Double blog assault

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Allison Campbell who alerted me to the integrated state schools that choose not to teach evolution through her posts here and here has taken a similar direction as I have in my post Blow by blow: part 1(see also here). Allison has lightened my load somewhat by commenting on section nine of the Ponatahi Christian School's statement on creation/evolution "[w]hat about archeopteryx?"  Many creationists see archeopteryx as some sort of silver bullet (among many others) to evolutionary theory. Allison does a nice job of showing how this the wrong stand to take.

A winner is crowned

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Pūkeko (Porphyrio porphyrio melanotus) from wikipedia
Forget bird of the week, here is bird of the year as voted by the New Zealand public (truthfully it was 7851 of them). This year it was taken out by the humble pūkeko (Porphyrio porphyrio melanotus). The pūkeko is a common rail that inhabits swamps and wetland, often seen at motorway verges. Sadly this tendency to hang out next to the motorway results in a fair number of deaths by car. Interestingly (to me at least), the pūkeko is a subspecies that belongs to a species complex with a broad distribution. Collectively known as the Purple Swamphen, the complex consists of 15 subspecies found in Europe, southeast Asia, Africa, New Guinea, Melanesia, western Polynesia, Australia and of course New Zealand. The Purple Swamphen is truly cosmopolitan. 


A takahē (Porphyrio hochstetteri)from here
In addition to the pūkeko, New Zealand is home to eight other species of rail. There is also evidence from middens that there were another eight species of endemic rails. But, as I have mentioned in previous posts on New Zealand birds (here and here), the arrival of humans resulted in their extinction. One species that was thought to be extinct, the takahē (Porphyrio mantelli hochstetteri), was 'miraculaously' rediscovered in 1948 G.B. Orbell. Orbell found a small population of about 250 indivuduals in a remote refuge in the Murchison, Kepler and Stuart Mountains in Fjordland on New Zealand's South Island. Following breeding and relocation efforts, takahē are now found on four predator-free offshore islands as well as at their rediscovery site.

Given their close relation to each other, the pūkeko and takahē are similar in appearance. Both species are bluish in colour with bright red legs and bills. However, the takahē is stockier and has a heavier bill. Furthermore, the takahē is flightless whereas the pūkeko is volant (i.e. it flies), albeit reluctantly, which is typical among rails. As with many New Zealand birds, and island birds in general, flightlessness is common and evolves in the absence of mammalian predators or competitors.

For some more pictures of pūkeko and other NZ native birds check out Chthoniid's Wildlife Photography and for some takahē videos check out the Deparment of Conservation. Also look out for a follow-up post on takahē that will be a little bit sciencier (that is a real word) demonstrating how modern genetic techniques have helped us learn so much more about species distributions. There is a hint about it in the species name for takahē.

Quote of some 'quotes'

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G.K. Chesterton: "The Bible tells us to love our neighbours, and also to love our enemies; probably because they are generally the same people."


Harsh but sometimes true.
From here
Noticing a trend in black and white images of the daily quoters. Did all the good things that people can say get used up before the invention of colour photography?

Return of the birds: the lazy parent

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 Is this the return of the failed ‘Bird of the week’ posts? Who knows? I won’t commit to a weekly bird post given that the last ‘Bird of the week’ was over nine months ago. I will, however, endeavor to post more about birds at more regular intervals.
Taxonomy

Kingdom
Animalia
Phylum
Chordata
Class
Aves
Order
Cuculiformes
Family
Cuculidae
Genus
Chrysococcyx
Species
lucidas
  
Today’s bird is quite a charismatic bird in terms of its interesting life history/survival strategy. These birds are brood parasites which means that they lay their eggs in the nests of other birds. The bird is obviously the cuckoo, more specifically the New Zealand Shining Cuckoo or pipiwharauroa (Chrysococcyx lucidus). Shining Cuckoos are so called due to their burnished metallic bronze-green plumage. Easily identified by their aforementioned plumage as well as their distinctive high-pitched call, Shining Cuckoos are a relatively common species found inhabiting native forest, scrub, parks and gardens though out New Zealand. During winter they migrate to Solomon Islands and Bismark Archipelago.



Although brood parasitism is found among other birds, among fish and insects, cuckoos are certainly the most famous of the brood parasites.  This is most likely because cuckoos are typically interspecific brood parasites (i.e. they use other species as host parents).  The Shining Cuckoo’s usual host is the Grey Warbler. Brood parasitism is more common in Old World cuckoos (~56 species) than in Old World cuckoos (~3 species). All of the former are members of the same family as the Shining Cuckoo, Cuculide, and all are obligate brood parasites. This means that they are ‘obliged’ to put their eggs in someone else's basket. However, whose basket is the question.

Photo credit: Peter Woods taken from http://www.nzbirds.com

 One of the common strategies for cuckoos to get a host to sit on their eggs is to mimic the appearance of the host’s eggs. As mentioned previously, the Shining Cuckoo uses the Grey Warbler as a host. Therefore, under an evolutionary arms race scenario, the cuckoo would be under selection to produce better and better mimetic eggs and the host would attempt to counter this with some sort of anti-parasitism defence (note: do not interpret the scenario as teleological). We should therefore expect that a single species of cuckoo would have a singly host species. Interestingly, this is not always the case. Some species of cuckoos have several host species and the way they get this right is by having polymorphic eggs. This means that within a species of cuckoo, different individuals lay eggs that look different and mimic the eggs of a different host species. But how does this happen and why do some individuals have different eggs?

The first question you would need to ask is how the females know which species has eggs that look like their own, and the second one would be why do females lay the same eggs as their mother if they mate with a male born to a female of a different egg type. The first question is relatively straight forward. The female is likely to carry some sort of imprint from the song and appearance of her surrogate mother making it easier for her to identify a host when she needs to lay her eggs. This is particularly important in areas where the different host species have overlapping geographic ranges. The second question has a remarkable potential answer. In mammals, males carry one X and one Y chromosome and females carry two X chromosomes. In birds, however, females carry one W and one Z chromosome and males carry two Z chromosomes. It is therefore possible that the gene related to egg colour determination in cuckoos is carried in the W chromosome. Therefore, it doesn’t matter what egg type male was born from, it is only the female that matters.

