This is not peer-review

Whoa, they are coming thick and fast this week.

A screen shot from the film Super of God touching Frank's brain

 This is inspired by my previous post that talked a little about peer-review. Actually it is the other way around. I got side tracked before I got started but was reminded about my initial idea after seeing this post over at Pharyngula about a terrible piece of Intelligent Design (ID) masquerading as science published. My idea initially came from a the list of peer-reviewed article by Discovery Institute (DI) members proudly displayed on their website. I scanned the list and noticed the journal called BIO-complexity popping up often. The name immediately set alarm bells off. It sounds very ID like: they love complexity as if it were some massive hurdle for evolution to overcome.

I googled BIO-complexity and guess what? It is just as I suspected. The opening line of their purpose statement is classic: "BIO-Complexity is a peer-reviewed scientific journal with a unique goal" (my emphasis). Unique indeed, peer-reviewed in the fairest sense, probably not. Although given that the journal has been around for two years and only has seven published articles could mean that they have such high standards very few manuscripts make it to publication. Again, probably not. Looking at the authors of the papers is no surprise, it is all the usual suspects, Gauger, Dempski, Axe et al. Moreover, in 2011 Axe was an author on two of the three articles in 2011 and two of the four in 2010. He is also the managing editor of the journal. A look at the editorial board shows that most of the authors are on the editorial board. Seems like bullshit to me. One the editors is the author of the paper criticised by PZ in the post linked above.

So is it appropriate for the DI to make claims about their members publishing in peer-reviewed journals if they are all just reviewing each others work? Well this is not unlike 'mainstream' science. In fact the word peer by definition means that is exactly what happens. But, the case of Lynn Margulis pulling a shifty to get Donald I. Williamson's paper published shows that there can be flaws in the peer-review process among mainstream journals. However, the science literature has a final line of defence in the form of commentary. If a published paper is found by another scientist in the field to be faulty, they can submit a comment to the journal arguing the case. This is exactly what happened with the above paper as with other famous cases like 'arsenic life'.

Not to worry though because according to BIO-Complexity they accept comments or Critiques as they call them. They also say that they "[all research articles] will followed by a brief published Critique when this becomes available." To date there have been no critiques published on any of their five research articles or critical reviews. In science, all comments are peer-reviewed as you would expect. Is it the same for BIO-Complextiy? Apparently not. Commentary is not peer-reviewed. Instead comments are published " at the sole discretion of the editor of the original article". So if I submit a comment challenging any of the papers published the editor is not likely to publish it because they look bad for publishing the original article. Basically because all the crap they publish is supportive of the underlying goals of the journal, all the authors who publish in the journal, and the most likely the ID community at large no comments will ever be published. How dishonest.

How does science work?

In my interactions with non-scientists there are some common misunderstandings about how science works. These misunderstandings are predominantly the result of a lack of exposure to science. At school science is offered as a subject but students rarely 'do' science. They get taught a bunch of facts and occasionally do some experiments with known outcomes. Realistically this is hardly science. Science is a way of approaching problems, questioning areas surrounding these problems and applying reason to get some understanding of the problem so we can begin to explain it.

Admittedly this procedure may be somewhat difficult to do at the high school level and indeed even at the tertiary level - at least it seems that way based on my very limited experience with teaching tertiary students. Nonetheless, certainly it can be achieved at tertiary and secondary level. I know that at the university I attended there has been some development in that area for first year students of science. The problem, however, is that science students are the only people with any semi-useful level of scientific literacy. The media reports on science on a daily basis but people are not qualified to make appropriate judgements on the science. What is worse is that the media always adds some slant to the reporting that often influences people into making up their mind about something with out actually being informed about it. I have written about a particular case in a previous post where the media got it quite wrong on the underlying scientific context that resulted in scores of ignorant comments on the news story.

