Tag Archives: quote

Trying to Find Pest Solutions While Hoping Evolution Doesn’t Exist Doesn’t Work

Melander wondered why some populations of scales were becoming able to resist pesticides. Could the sulfur-lime spray trigger a change in their biology, the way manual labor triggers the growth of callouses on our hands? Melander doubted it. After all, ten generations of scales lived and died between sprayings. The resistance must be hereditary, he reasoned. He sometimes would find families of scales still alive amidst a crowd of dead insects.

This was a radical idea at the time. Biologists had only recently rediscovered Mendel’s laws of heredity. They talked about genes being passed down from one generation to the next, yet they didn’t know what genes were made of yet. But they did recognize that genes could spontaneously change–mutate–and in so doing alter traits permanently.
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In the short term, Melander suggested that farmers switch to fuel oil to fight scales, but he warned that they would eventually become resistant to fuel oil as well. In fact, the best way to keep the scales from becoming entirely resistant to pesticides was, paradoxically, to do a bad job of applying those herbicides. By allowing some susceptible scales to survive, farmers would keep their susceptible genes in the scale population. “Thus we may make the strange assertion that the more faulty the spraying this year the easier it will be to control the scale the next year,” Melander predicted.
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What’s striking is how many different ways weeds have found to overcome the chemical. Scientists had thought that Roundup was invincible in part because the enzyme it attacks is pretty much the same in all plants. That uniformity suggests that plants can’t tolerate mutations to it; mutations must change its shape so that it doesn’t work and the plant dies. But it turns out that many populations of ryegrass and goosegrass have independently stumbled across one mutation that can change a single amino acid in the enzyme. The plant can still survive with this altered enzyme. And Roundup has a hard time attacking it thanks to its different shape.
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Another way weeds fight off Roundup is through sheer numbers. Earlier this year an international team of scientists reported their discovery of how Palmer amaranth resists glyphosate. The plants make the ordinary, vulnerable form of the enzyme. But the scientists discovered that they have many extra copies of the gene for the enzyme–up to 160 extra copies, in fact.
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What makes the evolution of Roundup resistance all the more dangerous is how it doesn’t respect species barriers. Scientists have found evidence that once one species evolves resistance, it can pass on those resistance genes to other species. They just interbreed, producing hybrids that can then breed with the vulnerable parent species.

Another great article from Carl Zimmer.

Why Wasn’t the Earth Covered in Ice 4 Billion Years Ago – When the Sun was Dimmer

Climate scientists from all over the globe are now able to test their climate models under extreme conditions thanks to Professor Minik Rosing, University of Copenhagen. Rosing has solved one of the great mysteries and paradoxes of our geological past, namely, “Why the earth’s surface was not just one big lump of ice four billion years ago when the Sun’s radiation was much weaker than it is today.” Until now, scientists have presumed that the earth’s atmosphere back then consisted of 30% carbon dioxide (CO2) which ensconced the planet in a protective membrane, thereby trapping heat like a greenhouse.

The faint early sun paradox
In 1972, the late, world famous astronomer Carl Sagan and his colleague George Mullen formulated “The faint early sun paradox. ” The paradox consisted in that the earth’s climate has been fairly constant during almost four of the four and a half billion years that the planet has been in existence, and this despite the fact that radiation from the sun has increased by 25-30 percent.

The paradoxical question that arose for scientists in this connection was why the earth’s surface at its fragile beginning was not covered by ice, seeing that the sun’s rays were much fainter than they are today. Science found one probable answer in 1993, which was proffered by the American atmospheric scientist, Jim Kasting. He performed theoretical calculations that showed that 30% of the earth’s atmosphere four billion years ago consisted of CO2. This in turn entailed that the large amount of greenhouse gases layered themselves as a protective greenhouse around the planet, thereby preventing the oceans from freezing over.

Mystery solved
Now, however, Professor Minik Rosing, from the Natural History Museum of Denmark, and Christian Bjerrum, from the Department of Geography and Geology at University of Copenhagen, together with American colleagues from Stanford University in California have discovered the reason for “the missing ice age” back then, thereby solving the sun paradox, which has haunted scientific circles for more than forty years.