Mimetic eggs are not the only way that cuckoos get away with brood parasitism. In some species the egg does not resemble the hosts’ eggs. How then does the cuckoo get away with it? Historically it has been suggested there might be lag in the evolution of the host such that there has not been enough time to evolve defenses or, the host is genetically constrained somehow and unable to evolve a defense. This means that the evolutionary arms race is in disequilibrium. A recent study of the Jacobin Cuckoo (Clamator jacobinus) and its host the Cape bulbul (Pycnonotus capensis) suggests that in this case it might actually be stable. This is an example of a non-mimetic egg host–parasite relationship because eggs of the Jacobin Cuckoo are almost twice the size of the eggs of the Cape Bulbul. Given this non-mimetic nature of the cuckoo eggs it would be easy for the Bulbul to recognise the imposter but the eggs are probably too heavy to eject from the nest and too thick to break open. Why does the Bulbul not just desert the nest in the presence of a cuckoo egg? Despite cuckoo eggs and/or chicks being present in the nest the author found that the fitness of the Bulbul was not reduced to zero. In other words some Bulbul offspring did survive to fledge in the presence of cuckoo chicks. Thus, if the Bulbul does abandon the nest its own chicks would die, effectively reducing its own fitness. This work is interesting because evolutionary lag has tended to be the typical explanation for the non-mimetic phenomenon among cuckoos. It also indicates the importance of questioning ideas carefully in science and not sticking to the status quo.

Quaily Dote

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 I am literally (Paul) not going to introduce today's quoter. I propose guessing who it is without the use of google and posting your guess in the comments.

"We must, however, acknowledge, as it seems to me, that man with all his noble qualities . . . still bears in his bodily frame the indelible stamp of his lowly origin"

Online science

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Over the last decade blogging and other social media has become a part of most of our lives. This surge has been seen in the science community too. Platforms like freethoughtblogs, home to PZ Myers' blog Pharyngula, New Zealand's own sciblogs exemplify this growth. It has got to a point where you need to have an online presence to be noticed. I have taken this route too. I have a blog (obviously) and I have a twitter account as of this week.

Social media has been a hugely positive for science. Disseminating of ideas and new discoveries can be notoriously slow in the scientific literature, particularly in high impact journals that receive literally hundreds of submissions from hopeful scientists every day. Social media and blogging on the other hand allows rapid sharing of ideas, and in recent times it has been the vehicle of criticism. There are two notable examples that come to mind although I am sure there are many others: (1) the famous 'arsenic-life' paper, and (2) the 'velvet worm--insect hybrid' paper.

The first example, 'arsenic life', exploded in the scientific blogging community. A Google search of arsenic life yields 11,300,000 hits. The original work was published in one of the most prominent journals, Science, but was preceded by a press release by NASA  who funded the research. The press release was tantalizing and alluded to the discovery of extraterrestrial life. This was not the case. What the research apparently showed was that bacteria, named GFAJ-1, was not only growing in high levels or arsenic, but actually incorporating arsenate into it's DNA 'backbone'. This is significant because all life on Earth as we knew it until then used phosphate in it's DNA backbone--GFAJ-1 was essentially replacing phosphate with arsenate.

Unsurprisingly, such a bold claim is always approached with skepticism in the science community. However, this work was met with more than just skepticism. It was met with disbelief and harsh criticism. I have taken the time to Google that for you, all you need to do is click here to see the results. In fact about six months later Science published no less than eight technical comments on the original arsenic life paper along with a reply from the original authors. However, it was blogging that started it all. Probably the most outspoken and prominent critics was Rosie Redfield. Rosie is now trying to reproduce the results of the arsenic life paper with a live diary of her progress. To date she has been unable to replicate the growth reported by Wolfe-Simon et al. (arsenic life). We are left with several different conclusions we can draw thus far. One of them is clearly that Wolfe-Simon et al are did something dodgy. Another is that Rosie Redfield is doing something different that is inhibiting the growth of GFAJ-1 in her arsenate medium. Because Rosie is live blogging her progress and getting advice from readers the second seems unlikely, but who knows. None the less, it is an excellent example of a scientist using social media to improve science in general.

The second example is a paper by Donald I. Williamson published in another high impact journal, the Proceedings of the National Academy of Science. The paper proposed a bold new idea that Williamson claimed would change the way we should view evolution. He claimed that holometabolous species (e.g. butterflies) are not decedents of a single lineage, but rather the result of an ancient hybridization between two lineages; one that resembles the larval form and one that resembles the adult form.

The example that Williamson put forward in his 2009 paper was Lepidoptera.Williamson claimed that the two distinct forms that butterflies and moths take in their life cycle (i.e. caterpillar and flying adult) resulted from the 'unholy matrimony' between a velvet worm and an butterfly or moth-like insect. To the casual observer this might sound crazy, but at the same time wonderfully appealing. In fact, looking at a caterpillar it might be easy to believe that they are more closely related to velvet worms than butterflies. See the picture below. However, there are several lines of argument along with empirical evidence that demonstrates that caterpillars and butterflies are indeed one lineage separate from velvet worms. This evidence was presented by several authors in follow-up commentary published in PNAS that severely criticised Williamson's work. See here and here.

Caterpillar of Theretra oldenlandiae I think. Taken from here

Velvet worm from New Zealand (peripatus). Photo by S. Moore
The formal criticisms published in PNAS are an example of science in working and PNAS should be applauded for this. However, the biggest question that should be asked is, how was this work published in the first place given the significant flaws? This was discussed and debated heavily online and it was the online science community that really got people interested in making formal comments. My favourite quote from an online source is from Fred Nijhout saying that the paper would be better suited to "National Enquirer than [PNAS]."

Pirate quote, arghhhhh

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Sir William Schwenck Gilbert: "[a]nd isn't you life extremely flat whit nothing whatever to grumble at!"

Sir W.S. Gilbert: image from Encyclopedia Britannica


Well said Sir Gilbert. A life without grumbling would be boring indeed. W.S. Gilbert is the Gilbert of Gilbert and Sullivan who produced the musicals The Pirates of Penzance and The Mikado.

