Novel Coronavirus Update

Filed under: — Bravus @ 12:54 pm

Stats and graphs are from: https://www.worldometers.info/coronavirus/

The novel coronavirus statistics are still very worrying, with more than 31,000 cases now and more than 630 fatalities.

There is some reason for hope, though: have a look at the slope of each of these curves. The deaths curve seems to have gone from exponential to linear, and the slope of the infections curve has actually started to decrease.
The impact will still be immense, but this pandemic is not growing in an out-of-control exponential way.

Fatality rates for those infected are estimated (on a fairly small sample size) at about 2%, and as with most other flus, those already frail – old people, children, ill people – are over-represented in the fatalities. That rate may also fall as more medical resources are deployed more effectively.

Comparisons between the fatalities from this novel virus versus the ‘normal’ seasonal flu don’t work very well, because the infected populations and even exposed populations are vastly different at this point.


Evolution and entropy

Filed under: — Bravus @ 8:05 am

The claim is sometimes made that entropy, or the laws of thermodynamics, prohibit the possibility of evolution.

The laws of thermodynamics can be stated in a number of ways in words, and more precisely in equations, but here is one way of stating them:

  1. Energy cannot be created or destroyed in an isolated system.
  2. The net entropy of an isolated system always increases.
  3. The entropy of a system approaches a constant value as the temperature approaches absolute zero (-273.15o C).

A more amusing but less accurate version I have seen is:

  1. You can never win, you can only break even.
  2. You can only break even at absolute zero.
  3. You can never reach absolute zero.

Returning to the first set of laws, the First Law obviously needs to be slightly modified in the light of General Relativity and Einstein’s famous equation E = mc2 to ‘matter-energy cannot be created or destroyed’, but the bottom line remains the same.

Entropy has a technical definition, or rather a number of different technical definitions, expressed in equations, but it is often understood as the ‘disorder’ of a system. So an increase in entropy is a decrease in order, and so on. Essentially, energy tends to change from more useful forms, that can do work, to less useful forms, over time.

The claim I referenced in the first sentence – that entropy forbids evolution – relies on the notion that evolving from a single-celled organism to something like a human being (with a human brain, perhaps the most complex matter we know of) requires a considerable increase in order, and therefore a net decrease in entropy.

The answer is right there in the Second Law, though: the words ‘in an isolated system‘. A single-celled organism does not evolve into a human being if it is placed in a sealed chamber and isolated from incoming energy – in the forms of heat, light, food and air – from the environment.

Perhaps the people who make this claim want to regard the whole of Earth as an isolated system, and argue that the evolution of all lifeforms from simpler (less-ordered) lifeforms is prohibited by the Second Law of Thermodynamics?

But the answer to that involves stepping outside and looking up, even on a cloudy day. Earth is not an isolated system, because it receives vast amounts of energy from that big nuclear fusion generator in the sky, the Sun.

Local increases in order – decreases in entropy – are certainly not prohibited: a human brain is much more ordered than all the food that goes into making it.

In practical terms, no system in the universe is closed and isolated. Even the Solar System emits solar energy to the space around it. But certainly, in considering Earth, the energy coming in from the Sun is a huge part of the overall energy picture.

(As a side note, high energy, short wavelength visible light arrives with the ability to do work, including the work of photosynthesis. It passes through various processes, and then is emitted as low energy, long wavelength infrared radiation, which radiates off into space. Unless intercepted by greenhouse gases, in which case it hangs around a bit longer, warming the globe…)

And it turns out that the nuclear fusion process of hydrogen combining to form helium that produces the Sun’s energy involves a net increase in entropy – a net decrease in order. And, given that Earth receives only a tiny fraction of the energy the Sun puts out, this increase in entropy occurring in the Sun completely dwarfs the local decrease in entropy involved in evolution. So, in the local system of our Solar System, net entropy increases, in agreement with the Second Law

No rules of thermodynamics are contravened by the processes of evolution.

For ease of navigation I will include links to each of the other posts in this series at the bottom of each post.

