Wednesday, May 30, 2007

The Splendour that is the Historical Sciences

I had the good fortune to attend a lecture on Friday by Dr John Paterson about the Cambrian Explosion, and how good inferences about the behaviour of organisms from that distant springtime of life can be made by considering such things as fossilized organisms that have healed after an injury, fossilized gut contents, and the size distribution of ensembles of organisms fossilised in different environments. The earliest dates for things like predation and herd/school behaviour seem to be being pushed further and further back.
Once again I was inspired by the magnificent beauty and complexity of the vision that is deep time, and how the contingent, irreproducible events of history have shaped the world that we know.

Best of all, I now realise there is an excellent way to push our search for the origins of life back beyond the fossil record. Molecular fossils! While most of the actual molecules that comprise ancient organisms are long gone, in some strata some of these molecules are tenacious and remain, and others have been transformed in systematic ways into compounds that still preserve some information about their origin. Perhaps succeeding generations of proto-life have not truly eradicated all traces of their predecessors as effectively as I thought.

These molecular fossils also seem to be a fantastic way to answer a question of great relevance to the 'Dr Jumba' theory of intelligent design. How closely related to the Cambrian Explosion beasties were the Ediacaran beasties? The Ediacaran world was very different, Dr Paterson told us- flat microbial mats with flat beasties: nothing that dug beneath the mats, nothing that ate anything else. Were those beasties based on the same chemistry as us? Or not? Surely the chemicals associated with them would give us a clue. I will explore the literature and return with a report.

Wednesday, May 16, 2007

Here tis

John Ashton rang me up the other day, after I wrote to that creationist website to complain about the same thing I have complained about here (i.e., the implication that Francis Collins supports young earth creationism). One of the things they make a lot of on that same creationist website is that we haven't bothered to refute John Ashton's arguments, we've just shouted 'rubbish!' and I told him I would put up a refutation here.

This is it.

John Ashton’s essay conflates two very different things.

(1) Does the variability of living organisms in space, and the inferred variability of living organisms in time, arise partly or completely from supernatural factors?

This is what I have called ‘Intelligent Design’ with capital letters, in previous posts. This is not a testable hypothesis, and is not a scientific hypothesis, but it is not necessarily stupid. Science is concerned with the reproducible features of the universe, and when we claim that the universe can be explained entirely through study of those reproducible features we are making a statement of faith. We cannot exclude, through science, the existence of supernatural factors or the possibility that they act or acted upon the Earth now or at some other time. We can only demonstrate that there are entirely plausible explanations that do not invoke supernatural phenomena to explain features of the observable world that other people invoke supernatural phenomena to explain. That is as far as we can go.

Some scientists have argued that it is useless to debate people whose worldviews are orthogonal to that of science. This is probably true for completely orthogonal views, but I think it is possible that a person could answer ‘yes’ to this question while holding a worldview that overlaps to an extent with a scientific worldview.

(2) Are the creation accounts given in the Book of Genesis literally true? That is, the world is 6000 or so years old, and the apparent age of the world is a cruel trick played on us by a God who created the world so it looked that way?

This is not a supernatural explanation of experimentally verifiable facts, but a denial of those facts. This was a position abandoned by all reputable thinkers long before Darwin was born. Every roadside cutting, every hill, every meadow, every map, every cell in our own bodies testifies that this is false. Si contradictio requiris, circumspice. This position can only be maintained by postulating a God who intentionally set out to mislead us and make a mockery of our faculty of reason. I think anyone who has been appraised of the experimentally verifiable facts who answers ‘yes’ to this question has lost the good of the intellect and can be considered to hold a worldview completely orthogonal to that of science. I have no common ground to argue with such people.

