Category Archives: quote

Saving Fermilab

Fermilab was once the premiere particle physics research lab. It is still a very important research lab. But, I have said before, other countries are the ones making the larger efforts lately to invest in science and technology centers of excellence that the US was making in the 1960’s and 1970’s: Economic Strength Through Technology Leadership, Investing in Technology Excellence, etc..

I have also said that the past success of the US has left it in a still very strong position. For example, the anonymous donor that saved Fermilab with a $5 million donation likely benefited from the successful investments in science centers of excellence in the past (few countries – maybe 30, can rely on large donations from wealthy individuals, to sustain centers of excellence and I don’t think any approach what the USA has now – Howard Hughes Medical Institute, Standford, MIT…).

Excellent post on the the saving of Fermilab, To the person who saved Fermilab: Thank You.:

The facility has recently seen financial difficulties which have resulted in the layoffs of research staff and dramatic cuts in experiments. The world class research facility has been left to scrape together funds to pay the bills and has even had to auction off equipment and ask staff members to take pay cuts just to keep the lights on in the laboratories.
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Fermilab also has an illustrious history of achievements in the field of supercomputer development and parallel processing. Fermilab has been on the forefront of applying supercomputing to physics research and is one of the top supercomputing centers of the world. Fermilab has claimed the world’s most powerful supercomputer on multiple occasions – although the title is rarely held long by any system due to the continuous advancements in computing. In recent years, Fermilab has been a leader in the development of “lattice” supercomputing systems and has developed methods for efficiently utilizing the power of multiple supercomputers in different locations through more [efficient] distribution practices.

To some, the construction of the Large Hadron Collider at CERN may seem to reduce the importance of Fermilab’s capabilities, but this is not at all the case. Although the LHC may take the title for the overall size and energy levels of a particle accelerator, Fermilab remains a uniquely capable particle physics research institution. Though less powerful, the Tevatron is able to operate for longer periods of time than the LHC and will likely require less downtime for maintenance, allowing for greater access and numerous types of research activities.

Viruses Eating Bacteria

All the World’s a Phage by John Travis:

“Believe it or not, nobody had looked before,” says Suttle. “On average, there are 50 million viruses per milliliter in seawater. The question is, What the heck they’re doing there?” Microbiologists then documented similar, and even higher, concentrations of phages in soil samples. This led to estimates of 10³¹ bacteriophages worldwide, a staggeringly large number that many scientists initially dismissed. “We can’t wrap our brains around it,” says Pedulla. “If phages were the size of a beetle, they would cover the Earth and be many miles deep.”
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According to estimates put forth by Suttle, phages destroy up to 40 percent of the bacteria in Earth’s oceans each day.
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The students collected soil from barnyards, gardens, and even the monkey pit at the Bronx Zoo. The scientists then taught the students how to isolate a bacteriophage from the soil by growing the viruses in Mycobacterium smegmatis, a harmless bacterial relative of the microbe that causes tuberculosis. “We guarantee them that the bacteriophage they find will never have been discovered before. We know that because the diversity is so high, and we’ve never isolated the same bacteriophage twice,” says Hatfull.

In the April 18 Cell, Hatfull and his professional and teenage collaborators describe the genomes of 10 soil-dwelling bacteriophages that they had isolated. Of the more than 1,600 genes that the team identified, about half are novel, that is, they don’t match any previously described genes in any other organism.

Science is full of amazing new frontiers. Some other amazing stuff: Thinking Slime Moulds – Tracking the Ecosystem Within Us – Retroviruses – Energy Efficiency of Digestion – One Species’ DNA Discovered Inside Another’s

Drug Price Crisis

I don’t think the suggestion below really solves the drug price crisis. But I do think it is an example of an educational and research institution actually proposing sensible role for themselves. As I have said too many universities now act like they are for-profit drug or research companies: Funding Medical Research. For some background on drug prices read my post on the Curious Cat Management blog from 2005.