Why I think it’s important to understand evolution
Cosmogenesis, abiogenesis and evolution
Facts, Theories and Laws
Radiocarbon dating
Radiometric dating and deep time
Four Forces of the Universe
Probability and evolution
Species and ‘baramin’, macro- and micro-evolution
Mitochondrial Eve and Y-chromosomal Adam
Transitional fossils
Complexity – irreducible and otherwise


Why I think it’s important to understand evolution

Filed under: — Bravus @ 6:38 pm

I’ve decided to re-animate this blog for a while to post a short series of clear, simple discussions of some of the common arguments that are used to reject evolutionary theory as an explanation for the current diversity of living things on Earth.

When I raised the issue on Facebook, a friend asked “Why is it so important to you to persuade people to believe the Theory of Evolution?”, which is a great question. So this post is both an introduction to the series (initially I think there might be about 10 posts in total, but it may well grow), and my attempt to answer that question.

First, I think there’s value in clarifying that evolution is not something we ‘believe in’ in any religious sense. Rather, we ‘believe that’ it is the theory that best explains all of the available evidence… until a better one comes along. This is true for all scientific theories.

With that in mind, then, I care that people understand evolutionary theory because I care about what is true, and because it is a theory that we use in things like medical and pharmaceutical advances that save lives. Rejecting it is also strongly associated with rejecting science in other domains such as vaccines and climate change. It also makes people very vulnerable to liars and charlatans.

I suppose there’s one or two other notes worth including in this introductory post: I’ve been using the words ‘evolution’ and ‘evolutionary theory’, but it is probably more accurate to talk about the ‘modern evolutionary synthesis’ – the sum of the best current understanding on the part of evolutionary biologists of the mechanisms through which life perpetuates itself and changes.

Those who reject evolution often talk of ‘Darwinism’, but this is inaccurate for two reasons:

  1. Evolutionary theory is a scientific theory, not an ideology. It is not an ‘ism’. Confusing the kind of thing an idea is confuses our thinking.
  2. While Charles Darwin was important in outlining the broad lines of evolution, others also did so before and since. He wrote in a time when he did not know of the existence of genes or DNA, so he got some things wrong. Science, by its nature, moves on, and evolutionary science is no exception. Refuting Darwin may not refute the modern evolutionary synthesis, and vice versa. (A related point is that traducing Darwin’s character or motivations does not refute evolutionary theory.)

The other point is about the use of ‘theory’ in relation to evolution, and this is something I’ve already written about elsewhere: Facts, Theories and Laws

I hope that the journey will be interesting and useful for all of us.

For ease of navigation I will include links to each of the other posts in this series at the bottom of each post.

Cosmogenesis, abiogenesis and evolution
Evolution and entropy
Facts, Theories and Laws
Radiocarbon dating
Radiometric dating and deep time
Four Forces of the Universe
Probability and evolution
Species and ‘baramin’, macro- and micro-evolution
Mitochondrial Eve and Y-chromosomal Adam
Transitional fossils
Complexity – irreducible and otherwise


Up Here’s For Thinkin’

Filed under: — Bravus @ 6:02 pm

Here’s a graph I made and posted here a while ago:

The post in question is here: http://www.bravus.com.au/blog/?p=1911

Sorry about the lack of labels – x-axis is years, y-axis is million square km of Antarctic sea ice.

These data are for Antarctica, but the Arctic picture is similar. Why do I bring it out?

Because the claim ‘Arctic ice is growing at record rates’ is being bandied about to ‘debunk’ climate change.

Yes, the extent (area) of the ice is growing fast for part of the year. The onset of winter runs for a finite time in the year. And if you look at the graph above, you will note that the minima are getting smaller quicker than the maxima – there is a lot less ice in summer, and a little less in winter.

That means that, to get from the new lower minimum to the new also-lower-but-not-as-dramatically maximum, in the same amount of time, of course the ice extent has to grow faster – maybe even at record rates.

It also means, of course, that to get from the maximum to the new ever-lower minimum at the beginning of summer the ice is also shrinking at record rates… but that stat doesn’t get bandied about at all by the (and I use the term quite wrongly) ‘skeptics’.

Doesn’t mean the ice is actually expanding over time – quite the reverse. The total ice is shrinking, and markedly so. This is not evidence against climate change, but for it.


