Posts tagged ‘funding’

There are  budget cuts and layoff everywhere. We have already heard before that Florida State dissolved academic departments to fight the financial crisis. And now the University of Florida is going to eliminate Computer Science Department, a really disturbing move. From Steven Salzberg’s blog:

The University of Florida announced this past week that it was dropping its computer science department, which will allow it to save about $1.7 million.  The school is eliminating all funding for teaching assistants in computer science, cutting the graduate and research programs entirely, and moving the tattered remnants into other departments.

 

I am so envious of these people who can build a useful machine by LEGO which can save money. The building part itself must be a lot of fun!


From boingboing.net:  LEGO robots in the laboratory

Stem cells/ regeneration

  1. Makkar RR, Smith RR, Cheng K, Malliaras K, Thomson LE, Berman D, Czer LS, Marbán L, Mendizabal A, Johnston PV, Russell SD, Schuleri KH, Lardo AC, Gerstenblith G, Marbán E. Intracoronary cardiosphere-derived cells for heart regeneration after myocardial infarction (CADUCEUS): a prospective, randomised phase 1 trial. Lancet. 2012 Feb 13. [Epub ahead of print] PubMed PMID: 22336189.
    • News coverage by the BBC

Genetics/Genomics

  1. MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG; 1000 Genomes Project Consortium, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C. A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012 Feb 17;335(6070):823-8. PubMed PMID: 22344438.
    • Commentary: Quintana-Murci L. Genetics. Gene losses in the human genome. Science. 2012 Feb 17;335(6070):806-7. PubMed PMID: 22344433.

Development

  1. Inaba M, Yamanaka H, Kondo S. Pigment pattern formation by contact-dependent depolarization. Science. 2012 Feb 10;335(6069):677. PubMed PMID: 22323812.

Funding

  1. Mervis J. U.S. budget. Science spared brunt of ax in budget request. Science.  2012 Feb 17;335(6070):783-4. PubMed PMID: 22344417.

Academic career

  1. Kaminski D, Geisler C. Survival analysis of faculty retention in science and engineering by gender. Science. 2012 Feb 17;335(6070):864-6. PubMed PMID: 22344445.

Development

  1. Balaskas N, Ribeiro A, Panovska J, Dessaud E, Sasai N, Page KM, Briscoe J, Ribes V. Gene regulatory logic for reading the sonic hedgehog signaling gradient in the vertebrate neural tube. Cell. 2012 Jan 20;148(1-2):273-84. PubMed PMID: 22265416; PubMed Central PMCID: PMC3267043.
  2. Lassar A. Finding MyoD with a little help from my friends. Nat Cell Biol. 2012 Feb 2;14(2):116. doi: 10.1038/ncb2421. PubMed PMID: 22298038.
    • An interesting personal account of the discovery of MyoD.

Retinal Regeneration

  1. Qin Z, Kidd AR 3rd, Thomas JL, Poss KD, Hyde DR, Raymond PA, Thummel R. FGF signaling regulates rod photoreceptor cell maintenance and regeneration in zebrafish. Exp Eye Res. 2011 Nov;93(5):726-34. Epub 2011 Sep 17. PubMed PMID: 21945172; PubMed Central PMCID: PMC3243491.
  2. Hochmann S, Kaslin J, Hans S, Weber A, Machate A, Geffarth M, Funk RH, Brand M. Fgf Signaling is Required for Photoreceptor Maintenance in the Adult Zebrafish Retina. PLoS One. 2012;7(1):e30365. Epub 2012 Jan 26. PubMed PMID: 22291943; PubMed Central PMCID: PMC3266925.

Genetics

  1. Visscher PM, Brown MA, McCarthy MI, Yang J. Five Years of GWAS Discovery. Am J Hum Genet. 2012 Jan 13;90(1):7-24. PubMed PMID: 22243964.

Genomics

  1. Baker M. Structural variation: the genome’s hidden architecture. Nat Methods. 2012 Jan 30;9(2):133-7. doi: 10.1038/nmeth.1858. PubMed PMID: 22290183.
  2. Xiong Q, Ancona N, Hauser ER, Mukherjee S, Furey TS. Integrating genetic and gene expression evidence into genome-wide association analysis of gene sets. Genome Res. 2012 Feb;22(2):386-97. Epub 2011 Sep 22. PubMed PMID: 21940837.

Imaging

  1. Cox S, Rosten E, Monypenny J, Jovanovic-Talisman T, Burnette DT, Lippincott-Schwartz J, Jones GE, Heintzmann R. Bayesian localization microscopy reveals nanoscale podosome dynamics. Nat Methods. 2011 Dec 4;9(2):195-200. doi: 10.1038/nmeth.1812. PubMed PMID: 22138825.
    • Commentary: Lidke KA. Super resolution for common probes and common microscopes. Nat Methods. 2012 Jan 30;9(2):139-41. doi: 10.1038/nmeth.1863. PubMed PMID: 22290184.
    • This looks like an interesting article that talks about how to use common fluorescent setup for super-resolution imaging.
  2. Xu K, Babcock HP, Zhuang X. Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nat Methods. 2012 Jan 8;9(2):185-8. doi: 10.1038/nmeth.1841. PubMed PMID: 22231642.

