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Many Great, Free, Online Courses in Science, Engineering and More

The video, above, provides an overview of an online course, Calculus: Single Variable, via coursera from the University of Pennsylvania. This course provides a brisk, entertaining treatment of differential and integral calculus, with an emphasis on conceptual understanding and applications to the engineering, physical, and social sciences.

Robert Ghrist is the Andrea Mitchell University Professor of Mathematics and Electrical & Systems Engineering at the University of Pennsylvania. Coursera offers many courses in all sorts of disciplines including: Introduction to Genetics and Evolution (Duke), Scientific Computing (University of Washington), Principles of Economics for Scientists (California Institute of Technology), Game Theory (Stanford University and The University of British Columbia), A Beginner’s Guide to Irrational Behavior (Dan Ariely, Duke University), The Modern World: Global History since 1760 (University of Virginia), Microeconomics for Managers (University of California, Irvine), Data Analysis (Johns Hopkins University), Fundamentals of Human Nutrition (University of Florida), Algorithms, Part I (Princeton University), The Ancient Greeks (Wesleyan University), Astrobiology and the Search for Extraterrestrial Life (University of Edinburgh) and Epigenetic Control of Gene Expression, (University of Melbourne).

All the classes are free. These courses, and many more, are extremely appealing. I signed up for 2. I would be interested in signing up for much more but I worry about having the time to commit to keeping up with the coursework. I hope the first two go well and I can sign up for more in the future.

Related: Top Online Graduate Engineering Programs in the USAOpen Source Education CurriculaScience and Engineering Education ResourcesExploring Eukaryotic Cells

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Drug Company Funding Taints Published Medical Research

Science provide the opportunity for us to achieve great benefits for society. However, especially in medical research money can make what are already very difficult judgments even less reliable. Add that to a very poor understanding of science in those we elect and you have a dangerous combination. That combination is one of the largest risks we face and need to manage better. I wish we would elect people with a less pitiful appreciation for science but that doesn’t seem likely. That makes doing a better job of managing the conflicts of interest money puts into our current medical research a top priority.

How Drug Company Money Is Undermining Science by Charles Seife

In the past few years the pharmaceutical industry has come up with many ways to funnel large sums of money—enough sometimes to put a child through college—into the pockets of independent medical researchers who are doing work that bears, directly or indirectly, on the drugs these firms are making and marketing. The problem is not just with the drug companies and the researchers but with the whole system—the granting institutions, the research labs, the journals, the professional societies, and so forth. No one is providing the checks and balances necessary to avoid conflicts.

Peer-reviewed journals are littered with studies showing how drug industry money is subtly undermining scientific objectivity. A 2009 study in Cancer showed that participants somehow survived longer when a study’s authors had conflicts of interest than when the authors were clean. A 1998 study in the New England Journal of Medicine found a “strong association” between researchers’ conclusions about the safety of calcium channel blockers, a class of drugs used to reduce blood pressure, and their financial relationships with the firms producing the drugs.

Most of those in the system have an interest in minimizing an effort to clean this up. It is just more work they don’t want to do. Or it goes directly against their interest (drug companies that want to achieve favorable opinions by buying influence). The main political message in the USA for a couple decades has been to reduce regulation. Allowing research that is tainted because you find regulation politically undesirable is a bad idea. People that understand science and how complex medical research is appreciate this.

Sadly when we elect people that by and large are scientifically illiterate they don’t understand the risks of the dangerous practices they allow. Even if they were scientifically illiterate but understood their ignorance they could do a decent job by getting scientific consultation from experts but they don’t (to an extent they listen to the scientists that those that give them lots of money tell them to which does help make sure those giving the politicians cash have their interests served but it is not a good way to create policy with the necessary scientific thinking needed today).

Related: Problems with the Existing Funding System for Medical ResearchMedical Study Integrity (or Lack Thereof)Merck and Elsevier Publish Phony Peer-Review JournalAnti-Science PoliticsStand with Science, Late is Better than Never

Key Indicator for Malignant Melanoma Found

Skin cancer detection breakthrough

The researchers found that certain biochemical elements in the DNA of normal pigment-producing skin cells and benign mole cells are absent in melanoma cells. Loss of these methyl groups — known as 5-hmC — in skin cells serves as a key indicator for malignant melanoma. Loss corresponded to more-advanced stages of melanoma as well as clinical outcome.

Strikingly, researchers were able to reverse melanoma growth in preclinical studies. When the researchers introduced enzymes responsible for 5-hmC formation to melanoma cells lacking the biochemical element, they saw that the cells stopped growing.

