Thursday, May 2, 2013

Carnival of Evolution #59: A letter from the Doctor



Dear Wilfred,

Are you still watching the stars with your new telescope?  I bet you can see what I see outside the windows of my TARDIS. The star you're searching for is still there, it just tends to fall out of view occasionally. 

Do you remember how you always said how you'd love to be travelling with me again through the skies? I envy you right now, living on this wonderful planet in your lovely little house treating yourself to a flask of tea on your porch while you look at the stars. They're beautiful, I would know, I live amongst them and I've traveled to so many. I’ve seen galaxies born and fading away.

But what is it with your little blue planet that makes me coming back so often?  Is it its people that are so brilliant and clever and funny and everything I'd ever want in companions? I don’t know and that means a lot to somebody who has been at the beginning and the end of the universe. Or maybe it’s the way how life evolved since the days your planet was not more than just another rock in a sidearm of an inconspicuous galaxy. 

Oh, you humans are so clever. Take this evolution thing. I watched you over the last month.  It is fascinating want you are working on and what you have found out so far (and what not). Who would have thought how much playing games can advance your knowledge? So much more...

...Let me see - there was the question if humans think that cancer can evolve. Here a brilliant answer from students of Emory University:



At Bioblog by Biotunes I found another piece on the fact that tumors are heterogeneous populations of cells that evolve, and should be treated as such.

Poor little mortal humans, a lot of what I learned revolved around your own species and people reflected on an old question tested by research (is size really that important?), or on an old debate about why menopause exists, and finally you wonder how humans developed the ability to talk about all this.

So many fascinating creatures inhabit your little blue ball. There is the fossa with its unique mating system. During the breeding season large numbers of males gather at traditional mating trees which are occupied by small groups of up to three females. Another piece in the puzzle of the evolution of group-living from solitary ancestors as some male fossas go it alone while others form associations.

Or the little mites that can teach us something about the theory of harvest-induced selection, a framework in which it is thought that high trait-selective harvesting rates lead to a change in the frequency of traits in a population, diminishing the type of animal or plant that the harvester is seeking.

Or the unique mud snails unique in New Zealand with sexual and asexual individuals of the same species teaching you something about how sexual and asexual reproduction affect the genome.

Or moths that might play a role in the pollinator-mediated speciation of the Joshua tree. Or how the salt-loving halophile bacteria evolved through massive horizontal gene transfer. Or that whales and monkeys helped you to understand that animals can learn from each other in ways that create different cultures in the wild.

Ah, yes, and the coelacanth genome has been sequenced. Great news, but a couple of earthlings stumbled over the idea of them evolving slowly, questioning the interpretation of the data, while others simply celebrated the accomplishment.

You wonder if evolution is predictable and if results are unpredictable, does it make them any less true?


I have so much enjoyed reading about the old thinkers such as Huxley, Williams, Bintliff and Gould, and this new book on randomness in evolution. Marc Srour is not the only one wondering why there is such a kerfuffle about this as evolution has a significant random component. Mutations can be random, genetic drift is random and there is hopefully no doubt that both play a big role in the evolution of species. Well, there is but don't get me started on this group of inveterate ignorants. You have a couple of eloquent, outspoken, wise proponents of reason that can deal with them much better. By the way, don't miss this one:






It's sort of quiet...The TARDIS and I have decided to be alone for a while. Don't want to cause too much trouble (you are very good in that without me)! We also have a paradox to solve. Who is she?

Well...must be off now...got things to do and shelves to put up!

You'll see me again one day. Until Then...keep watching!

Your ever grateful and faithful friend,

The Doctor.



Thanks to everyone who contributed to this month's Carnival of Evolution (CoE)! Want to submit posts for next month? Go to the BlogCarnivals form. Just as importantly, the Carnival always needs hosts! If you'd like to host the Carnival, please send an email to Bjørn Østman (I think there is still no host for the coming 60th Carnival).

CoE on Facebook (https://www.facebook.com/pages/Carnival-of-Evolution/181930561831085),
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CoE blog (http://carnivalofevolution.blogspot.com)

Wednesday, May 1, 2013

Genome Socks

Did you see my post on the Mongolian Death Worm? The specimen photo that came with it showed some mastery in the art of knitting. I am not into knitting so much. My abilities in this craft are extremely limited. More than 25 years ago I was able to produce approximately half a shawl but that was it.

However, I do admire all these knitting masters that can produce pretty much everything and come up with new knitting patterns.

I have been made aware that DNA has also found its way into knitting design. Here I present the Genome Socks (Meema Spadola, 2007):

While watching a TV documentary about human reproduction, Meema noticed how much human DNA resembles a knitted cable. In honor of her first child, she added her version of a DNA cable chart to these charming toe-up socks. 

This strikingly beautiful sock pattern consists of a cabled twist that goes down the center, making for a remarkable design. Perhaps Meema Spadola's unique inspiration will speak to you as well, making this hand knit sock a cozy reminder of those closest to you.
 