Gene Regulatory Network

  1. Damle SS, Davidson EH. Synthetic in vivo validation of gene network circuitry. Proc Natl Acad Sci U S A. 2012 Jan 11. [Epub ahead of print] PubMed PMID: 22238426.
  2. Weaver J. New signaling chemicals spur worms to seek company. PLoS Biol. 2012 Jan;10(1):e1001240. Epub 2012 Jan 10. PubMed PMID: 22253575; PubMed Central PMCID: PMC3254651.
  3. Gross L. Built-in Timer Delays Differentiation. PLoS Biol. 2012 Jan;10(1):e1001254. Epub 2012 Jan 31. PubMed PMID: 22303284.
  4. van Dijk AD, van Mourik S, van Ham RC. Mutational robustness of gene regulatory networks. PLoS One. 2012;7(1):e30591. Epub 2012 Jan 25. PubMed PMID: 22295094; PubMed Central PMCID: PMC3266278.

Ageing

  1. Heidinger BJ, Blount JD, Boner W, Griffiths K, Metcalfe NB, Monaghan P. Telomere length in early life predicts lifespan. Proc Natl Acad Sci U S A. 2012 Jan 9. [Epub ahead of print] PubMed PMID: 22232671.

Brg1

  1. Curtis CD, Griffin CT. The chromatin-remodeling enzymes BRG1 and CHD4 antagonistically regulate vascular Wnt signaling. Mol Cell Biol. 2012 Jan 30. [Epub ahead of print] PubMed PMID: 22290435.

Funding

  1. Macilwain C. Funding in 2012: “great recession” starts to bite. Cell. 2012 Jan 20;148(1-2):14-6. PubMed PMID: 22265395.

This is a cross post from a discussion thread on my facebook, after the UC Davis pepper spray incidence. There are interesting ideas that are worthwhile to think further. It is also interesting to see that there are scientists joining the actual Occupy protests… um..  I still think the problem is not merely the lack of funding, but is a fundamental issue of the business model for the contemporary scientific research.

—-

Fai: After seeing what is happening in the Occupy Wall Street movement, especially the very recent episodes at UC Davis, I cannot stop thinking about the resemblance between the current social issues and the problems that sincere research scientists at all levels are facing. In fact, part of the problems is caused by these social issues related to business and government policy; and many of us can easily tell a few personal stories. We have been trained to be critical of our work, why can we not be critical about the system as well? For example, if we were allowed to redesign our university and research system, what should we do to ensure that we will build a sustainable system for the society, students and scientists? I am intrigued in hearing from my friends who have been contributing in the field across the world.

Abel Chun: But the fact seems to be that politics rules the world. Like in HKU, there’re many good scientists for life science but they’re “workers” under the command of professors who come from Medicine, not PhD. After all, we have to apply for grants to survive but those who review the grants are bearing lot of power, managerial levels, and even some so-called scientists (eg. from ITF). If we write a grant proposal simply for “understanding the nature”, U will never get a penny. But if U say your research can lead to drug development, can make big $, ok, here U go.

Albert Hui:  Changes only ever happen top-down. See what George Soros did to advance his open society movement? First make big money.

Winnie Tong: We are too specialised. Research training nowadays is very concentrated in speacilised techniques for specific narrow subject area and often one is pretty much stuck within one research area. It just limits our choices for jobs and power for negotiation. I knew some people would not mind being ‘workers’ for life. What they hate is the job insecurity every 2-3 years for all their working life. Even the universities offer some help at the end of each contract, usually it’s just putting you on a list for other research groups. You will be lucky if they are looking for your specific skill set, otherwise it’s good bye and good luck after a few months. If I can redesign the university and research system, everyone should have at least a few weeks of sabbatical time to actually work in a completely different research area.

Fai: Abel: it’s the same (censored) everywhere.

Fai: Albert: I always want to be a philanthropist.

Fai: Winne: that is indeed the core problem! Many good-hearted, intelligent people did not realize that the business model is actually a contest. And that is often not taught explicitly at school. I don’t think merely providing time to learn new skills without a wholesale improvement if the business model can alleviate the frustration of most participants.

Fai: Abel: and you would agree much of the creativity of the whole community is wasted on irrelevant stuff because of the business model.

Winnie Tong:  True. But it’s something that can be done on our end now, at least if you have a good boss. Like what google does, allowing 10% time for blue-sky development. And say two weeks is like a long conference time, long enough to actually gain some hands on experience and network to other research groups. 1-3 days is just way too short. You tend to forget and less chance to touch any buttons. It would be much easier, say, instead of small little pots of funding within individual research groups, perhaps some of it can go to a centralised place. This pool of fund can be use to hire some more permenant research staffs, who can rotate between labs and groups. This is a bit like the industry where the same scientists may be put in several different projects instead of just one. This way you can utilise the avaliable man power better for more urgent projects. It will be great if the University and funding bodies can think of a way to adopt some of this industrial approach, but that probablywould mean PIs will have to let go of their control over their own funding and it is unlikely to happen.

