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.