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A medical controversy 3 July, 2011

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Let’s look at different kind of controversy – a medical one.  Multiple sclerosis (MS) is a disease that causes the body’s immune system to attack the central nervous system, leading to a range of neurological symptoms. There is no cure, only some drug treatments that attempt to relieve some short term symptoms. So when Italian researcher Paulo Zamboni proposed in 2008 that a relatively simple procedure could provide significant long term relief from MS, it caused a big reaction.

Dr Zamboni believed that decreased blood flow in veins in the neck and chest (known as chronic cerebro-spinal venous insufficiency – CCSVI) could be partly responsible for MS. He reported that MS sufferers were much more likely to have CCSVI than healthy people, and that balloon angioplasty and stenting (two slightly different techniques for stretching a vein to increase blood flow) could reduce MS symptoms.

This set off a rush by some patients and doctors to try the treatment, with people travelling around the world to countries where the treatment was offered. Meanwhile, many researchers were concerned that Dr Zamboni’s studies weren’t done properly. Recently the news has not been good for supporters of the treatment. The NY Times reported on the reluctance of hospitals to perform the procedure, fearing that it hasn’t been proven reliable enough, and the Wall Street Journal wrote about a research program at Stanford University that was halted after one patient died and another required emergency surgery.

From a strictly scientific point of view, there simply doesn’t seem to be any convincing evidence to say that the treatment works. Here is a particularly passionate blog arguing that Zamboni and CCSVI are a scam.

What makes this different from the other controversies I’ve looked at are the patients. A large, well-organised group of people who are (understandably) pushing for the widespread adoption of the treatment; the pressure they bring to bear on researchers and governments will keep this debate going for longer than it would otherwise.  From what I’ve read, I think it’s unlikely that CCSVI plays a role in MS, so I don’t think the angioplasty and stenting techniques will prove to have any positive impact – but if I’m wrong then the patients deserve credit for sticking to their guns.

Checking your work 27 June, 2011

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Carl Zimmer has an excellent piece in the NY Times about science’s failure to correct its own mistakes, which is often touted as one of its most important qualities.  He points out numerous recent examples (including ESP and arsenic-based life) of controversial research where other scientists don’t actually attempt to replicate the research (or journals refuse to publish their results when they do). Scientists quoted in the story point out that they don’t want to put their own research programs on hold to check someone else’s findings, especially when they’re sure that the initial research was wrong.

When the only published research on an important issue reaches conclusion A, but the majority of the scientific community believes in conclusion B, it seems to me that we’re devaluing the importance of research journals. Zimmer concludes his piece with an appeal for those in science to put more resources into replicating important experimental results. This strikes me as slightly naive – what are the incentives for people to act this way? – but I don’t know what else might work.

Arsenic followup 28 May, 2011

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Carl Zimmer has a great article in Slate about how the arsenic based controversy has changed the way that peer review is happening – he says we’re moving to a post-publication peer review process, where the merits of a paper are debated (often via blogs or Twitter) after it’s been published. The key point is that it’s not just amateurs or journalists writing about the research – other scientists are getting involved.

Zimmer notes that in the case of arsenic-based life, the original researchers have avoided this online debate (which was almost universally critical of their work), and only in the 3 June issue of Science will they respond to the critics. No matter which side is actually right, that’s simply too late. By staying out of the debate for over 6 months they’ve missed their chance to change people’s minds, and made it that much harder for themselves to be heard in the future.

Mantle plumes! 13 May, 2011

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Time to jump away from human evolution and look at a different field.

“Mantle plumes” is not a phrase that you hear very often, but it’s at the heart of an important controversy in geophysics. All over the world there are long chains of volcanic mountains that can’t be explained by classical plate tectonics, and the debate about what’s responsible for them is growing in intensity.

This post will require a little more background than usual, so let’s dive in. We’ll start at one my favourite places in the world – Hawaii. Most people think of Hawaii as a small chain of islands, known for active volcanoes like Kilauea (click here for a live picture of Kilauea’s Puʻu ʻŌʻō crater) . But if you look under the Pacific ocean, you see that the Hawaiian islands are just the end of a very long chain of mountains, most of which are completely submerged. It’s known as the Hawaiian-Emperor seamount chain, and it stretches nearly 6,000km from Hawaii to the Kamchatka Peninsula in Russia.

The Hawaiian - Emperor seamount chain

Hawaii sits in the middle of the Pacific plate, far away from the edge of the plate known as the “Pacific Ring of Fire”. It gets its name from the many volcanoes found there, and they are easily understood by classical plate tectonics – as one plate dives under another, rock is melted and it rises up to form a volcano near the plate boundary. For something like the Hawaiian – Emperor seamount chain, though, a new theory is required.