Beauty in creation.

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Update: Paul points out a major flaw in my and David's argument for why suffering exists: the Fall. You can read all about it at Creation Ministries, a wonderful source of factual information. I haven't and I won't subject my brain to that torture.

Religious people often cite the beauty of nature as evidence of god. Butterflies and flowers come to mind. What about this, this and this? Warning, contains disturbing images. The second example is discussed by David Attenborough as follows:

My response is that when Creationists talk about God creating every individual species as a separate act, they always instance hummingbirds, or orchids, sunflowers and beautiful things. But I tend to think instead of a parasitic worm that is boring through the eye of a boy sitting on the bank of a river in West Africa, [a worm] that's going to make him blind. And [I ask them], 'Are you telling me that the God you believe in, who you also say is an all-merciful God, who cares for each one of us individually, are you saying that God created this worm that can live in no other way than in an innocent child's eyeball? Because that doesn't seem to me to coincide with a God who's full of mercy'.
For me is the most compelling argument against the existence of god of the bible.

Quoting a famous guy

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Mark Twain: "Such is the human race. Often it does seem such a pity that Noah . . . didn't miss the boat."

Thanks Wikipedia


While the story of Noah's Ark, and the great flood are obviously a fairy tales, the quote is a great one. We can know that the idea of a global flood is a myth is from geological evidence.

Mark Twain is obviously famous for writing The Adventures of Tom Sawyer and The Adventures of Huckleberry Finn. The former is rather light-hearted, but the latter addresses some important contemporaneous themes, most importantly racism, which was rife in the southerns US states. From a  religious perspective,  Twain could be be described as a deist, at least that is what I can gather from Wikipedia.

Today's quote and a little more

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“Many people would sooner die than think. In fact, they do”

The quote in my journal is from Bertrand Russell, although I prefer this one; “[t]he trouble with the world is stupid people are cocksure and the intelligent are doubtful.” This is so true and is exemplified by my previous post. The statement is written authoritatively, yet is in several instances well off the mark. Although I am jumping the gun there is an elegant example of the cocksureness of Ponatahi School’s taken from point nine:

Update: The February 2011 National Geographic stated that the archaeopteryx, whose well developed feathers causes a problem for dino to bird dating, was probably such a good flier, that it probably could take off from the ground. Well done National Geographic! We hope that the corrections flow down to the texbooks, but this may be hoping too much
Firstly, there is a clear misunderstanding of how science works. Science is a work in progress, and as Russell said, the intelligent are doubtful. Scientists are usually tentative in presenting their results and others are often quick to scrutinise new or unusual results. Furthermore, taking something from National Geographic as scientific consensus is unwise. When an idea is proposed in science is remains a testable hypothesis and tends to stay out of text books until it has very strong evidence to support it. Therefore, suggesting that text books should be changed based on presumably a single study is not generally going to happen. Sorry Ponatahi but you are hoping probably too much.
Note: I make no comment on the validity of the findings of the original study from which Nat Geo got their information because I have read neither the Nat Geo nor the original paper/s.  I am suggeting rather that one must always be careful of scientific ‘facts’ published in popular press.

Blow by blow: part 1

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As a follow-up to my earlier post about two schools in New Zealand that teach creationism and reject evolution I have decided to do a section-by-section critique of the statement published on Ponatahi Christian School’s website. The reason why I am doing this is twofold: (1) I am appalled that teachers paid by the government (i.e. my tax money) can teach this in New Zealand and (2) because their statement about creation/evolution contains several inaccuracies and internal contradictions. The fact that it contains inaccuracies that border on deceit is in my mind a serious concern for the “[t]hou shall not bear false witness against thy neighbor” commandment, but that is really a side in issue and doesn’t concern me. Many of the inaccuracies have been discussed thoroughly by several people, most notably Richard Dawkins in The Greatest Show on Earth: The Evidence for Evolution and Jerry Coyne in Why Evolution Is True. I have read the former and found it compelling and well written in a way that can be understood easily by the lay person. If read with an open mind, I would say that you would be hard pressed to not accept the theory (said: fact) of evolution. Unfortunately it is the ‘open-mind’ part that appears to be missing from the statement published by Ponatahi Christian School. Their view, as stated by them, is first and foremost the word of god. Thus, if evidence contradicts the word of god, it must be wrong. The introduction to their statement about creation/evolution testifies to this:

It is important that children and adults are clear that there is one universal truth. There can only be one truthful explanation for origins which means that all other explanations are wrong. Truth is truth. Biblical truth, scientific truth, mathematical truth, and historical truth are in harmony. Truth can never contradict truth. We do not have to be afraid of history or science if rightly understood. True science is our friend, it is the manifestation of God’s wisdom. Design demands a Designer. Creation demands a Creator, and it is not feasible that a Creator would not communicate to us who He is. We are privileged to have the great Creator’s communication to us in our homes and school: The Holy Word of God; the Bible. In this we can learn about the Creator, our relationship to the Creator, and how that relationship can be enhanced. We can also learn things which science is too limited to teach us.
Note: head nod to PZ Myers for comic sans quoting.

The claim that there is one universal truth is an odd one. Logically there is no way to explain a single universal truth. Of course they mean is that god is universal truth, but applied to the universe in a general sense is a logical fallacy; everybody knows the only universal truth is 47. Joking aside, this claim is the justification to reject anything that contradicts the bible. Therefore, we know from the get go that there is no critical thinking applied to the creation/evolution statement. The motivation is anti-science because they start with a ‘fact’ and try to prove it. Here is where there is a contradiction: “it is not feasible that a Creator would not communicate to us who He is.” Absolutely, yet there are no recorded moments in time where it can be said, without a shadow of a doubt, god did that, or that IS god. They provide no evidence of god yet use god as a reason to reject evidence. The ridiculousness is glaringly obvious.


