Category Archives: SciBlogs

November ’15 – NZ blogs sitemeter ranking


There are about 300 blogs on the list, although I am weeding out those which are no longer active or have removed public access to sitemeters. (Let me know if I weed out yours by mistake or get your stats wrong).

Every month I get queries from people wanting their own blog included. I encourage and am happy to respond to queries but have prepared a list of frequently asked questions (FAQs) people can check out. Have a look at NZ Blog Rankings FAQ. This is particularly helpful to those wondering how to set up sitemeters. Please note, the system is automatic and relies on blogs having sitemeters which allow public access to the stats.

Here are the rankings of New Zealand blogs with publicly available statistics for November 2015. Ranking is by visit numbers. I have listed the blogs in the table below, together with monthly visits and page view numbers. Meanwhile I am still keen to hear of any other blogs with publicly available sitemeter or visitor stats that I have missed. Contact me if you know of any or wish help adding publicly available stats to your bog.

You can see data for previous months at Blog Ranks

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The problem with reasoned discussion


Why is  a straightforward logical discussion so impossible? Why do our discussion partners refuse to accept our reasoned arguments? And, if we are honest, why do we ourselves find it so difficult to accept the reasonable logic of our discussion partners?

Well, a recent article at the blog “Why We Reason” provides an answer. It is  Psychology’s Treacherous Trio: Confirmation Bias, Cognitive Dissonance, and Motivated Reasoning and reinforces what I have often felt – we are not really a rational species – more a rationalising one.

Beliefs dictate what and how we see

The article gets to the root of the matter – the psychological forces that fuel our conversations:

“While many like to believe that they have a special access to the truth, the reality is that we all see the world not as it is, but as we want it to be: Republicans watch Fox while Democrats watch MSNBC; creationists see fossils as evidence of God, evolutionary biologists see fossils as evidence of evolution; a mother sees abortion as the best thing for her daughter, and the church sees it as unholy and sinful. You get the point – our beliefs dictate what we see and how we see.”

The article goes on to discuss “a few psychological tendencies that when mixed together form a potent recipe for ignorance.”

Confirmation bias


Confirmation bias sticks out like a sore thumb when participants in discussion cherry-pick authorities and citations to support their arguments. Well, it sticks out like a sore thumb to the discussion partner anyway (who may also be cherry-picking to confirm an opposite bias).

“Confirmation bias is exactly what it sounds like – the propensity for people to look for what confirms their beliefs and ignore what contradicts their beliefs while not being concerned for the truth.”

Hard not to fall into that trap when discussing complex issues within the constraints of limited space and time. But, nevertheless, something we should attempt to avoid.

Cognitive dissonance


“Then there’s cognitive dissonance, which describes a “state of tension that occurs whenever a person holds two cognitions that are psychologically inconsistent.” “

The article provides an example:

“Leon Festinger introduced it in 1957 after he infiltrated and studied a UFO cult convinced the world would end at midnight on December 21st, 1954. In his book When Prophecy FailsFestinger recounts how after midnight came and went, cult members began to look for reasons for why the end of the world had not come. Eventually the leader of the cult, Marian Keech, explained to her members that she received a message from automatic writing, which told her that the God of Earth decided to spare the planet from destruction. Relieved, the cult members continued to spread their doomsday ideology to non-believers. Although Festiner’s example is extreme, all of us do this everyday. Take unhealthy food; we all know that pizza is bad for us, but we still eat it. And after finishing a few slices we say “it was worth it,” or “I’ll run it off tomorrow.” Or take smokers; they know that smoking kills but continue to smoke. And after unsuccessfully quitting, they justify their failures by claiming that, “smoking isn’t that bad” or that “it is worth the risk.” Whether it’s UFO’s, food, or smoking we all hold inconsistent beliefs and almost always side with what is most comfortable instead of what is true.”

Motivated reasoning

Dilbert - mot reason

The article describes this as “our tendency to accept what we want to believe with much more ease and much less analysis than what we don’t want to believe.”

