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Curious Cat Science and Egineering blog full tag cloud
Why you can get ‘500 year floods’ two years in a row by Anne Jefferson:
This post is a good explanation that the 500 year flood idea is just way of saying .2% probability (that some people confuse as meaning it can only happen every 500 years). But I actually am more interested in the other factor which is how much estimation is in “500 year prediction.” We don’t have 500 years of data. And the conditions today (I believe) are much more likely to create extreme conditions. So taking comfort in 500 year (.2%), or even 100 year (1% probability) flood “predictions” is dangerous.
It would seem to me, in fact, actually having a 500 year flood actually increases the odds for it happening again (because the data now includes that case which had not been included before). It doesn’t actually increase the likelihood of it happening but the predictions we make are based on the data we have (so given that it happens our 500 year prediction is questionable). With a coin toss we know the odds are 50%, getting 3 heads in a row doesn’t convince us that our prediction was bad. And therefore the previous record of heads or tails in the coin toss have no predictive value.
I can’t see why we would think that for floods. With the new data showing a flood, (it seems to me) most any model is likely to show an increased risk (and pretty substantial I would think) of it happening again in the next 100 years (especially in any area with substantial human construction - where conditions could well be very different than it was for our data that is 20, 40… years old). And if we are entering a period of more extreme weather then that will likely be a factor too…
The comments on the original blog post make some interesting points too - don’t miss those.
Related: Two 500-Year Floods Within 15 Years: What are the Odds? USGS - All Models Are Wrong But Some Are Useful by George Box - Cancer Deaths - Declining Trend? - Megaflood Created the English Channel - Seeing Patterns Where None Exists - Dangers of Forgetting the Proxy Nature of Data - Understanding Data
A few weeks ago we posted about Tracking Down Tomato Troubles as another example of the challenges of scientific inquiry. Too often, in the rare instances that science is even discussed in the news, the presentation provides the illusion of simple obvious answers. Instead it is often a very confusing path until the answers are finally found (posts on scientific investigations in action). At which time it often seems obvious what was going on. But to get to the solutions we need dedicated and talented scientists to search for answers.
Now the CDC is saying tomatoes might not be the source of the salmonella after all: CDC investigates possible non-tomato salmonella sources.
Three weeks after the Food and Drug Administration warned consumers to avoid certain types of tomatoes linked to the salmonella outbreak, people are still falling ill, says Robert Tauxe with the Centers for Disease Control and Prevention. The latest numbers as of Monday afternoon were 851 cases, some of whom fell ill as recently as June 20, says Tauxe, deputy director of the CDC’s division of foodborne diseases.
The CDC launched a new round of interviews over the weekend. “We’re broadening the investigation to be sure it encompasses food items that are commonly consumed with tomatoes,” Tauxe says. If another food is found to be the culprit after tomatoes were recalled nationwide and the produce industry sustained losses of hundreds of millions of dollars, food safety experts say the public’s trust in the government’s ability to track foodborne illnesses will be shattered.
“It’s going to fundamentally rewrite how we do outbreak investigations in this country,” says Michael Osterholm of the Center for Infectious Disease Research and Policy at the University of Minnesota. “We can’t let this investigation, however it might turn out, end with just the answer of ‘What caused it?’ We need to take a very in-depth look at foodborne disease investigation as we do it today.”
I am inclined to believe the FDA is not enough focused on food safety. Perhaps we are not funding it enough, but we sure are spending tons of money on something so I can’t believe more money needs to be spent. Maybe just fewer bills passed (that the politicians don’t even bother to read) with favors to special interests instead of funding to support science and food safety. Or perhaps we are funding enough (though I am skeptical of this contention) and we just are not allowing food safety to get in the way of what special interests want (so we fund plenty for FDA to have managed this much better, to have systems in place that would provide better evidence but they are either prevented from doing so or failed to do so). I am inclined to believe special interests have more sway in agencies like (NASA, EPA, FDA…) than the public good and scientific openness - which is very sad. And, it seems to me, politicians have overwhelmingly chosen not to support more science in places like FDA, CDC, NIH… while increasing federal spending in other areas dramatically.