 That “[t]here can only be one truthful explanation for origins which means that all other explanations are wrong” is correct. And indeed truth is truth. Scientific truth, mathematical truth, and historical truth are in harmony. Biblical ‘truth’ is the odd one out.  The bible contains several instances that are absolutely not in harmony with science and/or historical truth. Coming back from the dead, turning water into wine, walking on water, the global flood and the six day creation are inconsistent with scientific observations of geology, biology and physics. This is not harmonious. Indeed, history also contradicts the bible. The book of Matthew recounts the Massacre of the Innocents whereby Herod ordered the slaughter of young males after hearing of the forthcoming birth of Jesus. However, it turns out that the only place this event was ‘recorded’ is the book of Matthew. Matthew was not present at the time of Jesus’ birth and so he did not observe this event. It was not recorded in any contemporary texts suggesting that Matthew was mistaken. While these are only a few examples they demonstrate a point: the lack of harmony.

Overall the introduction holds science in contempt: the closing remark that science is limited with the qualifier ‘too’ which tantalizingly alludes to weakness or inferiority. This suggestion of limitation is expanded in sections two and three but I will save comment on that for another time. All in all not a great start from Ponatahi but it might get better.If you have any thoughts, comments or criticisms of my critique post them below and I will respond accordingly.

I remembered

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Today's quote comes from the great Albert Einstein.

 Only two things are infinite, the universe and human stupidity, and I'm not sure about the former



Albert is unquestionably one of the greatest minds to have ever lived and almost certainly who ever will live. His contributions to humanity are virtually unmatched. He was an archetypal genius most famous for developing the theory of relativity.

I knew they were here

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I have met young earth creationists in New Zealand, but they have seemed to be few and far between. New Zealand is a secular society and religious people tend to be moderate, bar the kooks on Queen Street on Friday and Saturday nights. Evolution is the principle that ties all of biology together. Insert Dobzshansky's famous quote here. Thus, it should be taught in biology, and as such it is in New Zealand.

The science curriculum is grouped into several strands linking to the major areas of science. Biology is called "the living world" strand under which the following descriptions is provided:

The living world strand is about living things and how they interact with each other and the environment. Students develop an understanding of the diversity of life and life processes, of where and how life has evolved, of evolution as the link between life processes and ecology, and of the impact of humans on all forms of life. As a result, they are able to make more informed decisions about significant biological issues. The emphasis is on the biology of New Zealand, including the sustainability of New Zealand’s unique fauna and flora and distinctive ecosystems
Furthermore, from level 1--8 (ages 11 to 18) students are taught evolution as evidenced by the achievements and aims of the living world strand. We should expect then that all students who attend state school in New Zealand are exposed to, and taught the basic principles of evolutionary biology.

It turns out that this is not true. Two recent posts (here and here) by Allison Campbell from Wiakato University highlighted two examples of state funded school discarding evolution from their teaching in favour of creationism. The two schools in question are Westminster Christian School and Ponatahi Christian School. Westminster has a pdf of their prospectus that outlines how they have replaced the word 'evolution' with 'creation' and also have a special course called Creation Studies where they seem to go through the days of creation presumably in a literal sense and brainwashing the kids. Ponatahi, on the other hand, has an entire section on their website dedicated to evolution/creation.



I have very little to say on this other than I find these two examples really disgraceful. It makes a mockery of science and how it should be presented to students. The creationist/ID lot love claiming that presenting the "alternative" ideas and letting kids decide for themselves is exactly in the spirit of science. However, when you imply that accepting evolution you are essentially rejecting god and resigning yourself to an eternity of torture. This is mental child abuse and should be stamped out. What I find worse is that these are state funded schools and they are blatantly misteaching those kids. My taxes pay for that and I don;t think it is OK.

Quote of the day

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Today's quote is from Douglas Adams, author of The Hitchhiker's Guide to the Galaxy. I have only seen the film which I enjoyed, although I believe the books are better as is usually the case.


The quote is quite appropriate given subjects covered previously:

" Human beings, who are almost unique in having the ability to learn from the experience of others, are also remarkable in their disinclination to do so."

Daily? quote

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My wife gave me a diary last christmas. I have kept three diaries in the past: one was a diary of a trip to Europe when I was 11, the second was from a trip to New Zealand when I was 15, and the final one started on my OE to England, it didn't last.

To date I haven't used the diary from my wife but I thought now might be a good time to start. I was reminded of the diary by a quote a friend of mine posted on facebook this week "It isn't that I'm not a people person, I'm just not a stupid people person." Why does that remind me of the diary? See the front cover of the diary below for a hint.


Each day in the diary has a quote from an historical figure including scientists, philosophers and musicians. All quote are in the theme of the title of the journal. I think I might try and post one each day, or at least as often as I write in the journal. Who knows? I might publish my memoirs including statements from the journal which themselves will be pyblished in a similar journal in the future.

Todays quote comes from Jean-Paul Sartre. It is rather simple and straight to the point although it does seem a bit too general and I'm not sure how much I agree with it.
Hell is other people

A persons right to choose

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Saw this video over at Pharyngula and it initially made me proud to be a New Zealander.


Same sex civil union has been legal in New Zealand since 26 April 2005. A civil union basically affords the same rights to each member of the partnership in the same way as marriage does. As is said I was proud of being a New Zealander and it is because we have the Civil Union Act. However, a little reading reminded me of the controversy that surrounded the implementation of the act. The parliamentary vote was close, 65 for and 55 against. What I find more shocking is that only three of the nine parties voted predominantly yes. The three parties that voted predominantly yes were the Labour Party (45 yes, 6 no), who were leading the government, the Green Party (9 yes, 0 no) and the Progressive Party (2 yes, 0 no). The Act Party did have 5 for and 4 against surprisingly. The National Party, our current government, voted 3 for and 24 against. We have an election soon and it is likely that National will remain the governing party. I hate the thought of bigots being in charge and that is without considering their formal policies per se.

This year the election campaign has been cut quite short because of a certain event that will remain unnamed. However, there have been several campaign videos as well as the usual signs placed on street corners. I haven't watched most of the videos all the way through. I find them quite boring and I have already made up my mind so John Key talking to a fake audience and answering fake questions, or Labour harping on about the past is going to change it. My vote is firmly with the Greens.

