Fear and uncertainty in politics

The New York Times has a long and interesting article about one politicians truth seeking process, when trying to decide what to vote on the issue of a ban on genetically modified crops in Hawaii.

A Lonely Quest for Facts on Genetically Modified Crops

It is not unreasonable to have some concerns when discussing genetically modified crops, especially related to cross-pollination, patents, and the business practices of the companies providing such crops. All of these things are touched upon in the article, as the politician, Greggor Ilagan, tries to understand the issue, and the science relating to it.

Unfortunately, as Mr. Ilagan, also finds out, there is a lot of FUD (Fear-Uncertainty-Doubt) going on when it comes to G.M.O.s. None of it fact-based, but it sounds just plausible enough that people will believe it (especially when used in connection to phrases like "Frankencrops").

There have been some studies that indicates higher risks of cancer when eating G.M.O.s, but the scientists behind these studies appear to have been ideologically against G.M.O.s, and the studies have been found to flawed and has largely been retracted (including the much spoken about 2012 rat study from France). Indeed, the general consensus among scientists doing research into the subject, is that there is no difference in risks between conventional crops and modified crops - something which is hardly surprising, considering the biology behind it.

In 2010, the European Commission (hardly a strong proponent of G.M.O.s) released their research into the harms from G.M.O. In the press release it was described thus:

In order to help inform debate on genetically modified organisms, the European Commission is publishing today a compendium entitled "A decade of EU-funded GMO research". The book summarizes the results of 50 research projects addressing primarily the safety of GMOs for the environment and for animal and human health. Launched between 2001 and 2010, these projects received funding of €200 million from the EU and form part of a 25-year long research effort on GMOs.

As I said before, the EU and the European Commission can hardly be considered strong proponents of G.M.O.s. Indeed they put off allowing G.M.O.s for a long time, while researching the potential side-effects. This is part of the general principle of caution, under which the EU usually handles these things - in the EU it generally has to be demonstrated that there are no harmful side-effects, before it is allowed, while in the US, the tendency is to demand that a harmful side-effect be proven, before not allowing it.

The summarization of 25 years of research into the potential side-effects of G.M.O.s was summed up thus in the press release:

According to the projects' results, there is, as of today, no scientific evidence associating GMOs with higher risks for the environment or for food and feed safety than conventional plants and organisms.

I highly recommend downloading and reading the book (pdf).

Back to the NY Times article. Mr. Ilagan spent the time necessary, and talked to the people with the proper expertize, in order to get to understand the subject well enough to make an informed vote. He appears to have been alone, or nearly alone, in this, and instead the anti-science ignorance spread by anti-GMO advocates were allowed to carry the day. The ban was approved 6 votes to 3.

Many issues related to science are complex, and it is even harder to get to understand them when there are people actively promoting misinformation, no matter whether they are grassroots organizations or think-tanks.

When politicians face decision making relating to such an issue, they could much worse than try to follow in the footsteps of Mr. Ilagan. As the EC compendium correctly states:

Sound policy, while needing to take account of a wide range of views, must be based on sound science.

All to often, anti-science is allowed to carry the day.

Repost: Nothing in Medicine Makes Sense in the Light of Homeopathy

Note: Due to an upcoming job change, and a number of deadlines before then, I don't have time to do any blogging at the moment. Instead I will try to re-post some of my better posts from the past. The original post can be found here

I am not the first person to state this, but I think that it's important that we all keep up saying this: Testing of homeopathic medicine should end.

Why do I say this? Well, for a very simple reason: There is no evidence that homeopathy works. And what's more, the whole concept of homeopathy flies against everything we know about chemistry, physics, and physiology.

This blog post is triggered by a truly abysmal study where homeopathic medicine was compared to proper medicine used for treating moderate to severe depressions - there were numerous flaws in the study (which I plan to address in a later post), but the fundamental problem was that it was comparing medicine with remedies based on nonsense.

There is a famous essay by Theodosius Dobzhansky called "Nothing in Biology Makes Sense Except in the Light of Evolution", which goes on to explain how our knowledge of biology wouldn't make sense except if evolution is true. One could write a similar essay, called say "Nothing in Medicine Makes Sense in the Light of Homeopathy", in which one explains how all our knowledge of medicine and physiology doesn't make sense if homeopathy is true.

I don't think this can be stressed enough.

It's not just a matter of science not understanding homeopathy. If homeopathy was true, it would mean that the basic building blocks upon which our knowledge is built would be wrong.

Given we know that this is not the case, homeopathy must be wrong. No, that's too mild; homeopathy must be absolute nonsense.

The basic concepts of homeopathy are things like "like cures like", miasms, and and the concept of "memory" in water, all of which is nonsense.

"Like cures like" (or law of similars) is the idea that medicine should be based upon things which gives the same symptoms as the original disease. This was perhaps plausible back when Hahnemann first proposed it two hundred years ago, but we now know that there is no truth to this idea. Sometimes the medicine will be based upon substances which gives similar symptoms, but mostly it won't.

Miasms are an old concept, in which diseases are caused by pollution or bad air. This idea was replaced by the germ theory of diseases, and is not taken serious by anyone except for certain branches of alternative "medicine" such as homeopathy, where they have added their own twists to the concept, but still stay largely true to the old Medieval concept.

The "memory" of water (or sugar for that matter) is the explanation used to explain how homeopathic medicine can have any effect. Homeopathic remedies are based upon the concept of diluting, in which the remedies are diluted to a degree where none of the original molecules are left (see this rather poor Wikipedia article for the numbers).