Solving the drug price crisis

The mounting U.S. drug price crisis can be contained and eventually reversed by separating drug discovery from drug marketing and by establishing a non-profit company to oversee funding for new medicines, according to two MIT experts on the pharmaceutical industry.
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Following the utility model, Finkelstein and Temin propose establishing an independent, public, non-profit Drug Development Corporation (DDC), which would act as an intermediary between the two new industry segments — just as the electric grid acts as an intermediary between energy generators and distributors.

The DDC also would serve as a mechanism for prioritizing drugs for development, noted Finkelstein. “It is a two-level program in which scientists and other experts would recommend to decision-makers which kinds of drugs to fund the most. This would insulate development decisions from the political winds,” he said.

Book – Reasonable Rx: Solving the Drug Price Crisis by Stan Finkelstein and Peter Temin

Scientists and Engineers in Congress

A list of Congressmen with science PhDs: Vernon Ehlers, Michigan, physics PhD; Rush Holt, New Jersey, physics PhD; John Olver, Massachusetts, chemistry PhD; Brian Baird, Washington, psychology PhD; and now Bill Foster, Illinois, physics PhD. Other scientists, engineers and mathematicians include: Ron Paul, Texas, biology BS, MD; Jerry McNerney, California, math PhD; Dan Lipinski, Illinois, mechanical engineering BS, engineering-economic systems MS; Nancy Boyda, Kansas, chemistry BS; Cliff Stearns, Florida, electrical engineering BS; Joe Barton, Texas, industrial engineering BS. Please comment with additions.

Another Scientist in Congress!

He is not just any old particle physicist, but quite an accomplished one, having been a co-inventor of Fermilab’s antiproton Recycler Ring. Once you’ve mastered antiprotons, the Washington political process should be child’s play. Congratulations!

Vernon Ehlers – “After three years of studying at Calvin College in Grand Rapids, Ehlers transferred and received his undergraduate degree in physics and his Ph.D. in nuclear physics from the University of California at Berkeley in 1960. After six years teaching and research at Berkeley, he moved back to Grand Rapids to Calvin College in 1966 where he taught physics for 16 years and later served as chairman of the Physics Department. During his tenure at Calvin, Ehlers also served as a volunteer science advisor to then-Congressman Gerald R. Ford.”

Russ Holt – Rep. Holt earned his B.A. in Physics from Carleton College in Minnesota and completed his Master’s and Ph.D. at NYU. He has held positions as a teacher, Congressional Science Fellow, and arms control expert at the U.S. State Department where he monitored the nuclear programs of countries such as Iraq, Iran, North Korea, and the former Soviet Union. From 1989 until he launched his 1998 congressional campaign, Holt was Assistant Director of the Princeton Plasma Physics Laboratory, the largest research facility of Princeton University and the largest center for research in alternative energy in New Jersey. He has conducted extensive research on alternative energy and has his own patent for a solar energy device. Holt was also a five-time winner of the game show “Jeopardy.”
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Phun Physics

Coolest science toy ever

Phun is without question the greatest computer toy in the history of the universe, if this had been around when I was a kid I would be a frickin genius by now. You don’t need things any more. It’s extremely easy to use. As a starter tip, turn gravity off when you’re attaching stuff to the background (right click after selecting “affix” tool).

Very cool. Get your Phun (2D physics software) for free. Phun is a Master of Science Theises by Computing Science student Emil Ernerfeldt.

Some other very cool stuff: Cool Mechanical Simulation System – Scratch from MIT – What Kids can Learn – Lego Autopilot First Flight – Awesome Cat Cam

Funding Medical Research

Cheap, ‘safe’ drug kills most cancers

It sounds almost too good to be true: a cheap and simple drug that kills almost all cancers by switching off their “immortality”. The drug, dichloroacetate (DCA), has already been used for years to treat rare metabolic disorders and so is known to be relatively safe. It also has no patent, meaning it could be manufactured for a fraction of the cost of newly developed drugs.

Evangelos Michelakis of the University of Alberta in Edmonton, Canada, and his colleagues tested DCA on human cells cultured outside the body and found that it killed lung, breast and brain cancer cells, but not healthy cells. Tumours in rats deliberately infected with human cancer also shrank drastically when they were fed DCA-laced water for several weeks.