The return of a procrastinator: nothing to see here

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Inspired by the arrival of my fellow apomorphic hominid over at Still Monkeys (read it) I return from my hiatus. My reason for not posting over the last few months is that I haven't had any pressing deadlines like a thesis for example. I used blogging as a tool for procrastinating in the months leading up to submission followed by a complete halt weeks out from submission and nothing since then. I can quite confidently say that the last few weeks of working on my thesis was the most stressful time in my life. Nonetheless, I came out alive and I was happy with what I produced.

Since handing my thesis is I have been doing some work at the university working on a couple of papers, one of which has been submitted to Ecology and is currently in review (fingers crossed). Having a paper published in Ecology would be fantastic and hopefully be the beginning of a lifetime of publishing research, but who knows. I have be thinking about several lines of future work that seem fruitful but I will divulge more about that in later post. In fact, I haven't posted about my current/masters research although I might wait until the paper is published before I do. Until then you will have to deal with my maniacal ramblings about trees, birds and other things.

Make a difference with food

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I became vegetarian about 5 years ago. Very shrtly afterwards I became a vegan. I have since fallen off the wagon and eat cheese and eggs. I LOVE CHEESE. Nonetheless vegansism and vegetarianism are the best way to reduce you consumption of fossil fuels among other things. There is a doco coming out soon called PlanEAT about how the food we eat impacts the planet. Watch the trailer below.

Lazy me

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It's been ages since my last post (sounds like confession to the priest). I have been writing my thesis so have not had much time for blogging lately.

Here is something that I read today. It explains how I felt in my last post about the disparities within christianity. Again I stress the point about god's infallible nature. If god were all powerful, with complete power over the universe there is no way this could happen. His word should not lead to confusion. All people who read it should interpret it the same way. And, if they don't god should magically make them understand it in the same way.

Here are some bits that I like from the above link

Some of us, on the basis of our relationship with God, knew him to be loving, compassionate, generous, always reaching out to us, pitying our mistakes rather than condemning them. Others, on the basis of their relationship with God, knew him to be angry, jealous, punitive.

Some of us knew that God had more important things to worry about than our sex lives; others knew that human sexual impurity was deeply offensive to him.

Some of us knew that God wanted us to respond to other people’s shortcomings with tolerance and forbearance and humility; others knew that he wanted sin to be made an example of, to be held up and publicly rebuked.

Some of us knew that God was offended by conspicuous consumption when so many people had nothing; others knew that God showered wealth along with other good things on those of whom he approved.

Some of us knew that God saw all religions as different expressions of people’s yearning for him; others knew that traditional, orthodox Christianity was the only route to him.

Some of us knew that the devil was just a myth to explain the existence of evil; others knew that the devil was very real and a genuine threat to our souls.

Some of us knew that there was no way God could ever allow such a thing as hell; others knew that hell was very much a part of God’s ordained order.

Let people believe. Who does it harm?

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I have often heard the argument that religion or belief in the supernatural does not harm, from  religious and non-religious alike. I have also had a discussion in which it was suggested that people are free, and should be free to interpret their particular holy texts in the way that 'suits' them. These two points are both fallacious, the first being completely, and the second is not in line with  fundamental and underlying elements of the current large, popular religions.

I have recently thought quite a bit about these two points, but this morning, while scanning the news paper (dangerous I know) I noticed two articles that reminded me of the first point. The first article 'Church and and state war over condom plan' relates to the archaic and completely irrational doctrine contraception in the catholic church. People have sex. Sex makes babies. Sex is also a 'vector' for disease, most frighteningly HIV/AIDS. Condoms can prevent both of these things. Sure babies are great for those who can afford to have them, and I mean afford in a broad sense not just financially. The world is overpopulated and we are struggling to provide even the most basic human needs in some cases. Yet clowns like the ex-boxing champion Manny Paquiao make stupid statements like this: 'God said go forth and multiply. He did not say just go and have one or two children.' What an idiot! The Filipino catholic church want to excommunicate the president because he wants to give out free condoms. He should be grateful that the church want to publicly separate themselves from him. Who would want to be associated with idiocy like that?

The second article I saw related to a suggestion to introduce sharia law to Australia. I know very little about sharia except that it is a set of principles or a code of conduct for muslims. Also, it covers much of the same areas of law as secular laws with some other inclusions. There are apparently four schools of sharia that vary in their level of conservatism among other things. Nonetheless, I do not want to discuss sharia since I am largely ignorant of it. I do however, want to point out the impact the above suggestion in Australia has had. Given the events of recent history regarding terrorism and the demonisation of Islam, it is unsurprising that the crazies have come crawling out of the woodwork in opposition of the idea including: right wingers, jews and christians according to the article. The christian outcry is the most hypocritical. If you have time watch the video to see why. Otherwise go to pharyngula to read a brief summary. While agree that it might not be the same group or people opposing the idea of sharia in Aus, they still represent a collective who identify themselves with a common core philosophy. The same way that extremists tar all muslims with the same extremist brush.


Abrahamic religions have monotheistic beliefs, and this one god is regularly purported to be just, unchanging and infallible. However, apply a little scrutiny and these characteristics fall apart. God is just. I have discussed this in another post about morality and religion, and atrocities at the hand of god in the bible, most of which fall in the old testament and thus the torah. God is unchanging. I also mentioned this in the morality post. Here we see an old testament god hell bent on destroying huge numbers of enemies in genocides, not to mention flooding the entire earth killing every human being, except Noah and his family. And then in the new testament Jesus claims that if we are struck on the cheek, rather than killing the enemy, we should turn the other cheek. God is infallible. This can be developed from the last point about extremists and different groups within religions. God had a direct hand in influencing those who wrote religious texts, yet so often these texts are interpreted in vastly different ways. Extremist muslims and their acts of terror against infidels is one example. Another is immediately relevant. According to a group in the US that have done some excellent calculations based on dates or numbers (not too sure and not interested in reading about it) gleaned from the bible, Saturday 21 May is Judgement Day. The surprising thing is that other churches or groups haven't picked up on this, despite it being clear as day in the bible - according to Mr. Harold Camping at least. How does an all powerful, infallible god allow this to happen? Who is right and who is wrong? Will I still be here on Monday? I hope, and suspect i probably will, that I am because my wife and I are finally moving out of my mum's place.