I think religious apologists often provide the most obvious examples of motivated reasoning – probably because they are often trained in philosophy and logic. They will argue that their beliefs are based on reason and not faith, and seem to enjoy constructing logical arguments for their claims which seem to be built on simple logical steps. Yet, they gloss over, or ignore, the huge jumps in logic which are inevitably part of their reasoning.

Maybe a faith-based belief reinforced by motivated reasoning is the hardest to defeat because the proponent actually believes their arguments are completely rational.

The article concludes:

“So what’s the difference between confirmation bias, cognitive dissonance, and motivated reasoning? The short answer is that there really aren’t any differences. Generally speaking, they serve the same purpose, and that is to frame the world so it makes sense to us. But there are a few nuances worth mentioning. For one, motivated reasoning is like an evil twin to cognitive dissonance in that it tries to avoid it. And for another, and I quote NYU psychologist Gary Marcus who says it perfectly, “whereas confirmation bias is an automatic tendency to notice data that fit with our beliefs, motivated reasoning is the complementary tendency to scrutinize ideas more carefully if we don’t like them than if we do.””

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Science is never done – some scientific terms explained

The above great video by It’s Okay To Be Smart explains words such as theory, hypothesis, fact and law in the way that scientists use them, not the way we use them in everyday speech.

As the article at Sciencedump, You might think you know, but do you really? Important scientific words explained!, says:

“I don’t know about you, but I’m getting kind of sick of people misunderstanding the words theory and hypothesis and turning them into something bad. Whenever I hear someone say that evolution is only a theory, I am immediately reminded of Wallace Shawn’s character Vizzini from The Princess Bride going around yelling “inconceivable!” at every turn, and in really having no clue what it actually means.”

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Studies show – or do they?


This article from The Spud – Sentences that start with “studies show” usually followed by bullshit, study shows really resonates with me. I have had a gutsful of terms like “studies show” or “scientists have found,” etc. They are simply used to give authority to all sorts of claims – but authority requires the reader to do a bit of work. Check out these studies. Find out exactly what they do say. Don’t take such claims at face value.

A recent study in the Journal of Studying Studies, concluded that sentences which start with “studies show” tend to be followed by inaccurate information.“We looked at several health news stories, anti-vaccine websites, pseudoscience pages which cover things like homeopathy and naturopathic medicine, and found that in almost all cases when a story or headline begins with “studies show” it usually meant the studies were very poor and the author didn’t fully understand the evidence they were presenting,” said researcher Dr. Ernest Young.In response to this latest news, Natural News founder Mike Adams replied with “Studies show that almost all of the studies going against natural medicine are funded by big pharma and all part of the global conspiracy perpetuated by the Illuminati and Agenda 21. I know how to juggle.”The report will be available in next months issue.

Source: Sentences that start with “studies show” usually followed by bullshit, study shows – The Spudd

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Should we trust science? – Wellington talk


Naomi Oreskes is Professor of the History of Science and Affiliated Professor of Earth and Planetary Sciences at Harvard University, and an internationally renowned geologist, science historian, and author.

If you are in Wellington next Tuesday this should be an interesting talk. I would certainly be in the audience if I was able.

Should we trust science?

Perspectives from the history and philosophy of science

Naomi Oreskes

Professor of History of Science at Harvard University.

6pm Tuesday 24 November 2015
Paramount Theatre, 25 Courtenay Place, Wellington

In this talk Professor Naomi Oreskes offers perspectives from the history and philosophy of science, argues that we should trust science and explains why.

Many readers will know Professor Oreskes as one of the authors, together with Eric M. Conway, of 
Merchants of Doubt: How a Handful of Scientists Obscured the Truth on Issues from Tobacco Smoke to Global Warming
I highly recommend this excellent book.

These two authors have also written a science-based book of fiction The Collapse of Western Civilization: A View from the Future. I haven’t read it yet, but it’s certainly on my list (and in my eReader).

The Royal Society of NZ has organised the event – for more information see Should we trust science? « At Six « Events « Royal Society of New Zealand.

