Bench Press

If you’ve never used Google Earth, I’d recommend trying it out, at least once. For those of you not in the know, its an amazing piece of software which lets you access Google’s wealth of geographical and geological information (although with its layers feature, it also gives you access to the oceans, the moon, the sky, historical sites of interest, and Mars).

The magic of new, cheap and powerful technologies and information sources like Google Earth is that they can also be used to push additional experiments and discoveries. Widely available mathematical analysis tools like Mathematica let a professor figure out what instruments made up the mysterious “twang” at the beginning of the Beatles classic “It’s Been a Hard Day’s Night.” Advances in gaming and graphics technology make it possible for gaming consoles and personal computers to do sophisticated number-crunching. And, Google Earth helped make it possible for a team of students to take pictures from near-space for only $150.

More recently, Google Earth helped a team of researchers led by the University of the Witwatersrand’s Professor Lee Berger to find and unearth new fossil remains, including those of the newly discovered Australopithecus sediba (pictured right) in the Cradle of Humankind World Heritage Site in South Africa.

Berger and his associates used Google Earth to learn how to identify cave sites from satellite imagery and to help supplement on-foot exploration to map out ~500 previously unknown caves and, subsequently, 25 new fossil sites!

This discovery has been especially exciting as some have argued it could potentially be “the point from which the genus Homo [the genus we humans are a part of] arises” and “a good candidate for being the transitional species between the southern African ape-man Australopithecus africanus (like the Taung Child and Mrs. Ples) and either Homo habilis or even a director ancestor of Homo erectus (like Turkana Boy, Java man, or Peking man).”

Check out the University’s web coverage of the discovery as well as the Google blog’s coverage of the event as well as the video celebrating Professor Berger’s find (below):

(Image credit – University of the Witwatersrand website)

Science papers by Berger’s group: (1) and (2)

Happy belated 200th, Charles Darwin.

Charles Darwin brought to the field of biology a revolutionary insight into how species came about. But beyond merely synthesizing a  coherent theory of evolution, Darwin was also responsible for popularizing a way of conceptualizing evolution which continues to be used today: the evolutionary tree.

Darwin’s first (and quite possibly the first ever) evolutionary tree is depicted to the left (dated 1837, from Darwin’s First Notebook on Transmutation of Species on view at the Museum of Natural History in Manhattan) and is, almost ceremonially, directly underneath the words “I think”.

The tree depicts the relationships between a number of species in terms of how they are all related. And, while the concept itself is relatively simple, the actual tree itself is highly complex for three reasons.

First, as the number of species increases, it becomes much harder to generate complete and accurate evolutionary trees to cover all the possible evolutionary relationships. Knowing that A and B are related does not tell you if A and B are more closely related to each other than they are to C, for instance.

Secondly, Darwin’s tree only considered the possibility of branches – it never considered the possibility that branches may merge or that relationships other than branching out could exist. For instance, bacteria have at least three ways of obtaining genetic material through a method other than replicating:

• Transformation: a bacterium absorbs genetic material from its surroundings
• Conjugation: a bacterium exchanges genetic material with a neighboring bacterium
• Transduction: a virus inserts genetic material into the bacterium’s genetic code

Third, evidence linking two species in terms of an evolutionary tree is difficult to interpret. The challenge is that evolution occurs over millions of years – what we can see are end-results and fossils. What we don’t see is that evolution can change “directions” or affect different genes and characteristics differently over time.

So, what do we do? How do we present the richness of information encoded in an evolutionary tree, but updated with a contemporary understanding of evolutionary biology and genetics, and yet presented in a way which is actually useful and meaningful to scientists?

Enter Tree 2.0. Scientists (including Michael Sanderson’s group at the University of Arizona who developed the Paloverde software to visualize dense “tree of life”’s) have apparently partnered with web technology super-specialists Google and Adobe (HT: New York Times) to develop a new way of visualizing and storing the massive amounts of information needed to fully characterize the tree of life.

While very little in the way of details of the partnership have emerged, I think this is a clear example of where advances in computational and visualization technology can play in helping biologists better understand evolution, on three levels:

• First, sophisticated software can be used to help scientists crunch through the myriads of genetic data that needs to be understood in order to synthesize a proper evolutionary tree; it’s simply too difficult for humans and non-automated systems to sift through data from thousands of species at once to pick out all the relevant relationships; we posted before about how algorithms used to detect cheating may help in picking out evolutionary relationships – we probably need many more to detect and assemble the total tree of life structure
• Second, new technology and standards are needed to store the information within the tree to depict the types of relationships which can emerge between species (e.g. horizontal gene transfer, how certain genes have converged between species while others have diverged, etc)
• Third, visualization technology akin to what is used by Google Earth to depict rich and complex information quickly can help scientists quickly query and use to advance our understanding of biology – not to mention it would just look cool and be something everyone could easily browse

I can’t wait for what comes out of the collaboration with Google – and I do believe that this is the best birthday present Charles Darwin could ask for – even if he has to wait a little after his 200th birthday to get it.