Oh, and the homeopaths also claim that the more diluted a remedy is, the more potent it is. Yes, this is really what they claim. No, it doesn't make any sense.

So, all in all, we know that homeopathy doesn't work. So, why the hell are we continuing to test it against proper medicine?

There are a lot of alternative "medicines" which might work, even if the concepts they are based upon are nonsense (e.g. acupuncture), and it makes sense to test these (so far, the effect of acupuncture seems to be placebo), but this is most certainly not the case with homeopathy. There is no way in which that can work.

Homeopaths might claim otherwise, but then it's up to them to explain how our basic understanding of chemistry, physics, physiology, and medicine is wrong in this matter, and yet works in every other case. In other words, it's up to the homeopaths to propose new theories in which homeopathy works, and which still supports our current state of knowledge, and until then, they should be ignored.

Not shunned, but ignored. Like we ignore perpetual motion machine builders, flat-earthers, and other weirdos.

Conventional medicine is not perfect, and our knowledge is expanding all the time, but theories like the germ theory of diseases are well established through science. We understand the mechanisms at play, and this knowledge enables us to fight diseases more efficiently. Much like our understanding of vira has helped us fighting other diseases more efficiently.

Why does claims of memory in water and strength through dilution bring to the table? In what ways are they expanding our knowledge? What diseases are we able to cure because of them? Nothing, none, and none are the answers. So stop bringing them to the table. Instead focus on the many valid ideas, which don't fly in the face of all the collective knowledge of the sciences.

Woos like to bring up Nobel Laureates Barry Marshall and Robin Warren, and their discovery that ulcers were caused by the bacterium Helicobacter pylori as an example of how outsiders can turn conventional knowledge on its head.

This is of course pure wishful thinking from their side. Marshall and Warren were very much part of the established scientific community, and while their proposal was received skeptically at first, it was not dismissed out of hand for some very simple reasons:

• It was built upon evidence.


• The mechanisms etc. all worked within conventional science and the mechanisms known at the time.


• There seemed to be some problems with the prevalent hypothesis at the time.

In other words, not only did they work within the established science, they actually addressed some known issues and presented evidence for their claims.

Yes, it took some time (and a very drastic demonstration) to convince people, but the scientific and medical community was very willing to be convinced, and as soon as there were sufficient evidence, the new explanation was universally accepted in quite a short time.

This is how it is done.

So, in what way has proponents of homeopathy done any of this?

The truth is that most people with a basic understanding of science understands that homeopathy is nonsense of the worst order, yet money is still spent on testing this nonsense, demonstrating again and again that it doesn't work. Why? We know that it doesn't work, since we understand the fundamental flaws in the premises behind homeopathy, and we know that homeopathic remedies are nothing but water, alcohol, or sugar (depending on whether they are liquid or in pill form), so they cannot work any better than placebo - they ARE placebo.

Let's put an end to this.

All it does is to lend credibility to homeopathy in the eyes of observers who don't know any better. They think that since homeopathic remedies are continuously being tested, there must be something to them. Why do we let this misconception continue? Science wins nothing from these sham studies, and it only lends cranks an aura of respectability. Stop it.

Yes, I am very passionate about this - we are allowing a lie to continue perpetually. That's wrong. Homeopathy has been around for 200 years, providing no value to society as a whole, and generally decreasing the general level of health, and it's time to stand up and say so.

It goes without saying that I have only contempt for hospitals and doctors who provide homeopathic remedies to their patients. Homeopathic practitioners are usually acting in good faith, believing in their nonsense, but doctors and nurses should know better - they have an education behind them, which provides them with the knowledge necessary to understand what nonsense homeopathy is.

Re-post: Prosopagnosia [slightly edited]

Note: This was an early post on this blog, back when I only had a handful of readers. Given the fact that my readership has grown somewhat, I thought it might be a good idea to re-post it, as it's a fascinating subject.

I first came across the phenomenon of Prosopagnosia, or face blindness, back when I read an article in Wired about the subject.

Basically it's the phenomenon of not being able to recognize faces. Not in the sense of not being good at remembering faces, but in the sense of not being able to recognize faces, including those of your own family and yourself.

Until recently it was thought it was only a phenomenon among people who damaged their brain through some kind of accident (the first well know example was apparently a soldier who was hit in the head, and after that was unable to recognize even his own wife), but now scientists have realized that it's much more widespread than that, and that people can suffer from this from birth. Brad Duchaine, a scientist studying this subject, estimates that 2 percent of the population is face blind.

One of the reasons why face blindness has gone undetected for so long, is the fact that people who suffer from it, are not aware how other people percept faces. This is of course not the case for people who get it later in life.
Another reason could also be that people are good at compensating. When I started needing glasses (when I was about 13 or 14), I learned to compensate for the lack of them, by being able to recognize people in the distance by how they moved. Since I stated wearing glasses I've mostly lost that ability again.

A most fascinating aspect of prosopagnosia is that it's very specific to faces. People who suffer from it, can recognize (and remember) other things as well as everyone else. This is probably due to the fact that faces are much more complex than other things, and demands more from the brain.
However, based on this abstract, it seems that at least some of the brain is able to recognize the person, yet the end result doesn't reflect this.

The reason for face blindness is probably genetic, since the trait has a inheritance pattern that is consistent with the trait being carried by a single gene.