For those of us who can’t make Professor Oreskes talk there is a video of a similar talk she gave at Virginia Tech recently at Distinguished Lecture 2015: Dr. Naomi Oreskes, Harvard University

About Naomi Oreskes

Naomi Oreskes is Professor of the History of Science and Affiliated Professor of Earth and Planetary Sciences at Harvard University, and an internationally renowned geologist, science historian, and author.

Oreskes is the author of many scholarly and popular books and articles on the history of earth and environmental science. She has lectured widely and won numerous prizes, including the 2009 Francis Bacon Medal for outstanding scholarship in the history of science and technology, the 2011 Climate Change Communicator of the Year, and the 2014 American Geophysical Union Presidential Citation for Science and Society.

For the past decade, Oreskes has been primarily interested in the science and politics of anthropogenic climate change. Her 2010 book, Merchants of Doubt, How a Handful of Scientists Obscured the Truth on Issues from Tobacco to Global Warming, co-authored with Erik M. Conway, was shortlisted for the Los Angeles Times Book Prize and won the Watson-Davis Prize from the History of Science Society. The film version was released in late 2014.

Oreskes’s current research projects include completion of a scholarly book on the history of Cold War oceanography.

Naomi Oreskes is brought to New Zealand by History of Science 2015 conference in partnership with the Royal Society of New Zealand.

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Anti-fluoride hypothyroidism paper slammed yet again


Credit: Display of Statistical Data

Anti-fluoride campaigners often cite a limited number of papers published in scientific journals as evidence for their claims that community water fluoridation (CWF) is harmful. They do this to give some sort of scientific credibility to their claims – but the citations are far from scientific as they are usually cherry-picked, misrepresent the cited papers or use poor quality papers which are often not peer-reviewed, or poorly peer-reviewed, and written by fellow anti-fluoride campaigners.

This year, anti-fluoride campaigners have heavily promoted two such papers claiming harmful effects of CWF:

The hypothyroidism paper (Peckham et al., 2015) received negative reviews immediately after publication and a number of peer-reviewed responses have since been published. The latest response by Foley (2015) is useful because it gives a thorough critique of several faults in the Peckham paper. It is available in full text on-line:

Foley, M. (2015). Fluoridation and hypothyroidism – a commentary on Peckham et al. British Dental Journal, 219(9), 429–431.

Here is a summary of some of the points covered by Foley:

Confounding effects almost ignored

The sort of statistical analysis of data used in the Peckham et al., paper should always consider confounding effects – otherwise the analysis is simply an exercise in confirmation bias.  Foley says:

“Peckham et al. show little understanding of confounding factors, and have made only a token attempt at considering their impact. The authors mention the ecological fallacy, but then ignore its implications in strongly implying a causal link between water fluoridation and hypothyroidism.”

The confounding factor that sticks out like a sore thumb is iodine – or its deficiency. Iodine deficiency is associated with hypothyroidism and there are moderately to severely deficient levels of iodine across the UK. Foley points out:

“Vanderpump et al. have already shown that schoolgirls in fluoridated Birmingham appear to be more likely to show moderate-to-severe iodine deficiency than schoolgirls in many non-fluoridated UK cities . .”


Credit: Mu-Peter

Iodine intake could potentially be associated with fluoridation status, yet Peckham et al. discounted its effects claiming “it is unlikely that there are significant differences [in dietary iodine intake] between people, living in fluoridated and non-fluoridated areas.” That is just not good enough and simply confirms the bias of the authors – especially as they had already referenced a study showing “greatly differing urinary iodine levels in groups of schoolgirls from major UK cities, with 17% of participants showing moderate to severe deficiency.”

As Foley points out:

“. . iodine intake is associated with the outcome variable, hypothyroidism. Iodine intake could certainly confound any statistical association between fluoridation status and hypothyroidism. So why wasn’t this considered by the authors? Authors also failed to consider the impacts of smoking, medications and other factors known to contribute to hypothyroidism.”

