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

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

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

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

Part 2: do you believe in evidence?

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

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

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

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

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

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

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

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

Double blog assault

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

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.

Return of the birds: the lazy parent

 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.

Online science

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]."

Blow by blow: part 1

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.