Science and Morality

Filed under: — Bravus @ 7:50 am

P Z Myers is almost always worth reading. I disagree with him on many things, and agree on many more, but a blog is not worth reading only based on agreement – no doubt many who read my blog also disagree with me on some things. A blog is worth reading, in my opinion, for the ways in which it (a) points us to things that we find interesting but might not have discovered on our own and/or (b) works through ideas in a thoughtful, interesting way.

I’ve talked before about why I think Sam Harris’ claim that morality can be founded in science is a mistake, and could talk more about that, but this post by P Z does a great job, using an illustration from history:


The short-sighted lesson would be ‘oh, those silly 19th century folk who thought eugenics was a Good Thing’. The longer-sighted one is, I think, ‘Hmm, I wonder what things we silly 21st century folk remain blind to?’

The moral (heh) is that we must seek our morality somewhere other than in science. Where that is has been an on-going theme for me, some of it represented here and some in other places. To be continued…



Filed under: — Bravus @ 5:10 pm

So, I got my lab book – the crucial and closely-guarded document in which working scientists record their experiments each day to establish who got there first – this afternoon, and spent the whole afternoon working in the lab.

Nothing particularly security-conscious today, but in these social media days, in which I know I share a lot more than many people, I need to get in the habit where it’s OK to say that I’m doing research but not to share what I’m working on lest some other team elsewhere scoop us.

Anyway, definitely a buzz to be working as a real scientist in a biophysics lab.

I guess the first publication of a paper in that field will be the really big milestone – perhaps even more so than getting the degree itself. That’s some distance off, of course, but not that far… stay tuned!

Only then will I feel I can call myself ‘a physicist’ and/or ‘a scientist’.


Evolutionary Psychology (again) – and why it matters

Filed under: — Bravus @ 1:03 pm



Literature Reviews

Filed under: — Bravus @ 8:14 pm

I’m working on the literature review for my Masters of Philosophy (Physics) (henceforth to be known by the more familiar title ‘M Phil’ – sounds French!). I’m writing something that will end up being (much tweaked near the end) a chapter of the thesis, but I also have to present a lit review seminar in a couple of months.

(one of the interesting things is that I’m one of 2-3 physicists, labelled as biophysicists, in the Institute for Glycomics, which is full of biologists and chemists and biochemists. If anyone at all turns up for my talk, it will be a heap of smart non-specialists… and perhaps a couple of serious physicists from the other campus, charged with putting my feet to the fire)

In education, a literature review really needs to have three parts: some on the theoretical framework, some on the methodology and some on the empirical stuff – what we have learned from the research done so far.

The difference in (bio)physics – or at least my particular branch – is that the theoretical framework has pretty much been in place since Maxwell. If we get down to the ionic level we might have to get a little bit quantum on it – but even that’s a century old. So, guess I don’t really need to write too much about the theoretical framework in general: a bit about the specifics of the relevant theory and its implications for our work, but not a lot more.

In Kuhn’s terms, education can be thought of as ‘pre-scientific’. It doesn’t have a single dominant paradigm, it has dozens of competing paradigms. While they can be roughly sorted into qualitative and quantitative methods, the underlying paradigms are much more disparate. It’s necessary to say quite specifically where one’s research is located on this map – or possibly on a couple of different maps.

Physics, of course, is kind of the paradigm case (a slightly different use of the term – never mind, Kuhn apparently uses it 23 different ways) of a discipline that is ‘scientific’ in Kuhn’s sense. That means the methodology can largely be ‘taken as read’, since it’s shared by everyone in the field. It’s so foundational as to be pretty much invisible, and it’s certainly not necessary to waste words saying what everyone knows.

So this lit review I’m working on, while it’s complicated and technical in terms of the physics involved, and the maths used to tell that story, is actually more straightforward in some ways than the ones I routinely help students prepare in education.



Filed under: — Bravus @ 2:25 pm

Great little article on the ways words and language can confuse us in relation to health – if we let them.



Research Funding Freeze Redux

Filed under: — Bravus @ 3:19 pm

So, the minibudget came out today, and I guess the news wasn’t as bad as it could have been. Looks like the competitive grant programs’ funding is safe, and the ARC Linkage grant funding round has been opened up for applications, a month or so late.

The Linkage program requires applicants to gain some industry funding to couple with the government funding. It’s a great program, but this hiatus won’t have helped with the already very tough process of finding industry partners in a tight economy.