To draw an analogy with another debate of much more relevance to public policy, the person who would answer ‘yes’ to question 1 is more-or-less equivalent to the sort of ‘Greenhouse skeptic’ who says: ‘global warming has nothing to do with humans and is caused by an as-yet-unidentified natural factor’. They are disputing the explanation for the facts. The person who would answer ‘yes’ to question 2 is more-or-less equivalent to the sort of ‘Greenhouse skeptic’ who would say ‘The earth is not warming, but rapidly cooling. What’s more, there is no such thing as carbon dioxide.’ They are disputing the existence of a large number of well-attested facts.

Accordingly I will take the liberty of slicing John Ashton’s essay into two pieces.

For that part of his essay addressing (1) which is not entirely orthogonal to a scientific worldview, I will offer a plausible non-supernatural explanation for the observed variations of living organisms in space and time and explain why it is more consistent with the hypothesis of a benevolent God than his hypothesis.

For that part of his essay addressing (2), I can only rend my raiment and emote about how a God who would create such a stupid universe would be utterly unworthy of human worship.

My glosses are in brackets, [like so].

Essay One. Quoth John Ashton:

One rarely reads creationist perspectives on science first hand in journals such as Chemistry in Australia. Secular and atheistic views have dominated western education for many years and it is now very difficult to get a theistic based theory taught or discussed as illustrated by the uproar in 2005 about a proposal to teach evidence for intelligent design.

However, I believe there is a sufficient case for the alternative view that in the beginning God’s creative power brought everything into existence to warrant teaching the evidence for this view in science classes.
My first observation is that a number of unproven scientific hypotheses have become widely accepted (or talked about) as fact. This makes it very difficult for the non-expert or layperson to distinguish what is a proven fact from what is merely a theory about origins.

Evolution is a case in point.
There is no denying that biological change occurs. However, Darwinian evolution, as the origin of Life on earth, is now known to be impossible.

[This is a category mistake: Darwinian evolution has nothing to say about the origin of Life on earth. It is a model for how biological change occurs. Given some simple organism to start with- Gilbert and Sullivan’s ‘primordial protoplasmic globule’- it provides an entirely plausible picture for how changes arising by whatever means are spread by natural selection, and the aggregate of beneficial changes can lead to the variety of living organisms we see today.]

Let me illustrate the difference. Over the past 30 to 40 years a number of new strains of food poisoning bacteria have evolved. That is before the 1970s or thereabouts they did not exist (or were at least unknown). Now they are a threat to food safety. The evolution of these bacteria has been traced to the transfer of genetic information (toxin genes or acid resistance genes etc.) from one type of organism to another.

[Exactly! These changes have arisen, and then they have been spread by a Darwinian process of natural selection. Darwin’s theory does not depend on any particular mechanism for introducing changes. I agree that horizontal transfer of genetic information is an extremely important mechanism for introducing these changes. But this does not preclude other mechanisms. A copying error in which the daughter gene is not quite the same as the mother gene may be a felix culpa: indeed, given the vast numbers of genes being copied all the time, it is certain that beneficial errors are happening all the time. When these mutations affect genes that are involved in regulating embryonic development, for example, quite marked changes in an organism can be induced from minor genetic changes.]

And it is a similar situation for all the observed cases of evolution involving mutations. They all involve either the transfer of existing (i.e., created) genetic information from one organism to another or the loss of some pre-existing (created) genetic information.

On the other hand, there are no known instances of meaningful or purposeful genetic information arising spontaneously by chance- not a single known example- yet this is a fundamental requirement of Darwinian evolution, which teaches that microbes evolved into higher organisms, etc.

[While I am also unaware of any cases where a beneficial change has been unambiguously demonstrated under laboratory conditions, the mechanism is entirely plausible. There have certainly been many instances of heritable genetic damage, and this is not a ‘loss’ of genetic information, just a change. Out of a large ensemble of changes, some will doubtless be beneficial under certain conditions. Mutations do not have any meaning or purpose, and their utility will be dependent on the environment. Mutations that are harmful under one set of conditions may be beneficial under another.]

