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All the World’s a Phage by John Travis:
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
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.
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
Related: Lifestyle Drugs and Risk - From Ghost Writing to Ghost Management in Medical Journals - USA Spent $2.1 Trillion on Health Care in 2006 - Measuring the Health of Nations - Economic Strength Through Technology Leadership - USA Paying More for Health Care
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!
Related: China’s Technology Savvy Leadership - Scientists and Politics - Why Congress Needs More Scientists - At Last, a Politician Who Knows Quantum Mechanics
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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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
Cheap, ’safe’ drug kills most cancers
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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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
Related: Van Gogh self portrait - Mars Rovers Getting Ready for Another Adventure - NASA Robotics Academy
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?
Related: Worldwide Science and Engineering Doctoral Degree Data - Views on Evolution by Country - Science and Engineering Doctoral Degrees Worldwide - Top 10 Manufacturing Countries 2006 - USA Teens 29th in Science - Ranking Universities Worldwide - Diplomacy, Science Research and Economics
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:
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 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
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.
Related: Understanding Evolution (from Berkeley) - Teaching Evolution and the Nature of Science - Evolutionary Design - Real-Time Evolution - Evolution at Work with the Blue Moon Butterfly - 200 Million Americans Are Scientifically Illiterate - Evolution In Action - Retroviruses - Evolution in Darwin’s Finches - Two Butterfly Species Evolved Into Third - Evolution of Antibiotic Resistance
Great paper looking at DNA from the perspective of a computer programmer. DNA seen through the eyes of a coder by Bert Hubert:
A typical example of a DNA codon is ‘GCC’, which encodes the amino acid Alanine. A larger number of these amino acids combined are called a ‘polypeptide’ or ‘protein’, and these are chemically active in making a living being.
…
Furthermore, 97% of your DNA is commented out. DNA is linear and read from start to end. The parts that should not be decoded are marked very clearly, much like C comments. The 3% that is used directly form the so called ‘exons’. The comments, that come ‘inbetween’ are called ‘introns’.
Related: RNA Interference Webcast - Hiring Software Developers - Donald Knuth, Computer Scientist
This is a pretty counter-intuitive statement, I believe:
But some simple math shows it is true. If you drive 10,000 miles you would use: 667 gallons, 556 gallons, 200 gallons and 100 gallons. Amazing. I must admit, when I first read the quote I thought that it must be an wrong. But there is the math. You save 111 gallons improving from 15 mpg to 18 mpg and just 100 improving from 50 to 100 mpg. Other than those of you who automatically guess that whatever seems wrong must be the answer when you see a title like this I can’t believe anyone thinks 15 to 18 mpg is the change that has the bigger impact. It is great how a little understanding of math can help you see the errors in your initial beliefs. Via: 18 Is Enough.
It also illustrates that the way the data is presented makes a difference. You can also view 100 mpg as 1/100 gallon per mile, 2/100 gallons per mile, 5.6/100 gpm and 6.7 gpm. That way most everyone sees that the 6.7 to 5.6 gpm saves more fuel than 2 to 1 gpm does. Mathematics and scientific thinking are great - if you are willing to think you can learn to better understand the world we live in every day.
Related: Statistics Don’t Lie, But People Can be Fooled - Understanding Data - Seeing Patterns Where None Exists - Optical Illusions and Other Illusions - 1=2: A Proof
This interesting and long report (I have not finished reading it yet - 120 pages) has been completed by the President Emeritus of at The University of Michigan (and current University Professor of Science and Engineering): Engineering for a Changing World by James J. Duderstadt.
Related: Science, Engineering and the Future of the American Economy - Engineering the Future Economy - China’s Economic Science Experiment - Economic Strength Through Technology Leadership - Educating the Engineer of 2020: NAE Report - The Future is Engineering - MIT Engineering Education Changes - Best Research University Rankings (2007) - Global Technology Leadership
My father, Willaim Hunter, a professor of statistics and of Chemical Engineering at the University of Wisconsin, was a guest speaker for my second grade class (I think it was 2nd) to teach us about numbers - using dice. He gave every kid a die. I remember he asked all the kids what number do you think will show up when you roll the die. 6 was the answer from about 80% of them (which I knew was wrong - so I was feeling very smart).
Then he had the kids roll the die and he stood up at the front to create a frequency distribution of what was actually rolled. He was all ready for them to see how wrong they were and learn it was just as likely for any of the numbers on the die to be rolled. But as he asked each kid about what they rolled something like 5 out of the first 6 said they rolled a 6. He then modified the exercise a bit and had the kid come up to the front and roll the die on the teachers desk. Then my Dad read the number off the die and wrote on the chart 
This nice blog post, reminded me of that story: Kids’ misconceptions about numbers — and how they fix them
But there’s a pattern to the second-graders’ responses. Nearly all the kids (93 were tested) understood that 750 was a larger number than 366; they just squeezed too many large numbers on the far-right side of the number line. In fact, their results show more of a logarithmic pattern than the proper linear pattern.
Politics of engineering by Patrick Mannion, EE Times:
If the science and engineering community are not well represented to our representatives the interests of the science and engineering community will get short changed. Especially since so few politicians in the USA have even a basic understanding of science and the scientific method. And a very small percentage have any advanced degrees in science and engineering fields or work experience in them. That being said the political arena is much like a tar pit: that is it is difficult to interact with without becoming entangled in a big mess. And it is not as though the scientific and engineering community are even close to unified but still the impact of political decisions is very significant and science and engineering leaders need to be heard.
China’s Economic Science Experiment - China’s 9 most senior government official are all engineers (in 2006 - I am not sure now):
Related: Larry Page on Marketing Science - The A to Z Guide to Political Interference in Science - Diplomacy and Science Research - Open Access Legislation - Proposal to Triple NSF Graduate Research Fellowship Awards - Science Interview with John Edwards - Proposed Legislation on Science and Education - House Testimony on Engineering Education - Germany’s Science Chancellor - Nanotechnology Investment as Strategic National Economic Policy - Singapore Supporting Science Researchers - Farming Without Subsidies in New Zealand
Humans Carry More Bacterial Cells than Human Ones
How cool is science? Very, I think
Related: Tracking the Ecosystem Within Us - Beneficial Bacteria - Energy Efficiency of Digestion - Large Number of Bacteria on our Skin - Where Bacteria Get Their Genes - Amazing Science: Retroviruses
xo-laptop: On the Open-Sourcing of Business - interesting post worth reading, though I disagree with some points:
There is a difference between your sole legal obligation and your sole obligation. I agree legally all you are obliged to do is comply with the legal requirements. That does not mean that is your sole obligation. I don’t see any problem making money in efforts involving open source efforts but I do believe that as that happens an obligation (perhaps not legal but real none-the-less) grows to give back to the community (Google’s summer of code is a great example of giving back). Most open source efforts require that any additions you make to the software be given back to the community (those involved in open souce know this, I add this just for the information of those not familiar with open source practices). Legal obligations are the minimum you can be forced to do, not the only obligations one has. Great quote (emphasis mine):
Simply put, free and open-source software is just the scientific model applied to programming: free sharing of work open collaboration; open publication; peer review; recognition of the best work, with priority given to the first to do a meaningful new piece of work; and so forth. As a programmer, it is the best arena in which to work. There are no secrets; the work must stand on its own.
Another great post on this topic: What Business Can Learn from Open Source.
Related: Open Source for LEGO Mindstorms - Young Scientists Design Open-Source Program at NASA - Open-Source Biotech - Publishers Continue to Fight Open Access to Science
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