Friday, 28 February 2014

UNSW Biological Sciences makes the Top 50 in QS World Rankings

I’m deep in grant- and lecture-writing at the moment (hence the lack of posts) but the QS World University rankings are out for 2013/2014 and UNSW is ranked 50th in Biological Sciences. Obviously, I haven’t been there long enough to have contributed to this but still good news and worth a mention! Overall, UNSW was ranked 52nd.

Pretty good result for the University of Southampton at 86 too. (U. Sydney is 38th but you can’t have everything! :op)

Wednesday, 19 February 2014

37 page views!

The blog hit a landmark today, so I am taking a brief break from grant writing for a quick reflection on the top posts and see how things have changed since my last reflection in January last year. Happily, the top three posts are all (kind of) science/technology related now, rather than the wine/kitten/celebratory/ sex influenced selection before! (I’m a little disappointed that Finding Nemo’s sex-changing father has dropped out of the top ten, though.)

Looking at the "Popular posts this week", the top three of all time are actually not too surprising, being the same top three as this week. What did surprise me was the gap to post number 4, with number 3 having nearly 2000 more pageviews! Here then, for posterity, are the top 3 pages of all time, as of today:

#1. (4002 views)

I’ve had my Macbook Air for over a year now (crazy how time flies) and I still love it. The only drawback really is the limited disk space ...

#2. (4000 views)

I want to preface this post by saying that it’s been one of the harder ones to decide whether to write. On the one hand, it feels a little u...

#3. (2662 views)

Teaching phylogenetics, it is clear that one of the things that causes a surprising amount of confusion is rooting the tree - defining the ...

Thursday, 13 February 2014

Belated Happy Darwin Day!

It’s still (just) Darwin Day in some places but I must confess that it came upon me too fast this year. Still, it’s a good excuse to revisit some of the previous Darwin posts about Darwin and Wallace, Darwin the gentleman scientist and last year's Darwin quotes for Darwin Day.

Better still, check out some Darwin Day posts from elsewhere: How Darwin took on Intelligent Design at the Rationalist Association, or a suite of posts at Why Evolution is True, including Darwin’s pet tortoise!

Monday, 10 February 2014

Observational versus Historical Science

One of the things that Ken Ham made a big deal about during the recent Nye vs Ham debate was his distinction between “Observational Science” - things we observe now - and “Historical Science” - inferences from the past that we can never know because we can never go back. Historical Science, he argues, can never be verified/falsified, is built on assumptions, and could therefore be wrong. He then makes the giant leap (of faith) that because it could be wrong, it can safely be dismissed when it does not fit his Young Earth Creationist (YEC) worldview. (A world-view, ironically, built on the trust of an historical text that he cannot go back and see written and therefore cannot know is authentic!) He then accused science textbooks of being misleading because they fail to make this distinction between the observational and historical.

Bill Nye dismissed this distinction. However, although he gave hints, he did not really explain why it was wrong. So, who’s right? It seems fair enough to divide what can be seen from what is only inferred, doesn’t it? Is Ken Ham right?


As was abundantly clear when Ken Ham tried to give examples of “observational science” that supported the YEC position versus “historical science” that did not, dividing scientific conclusions along these lines is confusing, meaningless and demonstrates a fundamental misunderstanding of how science works. The real division - the aspect of the argument that appears to have merit - is between data and interpretation.

In science, data is sacred. This is the “observational” aspect. A fossil either exists or it does not. A DNA sequencing machine returns a particular order of nucleotides. Light has a particular measured wavelength etc. But, data by itself does not mean anything. Its meaning is derived from the interpretations of that data, based on certain assumptions and interpretation in the context of other data and evidence.

Crucially, this interpretation - and the required for underlying assumptions - is true for all observations and all science. The methods, techniques and models etc. that we apply to contemporary data are the same as those applied to “historical” data. There is nothing inherently more or less reliable about one or the other. Contemporary “observations” are rarely direct observations - they also require assumptions and knowledge of technical error rates etc. DNA sequencing, for example, is not literally observing nucleotides: it is interpreting patterns of fluorescence, or changes in electric current. Technical errors - and human mistakes - can happen.

Now, that does not mean that all scientific conclusions are equally reliable. The confidence in a conclusion will depend on the confidence of the underlying assumptions and models; these in turn are determined by how consistently those assumptions and models fit/explain other data. This is another mistake of the Creationist crowd (including Intelligent Design Creationism): they mistake possibility for probability.

Confidence is also determined by how readily we could spot something awry with the model/assumption in question. In other words, if the assumption is wrong, how would we expect the results of a particular experiment to deviate from the expected results if the assumption is right. This is what it means to be falsifiable and this is what scientists do on a day-to-day basis: test their models and assumptions and try to break them. If the assumptions seem to hold, we keep the interpretation - or suite of possible interpretations - that result. If not, we go back to the drawing board and try to come up with new models and assumptions that work with the new data and still work with the old data. The interpretation of the data is then updated in the light of the new model. Critically, we do not build the assumptions on the conclusion. This is why science changes its best interpretation - and gets less wrong with time; YEC does not.