“It is difficult to repair the mutations in the actual DNA sequence that are believed to cause cancer,” said Christine Lian, a physician-scientist in the Department of Pathology at BWH and one of the lead authors. “So having discovered that we can reverse tumor cell growth by potentially repairing a biochemical defect that exists — not within the sequence but just outside of it on the DNA structure — provides a promising new melanoma treatment approach for the medical community to explore.”

Because cancer is traditionally regarded as a genetic disease involving permanent defects that directly affect the DNA sequence, this new finding of a potentially reversible abnormality that surrounds the DNA (thus termed “epigenetic”) is a hot topic in cancer research, according to the researchers.

In the United States, melanoma is the fifth most common type of new cancer diagnosis in men and the seventh most common type in women. The National Cancer Institute estimates that in 2012 there will be 76,250 new cases and 9,180 deaths in the United States owing to melanoma.

Thankfully scientists keep making great progress in understanding and finding potential clues to treating cancer. And big gains have been made in treating some cancers over the last few decades. But the research successes remain difficult to turn into effective solutions in treating patients.

I am thankful we have so many scientists doing good work in this difficult and important area (cancer).

Related: Webcast of a T-cell Killing a Cancerous CellNanoparticles With Scorpion Venom Slow Cancer SpreadDNA Passed to Descendants Changed by Your LifeResearchers Find Switch That Allows Cancer Cells to Spread

Virus Kills Breast Cancer Cells in Laboratory

Some very exciting and good news from Penn State. Researchers have found a virus that kills breast cancer cells. It is great to read about research breakthroughs like this. Of course, most of these announcements never become practical solutions, unfortunately. And if they do it is many many years later and almost always in much less exciting ways than the headlines. Still, the percentage that do make it through the process into workable solutions provide us great benefits.

Virus kills breast cancer cells in laboratory

Adeno-associated virus type 2 (AAV2) is a virus that regularly infects humans but causes no disease. Past studies by the same researchers show that it promotes tumor cell death in cervical cancer cells infected with human papillomavirus. Researchers used an unaltered, naturally occurring version of AAV2 on human breast cancer cells.

“Breast cancer is the most prevalent cancer in the world and is the leading cause of cancer-related death in women,” said Samina Alam, research associate in microbiology and immunology. “It is also complex to treat.”

“We can see the virus is killing the cancer cells, but how is it doing it?” Alam said. “If we can determine which viral genes are being used, we may be able to introduce those genes into a therapeutic. If we can determine which pathways the virus is triggering, we can then screen new drugs that target those pathways. Or we may simply be able to use the virus itself.”

AAV2 does not affect healthy cells. However, if AAV2 were used in humans, the potential exists that the body’s immune system would fight to remove it from the body. Therefore, by learning how AAV2 targets the death pathways, researchers potentially can find ways to treat the cancer without using the actual virus.

In ongoing studies, the Penn State researchers also have shown AAV2 can kill cells derived from prostate cancer, mesothelioma, squamous cell carcinoma, and melanoma. A fourth line of breast cancer cells — representing the most aggressive form of the disease — also was studied in a mouse breast tumor model, followed by treatment with AAV2. Preliminary results show the destruction of the tumors in the mice, and researchers will report the findings of those mouse studies soon.

The fight against cancer has many promising breakthroughs. We have made some great progress. Still the fight is extremely difficult and we have many more frustrations than successes.

Related: Webcast of a T-cell Killing a Cancerous CellSynthetic Biologists Design a Gene that Forces Cancer Cells to Commit SuicideResearchers Find Switch That Allows Cancer Cells to Spread

Harvard Steps Up Defense Against Abusive Journal Publishers

For a decade journals have been trying to continue a business model that was defensible in a new world where it is not. They have becoming increasing abusive with even more outrageous fees than they were already charging. As I said years ago it has become obvious they are enemies of science and should be treated as such. The time to find mutual beneficial solution past years ago.

Harvard University says it can’t afford journal publishers’ prices

Exasperated by rising subscription costs charged by academic publishers, Harvard University has encouraged its faculty members to make their research freely available through open access journals and to resign from publications that keep articles behind paywalls.

A memo from Harvard Library to the university’s 2,100 teaching and research staff called for action after warning it could no longer afford the price hikes imposed by many large journal publishers, which bill the library around $3.5m a year.

he memo from Harvard’s faculty advisory council said major publishers had created an “untenable situation” at the university by making scholarly interaction “fiscally unsustainable” and “academically restrictive”, while drawing profits of 35% or more. Prices for online access to articles from two major publishers have increased 145% over the past six years, with some journals costing as much as $40,000, the memo said.