Some further reading:
Face Blind - the original Wired article that got me interested in this subject.

Face blindness not just skin deep - CNN article about the subject.

Living in a world without faces - New Scientist podcast.

I’m Strange, You’re A Stranger - a blogpost from a blogger who suffers from prosopagnosia. The post is quite interesting, and also makes it clear that the problem is not only with human faces, but also animal faces.

I was doing some closet-cleaning the other week, and came across my portfolio of projects from when I took Commercial Art classes some years ago. One picture was an assignment: “Abstraction, select a natural object, create an abstract of that object”, cat, done in ink (dip-pen & pot of ink). I remember thinking about cats, and what qualities of the body shape define them as having “cat-ness”, and decided that it was the tail, the angularity of the limb joints, the pointed ears and the whiskers. But as I said, I tend to perceive things primarily by the mass and outline and by specific traits.

Most everyone did animals for that abstraction assignment, although the instructor pointed out that my drawing was the only one showing the animal from the back side, without the eyes. Mine was the only picture without a face!

Facebling.org - website of the Prosopagnosia Research Center Harvard University and University College London.

A bad time for anti-vaxxers

My, my - this is definitely a bad start of the year for the anti-vaxxers.

First Brian Deer's articles in the British Medical Journal (How the vaccine crisis was meant to make money and How the case against the MMR vaccine was fixed, with more on the way), and the BMJ editorial, where they put themselves on the line by making clear accusations of fraud against Wakefield (Wakefield’s article linking MMR vaccine and autism was fraudulent).

Most of the media picked up on this, and for once didn't try to "balance" the story, but instead actually made clear that Wakefield had no credibility.

Now, Salon.com has decided to removed a 2005 article by Robert F. Kennedy Jr. This article was one of the main reasons for me getting into the fight against anti-vaxxers (and more importantly, for Orac getting into the fight). It was co-published by Rolling Stones, which unfortunately hasn't removed the article.

Salon explains why they removed the article here

CERN traps antimatter atoms

It looks like the doomsday sayers were wrong - creating antimatter didn't destroy the planet (or was it the universe?). That's hardly surprising, as antimatter pops in and out of existence all the time, and both the universe and the planet seems to still be here.

CERN has created antimatter for nearly a decade, starting in 2002, but these particles have always been short-lived as the interact with the matter around them, and disappears.

This week, however, Nature published the news that scientists at CERN has managed to contain antimatter atoms, for more than 170 milliseconds, 38 times. This was done by using a "magnetic trap"

The ALPHA claim is the first major advance since the creation of thousands of antihydrogen atoms in 2002 by a forerunner experiment called ATHENA2 and by ATRAP3 [...]. Both experiments combined decelerated antiprotons with positrons at CERN to produce antihydrogen atoms. But, within several milliseconds, the atoms annihilated with the ordinary matter in the walls of their containers.

To prevent that from happening, the ALPHA team formed antihydrogen atoms in a magnetic trap. Although not electrically charged like antiprotons and positrons, antihydrogen — like hydrogen — has a more subtle magnetic character that arises from the spins of its constituent particles. The ALPHA researchers used an octupole magnet, produced by the current flowing in eight wires, to create a magnetic field that was strongest near the walls of the trap, falling to a minimum at the centre, causing the atoms to collect there.

Creating antimatter atoms this way has proven to be much more difficult than the "traditional" way

To trap just 38 atoms, the group had to run the experiment 335 times. "This was ten thousand times more difficult" than creating untrapped antihydrogen atoms, says Hangst — ATHENA made an estimated 50,000 of them in one go in 2002. To do spectroscopic measurements, Surko estimates that up to 100 antihydrogen atoms may need to be trapped at once.

Obviously, there is some work yet to be done before measurements can be made, but according to this National Geographic article, great advances have been made since the Nature article

Since the experiments covered in the Nature study, the researchers have created many more antihydrogen atoms and held them for much longer—fodder for a future report.

According to Fajans, "We're doing much better now."

If more antihydrogen atoms can be produced and trapped for longer periods, scientists might finally be able to study them in enough detail to explain their scarcity in our universe, he added.

That's a pretty big deal. Let's hope that the progress continues.

For the original paper, you can find it behind Nature's pay-wall here

In the pocket of Big Coffee?

Via ScienceDaily I became aware of this special supplement of Journal of Alzheimer's Disease

Therapeutic Opportunities for Caffeine in Alzheimer's Disease and Other Neurodegenerative Disorders

The special issue focuses only on the effects of caffeine on the brain, more specifically on caffeine's effect on Alzheimer and similar ailments.

What's interesting is that the issue, and the conference which lead to it, was funded by Associação Industrial e Comercial do Café - "Big Coffee" if you will. However, while the association has funded the conference and issue, they have not in any way tried to influence the research, and everyone has been entirely above board about the funding.

This is a very good way to deal with these things. Obviously, it is in the interest of the association to find any, especially positive, effects which caffeine might have, so it makes sense for them to fund this research. Yet, in order to reduce doubts about bias, everybody involved have been entirely open about the source of funding. Many other scientists and interest organizations could learn from this.

Lazy linking - science and skepticism edition

A few science and skepticism links that I thought I'd share.

* J. David Jentsch ask people in the LA area to Stand up for science on April 8. Jentsch is one of the scientists who has been targeted by animal rights terrorists because of his animal research.

* A new study shows that Spanking sparks aggression, does little to reduce behavior problems in children. One of the techniques studied (spanking) is illegal in Denmark, but the others are certainly still used.