The standard explanation for how such a long chain of volcanic mountains forms in the middle of a plate is called the hotspot theory. Hotspots are excessively hot places under the earth’s surface that seem to stay fixed in place while continental plates drift over them. Directly above the hotspot, a volcanic mountain is formed. As the plate moves, that mountain moves away from the hotspot and ceases to be volcanic. A new volcano then forms over the hotspot, and the process continues.

A hotspot producing a chain of volcanoes

But how do you explain the hotspots? That’s the controversial part of this story.  The standard theory says that they are caused by mantle plumes – rising columns of hot rock that start from deep within the earth, perhaps as deep as the earth’s core.

Mantle plumes rising from the earth's core. Source: http://faculty.weber.edu/bdattilo/shknbk/notes/htsptplm.htm

Opponents of this theory, who are in the minority, say mantle plumes simply don’t exist, and that the heat responsible for the volcanoes is generated much closer to the earth’s surface, just under the plate. They have organised themselves and maintain the website MantlePlumes.org to present their views.

As the debate intensified, each side organised conferences that tended to exclude their opponents. Eventually, in 2003, the Geological Society of London hosted The Great Plumes Debate in an attempt to bring both sides together. Some of the comments received at their website is eye-opening.

There are those who think the geophysical community has accepted a mantle plume model that is so flexible and poorly defined that it doesn’t actually explain anything:

I wouldn’t blame anyone for the state of thinking and publications about hotspots and mantle plumes except ourselves, as in Pogo’s dictum “we have met the enemy and they are us.” In the absence of any other clear model, we’ve accepted very vague ideas about plumes and allowed them to be the null hypothesis for excess ridge or intraplate volcanism… The hypothesis evolved from fairly rigorous criteria to a point where plumes don’t have to meet any particular test. Hence the hypothesis now always works… but increasingly doesn’t tell us anything or predict anything.

(emphasis mine)

And there are others who think that the anti-plumers aren’t as ostracised as they claim, and the differences between the camps may not be all that fundamental:

There is even some suggestion of long-lived conspiracies between referees and journal editors to stifle emerging non-plume hypotheses in their infancy, and thereby to suppress ‘the truth’. The reality is somewhat different. Some folk have never accepted the plume hypothesis, and their views, far from being suppressed, are widely published in the geological literature. For example, the ‘big daddy’ of non-plume hypotheses, Don Anderson, is credited with having published more than 30 ‘non-plume’ papers in the past 8 years, most of which appear in respected journals… Hardly a case of being stifled at birth by evil editors keen to hang on to the old ways!

Thus far, neither side has been able to prove their case conclusively. This suggests to me that ‘the truth’ is probably somewhere between the two opposite ends of the spectrum, i.e. some but not all of the largest volcanic outpourings were fed by hotspots in the mantle, whereas other, smaller, outpourings have their origin in plate tectonics.

(emphasis mine)

I think what strikes me about this controversy is how it has bubbled away without much public attention. Usually the mass media plays an important role in these debates, either by prolonging them in order to attract readers, or simply by increasing the bitterness as each side sees their opponent’s views get some publicity. The mantle plumes debate has developed differently. It will be interesting to see how it plays out, and I’ll look for any signs that it might be heading for a resolution.

The monkey problem 25 April, 2011

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This is a different kind of dispute – it’s about scientific words and what they mean.

Last week Martin Robbins, writing for The Guardian, complained about people confusing the terms “ape” and “monkey”. He seems particularly annoyed with entertainment journalists writing about the upcoming movie Rise of the Planet of the ApesHe quotes examples of headlines like

Fans go bananas for new Planet Of The Apes trailer which takes humanised monkey effects to a whole new level

and

Trailer for Rise of the Planet of the Apes Promises Monkey Invasion

Robbins points out that apes and monkeys are very different groups, and goes on to point out another common mistake – failing to recognise that humans are apes, too.

John Hawks picked up on this story, but he has a different take on these definitions. Looking at the groups based on their evolutionary history, he argues that if you include humans with the apes, then you have to conclude that monkeys are apes as well. So Hawks decides that “monkey” and “ape” aren’t defined well enough to be proper biological terms, preferring to use “hominoids” (apes + humans) and “anthropoids” (apes + humans + monkeys).

John Wilkins takes a deeper look at the problem of how people define and use these terms, and talks about a similar issue about birds and dinosaurs – introducing me to the BAD (Birds Are Dinosaurs) and BANDit (Birds Are Not Dinosaurs) groups on either side of the debate.

Is there any way to resolve this? Not that I can see. People will always use terminology that they are familiar with, even when it clashes with current biological understanding. If biologists avoid the common-use terms, and stick to biologically accurate words, they make it more difficult to communicate with the public.