A possible reason for decline

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Following on from the previous post here is a video of the famous kakapo male, Sirocco partaking in a bit of the old interspecies, homosexual proverbial in-out-in-out. Maybe this is why their numbers are so low. They can't tell head from tail (excuse the terrible turn of phrase, had nothing better).

Science journalism?

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A recent paper published in Frontiers in Ecology and the Environment (Clements et al. 2011) and subsequent press releases in New Zealand has resulted in a some public backlash. The paper proposes a new index for assessing the extinction risk of a species called SAFE (species ability to forestall extinction). In the paper the authors tested the strength of the SAFE index at predicting the most commonly used species threat measure, the International Union for Conservation of Nature (IUCN) Red List, and found it to perform better than other currently used measures.

The SAFE index is really quite simple. It takes into account two things, the total number of individuals in a species across it's entire known range and, the minimum viable population (MVP) of a species. The minimum viable population is the lowest number of individuals a population needs to sustain itself. A few years ago a cross species review of MVP and found that on average MVPs are around 4169 individuals (Traill et al 2007). The importance of this with regard to extinctions is obvious. If a species population size drops below this minimum, the chances of extinction are greatly increased. See I told you it was simple.
Photo credit: Shane McInnes, winner of The Worlds Rarest Birds photo competition
However, the backlash in New Zealand about this work was largely from ill informed people who have a chip on their shoulder. What chip you ask? Well it so happens that the authors of the SAFE paper are based at Australian institutions. So what? Well the crux of the story stems from the misrepresentation of the work and how it can be applied in a real world situation. Professor Cory Bradshaw was one of the authors who worked on the paper and talked about the work on radio here in NZ. There were also some news articles, one entitled 'Let the wonderfully wierd kakapo die--scientist' specifically got me riled up. The kakapo (pictured above) is a very unique bird in that is a flightless, nocturnal parrot, the only one of its kind in the world, but like so many NZ birds, it is endangered. And according to the SAFE index, with only 131 individuals of the species left, it has little chance of being saved. Luckily there are a huge number of dedicated people, both paid and volunteers, who are trying to get this bird back on it's feet. What Corey Bradshaw had to say was what people hated. He said that the massive expenditure on saving a single species that fell short on the SAFE index is unjustified because, where financial resources are limited, this happens to the detriment of countless other species. The other species may not be endangered but could be on the verge and thus excluded from the conservation effort. Therefore, by the time we realize that these species are becoming rare it may be too late, one because we spent too much money on a single species and don't have much left, and two because they may already be below the MVP threshold. 


You could go and read some of the comments on the news article but I have picked out some of my favourites:

This one is priceless for a couple of reasons. Firstly they cite positive as people who are slandering Corey Bradshaw, and secondly he talks about Darwineans. I think what he means is darwinians, but I have no idea what he means by it, particularly when he talks about saving money etc.


Glad to see so many positive (save the Po) comments, but am surprised at the number who agree with the Aussie! NZ has saved a bird before, and hopefully we will do it again. To those of you "Darwineans" who are against "wasting money" saving it....think of all the money we waste trying to save other humans?? Is that a waste too? Should the NZ government let nature take its course next time you have a treatable illness or injury?
 Another classic. I love how she  calls him a "so-called 'scientist'". And then goes on to attack him because he is Australian. If she had not just read the crap title of the article and bothered to find out about the source material she would ave realised two things. One, that Corey Bradshaw is a "real" scientist who is highly published and respected in his field, and two, that he is in fact Canadian who now lives in Australia. Additionally, he did his PhD in New Zealand.
Please everyone, don't give this so-called 'scientist' another minute of our time. BUT, I guess if we don't, he will think "yeah, no one is commenting about my statement" so he'll think we really don't care about saving our lovely little kakapo. wrong !!!! Keep your Aussie BS to yourself....
 Comments about being Australian were really common. Here's a couple more. These ones are the most ridiculous. Real geniuses!

As many others have said, how about the Australians keep to their own country?! Australia has their own problems to watch out for!

Typical comment from an Australian i mean they have a history with there Native people as well.
The worst part about this is obvious slant the media took and by having a title like it did, peoples minds were made up for them before they actually had any understanding of the topic.

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Clements, G. R., Bradshaw, C. J. A., Brook, B. W., & Laurance, W. F. The SAFE index: using a threshold population target to measure relative species threat. Frontiers in Ecology and the Environment, preprint.
Traill, L. W., Bradshaw, C. J. A., & Brook, B. W. (2007). Minimum viable population size: A meta-analysis of 30 years of published estimates. Biological Conservation, 139(1-2), 159-166.

The spectrum of sexuality

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I just read a post on Homologous Legs on bisexuality that reminded of a film I watched some months ago about Alfred Kinsey. Kinsey was an entomologist worked with gall wasps (Cynipidae) but, it was his work in human sexuality that he is best known for. In the 1930s, Kinsey became interested in human sexuality and began to pursue research in order to classify human sexual practices. The thing that I, and I am sure many others would find interesting is, "What is normal?"
The Kinsey scale of sexual preference: Image from Wikipedia
The ideas around what is normal is something that I have thought about quite a bit. People think they know what is normal and anything that deviates from their normality is just that, deviant or perverted. Kinsey and his colleagues addressed this by anonymously interviewing subjects about their sexual activity and preferences. The results were quite surprising with 'non-normal' activities proving quite 'normal'. Of particular interest was the apparent prevalence of bisexuality in men. This led to the development of the Kinsey Scale where sexual preference is viewed not as binary (i.e. gay or straight) or possibly three dimensionally, but more spectrally. In other words, zero on the scale is exclusively straight, and six is exclusively gay. What Kinsey and his colleagues found was that the majority of subjects fell outside of the exclusive zero or six, and had at least some bisexual tendency. That is not to say everyone acts on these feelings, but they are at least present.