Darwinian evolution also requires abiogenesis, that is living cells spontaneously arising from non-living molecules (chemicals). Again, as George Javor, Professor of Biochemistry at the Loma Linda Medical School in California, points out, this has never been observed despite experimental attempts, and on the basis of current biochemical knowledge is absolutely impossible.

[Please see my post here on why seeking an understanding of abiogenesis based on ‘current biochemical knowledge’ is futile. This in no way make abiogenesis ‘absolutely impossible’.]

Not surprisingly, Francis Collins, director of the National Human Genome Research Institute, believes that it was God’s creative power that brought everything into being in the first place.
Oxford educated philosopher Ronald Laura and myself have also shown that an intelligent design or ‘blueprint’ based model is more effective in predicted adverse health outcomes resulting from new technologies than are conventional reductionist science models.

And this is my brief response to essay 1.

We do not need a supernatural explanation for biological change.

The mechanisms by which beneficial genetic variation might arise (genetic damage leading to copying mistakes, or horizontal transfer of genetic material) are either well attested by experimental evidence, or entirely plausible in light of experimental evidence for heritable genetic damage.

Once a beneficial genetic variation arises, there is a vast amount of real-time experimental evidence that this can be rapidly communicated throughout a species.

There are many, many places where anyone who is interested in truth can go to find a clearer explanation for the process and the experimental evidence for it than I can provide.

Why would anyone possibly want a supernatural explanation for biological change, anyway? For millenia, a challenge to theodicists has been how to reconcile the suffering of the biological world with the workings of a just and merciful God. Evolutionary biology lets God off the hook. One no longer has to believe in a God who just decided the animal world would be full of misery and suffering. Who just happened to make countless species eminently adapted to a life of parasitism or carnivory. Instead, the biological world can be seen as a collaborative work between God and Life. Living things were offered choices, with whatever smidgen of free will you want to postulate they have, and the sum of All Decisions Antecedent to Mankind resulted in the fallen world we see around us.

Essay Two.Quoth John Ashton:

Scientists and educators have been taught for decades that the earth and the universe are billions of years old, and this message permeates our culture to the extent that it has many people doubting the Bible’s record of the history of the world. Yet the historical accuracy of the Bible has been consistently validated by archaeology and secular historical records to within two generations after Noah’s flood (e.g., ancient Egypt was founded by and named after Noah’s grandson).

Although it is true that, on the basis of radioactive dating methods, scientists have calculated certain rocks to be millions and even billions of years old, we need to remember that these methods cannot be validated for pre-historical dates. Furthermore the calculations can give inconsistent and even wild results for some historical objects, for example recent lava flows. This kind of knowledge is why some highly educated geologists, geophysicsts, and physicists reject the ‘billions of years’ hypothesis and believe the earth is only thousands of years old. Some of their testimonies are freely available on the internet.

[You don’t need atomic dating to know that the earth is really very old. You just need to look at any geological formation. The idea that the earth was ‘thousands’ of years old was discredited centuries before atomic dating was invented. And Noah's grandson was named after Egypt by the authors of Genesis, or I'm a spotted hyena.]

Most of us have heard of the Big Bang model for the origin of the universe. This model uses black hole cosmology and assumes the ‘cosmological principle’ which requires a hypothetical fourth dimension. Even though this model has now essentially been disproved because it fails to predict observed data (such as proton decay) it continues to be the dominant model. However, if we hypothesise ‘white hole’ cosmology, i. e., matter stretched out in three-dimensional space (no hypothetical fourth dimension) we would have an ‘event horizon’ mwhere the gravitational field would be enormous and the speed of light would be very much faster and atomic clocks would run almost infinitely fast. Using this model the earth and universe could be very young- only 6000 years old.

[Two things are conflated here: the observations that matter is flying away from other matter, which can be extrapolated back to the origin of all matter at a single ‘point’, and the precise mechanism for the ‘Big Bang’, which is a matter for debate. But an ‘old universe’ is not dependent on one or any of these models being true. Cosmologists hypothesise all sorts of things all the time: but they can’t be totally inconsistent with the facts we are living with on Earth. We are justified in immediately rejecting ‘white hole’ cosmology purely because of the weight of terrestrial evidence for an old earth.]