Professor Minik Rosing explains, “What prevented an ice age back then was not high CO2 concentration in the atmosphere, but the fact that the cloud layer was much thinner than it is today. In addition to this, the earth’s surface was covered by water. This meant that the sun’s rays could warm the oceans unobstructed, which in turn could layer the heat, thereby preventing the earth’s watery surface from freezing into ice. The reason for the lack of clouds back in earth’s childhood can be explained by the process by which clouds form. This process requires chemical substances that are produced by algae and plants, which did not exist at the time. These chemical processes would have been able to form a dense layer of clouds, which in turn would have reflected the sun’s rays, throwing them back into the cosmos and thereby preventing the warming of earth’s oceans. Scientists have formerly used the relationship between the radiation from the sun and earth’s surface temperature to calculate that earth ought to have been in a deep freeze during three billion of its four and a half billion years of existence. Sagan and Mullen brought attention to the paradox between these theoretical calculations and geological reality by the fact that the oceans had not frozen. This paradox of having a faint sun and ice-free oceans has now been solved.”

CO2 history iluminated
Minik Rosing and his team have by analyzing samples of 3.8-billion-year-old mountain rock from the world’s oldest bedrock, Isua, in western Greenland, solved the “paradox”.

But more importantly, the analyses also provided a finding for a highly important issue in today’s climate research – and climate debate, not least: whether the atmosphere’s CO2 concentration throughout earth’s history has fluctuated strongly or been fairly stable over the course of billions of years.

“The analyses of the CO2-content in the atmosphere, which can be deduced from the age-old Isua rock, show that the atmosphere at the time contained a maximum of one part per thousand of this greenhouse gas. This was three to four times more than the atmosphere’s CO2-content today. However, not anywhere in the range of the of the 30 percent share in early earth history, which has hitherto been the theoretical calculation. Hence we may conclude that the atmosphere’s CO2-content has not changed substantially through the billions of years of earth’s geological history. However, today the graph is turning upward. Not least due to the emissions from fossil fuels used by humans. Therefore it is vital to determine the geological and atmospheric premises for the prehistoric past in order to understand the present, not to mention the future, in what pertains to the design of climate models and calculations,” underscores Minik Rosing.

Full press release from the University of Copenhagen in Denmark.

Statistical Errors in Medical Studies

I have written about statistics, and various traps people often fall into when examining data before (Statistics Insights for Scientists and Engineers, Data Can’t Lie – But People Can be Fooled, Correlation is Not Causation, Simpson’s Paradox). And also have posted about reasons for systemic reasons for medical studies presenting misleading results (Why Most Published Research Findings Are False, How to Deal with False Research Findings, Medical Study Integrity (or Lack Thereof), Surprising New Diabetes Data). This post collects some discussion on the topic from several blogs and studies.

HIV Vaccines, p values, and Proof by David Rind

if vaccine were no better than placebo we would expect to see a difference as large or larger than the one seen in this trial only 4 in 100 times. This is distinctly different from saying that there is a 96% chance that this result is correct, which is how many people wrongly interpret such a p value.
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So, the modestly positive result found in the trial must be weighed against our prior belief that such a vaccine would fail. Had the vaccine been dramatically protective, giving us much stronger evidence of efficacy, our prior doubts would be more likely to give way in the face of high quality evidence of benefit.
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While the actual analysis the investigators decided to make primary would be completely appropriate had it been specified up front, it now suffers under the concern of showing marginal significance after three bites at the statistical apple; these three bites have to adversely affect our belief in the importance of that p value. And, it’s not so obvious why they would have reported this result rather than excluding those 7 patients from the per protocol analysis and making that the primary analysis; there might have been yet a fourth analysis that could have been reported had it shown that all important p value below 0.05.

How to Avoid Commonly Encountered Limitations of Published Clinical Trials by Sanjay Kaul, MD and and George A. Diamond, MD

Trials often employ composite end points that, although they enable assessment of nonfatal events and improve trial efficiency and statistical precision, entail a number of shortcomings that can potentially undermine the scientific validity of the conclusions drawn from these trials. Finally, clinical trials often employ extensive subgroup analysis. However, lack of attention to proper methods can lead to chance findings that might misinform research and result in suboptimal practice.