* An interesting take on the use of statistics in science: Odds Are, It's Wrong. Personally, I don't find the article entirely convincing. Yes, it's true that there are possibilities of false positives and negatives, but it seem to me that enough studies should clean up these problems. I find the complains about meta-studies puzzling, and while I can see the author's point in a perfect world, we have to work with the material at hand. Still, it's a good article, and I think scientists conducting studies would do well to keep its points in mind.

* I can't remember where I found this link (almost certainly at a feminist blog), but I thought that it was well worth sharing. It's an article in Stanford Magazine about Stanford professor Clelia Mosher who probably was the first to do research into female sexuality: The Sex Scholar.

* Occasionally I come across people who seem to think that the cause of ice ages are unknown, which puzzles me, since I thought it was well-established that they were caused by shifts in the Earth's axis. Apparently this wasn't quite as well-established as I thought, or at least not for as long as I thought - I came across a ScienceDaily article from August 2009 which explains that this was now the established explanation: Long Debate Ended Over Cause, Demise Of Ice Ages? Research Into Earth's Wobble

* David Colquhoun tells us that the University of Buckingham does the right thing. The Faculty of Integrated Medicine has been fired. One less place educating people in woo.

* Over at Alice in Galaxyland there is a great report about a recent event at Skeptics in the Pub in Wincester: Skeptics in the Pub: Unnatural Predators by Jourdemayne at Winchester. Certainly makes me wish I had been there (though I am happy to have been spared the journey described).

* And finally, a shout-out to a fairly new blog. When I was in Perth in January, I met up with the Perth Skeptics on the last day I was there (which is when they participated in the 10²³ mass suicide by homeopathy event). While I was there, I talked a bit about skepticism in Denmark (not much of it around) and blogging. One of the participants was thinking about starting his own blog, and after my talk he took the plunge - so I present to you Friend of Reason. There is some good stuff there.

Nothing in Medicine Makes Sense in the Light of Homeopathy

I am not the first person to state this, but I think that it's important that we all keep up saying this: Testing of homeopathic medicine should end.

Why do I say this? Well, for a very simple reason: There is no evidence that homeopathy works. And what's more, the whole concept of homeopathy flies against everything we know about chemistry, physics, and physiology.

This blog post is triggered by a truly abysmal study where homeopathic medicine was compared to proper medicine used for treating moderate to severe depressions - there were numerous flaws in the study (which I plan to address in a later post), but the fundamental problem was that it was comparing medicine with remedies based on nonsense.

There is a famous essay by Theodosius Dobzhansky called "Nothing in Biology Makes Sense Except in the Light of Evolution", which goes on to explain how our knowledge of biology wouldn't make sense except if evolution is true. One could write a similar essay, called say "Nothing in Medicine Makes Sense in the Light of Homeopathy", in which one explains how all our knowledge of medicine and physiology doesn't make sense if homeopathy is true.

I don't think this can be stressed enough.

It's not just a matter of science not understanding homeopathy. If homeopathy was true, it would mean that the basic building blocks upon which our knowledge is built would be wrong.

Given we know that this is not the case, homeopathy must be wrong. No, that's too mild; homeopathy must be absolute nonsense.

The basic concepts of homeopathy are things like "like cures like", miasms, and and the concept of "memory" in water, all of which is nonsense.

"Like cures like" (or law of similars) is the idea that medicine should be based upon things which gives the same symptoms as the original disease. This was perhaps plausible back when Hahnemann first proposed it two hundred years ago, but we now know that there is no truth to this idea. Sometimes the medicine will be based upon substances which gives similar symptoms, but mostly it won't.

Miasms are an old concept, in which diseases are caused by pollution or bad air. This idea was replaced by the germ theory of diseases, and is not taken serious by anyone except for certain branches of alternative "medicine" such as homeopathy, where they have added their own twists to the concept, but still stay largely true to the old Medieval concept.

The "memory" of water (or sugar for that matter) is the explanation used to explain how homeopathic medicine can have any effect. Homeopathic remedies are based upon the concept of diluting, in which the remedies are diluted to a degree where none of the original molecules are left (see this rather poor Wikipedia article for the numbers).

Oh, and the homeopaths also claim that the more diluted a remedy is, the more potent it is. Yes, this is really what they claim. No, it doesn't make any sense.

So, all in all, we know that homeopathy doesn't work. So, why the hell are we continuing to test it against proper medicine?

There are a lot of alternative "medicines" which might work, even if the concepts they are based upon are nonsense (e.g. acupuncture), and it makes sense to test these (so far, the effect of acupuncture seems to be placebo), but this is most certainly not the case with homeopathy. There is no way in which that can work.

Homeopaths might claim otherwise, but then it's up to them to explain how our basic understanding of chemistry, physics, physiology, and medicine is wrong in this matter, and yet works in every other case. In other words, it's up to the homeopaths to propose new theories in which homeopathy works, and which still supports our current state of knowledge, and until then, they should be ignored.

Not shunned, but ignored. Like we ignore perpetual motion machine builders, flat-earthers, and other weirdos.

Conventional medicine is not perfect, and our knowledge is expanding all the time, but theories like the germ theory of diseases are well established through science. We understand the mechanisms at play, and this knowledge enables us to fight diseases more efficiently. Much like our understanding of vira has helped us fighting other diseases more efficiently.