Ignoring or downplaying confounding effects is a common trick used by those who have a bias against CWF. I referred to this in my articles Connett misrepresents the fluoride and IQ data yet again, and Connett & Hirzy do a shonky risk assessment for fluoride. Connett uses data showing a correlation of IQ with urinary fluoride explaining only 3% of the variation in IQ. The statistical  analysis did not consider confounding effects which could easily have eliminated the correlation with fluoride.

Another example is the ADHD paper of Malin & Till where a significant correlation with CWF disappeared when confounding effects were included in the statistical analysis (see  ADHD linked to elevation not fluoridationADHD link to fluoridation claim undermined again).

Poor review and citation

Authors inevitably show some bias in the citations they select, but anti-fluoridation proponents carry this to the extreme. Citations are cherry-picked to support their case and the rest of the literature usually ignored (or ridiculed) to give the impression there is a large amount of scientific support for their case.

Foley criticises the Peckham paper for this sort of citation – and for “inappropriate self-citation.”


Credit: Self-citations, is it worth to work on them?

Peckham et al., demonstrates how to use self-citation as a way of getting claims from a poor journal into a  mainstream journal. Foley mentions their self-citation of a earlier paper opposing CWF – Peckham & Awofeso (2014), Water Fluoridation: A Critical Review of the Physiological Effects of Ingested Fluoride as a Public Health Intervention, The Scientific World Journal Volume 2014 (2014):

Scientific World Journal has a well-publicised history of colluding with other journals to self-cite authors’ papers to increase journal impact factors. The referenced Peckham and Awofeso paper is unusual in that many unattributed paragraphs, including factual errors, are almost identical to paragraphs from a previous Awofeso paper. This paper in turn has unattributed paragraphs almost identical to paragraphs on webpages belonging to the National Institute of Dental and Craniofacial Research and a popular chemistry website.

I discussed this journal and Peckham & Awofeso (2014) in my article Peer review, shonky journals and misrepresenting fluoride science.

So, get a biased article published in a shonky journal (usually by paying publication fees to avoid proper peer-review) and then cite it in later papers to give dubious credibility to current claims.

But again and again Peckham et al., (2015) cites papers which don’t really support the claims they make. For example, they cite Feltman & Kosel to support their statement that “the effects of fluoride on the thyroid have long been observed.”

“But Feltman and Kosel’s only mention of the thyroid is a single sentence that other researchers ‘…report that fluoride is a thyroid inhibitor’. Their only references for this statement are a personal communication with US Public Health Service researcher Floyd De Eds, and a 1954 paper that studied delayed tooth eruption in rats following removal of the pituitary gland. The evidence supporting Peckham et al.’s statement is extremely weak.”

Similarly, Peckham et al referenced a 1958 Galletti and Joyet paper to claim fluoride reduced thyroid activity:

“However, Galletti and Joyet only investigated the effect of fluorides on patients with hyperthyroidism, and did not find that fluoride was linked to goitre. . . . . Regarding the reduction in thyroid activity in patients with hyperthyroidism treated with fluoride, Galletti and Joyet concluded ‘…such an action appears only occasionally among persons subjected to massive doses of this substance’, a situation clearly not comparable to community water fluoridation.”

Peckham et al., concluded there are “questions about the safety of community fluoridation and consideration should be given to reducing all sources of fluoride in the environment.” But Foley points out:

“Three references are given to support this statement; however, two of the references provided make no such alarmist recommendation. The only one of the three that does so is Peckham’s own 2014 paper.”

Poor conclusions

Foley’s opinion is that “the paper’s conclusions can and should be dismissed” as it has “serious biases and flaws.”

He says:

“Literature reviews have been highly selective and critical analysis of that literature has been poor. The authors show a disturbing tendency to focus on a small number of poor quality studies that reinforce their own views, while ignoring contradictory evidence from much stronger studies and reviews.”

And provides a bit of advice:

“Peckham et al. should have heeded the adage ‘correlation is not causation’ before coming to a conclusion at odds with a large body of reputable evidence from around the world.”