Why Most Published Research Findings Are False by John P. A. Ioannidis
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$100,000 Lemelson-MIT Award for Sustainability

[Sadly the video was made private so I removed it. It is disappointing how often people fail to follow decade old usability advice to make internet urls permanent]

According to the United Nations, more than 40 percent of Africans live in poverty, subsisting on less than US$1 a day. As co-founder and CEO of the nonprofit social enterprise KickStart, Fisher develops and markets moneymaking tools such as low-cost, human-powered irrigation pumps that improve the lives of small-scale rural farmers – the majority of the poor in sub-Saharan Africa.

“These poor rural farmers have one asset: a small plot of land; and one basic skill: farming. The best business they can pursue is irrigated farming,” Fisher explained. “Once they employ irrigation, the farmers can grow and sell high-value crops, like fruits and vegetables. They can grow year-round and reap four or five harvests, instead of waiting for the rain to grow a staple crop once or twice a year.”

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Unless We Take Decisive Action, Climate Change Will Ravage Our Planet

Lake McDonald, Glacier National Park photo by John Hunter

photo by John Hunter at Glacier National Park.

Tomorrow 56 newspapers, in 45 countries, are taking the unprecedented step of publishing the same editorial. The editorial will appear in 20 languages, as the United Nations Climate Change Conference is set to begin in Copenhagen.

Unless we combine to take decisive action, climate change will ravage our planet, and with it our prosperity and security. The dangers have been becoming apparent for a generation. Now the facts have started to speak: 11 of the past 14 years have been the warmest on record, the Arctic ice-cap is melting and last year’s inflamed oil and food prices provide a foretaste of future havoc. In scientific journals the question is no longer whether humans are to blame, but how little time we have got left to limit the damage. Yet so far the world’s response has been feeble and half-hearted.

Climate change has been caused over centuries, has consequences that will endure for all time and our prospects of taming it will be determined in the next 14 days. We call on the representatives of the 192 countries gathered in Copenhagen not to hesitate, not to fall into dispute, not to blame each other but to seize opportunity from the greatest modern failure of politics. This should not be a fight between the rich world and the poor world, or between east and west. Climate change affects everyone, and must be solved by everyone.

The science is complex but the facts are clear. The world needs to take steps to limit temperature rises to 2C, an aim that will require global emissions to peak and begin falling within the next 5-10 years.
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Few believe that Copenhagen can any longer produce a fully polished treaty; real progress towards one could only begin with the arrival of President Obama in the White House and the reversal of years of US obstructionism. Even now the world finds itself at the mercy of American domestic politics, for the president cannot fully commit to the action required until the US Congress has done so.
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the rich world is responsible for most of the accumulated carbon in the atmosphere – three-quarters of all carbon dioxide emitted since 1850. It must now take a lead, and every developed country must commit to deep cuts which will reduce their emissions within a decade to very substantially less than their 1990 level.
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The transformation will be costly, but many times less than the bill for bailing out global finance — and far less costly than the consequences of doing nothing.

Many of us, particularly in the developed world, will have to change our lifestyles. The era of flights that cost less than the taxi ride to the airport is drawing to a close. We will have to shop, eat and travel more intelligently. We will have to pay more for our energy, and use less of it.
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Kicking our carbon habit within a few short decades will require a feat of engineering and innovation to match anything in our history. But whereas putting a man on the moon or splitting the atom were born of conflict and competition, the coming carbon race must be driven by a collaborative effort to achieve collective salvation.
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The politicians in Copenhagen have the power to shape history’s judgment on this generation: one that saw a challenge and rose to it, or one so stupid that we saw calamity coming but did nothing to avert it. We implore them to make the right choice.

Most of the newspapers have taken the unusual step of featuring the editorial on their front page. Even with the overwhelming evidence and tremendous consequences I don’t expect politicians to make the right decisions. We know full well what the choices are. We just decide to avoid the unpleasant choices. To bad so many that don’t get to choose are going to suffer. The politicians will be weak. They will play to those that pay them money. They will delay taking important steps now. We have chosen to elect non-leaders for quite some time. We can’t really expect them to act with courage, vision, wisdom and leadership given who we elect. The politicians are responsible for their failing but we are more responsible for electing them. Some politicians, even now, do possess fine qualities but not nearly enough. Maybe I will be proven wrong, but I doubt it.