Why does claims of memory in water and strength through dilution bring to the table? In what ways are they expanding our knowledge? What diseases are we able to cure because of them? Nothing, none, and none are the answers. So stop bringing them to the table. Instead focus on the many valid ideas, which don't fly in the face of all the collective knowledge of the sciences.

Woos like to bring up Nobel Laureates Barry Marshall and Robin Warren, and their discovery that ulcers were caused by the bacterium Helicobacter pylori as an example of how outsiders can turn conventional knowledge on its head.

This is of course pure wishful thinking from their side. Marshall and Warren were very much part of the established scientific community, and while their proposal was received skeptically at first, it was not dismissed out of hand for some very simple reasons:

• It was built upon evidence.


• The mechanisms etc. all worked within conventional science and the mechanisms known at the time.


• There seemed to be some problems with the prevalent hypothesis at the time.

In other words, not only did they work within the established science, they actually addressed some known issues and presented evidence for their claims.

Yes, it took some time (and a very drastic demonstration) to convince people, but the scientific and medical community was very willing to be convinced, and as soon as there were sufficient evidence, the new explanation was universally accepted in quite a short time.

This is how it is done.

So, in what way has proponents of homeopathy done any of this?

The truth is that most people with a basic understanding of science understands that homeopathy is nonsense of the worst order, yet money is still spent on testing this nonsense, demonstrating again and again that it doesn't work. Why? We know that it doesn't work, since we understand the fundamental flaws in the premises behind homeopathy, and we know that homeopathic remedies are nothing but water, alcohol, or sugar (depending on whether they are liquid or in pill form), so they cannot work any better than placebo - they ARE placebo.

Let's put an end to this.

All it does is to lend credibility to homeopathy in the eyes of observers who don't know any better. They think that since homeopathic remedies are continuously being tested, there must be something to them. Why do we let this misconception continue? Science wins nothing from these sham studies, and it only lends cranks an aura of respectability. Stop it.

Yes, I am very passionate about this - we are allowing a lie to continue perpetually. That's wrong. Homeopathy has been around for 200 years, providing no value to society as a whole, and generally decreasing the general level of health, and it's time to stand up and say so.

It goes without saying that I have only contempt for hospitals and doctors who provide homeopathic remedies to their patients. Homeopathic practitioners are usually acting in good faith, believing in their nonsense, but doctors and nurses should know better - they have an education behind them, which provides them with the knowledge necessary to understand what nonsense homeopathy is.

Local effects of global warming investigated

If you looked at the blogs and articles by deniers of anthropogenic global warming (AGW), it would appear that flaw after flaw has been demonstrated in the science and data behind our understanding of AGW, yet in the real world, this is not the case, and the scientists keep on working on expanding their, and our, understanding of the effects of AGW.

Generally, the effects have been considered on a global scale (the Earth as a whole), or very localized scale (e.g. individual glaciers), but our understanding of how certain types of climate will change have been somewhat lacking. It has been assumed that a climate belt would change more or less uniformly, but nobody has known for sure.

Now, we are a bit closing in knowing, and it appears that climate belts won't change uniformly.

ScienceDaily reports on a new study, which looks into this very subject: Tropics: Global Warming Likely to Significantly Affect Rainfall Patterns

Climate models project that the global average temperature will rise about 1°C by the middle of the century, if we continue with business as usual and emit greenhouse gases as we have been. The global average, though, does not tell us anything about what will happen to regional climates, for example rainfall in the western United States or in paradisical islands like Hawai'i.

Analyzing global model warming projections in models used by the Intergovernmental Panel on Climate Change, a team of scientists headed by meteorologist Shang-Ping Xie at the University of Hawaii at Mānoa's International Pacific Research Center, finds that ocean temperature patterns in the tropics and subtropics will change in ways that will lead to significant changes in rainfall patterns. The study will be published in the Journal of Climate this month, breaking ground on such regional climate forecasts.

Scientists have mostly assumed that the surfaces of Earth's oceans will warm rather evenly in the tropics. This assumption has led to "wetter-gets-wetter" and "drier-gets-drier" regional rainfall projections. Xie's team has gathered evidence that, although ocean surface temperatures can be expected to increase mostly everywhere by the middle of the century, the increase may differ by up to 1.5°C depending upon the region.

"Compared to the mean projected rise of 1°C, such differences are fairly large and can have a pronounced impact on tropical and subtropical climate by altering atmospheric heating patterns and therefore rainfall," explains Xie. "Our results broadly indicate that regions of peak sea surface temperature will get wetter, and those relatively cool will get drier."

So, not only will the climate get warmer, but the rainfall patterns are likely to change as well. This is pretty bad news, though not really that surprising, when one stops and think about it - the only reason why people have assumed otherwise, is because of lack of data and models. Now we have the data and models, and can make more precise predictions.

It doesn't look like the mentioned article has been published yet, though I could have overlooked it - Shang-Ping Xie has published quite a few articles on subjects related to climate.

Lazy linking

I used to do a lot of lazy linking posts, which are posts linking to things I find interesting. The main reason for the decline in these posts, is that I now link to such things from my Twitter account. Still, I'll try to make these posts from time to time, if nothing else then to give some linklove to other people.

First of, a fairly old blogpost about old atomic models in the past: The gallery of failed atomic models, 1903-1913

From the mainstream media, BBC reports on the findings of an rather interesting meteorite: Attic stored meteorite 'four billion years old'

Ed Brayton reports that the Innocence Project Frees 250th Innocent Person

And then there is the news that quack Kevin Trudeau has been hold in content of the court, because he asked his followers to write the judge, resulting in an email deluge.

