

Positions are subject to budget approval. Applicants should have fluent written and oral communication skills in English. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority. The University of Western Ontario is committed to employment equity and welcomes applications from all qualified women and men, including visible minorities, aboriginal people and persons with disabilities.

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If Spiders Are Arthropods then Where Are the Segments?

 
Christopher Taylor of Catalogue of Organisms has the answer [Attercop].

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[Image Credit: Commonwealth Scientific and Industrial Research Organisation (CSIRO)]

Get a Job

 

Assistant Professor, Tenure Stream
Dept. of Cell & Systems Biology
University of Toronto

The Department of Cell & Systems Biology at the University of Toronto invites applications for a tenure track faculty position to be appointed at the Assistant Professor level in the field of Systems Biology to begin July 1, 2009.

We particularly encourage applications from candidates who have demonstrated excellence in addressing fundamental questions in biology using high-throughput approaches or gene/protein network analyses with bioinformatic, genomic, proteomic, or imaging tools. Our vision is to advance systems biology-based research, with a specific interests in developing expertise in systems neurobiology, but we welcome applicants from all others areas of systems biology which complement existing strengths in the department (www.csb.utoronto.ca).

Candidates should have at least two years of research experience beyond their doctoral degree. In addition to pursuing a vigorous, internationally-recognized research program, the successful candidate will contribute to undergraduate and graduate teaching in the molecular life sciences. The successful candidate would also be expected to network with researchers university-wide to take advantage of the extensive resources in systems biology at the University of Toronto and its affiliated institutions. A generous start-up package will be provided. Salary will be commensurate with qualifications and experience.

We encourage qualified applicants to submit their applications online at: www.jobs.utoronto.ca/faculty.htm. Applicants should submit their curriculum vitae, copies of significant publications, and statements of research and teaching interests. Applicants should also arrange for three confidential letters of recommendation to be sent directly to: Professor Daphne Goring, Chair, Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario M5S 3G5, Canada; or by email to search@csb.utoronto.ca by January 31, 2009.

The University of Toronto offers the opportunity to teach, conduct research and live in one of the most diverse cities in the world, and is responsive to the needs of dual career couples. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.

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This Doesn't Seem Right ...

 
Scientific American is reporting on a growing trend among field biologists. When they discover a new species they sell the right to name it [Name that species--After yourself, Purdue auction suggests].

Naming your kid after you is one thing. But imagine if an entire species were named for you.

This week, Purdue University is auctioning off the rights to name seven newly discovered bats and two turtles, the Associated Press is reporting. The winners — who will shell out a minimum of $250,000 for at least one of the bats, a Purdue spokesman told ScientificAmerican.com — can link their own name or that of a pal to the animal’s scientific name.

"Unlike naming a building or something like that, this is much more permanent. This will last as long as we have our society," John Bickham, who co-discovered the nine species, told the AP.

In the ongoing battle between splitters and lumpers, you can bet that the splitters are going to gain the upper hand if they can earn so much money by creating a new species.

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Greg Laden on "Race" (Again)

 
Greg Laden is one of those people who want to abolish use of the word "race" to define genetic subpopulations. He claims that there is no such thing in humans (or in other species). But even if it were biologically correct we shouldn't use the word because is has been misused by non-scientists.

Here's an example of his reasoning from The Scientific, Political, Social, and Pedagogical Context for the claim that "Race does not exist.".

The race concept has been very successful in its many nefarious applications, but this is not what I wish to speak about here. Rather, I want to acknowledge that a concept that divides humans into a particular set of groups in a useful way might be, well, useful and not such a bad thing. The fact that medical researchers use race to divide subjects, and find differences between races, and that these differences are important to know about, is important, even if it does not validate the races. What it means is that an unworkable race concept works sometimes, even if the races themselves don't exist. Nonetheless, it is reasonable to acknowledge that even though races don't really exist and many, if not most, applications of the race concept are obnoxious, it may be that its use is not entirely inappropriate all the time.