DCA attacks a unique feature of cancer cells: the fact that they make their energy throughout the main body of the cell, rather than in distinct organelles called mitochondria. This process, called glycolysis, is inefficient and uses up vast amounts of sugar.

Until now it had been assumed that cancer cells used glycolysis because their mitochondria were irreparably damaged. However, Michelakis’s experiments prove this is not the case, because DCA reawakened the mitochondria in cancer cells. The cells then withered and died

The University of Alberta is raising funds to further the research. Some look at this and indite a funding system that does not support research for human health unless there is profit to be made. Much of the blame seems to go to profit focused drug companies. I can see room for some criticism. But really I think the criticism is misplaced.

The organizations for which curing cancer is the partial aim (rather than making money) say government (partial aim or public health…), public universities (partial aim of science research or medical research…), foundations, cancer societies, private universities… should fund such efforts, if they have merit. Universities have huge research budgets. Unfortunately many see profit as their objective and research as the means to the objective (based on their actions not their claims). These entities with supposedly noble purposes are the entities I blame most, not profit focused companies (though yes, if they claim an aim of health care they I would blame them too).

Now I don’t know what category this particular research falls into. Extremely promising or a decent risk that might work just like hundreds or thousands of other possibilities. But lets look at several possibilities. Some others thoughts on where it falls: Dichloroacetate to enter clinical trials in cancer patients, from a previous post here – Not a Cancer Cure Yet, The dichloroacetate (DCA) cancer kerfuffle, CBC’s ‘The Current’ on dichloroacetate (DCA), Dichloroacetate (DCA) Phase II Trial To Begin (“Like hundreds (if not, thousands) of compounds being tested to treat cancer, DCA was shown by Michelakis’ group earlier this year to slow the growth of human lung tumors in a preclinical rodent model.”).
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Great Self Portrait

photo of astronaut's faceplate reflecting earth

Photo by, and of, Astronaut Clay Anderson, Expedition 15 flight engineer. He used a digital camera to expose a photo of his helmet visor during the mission’s third planned session of extravehicular activity (EVA) on the International Space Station (15 August 2007). Also visible in the reflections in the visor are various components of the station and a blue and white portion of Earth. During the 5-hour, 28-minute spacewalk, Anderson and astronaut Rick Mastracchio (out of frame), STS-118 mission specialist, relocated the S-Band Antenna Sub-Assembly from Port 6 (P6) to Port 1 (P1) truss, installed a new transponder on P1 and retrieved the P6 transponder.

NASA provides their content, photos etc. online in an open access spirit. When linking to content (especially images) it is best to provide context (and with the internet the easiest way to do is so is relevant links). You can find many low resolution pictures of the image above around the internet. Trying to find the context around the image is not so easy – it took me quite awhile to do so. I try to provide the context and links. Lately some more sites will link to some original sources but this is still done far to infrequently.

There are also still far too many pointy haired bosses (PHB) making decisions to break the web by killing pages: web pages must live forever. Those PHB’s decisions do reduce the great benefit of linking but it is still worth doing for those cases where web sites are managed by people with the knowledge and ability to manage an internet resource properly.

Photo: NASA – high resolution version

Country H-index Rank for Science Publications

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database. As stated in previous posts these types of rankings have limitations but they are also interesting (such as the best research universities 2007). The table shows the top 6 countries by h-index and then some others I chose to list.

Country	h-index	% of World Population	% of World GDP	total Cites	% Top 500 Schools
USA	793	4.6%	27.4%	43,436,526	33%
United Kingdom	465	0.9	4.9	9,895,817	8
Germany	408	1.3	6.0	8,377,298	8
France	376	0.9	4.6	5,795,531	4
Japan	372	2.0	9.0	7,167,200	6
Canada	370	0.5	2.6	4,728,874	4
Additional countries of interest
20) China	161	20.1	5.5	1,629,993	3
20) South Korea	161	.7	1.8	1,018,532	2
24) Brazil	148	2.9	2.2	752,658	1
25) India	146	17.0	1.9	994.561	.4

Read more about the h-index (Hirsh index). Country population and GDP data taken World Development Indicators 2007, by the World Bank.

via: Stat freaks, are you ready to play with the SCImago Journal & Country Rank?

