Category Archives: Science

Funding Sources for Independent Postdoctoral Research Projects in Biology

Here is a nice list of funding sources for independent postdoctoral research projects in biology.

Some examples:

Banting Postdoctoral Fellowships. Eligibility: Canadian citizens, foreign citizens – so about everybody 🙂
Starting Grants, European Research Council, Europe. “ERC grants are open to researchers of any nationality in the world, any scientific field, any age.”
Max Planck Research Group, Germany – “The Max Planck Society is committed to support Open Access on all levels. We therefore ask applicants to highlight in their list of publications all items which are freely available in an open access repository or on a journal’s website.”
Research Fellowships for Young Scientists, Japan Society for the Promotion of Science – “Young researchers in all fields of the humanities, social sciences and natural sciences are eligible to apply.” “This fellowship program is Japan’s core program for cultivating young Japanese researchers. However, there is no nationality requirement for applications.”
NSF Postdoctoral Fellows. For at least some, maybe all, “be a U.S. citizen (or national) or a U.S. permanent resident, i.e., have a “green card,” when applying; “
Research Associateship Programs, The National Academies of Sciences, Engineering, and Medicine, “Citizenship requirements for the NRC Research Associateship Programs vary depending on the sponsoring federal laboratory.”

Directory of select science and engineering scholarships and fellowships for undergraduates, graduates and faculty on our blog.

Youyou Tu: The First Chinese Woman to Win a Nobel Prize

The Nobel Prize in Physiology or Medicine 2015 was divided, one half jointly to William C. Campbell (born Ireland, now USA) and Satoshi ÅŒmura (Japan) “for their discoveries concerning a novel therapy against infections caused by roundworm parasites” and the other half to Youyou Tu (China) “for her discoveries concerning a novel therapy against Malaria”.

Youyou Tu is the first Chinese woman to win a Nobel Prize.

Diseases caused by parasites have plagued humankind for millennia and constitute a major global health problem. In particular, parasitic diseases affect the world’s poorest populations and represent a huge barrier to improving human health and wellbeing. This year’s Nobel Laureates have developed therapies that have revolutionized the treatment of some of the most devastating parasitic diseases.

William C. Campbell and Satoshi ÅŒmura discovered a new drug, Avermectin, the derivatives of which have radically lowered the incidence of River Blindness and Lymphatic Filariasis, as well as showing efficacy against an expanding number of other parasitic diseases. Youyou Tu discovered Artemisinin, a drug that has significantly reduced the mortality rates for patients suffering from Malaria.

These two discoveries have provided humankind with powerful new means to combat these debilitating diseases that affect hundreds of millions of people annually. The consequences in terms of improved human health and reduced suffering are immeasurable.

via Noble Prize website

Malaria was traditionally treated by chloroquine or quinine, but with declining success. By the late 1960s, efforts to eradicate Malaria had failed and the disease was on the rise. At that time, Youyou Tu in China turned to traditional herbal medicine to tackle the challenge of developing novel Malaria therapies. From a large-scale screen of herbal remedies in Malaria-infected animals, an extract from the plant Artemisia annua emerged as an interesting candidate.

However, the results were inconsistent, so Tu revisited the ancient literature and discovered clues that guided her in her quest to successfully extract the active component from Artemisia annua. Tu was the first to show that this component, later called Artemisinin, was highly effective against the Malaria parasite, both in infected animals and in humans. Artemisinin represents a new class of antimalarial agents that rapidly kill the Malaria parasites at an early stage of their development, which explains its unprecedented potency in the treatment of severe Malaria.

Youyou Tu was born in 1930 in China and is a Chinese citizen. She graduated from the Pharmacy Department at Beijing Medical University in 1955. From 1965-1978 she was Assistant Professor at the China Academy of Traditional Chinese Medicine, from 1979-1984 Associate Professor and from 1985 Professor at the same Institute. From 2000, Tu has been Chief Professor at the China Academy of Traditional Chinese Medicine. She doesn’t have a doctorate, very rare for a Nobel Prize winner in the sciences.

Read the full press release

Cancer Rates Consistent Across Species Instead of Increasing Due to Body Mass

It would seem sensible to think cancer should be more prevalent in species with a huge number of cells, and thus more cells to become cancerous. But cancer risk doesn’t increase in this way. This interesting, open source paper, sheds some light on what is behind this.

