Monthly Archives: March 2012

Representative Cummings's office

ASBMB Hill Day: Part 2

Day number two of the ASMBM hill visit was busy, busy, busy. Each group of two students/postdocs and one or two PAAC members grabbed a light breakfast, and then it was off on the Metro to the Senate/Congressional offices.

Representative Cummings's office

Something I was not ready for was the actual size of the congressional offices. Some are really, really tiny, and others (especially the Senators’ offices) are rather large. In the older buildings, there are obvious additions – such as power outlets that protrude from the middle of the floor about three inches. Other offices have comfortable appointments such as couches and meeting areas. In the Hart Senate office building, there is a striking sculpture that looms in a sunny atrium. People seemed to have mixed opinions, but I really like it.

Pork barrel spending or support of the humanities?

Overall, even though it was tiring, it was great to meet with the staff of many congressional offices. The staff were all very well informed and well spoken. Most agreed with our message of funding the NIH at $32 billion for FY2013. Most also felt that this will be tough to make work during an election year. I also learned more about the details surrounding sequestration.

We were not able to meet directly with any senators or congressional representatives, except for Rep. Rush Holt from New Jersey’s 12th district. Rep. Holt was a keynote speaker for the AAAS FY2013 R&D seminar, which we were able to attend, and which was very informative.

Rep. Holt (NJ-12) shakes hands with Ann McCabe

The consensus among most staffers is that NIH funding comes back to the US economy many times over, and that under-funding the NIH for the past decade has been a mistake. After setting out to double the NIH budget over the course of 12 years with 6% increases, which was a bipartisan effort initiated by the Senate Republicans, funding efforts to the NIH have stopped. The president’s budget for this year calls for flat-funding which does not even account for a ~3% inflation.

We can not continue to let NIH funding stagnate. For PhD researchers, the average age for obtaining your first R01 is now over 42. This means that young and sometimes innovative research scientists are missing their peak period of productivity. With China increasing funding for science research and education over the past decade,  the United States needs to worry about our international competitiveness.

ASBMB Hill Day: Part 1

Day one of the ASBMB hill day was comprised of checking in to the hotel and attending an informational seminar about legislative procedure – School House Rock style. Tomorrow will be not only busy with meetings, but there will also be lots of people on the Hill for the “ObamaCare” hearings. We learned which Senators and Representatives we would be meeting with, and then proceded to have dinner at CESCO ostaria - which was quite good. Then off to bed, for tomorrow will bring lots of walking and talking…

Obamacare protesters in front of the Supreme Court

Chewy dogs? Add some pulp!

I intended to write about this earlier in the week, but now it has been picked up by other sources. An article I read in Scientific American mentions that researchers have figured out a way to replace the saturated fats in hot dogs with an emulsion of ethyl cellulose. By performing a bit of Wikipedia research, I found that ethyl cellulose is already used and approved by the FDA as an food emulsifier. The more interesting prospect is that the researchers are replacing a component of a complex food. It speaks volumes about the already processed nature of hot dogs that someone can just extract all the saturated fat from one and replace it with a different compound without completely ruining the hot dog experience. Science!

Source - http://www.scientificamerican.com/article.cfm?id=something-to-chew-on

Genomics + GPUs on the horizon

While most people may not consider computer gaming a scientific endeavor, keeping up with the latest computer gaming technology is exactly what some researchers are doing. Specifically, the graphics cards, or “GPUs”, are being used to speed up calculations that would normally take a vast amount of time on a CPU. Typically, these calculations are somewhat simple, but extremely repetitive. This is what a graphics processor is optimized for – rendering many simple bits and pieces of a game extremely rapidly (higher “frame rates” are universally sought by gamers).
A recent paper in the journal Bioinformatics outlines a short read sequence aligner that runs its calculations on GPUs at roughly an order of magnitude faster than the state of the art CPU based aligners. The SOAP3 aligner has an advantage in aligning sequencing reads with multiple mismatches, which can be computationally intensive for the other aligners. In addition, SOAP3 excels at aligning larger sequencing runs; an advantage that will become more important as the total cost of sequencing drops, and higher quality sequence is generated.
Along with the trend of increasing GPU programming in bioinformatics tools, GPUs are becoming more efficient. These advances may make possible a one business day genome sequence, alignment, and variant analysis. “Genomics lab”, meet phlebotomy lab.
Source – Liu C-M, Wong T, Wu E, Luo R, Yiu S-M, Li Y, et al. SOAP3: Ultra-Fast GPU-Based Parallel Alignment Tool for Short Reads. Bioinformatics. 2012 Mar 15;28(6):878–9.
Source – Engadget.com

Salzberg stakes creationists

In a recent post on his blog at Forbes, Steven Salzberg elaborates on the cover image for a new textbook, and uses “leaf insects” as an example of strong evidence in support of evolution. He points out that there is growing support for evolution with younger Americans.

So perhaps in another hundred years or so, Americans will start to “get” evolution. But it might take longer: apparently 18% of Americans still believe that the sun revolves around the earth.  So it’s taken us 500 years to get to 80% for that one.

Source - http://blogs.forbes.com/stevensalzberg/

A discussion of open-access publishing and comments

Faculty of 1000 Research has an intelligent post about the current debate about the future of open-access scientific publishing. The author also touches on the idea that scientific commentary is sometimes not useful in its current state, and that commentary might move in a similar direction as blogging systems.

I’m sure it’s something we’ve all experienced ourselves – ‘The Good, The Bad, and The Ugly’ of comments, if you will. What is the alternative? Disable commenting altogether, as some people do? What about ‘free speech’?

 

Source - http://f1000research.com/

A manifesto on science education

 

While browsing (stalking) the online presences of the other ASBMB hill day participants, I found this entry in Kristy Lamb‘s blog. It’s a well-formed thought about communicating science with “laypeople”, and why it isn’t working very well (out science education failures).

 

It’s almost a call to arms, to take off the lab coats and put down the furiously scribbling pens, leave the lab on a semi-regular basis, and take up conversation with some people who haven’t thought about science lately.

Source - http://thescientificsheep.wordpress.com/2011/10/15/hello-world/

Nanopore sequencing and the future of personal genomics.

Any person who has seen the movie Gattaca knows the future of human genomics involves getting a neat little printout of our genetic strengths and weaknesses. Also, it involves lots of beautiful actors. Many people would rightly agree that our future personal genomics readouts will look a lot more like a used car inspection and less like the US tax code, though, to get there will take a more comprehensive understanding of functional genomics, as well as more and cheaper genomic data.

The many labs that collaborated together to publish the first drafts of the human genome spent thousands of hours, and many millions of dollars just to assemble one personal genome. Now, Oxford Nanopore is bringing a new sequencing technology to market that promises a $1000 genome in under one day. I think that’s incredible. These sequencers also have embedded computers that start analyzing the sequence in real time. There will even be a model that is similar in size and function to a USB flash drive.

I couldn’t find any publications with any data from the GridION system the company currently produces, but it will be interesting to see what the error rates and throughput on these machines are like.

ASBMB capitol hill day.

Last week I was very excited to learn that I am selected for this year’s ASBMB capitol hill day visit. March 26th-27th I will have the opportunity to travel to DC and meet with congressional representatives from the Mid-Atlantic region. Amtrak tickets are booked, and I’m ready to go!