Parasite Rex

Parasite Rex is a great book by Carl Zimmer (one of the bloggers listed in the Curious Cat directory of science blogs). This is the first book read as part of my specific plan to read more about bacteria, cells, virus, genes and the like.

One of the most enjoyable aspects of writing this blog is that I have focused much more on cool things I read. And over time the amazing things I posted about related to these topics made me realize I should put some focused effort to reading more on these topics. Some of the posts that sparked that idea: Tracking the Ecosystem Within Us – Inner Life of a Cell: Full Version – Where Bacteria Get Their Genes, People Have More Bacterial Cells than Human Cells, Biological Molecular Motors – Energy Efficiency of Digestion – Old Viruses Resurrected Through DNA – Midichloria mitochondrii – Microbes – Using Bacteria to Carry Nanoparticles Into Cells – How Bacteria Nearly Destroyed All Life – New Understanding of Human DNA – Soil Could Shed Light on Antibiotic Resistance – Symbiotic relationship between ants and bacteria

Parasite Rex was a great place to start. Carl Zimmer is a great writer, and the details on how many parasites there are and how interconnected those parasites are to living systems and how that has affected, and is affecting, us is amazing. And the next book I am reading is also fantastic: Good Germs, Bad Germs. Here is one small example from Parasite Rex, page 196-7:

A person who dies of sickle cell anemia is less likely to pass on the defective gene, and that means the disease should be exceedingly rare. But it’s not – one in four hundred American blacks has sickle sell anemia, and one in ten carries a single copy of the defective gene. The only reason the gene stays in such high circulation is that is also happens to be a defense against malaria.

Malaria is a parasite. One of the amazing things with repeated examples in the book were parasites that seemed to have extremely complicated life cycles (that don’t seem like a great strategy to prosper but obviously work). Where they grow in one life form (an insect or mammal or whatever) but must leave that life form for some other specific life form for the next stage in life (they cannot have descendants without doing so…). Seems like a crazy way to evolve but it happens over and over again.
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Evolution is Fundamental to Science

Evolution is absolutely fundamental to scientific thinking. Any country, or part of a country (or those wishing to lead a country) that teaches evolution as though it is some alternative way of looking at the facts (that can be compared to creationism/intelligent design, as science, for example) is an embarrassment. Unfortunately the United States is home to far too much of this thinking – which explains why scientific literacy is so low. Luckily there are also plenty in the USA that understand science. The National Academy of Science has published, Science, Evolution, and Creationism, in which a

group of experts assembled by the National Academy of Sciences and the Institute of Medicine explain the fundamental methods of science, document the overwhelming evidence in support of biological evolution, and evaluate the alternative perspectives offered by advocates of various kinds of creationism, including “intelligent design.” The book explores the many fascinating inquiries being pursued that put the science of evolution to work in preventing and treating human disease, developing new agricultural products, and fostering industrial innovations. The book also presents the scientific and legal reasons for not teaching creationist ideas in public school science classes.

The scientific theory of evolution still has details that can be debated – which is what the scientists should and will do (seeking out evidence to support such details). The idea that people today can question evolution is beyond amazing to me. It is much easier to understand some people thinking you would sail off the edge of the earth 500 years ago than anyone in the USA thinking there is any serious debate about evolution (there are parts of the world where the educational system does not give everyone a chance to see the available evidence, so I can forgive some in the world for being ignorant – not having been exposed to the evidence). And I guess there are parts of the USA educational system that are nearly so poor also where a gullible student could not see the truth. But in the USA the evidence is easily at hand – you have to intentionally remain ignorant to somehow not understand the truth of evolution.

What Everyone Should Learn:

Dr. Vincent Cerf: “I would want people to really understand the theory of evolution and the origin of species. The power of cumulative, adaptive change in the genome, over the course of billions of years and changing conditions, is hard for many people to fully appreciate.”