Solutions to Peto’s paradox revealed by mathematical modelling and cross-species cancer gene analysis

Whales have 1000-fold more cells than humans and mice have 1000-fold fewer; however, cancer risk across species does not increase with the number of somatic cells and the lifespan of the organism. This observation is known as Peto’s paradox. How much would evolution have to change the parameters of somatic evolution in order to equalize the cancer risk between species that differ by orders of magnitude in size? Analysis of previously published models of colorectal cancer suggests that a two- to three-fold decrease in the mutation rate or stem cell division rate is enough to reduce a whale’s cancer risk to that of a human. Similarly, the addition of one to two required tumour-suppressor gene mutations would also be sufficient.

We surveyed mammalian genomes and did not find a positive correlation of tumour-suppressor genes with increasing body mass and longevity. However, we found evidence of the amplification of TP53 in elephants, MAL in horses and FBXO31 in microbats, which might explain Peto’s paradox in those species. Exploring parameters that evolution may have fine-tuned in large, long-lived organisms will help guide future experiments to reveal the underlying biology responsible for Peto’s paradox and guide cancer prevention in humans.

Elephants in Kenya by John Hunter. See more photos from my trip to Kenya.

In another way it would make sense that large animals would have hugely increased risks of cancer. As they evolved, extremely high cancer rates would be a much bigger problem for them. Therefore it wouldn’t be surprising to find they have evolved a way of reducing cancer risks.

Despite these limitations, we found genes that have been dramatically amplified in specific mammalian genomes, the most interesting of which is the discovery of 12 TP53 copies in the genome of the African elephant. We subsequently cloned those genes and identified 19 distinct copies of TP53 in African elephants and 15–20 in Asian elephants [1]. Another potential lead for solving Peto’s paradox is MAL, which is found to have eight copies in the horse genome and two in microbat. This could be an example of convergent evolution where a large animal (horse) and a small, long-lived animal (microbat) both evolved extra copies of the same gene to overcome their increased risk of cancer. Further analysis and experimentation would need to be performed to determine the function of these copies and whether or not they provide enhanced suppression of carcinogenesis.

The researchers have found an interesting potential explanation for how that has been accomplished.

Highest Paying Fields at Mid Career in USA: Engineering, Science and Math

Payscale has again provided details on average salaries by major for various fields. Once again engineering, math and science dominate. For this data they define mid-career as those with 10+ years of experience.

The top 15 bachelor degrees by mid-career salary were all from those 3 fields. And the median salary was $168,000 for petroleum engineering degrees (at the top) to $107,000 for Aerospace Engineering and Computer Science and Mathematics (tied for 14th).

The starting salaries for those with these degrees ranged from $58,000 for Actuarial Mathematics (though by mid-career salary they were in 3rd place at $119,000) to $101,000 for petroleum engineering. My guess is petroleum engineering salaries will decline from their current highs (as they have done in previous oil price busts). The second highest paying bachelor degree starting salary was for mining engineering at $71,500 – with most of the other fairly close to that amount.

Nuclear engineering pay started at a median of $68,200 before rising to the 2nd highest mid-career level of $121,000.

Payscale also provided data based on master’s degree field. Again petroleum engineering was in first place by mid-career ($173,000). Nurse anesthesia was in second at $159,000 and held the first spot for starting median salary ($139,000).

Taxation is the only filed that is obviously not STEM (science, technology, engineering and math) related which had the lowest initial median salary of $60,700 but was tied for 5th for mid career salary at $126,000. Technology management and operations research are also not STEM fields though are a bit related to the STEM area.

PhD degree’s with the highest mid-career median earning are again all STEM fields. Economics is one many people probably don’t think of as STEM but it is (as a social science) and really it is largely mathematics at this point.

Many of the PhD starting salaries are at $100,000 (or close). The disciplines with the highest mid-career median salaries are: Electrical and Computer Engineering $142,000; Computer Engineering $139,000; Chemical Engineering $138,000; Biomedical Engineering, $137,000; and Economics $134,000.

