Thursday, January 31, 2008
Four Things I Never Heard
* 70% of NSW canola is herbicide-resistant strains generated by conventional breeding.
These are mostly resistant to triazine herbicides, which build up in the environment. The genetically-modified versions available are resistant to glufosinate ammonium or glyphosate, herbicides which degrade rapidly and do not build up in the environment. So GM canola is unlikely to lead to increased herbicide use and there is a clear environmental benefit in introducing them in terms of the herbicides used.
* Our non-GM bulk canola gets the same price in world markets as Canadian GM canola.
So there is no question of us throwing away a 'premium' for a non-GM product. Our yields are just a lot lower because the triazine-resistant varieties are not as high-yielding.
* No 'organic' canola is grown in New South Wales.
So there is no chance of us jeopardising a small boutique industry which is getting a premium price for its product.
* EU and Japanese regulations on the labelling of non-GM foods allow up to 0.9% GM material (EU) and 5%(!) GM material (Japan).
This is far more than documented cases of accidental contamination of non-GM fields from the GM field across the fence, so if a premium non-GM market *did* develop, the fact that GM canola was being grown in the same part of the country would do nothing to stop farmers from participating in it.
This goes to show that there are great benefits to be gained in travelling to other institutions and attending seminars one wouldn't normally go to. I have known for years that the health and environmental arguments against GM foods were bogus, and is interesting to find that the economic ones are (at least in this case) bogus as well.
Wednesday, December 5, 2007
Google Shock
Monday, November 5, 2007
Good on him!
Sunday, November 4, 2007
My run of luck ends
I was 4/4 for letters to major newspapers over the last couple of years. (Finding these is left as a Googling exercise for the reader). This time I have had a go at Dr Karl, and my letter has passed into limbo.
In this article in the Sydney Morning Herald on Friday, Dr Karl is quoted as claiming that
Back in May we were told that Australians produce ‘more than five’ tonnes of carbon per capita per annum. That is, more than 18 tonnes of carbon dioxide per capita per annum.
This other site indicates that total Australian greenhouse gas emissions are of the order of 600 million tonnes of carbon dioxide per annum.
Thus, we can guess at 20-30 tonnes of carbon dioxide per capita per annum in
This gives 80-120 million tonnes of carbon dioxide per annum in
This is 1.8-2.7 trillion moles of carbon dioxide.
Which is 40-60 trillion (1012) litres of carbon dioxide at atmospheric pressure.
Which is admittedly a lot.
There are a trillion litres in a cubic kilometre.
So, we have 40-60 cubic kilometres of uncompressed carbon dioxide per annum. That is more like one a week, not one a day.
Week, day, whatever. Near enough is good enough, as my uncle who builds space probes for NASA says.
The article claims that
One mole of carbon dioxide at atmospheric pressure will occupy 22.4 litres. By pV= nRT, if we put it under a pressure of 100 atmospheres, it will occupy near enough to 1% of that. I don’t know what sort of pressure is appropriate for the zeroth-order ‘pumping it into empty oil and gas reservoirs’ sort of carbon capture technology. But I do know that the grail of this sort of thing is converting carbon dioxide into a solid.
One mole of carbon dioxide converted into, say, calcium carbonate, will occupy 37 cubic centimetres.
So, rather than ‘one cubic kilometre per day’ we have 0.10-0.15 cubic kilometres per day, which could be theoretically converted into 0.0002-0.0003 cubic kilometres of calcium carbonate per day. That would be about 20 times as much as the solid waste currently produced by
Here is how I ended my letter:
‘The fact that many different people are working on many different strategies to solve a problem should be a source of optimism and joy. That a group called the Climate Change Coalition would malign the motives of researchers pursuing carbon sequestration technologies is depressing, to say the least.’
Tuesday, October 30, 2007
O tempora! O mores!
Here are two more things I don't understand, which I will have a proper stab at real soon now:
(1) What is it with quantum teleportation? My gut feeling is that ‘teleportation’ is an illusion arising from us looking at things the wrong way.
(2) Ditto for the ‘collapse’ of a wavefunction.
What happens to these concepts in the De Broglie pilot-wave model? This is a model which can explain the mysterious double-slit experiments- where electrons (and neutrons, and helium nuclei) seem to interfere with each other as if they were waves *even if only one is sent through at a time* - in terms of each particle really being a particle but being guided by a 'pilot wave'. I find this much more satisfactory than wave/particle duality- which of course has no bearing on whether it is true or not.
De Broglie's abandoned this theory, but other people have been mucking about with it and optimising it from time to time. But, as a mere chemist, I don't really understand what they are saying.
“One singular deception of this sort ... is to mistake the sensation produced
by our own unclearness of thought for a character of the object we are
thinking. Instead of perceiving that the obscurity is purely subjective, we
fancy that we contemplate a quality of the object which is essentially
mysterious; and if our conception be afterward presented to us in a clear
form we do not recognise it as the same, owing to the absence of the feeling
of unintelligibility.”
- Charles Sanders Peirce, ‘How to Make Our Ideas Clear’
Friday, August 3, 2007
Sunday, July 22, 2007
Listening to the Sky
Curiously, I have come away with rather more scepticism about the Big Bang model than I had hitherto. I still think that the weight of the evidence is vastly in its favour. Declaring my biases, I still find it vastly more congenial to my worldview. However, I would no longer put it in the ‘that’s settled, then’ basket with continental drift and the evolution of all terrestrial life from a common ancestor.