Bird watching "Hall of famer"

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Ernst Mayr is one of biology's greatest sons (can I say that he is a son of biology?). He made many contributions to evolutionary biology, in particular, the biological species concept. The obvious outcome of this was that it allowed biologists to draw a line in the sand and say that this is this species and this is another species, although some argue that it is arbitrary and is more problematic than useful. For example, it is possible for two defined biological species to interbreed (hybridize) and have viable, fertile offspring. Commonly, people will cite lions and tigers hybridizing (the infamous Napoleon Dynamite Liger) in zoos or other man made facilities. However, this is highly improbable in a contemporary world since everybody knows (?) that tigers live in Asia and lions in Africa. None the less, it does speak to the potential power of the process. But, if we are in search of viable hybrids, we need to think less like a human. By this I mean we need to steer away from charismatic organisms and look at other life forms. Plants are a great place to start. There are countless example of naturally occur plant hybrids, and excitingly it occurs at relatively high taxonomic levels (i.e. inter-genus and even inter-familial hybridization). There are also examples of interfamilial bird hybrids such, particularly in the unfortunately named game birds.

I seem to have digressed from my initial topic but species concepts and modes of speciation are currently a particular interest of mine. Anyways all i really wanted to say was that Ernst started out as a bird watcher as a young man. He discusses it in the video below. I really love how, even though he is his 90s, he tells the story of observing a rare bird with such excitement, as though it was yesterday. The video comes from Web of Stories which is a website with videos of a wide range of interesting and influential people, including Ernst Mayr. The videos are broken down into small digestible sections only a few minutes long and are definitely worth a look.


Here is a piece Mayr wrote for Science in 2004 when he was 100 about the Modern Synthesis. He died the following year. Even after 100 years, 81 of which were spent as a student of biology his hunger for discovery, evolutionary biology in particular, is beautifully revealed by his last sentence "I only regret that I won't be present to enjoy these future developments".

Morality and it's origins?

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I once read a book by the well known christian author C.S. Lewis called 'Mere christianity'. The book centres largely around the concept of a supposed innate sense of morality governed by our conscience. Lewis argues that everybody knows the difference between right and wrong and our conscience is the proverbial 'angel' sitting on our shoulder that lets us know when we are being immoral. On the surface this concept seems quite simple and rather true when applied to a typical western, developed country. However, when you attempt to apply it to countries of various cultures it falls apart rather rapidly. For example, an extreme case can be found in Papua New Guinea where cannibalism is still probably practised to some degree, or at least was until very recent times. The people who practised cannibalism undoubtedly viewed human flesh as a substantial source of protein and probably felt little remorse (conscience wise) in the same sense that westerners feel when they eat cow, pig, chicken or sheep. Obviously being a christian author, Lewis believes that your governing conscience is a 'gift' from god. The PNG cannibals definitely didn't have the same monotheistic abrahamic god as Lewis does, but certainly had a polytheistic naturalistic gods that centred around the sun, moon and stars -- since for them these are their life givers.

Where I am going with this relates to a commonly held belief among religious people regarding morality. Many argue that without a god guiding us there is no basis for human morality. This is absurd. A relatively simple counter to that argument is that morality is guided rather by a desire to do good for the better of the humanity as a whole. This of course is not necessarily always a true reflection of what the world is like, but people are likely to be morally "good" to those that they like, and even more so to those they are related to. Moreover, religion can even be argued to be immoral if one were to read certain passages in the bible. The common notion of an all loving god is a wonderful thought, and is perpetuated in many modern churches. However, in addition to the love preached by Jesus is the new testament, the bible is full of horrific acts and rules. Below is a list of some of them. I have summarised them with a link to them too.

Numbers 31: 17 - Murder of men and woman as well as keeping virgins for yourself
Hosea 13: 16 - Murder of children and pregnant women
Leviticus 20:10 - Kill adulterers
Isaiah 13: 15 - Murder, including children "dashed to pieces", and "ravishing" wives. This is a strange one since Leviticus 20:10 says that adulterers should be put to death, but here god is saying that wives will be ravished.
Luke 19: 27 - More slaying, but this time from the mouth of Jesus.
Leviticus 20: 13 - Murder of homosexual men
1st Corinthians 14: 34  - Oppression of women
Exodus 31: 15 - People who work on the sabbath should be killed. Bear in mind this comes from the same book as the 10 commandments, one of which is about not killing.
Titus 2: 9 - How slaves should behave. Slavery come up quite a bit in the bible with not condemnation of it that I am aware of, although I am no biblical scholar so I can't be sure.

So my question is, how can the above selection be part of something that is supposed to be a moral guide? I acknowledge that the bible does have parts about love etc., but which parts are supposed to be followed, and which not?  Murder is morally wrong, but what about adulterers or homosexuals?


Sam Harris has a new book out called 'The moral landscape: how can science determine human values?'. The title is pretty self explanatory. I have as yet not read it but will get a copy of it asap and do my best to decipher it and maybe even review it here.

Singing it how it is

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Who hasn't been in the position where like Mr. Minchin (see video below) before and held their tongue for wont of not offending? It happens often and I always think to myself, why is it okay for them to offend me but not for me to offend them? I suppose they don't realise that I am offended.

It's award season

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Two in institutes that promote evidence as foundations of decision making have recently given some awards to a bunch of people that promote beliefs supported by little to no evidence. The first award is the first is the National Centre for Science Education's annual UpChucky award for creationist of the year and, the second are a set of awards from the James Randi Educational Foundation called the Pigasus Awards.

UpChucky award taken from the NCSE

I have mentioned Ken Ham is two previous posts here and, here. Ken received the UpChucky award from the NCSE and has finally be recognised for all his hard work at being an ignorant fool and spreading garbage or, as my friend Paul elegantly put it, "aurally raping" people. Nice one Hamo, you deserve it. Give yourself a pat on the back for being recognised for your genius. I actually just had a watch of a couple of videos over at the AiG website with Ken spurting something about how natural selection is not evolution. He reckons that evolution cannot occur in the way that evilutionsists "claim" it does because it requires new information to originate in the genetic material of plants and animals. It always blows me away to hear people making claims without any evidence (although Ken does have stories from a book that at its newest parts are about 2000 years old and not corroborated by any other source) that are completely contrary to what we can, and have observed. Gene duplication for example is a well documented occurrence that absolutely adds new information to the genome on which selection (or neutral processes) can act.