The final cuts – $500m is the headline number – are to future growth in the Sustainable Research Excellence (SRE) program. Slightly bitterly: apparently sustainable research excellence is no longer a priority.

That program gave funding to universities to cover the associated costs of research. Research grants cover things like infrastructure, researcher salaries, travel and so on, but there are lots of administrative costs, building space costs, electricity and water and a huge number of other costs that go into keeping research happening. Prior to the SRE program – and, to some extent in the future now – this money had to come out of recurrent federal funding for universities, and even be cross-subsidised by taking money the universities earned for teaching and using it to find the indirect costs of research.

That means today’s decision has the potential not only to impact on research in Australia – the thing that’s going to keep our living standards up once the resource boom winds down – but also to damage education at universities.

I’m a Labor supporter, as everyone knows, but this is a dumb decision, made for political reasons – to fulfil the stupid promise to return the budget to surplus this year, regardless of external factors. I hope that now that stupid promise has been fulfilled, we might see some smarter long term strategic decisions made about funding the things that will build our nation’s future.


Rifat Afeef in the Maldives – Deductive Science

Filed under: — Bravus @ 8:50 pm

I’ve received a couple of unsolicited emails from Rifat Ateef, who claims to have identified serious problems in international education and to be able to offer a solution that will transform education and the social sciences.

Rifat’s blog is here and contains a number of writings outlining these ideas.


I’m still reading them myself. The main contention seems to be that we have focused on induction – building up general laws from a large number of examples – rather than deduction – generating specific examples from general laws.

Thing is, we need to deduce from something. The general laws must exist without being empirically induced from our experiences.

I’m interested to see where Rifat goes with the ideas…


Science: The New Crusades

Filed under: — Bravus @ 11:34 am

OK, it’s not quite on the scale of the famous Billy Graham crusades in Melbourne in the 50s, which packed out the Melbourne Cricket Ground, but An Evening With Brian Cox in Melbourne sold 1800 tickets in one evening yesterday.

The fact that women tend to think he’s dreamy (pic at the link above) and he used to play keyboards in a band probably doesn’t hurt, but the fact that he’s talking about the universe and is a very good science communicator is the interesting bit.

Neil Degrasse Tyson is perhaps a bit less dreamy, but I’m sure would get a similar or greater reaction. There seems to be a real hunger for science – perhaps particularly astronomy, but other sciences too – in society. Which gives me hope, in a world that sometimes feels as though it’s being relentlessly dumbed down.

There’s a slightly different focus, but the big atheist conferences also tend to feature, as well as anti religious jeremiads, celebrations of science, and the audiences for those are growing year on year too.

Teachers who can find ways to ignite, rather than extinguish, that drive in their students are likely to be popular and influential too – even if they were never in a band.


Phj34r teh Mighty Ducks!!!1!

Filed under: — Bravus @ 8:34 am

I’m not posting this in relation to creationism and evolution, nor homosexuality and homophobia, although it touches on all those issues.


It’s about science education… which is what I do.

Students don’t have to ‘believe in’ evolution: but they do have to understand it.

And, honestly, they are in no position to make judgements about it if they don’t.


Science and Politics

Filed under: — Bravus @ 9:26 pm

It’s not *necessarily* the case that those on the right politically have to be anti-science: indeed, conservatism has typically supported science. This is a very disturbing trend.



Weak Measurements

Filed under: — Bravus @ 12:40 pm

Only for the very brave.

Here’s a paper I wrote for my course, about the concept of ‘weak measurement’ in quantum systems. http://www.bravus.com.au/weakmeasure.pdf

In that paper I mention an objection to the original paper by Leggett. That would be Nobel Prize Winner Sir Anthony Leggett. Here’s a lecture by him on weak measurement:



Filed under: — Bravus @ 12:09 am

I wanted to say ‘Happy Birthday’ to a couple of good friends, and since I’m in Portugal I looked up how to do it in Portuguese1. One way to say it is ‘Parabens!’ – and my chemistry ears pricked up a bit. In chemistry the parabens are a family of compounds derived from parahydroxybenzoic acid. They are widely used as preservatives.

