Posts about curiouscat

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:

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

Related: Science, Engineering and Math Fellowships (2008)Proposal to Triple NSF GFRP Awards and the Size of the Awards by 33% (2007)HHMI Expands Support of Postdoctoral ScientistsNSF Graduate Research Fellow Profiles (Sergy Brin, Google co-founder)

A Healthy Lifestyle is More About Health Care than the Sickness Management That We Call Health Care Is

American Heart Association Recommendations for Physical Activity in Adults

Being physically active is important to prevent heart disease and stroke, the nation’s No. 1 and No. 4 killers. To improve overall cardiovascular health, we suggest at least 150 minutes per week of moderate exercise or 75 minutes per week of vigorous exercise (or a combination of moderate and vigorous activity). Thirty minutes a day, five times a week is an easy goal to remember. You will also experience benefits even if you divide your time into two or three segments of 10 to 15 minutes per day.

For people who would benefit from lowering their blood pressure or cholesterol, we recommend 40 minutes of aerobic exercise of moderate to vigorous intensity three to four times a week to lower the risk for heart attack and stroke.

The simplest, positive change you can make to effectively improve your heart health is to start walking. It’s enjoyable, free, easy, social and great exercise. A walking program is flexible and boasts high success rates because people can stick with it.

It really is important for giving yourself the best chance for health by taking sensible steps to exercise based on your own situation (obviously some health conditions may limit your ability to exercise safely, which is something each person has to judge and see a doctor about if necessary).

Doing small things like using a treadmill while you watch TV or taking the stairs instead of the elevator for short trips can help. Another option is to walk instead of driving your car, or if you drive parking a few blocks away (or at the far side of the parking lot) walking, or if you are running several errands walk between those that you can even if you are using your car. Biking to work is another healthy lifestyle choice (if you city has made this safe – too often they fail to do sensible things).

photo of a forest

Forest hike on Hole in the Wall trail, Olympic National Park, Oregon, USA by John Hunter

Swimming is good exercise and something I took up several years ago (I was super lame at first but within a month or two it was better. I love hiking through national parks. A standing desk (or treadmill desk) is another option to reduce the damage of our sedentary lives.

Another thing to remember is losing weight is hard. It is better to avoid gaining too much weight in the first place. Avoiding the weight gain may also be a challenge but it is better than the alternative.

Too often we treat “health care” as sickness management. Doing things like creating a healthy lifestyle are are health care. Taking pills and antibiotics is mainly about sickness management.

Related: Better Health Through Exercise, Not Smoking, Low Weight, Healthy Diet and Low Alcohol IntakePhysical Activity for Adults: Inactivity Leads to 5.3 Million Early Deaths a YearHealthy Diet, Healthy Living, Healthy WeightStudy Finds Obesity as Teen as Deadly as Smoking

Refusal to Follow Scientific Guidance Results in Worms Evolving to Eat Corn Designed to Kill The Worms

An understanding of natural selection and evolution is fundamental to understanding science, biology, human health and life. Scientists create wonderful products to improve our lives: vaccines, antibiotics, etc.; if we don’t use them or misuse them it is a great loss to society.

There is also great value in genetic enhanced seeds and thus plants (through natural human aided processes such as breeding and providing good genetic material over a wide area – distances that would not be covered naturally, at least not in a time that helps us much). Genetic Modified Organisms (GMO) food, in which we tinker with the genes directly also holds great promise but has risks, especially if we forget basic scientific principles such as biodiversity.

Voracious Worm Evolves to Eat Biotech Corn Engineered to Kill It

First planted in 1996, Bt corn quickly became hugely popular among U.S. farmers. Within a few years, populations of rootworms and corn borers, another common corn pest, had plummeted across the midwest. Yields rose and farmers reduced their use of conventional insecticides that cause more ecological damage than the Bt toxin.

By the turn of the millennium, however, scientists who study the evolution of insecticide resistance were warning of imminent problems. Any rootworm that could survive Bt exposures would have a wide-open field in which to reproduce; unless the crop was carefully managed, resistance would quickly emerge.

Key to effective management, said the scientists, were refuges set aside and planted with non-Bt corn. Within these fields, rootworms would remain susceptible to the Bt toxin. By mating with any Bt-resistant worms that chanced to evolve in neighboring fields, they’d prevent resistance from building up in the gene pool.

