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Sunday diversion from earthquake news with some space science – and a little reminiscing from my Ph.D. studies.

At the end of second of the two videos below Chris Davis refers to ’the space weather forecast’, hence my title.

Basically, he’s talking about the magnetic atmosphere of the earth and the influence of the sun on it.

As everyone here knows I’m not an astronomer (I’m a computational biologist), but Chris explains what he’s doing so well I’m getting the picture too.

In the first video he’d dug up old paper recordings of atmospheric activity. Scientists are fond of datasets in their field. Dataset have all the clues to the mysteries they’d like to dig into and solve. You hate to see the stuff get thrown away or sit there idle.

Chris ponders how to add years of paper (film) records to the modern digital ones. It’s a problem in many other fields too, and brings up issues of data formats–even electronic data formats age and present problems in time, something people in my field deal with from time to time.

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Now that I think back, in a sense I’ve done a little of what Chris is up to here myself.

During my Ph.D. research I developed a database of zinc finger proteins, proteins with an array of small domains formed by binding a zinc ion that bound to DNA to regulate genes.

After I’d completed my database I was quizzed by a scientist who wondered how I had so many more examples of these proteins that he could find in the electronic databases. I’m not sure if I ever explained to him that I’d entered many of them by hand from paper publications.

In the earlier period of bioinformatics–even when the early databases were available–many experimental researchers didn’t submit their data to the databases. Most of these sequences were published as figures in the research papers. Short of writing to these researchers asking for their data it was just as easy for me to type them in manually, which I did. Being very dogged–as Ph.D. students often are–I tracked down zinc finger proteins all over the literature and manually transcribed them into the FASTA file format for my database.

In time the scientific journals, with some encouragement, adopted a policy that to present DNA (gene) sequence data in a research paper the researcher had to deposit the sequence in one of the international databases. With this in place, there’s now no need to go out and look for what might be in the electronic databases, as I did.

But back to space science. Below Chris talks about some of his work tracking solar events (e.g. flares) that affect the earth’s ionosphere:

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Other videos on Code for Life:

Capturing bodies – medical imaging data

On learning the sounds of a new (spoken) language

Understanding the brain through controlling it

Russell Doolittle on Life before Bioinformatics

Consumer brain-computer interface

Oliver Sacks on Hallucinations