More than 10,000 academics have already joined a boycott of Elsevier, the huge Dutch publisher, in protest at its journal pricing and access policies. Many university libraries pay more than half of their journal budgets to the publishers Elsevier, Springer and Wiley.

Research Libraries UK negotiated new contracts with Elsevier and Wiley last year after the group threatened to cancel large subscriptions to the publishers. The new deal, organised on behalf of 30 member libraries, is expected to save UK institutions more than £20m.

These journals have continuously engaged in bad practices. Scientists should publish work in ways that enrich the scientific community not ways that starve the scientific commons and enrich a few publishers that are doing everything they can to hold back information sharing.

In 2008 Harvard’s liberal arts faculty voted to make their research open source.

Related: Fields Medalist Tim Gowers Takes Action To Stop Cooperating with Anti-Open Science CartelScience Commons: Making Scientific Research Re-usefulMIT Faculty Open Access to Their Scholarly ArticlesMerck and Elsevier Publish Phony Peer-Review JournalOpen Access Journal Wars

How Lysozyme Protein in Our Tear-Drops Kill Bacteria

A disease-fighting protein in our teardrops has been tethered to a tiny transistor, enabling UC Irvine scientists to discover exactly how it destroys dangerous bacteria. The research could prove critical to long-term work aimed at diagnosing cancers and other illnesses in their very early stages.

Ever since Nobel laureate Alexander Fleming found that human tears contain antiseptic proteins called lysozymes about a century ago, scientists have tried to solve the mystery of how they could relentlessly wipe out far larger bacteria. It turns out that lysozymes have jaws that latch on and chomp through rows of cell walls like someone hungrily devouring an ear of corn.

“Those jaws chew apart the walls of the bacteria that are trying to get into your eyes and infect them,” said molecular biologist and chemistry professor Gregory Weiss, who co-led the project with associate professor of physics & astronomy Philip Collins.

The researchers decoded the protein’s behavior by building one of the world’s smallest transistors – 25 times smaller than similar circuitry in laptop computers or smartphones. Individual lysozymes were glued to the live wire, and their eating activities were monitored.

“Our circuits are molecule-sized microphones,” Collins said. “It’s just like a stethoscope listening to your heart, except we’re listening to a single molecule of protein.”

It took years for the UCI scientists to assemble the transistor and attach single-molecule teardrop proteins. The scientists hope the same novel technology can be used to detect cancerous molecules. It could take a decade to figure out but would be well worth it, said Weiss, who lost his father to lung cancer.

“If we can detect single molecules associated with cancer, then that means we’d be able to detect it very, very early,” Weiss said. “That would be very exciting, because we know that if we treat cancer early, it will be much more successful, patients will be cured much faster, and costs will be much less.”

The project was sponsored by the National Cancer Institute and the National Science Foundation. Co-authors of the Science paper are Yongki Choi, Issa Moody, Patrick Sims, Steven Hunt, Brad Corso and Israel Perez.

Related: full press releaseWhy ‘Licking Your Wounds’ WorksHow Bleach Kills BacteriaAlgorithmic Self-Assembly

Top Online Graduate Engineering Programs in the USA

Online degree programs are growing quickly in popularity in the USA. Over 6 million students took online courses in 2011. The costs of traditional education continue to rise at extremely high rates – schools have done a horrible job of dealing with this. I personally, don’t understand how they have done so horribly on this measure. Administration costs have exploded. Building vanity projects that costs tens of millions of dollars add little to student achievement and waste limited resources driving up costs.

We really need to find administrators that will reduce administrative staffing levels and costs. Let some schools continue on the ego driven spiraling costs, but let us at least find some who will focus on reducing education costs and providing good education at reasonable costs. For engineering, more than maybe any other discipline, I can excuse some of the costs. But given the universal failure to manage costs I think the failure to manage costs is the primary issue (the extra demands for spending on engineering education, I understand).

The failure to stop the lavish spending has greatly increased the demand for online education. Given the unreasonable cost increases for traditional education many are priced out of considering that option. Given how unable schools have proven to be at providing good education for reasonable rates the last few decades it is reasonable to assume online education will continue to gain popularity. I don’t see the top tier schools facing much competition from online efforts (even if some students are drawn away there are plenty wanting to upgrade their school choice at whatever the cost – as the administrators know as they continue to drive up costs).