It is certainly true that some data is easier to come by than others and, as a general rule, we have less confidence about things the further back in time we go. But, this is nothing to do with observation versus history; it is everything to do with abundance (or paucity) and variety of data. We have more confidence about recent things because we can generally get more - and more varied - data more easily. This is not universal, though, and when the data is absent we have little confidence regardless of the age. We have far more confidence in the age of the Earth than the Higgs boson, for example. Likewise, where we have weak, untested models and assumptions - or messy data for which the correct assumptions cannot be established - we have little confidence. Where we have robust well-validated models, we have high confidence.

Radiometric dating is a case in point. As exemplified by Ken Ham, the YEC crowd love to pull out examples where radiometric dating goes wrong - usually featuring recent volcanic eruptions. When doing so, they completely neglect whether we expect those examples to give reliable dates. We don’t! They are often messy scenarios where the inherent assumptions of the dating techniques are likely to be violated. (Sometimes, they are completely inappropriate scales and/or ignore measurement error.) This does not mean that those assumptions are always questionable and the techniques are always unreliable. Whether the conditions give us confidence that the underlying assumptions are correct - clear strata, for example - dating methods are incredibly accurate and consistent. (For a good discussion of when radiometric dating is (not) reliable, see here.) If you want to go after a scientific theory, you have to attack the strongest evidence, not the weakest.

All science is both observational and historical. The science of an Old Earth and the common ancestry of all (known) life on Earth are as confident and observational as the particle physics that made possible the computer on which I type these words. Ken Ham is just plain wrong. Again.

Wednesday, 5 February 2014

Ken Ham demonstrates that Young Earth Creationism is a purely religious theory and not scientific

Like many evolutionary biologists (and scientists in general), I had deep reservations about Bill Nye’s decision to debate Ken Ham today at the Creation Museum in Kentucky. My reservations were three-fold:

  1. Debates are not about truth, they are about winning - science, the complete opposite. Science is settled by data and lengthy rational discussion in the scientific literature, not by one hour grandstanding without any real-time fact-checking.

  2. All the ticket and DVD sales go to directly undermine his life’s work. (i.e. funding The Creation Museum.)

  3. Bill Nye is not an evolutionary biologist and I was not sure that he would have the knowledge at his fingertips required to counter the bizarre unusual examples that Creationists always like to drag out in an attempt to discredit some aspect of evolutionary theory. (I know I couldn’t without the internet and time to look into them!)

I even uttered the words (or whatever the online equivalent of utterance may be): He’s “lost” before he even starts.

Like many evolutionary biologists (and scientists in general), I also did not intend to watch the debate, believing it to be a train-wreck in the making. When, however, a reminder from Why Evolution is True popped up in my inbox just after I had got myself a coffee, I changed my mind - I hadn’t even realised it would be on at a sensible time Down Under. (11am as it happens.)

Happily, I was wrong on a few counts. Bill Nye made a very good account of himself. Ken Ham did not wind me up like Creationists are prone to do and, whilst contradicting himself in places and misrepresenting specific scientific techniques on occasion, he was actually fairly easy to listen to and made a compelling case: just not the case I think that he thought he was making - but I’ll come back to that.

I’m still not sure that Bill Nye should have agreed to do it but three realisations/revelations (four if you count his performance) have certainly made me question my earlier judgement:

  1. The topic. Crucially - and in a big mistake by Ken Ham - the debate was not “Creation versus Evolution”. Ham was not able to pull out the usual Creationists smoke and mirrors, partly because he is a Young Earth Creationist (YEC) and has little room for manoeuvre. Instead, the topic was: “Is creation a viable model of origins in today’s modern scientific era?” By putting the focus on YEC and not evolution, there was less of the focusing on gaps in our knowledge (as if they somehow invalidate the positive evidence) and more focus on the evidence - or lack of it - for YEC.

  2. Apparently, the ticket sales would not be sufficient to cover the costs of running the event, so the Creation Museum might actually make a loss. I am sure that they will recover this from DVD sales to the faithful, although given how exposed the YEC position was in the debate, I’m not sure they’ll want to.

  3. Rather than simply being a debate between the two, they also had to answer questions handed in by the public. These were some of the most revealing of all.

There are a lot of points from the debate that are worthy of discussion, and I might write a few more posts in future if I have the time/energy. One point really stood out, though, so it is worthy of a mention now.