Related: USDA’s failure to protect the food supply - FDA May Make Decision That Will Speed Antibiotic Drug Resistance - Food safety proposal: throw the bums out - The A to Z Guide to Political Interference in Science
The graph shows college degrees granted in the USA. This topic sets up one for criticism, but I believe it is more important to examine the data and explore the possible ideas than to avoid anything that might be questioned by the politically correct police. An import factor, to me anyway, is that women are now graduating from college in far higher numbers than men. And in many science fields female baccalaureate graduates outnumber male graduates (psychology [67,000 to 19,000], biology[42,000 to 26,000], anthropology, sociology [20,000 to 8,000]) while men outnumber women in others (math [7,000 to 6,000], engineering [53,000 to 13,000], computer science [39,000 to 11,000], physics [3,000 to 900]).
| Field | Bachelors | Master’s | Doctorate | ||||
|---|---|---|---|---|---|---|---|
| Women | Men | Women | Men | Women | Men | ||
| Biology | 42,283 | 25,699 | 4,870 | 3,229 | 3,105 | 3,257 | |
| Computer Science | 11,235 | 39,329 | 5,078 | 12,742 | 225 | 909 | |
| Economics | 8,141 | 17,023 | 1,391 | 2,113 | 355 | 827 | |
| Engineering | 13,197 | 52,936 | 7,607 | 26,492 | 1,174 | 5,215 | |
| Geosciences | 1,660 | 2,299 | 712 | 973 | 243 | 470 | |
| Physics | 903 | 3,307 | 427 | 1,419 | 200 | 1,132 | |
| Psychology | 66,833 | 19,103 | 12,632 | 3,444 | 2,264 | 211 | |
| Sociology | 20,138 | 8,438 | 920 | 485 | 343 | 211 | |
| All S&E | 235,197 | 230,806 | 53,051 | 66,974 | 10,533 | 17,405 | |
What does this all mean? It is debatable, but I think it is very good news for the efforts many have made over the last few decades to open up opportunities for women. I still support efforts to provide opportunities for girls to get started in science and engineering but I think we have reached the day when the biggest concern is giving all kids better math and science primary education (and related extracurricular activities). Also continued focus and effort on the doctorate and professional opportunities for women is warranted.
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Merck wrote drug studies for doctors
The article, based on documents unearthed in lawsuits over the pain drug Vioxx, provides a rare, detailed look in the industry practice of ghostwriting medical research studies that are then published in academic journals.
…
“It almost calls into question all legitimate research that’s been conducted by the pharmaceutical industry with the academic physician,” said Ross, whose article, written with colleagues, was published Wednesday in JAMA, The Journal of the American Medical Association, and posted Tuesday on the journal’s Web site.
Merck acknowledged Tuesday that it sometimes hired outside medical writers to draft research reports before handing them over to the doctors whose names eventually appear on the publication. But the company disputed the article’s conclusion that the authors do little of the actual research or analysis.
It is sad that the integrity of journals and scientists is so weak that they leave them open to such charges. The significant presence of the corrupting influence of too much money leaves doubt in my mind that the best science is the goal. Which is very sad. In, Funding Medical Research, I discussed my concern that universities are acting more like profit motivated organizations than science motivated organizations. I am in favor of profit motivated organization (those getting the micro-financing in this link, for example) but those organization should not be trusted to provide honest and balanced opinions they should be expected to provide biased opinions.
If universities (and scientists branding themselves as … at X university) want to be seen as honest brokers of science they can’t behave as though raising money, getting patents… are their main objectives. Many want to be able to get the money and retain the sense of an organization focused on the pursuit of science above all else. Sorry, you can’t have it both ways. You can, and probably should, try stake out some ground in the middle. And for me right now, partially because they fail to acknowledge the extent to which money seems to drive decisions I don’t believe they are trying to be open and honest, instead I get the impression they are leaning more toward trying to market and sell.
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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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Millions of users around the globe could not access YouTube for a couple hours yesterday. Why?
Well to understand, we need to start with how you normally connect to a web site. You click on a link to youtube.com. Your ISP looks up the internet address for youtube.com by looking at internet routing tables. Each domain has a name server that provides the IP address for where it should be found (for example, an IP address that shows youtube.com is 208.65.153.238).
Well what happened in this case is Pakistan decided to prevent anyone in Pakistan from accessing YouTube because the government didn’t like some video. The way Pakistan decided to accomplish this was to update their routing table to just direct all traffic that was meant to go to YouTube to a phony address which would then return nothing.
Why did many outside of Pakistan lose access to YouTube? Well their version of the routing table leaked out of Pakistan through PCCW (large internet provider), Then other internet providers adopted the incorrect information, until many around the globe were being directed to the wrong place.
You might find it amazing the routing system could allow such a thing to happen - it doesn’t seem very secure. You are right, that it doesn’t seem very sensible. When the internet was created some protocols were established that made sense then but don’t necessarily make sense for what the internet has become.
The problem was fixed when Google’s YouTube engineers contacted PCCW to inform them of the problem and have them correct it. I think if it was my site instead, I would have had difficulty figure out what was going on 
Once PCCW corrected their routing tables the fixed flowed through the system and everyone was able to see the great stuff like Marissa Mayer discussing Innovation at Google.