I will argue, however, that the down side of the use of race requires its abolition among scientists. Since race is usually not a biologically useful concept for humans (or many other species), and is never a truly valid concept, it is difficult to justify its use given the negative political and social consequences it carries.

Greg and I have been over this ground before. It think it's silly to pretend that races don't exist. That's carrying the anti-racist agenda too far.

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Identity of the Product of Mendel's Green Cotyledon Gene (Update)

Last year I drew your attention to the identification of one of Gregor Mendel's original seven mutants [Identity of the Product of Mendel's Green Cotyledon Gene]. At the time, I thought that a recent 2007 paper by Sato et al. was the first publication to make this identification. Now I realize that I slighted the original discoverers Armstead et al. (2007) and earlier publications. The Armstead et al. paper is referenced in the later Sato et al. paper but the reference does not give appropriate credit to the work done by Armstead et al. in identifying the Mendelian gene. It was easy to get the impression that the Japanese group was the first to make the definite connection between Mendel's gene and work done in other species. I suspect that this was deliberate.

Here's a revised version of my original posting. Thanks to a reader who alerted me to the proper credit.

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Another of Mendel's seven genes has been identified. This one is described in his 1865 paper Experiments in Plant Hybridization [MendelWeb] as character number 2.

2. To the difference in the color of the seed albumen (endosperm). The albumen of the ripe seeds is either pale yellow, bright yellow and orange colored, or it possesses a more or less intense green tint. This difference of color is easily seen in the seeds as their coats are transparent.

Mendel's reference to the color of albumin, or endosperm, is inaccurate. He was actually observing the color of the cotyledons—the "seed leaves" that surround the embryo in the pea seed. These tiny leaves are covered by a seed coat that is partially transparent.

In wild-type peas the seeds turn yellow as they mature (I) but certain mutants exhibit a "stay-green" phenotype where the peas retain their green color (i). The figure shows seeds from a plant with the II genotype (top) and the ii genotype (bottom). The seed coat has been removed from the lower pair of each group of four peas.

A paper published in Science identifies the "stay-green" gene that Mendel worked with (Armstead et al. 2007). This work is based on several decades of study of the "stay-green" phenotype by Howard Thomas and his colleagues at the Institute of Grassland and Environmental Research, Aberystwyth, UK (Armstead et al. 2006; Thomas, 1987; Thomas et al. 1996; Thomas and Stoddart, 1975).

It turns out that the gene, called sgr (stay-green), encodes an enzyme that is localized to chloroplasts and plays a role in the degradation of chlorophyll during senescence and maturation of seeds. When the enzyme is defective chlorophyll isn't broken down and the tissue stays green.

This brings to three the number of Mendel's genes that have a known function. The wrinkled pea phenotype is caused by a defect in the gene for starch branching enzyme (Bhattacharya et al., 1990) [Biochemist Gregor Mendel Studied Starch Synthesis]. The tall/short phenotypes are caused by defects in the gene for gibberellin 3β-hydroxylase (Martin et al., 1997). Gibberellins are plant growth hormones.

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[Photo Credit: The photograph of mutant and wild-type pea seeds is taken from Figure 1 of Sato et al. (2007)]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2007) Cross-species identification of Mendel's I locus. Science 315: 73. [DOI: 10.1126/science.1132912]

Armstead, I., Donnison, I., Aubry, S., Harper, J., Hörtensteiner, S., James, C., Mani, J., Moffet, M., Ougham, H., Roberts, L., Thomas, A., Weeden, N., Thomas, H., and King, I. (2006) From crop to model to crop: identifying the genetic basis of the staygreen mutation in the Lolium/Festuca forage and amenity grasses. New Phytologist 172: 592-597.

Bhattacharyya, M. K., Smith, A. M., Ellis, T. H., Hedley, C., and Martin, C. (1990) The wrinkled-seed character of a pea described by Mendel is caused by a transposon-like insertion in a gene encoding starch-branching enzyme. Cell 60:115-122.