(1) Briefly, the basic big bang model predicts background radiation in the universe that fits the blackbody radiation curve and is homogeneous with the same intensity in all directions. The steady-state model doesn’t. We have found background radiation which beautifully, definitely, fits the blackbody radiation curve. However, it is not homogeneous. Is it easier to tweak the big bang theory so that the radiation isn’t homogeneous, or the steady-state theory so that the background is thermal? Probably the former. And there are a lot of other problems with the steady state theory. Still, I can’t help wondering- if for purely historical reasons most theorists had stayed in the steady-state paradigm and devoted their lives to tweaking it, and only a few crackpots had kept beavering away at the big-bang model, would we have an elegant steady-state model today that fit all the data perfectly? Maybe we wouldn’t, but maybe we would. I just am not as sure as I was before that the universe is busily beating us over the head with the right answer.
(2) This is not an objection to the theory at all, but it is something I hadn’t known before, and it would certainly be something that would be shouted to the rooftops if a similar situation were to arise today- e.g., if a researcher affiliated with an oil company came up with a theory for climate change that confirmed the expected biases of their employer, even if it fit the data better than the anthropogenic global warming one. The Catholic church is not just perfectly happy with the Big Bang because it is consistent with Catholic ideas: it was a Catholic priest who came up with the theory.
Friday, July 13, 2007
The Clone Wars
I think it would be handy for all sorts of people who because of disease, accident, sexual orientation, or vocation, are unable to pass on their genetic material in the regular way. It has two problems, but these are problems shared by other assissted reproductive technologies:
(1) Wastage of ‘surplus’ embryos. I know nature does this, but I still think we should strive to keep it to a minimum.
(2) Health problems in the offspring. These are well documented but relatively minor for children put together by in vitro fertilisation. With cloning on the other hand, in the mammals we have looked at so far there are all sorts of peculiar and unexplained health problems. It would be criminal to experiment on human reproductive cloning at the moment because of these problems.
But there is no reason we should not keep on experimenting on our near relatives. Primates seem to be tricky things to clone. By all means let us try to clone chimpanzees. Once we can reliably clone perfectly healthy chimpanzees with a minimum of embryo wastage, why not apply the same technology to ourselves? I see no rational reason not to.
I do see therapeutic cloning as intrinsically wrong.
I think deliberately creating human embryos in order to destroy them is going too far. I don’t lose a great deal of sleep over it, because I was lucky enough to hear a talk in February 2006 by Graham Parker who is on the board of the journal ‘Stem Cell Research’ and works at a research hospital in Michigan. I learned the following things:
(1) The more differentiated a stem cell is when you start messing around with it, the more effective it is. This is why we still need to donate blood, and don’t just culture haemotopoetic stem cells. Inner-cell-mass-derived (aka embryonic) stem cells are less differentiated than somatic (aka adult) stem cells and appear much more likely to turn into invasive cancers when you inject them into mice.
(2) Nobody has a clue how stem cells really work clinically. It does not look like they just move in and turn into the sort of cells that are around them. They do other weird things that nobody understands yet.
(3) The chaps who first discovered inner-cell-mass-derived stem cells never claimed they had clinical uses. They still don’t. They are of fundamental importance in understanding developmental biology, which is important fundamental research and will eventually lead to all sorts of innovations- but they won’t involve injecting people with stem cells. 97+% of this fundamental research could (and should) be done with stem cells of the other mammals that we share so much of our DNA with.
This suggests to me that we are not likely ever to have a situation where therapeutic cloning would be done on an industrial scale and would be a big moral quandary for anyone with a serious illness. And if someone says, ‘I want to experiment on human embryonic stem cells’, the correct response is, ‘go do your experiments on chimpanzee embryonic stem cells’. There is no justification for playing with human embryonic stem cells. Maybe, once you have demonstrated that you can reliably and safely repair damaged chimpanzee brains, or whatever, then we can sit down and have a debate on extending the technology to humans.
Thursday, June 14, 2007
Granddad's Biography
I was pleased to discover his philosophy of examinations:
I always felt that an exam should be a learning experience and, at a graduate level, all exams were take-home exams where a student could consult with any book or person. The catch, however, was that the questions had no answers, and the grade was based upon the approach to unanswerable questions. Students have come back later to tell me that this was the greatest experience they had in preparing them for the real world.
Tuesday, June 5, 2007
Monday, June 4, 2007
Had we but world enough and time
This means that the chemical phenotypes of these classes of organism were well-established at least 2.7 billion years ago. Thus the genetic differences between these classes, which are vast, either:
* Have to be compressed into the time between 2.7 billion years ago and the origin of life on Earth, which has to be after the crust solidified. This is vaguely possible, as there is no plausible reason that the ‘molecular clock’ has run at the same speed all the time.
* Arose, if one extrapolates the molecular clock sphexishally backwards, well before the Earth’s crust solidified.
Isotopic distributions of 12C:13C in organic deposits show no sharp discontinuity as we move further back in time, but are consistent with a biological origin (Schidlowski, Precambrian Research, 2001, 106(1-2), 117-134). Thus the essential biochemistry of today’s methanogens, or something very similar, were already established in the very oldest sedimentary rocks we know about, about 3.8 billion years old.
Wednesday, May 30, 2007
The Splendour that is the Historical Sciences
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
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.