Hobbit followup – the A. sediba story 20 April, 2011

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Here’s another interesting debate in the human evolutionary story. Last year scientists in South Africa found 2 partial skeletons that were approximately 2 million years old. Their analysis suggested it was a new species which they called Australopithecus sediba. Not only did they place it in the genus Australopithecus, which is the home of several early hominids including the Lucy skeleton, they claimed that A. sediba was the specific species that gave rise to our own Homo genus, including us – Homo sapiens.

That’s a pretty big claim, and not surprisingly was met with some resistance. Now the discoverers of A. sediba have revealed the results of further analysis, and their claim that it is a direct ancestor of our own species seems to be convincing more and more people.

The hobbits 17 April, 2011

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Here’s a scientific controversy that’s been out of the spotlight for a little while – the so-called ‘hobbit’ skeletons found in a cave on the Indonesian island of Flores. These human-like remains, found in 2003 and announced to the world in 2004, were from creatures just one metre high, and were relatively modern – just 12,000 years old.

When researchers made the discovery, they claimed that this was a new species which they called Homo floresiensis. This kicked off a controversy that received a lot of coverage in the press.

Did they really belong to previously unknown species in our family tree, or were they just a group of early humans that suffered from a medical condition (microcephaly being the prime suspect) that made them so small?

That debate has continued ever since, although it has faded from public view recently as further finds from the cave indicate that the hobbits probably were a separate species.

In a strange twist to the story, Teuku Jacob, a prominent Indonesian paleoanthropologist, removed most of the hobbit remains from the lab where they were stored in late 2004. Jacob conducted his own analysis of the remains and returned them a few months later, but they had suffered some damage while in his care. Jacob did not believe that the remains were a new species, so when the Indonesian government blocked access to the cave in 2005, some believed that it was in order to prevent excavations that might prove him wrong. The government allowed work to resume in the cave in 2007.

A recent development was the announcement that researchers at the University of Adelaide are going to attempt (for a second time) to extract DNA from one the hobbit’s teeth. By far the most interesting part of that link to the story in Nature is in the Comments section, where Maciej Henneberg, also from the University of Adelaide and a well-known opponent of the hobbit-as-a-separate-species idea, attacks the techniques and accomplishments of the lead scientist attempting the DNA analysis.

So what happens next? If the DNA testing is successful (which seems like a longshot), that should clarify things. If it’s not, the discovery of further remains from Flores seems like the best way to resolve the controversy.

One of the most interesting things about the controversy is that the stakes aren’t as high as the media coverage would have you believe. Even if the hobbits are a new species, that doesn’t cause a major rewrite of the human evolutionary story – it’s just an interesting little branch that wasn’t known before. Ralph Holloway from Columbia University, who hasn’t fully committed to either side in this debate, has been quoted as saying “I think it’s sort of a side issue.” It seems like the public’s fascination with the story have driven the level of acrimony in the scientific debate to heights that it wouldn’t reach otherwise.

Further reading:

John Hawks (Anthropologist who maintains an excellent blog)

What is the Hobbit? (2006 review article in PLoS Biology)

Arsenic based life 7 April, 2011

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Back in late November, NASA put out a press release about an upcoming news conference. The exact details of the research to be discussed weren’t revealed, because the research paper wasn’t published yet, but the release stated that the news conference would discuss

…an astrobiology finding that will impact the search for evidence of extraterrestrial life.

This vague wording sparked some wild speculation in the popular press.

Eventually it was revealed that a NASA-funded research team, led by Felisa Wolfe-Simon, had discovered microbes in California’s Mono Lake that appeared to have a slightly different kind of DNA from all other known living things. Mono Lake is an unusual (and hostile) environment – it’s about twice as salty as the oceans, extremely alkaline, and has very high levels of arsenic. Some microbes in Mono Lake are capable of using arsenic instead of water to help them photosynthesise, but this new research identified microbes that are actually incorporating arsenic into their DNA, in the place of phosphorus.

There’s many different angles to this story, but for now I’ll focus on the science and the media.

Almost immediately the experimental process came under attack – Rosie Redfield wrote a detailed review of the paper here. The main point of criticism was that the researchers simply weren’t careful enough with their experiment, so the conclusion can’t be trusted.  From her conclusion:

Lots of flim-flam, but very little reliable information.  The mass spec measurements may be very well done (I lack expertise here), but their value is severely compromised by the poor quality of the inputs.  If this data was presented by a PhD student at their committee meeting, I’d send them back to the bench to do more cleanup and controls.

I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda.  I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science’s editors in their eagerness to score such a high-impact publication.