So what is the answer? I don't have a clear-cut one but I have some possible ideas that might help. One of the misunderstandings that appears common - actually is is more of an ignorance - is how science is disseminated. It is very rare that I talk to people about what I do that have any clue about what the scientific literature is let alone how it works. I have found that when I tell people what it means to publish work in a journal they are surprised that it is common for work to be rejected for publication and, that many more manuscripts are rejected than accepted. They are also surprised that journals can charge you to publish, not the other way around.

Because publication is generally the final step in a research project (Note: How the knowledge gained from the project is a different discussion) I think that the public should know more about how it actually works, specifically peer-review. Peer-review is science's quality control and I think if more people understood the process they would be able to better gauge the merits of science. It might stop ridiculous phrases like "so-called scientists" when people disagree with the outcome of a study like the one I mentioned above. Rather they might realise that it is not just some persons pet idea that they have come up with, but actually something that has been scrutinised by other experts. When the work is controversial it will most likely be heavily scrutinised. It is of course important to admit that peer-review is not flawless, something I have briefly touched on before, but importantly this is the exception not the rule or anywhere near it. The University of California at Berkley has a good explanation of the peer-review process up on their website which I recommend for a brief introduction.

A bird with a plant name! How appropriate.

I think given my sporadic posting due to work in the field (no complaints here) I am no longer going to kid myself with rigid nomenclature for grouping posts. What I mean is that I am relaxing the (in fact already have) "Bird of the week" and "Quote of the day" posts. Despite this I will keep up with doing posts along the same lines without the strict time frames.

From here

I begin this new series of "not of the weeks" with a bird one, and given that this week was host to World Wetlands Day a wetland bird seems appropriate, and as the title suggests the bird has a plant name. According to Wikipedia early settlers called it the 'swamp sparrow' due to colouration (see pictured) and its typical habitat, Kōtātā or Mātātā  by maori. It is now commonly called the Fernbird.

 The Fernbrid (Bowdleria punctata) is a monotypic species (i.e. the only species in its genus) in the Locustellidae family although Fernbird collectively refers to a species complex of fives subspecies. Each subspecies is native to a single island or island group: North Island, veleae; South Island, punctata; Stewart Island, stewartiana; Codfish Island, wilsoni and Snares Island, caudata. Despite their widespread distribution Fernbirds numbers are generally quite low. This is due overwhelmingly due to habitat clearance and their relatively high habitat-specificity. As I have already mentioned, Fernbirds inhabit wetlands. Wetlands in New Zealand have declined because they have been cleared for farming particularly in the Waikato and southern regions of the North Island. What habitat that does remain is often in heavily modified pastoral landscapes. Yet, despite this, Fernbirds remain locally common in areas where habitat remains. This is particularly evident in low-fertility manuka mires or pahiki that are not suitable for agriculture. My colleague was fortunate enough to see several Fernbirds this week in just such habitat.

I tweeted today about being in some wetlands on World Wetlands Day but sadly I didn't see any Fernbird. I did possibly (yet to be confirmed) collect a regionally critical plant, Carex fascicularis which is quite 'cool' in a plant-geek way. In fact over the last few months i have been quite lucky to visit several places around the Auckland region looking at pockets of remaining bush, wetland and coastal cliffs and have found quite a few rare/endangered plants. But I think I will save the discussion on my recent escapades for another post.

Happy Birthday Bert!

Although I have previously featured a quote from Bertrand Russell I feel like today (a day late) is a good day for another. The reason in threefold: (1) my friend Holly owns an awesome cafe in Auckland central called Albert Park Cafe - which you should definitely go to if you are in Auckland - and she had a poster on the wall this morning depicting Albert Einstein (also previously featured in QOTD), Bertrand Russell and another 'Bert' that I don't know, (2) it was Bertrand Russell's birthday yesterday and (3) when I got out my quote book [Bertrand's] was on the page i opened to. It was destined by the spiritual woo inside me to happen. The quote itself warrants little discussion because it is quite direct and is unambiguous. Moreover, what more could I add, at least on his birthday.

"Many people would rather die than think. In fact, they do."