Martin D.N., Proebsting W.M., Hedden P. (1997) Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins. Proc. Natl. Acad. Sci. (USA) 94:8907–8911.

Sato Y., Morita R., Nishimura M., Yamaguchi H., and Kusaba M. (2007) Mendel’s green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway. Proc. Natl. Acad. Sci. (USA) 104: 14169-14174. [doi: 10.1073/pnas.0705521104].

Thomas, H. (1987) Sid: a Mendelian locus controlling thylakoid membrane disassembly in senescing leaves of Festuca pratensis. Theoretical and Applied Genetics 73: 551 555.

Thomas, H., Schellenberg, M., Vicentini, F., Matile, P. (1996) Gregor Mendel's green and yellow pea seeds. Botanica Acta 109: 3-4.

Thomas, H., and Stoddart, J.L. (1975) Separation of chlorophyll degradation from other senescence processes in leaves of a mutant genotype of meadow fescue (Festuca pratensis). Plant Physiology 56: 438-441.

A Fondness for Beetles

 
By now everyone has heard the story. There are almost as many species of beetle as all the rest of the insects put together. This is what prompted J.B.S. Haldane to say that God has "an inordinate fondness for beetles."

Now that's fine if you're an ordinary person, but if you're into taxonomy the huge diversity of beetles presents some really tough problems. Christopher Taylor describes one of the problems of classifying beetles in The Diversity of Ground Beetles.

Apparently God isn't the only one who likes beetles.

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Riding in the Car to Get Cherries

 
Riding in the Car to Get Cherries is a painting by Kanzi who also gave it the title. The painting is part of Apes Helping Apes.

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Schizophyllum commune Has 28,000 Distinct Sexes

 
This is the Botany Photo of the Day from The University of British Columbia Botanical Garden and Centre for Plant Research. The organism is the fungus Schizophyllum commune which is reported to have 28,000 sexes according to Tom Volk's Fungus of the Month for February 2000. Check out the Botany Photo of the Day blog for a much better picture.

In some parts of the world sex is legally restricted to arrangements involving single members of specified gender. I wonder which sexes of Schizophyllum commune would qualify? Personally, I think that members of sex 408 should be allowed to marry members of sex 12,105 but all other marriages are immoral and should be illegal.

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Botany Photo of the Day and the Oldest Living Organism

 
The oldest known organism on the planet is about 4,800 years old. Find out what that has to do with the Botany Photo of the Day.

It is often very hard to tell the difference between various species of pine. One of the distinguishing characteristics of this species (left) is that it has five needles per cluster. Other species have one, two, or three. I don't know if there is a species with four needles per cluster, or six.

Here's a question for all the adaptationists, is number of needles per fascicle an adaptation or is it just an allele that was fixed by accident? Is it an example of a morphological characteristic that is not an adaptaion?

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Which Animal Phylum Has the Most Species?

 
I bet almost all of you think it's Arthropoda since there are so many insects and especially beetles, which God was very fond of.¹

However, recent advances in taxonomy have suggested that there are one million species of nematode. This is about the same number of species as arthropods so the primacy of insects has been challenged.

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1. This is a reference to a famous quip by J.B.S. Haldane. When asked to name the most important thing he has learned about God from studying biology he reportedy said, "I'm not sure, but He seems to be inordinately fond of beetles."

[Photo Credit: Iowa State University Plant Disease]

Alternating Generations

 
Check out When Ferns Don't Look Like Ferns by Christopher Taylor on Catalogue of Organisms. The concept of alternating generations is an important concept that everyone should understand.

All plants undergo alternation of generation to a greater or lesser degree. Here's an interesting way to think about the concept from the Biology course notes at the University of Miami.

If animals were to undergo alternation of generations, then imagine that you are the diploid individual (sporophyte). Your mother, the gametophyte, would be haploid, and would look completely different from you (maybe like a SmurfTM). Your grandmother would be diploid, and look like you. Your own offspring would look like your mama the SmurfTM, your grandchildren would look like you, and so on.