The end is Nye for Young Earth Creationism as “Science”

One of the most interesting things was how Ken Ham did not even try to pretend that his YEC was not wholly and utterly derived from his religious belief. This was not a matter for debate and it was Ham, not Nye, that exposed it. He made it clear that, in his view, Christian theology does not make sense without a literal Biblical Creation. (I happen to agree with him there but that’s definitely another post!) He also made it clear that Genesis was the starting point, had to be true and there was absolutely no way that he would ever accept any evidence or interpretation that contradicted it.

One of the questions from the public was what it would take for the speakers to change their mind. For Nye: a bunch of different observations incompatible with naturalistic evolution and/or an old Universe. For Ham: nothing.

Ham’s tactic to cover this up was a new one to me, I must confess. Rather than claim that YEC is not a religious position, he claims that “molecules to man” evolution is a religious position. (Rather odd given the number of “Theistic evolution” religious believers out there.) Apparently, not believing the Bible is a literal God-inspired manual for life that trumps all evidence - even if that opinion is itself based on external evidence - is religion.

He then made a big effort to convince people that YEC is consistent with the evidence. There were the usual quotes from YEC PhDs and a big thing about distinguishing “observable science” and “historical science”. (From what I can gather, anything that can be shoehorned into being “consistent” with YEC is “observable science”, and anything that cannot is “historical science” and therefore “impossible to know” and open to other interpretations.) He also made a big thing of scientific interpretations being based on “assumptions” and therefore quite possibly wrong, whereas he could present a different set of assumptions and suddenly the data is consistent with the Bible.

And here is the crux of the matter. With these admissions, Ken Ham is demonstrating exactly why YEC is not science - and why a scientific interpretation of evidence is not religion...

Religion starts with the conclusion and makes up assumptions to fit the data to it. Science, on the other hand, starts with a set of assumptions and then asks what conclusions are most feasible given the data and these assumptions. This is big difference between science and religion - between evolution and YEC. Does the conclusion lead the interpretation of the data or does it fall out of it?

Crucially, where YEC invents assumptions to make the data fit, the assumptions of science are themselves scientific conclusions and/or explicitly tested. For science, it is not enough to simply say that data X is consistent with explanation Y. For science to accept Y as the current working explanation, data X has to be more consistent with Y than competing explanations. Certainly, Ken Ham’s team can come up with all manner of just-so unlikely explanations as to why apparent evidence for an old earth or shared ancestry can be explained away but are they likely? More to the point, what are the chances of them all being right? YEC ignores the weight of consistent probability that opposes their position - because their position is not derived from evidence. As Ham and Nye made clear together: in the modern scientific era, this is just not a viable model of origins without extraordinary faith in deceptive powers.

Of course, YEC starting with its conclusion and therefore not being science is an old chestnut but I still find it interesting that Ham did nothing to dispel this and actually reinforced it. I’m doubtful that this debate will make any difference but it really should have put the misguided representation of YEC as science to bed, once and for all.

Tuesday, 4 February 2014

A pair of top quality bargain white wines from Tyrrell's

Ever since our Hunter Valley wine tour last month, I’ve been on the lookout for Tyrrell’s Wines in the local bottle shops. At the weekend, we had friends over for curry and I was therefore very happy to find a Tyrrell’s 2013 Old Winery Sauvignon Blanc for a snip at $12.99, which was suggested to make “an ideal accompaniment to fresh seafood and spicy Asian dishes”. Ideal, it was!

The Old Winery Sauvignon Blanc exhibits a wonderfully fragrant nose of snow peas, guava and a little passionfruit. With its classic varietal character, this full flavoured and refreshing sauvignon blanc delivers herbal and grassy notes with vibrant, zesty citrus fruit character.

Tonight, we sampled a second one from the range, the 2013 Old Winery Semillon Sauvignon Blanc, “an ideal accompaniment to a wide variety of cuisines such as seafood, vegetarian, chicken and creamy pasta dishes” - it paired very nicely with our pasta carbonara.

Citrus semillon fruit characters and lifted herbaceous sauvignon blanc overtones combine perfectly to produce this zesty wine style with a fresh and lively finish.

If cheap (but delicious) whites are not your thing, I can also thoroughly recommend the 2011 Stevens Single Vineyard Shiraz.

Medium to full bodied with a lively, intense purple colour. Black cherry, rapsberry and fresh, spicy flavours dominate the palate with a vibrant, fresh acidity that make the wine a wonderful example of the modern, balanced style of Hunter Valley shiraz.

You have to go to the winery in Hunter Valley to get it (and it’s a tad more than $13) but it’s worth the trip!

Sunday, 2 February 2014

The world's best bacon sandwich?

We’ve been to One Six Nine Cafe in Randwick a few times for brunch or lunch and never been disappointed. The menu is good and all the food is made with quality ingredients in decent portions, so great value for money as well as taste. The sandwiches are particularly excellent. Today, I had the bacon, rocket, avocado, tomato and spicy slaw and I can’t think of how it could have been made better. (A bigger mouth, maybe?) Highly recommended if you find yourself in Randwick for lunch!