Fai: Google’s approach is nice and is indeed the approach for many postdocs and graduate students. You always want to try something new. However that may not be for every one. The idea for centralizing and rotating staff is interesting, but I can imagine strong resistance at the administration level. The current model is project based and the school earns money from the government by getting support for new projects. Since staff who can perform a specific skill is related to a project, it is a budgeting nightmare to figure out how to rotate some core people around between different projects. It does require a whole new way of funding and administration. In addition, given the expensive staff and the financial situation, having centralized staff may not be a sustainable solution.

Winnie Tong: I think what’s demaging is that many people are only hired and involved in a single project. I think we can start small, say, two PIs share their research staffs between their projects. If each PI has one full-time staff, it means there will be two full-time people for two projects.

Fai: Without a concomitant change in the system, this bottom-up approach can be problematic. Project time will vary, who is going to pay for the staff when one project is terminated? Also the resolution on the staff time can also be problematic… this is the fundamental dilemma between the award-based system and the desire of many who would opt for a stable life.

—–

 

These days with tight budget and poor economy, I am always intrigued in finding ways to conserve my research funding, which I think is a responsible approach to research rather than the big spending and throwing-away-old-but-good-equipment mentality. For example, all monitors in my office are old, unwanted CRT monitors. The oldest one is a Sony Trinitron that I picked up as a postdoc at Harvard in 2004, when they were throwing away many CRTs and replacing them with the sexy LCD monitors. It is still running great and I wish I could pick up more at that time.

Anyway, there is an interesting new consumer camera called Lytro that has just been launched recently. It is based on a revolutionized light field concept that can capture not just the color and intensity, but also the vector direction of the light. Thus, information with regards to the location of the object be extracted after image acquisition; in other words, one can “focus” after image acquisition in the computer. This concept is originated from the Ph.D. research of Ren Ng, Lytro’s CEO, at Stanford.

I think the concept can potentially be applicable to research imaging in life-science. For example, in fluorescent imaging, we always want to acquire information from a very specific focal plane of the specimen. One fancy way to exclude the out-of-focus information is by confocal microscopy,  a fancier way of imaging which is not a cheap at all. From my limited understanding, Lytro’s principle can potentially be applicable to generate an effect that is similar to confocal on a regular fluorescent microscope, perhaps with some essential modifications of the algorithms. If that is possible, then Lytro can be a very economical replacement (a few hundreds) of confocal (hundreds of thousands). I immediately emailed them about that and asked for the possibility of getting a unit to play with. Of course they said thank you for the great idea, but no, we won’t be able to send you one.

I do hope someone, including Lytro, who has time and interest, can figure this application out… then we can have a $400 confocal! Think about capturing all the confocal market in the field!

Development

  1. Lander AD. Pattern, growth, and control. Cell. 2011 Mar 18;144(6):955-69. Review. PubMed PMID: 21414486; PubMed Central PMCID: PMC3128888.
  2. Braendle C, Felix MA. The other side of phenotypic plasticity: a developmental system that generates an invariant phenotype despite environmental variation. J Biosci. 2009 Oct;34(4):543-51. Review. PubMed PMID: 19920340.
  3. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, Duboule D. The dynamic architecture of Hox gene clusters. Science. 2011 Oct 14;334(6053):222-5. PubMed PMID: 21998387.

Genomics

  1. Sadeh R, Allis CD. Genome-wide “Re”-Modeling of Nucleosome Positions. Cell. 2011 Oct 14;147(2):263-6. PubMed PMID: 22000006.
  2. Lupski JR, Belmont JW, Boerwinkle E, Gibbs RA. Clan genomics and the complex architecture of human disease. Cell. 2011 Sep 30;147(1):32-43. PubMed PMID: 21962505.
  3. Raychaudhuri S. Mapping rare and common causal alleles for complex human diseases. Cell. 2011 Sep 30;147(1):57-69. PubMed PMID: 21962507; PubMed Central PMCID: PMC3198013.

Genetics

  1. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011 Oct 14;147(2):358-69. PubMed PMID: 22000014.

Funding

  1. Mervis J. Peer review. Beyond the data. Science. 2011 Oct 14;334(6053):169-71. PubMed PMID: 21998363.

Systems biology

  1. Liu C, Fu X, Liu L, Ren X, Chau CK, Li S, Xiang L, Zeng H, Chen G, Tang LH, Lenz P, Cui X, Huang W, Hwa T, Huang JD. Sequential establishment of stripe patterns in an expanding cell population. Science. 2011 Oct 14;334(6053):238-41.  PubMed PMID: 21998392.

Medical research

  1. Novarino G, Akizu N, Gleeson JG. Modeling human disease in humans: the ciliopathies. Cell. 2011 Sep 30;147(1):70-9. PubMed PMID: 21962508.