Re-engineering the Food System for Better Health

Good food nation

According to the Centers for Disease Control, between 1980 and 2006 the percentage of obese teenagers in the United States grew from 5 to 18, while the percentage of pre-teens suffering from obesity increased from 7 to 17.
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Obesity is widespread due to our national-scale system of food production and distribution, which surrounds children – especially lower-income children – with high-calorie products…
90 percent of American food is processed – according to the United States Department of Agriculture – meaning it has been mixed with ingredients, often acting as preservatives, that can make food fattening.
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Now, in another report finished this October after meetings with food-industry leaders, the MIT and Columbia researchers propose a solution: America should increase its regional food consumption.
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Only 1 to 2 percent of all food consumed in the United States today is locally produced. But the MIT and Columbia team, which includes urban planners and architects, believes widespread adoption of some modest projects could change that, by increasing regional food production and distribution.

To help production, the group advocates widespread adoption of small-scale innovations such as “lawn to farm” conversions in urban and suburban areas, and the “10 x 10 project,” an effort to develop vegetable plots in schools and community centers. Lawns require more equipment, labor and fuel than industrial farming nationwide, yet produce no goods. But many vegetables, including lettuce, cucumbers and peppers, can be grown efficiently in small plots.
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As Albright sees it, the effort to produce healthier foods “fits right in with the health-care reform effort right now because chronic diseases are so costly for the nation.” America currently spends $14 billion annually treating childhood obesity, and $147 billion treating all forms of obesity.

Good stuff. We need to improve health in the USA. The current system is unhealthy and needs to be improved. The public good from improving the health of society is huge (both in terms of individual happiness and economic benefits).

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
Continue reading →

Scientific Illiteracy Leaves Many at Risk in Making Health Care Judgements

Scientific literacy is important for many reasons and that importance has increased greatly over the last century. Medical research is often difficult to interpret. Often various studies seem to contradict each other. Often the conclusions that are drawn are far too broad (especially as the research conclusions are passed on and people hear of them overly simplified ways).

Many health care options are not obviously all good, or all bad, but instead a mix of benefits and risks, both of which include interactions with the individuals makeup. So we often see contradictory (and seemingly contradictory) advice. Without a level of scientific literacy it is very difficult for people to know how to react to medical advice.

We have numerous posts on the scientific inquiry process showing that acquiring scientific knowledge is complex and can be quite confusing in many instances. While understanding things are often less clear cut than they are presented it is still true that most often strategies for healthy living have far better practices that will provide far better results than alternatives.

The scientific illiteracy that has some think because their are risks no matter what is done that means there is no evidence some alternatives are far superior is very dangerous. As you can see in action now with those that risk their and others lives and health by doing things like not vaccinating their children, or driving when drunk, or driving when talking on a cell phone.

Without a scientifically literate society even completely obvious measures like not using antibiotics on viral infections are ignored.

The Value of Displaying Data Well

Anscombe’s quartet: all four sets are identical when examined statistically, but vary considerably when graphed. Image via Wikipedia.

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Anscombe’s quartet comprises four datasets that have identical simple statistical properties, yet are revealed to be very different when inspected graphically. Each dataset consists of eleven (x,y) points. They were constructed in 1973 by the statistician F.J. Anscombe to demonstrate the importance of graphing data before analyzing it, and of the effect of outliers on the statistical properties of a dataset.

Of course we also have to be careful of drawing incorrect conclusions from visual displays.

For all four datasets:

Property	Value
Mean of each x variable	9.0
Variance of each x variable	10.0
Mean of each y variable	7.5
Variance of each y variable	3.75
Correlation between each x and y variable	0.816
Linear regression line	$y = 3 + 0.5 x$

Edward Tufte uses the quartet to emphasize the importance of looking at one’s data before analyzing it in the first page of the first chapter of his book, The Visual Display of Quantitative Information.