The US mathematician Robert Herrmann, former professor of mathematic at the United States Naval Academy, gives powerful arguments for scientific observations upholding a plain interpretation of Genesis chapter one, while allowing for starlight to travel for billions of light years.

[If the arguments are powerful arguments, why are they not given? The argument from authority ('Dr X says so') is the weakest form of argument. And argument from authority is all the next paragraph amounts to:]

My second observation is that while we regularly read about scientists who believe in the Big Bang and life on earth being billions of years old, such as Stephen Hawking, Paul Davies and Richard Dawkins, we rarely read articles in the media about scientists like Professor Herrmann who believe that the heavens and the earth were created in just six days about 6000 years ago. Yet scientists who believe the creation account and a young earth include dmany eminent scientists such as Professor David Gower DSc (London), Emeritus Professor of Steroid Biochemistry at the University of London; Dr Ker Thomson DSc (Colorado School of Mines), former director of the US Air-force Terrestrial Sciences Laboratory; and Professor Werner Gitt D. Eng (Aachen) a former director of the German Federal Institute of Physics and Technology (the same institute where Einstein studied). These scientists emphasise the observation that much about origins that is often presented as facts is actually based on unproven hypotheses and that the weight of factual evidence favours creation.

[Why not give the titles and potted CVs of Hawking, Davies, and Dawkins? Once you start arguing from authority, you have lost this game. These eminent scientists are not household names, like the first three are, because they are not really all that eminent. We don’t hear about scientists who hold creationist views because there aren’t any working in fields of relevance to the questions of the origins of life and the universe who hold such views.]

On re-reading this I can’t help but feeling a sneaking suspicion that maybe John Ashton is having us all on and is going to shout ‘gotcha!’ any minute now. Essay (2) is just so very, very, very silly.

There is an overwhelming mass of evidence that the earth and the universe are very, very old. I will requote Francis Collins because I am still upset about the shabby way he was quoted to make it look as if he was in favour of the content of essay (2).
'If the tenets of young-earth creationism were true, basically all the sciences of geology, cosmology, and biology would utterly collapse. It would be the same as saying 2 plus 2 is actually 5. The tragedy of young-earth creationism is that it takes a relatively recent and extreme view of Genesis, applies to it an unjustified scientific gloss, and then asks sincere and well-meaning seekers to swallow this whole, despite the massive discordance with decades of scientific evidence from multiple disciplines. Is it any wonder that many sadly turn away from faith concluding that they cannot believe in a God who calls for an abandonment of logic and reason?'

If, in the face of all this evidence, anyone persists in believing that the earth and the universe are 6000 years old, than this requires belief in a God who set out to make all the evidence point to a wrong conclusion. This requires a God who wants to frustrate rationality. This God is more like the jumped-up fraud of Robert Heinlein’s Job than anyone worthy of human respect. Could our ideals of justice and mercy possibly derive from such an entity? I think not.

Monday, May 14, 2007

I know you're out there!

Just was informed that there is a link, established on the 24th of April, from a creationist website to the letters catigating the Royal Australian Chemical Institute for publishing a creationist article that I posted so I could link to them here. There is *no link* to those letters on the Polymer Division website. Either Google found them, even though they were parked nigh-linkless, or someone has been through here and found them.

The creationist article says that our criticism is ill-founded because we have not specifically refuted the claims made in John Ashton's article. I will specifically refute them all here, real soon.

Chris Barner-Kowollik tells me that since the creationist website linked to his letter, he has been receiving hate mail from certain Christians, saying things like: "Your days are numbered and the wrath of god will hit you hard." He says I should leave the letter up on the web anyways, because he is a man of principle and integrity.