Credit: xkcd – correlation

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Cyberchondria and similar “illnesses”

Came across this new word today and realised immediately what it means.


What I need now is a word for a troll who makes claims to all sorts of personal illnesses and symptoms (not professionally diagnosed of course) which are highly exaggerated or invented.

Onehunga and the “fluoride-free” myth

Onehunga Aquifer optimised

An aerial view of the Onehunga Water Treatment Plant

Recently I discussed the fluoridation issue with a self-diagnosed sufferer from fluoride sensitivity. He claimed to have irritable bowel syndrome (IBS) brought on by fluoride in drinking water. His doctor didn’t believe him but he knew better – every time he left his hometown (which is unfluoridated) for fluoridated areas his IBS returned. He assured me that the water in his city is “fluoride-free.”

I checked the published data for his city and found the natural levels of fluoride in the tap water is 0.4 ppm – not too much less than the recommended 0.7 ppm where community water fluoridation is used. He didn’t respond to my comment passing on this information – maybe it brought on an attack of IBS as stress is one of the known factors causing this.

This issue came up again at a recent Auckland City Council meeting which considered a request for fluoridation of the Onehunga water supply. Unlike most of Auckland Onehunga’s water is pumped from the Onehunga springs and is not fluoridated. In fact, a referendum in 2001 voted against a proposal to fluoridate.

But what struck me is the argument presented by one councillor that some resident of Onehunga moved there because the water is “fluoride-free” and it would violate their rights if the water supply is now fluoridated. That seems a very poor argument as anyone with a hangup about fluoride can buy and use a cheap water filter – far cheaper than shifting house. But the claim that Onehunga’s water is “fluoride-free” motivated me to check out the published data for fluoride in the Onehunga water.

This graph summarises the data from reports covering the years 2010 – 2014 (a single report covered 2011-2012):

So, Onehunga water is not “fluoride-free.” The average concentration is about 0.2 ppm (not too unusual for ground-water sources in New Zealand) but the actual concentrations can vary a lot. Customers would have occasionally been drinking water with a concentration as high as 0.9 or 1.1 ppm F during that time period.

Surely this would occasionally send any fluoride sensitive person into a bout of IBS, skin rash, or one of the myriads of other symptoms propagandists against community water fluoridation claim. Or perhaps only if they had been told about the high concentrations (see Fluoride sensitivity – all in the mind?).

Fluorine is the 13th most common element in the earth’s crust so it is inevitable that our food and drink contain traces derived from natural sources. In the real world, there is no such thing as “fluoride-free.”

Note: I don’t know if such variation is common with underground freshwater sources. The Onehunga aquifer  derives from rainwater soaking through lava flows around One Tree Hill. It could well be prone influences from historical industrial or other sources in the locality. Apparently it has high nitrogen levels and may also be influenced by broken sewer pipes.


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Thames voters decisively support fluoridation

Fluoride Referendum Web Page Banner-01

Voters in the Thames water supply area of service have resoundingly defeated attempts to stop fluoridation of their water supply.

The Thames-Coromandel District Council has released the result of a referendum  which had been imposed on the town because of activities of anti-fluoridation campaigners. The results show a resounding defeat for these campaigners with 73% of voters supporting retention of community water fluoridation.

This is a decisive result, made even more decisive by the high turnout in the postal vote – almost 57 %. This is an unusually high turnout for local body votes in New Zealand.

Anti-fluoride campaigners were very active during this referendum, publishing about six full-page advertorials in the local papers as well as having a strong presence on the streets. It appears this aggressive approach could have turned residents off, even encouraged them to vote.

In fact, the advertising and billboard claims of the anti-fluoride campaigners have been the subject of several complaints to the Advertising Standards Authority (ASA). The Authority released the first decision on these complaints today finding that anti-fluoride advertising had violated advertising ethics. There will be more decisions released by ASA in the coming days and weeks.

The council had decided this would be a binding vote so approval of the decision to continue fluoridation is just a formality.