The second set of awards from James Randi include a few different categories:

  • The Scientist Pigasus Award goes to NASA Engineer Richard B. Hoover, who recently announced for the third time in 14 years that he had found evidence of microscopic life in meteorites. Along with the crackpot Journal of Cosmology—a now-defunct publication founded in 2009 to publish articles advancing the scientifically unsupported idea that life began before the first stars formed and was spread throughout the early universe on meteors—Hoover pitched his warmed-over ideas to Fox News, an outlet not known for their attention to facts. Predictably, Fox News ran with the story, convincing many people that NASA had discovered extraterrestrial life.
  • The Funder Pigasus Award goes to CVS/pharmacy, for their work to support the manufacturers of scam “homeopathic” medications who sell up to $870 million a year in quack remedies to U.S. consumers. Homeopathic remedies contain none of the active ingredient they claim, and homeopathy has been shown to be useless in randomized clinical trials. CVS/pharmacy sells these quack products in thousands of stores across the U.S., right alongside real medicine, with no warning to consumers. Instead of giving their customers the facts about homeopathy, CVS/pharmacy executives are cashing in themselves by offering their own store-brand of the popular homeopathic product oscillococcinum. Oscillococcinum is made by grinding up the liver of a duck, putting none of it onto tiny sugar pills—that’s right, none of it—and then advertising the plain sugar pills as an effective treatment for flu symptoms.
  • The Media Pigasus Award goes to Dr. Mehmet Oz, who has done such a disservice to his TV viewers by promoting quack medical practices that he is now the first person to win a Pigasus two years in a row. Dr. Oz is a Harvard-educated cardiac physician who, through his syndicated TV show, has promoted faith healing, "energy medicine," and other quack theories that have no scientific basis. Oz has appeared on ABC News to give legitimacy to the claims of Brazilian faith healer “John of God,” who uses old carnival tricks to take money from the seriously ill. He's hosted Ayurvedic guru Yogi Cameron on his show to promote nonsense "tongue examination" as a way of diagnosing health problems. This year, he really went off the deep end. In March 2011, Dr. Oz endorsed "psychic" huckster and past Pigasus winner John Edward, who pretends to talk to dead people. Oz even suggested that bereaved families should visit psychic mediums to receive (faked) messages from their dead relatives as a form of grief counseling.
  • The Refusal to Face Reality Award goes to Andrew Wakefield, the researcher who launched the modern anti-vaccine panic with unfounded statements linking the MMR vaccine with autism that were not borne out by any research, even his own. In 2010, The Lancet retracted his paper on the MMR vaccine, and this year the British medical journal BMJ called Wakefield’s paper an outright fraud, finding “clear evidence of falsification of data” and that “he sought to exploit the ensuing MMR scare for financial gain,” taking more than $674,000 from lawyers who intended to sue vaccine manufacturers. Yet Wakefield continues to ask the public to believe he is the victim. In a recent article in NaturalNews, Wakefield called the American Academy of Pediatrics and The Lancet “instruments of a state that I don't really want to be associated with.”
But probably the best award of them all must be the "comback award" for Peter Popoff.

The Performer Pigasus Award—this year for “Best Comeback”—goes to televangelist Peter Popoff. Popoff made millions in the 1980s by pretending to heal the sick and receive information about audience members directly from god. He went bankrupt in 1987 after JREF founder James Randi exposed him for using a secret earpiece to receive information about audience members from his wife. Now he’s back to prey on victims of the economic recession. In paid infomercials on BET, Popoff offers “supernatural debt relief” in exchange for offerings of hundreds or even thousands of dollars. This business is so lucrative that according to recent IRS documents, Popoff took in $23.5 million and paid himself and his immediate family more than $1 million in one year alone.
How ridiculous. Are people buying his shit after he was publicly debunked.  

Is the world ending?

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Myagi prefacture, Japan following the devastating tsunami: Kyodo News/Associated Press

The recent spate of earthquakes in Haiti, New Zealand, Chile and, the huge Mw 8.8 9.0 (Mw is a scale used for large earthquakes, modified from the well known Richter scale) in Japan appear particularly unusual. This has led people to ask if we are having more large quakes than previously. But, it seems that this trend is not anything special, albeit tragic. Rycharde Manne discusses this in some depth using data collected over the past 30 years, and finds that there is no trend of increasing large earthquake frequency. Apparently, three large earthquakes (greater than Mw 6.0) per year across the globe is about normal when we consider long term averages. And, despite having a seemingly bad run recently, during the 60s it was worse, with two of the biggest recorded earthquakes in Chile (1960) and Alaska (1964) at Mw 9.5 and Mw 9.2 respectively.

There are a couple of reasons why I think that things seem worse than before. The world is more populated than before. Therefore, when large earthquakes, an their accompanying tsunamis hit, there are more people to injure and kill, and more infrastructure to damage and destroy. In addition, information is so easily and rapidly transmitted these days, the devastation can be seen immediately, rather than taking days, as it would have in the 60s . The video below is an example of modern information technology, showing the havoc caused by the Japanese tsunami. 

I also think that people forget quickly. When something new and "exciting" comes along we tend to forget things from the past. It seems to be human nature. It can be easily observed at the small scale in our own lives. Kids, and adults, get new toys and the old ones fall by the wayside. I know I've done it.


Most of what I have discussed comes from an article on The Panda's Thumb by Matt Young. Matt also discusses the problems around predicting earthquakes and how it basically cannot be done. Of course there are some that claim it can be. One such fellow is Ken Ring, or the "moon man". Ken Ring is known for his weather forecasting almanac based on lunar cycles. I don't know too much about it but apparently he can be broadly accurate. But I suspect that it comes less from the moon and more from studying trends. However, it seems Ken has decided that earthquakes can be predicted using the moon and tides. Ken recently appeared on the current affairs programme in NZ, Campbell Live. The average "interviewing" aside, John points out some obvious flaws in Ring's methods. For example, Ken Ring says that earthquakes are most likely to occur one week either side of new, or full moon. Now I would be the first to admit that my mathematics is poor but, seriously. One week either side of new or full moon makes four weeks. Four weeks makes a month. That is some ridiculously broad predicting. Not only that, but it is pseudosience that is misleading and actually quite dangerous. If you want to read more, Phil Plait has the details here.