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."

Keeping up with the Railses: New Zealand's flightless rails

In a previous post I touched briefly on two species of New Zealand rail in the genus Porphyrio. As mentioned, the pūkeko is one subspecies (Porphyrio porphyrio melanotus) that belongs to a cosmopolitan species complex. The takahē (Porphyrio hochsetterii), on the other hand, is endemic to New Zealand.  In addition to these two extant species there is an extinct member of the genus, the mōho (Porphyrio mantelli), also known as the North Island takahē. The pūkeko and takahē are morphologically similar as would the mōho have been, which is what you expect given that they are congeneric (i.e. in the same genus). From fossil evidence we know that the mōho and the takehe were more similar to each other than to the pūkeko: the main difference being that the mōho had longer legs, was larger and was more slender than the takahē. The strong morphological similarity between the mōho and takahē led early taxonomists to classify them as two subspecies, Porphyrio mantelli mantelli  and Porphyrio mantelli hochsetterii respectively. Because all three species are in the same genus, we know that they share a common ancestor. Therefore, pragmatically we might expect that they all evolved from this common ancestor in New Zealand.

However, this expectation is not supported by both fossil and molecular (DNA) evidence. In the mid-nineties, Steven Trewick (note the link to his personal page is broken but this takes you to his lab website) undertook a study of New Zealand rails to determine their origins, evolutionary history and the relationships among them. What he found was somewhat surprising in regard to the mōho and takahē. Rather than sharing a common ancestor with an in-situ divergence event, the mōho and takahē were the result of two separate colonisations by similar volant ancestors—probably a species similar to the pūkeko. This evidence resulted in a revision of the two subspecies into two separate species as indicated above. It also raised some interesting questions regarding the evolution of flightlessness among New Zealand rails.

New Zealand has (including recently extinct species) a relatively high diversity of rails (18), about half of which are flightless. An interesting question that Steve Trewick and his research group are asking is why seemingly mobile, volant species evolve into flightless range-restricted species. This comes partially from the fact that the likely ancestors of the mōho and the takahē came from the same lineage as the pūkeko. Because birds are highly mobile - the pūkeko being a perfect example in this case the - gene flow tends to be high reducing the probability of speciation. In fact, there is little evidence for speciation among birds on islands. In other words, it takes a substantial barrier to stop gene flow in birds which reduces the probability of speciation. Yet there have been several independent rail colonisations in NZ with many resulting in a flightless species. To me this indicates that there is strong selection for rails to fly when necessary (i.e. in the presence of predators) but it is easily relaxed without predators. But the question of even rates of gene flow remains.

A quote about us all

"The chief obstacle to the progress of the human race is the human race." - Don Marquis

This statement is often quite true. I have just started reading The Moral Landscape by Sam Harris (on my new kindle-get one). Early on, and I am sure later (actually I know later because I can word search with my kindle-see I told you to get one), Harris talks about stem-cell research and the opposition it faces in the US. Sadly, this opposition has significant negative impact on our ability to develop medical treatments that would save countless lives.

Note: sorry no photo this time.

Part 2: do you believe in evidence?

The second part of my analysis of the statement on creation/evolution published by Ponahui Christian School picks up where part one left off: it might get better.

Indeed, it seemed like it might with a promising title. The title of the second part of the statement “[c]ommonly accepted science we believe in.” It is better because at least they accept some science, but inserting the world ‘believe’ in reference to science is cringe worthy. Science is not based on beliefs, science is based on evidence. Accept would have been better but it would hardly change their intent. The second part of the statement is as follows:

We believe in all the experimentally verifiable laws of science. We also teach that the laws of physics and chemistry are purposely designed by the Creator to support life. If the known physical constants of the universe are slightly different, or the angle in a water molecule was slightly different, or the chemical laws of equilibria, etc, are any different then life would be impossible. (Imagine a universe without gravity for example.) Even something as simple as burning wood in a controlled campfire requires several laws of physics and chemistry to be just right, and several conditions on planet Earth to be just right also. This paradox is a puzzle to evolutionists who base everything on chance, but not to the creationist who believe that even something as simple as controlled fire, and something more complex such as life, is God’s design. The unproven and unprovable theory of the existence of millions of universes is based solely on trying to explain this paradox. If there are millions of universes is has to be just right somewhere! (We don’t subscribe to this.)

This means that we believe in the overwhelming majority of science in the NZ curriculum and teach it accordingly, and we feel privileged to be part of the NZ education system. Our students have consistently scored above the national average in all external science exams, including biology.

In the area of biology we believe in natural selection, genetic drift, speciation, and adaptive radiation. We believe that God has designed these processes to enable living things to change slightly, within their kind, to enhance population health in new or changing environments. These processes are all re-arrangements, frequency shifts, and net losses of genetic information which is already present.

Following on from using ‘believe’ in the title, the word is inserted here again, although in reference to “experimentally verifiable laws of science.” If something is an experimentally verifiable law belief is entirely redundant. A scientific law is a phenomenon of nature that has been proven to invariably occur whenever certain conditions exist or are met. Therefore, it is ironic, that people who believe in the unverifiable nature of the supernatural require something to be verified experimentally. Also, there are very few laws in science yet they suggest that “[they] believe in the overwhelming majority of science in NZ curriculum” which cannot be true if they only ‘believe’ in laws. Science is built upon laws, theories, principles and hypotheses and the NZ science curriculum is built on all of these, not just laws.

It is true that the physical constants on Earth are just right for the way the world is now. However, while we can speculate that life as we know it would not exist if the earth and universe were not exactly as it is now, we cannot be sure that life in any other form would not. Things would be different, but that is what they would be. I would most likely not exist and neither would you. The suggestion of a paradox is quite difficult to understand. I see no paradox. The conditions on Earth are just right for the life that exists on it is in no way paradoxical, it just is. The claim that the multiverse concept was proposed is an attempt to account for the ‘paradox’ is patently incorrect. These ideas arose independently of evolutionary biology given that it comes from the field of theoretical physics and have been around for a long time. Recent empirical observations of the universe appear to support the concept of a multiverse. See here for a paper on a concept called Eternal Inflation. Warning! It is not straight forward. Also note that authors do not talk about resolving any paradox. Further note that I am not a physicist and cannot verify the work I am simply putting trust in those who do know about physics in the same way that I, and most other people, trust bridge builders and car manufacturers.

I have purposely left the final paragraph about biology because I think it is best addressed along with the next few sections that cover biology and evolution in more ‘detail’. What I will do is congratulate Ponatahi for their “consistently. . . above the national average in all external science exams, including biology.” However, I will add that it seems odd that their students achieve above results in biology exams based on a curriculum that explicitly covers evolution. It is fishy and reeks of dishonesty somewhere down the line. I have no evidence so I am just speculating.