But the scientists’ own recommendations — an advisory panel convened in 2002 by the EPA suggested that a full 50 percent of each corn farmer’s fields be devoted to these non-Bt refuges — were resisted by seed companies and eventually the EPA itself, which set voluntary refuge guidelines at between 5 and 20 percent. Many farmers didn’t even follow those recommendations.

Using extremely powerful tools like GMO requires society to have much better scientific literacy among those making decisions than any societies have shown thus far. The failure of our governments to enforce sensible scientific constraints on such use of genetic engineering creates huge risks to society. It is due to this consistent failure of our government to act within sensible scientific constraints that causes me to support efforts (along with other reasons – economic understanding – the extremely poor state of patent system, risk reduction…) to resist the widespread adoption of GMO, patenting of life (including seeds and seeds produced by seeds).

Wonderful things are possible. If we grow up and show a long term track record of being guided by scientific principles when the risks of not doing so are huge then I will be more supportive of using tactics such as GMO more easily. But I don’t see us getting their anytime soon. If anything we are much less scietifically minded and guided than we were 50 years ago: even while we bask in the glorious wonders science has brought us on a daily basis.

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Math Education Results Show China, Singapore, Korea and Japan Leading

The most comprehensive comparison of student achievement in math and science around the globe undertaken by the Organisation for Economic Co-operation and Development (OECD). The 2012 Program for International Student Assessment (PISA) focuses on math understanding of 15 year olds (the 2014 report will focus on science). The 2009 report focused on the results of science education student achievement around the globe.

2012 results for the math portion (rank – country – mean score)(I am not listing all countries):

  • 1 – Singapore – 573
  • 2 – Korea – 554
  • 3 – Japan – 536
  • 5 – Switzerland – 531
  • 6 – Netherlands – 523
  • 7 – Estonia – 521
  • 8 – Finland – 519
  • 9 – Canada – 518
  • 12 – Germany – 514
  • 24 – UK – 494 (this is also the OECD average)
  • 34 – USA – 481
  • 49 – Malaysia – 421
  • 50 – Mexico – 413

All 34 OECD member countries and 31 partner countries and economies participated in PISA 2012, representing more than 80% of the world economy. Portions of China participated and did very well including Shanghai-China (highest mean score of 613 points – if you ranked that as a country, I ignored these “regional results” in the ranks I shown here), Hong Kong-China (561, 3rd if including countries and regions together), Chinese Taipei [Taiwan] (560, 4th), Macao-China (538, 6th).

Boys perform better than girls in mathematics in 38 out of the 65 countries and economies that participated in PISA 2012, and girls outperform boys in 5 countries.

Related: Playing Dice and Children’s NumeracyNumeracy: The Educational Gift That Keeps on GivingMathematicians Top List of Best OccupationsThe Economic Consequences of Investing in Science EducationCountry H-index Ranking for Science PublicationsEconomic Strength Through Technology Leadership

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Our Dangerous Antibiotic Practices Carry Great Risks

Our continued poor antibiotics practices increase the risk of many deaths. We are very poor at reacting to bad practices that will kill many people in the future. If those increased deaths happened today it is much more likely we would act. But as it is we are condemning many to have greatly increased odds of dying from bacterial causes that could be prevented if we were more sensible.

Resistance to antibiotics is becoming a crisis

Increasingly, microbes are becoming untreatable. Margaret Chan, director general of the World Health Organization, warned in March of a dystopian future without these drugs. “A post-antibiotic era means, in effect, an end to modern medicine as we know it,” she said. “Things as common as strep throat or a child’s scratched knee could once again kill.”

evidence is mounting that antibiotics are losing efficacy. Through the relentless process of evolution, pathogens are evading the drugs, a problem known broadly as antimicrobial resistance.

Europe has launched a $741 million, seven-year, public-private collaborative research effort to accelerate drug development.

Seeking new antibiotics is wise but the commentary completely ignores our bad practices that are causing the problem to be much worse than it would be if we acted as though bad practices that will lead to many deaths should be avoided.