On the anthropogenic global warming front, Climate Progress reports that Penn State inquiry finds no evidence for allegations against Michael Mann.

Via Sheril Kirshenbaum, I became aware of the Under the Microscope website, dedicated to women in science.

Over at Majikthise, Lindsay Beyerstein takes on the claims that the fathers of modern obstetrics murder more women than Jack the Ripper. Personally I find Lindsay's speculations more convincing than the new claims.

Over at Alternet, Greta Christina writes about Why We Don't Need Religion to Give Life Mystery (also at her own blog)

Ancient Greenlandic Genome Decoded

As one might expect, this has been fairly big news in Denmark, and it has now also been reported in the NY Times

Ancient Man in Greenland Has Genome Decoded

The genome of a man who lived on the western coast of Greenland some 4,000 years ago has been decoded, thanks to the surprisingly good preservation of DNA in a swatch of his hair so thick it was originally thought to be from a bear.

This is the first time the whole genome of an ancient human has been analyzed, and it joins the list of just eight whole genomes of living people that have been decoded so far. It also sheds new light on the settlement of North America by showing there was a hitherto unsuspected migration of people across the continent, from Siberia to Greenland, some 5,500 years ago.

The genome came from some hair which had been in a bag at the Danish National Museum since 1986. The hair were found in an ancient garbage heap.

The study was published in Nature and can be found here: Ancient human genome sequence of an extinct Palaeo-Eskimo

As the NY Times mentions, the research has now given new insight into the migration patterns of the ancient humans, demonstrating some unexpected paths.

This is probably something we'll continue to see when more and more ancient genomes are decoded, expanding our knowledge in this area.

The Copenhagen Diagnosis

Some of the world's best climate researchers have put together a report, the Copenhagen Diagnosis, which updates the readers on what has happened in climate research since the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report.

The report is targeted towards policy makers, the media, and the general public, and as such it "synthesize the most policy-relevant climate science published since the close-off of material for the last IPCC report", allowing policy makers to make informed decisions based on all available (peer-reviewed) material, and not just material available 3 years ago.

If you want to be informed about the current state of climate research, and on our knowledge of AGW, then read this report. It won't include any of the many manufactured controversies, just the pure science, which has been through a proper peer-review process.

Food Waste in US and its environmental impact

PLoS One has an interesting article The Progressive Increase of Food Waste in America and Its Environmental Impact by Kevin D. Hall et al

Food waste contributes to excess consumption of freshwater and fossil fuels which, along with methane and CO2 emissions from decomposing food, impacts global climate change. Here, we calculate the energy content of nationwide food waste from the difference between the US food supply and the food consumed by the population. The latter was estimated using a validated mathematical model of metabolism relating body weight to the amount of food eaten. We found that US per capita food waste has progressively increased by ~50% since 1974 reaching more than 1400 kcal per person per day or 150 trillion kcal per year. Food waste now accounts for more than one quarter of the total freshwater consumption and ~300 million barrels of oil per year.

As this study shows, this is a serious issue which should be addressed. One quarter of all freshwater consumption wasted is simply way too much, especially considering the fact that we will encounter increased water shortage in the future.

The oil consumption sounds very high, but given the fact that the US uses approximately 19.5 billion barrels of petroleum per day, it's a very small percentage of the US consumption. Still, everything helps, and reducing this waste would be one step among many to reduce the US consumption of fossil fuel.

Also, as the abstract says, "methane and CO2 emissions from decomposing food, impacts global climate change". Since anthropogenic global warming probably is the most pressing issue of our times, any possible steps towards reducing AGW should be taken.

Want to avoid errors? Sleep more

I thought this was pretty well established science, but apparently it's not. A new study has found that sleep deprivation can negatively affect information processing.

A study in the Nov.1 issue of the journal Sleep shows that sleep deprivation causes some people to shift from a more automatic, implicit process of information categorization (information-integration) to a more controlled, explicit process (rule-based). This use of rule-based strategies in a task in which information-integration strategies are optimal can lead to potentially devastating errors when quick and accurate categorization is fundamental to survival.

Results show that sleep deprivation led to an overall performance deficit on an information-integration category learning task that was held over the course of two days. Performance improved in the control group by 4.3 percent from the end of day one to the beginning of day two (accuracy increased from 74 percent to 78.3 percent); performance in the sleep-deprived group declined by 2.4 percent (accuracy decreased from 73.1 percent to 70.7 percent) from the end of day one to the beginning of day two.

According to co-principal investigators W. Todd Maddox, PhD, professor of psychology, and David M. Schnyer, PhD, associate professor of psychology at the Institute for Neuroscience at the University of Texas in Austin, fast and accurate categorization is critical in situations that could become a matter of life or death. However, categorization may become compromised in people who often experience sleep deprivation in fast-paced, high pressure roles such as doctors, firefighters, soldiers and even parents. Many tasks performed on a daily basis require information-integration processing rather than rule-based categorization. Examples include driving, making a medical diagnosis and performing air-traffic control.

I think we've all experience times where we have been sleep deprived, and have our ability to use information be compromised as a result. So the findings of this study shouldn't come as a surprise.

Still, it's good that such things are researched, so it can be quantified how badly peoples' performance is affected. Studies, such as this one, can lead to changes in watch schedules etc. Or, given the fact that the effect is not universal, it could lead to better monitoring of those who have the type of jobs where this might cause problems.