If Google is not nigh-omnicompetent, and you, dear reader, found those letters through here, please feel free to publicise my name and contact details to receive abusive messages as well. For the God of young-earth creationism is a despicable God, a God who holds his creatures in contempt by filling the natural world with suffering for no good reason and mocks sentience by constructing a universe made to look in every way like it is billions of years old and governed by rational laws. I want no truck with him. Humanity deserves a better God than that.

Wednesday, May 9, 2007

Things I Don't Understand: The Gibbs Paradox

I was told a while back that there is no such thing as entropy of mixing for ideal gases, and it makes sense to me.

In an ideal gas, the components of the gas don’t take up any volume, and they don’t have any specific interactions with each other.

If you start out with two ideal gases, A and B, in a container separated by a partition, and remove the partition, then gas A will expand into the whole of the volume previously occupied by A and B. Each molecule of A will have more options available to it than it had previously, and entropy will increase. Similarly, gas B will expand into the whole of the volume, etc. See, there is no entropy of mixing. There is only the entropy of expansion. If the volume of A equals the volume of B, this entropy of expansion turns out to be R.ln2, where R is the ideal gas constant.

But, let’s say we had equal pressure of gas A on both sides of the partition. We remove the partition, and gases A and A mix. Both of them expand, so we ought to get an entropy increase. But the pressure and volume and temperature of the final A + A system is exactly the same as the initial one: there has been no change, and the entropy of expansion turns out to be 0.

This is the Gibbs Paradox.

It bugs me because, let’s say we didn’t stop at one partition, but kept putting in more and more partitions until every particle was in its own little box, surely that would mean we had a system with less entropy?

Or not?

I keep looking for experiment data on entropy of mixing of gases, and all I find is people writing theoretical papers explaining the paradox away in different ways.

This one is particularly good, and says more or less- I think- that the thermodynamic entropy that we can use to do work with is not really a well defined function in the same way that energy is. It will depend on the things we have selected to characterise the system, and if we were to find out new ways of distinguishing particles that were indistinguishable before, we could exploit these to do work, and see an entropy change on mixing. This seems perfectly valid, but troubles me because I have been teaching first year in such a way that energy is an abstraction from entropy as a more fundamental concept. Which I will have to rethink without confusing myself totally.

Another paper that I have to read over again to try and start thinking clearly is this one, which is about the confusion between thermodynamic entropy and informational’entropy’.

So it seemed to me that when we remove the partition between A and A′, we had to be increasing the informational ‘entropy’ of the system, but maybe because there is no way to exploit this to do work, we haven’t done anything to the thermodynamic entropy.

I was talking about putting particles in boxes before, so I thought I should go all quantum and actually put our particles in boxes.

Let’s say we have some energy kT available for partitioning all our particles into translational states. These translational states will be separated by energies proportional to 1/a2, where a is the size of the box. So the number of translational states available if the temperature stays the same but we double the size of the box doesn’t go up by a factor of 2, but by a factor of 4.

So I was thinking that there seemed to be a lot more ways of putting 2n objects in 4m boxes than of n objects in 2m boxes, and so there ought to be an increase in informational ‘entropy’ when we double the size of the box. Sure enough, when I looked up how to calculate the number of permuations there are a whole lot more permutations. But informational entropy is related to the log of the number of permutations. The log of the number of permutations at the end seems to be converging to twice the log of the number of the permutations I had in a box half the size... but it is converging towards one too slowly for the factorials I can do in Excel to cope. Is it going to go to one or not? Does ‘entropy’ of A + ‘entropy’ of A = entropy of (A+A)?

So I have to say this is something I don’t understand.

Next up: Quantum Teleporation.

Wednesday, May 2, 2007


It would seem that there is more positive selection in a large population than a small population, because statistically more beneficial mutations will arise and spread throughout the population. This seems logical.

Here is a link to Zhang's article on the human and chimpanzee genomes, which I admit is well beyond me as a mere chemist. :P