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[Image Credit: Lewis & Clark]

This Is Not a Spider

 
It's not a spider but I'm not going to tell you what it is. In order to find out, you'll have to go to Catalogue of Organisms and read up on these species. At the same time you'll discover why Christopher Taylor posts an article with the title: In Which I Reveal Just How Much of a Freak I Am.

Good luck Christopher, I don't think that's a freaky thing to do. I think it's cool.

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I'm so glad I took Latin

 
It means I can understand Christopher Taylor at Catalogue of Organisms when he writes about The Gender of a Table.

Eat your hearts out, all you speakers of living languages!

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[Photo Credit: AP Photo]

Epigenetics Revisited

I'm still struggling with the concept of epigenetics [see Epigenetics]. Most of the modern definitions are so broad that they become meaningless. It's impossible to distinguish between epigenetics and plain old regulation of gene expression.

One of my colleagues, Craig Smibert, was so annoyed by my questions about epigenetics that he pointed me to a series of articles in Nature in the hopes it would shut me up. The relevant article is Perception of Epigenetics by Adrian Bird (Bird 2007).

It's not going to help. After describing several examples like methylation and histone modifications, Bird then points out that these modifications are not necessarily stable ...

So how accurately transmitted should an epigenetic mark be? Variation due to faulty copying is compounded by current evidence that all histone modifications, as well as DNA methylation itself, can be abruptly removed during development, thereby preventing the persistence of these modifications in a heritable epigenetic sense.

In other words, an epigenetic phenomenon doesn't really need to be heritable in order to qualify as epigenetic.

Furthermore, an epigenetic phenomenon doesn't even have to be passed on to progeny to qualify.

The restrictiveness of the heritable view of epigenetics is perhaps best illustrated by considering the brain. A growing idea is that functional states of neurons, which can be stable for many years, involve epigenetic phenomena, but these states will not be transmitted to daughter cells because almost all neurons never divide.

That's not very helpful. It's beginning to look like any activation or repression of eukaryotic genes will count as epigenetics. (According to some, it doesn't have to be eukaryotes. There is epigenetic regulation in bacteria as well, Casadesús and Low (2006).)

Here's the definition ...

Given that there are several existing definitions of epigenetics, it might be felt that another is the last thing we need. Conversely, there might be a place for a view of epigenetics that keeps the sense of the prevailing usages but avoids the constraints imposed by stringently requiring heritability. The following could be a unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states.

Does this include simple activation and repression of genes during development in the manner of control of lac operon expression? You betcha.

Bird may be thinking mostly of histone modifications and DNA methylation but he's well aware of the fact that these are often consequences, not causes, of activation and repression. He says,

For example, transcriptional activation through sequence-specific DNA-binding proteins brings in histone acetyltransferases, which then epigenetically adapt the promoter region for transcription (for histone acetyl groups, although ephemeral, would now be epigenetic).

So we're right back where we started, Craig will not be happy. Just about anything that modifies or regulates gene expression in eukaryotes (multicellular?) counts as epigenetics.

One could ask, what's the point? Why create a special word to describe regulation of gene expression in eukaryotes (and prokarotes) using mechanisms that we've known about for thirty years?

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Bird, A. (2007) Perceptions of epigenetics. Nature 447:396-398. [doi:10.1038/nature05913]

Casadesús, J. and Low, D. (2006) Epigenetic Gene Regulation in the Bacterial World. Microbiology and Molecular Biology Reviews 70:830-856. [doi:10.1128/MMBR.00016-06

Species-Scape

 
This is a snapshot of an animated picture of a "species-scape." The size of the organisms represent their relative abundance on Earth. See Species-Scape on the Cornell University website.

Another version is shown on Christopher Taylor's blog Catalogue of Organisms [The Species-Scape Picture].

Notice how insignificant mammals are, yet one particular species of mammal has the potential to ruin the entire planet for all other species.

Some groups seem to be missing, bryophytes (moss) for example. Can you find any others?

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