The study is behind the paywall at SLEEP, but the abstract can be found here

Bad pun, but interesting article

Normally, there is nothing that turns me away from an article faster than a pun in the headline, but for once, curiosity got the better of me when I came across this Wired article.

Scanning Dead Salmon in fMRI Machine Highlights Risk of Red Herrings

Neuroscientist Craig Bennett purchased a whole Atlantic salmon, took it to a lab at Dartmouth, and put it into an fMRI machine used to study the brain. The beautiful fish was to be the lab’s test object as they worked out some new methods.

So, as the fish sat in the scanner, they showed it “a series of photographs depicting human individuals in social situations.” To maintain the rigor of the protocol (and perhaps because it was hilarious), the salmon, just like a human test subject, “was asked to determine what emotion the individual in the photo must have been experiencing.”

The salmon, as Bennett’s poster on the test dryly notes, “was not alive at the time of scanning.”

If that were all that had occurred, the salmon scanning would simply live on in Dartmouth lore as a “crowning achievement in terms of ridiculous objects to scan.” But the fish had a surprise in store. When they got around to analyzing the voxel (think: 3-D or “volumetric” pixel) data, the voxels representing the area where the salmon’s tiny brain sat showed evidence of activity. In the fMRI scan, it looked like the dead salmon was actually thinking about the pictures it had been shown.

The article is about the perils of false positives when using fMRI machines, and raises the question whether we can trust the results from such scanning. This question is hard to answer, but the answer is probably "it depends". The trustworthiness of such results depends on the rigorousness of the statistical methods used.

One things this experiment also highlights, which I believe strongly in, is that one should not just test for whether things works when you expect it to work, but also that it fails to work when it's expected to not work. This is something I preach when making IT systems, and it is something which everyone who do any type of tests or measurements should keep in mind.

The Human Family Tree | Interactive - National Geographic Channel

Interesting interactive page at National Geographic about how closely related humans really are.

Explore the haplogroups from participants in the National Geographic Channel show The Human Family Tree.

View >>

Chimpanzees get AIDS too

This is really more the area of Tara or ERV but I still thought I'd comment on this piece of news.

African primates can be infected with over 40 different simian immunodeficiency viruses (SIVs). These diseases are related to two diseases which infects our particular species of primates, Homo sapiens, human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) - indeed the two types of HIV are the result of SIVs crossing the species barrier.

HIV is considered an epidemic with more than 30 million people suffering from it worldwide (source - .pdf). As people hopefully know, HIV 1 and 2 will, if not treated by medicine, result in acquired immune deficiency syndrome (AIDS), which is fatal. 2 million people died from AIDS in 2007.

HIV and AIDS is one of the top prioritized areas of medical studies, and both the evolution of HIV from SIV and the connection between HIV and AIDS are well understood. This doesn't, however, keep some people from either claiming that HIV/AIDS is man-made, or that AIDS doesn't exist.

One of the arguments used by both groups is that SIV doesn't lead to AIDS in primates - the one group to argue that HIV couldn't have evolved from SIV, the other to argue that AIDS is not real.

Neither group makes sense. The lack of development of AIDS in SIV carrying primates is by no means evidence of there being no SIV-HIV connection, nor evidence of there being no HIV-AIDS connection.

Still, this matters even less now. Researchers have found out that some primates can get AIDS.

Nature has a new paper by Beatrice Hahn et al.

Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz (link takes you to the abstract, the paper is behind a paywall)

African primates are naturally infected with over 40 different simian immunodeficiency viruses (SIVs), two of which have crossed the species barrier and generated human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2)1, 2. Unlike the human viruses, however, SIVs do not generally cause acquired immunodeficiency syndrome (AIDS) in their natural hosts3. Here we show that SIVcpz, the immediate precursor of HIV-1, is pathogenic in free-ranging chimpanzees. By following 94 members of two habituated chimpanzee communities in Gombe National Park, Tanzania, for over 9 years, we found a 10- to 16-fold higher age-corrected death hazard for SIVcpz-infected (n = 17) compared to uninfected (n = 77) chimpanzees. We also found that SIVcpz-infected females were less likely to give birth and had a higher infant mortality rate than uninfected females. Immunohistochemistry and in situ hybridization of post-mortem spleen and lymph node samples from three infected and two uninfected chimpanzees revealed significant CD4+ T-cell depletion in all infected individuals, with evidence of high viral replication and extensive follicular dendritic cell virus trapping in one of them. One female, who died within 3 years of acquiring SIVcpz, had histopathological findings consistent with end-stage AIDS. These results indicate that SIVcpz, like HIV-1, is associated with progressive CD4+ T-cell loss, lymphatic tissue destruction and premature death. These findings challenge the prevailing view that all natural SIV infections are non-pathogenic and suggest that SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild.

In other words, there is a non-trivial health cost in being infected with SIVcpz.

This is not a trivial finding. As Nature makes clear in it's news release on the story (Wild chimpanzees get AIDS-like illness) this will impact future research.

The results suggest that it will not be possible to find the key to HIV immunity in the chimpanzee genome, as scientists had hoped. However, the study, published in Nature, sets the stage for researchers to gain insight into how HIV and SIV cause disease in their hosts by studying the responses of different primates to the viruses. Wild monkeys that have coexisted with SIV for a long time — such as sooty mangabeys and African green monkeys — seem to have evolved the ability to control SIV, and so do not become ill when exposed to the virus. The new paper, however, shows that chimpanzees — which, like humans, were exposed to SIV more recently — are sickened by the virus.