One danger is that online education is hardly a proved commodity yet. Both in terms of what you learn and the acceptance and desirability of degrees. So right now students are having to make guesses that are more challenging with online programs than the traditional choices. US News and World Report has selected 3 online engineering master’s programs for the honor roll.

Related: Engineering Education in the 21st CenturyHow the Practice and Instruction of Engineering Must ChangeGlobal Engineering Education Study

Dennis Hong, Virginia Tech Mechanical Engineering Professor, Leading Robotics Innovation

Dennis Hong is the U.S. star in humanoid robotics

Hong came by his interest in science naturally. He was born in 1971 on the exclusive Palos Verdes Peninsula, outside Los Angeles, and his father, Yong Shik Hong, worked as an aerospace engineer at the federally funded Aerospace Corp. The family returned to Seoul in 1974 so the elder Hong could lead South Korea’s short-range missile program, at the bidding of then-President Park Chung Hee.

Korean fathers of that era were strict and remote. Hong’s father was engaged and intellectually indulgent. He installed a work bench in Dennis’s room when he was 4, complete with a hammer and saw. He led the children in chemistry experiments and brought home model airplanes from America.

Dennis Hong built things with scraps of wood and metal and bits of plastic. He disassembled toys and stored the parts in a chest beneath his bed.

“We spent a lot of time building things and breaking things,” said Julie Hong, Hong’s older sister. “He was the one who broke things the most and built things the most.”

Hong traveled to America to complete his university study, following his father’s credo, “Big fish must swim in the big sea.” He earned a bachelor’s in mechanical engineering at the University of Wisconsin and a master’s and doctorate at Purdue.

Dennis’ success illustrates several themes repeated in posts on this blog: the USA attracting talent from overseas, kids curiosity and exposure to science and engineering leading to great things, the value of strong science and engineering programs and professors. Robotics continue to progress very quickly. The economic impact of robotics is large already (largely in manufacturing) and will continue to grow dramatically. Likely robots will find their way into much more diverse areas over the next 2 decades. The Robotics and Mechanisms Laboratory, lead by Dennis Hong, seems poised to play a big role in that future.

Related: Robocup 2010, Robot FootballSoft Morphing Robot FutureEvolution of Altruism in RobotsToyota Develops Thought-controlled Wheelchair

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I Always Wanted to be Some Sort of Scientist

A nice simple post by a soon to be Dr. of Genetics and Molecular Biology on what being a scientist is like for her. I like her take, which I think is much more accurate than some of the generalities people use. The main reason people (men or women) become scientists because they want to be scientists.

photo of almost-Dr. Caitlin

Photo the almost-Dr. Caitlin

The truth is science requires you to be social. We share ideas, techniques, and equipment. A good scientist knows her limitations and uses someone else’s expertise when her own is not enough. The modern scientist communicates not only through conferences and journals, but also through blogging and Facebook.

When a non-scientist (usually my parents or some other close relative) asks me about what I do, they inevitably want to tie it back to how I’m curing a disease and saving the world. I am not curing a disease or saving the world.

I study science because it’s cool. I study basic science — asking questions for the purpose of learning the answer. That doesn’t mean what I do isn’t important. Lots of ground-breaking medical advances have been made just because someone asked a question no one else thought to ask.

To all you ladies fighting the good fight in other fields, keep at it, because the numbers are going up for women with advanced degrees.

I’ve always wanted to be some sort of scientist. When I was in elementary school I wanted to be a paleontologist because dinosaurs are awesome (and so was “Jurassic Park”). When I was 11, I read the Hot Zone and knew I wanted to be a biologist. Though there were times that I flirted with the Dark Side, i.e., medical school, but mostly only because when my teachers figured out I was good at science they said go to medical school. No one even suggested becoming a scientist.

Great stuff. Good Luck, Caitlin.

Related: Movie Aims to Inspire College Students With Tales of Successful Minority ScientistsKids on Scientists: Before and After Talking to Real Live ScientistsWomen Choosing Other Fields Over Engineering, Math, Physics and Computer Science

Molecule Found in Sharks Kills Many Viruses that are Deadly to People

photo of 3 dogfish sharks
Shark Molecule Kills Human Viruses, Too

“Sharks are remarkably resistant to viruses,” study researcher Michael Zasloff, of the Georgetown University Medical Center, told LiveScience. Zasloff discovered the molecule, squalamine, in 1993 in the dogfish shark, a small- to medium-size shark found in the Atlantic, Pacific, and Indian Oceans.