I would imagine Internet2 (well on its way to a computer near you) and IPv6 will take not be so venerable to such a mistake.
Related: Insecure routing redirects YouTube to Pakistan - YouTube outage blamed on Pakistan - YouTube Censorship Sheds Light on Internet Trust - The Web is 15 Years Old - Internet Undersea Cables - Harvard Course: Understanding Computers and the Internet - Net Neutrality - The Next Generation Internet - The Journey of Internet Packets - mistake proofing (the opposite of the current setup)
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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I recently wrote about evolution and scientific literacy. The graph on the left shows the percentage of the population that understands evolution is a core scientific principle. The graph based on data from 2005 for 34 countries.
Blue indicates those that know that “human beings, as we know them, developed from earlier species of animals.” Evolution Less Accepted in U.S. Than Other Western Countries, Study Finds, from National Geographic News: A study of several such surveys taken since 1985 has found that the United States ranks next to last in acceptance of evolution theory among nations polled. Researchers point out that the number of Americans who are uncertain about the theory’s validity has increased over the past 20 years.
The United States is is second to last place in this question of scientific literacy with only 40% of the population knowing the truth. The USA was between Cyprus and Turkey in this measure of understanding of scientific knowledge. The most knowledgeable countries have about twice the rate of knowledgeable respondents (with nearly 80% knowing). Related: Scientific Illiteracy by Country (the USA managed to stay in the top 10 for overall scientific literacy rate of 8th graders in 2003) - Understanding Evolution (University of California at Berkeley) - Scientifically Illiteracy - Retroviruses - DNA Repair Army - Massive Project Will Reveal How Humans Continue to Evolve - Gene Study Finds Cannibal Pattern - Nigersaurus - Rare Chinese Mountain Cat |
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
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.
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
The Science Education Myth by Vivek Wadhwa:
The study certainly sounds interesting. I can’t find it (update Vivek Wadhwa provided the link - which will work Monday, also see his comment below), but found an article (which wasn’t easy) by the authors of the report: The Real Technology Challenge. The main point of the article, The Real Technology Challenge, seems to be that the USA should focus on globalization (and focus on educating scientists and engineers to work in a global world).
As I have said before I disagree with those that believe the USA is producing more science and engineering graduates than the market demands. Smart leaders know the huge positive impacts of a large, well educated science and engineering workforce.
Countries that succeed in producing more quality graduates while creating the best economic environment to take advantage of technology innovation (follow this link - it is one of the most important posts about what makes silicon valley so powerful a force at doing just that) are going to benefit greatly. My guess is the USA will be one of those countries; not by reducing the focus on science and engineering education but by increasing it. If not, other countries will, and the USA will suffer economically. The USA also needs to continue to push the economic and entrepreneurship advantages - doing that well is very difficult to achieve and the USA maintains a stronger advantage in that realm - but I will be very surprised if other countries don’t continue to make gains in this area. Even so doing so is much more challenging than just improving education (which is difficult itself just not nearly as difficult) and the USA can continue to benefit from this combination with the right policies.
Related: Economic Strength Through Technology Leadership - House Testimony on Engineering Education - Filling the Engineering Gap - Best Research University Rankings (2007) - Most IT Jobs Ever in USA Today - USA Under-counting Engineering Graduates - Science, Engineering and the Future of the American Economy - S&P 500 CEOs - Again Engineering Graduates Lead - Highest Paid Graduates: Engineers
Three ways to make the world better. First, Kiva is lets you loan money directly to an entrepreneur of your choice. Kiva provides loans through partners (operating in the countries) to the entrepreneurs. Those partners do charge the entrepreneurs interest (to fund the operations of the lending partner). Kiva pays the principle back to you but does not pay interest. And if the entrepreneur defaults then you do not get your capital paid back (in other words you lose the money you loaned). See my post: Helping Capitalism Make the World Better (if you donate to Kiva I have a Curious Cat Kivan - comment to have you link added).
Second, donate using the widget displayed in this post: to William Kamkwamba who built his own windmill in Malawi to get electricity for his home. The donations go to help him with his education and engineering projects. He is a young student and engineer. I have donated $50, I would love to see readers donate - do so and send me a link to your personal blog or personal home page and I will update this post with a link (only to a site obviously associated with you - I reserve the right to link or not link to whoever I want). [the campaign is over so I removed the widget - $943 was raised, the goal was $2,000]. A recent post to his blog: My sisters and cousins with their first books:
Third, create a Kiva like setup for donations that could be used to provide a source for finding remarkable people that have plans for possible donated funds. The potential is huge.
Related: Children’s books - Appropriate Technology - What Kids can Learn - Lesson on Life - $100 Laptop Update - Millennium Development Goals
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