Discovering Biology in a Digital World

A ScienceOnline 2010 session mash-up review: Fact checking and trust

Tue, 19 Jan 2010 07:00:19 -0500

One of the many interesting sessions I attended at ScienceOnline 2010 (#scio10) covered the questions of trust and critical thinking.

Sitting in the audience, I couldn't help but think of a mash-up (like on Glee!) between this session the one on Fact checking.

Granted, I know I'm a nitpicky scientist with an obsession for minutiae but I kept hearing statements during the session that I either wondered about or I knew were completely wrong.

Here's our first mashup tweet from docfreeride from David Dobbs:

Writing 1st book, description of bit character in mid/late 60s... after book came out, found out she was 48. D'oh #scio10

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MLK day and making the world a better place

Mon, 18 Jan 2010 17:13:33 -0500

Have you ever wanted to volunteer your talents and help with fun projects like these:

* Refurbish computers for schools
* Teach students how to use popular software or online services
* Build a database for a nonprofit
* Help out in your school's computer lab
* Become an online mentor for students across the country

In the spirit of MLK day, Serve.gov is calling on educators and tech people to participate in connecting schools and non-profits with tech needs to those who can help. You can use the widget below to find projects in your area.

To quote Serve.gov, and Dr. King:

"Life's most persistent and urgent question is: what are you doing for others?"

BTW - MLK day is only the beginning. The projects will last more than one day.

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Eight things I learned at ScienceOnline 2010 #scio10

Mon, 18 Jan 2010 14:55:01 -0500

ScienceOnline 2010 was one of the most amazing meetings I've attended in a long time and it's going to take some time to process it all, but in the mean time, it seems other bloggers (phylogenomics, CogSci, and Ed) have started one of those meme things and so, here goes.

At ScienceOnline 2010, I learned:

More than I ever wanted to know about the intimate details of duck sex. courtesy of Carl Zimmer!

Likewise for dolphins. courtesy of Kevin Zelnio!

Why the instantiation of Baked Alaska will never be as good as the Platonic Ideal. (courtesy of Dr. Freeride)

What DNA Jesus would sequence (courtesy of phylogenomics)

The number of times a day that rats have sex. (courtesy of Rebecca Skloot's quiz)

more than I ever expected to know about an SP3! (courtesy of Ms. Baker's wonderful students)

Water marbles aren't real (but look cool!) and If you're going to give someone a diamond, don't go by the structure in PubChem.(courtesy of ChemSpider)

That meeting all you - bloggers, educators, librarians, mathematicians, journalists, scientists - in person would be more wonderful than I could imagine.

Thank you all and extreme kudos to Bora and Aton! I can hardly wait for ScienceOnline 2011!

Hey readers, did anyone learn anything unexpected either at ScienceOnline 2010 or via all the social media? Read the comments on this post...

No room for your body at ScienceOnline 2010? Follow along in SecondLife!

Fri, 15 Jan 2010 10:15:46 -0500

Okay, I'll grant that visiting Second Life can seem a bit uncomfortable, especially at first, but it does open some new doors and present an alternative to travel.

In flu season, virtual visits could be the next best thing to being there. (Yikes, that sounds like an ad. No more yahoo news for me!)

Here's where you can attend ScienceOnline 2010 in Second Life (http://slurl.com/secondlife/Research%20Triangle%20Park/128/129/25).

The next excuse might be that you don't know how to use Second Life or what to do. Never fear. That's a solvable problem.

I have a primer on attending a conference in Second Life. I've done it and survived.

Jump right in! The water's fine.

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Citizen Science and Digital Biology: ScienceOnline 2010

Wed, 13 Jan 2010 15:11:25 -0500

Is there a place for citizen scientists in the world of digital biology?

Many of the citizen science projects that I've been reading about have a common structure. There's a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting data.

After the data are collected, they end up in a database somewhere and the University researchers analyze them and write papers. At least that's my impression so far.

It seems to me, that with all kinds of databases out there, on-line, there should be plenty of opportunity for both citizens and student groups to participate in analyzing the data.

But do they?

#scio10

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On the importance of citizen science

Wed, 13 Jan 2010 12:24:04 -0500

A common theme I hear in talks on personalized medicine, is that increased access to genomic data and medical literature are changing the relationship between doctors and patients. Patients are through being passive recipients of paternalistic health care. They are demanding to participate and be treated as partners with health care providers.

Citizen science can serve a similar role.

Just as personalized medicine is starting to make it possible for individuals to monitor and participate in their own personal health, citizen science is making it possible for people to participate and monitor the health of their communities.

With our environment endangered by growing concentrations of CO2, and global climate change happening faster than predicted, these efforts are timely and greatly needed. The best tool we have for fighting ignorance is to get citizens involved in science. I'm sure we'd have fewer people believing silly things on Fox news if they were doing experiments and looking at the world outside instead of listening to ideological nonsense on TV.

Communities don't have to be passive receptacles for pollution and waste. They don't have to sacrifice biodiversity for development or clean water and air for jobs. They can make a choice.

Making good environmental choices however, depends on information. You can't protect or monitor the environment without knowing what's in it. Citizen science empowers communities by making the scientific process transparent and allowing citizens to become involved.

Thank you all for posting an amazing collection of links to citizen science projects going on throughout the world. I never realized there were so many projects out there. It's encouraging to know there are so people out there who care about our world.

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From science research to science teaching: how to pay for a change

Tue, 12 Jan 2010 10:05:34 -0500

When I was a post-doc, I spent a few months seriously thinking about changing careers and teaching high school. I might have followed through on that plan, too, but I didn't know how to pay for it.