Well, I guess really it was my ‘teacher ears’ that pricked up, because a possible approach to teaching a chemistry lesson about the parabens seemed to arrive. As a lesson plan it would need to include a lot more action and involvement from the students, but I thought I’d share a little bit of the explanatory portion here, just for fun2.

In teaching, I might start with the ‘Parabens means Happy Bithday in Portuguese’ thing, just as a quirky mnemonic device, but then get into the explanation. I’d probably bring in some cosmetics, pharmaceuticals and other products and point out the ‘methylparaben’ and ‘propylparaben’ in the list of ingredients. The lesson would probably come as part of an organic chemistry topic in a high school chemistry course, at a point where students already understood chemical bonding and some of the conventions of how organic molecules are represented:

This structure is for the actual parahydroxybenzoic acid (italics indicate where the name comes from). The other chemicals in the family are made by adding methyl, ethyl, propyl and so on groups where the R is on the diagram above, and that’s a discussion for a later time.

So, what do we see in this structure, and why does it have the name it has? The first feature is the hexagonal ‘ring’ structure. This is known as the ‘benzene ring’, and the chemical compound benzene, which used to be used in things like drycleaning and decaffeinating coffee, would be just the ring without the extra things sticking out at the top and bottom. They even used to use it as aftershave – it smells… interesting, but I personally wouldn’t like to smell of it.

(Because there are so many carbons in organic chemistry, we save time and energy by not drawing them in diagrams, they are just ‘taken as read’. Everywhere the lines join there is a carbon atom.) The ring is shown here with alternating single and double bonds, three of each. The ring is made up of carbon atoms bonded to each other, with a ‘spare’ bond on each pointing outward. Remember, carbon can form a total of 4 covalent bonds, and if you look at each of the corners of the hexagon and imagine an extra line pointing outward, linked to a hydrogen atom you’ll see that there are 4 lines in total connected to it. In benzene itself, hydrogen atoms are connected to the ends of the ‘spare’ bonds.

But we know a few things about double and single bonds. We know that they come out at an angle, and we know that double bonds are shorter than single bonds. So if the benzene ring really was as it looks in this diagram, the hexagon would not be regular, it would have 3 short sides (the double bonds) and 3 longer sides (the single bonds). It would also be kind of ‘crownshaped’, going up and down, if we rotated it around and looked at it from the side.

When we actually do the measurements on the benzene ring, though (and how those measurements are done on something as tiny as a molecule is a story for another day), we find that it’s flat, not crownshaped, and all six bonds are the same length.

That means the picture we have above is not quite right: they’re not double bonds and single bonds, they’re sort of ‘one and a half’ bonds. We won’t get to talk about it here in high school, but at university you can look forward to the discussion of how the p electrons in the carbon atoms form new π molecular orbitals above and below the ring… anyway, that’s for later.

I said benzene ‘used to be used’ for quite a lot of purposes, including drycleaning, but it’s not used as much any more, because it’s quite carcinogenic (cancer causing). It turns out that those unusual bonds mean it’s very good at attacking DNA, and broken DNA is what causes cancers.

Some of the health concerns around the use of parabens arise from the idea that, because it contains a benzene ring, it might have some of the same bad properties. You’ll be doing some research for your assignment about the chemistry of those claims and the scientific evidence, and will be asked to take and support a position on whether parabens should be banned, or used for a narrower range of purposes.

OK, so we’ve got the ring, now what about the stuff hanging off it? We’ll start with the easy one first, at the bottom. This is a ‘hydroxy’ group – hence the ‘hydroxy’ in the name – and is just an oxygen atom bonded to a hydrogen atom and the ring. The hydroxy group is the characteristic group of the alcohols, and we’ve looked at its properties a bit already.

At the top of our diagram, across the ring from the hydroxy group, is a carboxylic acid group. This involves a carbon atom that is double-bonded to an oxygen atom and single-bonded to another oxygen atom that in turn is bonded to a hydrogen atom (in this diagram they’ve represented it with an R instead of an H because it’s also possible to add other groups on in place of the hydrogen). That last part looks a bit like the hydroxy group, and has some similar properties, but it’s not a hydroxy group, it’s part of the larger acid group. There’s more to say here about electronegativity and electron density, but we’ll get to that later.