Previous posts about practices we taking that create great risk for increased deaths: Antibiotics Too Often Prescribed for Sinus Woes (2007)Meat Raised Without Antibiotics is Sadly Rare Today (2007)Overuse of Antibiotics (2005)CDC Urges Increased Effort to Reduce Drug-Resistant Infections (2006)FDA May Make Decision That Will Speed Antibiotic Drug Resistance (2007)Antibacterial Soaps are Bad (2007)Waste Treatment Plants Result in Super Bacteria (2009)Antibiotics Breed Superbugs Faster Than Expected (2010)Antibiotics Use in Farming Can Create Superbugs (2010)What Happens If the Overuse of Antibiotics Leads to Them No Longer Working? (2011)Dangerous Drug-Resistant Strains of TB are a Growing Threat (2012)

Obviously bacteria evolve to survive the counter measures we currently have. The foolish practices of promoting ignorance of evolution leads to a society where the consequences of actions, and the presence of evolution, lead to bad consequences. We find ourselves in that society.

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Star Stuff: The Universe is In Us

Great statement from Neil DeGrasse Tyson on “what is the most astounding fact you can share with us about the universe.”

“The atoms that comprise life on earth, the atoms that make up the human body, are traceable to the crucibles that cooked light elements into heavy elements in their core under extreme temperatures and pressures. These stars, the high mass ones among them, went unstable in their later years. They collapsed and then exploded scattering their enriched guts across the galaxy. Guts made of carbon, nitrogen, oxygen, and all the fundamental ingredients of life itself. These ingredients become part of gas clouds that condense, collapse, form the next generation of solar systems: stars with orbiting planets. And those planets now have the ingredients for life itself. So when I look up at the night sky and I know that, yes we are part of this universe, we are in this universe, but perhaps more important than both of those facts, is that the universe is in us… my atoms came from those stars….”

I think this might well be my thought on the most astounding fact also. Ever since I learned the atoms we are made of were created inside stars it has never ceased to amaze me.

Neil DeGrasse Tyson is amazing. I would edit his statement a bit myself, though, to make it:

“The most astounding fact is that the atoms that comprise life on earth, the atoms that make up the human body, were created in the crucible of stars that cooked light elements into heavy elements. Those stars went unstable, in their later years: they collapsed and then explored scattering their enriched cores across the galaxy. Those stars made the carbon, nitrogen, oxygen, and all the fundamental ingredients of life itself. Those ingredients became part of gas clouds that condensed to form the next generation of solar systems: stars with orbiting planets. And those planets have the ingredients for life. So when I look up at the night sky, I know that my atoms came from the predecessors of the stars I see.”

Related: Scientifically Literate People See a Different WorldTen Things Everyone Should Know About ScienceGravity and the Scientific MethodThe Importance of Science Education

Healthy Diet, Healthy Living, Healthy Weight

Living and eating healthily is tricky but not entirely confusing. The whole area of eating healthy food and what is a healthy weight is one where the scientific inquiry process and the complexity of scientific research on what is healthy for us is clear. Scientists study various issues and learn things but creating simple rules has proven difficult. Different studies seem to show benefits of contradictory advice, advice once seen as wise is now seen as wrong…

This is an area I am far from knowledgable about. Still I try to pay some attention as I like being healthy. Being sick is the quickest way to appreciate how great it is to be healthy. From various things I have skimmed it seems there is more evidence from several studies about how difficult it is to lose weight. Our bodies seem to work against our efforts.

And this, it seems to me, makes the problem of increasing childhood and teen obesity even more important to deal with as soon as issues arise.

It seems to me the most important thing to take from this, is the importance of maintaining a healthy weight: since you can’t just easily make up for a bad year of weight gain. I am not sure why I haven’t seen this note in most of what I have read – I suspect it is our reluctance to make value judgements about what is healthy. The problem I see with that is, the best advice we have is confusing enough without people with more knowledge being reluctant to state their best advice given the current knowledge. That doesn’t mean the suggestions are right, but at least they are educated guesses.

I try to eat relatively healthily. Which for me means taking steps to increase the amount of vegetables I eat (especially greens and some fiber) and decrease the amount of sweets and heavily processed food I eat (I still eat way too much heavily processed food). And I try to exercise as it seems to have many benefits including helping make up for some weaknesses in your diet (like eating too many calories and too many “empty calories). In my opinion (which on this topic may well not be worth much) eating a bit more stuff that really isn’t so good for you and exercising more is an easier tradeoff than trying to eat perfectly and do the minimum amount of exercise needed to stay healthy.