In Many Crops Ants Can Provide Pest Protection Superior or Equal to Chemicals at a Much Lower Cost

Ants are as Effective as pesticides

The review [of over 70 studies] was conducted by Aarhus University’s Dr Joachim Offenberg, an ecologist who has studied ants for almost 20 years. It includes studies of more than 50 pest species on nine crops across eight countries in Africa, South-East Asia and Australia.

Most of the studies in Offenberg’s review are on weaver ants (Oecophylla), a tropical species which lives in trees and weaves ball-shaped nests from leaves. Because weaver ants live in their host trees’ canopy, near the flowers and fruit that need protection from pests, they are good pest controllers in tropical orchards.

All farmers need to do is collect ant nests from the wild, hang them in plastic bags among their tree crops and feed them a sugar solution while they build their new nests. Once a colony is established, farmers then connect the trees that are part of the colony with aerial ‘ant walkways’ made from string or lianas.

After that, the ants need little, except for some water in the dry season (which can be provided by hanging old plastic bottles among the trees), pruning trees that belong to different colonies so that the ants do not fight, and avoiding insecticide sprays.

The review shows that crops such as cashew and mango can be exceptionally well protected from pests by weaver ants.

One three-year study in Australia recorded cashew yields 49% higher in plots patrolled by ants compared with those protected by chemicals. Nut quality was higher too, so net income was 71% higher with ants than with chemicals.

Similar studies in Australian mango crops found that ants could produce the same yield as chemical control, but because the ants were cheaper, and fruit quality better, net income from mangoes produced with ant protection was 73% higher.

Those crops are special cases in which the ants are vastly superior. But in many other cases ants are as effective and much cheaper than chemical options. Different species of ants are suited to protecting different types of drops. Weaver ants require a canopy, other ants can protect crops without a canopy.

I hope more farmers adopt ants to help protect their crop yields.

Computer Code for NASA’s Apollo Guidance System

Margaret Hamilton, NASA. Standing next to a printout of the source code she and her team wrote for the Apollo guidance computer that made the moon landings possible.

Meet Margaret Hamilton, the badass ’60s programmer who saved the moon landing

The software for the guidance computer was written by a team at the MIT Instrumentation Laboratory (now the Draper Laboratory), headed up by Margaret Hamilton.
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The guidance computer used something known as “core rope memory“: wires were roped through metal cores in a particular way to store code in binary. “If the wire goes through the core, it represents a one,” Hamilton explained in the documentary Moon Machines. “And around the core it represents a zero.” The programs were woven together by hand in factories. And because the factory workers were mostly women, core rope memory became known by engineers as “LOL memory,” LOL standing for “little old lady.”
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Hamilton is now 78 and runs Hamilton Technologies, the Cambridge, Massachusetts-based company she founded in 1986. She’s lived to see “software engineering” — a term she coined — grow from a relative backwater in computing into a prestigious profession.
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In the early days, women were often assigned software tasks because software just wasn’t viewed as very important. “It’s not that managers of yore respected women more than they do now,” Rose Eveleth writes in a great piece on early women programmers for Smithsonian magazine. “They simply saw computer programming as an easy job. It was like typing or filing to them and the development of software was less important than the development of hardware. So women wrote software, programmed and even told their male colleagues how to make the hardware better.”

My aunt was one of those early software engineers. She wrote a chapter for a book, Programming the IBM 360, in the 1960s. My uncle was one of the first employees at NASA and rose to be one of the senior administrators there over his career.

It is great when society is able to capture the value individuals are capable of providing. We need to make sure we allow everyone opportunities to contribute. We do well in many ways but we also do lose from discrimination and also just making it uncomfortable for people to contribute in certain roles when we need not do so.

We have accomplished great things with software in the last 40 years. We could have accomplished more if we had done a better job of allowing women to contribute to the efforts in this field.

Intel International Science and Engineering Fair 2015

Raymond Wang, 17, of Canada was awarded first place for engineering a new air inlet system for airplane cabins to improve air quality and curb disease transmission at this year’s Intel International Science and Engineering Fair.

Wang’s system improves the availability of fresh air in the cabin by more than 190% while reducing pathogen inhalation concentrations by up to 55 times compared to conventional designs, and can be easily and economically incorporated in existing airplanes. Wang received the Gordon E. Moore Award of US$75,000. The system uses vents to create a “bubble” around passengers that deflects incoming air.