The last part of the name we need to explain is the ‘para’. It’s a way of saying where the two groups are around the ring. We start from the biggest attached group, which in this case is the acid group at the top. You can see that we could then put the hydroxy group on any of the other 5 carbon atoms in the ring. We need to be able to say where it is, because different locations will give the molecule slightly different properties.

Going clockwise around the ring, if the hydroxy group was next to the acid group, on the right, that position is called ‘ortho’. It would be possible (maybe, depending on the space in the molecule) to make ‘orthohydroxybenzoic acid’. I’ll give you a minute to draw that in your book and name it. Moving to the next position, that position is called ‘meta’. And then, when the molecule is as it actually is here, which the two groups opposite each other, the position is called ‘para’.

(I’d probably tie ‘ortho’ to ‘orthodox’, ‘meta’ to meta discussions, but this is already too long!)

You might think we’d need to have 5 labels since there are 5 positions, but if you imagine the hydroxy group in that bottom left corner, you can always just flip the molecule around its vertical axis, and the group will be in the bottom right ‘meta’ position… so it turns out we only need 3 labels, since it is how close that is important, not which side.

In a real lesson there’d be lots more questions, discussion, linking to past lessons and students’ life experience, discussion of how to answer exam questions on the topic, digressions into the conventions of how diagrams are drawn and what they really mean, and so on. But hopefully, at least, this has given you some sense of the kinds of processes that go on in a teacher’s head when preparing a lesson… and why it’s so much more than just information transfer. (And, linked to that, why a teacher can do a much better job than a textbook, all other things being equal.)

Oh, and for further reading, here’s the (excellent) Wikipedia article on the parabens: http://en.wikipedia.org/wiki/Paraben

  1. I’m fascinated with foreign languages and tend to try to figure out things like the words on labels. The Romance languages share enough Latin roots with English that it’s usually possible to piece together what’s going on with a little work. I’m fascinated by why Portuguese and Spanish are so different from one another when the countries are right next door with a land border (which makes it more mystifying to me than French and English).
  2. …and because it’s 3 am here and there’s nothing else to do. My efforts at synching my sleep cycle with here, coupled with the looong flight meant that I got my 9 hours of sleep from 6 pm to 3 am.







Christians and Evolution: A Different Take

Filed under: — Bravus @ 10:17 am

I think this relates to some of what Cadmann commented a little while ago, and is a very interesting take on the issue: http://www.huffingtonpost.com/jonathan-dudley/christian-faith-requires-_b_876345.html


Financial theory for fighting HIV?

Filed under: — Bravus @ 8:50 am

Ain’t science fascinating? http://www.salon.com/life/aids/index.html?story=/news/feature/2011/06/21/hiv_research


If you could, would you?

Filed under: — Bravus @ 10:20 am

Hack your mind, that is. http://www.salon.com/books/neuroscience/index.html?story=/news/david_sirota/2011/05/31/memory_mechanics_science_fiction

I’m ambivalent about the whole thing. My worst memories are pretty mild… just embarrassments and stupid things I did. Without a ‘do-over’ that would change the memories of other people or, say, the financial consequences in the real world, just getting rid of the memories wouldn’t do me much good.

For those with truly horrible memories, it might be more tempting… but as the linked story explores, what if those are an essential part of what makes you, you? Would you be willing to become a different person in order to get rid of those memories? And how would that effect your relationships?

Lots to think about, that goes right to the core of who we are.


Praying for the sick simply does not work

Filed under: — Bravus @ 10:10 am

I probably shouldn’t have to make the disclaimer after all this time, but it seems I do: I’m not attacking religion, Christianity or God. I’m challenging our (necessarily, inevitably) limited understanding of those things.

Here’s a big analysis of the research evidence: http://www.springerlink.com/content/ql345l2h434666l5/

It’s pretty conclusive: praying for the sick to be healed simply does not work.

Where it gets interesting is what we do with that. Rather than perhaps thinking again about what prayer means and what it is for, the most typical responses are to either try to impeach the science in some way as a godless plot or else to mutter about the inscrutable will of God.

His will must indeed be inscrutable if it turns out that praying for someone yields *exactly* the same medical outcomes as not praying for them… and if most Christians’ current understanding of the power of prayer is correct.

It’s not simple, and it’s not meant to be simple: but just pretending reality is not as it is doesn’t cut it any more.