The knitting pattern is open access and if you are interested you can download the pdf here.

Maybe we should show Meema Spadola some DNA Barcodes.


h/t Pat Shaver

Tuesday, April 30, 2013

DNA Barcoding Online Course

One of the projects that currently keep me busy is the development of an online course that introduces attendees to the principles of DNA Barcoding. We are working closely with our experts for distance education here at the UofG and this week is the start of the advertisement campaign for the first offering. This course is an exclusively web-based course which is offered over an eight week period starting on July 8th. On average, six to eight hours of study time are required each week to study the course material which will consist of reading, audio and video material. Participants will have weekly assignments/quizzes and have plenty of opportunities to participate at discussions that are happening in designated chatrooms. The number of participants is limited to ensure adequate mentoring by the instructor.


I am a big fan of distance learning as it provides access to learning when the source of information and the learners are separated by time and distance, or even both. Especially its asynchronous nature makes it very attractive to many as learning is self-paced and allows participants to engage in the exchange of ideas or information without the dependency of other participants involvement at the same time or the need to show up at a particular time for a lecture or seminar. It requires some learning skills and self discipline though.

Eventually this will hopefully develop into a full university course that includes a suite of modules and a hands-on unit. However, first things first. We will start with the Introduction to DNA Barcoding Course in July. I am currently working on the course content and I will also be the instructor.

If you are interested please have a look at www.dnabarcodingcourses.com. The site details course content, tuition fees, requirements, etc.

Coming this week!

The DNA Barcoding blog is the proud host of the 59th Carnival of Evolution.

In case you don't know what the Carnival is all about:

Do you care about the science behind evolution? Do you marvel at the tiny molecular machines spewing out coded messages to the microscopic inhabitants of your own bodied world? Do you grow irate at the ignorance pushers and the disintegration of evolution education in the modern world? Do you like to stay abreast of current topics and scientific findings in the study of the organismal existences surrounding us or those long gone?

If so, this is the blog carnival for you. (Don't know what a "blog carnival" is? Read this.)




I am working on my hopefully creative contribution. Stay tuned.

Friday, April 26, 2013

60 schools later

Today was the last day of school visits with the BIOBus for our School Malaise Trap program. 

Now we have 83 traps in 60 schools and a few adjacent National Parks and Conservation Areas. They are up and running since Monday and will hopefully fill up quickly. One more week and all those samples will come back. Then the big sorting, imaging, sub-sampling and sequencing will begin. All schools need their results back by early June.


Meet our Team! These folks have been on the school visits and will be working hard to barcode perhaps some 20 000 samples collected over two weeks.


Thursday, April 25, 2013

B for Brazil

The second stop on my virtual journey through the DNA Barcode cosmos is Brazil. 

If you are interested in Brazil's DNA Barcoding efforts the best way to start is having a look at the BrBOL website from which I stole this pretty cool banner image. 

Home to 60% of the Amazon Rainforest, which accounts for approximately one-tenth of all species in the world, Brazil is considered to have the greatest biodiversity of any country on the planet. It is also the country with the most known species of plants (55,000), freshwater fish (3000) and mammals (700). With 170,000 to 200,000 species Brazil is home to around 9.5% of all the species worldwide but researchers have estimated the country's total biota at 1.8 million species. A quick search on BOLD told me that about 5,000 of those species have been assigned a DNA Barcode.

A Brazilian consortium with almost one hundred member institutions aims to increase this number considerably. The Brazilian Barcode of Life (BrBOL) project consists of 11 projects aimed at different taxonomic groups and scientific fields.

As I am still very much into ichthyology I had a closer look the current status for the fishes of Brazil for which there is also a BrBOL project that plans to generate DNA Barcodes for 2,100 species. A search for "Brazil" and "Actinopterygii" in BOLD's public record section showed 4192 public records forming 646 BINs which likely represent species. I believe it is fair to say that 600 species of the Brazilian bony fish have been barcoded and are publicly accessible. More than 28% of the planned work has been done already and for those that are interested in more detail there is an interesting paper that was recently published in BMC Genetics.

More than one-fifth of the Amazon Rainforest in Brazil has been completely destroyed, and more than 70 mammals are endangered. The threat of extinction comes from several sources, mostly deforestation and poaching. Currently, 15.8 million acres of tropical ecosystem have been completely eliminated to farm sugarcane for ethanol production. There are plans to plant an additional 4.5 million acres during the next four years. 70-85% of Brazil's transportation energy is derived from ethanol, or various mixtures of ethanol and petroleum-based fuels. Only about 15-20% comes from imported petroleum. This massive national biofuel program has been devastating to tropical wildlife diversity, and to the global climate.

A national program such as BrBOL represents a modern approach to speed up cataloging a country's biodiversity.  The more we know about what lives around us the more we appreciate and care about it. And only that will motivate us to be creative when it comes to protect it.


Wednesday, April 24, 2013

Engaging kids in science

Five reasons why I really enjoy these school outreach activitites: