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]."

Pirate quote, arghhhhh

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.

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

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

“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

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

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.