Posted: 20 Sep 2008 08:08 PM CDT
Hey high school teachers! Are your students interested in the brain?
Three winners will win all-expense-paid trips to present their work in a poster session in Seattle at the 2009 Annual Meeting of the American Academy of Neurology. Their teachers get to come too! I can tell you, Seattle is a fun place to visit.
Low tide at Golden Gardens, July 2008
Plus, three student winners will get $1000 in cash in addition to the trip.
Find out more at www.aan.com/achieve.Read the comments on this post...
Posted: 20 Sep 2008 09:17 AM CDT
I just read this post at Gene Expression.
The opening paragraph is:
(emphasis from the link).
I don’t know what to say to that, really. You have freedom of expression, but you cannot say anything that is insulting?
Posted: 20 Sep 2008 09:01 AM CDT
Didn’t they already do roughly the same thing back in 2005?
The Spanish flu
The Spanish flu is a nasty virus. It’s an influenza that from 1918 to 1920 killed between 20 and 100 million people worldwide. In comparison, only about 20 million were killed in the entire First World War, so if you look at deaths per year in the early 20th century, it is the Spanish flu that will show a spike, more than the war.
It was a truly global epidemic. It is called the Spanish flu because the Spanish press wrote about it (most other countries had the press censored during the war, but Spain wasn’t involved in the war), but really it was found everywhere across the globe, with as much as 20% of the world population infected and killing 2.5-5% of the worldwide population.
With the danger of sounding like a mad scientist, I am really fascinated by this epidemic.
Digging up victims, to try to recreate the flu, might not be the brightest idea ever, but the reason people want to do this is to learn more about influenza epidemics. With all the scare about the bird flu, we might need all the knowledge about influenza we can get.
There is absolutely nothing preventing a new worldwide epidemic like the Spanish flu, and we really want to be prepared if that happens.
Reconstructing the Spanish flu
I’m not sure exactly what the plan is for Sir Mark Sykes — the guy they are digging up now — but what they did in the Science paper was to re-create the Spanish flu virus from the samples they got there.
They managed to get the sequence of the Spanish flu virus genome and then combine it with (the modern) H1N1 virus, to get viruses with more or less of the Spanish flu in them. These they then grew to learn about the virus.
Knowing the sequence of the Spanish flu will let us analyse the evolution of it and maybe tell us where it came from (jumping from another species; recombining or mutating to that particular variant; etc.)
Actually growing the virus lets us experiment with it, learn how deadly it really is and how it works (see e.g. this story), maybe develop vaccines (not that that would be much help against a new epidemic variant, but we might learn something from it).
T. M. Tumpey, Christopher F. Basler, Patricia V. Aguilar, Hui Zeng, Alicia Solórzano, David E. Swayne, Nancy J. Cox, Jacqueline M. Katz, Jeffery K. Taubenberger, Peter Palese, Adolfo García-Sastre (2005). Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus Science, 310 (5745), 77-80 DOI: 10.1126/science.1119392
Posted: 20 Sep 2008 06:17 AM CDT
The Spanish Flu killed an estimated 20 to 100 million people across the globe in the years 1918-1920. Towards the end of the pandemic soldier and diplomat Sir Mark Sykes was killed by the virus and buried in a lead coffin.
With lingering fears of a possible bird flu (H5N1) pandemic, and with a dearth of samples from Spanish flu (a subtype of avian flu H1N1), he has recently been exhumed by scientists -- paging Dr. Frankenstein!
Taking tissues from his body, well preserved by his lead casket, the team is trying to learn more about the Spanish flu and how it killed him in the hope of transferring that knowledge to the understanding and treatment of H5N1. His body was re-interred after removing samples in a special laboratory, airtight to avoid any risk of contamination.
Posted: 20 Sep 2008 06:12 AM CDT
There’s a very interesting post on Google’s blog: The Future of Mobile.
Where is the mobile phone heading? How will it change the future?
Posted: 20 Sep 2008 04:24 AM CDT
It is a quiet Saturday morning. I am slightly hung over. My scripts are scanning through a genome and I am just sitting here waiting for them to finish with nothing much to do.
So I started thinking. How much does it actually cost to get a new genome, these days? If I wanted my own genome sequenced, how much would I have to pay and how long would it take to get it?
The (first) human genome project cost about $3 billion (about $300 million for Celera) and took about 10 years (1990 to 2000 for the first assembly, then three more years for completion, but let’s just say 10 here).
Now they want to sequence 1000 humans in three years for $30-50 million. Next generation sequencing techniques lowered the cost of that project by a factor of 10. Of course, it helps a lot to have the original genome to assemble up against as well.
I’ve asked Roald about the price for the first “arab genome”, but I haven’t gotten an answer yet. I guess he doesn’t work Saturday mornings ;-)
The genomics age
Some people say we are in the “post genomic” age, but really we are just in the middle of the genomics age if anything. We are seeing an explosion in new genomes sequenced.
From GOLD you can download some statistics on genome projects. Plotting the total number of genomes published against years, you clearly see the explosive increase in data:
It is even more impressive when you consider all genome projects and not just the published genomes so far:
Statistics at NCBI says we have 22 complete Eukaryote genomes, 161 with a draft assembly and 176 in progress. For Prokaryotes the numbers are 749 complete, 540 draft and 676 in progress.
It doesn’t say anything about the cost of sequencing genomes, though, so I don’t know how much the price has dropped over time.
I was a bit surprised to learn that the only mammals considered complete are mouse and man. There are 22 mammals with draft assemblies and another 26 in progress. Will the draft genomes be completed any time soon?
Posted: 19 Sep 2008 11:01 PM CDT
Our friendly government lists some available genetic tests: these are the real deal, high penetrance tests for things you already have or conditions you will get.
Unlike Sergey Brin, I don’t particularly care about a mutation that gives me a slightly increased risk for a disease. That’s not significant, though if the placebo effect of a 23andMe test gets you to exercise more, congratulations.
However, if I knew I was bound to get Huntington’s Disease, I would really live my life differently with the moral superiority provided by knowing that my time on this earth was sadly limited by my genetics. I would just take things so much more seriously than all those suckers blissfully unaware of the cold, cruel nature of reality.
For now, it’s prohibitively expensive to get every single genetic test. With how much I would have to spend today to get 50 patented tests I would be better off waiting a year and getting my genome sequenced, then analyzing the data myself to (illegally?) check for every high penetrance mutation.
Posted: 19 Sep 2008 07:19 PM CDT
This was in response to a question on our abilities to make sense of complex data. I am very curious about how futuristic, or should we say modern since they’re here, will help our abilities to manipulate data, visualize it, etc. We have already seen the Google Maps API utilized to build genome browsers, and there is the stuff that Andrew has done. I have had the chance to see some very excellent visualizations, but they tend to have poor UIs and interaction models. That’s where I suspect we are going to see the most innovation in the coming years.
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Posted: 19 Sep 2008 07:10 AM CDT
No, contrary to popular belief no aliens are involved in my longest blog silence in a long time. Thanks to a hectic road trip, mostly at Web 2.0 Expo, haven’t had much of a chance to write about anything.
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