(Image credit – Darwin’s tree: Wikipedia) (Image credit – Circle Tree of Life: Hillis and Bull laboratory)

Inspiring students to be interested in (or at least to value and respect) science is something which the scientific community has unfortunately passed on to under-prepared teachers. This has serious consequences. When leading US politicians can pander to the public by asserting that vaccines can cause autism or that fruit fly research is pointless, I would like to think that the scientific community would be scrambling to find ways to reach out to more properly educate people about why and how to think about science.

Allyson, over at the Systems Biology & Bioinformatics blog, recently wrote an interesting post about her volunteering experiences with the Teacher-Scientist Network which pairs teachers and scientists in an attempt to help educate children about science. The post is fascinating, but I think her tips for scientists reaching out to students are especially useful:

1. My method of using no text on the vast majority of the slides really worked. It was especially useful as it meant I could stop anywhere in my slides if I was running out of time, and the littlest ones were not distracted by trying to read the words rather than listening to me.
2. Pictures of fluffy, pretty, cute, or “gross” animals were very, very popular. The number of “Awwwws” I got when showing pictures of cats was astounding. Equally, all the older ones wanted to see my pictures of the newborn mice (pretty gross with no hair!), and all ages enjoyed trying to figure out what the photo of e.coli was.
3. As soon as you ask a question, they all raise their hands to answer it. Not sure when this stops, but I know that by the time I was in high school the teachers had a hard time prying any answers out of the majority of us! However, on Monday I was at a school where the eldest was 11, and they all wanted to contribute. So, ask them questions. I found there were two types: the question where I wanted to get an answer (such as “What traits make a good horse?” or “What do you think makes these two cats different?”) and the type where I just wanted them to feel included in the talk, and just wanted a show of hands (such as “How many of you have a cat?” or “Who has heard of diabetes?”).
4. Introduce some ethics, and show how scientists think very carefully before doing research. We talked about genes a lot, and how putting new genes in bugs like e.coli can help us, e.g. the human insulin gene into e.coli to help with diabetes. I told all the older kids that it wasn’t the tool that is a problem: a tool is neither good nor evil. It’s how that tool is used, and people need to make a fresh decision, and think about the benefits and downsides each time that tool is used. I said genetic modification is like a knife: it is neither good nor bad, and that scientists try very hard to make sure that it is used for the right reasons, and in a safe way.
5. Visually-arresting analogies: Even though DNA is a double-helix and not a spiral staircase, I found it a very useful analogy, especially for the younger ones.
6. My partnered teacher had prepared some slides to show the kids prior to my arrival. They dealt with Mr. Green Genes, the GFP-glowing cat. Some of the other teachers also talked to their kids about inheriting some of your traits from your mom, and some from your dad, and used the labradoodle as a visual aid. This prepped them for my talk, which I think was really helpful.
7. Make your talk inclusive. It keeps their interest, I think. When I showed pictures of cats, I included one picture of my own cat, and told them a little about her. I often asked them questions about if they had pets, or scientists in the family, or liked the look of a picture, or knew what something was.

I think Allyson makes a lot of great points. But, in keeping with the theme of this blog to talk about technology, I think we can add a few suggestions to her list:

• Put up a science website – The best learning happens outside of the classroom. Now, I don’t advocate scientists to turn their labs over to 8-year-olds, but I do think that giving students a resource to look at outside of class.
• Edit wiki’s - It’s astounding how many people use Google and/or Wikipedia to find information about science and medicine. This represents an incredible opportunity for the scientific community to properly inform the public — fail, and let vaccine fear-mongers, Creationists, global warming deniers, and their kind guide the public discussion.
• Put up online video - A few years ago, online videos were clunky and difficult to use. So you had an excuse back then to not put up videos on your website. Today? Different story. When YouTube is a household name, there is no excuse for people not to put up engaging demo videos — because people who don’t know what they’re talking about are.
• Use feeds - Twitter. Flickr. Del.icio.us. RSS. These are becoming increasingly more mainstream, especially among students, so scientists should learn to use them. Who knows, your picture of GFP-tagged Neurons may be what inspires the discoverer of the cure for Alzheimers?
• Interactive applications - Show the public what you’re researching in a way which actually speaks to them. No, don’t show them your NSF grant application, show them a Google Earth layer highlighting your research on Ancient Rome, the impact of global sea levels rising, or the beautiful nebula that you’re telescopes are pointing at. Present an applet which shows the beauty of a Lorentz attractor, or examples of simple machines in your household.