I also eat yogurt – I like it and the beneficial benefits of some bacteria seems likely. I heard recently something that surprised me which is that the beneficial bacteria remain for close to 2 weeks. I figured they would be gone in a couple days. I only heard that from one source (I can’t remember now but some seemingly knowledgable source – scientist researching the area), so it might not be accurate but it was interesting.

Here is an example of one of these health studies. They find that a low protein diet resulted in a loss of “lean weight” (muscle…) and more fat than a comparable diet with more protein. The same weight with a higher percentage of fat is not a good thing for human health. Thus the message is that a lower protein diet has this risk that must be considered (and therefor higher protein diets may well be wise). Of course things get much more complicated than that when we actually try to live by a diet.

Effect of Dietary Protein Content on Weight Gain, Energy Expenditure, and Body Composition During Overeating

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Encouraging Curiosity in Kids

How do you help make your children scientifically literate? I think the biggest thing you can do is encourage curiosity.

One way to encourage curiosity it is by answering their questions (and not saying: I am too busy, don’t bother me, don’t ask me?, stop asking why…). I know adults are busy and have all sorts of stuff we are trying to get done; and the question about why I need to wash my hands doesn’t seem worth answering. But I think anytime a kid is asking why is an opportunity to teach and encourage them to keep being curious.

It is very easy to shut off this curiosity, in our society anyway (we do it to the vast majority of people). The biggest difference I see between adults and kids is not maturity or responsibility but curiosity (or lack thereof in adults) and joy (versus adults who seem to be on valium all the time – maybe they are).

As they grow up kids will have lots of science and technology questions that you don’t know the answers to. If you want them to be curious and knowledgeable, put in the effort to find answers with them. You have to help them find the answers in a way that doesn’t turn them off. If you just say – go look it up yourself (which really they can do), maybe the 2% that are going to become scientists will. But most kids will just give up and turn off their curiosity a little bit more (until eventually it is almost gone and they are ready to fit into the adult world). Which is very sad.

Once you get them used to thinking and looking things up they will start to do this on their own. A lot of this just requires thinking (no need to look things up – once a certain base knowledge is achieved). But you need to set that pattern. And it would help if you were curious, thought and learned yourself.

Photo of kids intently studying on a Malaysian beach

My mom with a group of Malaysia kids apparently intent on learning something. I am there, but not visible in this photo. Photo by my father.

While walking in the park, see one of those things you are curious about and ask why does…? It is good to ask kids why and let them think about it and try and answer. Get them in the habit of asking why themselves. And in those cases when no-one knows, take some time and figure it out. Ask some questions (both for yourself – to guide your thinking – and to illustrate how to think about the question and figure things out). If you all can’t find an explanation yourselves, take some time to look it up. Then at dinner, tell everyone what you learned. This will be much more interesting to the kids than forcing them to elaborate on what they did today and help set the idea that curiosity is good and finding explanations is interesting.

It is fun as a kid if your parent is a scientist or engineer (my father was an engineering professor).

You often don’t notice traits about yourself. In the same what I know what red looks like to me, I figure we both see this red shirt you see the red that I do. But maybe you don’t. I tend to constantly be asking myself why. If I see something new (which is many, many times a day – unless I am trapped in some sad treadmill of sameness) I ask why is it that way and then try and answer. I think most of this goes on subconsciously or some barely conscious way. I actually had an example a few months ago when I was visiting home with my brother (who is pretty similar to me).

As we were driving, I had noticed some fairly tall poles that seemed to have really small solar panels on top. I then noticed they were space maybe 20 meters apart. Then saw that there seemed to be a asphalt path along the same line. I then decided, ok, they are probably solar panels to power a light for the path at night. Then my brother asked why are there those small solar panel on top of that pole?

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What Happens If the Overuse of Antibiotics Leads to Them No Longer Working?

Antibiotics have been a miraculous tool to keep up healthy. Like vaccines this full value of this tool is wasted if it is used improperly. Vaccines value is wasted when they are not used enough. Antibiotics lose potency when they are overused. The overuse of anti-biotics on humans is bad (especially the huge amount of just lazy, not scientific use). But the massive overuse in livestock is much worse, it seems to me.