“It looked like no other compound that had been described in any animal or plant before. It was something completely unique,” Zasloff said. The compound is a potent antibacterial and has shown efficacy in treating human cancers and an eye condition known as macular degeneration, which causes blindness.

By studying the compound’s structure and how it works in the human body, Zasloff thought it might have some antiviral properties. He saw that the molecule works by sticking to the cell membranes of the liver and blood vessels. While there, it kicks off other proteins, some of which are essential for viruses to enter and survive in the cell.

The researchers decided to test the compound on several different live viruses that infect liver cells, including hepatitis B, dengue virus and yellow fever. They saw high efficacy across the board.

Zasloff hopes to start human trials in the next few years.

Marc Maresca, a researcher at Paul Cézanne University in Aix-en-Provence, France, who wasn’t involved in the study, agreed that the concentrations used were quite high, possibly in toxic ranges for some cells, but in an email to LiveScience Meresca also called the study “very exciting.”

Related: Alligator Blood Provides Strong Resistance to Bacteria and VirusesFemale Sharks Can Reproduce AloneMonarch Butterflies Use Medicinal Plants

Gamers Use Foldit to Solve Enzyme Configuration in 3 Weeks That Stumped Scientists for Over a Decade

Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, a very cool online game that allows players to collaborate and compete in predicting the structure of protein molecules that I wrote about before: Foldit – the Protein Folding Game. You can download it, play, and help move our understanding forward.

After scientists repeatedly failed to piece together the structure of a protein-cutting enzyme from an AIDS-like virus, they called in the Foldit players. The scientists challenged the gamers to produce an accurate model of the enzyme. They did it in only three weeks.

This class of enzymes, called retroviral proteases, has a critical role in how the AIDS virus matures and proliferates. Intensive research is under way to try to find anti-AIDS drugs that can block these enzymes, but efforts were hampered by not knowing exactly what the retroviral protease molecule looks like.

“We wanted to see if human intuition could succeed where automated methods had failed,” said Dr. Firas Khatib of the University of Washington Department of Biochemistry. Khatib is a researcher in the protein structure lab of Dr. David Baker, professor of biochemistry.

Remarkably, the gamers generated models good enough for the researchers to refine and, within a few days, determine the enzyme’s structure. Equally amazing, surfaces on the molecule stood out as likely targets for drugs to de-active the enzyme.

“These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs,” wrote the authors of a paper appearing Sept. 18 in Nature Structural & Molecular Biology. The scientists and gamers are listed as co-authors.

This is the first instance that the researchers are aware of in which gamers solved a longstanding scientific problem.

“The focus of the UW Center for Game Sciences,” said director Dr. Zoran Popovic, associate professor of computer science and engineering, “is to solve hard problems in science and education that currently cannot be solved by either people or computers alone.”

The solution of the virus enzyme structure, the researchers said, “indicates the power of online computer games to channel human intuition and three-dimensional pattern matching skills to solve challenging scientific problems.”

With names like Foldit Contenders Group and Foldit Void Crushers Group, the gamer teams were fired up for the task of real-world molecule modeling problems. The online protein folding game captivates thousands of avid players worldwide and engages the general public in scientific discovery.

Direct manipulation tools, as well as assistance from a computer program called Rosetta, encourage participants to configure graphics into a workable protein model. Teams send in their answers, and UW researchers constantly improve the design of the game and its puzzles by analyzing the players’ problem-solving strategies.

Figuring out the shape and misshape of proteins contributes to research on causes of and cures for cancer, Alzheimer’s, immune deficiencies and a host of other disorders, as well as to environmental work on biofuels.

Dr. Seth Cooper, of the UW Department of Computing Science and Engineering, is a co-creator of Foldit and its lead designer and developer. He studies human-computer exploration methods and the co-evolution of games and players.

“People have spatial reasoning skills, something computers are not yet good at,” Cooper said. “Games provide a framework for bringing together the strengths of computers and humans. The results in this week’s paper show that gaming, science and computation can be combined to make advances that were not possible before.”

Games like Foldit are evolving. To piece together the retrovirus enzyme structure, Cooper said, gamers used a new Alignment Tool for the first time to copy parts of know molecules and test their fit in an incomplete model.

According to Popovic, “Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries. We are currently applying the same approach to change the way math and science are taught in school.”

Related: Letter on the discoveryAlgorithmic Self-AssemblyPhun Physics Software GameCool Mechanical Simulation System

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