Nicole Ticea, 16, of Canada received one of two Intel Foundation Young Scientist Awards of US$50,000 for developing an inexpensive, easy-to-use testing device to combat the high rate of undiagnosed HIV infection in low-income communities. Her disposable, electricity-free device provides results in an hour and should cost less than US$5 to produce. Ticea has already founded her own company, which recently received a US$100,000 grant to continue developing her technology.

Karan Jerath, 18, of Friendswood, Texas, received the other Intel Foundation Young Scientist Award of US$50,000 for refining and testing a novel device that should allow an undersea oil well to rapidly and safely recover following a blowout. Jerath developed a better containment enclosure that separates the natural gas, oil and ocean water; accommodates different water depths, pipe sizes and fluid compositions; and can prevent the formation of potentially clogging methane hydrate.

This year’s Intel International Science and Engineering Fair featured approximately 1,700 young scientists selected from 422 affiliate fairs in more than 75 countries, regions and territories.

Images of 200 Calorie Portions of Various Foods

Wisegeek has photographed what 200 calories of various foods looks like. A small sample is shown here:

photos of 200 calorie portions of various foods

Some of the other 200 calorie portions they show are 1425 grams of celery, 588 grams of broccoli, 385 grams of apples, 333 ml of whole milk, 290 grams of grapes, 204 grams of sliced smoked turkey, 150 grams of eggs, 72 grams of a blueberry muffin, 53 grams of brown sugar and 52 grams of a donut or pretzel.

Chimpanzees Use Spears to Hunt Bush Babies

Video replaced with new one because original was removed 🙁

Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools by Jill D. Pruetz and Paco Bertolani

Although tool use is known to occur in species ranging from naked mole rats to owls, chimpanzees are the most accomplished tool users. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these.

Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.

The full paper, from 2007, was available as a pdf when I visited (I don’t really trust these publishers and what articles by professors they will block access to later when they don’t clearly say it is open access – in fact the journal broke the link on the post I made about this in 2007 now that I checked – sigh).

The full paper isn’t filled with overly complex scientific jargon (as scientific papers can be). In that sense it is an easy read; it is a bit graphic for those that are squeamish.

Dr. Jill Pruetz maintains an interesting blog the Chimpanzees she studies: Fongoli Savanna Chimpanzee Project

Scientific Inquiry Leads to Using Fluoride for Healthy Teeth

This webcast, from the wonderful SciShow, explores how we discovered fluoride helps prevent tooth decay and how we then used that knowledge and finally discovered why it worked.

I love stories of how we learn for observing what is happening. We don’t always need to innovate by thinking up creative new ideas. If we are observant we can pick up anomalies and then examine the situation to find possible explanations and then experiment to see if those explanations prove true.

When working this way we often are seeing correlation and then trying to figure out which part of the correlation is an actual cause. So in this dental example, a dentist noticed his patients had bad brown stains on their teeth than others populations did.

After investigation the natural fluoridation of the water in Colorado Springs, Colorado, USA seemed like it might be an explanation (though they didn’t understand the chemistry that would cause that result). They also explored the sense that the discolored teeth were resistant to decay.

Even without knowing why it is possible to test if the conditions are the cause. Scientists discovered by reducing the level of fluoridation in the water the ugly brown stains could be eliminated (these stains took a long time to develop and didn’t develop in adults). Eventually scientists ran an experiment in Grand Rapids, Michigan and found fluoridation of the water achieved amazing results for dental health. The practice of fluoridation was then adopted widely and resulted in greatly improved dental health.

In 1901, Frederick McKay, a recent dental school graduate, opened a dental practice in Colorado Springs, Colorado. He was interested in what he saw and sought out other dentists to explore the situation with him but had little success. In 1909, he found some success when renowned dental researcher Dr. G.V. Black collaborate with him.
Dr. H. Trendley Dean, head of the Dental Hygiene Unit at the National Institute of Health built on their work when he began investigating the epidemiology of fluorosis in 1931. It wasn’t until 1945 that the Grand Rapids test started. Science can take a long time to move forward.

Only later did scientists unravel why this worked. The fluoride reacts to create a stronger enamel than if the fluoride is not present. Which results in the enamal being less easily dissolved by bacteria.
Health tip: use a dental stimudent (dental picks) or floss your teeth to maintain healthy gums and prevent tooth decay. It makes a big difference.