NASA’s approach to publicising this research – putting out a teasing press release and letting the wild ideas build up before announcing the results – has angered a lot of scientists and no doubt fuelled some of the criticism. During the days leading up to the press conference, those who had actually read the paper couldn’t jump in and tamp down some of the speculation, because the paper was still under an embargo.

For some excellent summaries of the whole saga, see Carl Zimmer in Slate here, and the prolific Ed Yong at Discover here, here, here and here. In a recent update, Michael Eisen attended a seminar with Wolfe-Simon and was disappointed with her response to the criticisms.

So what do I make of all this? I think it’s probably an unfortunate mix of too much hype and sloppy science. Sounds similar to ALH84001, but in that case the debate was mostly about how to interpret observations, and that can take a long time to resolve. Here the main issue is the experimental process, and that can be resolved relatively quickly if others attempt to replicate the results – it will be interesting to see if there are any takers.

Skip the meteorite middleman – shop direct from the Martian factory 10 March, 2011

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Just one more meteorite comment (I promise!) – back when I was analysing the ALH84001 controversy, I speculated about some ways that the controversy could be resolved. My first thought was that the discovery of more Martian meteorites like ALH84001 would settle it one way or another, but later I realised that the broader question about life on Mars could be resolved in several different ways , including a manned mission to Mars or a robotic mission to return samples of the Martian surface to earth.

Well, it turns out that the American planetary science community have thought about this too. In their 10 year strategy paper, which outlines which planetary missions should receive funding over the next 10 years, they have chosen a Mars sample return mission as the highest priority. In particular, the report states:

It is now possible to select a site on Mars from which to collect samples that will address the question of whether the planet was ever an abode of life. The rocks from Mars that we have on Earth in the form of meteorites cannot provide an answer to this question. They are igneous rocks, whereas recent spacecraft observations have shown the occurrence on Mars of chemical sedimentary rocks of aqueous origin, and rocks that have been aqueously altered. It is these materials, none of which are found in meteorites, that provide the opportunity to study aqueous environments, potential prebiotic chemistry, and perhaps, the remains of early martian life.

And that is not a positive message for those who are looking at meteorites for signs of Martian life!

Tomorrow – an analysis of the ESP controversy.

Is ESP real? 9 March, 2011

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In January, the Journal of Personality and Social Psychology published research by Daryl Bem of Cornell University that measured an actual effect of extra sensory perception (ESP) (the link is to a preprint copy of the paper). Basically, the subjects in his experiments were able to guess the outcome of a random event – before it happened – with a small, but statistically significant, margin greater what you expect from just random luck. Jonah Lehrer of Wired has a good summary.

It’s pretty startling to find something like this in a mainstream journal – the journal felt the need to include an editorial comment stating

To some of our readers it may be both surprising and disconcerting that we have decided to publish Bem’s article … We openly admit that the reported findings conflict with our own beliefs about causality and that we find them extremely puzzling. Yet, as editors we were guided by the conviction that this paper—as strange as the findings may be—should be evaluated just as any other manuscript on the basis of rigorous peer review. Our obligation as journal editors is not to endorse particular hypotheses but to advance and stimulate science through a rigorous review process.

The research sparked a number of different responses in the scientific community. First, there was the “there must be something wrong with the experiment” view. Generally, this view starts from the assumption that the paper’s conclusion (that ESP is real) must be incorrect, therefore some error was committed in the course of the research – example here. In the same issue of the journal, a group of scientists from Holland point to the statistical analysis as the source of the error, and warn that many psychology experiments many suffer from the same flaw.

Another response was “this never should have been published”. An article in the NY Times quotes psychology professor Ray Hyman as saying:

It’s craziness, pure craziness. I can’t believe a major journal is allowing this work in… I think it’s just an embarrassment for the entire field.

If I was going to be completely objective about this, I would reserve judgement on the research and wait for the results to be replicated by other researchers. To his credit, Bem details his experimental setup and analysis techniques in great detail, and states:

The major empirical challenge … is to provide well-controlled demonstrations of psi (ESP) that can be replicated by independent investigators. That is the major goal in the research program reported in this article. Accordingly, the experiments have been designed to be as simple and transparent as possible…

Many other findings of positive results for ESP have disappeared when others tried to replicate them.

The main reason for people to assume that the paper’s conclusion is wrong is that there is no way to explain how ESP could possibly work. Bem attempts to address this, pointing out that the mechanisms behind many physical phenomena effects were only found many years after the first evidence of their existence. In this particular case, I don’t think that’s a satisfactory answer. The issue with ESP isn’t just that we can’t explain how it could work; it’s that any explanation would require a complete rewrite of the laws of physics. That’s an unbelievably tall order – the biggest scientific revolution ever, so I think it’s understandable (and even reasonable) to assume that the research is flawed, until many more irrefutable experiments show otherwise.