NY Times also writes about this study: Chimpanzees Do Die From Simian AIDS, Study Finds

Update: Carl Zimmer has written a great blog post about this.

Scientia Pro Publica

Image: wemidji (Jacques Marcoux).

Nam et ipsa scientia potestas est (And thus knowledge itself is power)
-- Sir Francis Bacon.

Welcome to the 5th round of Scientia Pro Publica. The Scientia Pro Publica (Science for the People) blog carnival celebrates the best science, nature and medical writing targeted to the public (instead of to other scientists) that has been published in the blogosphere within the past 60 days.

I apologize in advance if the carnival seems a bit incoherent, but due to a mild allergic reaction to something I ate yesterday, my tongue started to swell up, and I didn't sleep as much as I'd have liked. Apparently it's possible to get allergic reactions to food, without being allergic. This is a piece of medical knowledge I'd been perfectly happy to have gained through a blogpost somewhere.

Before starting on the submissions, I should probably mention that a number of the submissions didn't make it to the carnival. The aim of the carnival is to bring science to the public, which means that submissions should both contain science and be suitable for the general public. A number of submissions failed to live up to the science criteria, and thus haven't been included. Some of the submissions that did make it, might not be as suitable for the general public as one would have liked, but overall I felt that they merited inclusions.

Biology/Evolution
GrrlScientist presents a book review of Jerry Coyne's Why Evolution is True

Bora Zivkovic presents Yes, Archaea also have circadian clocks!

Given the media coverage of the discovery of Ida, I was surprised that there wasn't more submissions on that subject. Luckily Greg Laden has submitted a great post on Ida the Fossil Primate

Bob O'Hara presents Help! How Do I Deal With Microarrays?

Chemistry/Biochemistry
AK presents Wiring the Cell for Power

Human/Veterinary Medicine
jarofthoughts presents Stem Cell Research and you

Mike presents Neuro Brain Thermodynamics

Romeo Vitelli writes about the Vaccination Wars in two parts. Part 1 and part 2

Psychology/Psychiatry/Pharmacology
Michelle Dawson presents The autistic way of laughing

I will be rude enough to include my own post on the Dunning-Kruger effect.

Physics/Astronomy
DrKuha describes his submission as "Attempting to draw comparisons between Phlogiston Theory and the Higgs boson and String Theory in an effort to shed some light on how scientific insight is gained."
The Phlogiston: Not Quite Vindicated

Martial Development takes a good, hard look at Spike TV's new show "Deadliest Warrior", and is not impressed.
Inside Deadliest Warrior’s Combat Simulator

Phil for Humanity describes his submissions thus: "Finally, a plausible explanation as to why time travelers from the future have never arrived into our past or present, assuming time travel will be possible."
Time Travel Theories « Phil for Humanity

Behavioral Ecology/Conservation
Mesquite Pete explains that ets are at risk from mosquitoes as well in his post Pets and Mosquitoes

Jeremy presents Churros and peaches in the Canyon de Chelly

Oceanography/Marine Biology
At Mauka to Makai Overfishing Simplified... Then Complexified

Scientists and Society
Arj presents a book of Perfectly Reasonable Deviations From the Beaten Track in The Inner Feynman

Russell Blackford disagrees with NAS and writes about it in NAS on the compatibility of science and religion

Rick Foreman presents Robotics and Artificial Intelligence - The Next Step in Human Evolution?. I should perhaps note that I am not in agreement with his premises, but I think it's a pretty good fit for the "scientists and society" category, as it reflects on how science might influence society.

Southern Fried Science has a Guestpost: What is Social Science?

Bob O'Hara presents Publicity and Outreach Done Wrong. Sounds like he has found the right way to promote his papers.

The final submission I'm going to include, is one I had to debate whether really fitted the format or not. I've pretty much reached the conclusion that it doesn't but, thought "what the heck".

Hank Roberts submitted a link to a YouTube video, which I've embedded. He writes the following:

I've known about these folks for quite a while; they're completely serious and dedicated to what they're doing. I"m not involved with them, just a fan. If their video qualifies as a blog article, this is worth attention.

As I said, this is not really the right format for this carnival, and people should not expect future YouTube submissions to be included.



This ends this round of Scientia Pro Publica. I hope you have enjoyed the posts, and that my lack of sleep hasn't been too apparent.

The next edition of Scientia Pro Publica will be up at target="window" href="http://maukamakai.wordpress.com/">Mauka to
Makai in two weeks, so make sure to submit all your science posts aimed at the public.

Seeking science posts

As Grrlscientist explains I am the host of the next edition of Scientia Pro Publica, which will go up on the June 1st.

If you have a good science post, explaining science to the public in one way or another, please submit the post to the carnival (see Grrlscientist's post for explanation of how).

Open Laboratory 2008 is out

As a bit of a bibliophile and as an active participant¹ in the science blogsphere, I like the Open Laboratory books very much. For those of you who don't know what I am talking about, the Open Laboratory is an annual book collecting (some of) the best posts of the science blog sphere.

Bora started this a couple of years ago, covering 2006 - now the 3rd version has come out, covering 2008.

It can be bought at Lulu.

For more on this anthology, see Bora's post about it.

¹I hasten to say that I am not a particular talented part of the science blogsphere, just some one who participates.