See also: Thames-Coromandel District Council – Thames voters opt to continue fluoridation of town water supply

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Scientific papers, civil disobedience and personal networks


Image credit: 4 tips on finding and reading scientific papers…

Jerry Coyne raises an important issue about science publishing on his blog, Why Evolution is True. That is the problem of most published scientific journals being behind a firewall and so inaccessible to readers who do not have an institutional subscription – unless they pay an exorbitant fee – US$30 or more per paper.

His article, Scientists engage in civil disobedience, share copyrighted papers, is aimed mainly at scientists, but the problems is probably greater for the non-scientist, as most working scientists already have institutional subscriptions and libraries which can source papers where there is no subscription.

Incidentally, this is also a big problem for the retired scientist. Since the advent of Human Resources Departments, one loses all privileges and accesses on retirement. Cards and pin numbers for access to buildings no longer work. Emails addresses are lost. And access to institutional networks, databases, libraries and journal subscriptions also disappear.

It is particularly a problem for people who wish to discuss scientific evidence online – whether they have a scientific background or not. Firewalls often mean that discussion is hindered because people rely only on abstracts (and sometimes only titles!). Sure, we are all familiar with trolls who will make confident assertions on even less evidence – but they are dishonest. I strongly believe that participants in these discussions have a responsibility to at least read the papers they cite.

So, it is frustrating to post a blog article about a new paper knowing that many readers simply don’t have access to more than the abstract. Providing a link to a copy of these papers violates copyright and there are limits to the amount of text that can be quoted in a blog post.

So what is a reader to do? I wouldn’t recommend paying exorbitant fees for a paper which may or may not be useful – and that only encourages science publishers in a practice which is little more than  blackmail or piracy.

Here are two suggestions – first the “civil disobedience” described by Jerry Coyne, which is most probably illegal because of copyright violations. Secondly, one that is far more legal and better for one’s conscience.

Sharing copyrighted papers by civil disobedience.

i-can-haz-pdf-memeJerry describes a method using the hashtag  #icanhazpdf on Twitter. The procedure is described in the Atlantic article, How to Get Free Access to Academic Papers on Twitter. Have a read – but I find it impersonal and a bit sneaky (it involves deleting one’s tweet once a paper is downloaded and there is no real contact with the person who made the paper available). However, it will appeal to some people attracted to the idea of civil disobedience and “putting it to the man.”

This method is also discussed in the articles The scientists encouraging online piracy with a secret codeword and I can haz PDF: Academics tweet secret code word to get expensive research papers for free.

Using personal and online networks

One could always try a public library for a personal inter-loan – but that hardly appeals to the modern person who desires more immediate access.

I have found using Google Scholar to search for a title will often produce a link to a pdf copy already online, maybe already in violation of copyright. It’s amazing how many papers used by anti-fluoride activists are available from links on anti-fluoride web pages.

And, in the old days we used to request reprints from authors. Why not give that a go – send an email to the corresponding author asking if they could send you a pdf.

But what about considering your own personal and online networks.

Do you have a family member, friend or even an acquaintance (or several) who works in a scientific institution? It wouldn’t hurt to politely ask if they could get a pdf of the paper you are after and send it to you. Surely it is legally OK for staff in such institutes to discuss their work, and other aspects of science, with interested people via email. I can’t see that such communications, sometimes involving attached scientific papers, violate copyright – at least in spirit.

Then there are the online networks we seem to have these days – usually via Facebook groups. Most scientists would be cagey about attaching a link to a Facebook comment but sending a pdf via personal message or email would be OK. If you don’t already belong to a science or sceptical group then this is a good reason for joining. There will be people in these groups willing to help – and if the group is a closed one there is little risk.

Perhaps join several groups – after all if you have several people or networks to call on you will feel less guilty about asking others to spend time on your request.

Finally, it is not enough to acquire these pdfs – one should always read them before discussing them. And I mean read them critically and intelligently. This infographic gives you an idea of what can be involved.


Credit: Natalia Rodrigue –  Infographic: How to read a scientific paper

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