Today, if you have a background in science, technology, math, or engineering, you can retrain to become a teacher and the National Science Foundation will help. The Robert Noyce scholarship program has funds to help ease that transition to the classroom.

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Citizen Science: all fun and no data? ScienceOnline 2010

Mon, 11 Jan 2010 14:10:28 -0500

Do citizen science efforts ever go beyond "feel good" contributions? Do the data get published in peer-reviewed journals?

In an earlier post, I started a list of citizen science projects that allow students to make a contribution. Many commentors are graciously adding to that list and I thank you all! I'm glad to learn there are so many interesting projects and ways for people to get involved. Science is so empowering!

My question today concerns things like outcomes and deliverables. We'd like to assume that good things are coming from citizen science because people are involved, but I don't know if that's really true and being a scientist, I want to avoid over-doing the assumptions.

Does the research from citizen science ever get published?

Last Wednesday, at the University of Washington, I learned about one such study. If you know of others, I'd love to see citations in the comments.

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In the cloud, Next Gen DNA sequencing computes

Fri, 08 Jan 2010 18:24:50 -0500

These days, DNA sequencing happens in one of three ways.

In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this.

Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can learn more about this and go on a virtual tour in this nice video from Washington University).

At the same time, Universities expanded their core service laboratories and these labs began offering a greater number of sequencing services. Today, much the non-genome center sequencing happens in core labs. Scientists obtain samples and send them to the core labs. The core lab staff prepare the samples, carry out the sequencing reactions, and deliver data to their customers.

This system worked fine until the Next Generation DNA sequencing (NGS) instruments came along.

This January issue of Nature Biotechnology has two articles (1, 2) that address the role cloud computing can play in helping smaller laboratories cope with the large volumes of data produced by NGS.

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Citizen Science projects on-line

Fri, 08 Jan 2010 14:42:15 -0500

Next Saturday afternoon, at ScienceOnline2010, the science goddess, the chemspider, and I will be presenting a workshop on getting students involved in citizen science.

In preparation, I'm compiling a set of links to projects that involve students in citizen science. If you know of any good citizen science efforts, please share them in the comments.

Here we go!

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Can you spot the mistake?

Thu, 07 Jan 2010 21:24:31 -0500

This month's cover of The Scientist has a mistake that makes me cringe.

Can you spot what's wrong?

And they call themselves "The Scientist" humph!

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Curious about personal genomics?

Thu, 07 Jan 2010 13:11:14 -0500

Blaine Bettinger has an absolutely wonderful post where he compares his results for type 2 diabetes from 23andMe and DeCODEme.

I really liked his post and I appreciated the way he showed the data from the two companies and elaborated on their interpretation of his genotype and his risk.

Interestingly, his story goes beyond a simple relationship, where one base changes, one amino acid changes, and voila! you've got the disease.

Bettinger describes what happens when there are changes in multiple genes and how those changes can have a cumulative effect on evaluating the risk of developing a disease.

H/T The Daily Scan

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Digital biologists, bioinformaticists, and computational biologists: more thoughts on the question of names

Wed, 06 Jan 2010 18:06:01 -0500

"What's in a name? that which we call a rose
By any other name would smell as sweet"

- Juliet, from Romeo and Juliet by William Shakespeare

I realized from the comments on my previous post and from Mike's post that more explanations were in order.

It seems we have two topics - why do we need a new name at all? and why the current names (biologist, computational biologist, bioinformatician, etc.) don't work. What really distinguishes a digital biologist from a regular, garden variety biologist? Why isn't a digital biologist a computational biologist?

So, I brought along two "show and tell" items today, a picture and job posting, to help me explain.

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Bruce Alberts at the Seattle Aquarium and UW

Mon, 04 Jan 2010 13:41:24 -0500

If you're in Seattle, Dr. Bruce Alberts will be talking tomorrow night (Jan 5th) at the Seattle Aquarium on science education and the role that scientists play.

There are also some really interesting talks at a day-long workshop, Wednesday (Jan 6th) at the UW South Campus Center.

The details and registration info are below:

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

Tuesday:

COSEE Ocean Learning Communities & Washington SeaGrant Present

Redefining Science Education and the
Roles that Scientists Play in Society

Dr. Bruce Alberts

Tuesday, January 5th, 6:30 to 9pm, Seattle Aquarium Great Hall

To register for this event, please go to: http://www.coseeolc.net/for-scientists.cfm

Wednesday:

Some of Wednesday workshop highlights cover using citizen science for scientific gain, and your education and outreach requirements, leveraging your lab through outreach, and communicating science to the public and media.

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You may think you're African-American, but...

Mon, 04 Jan 2010 12:13:32 -0500

An NSF post on Twitter this morning described an interesting study from the University of Pennsylanvia and Cornell University, that found that some people who call themselves "African Americans" may only be 1% West African, according to their DNA.

The University of Pennsylvania press release contains other interesting findings as well. 365 individuals were studied and 300,000 genetic markers were examined.

Some of the findings were:

If you're African American, the genes most likely to have an African origin are those on your X chromosome. The article didn't mention it, but I would guess that also be true of your mitochondrial genes since X chromosomes and mitochondria are inherited from your mother.
The median amount of European DNA in African Americans was 18.5 percent.
The researchers were able to distinguish between genes that came from different parts of West Africa. This finding will probably help improve the accuracy of personal ancestry tests and give people better information about the homes of their ancestors.

One bit of frustration, though. I tried to find the original article and the most recent paper in PubMed was from May. I wish press releases would include links to these. Even the title of the paper would be nice.

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