The health system in the USA is broken in a huge way in which it is broken is the failure to address creating systemic behavior that promotes human health and instead just treating illness. It is much better to avoid a situation where we breed super bugs and then try to treat those super bugs that have evolved to be immune to the antibiotics we have to use.

When antibiotics no longer work

While the source of the current salmonella outbreak remains murky, we can reasonably speculate about the genesis of the bug’s drug-resistance: the reportedly endemic overuse of antibiotics by the agricultural industry.

Drugs are given to livestock for multiple reasons. An obvious one is for the treatment of diseases. When livestock are sick, veterinarians administer a significant dosage in hopes of eliminating the animal’s affliction. Another reason is preventative. Animals in close quarters are more susceptible to infection, so farmers will often administer medicine to healthy animals in order to nip anything nasty in the bud. Most controversially, though, members of the agricultural industry use antibiotics for the express purpose of promoting livestock growth.

It’s a well-known, if not entirely intuitive, fact that healthy animals who are fed small, or “sub-therapeutic,” doses of antibiotics will wind up larger than their unmedicated counterparts. In many such cases, these drugs are given to livestock through their feed or water, and without the prescription or oversight of a veterinarian, according to Dr. Gail Hansen, a senior officer at the Pew Campaign on Human Health and Industrial Farming.

An estimated 80 percent of all antibiotics in the U.S. are given to food-producing livestock, according to the FDA. And approximately 83 percent of that medicine is “administered flock- or herd-wide at low levels for non-therapeutic purposes, such as growth promotion and routine disease prevention,” according to a lawsuit filed against the FDA in May. These figures could have very real consequences for public health, because the Catch-22 of this antibiotic abandon is the widespread development of drug-resistant bacteria, colloquially referred to as “super-bugs.”

In 2006, the European Union banned all use of antibiotics on livestock for growth promotion. And the U.S. Senate will consider similar legislation this year. Sen. Dianne Feinstein, D-Calif., reintroduced the “Preservation of Antibiotics for Medical Treatment Act” last month, which would significantly rein in agricultural drug use, and strictly prohibit the application of sub-therapeutic doses of drugs that have benefits for humans.

Still, the agricultural industry disputes data about its use of antibiotics and the rise of super-bugs, and it has aggressively fought efforts to legislate the matter. As a result, it’s hard to tell how far the legislation might proceed.

Related: Antibiotics Too Often Prescribed for Sinus WoesOveruse of Antibiotics (2005)FDA May Make Decision That Will Speed Antibiotic Drug Resistance (2007)

The end of the era of antibiotics

How did this happen? The driving forces are Darwin and human carelessness. Bacteria are constantly evolving, adapting to the changing conditions they face. Antibiotics usually kill bacteria. But sometimes a bacteria will develop a biological defense – particularly if too small a dose is used.

Antibiotics require a prescription in America, but our nation is still very much a part of the problem. Patients routinely demand these drugs, and doctors acquiesce, for respiratory infections and other ailments that will not respond to antibiotics because they are caused by a virus. We use soap with antimicrobial agents when regular soap does equally well. And we allow farmers to feed antibiotics to livestock in horrifying amounts, not to treat illnesses but to make farming more efficient.

The Potential Role of Concentrated Animal Feeding Operations in Infectious Disease Epidemics and Antibiotic Resistance

This working group, which was part of the Conference on Environmental Health Impacts of Concentrated Animal Feeding Operations: Anticipating Hazards—Searching for Solutions, considered the state of the science around these issues and concurred with the World Health Organization call for a phasing-out of the use of antimicrobial growth promotants for livestock and fish production. We also agree that all therapeutic antimicrobial agents should be available only by prescription for human and veterinary use.

Antibiotic Resistance in Livestock: More at Risk Than Steak
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Gravity and the Scientific Method

One of the topics I return to repeatedly is the scientific method – theories must to tested. As evidence mounts that new ideas do a good job of explaining theories they become more accepted. But they continue to be tested in new ways as the ideas are extended and ramification are explored. And science progress means that old conventions can be overturned as new evidence is gathered.

Science is not about current beliefs. Science is about seeking knowledge. If the search for knowledge leads to evidence that old ideas were wrong those ideas are overturned. Since people are involved that process isn’t as clean as it sounds above. People get comfortable with beliefs. They build careers on expanding those beliefs. Most are uncomfortable when they are challenged and don’t accept new ideas even when the evidence mounts. But some do accept the new ideas. Some challenge the new ideas by running experiments. And some of those prove the new ideas faulty. Some become convinced of the new ideas as the results of their experiments make the new ideas seem more sensible (instead of getting the results they expected).

Building the body of scientific knowledge is not nearly as clean and simple as most people think. It isn’t a simple process, what is the underlying truth can be debatable. But the beauty of the scientific process is how it helps us overcome our biases and provide evidence to support the theories we support. The scientific method (combined with our human involvement) doesn’t mean new ideas are accepted easily but it does mean new ideas compete on the basis of evidence not just the power of those that hold the beliefs.

Is gravity not actually a force? Forcing theory to meet experiments
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Ten Things Everyone Should Know About Science

As the writer of this blog (which is located at engineering.curiouscatblog.net) I am a strong believer in the importance of scientific literacy. Neil Degrasse Tyson stated the importance very well, as I mentioned in a previous post, the scientifically literate see a different world

If you are scientifically literate the world looks very different to you. Its not just a lot of mysterious things happening. There is a lot we understand out there. And that understanding empowers you to, first, not be taken advantage of by others who do understand it. And second there are issues that confront society that have science as their foundation. If you are scientifically illiterate, in a way, you are disenfranchising yourself from the democratic process, and you don’t even know it.

The Financial Times has complied a list of the 10 things everyone should know about science

  1. Evolution – previous posts: Evolution is Fundamental to Scienceposts tagged: evolution
  2. Genes and DNA – tags: genesgeneticsDNARNA
  3. Big bang – tags: physics, posts mentioning big bang
  4. Relativity – General Relativity Einstein/Essen Anniversary Test – posts mentioning relativity
  5. Quantum mechanics – Quantum Mechanics Made Relatively Simple Podcasts, Quantum mechanics
  6. Radiation
  7. Atoms and nuclear reactions
  8. Molecules and chemical reactions – posts on chemistry
  9. Digital data – I must admit, even reading their comments, I don’t understand what they are thinking here. There certainly is a great deal of digital data and the future certainly going to involve a great deal more, but this just doesn’t fit, in my opinion.
  10. Statistical significance – Seeing Patterns Where None Exists, Statistics Insights for Scientists and Engineers, Correlation is Not Causation post on statisticsexperimentation

It is a challenge to create such a list. I agree with most of what they have. I would like to look at changing the last 2 and radiation, though. I would probably include something about the scientific method rather than statistical significance. Another area I would consider is something about bacteria and/or viruses. You can maybe include them under genes, but viruses and bacteria are amazing in the very strange things they do with genes and I think that is worthy of its own item. Another possibility is thinking of separating out a second spot for things related to the scientific method – causation, randomized testing, multivariate experiments… I would also consider one, or more of the following or something related to them biology – chlorophyll, the the life of bacteria in our bodies, something related to human health (how drugs work, medical studies…), etc..

The Ten Things Everyone Should Know About Science

Evolution through natural selection remains as valid today as it was 150 years ago when expressed with great elegance by Charles Darwin in The Origin of Species. The mechanism of evolution depends on the fact that tiny hereditable changes take place the whole time in all organisms, from microbes to people.

An important feature of Darwinian evolution is that it operates at the level of the individual. There is no mechanism for natural selection to change the species as a whole, other than through the accumulation of changes that lead to the survival of the fittest individuals.

The rate of evolution varies enormously between different types of organism and different environmental circumstances. It can proceed very quickly when the pressure is great, as, for example, with bacteria exposed to antibiotics, when drug-resistant mutations may arise and spread through the bacterial population within months.

Why does it matter? Evolution is coming under renewed assault, particularly in the US, from fundamentalist Christians who want creationism to be taught in schools. Although evolution has had virtually unanimous support from professional scientists for at least a century, polls show that American public opinion still favours creationism.

Related: Poor Results on Evolution and Big Bang Questions Omitted From NSF ReportNearly Half of Adults in the USA Don’t Know How Long it Takes the Earth to Circle the SunScience Knowledge Quiz