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 30, 2007
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, 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.
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.
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.
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
Aha!
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
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
Tuesday, April 24, 2007
What is Chemistry? A Preface to an as-yet unwritten Book.
Chemistry is the science of things that we can see and that we can control.
When I was young, I never gave chemistry a second thought. I loved the grand sweep of biological evolution, with its single unifying idea and its endless ramifications, every twig on life’s branch subjected to a neat exegesis by my idol, Stephen Jay Gould. I loved the vastness of space, the unimaginably gigantic and inhuman universe subjected to the breathless exposition of Carl Sagan. I was brought up in an atmosphere suffused with geology, and I cannot remember ever not knowing that I lived on a thin chunk of crust moving inexorably towards Asia. These, the descriptive sciences, the historical sciences, were where I lived. I wanted to know where I was; I wanted to know where I was going.
But...
It is not enough to know. If you actually want to do something, all of these sciences have serious flaws. You cannot crash galaxies together to see what will happen. You cannot evolve your own species of toothed whale. You cannot smear an archipelago onto the Pacific coast of North America. You can only watch, and collect data, and hope for a ‘natural laboratory’ which will test whatever hypothesis you have developed. The essential bits of the historical sciences, the most interesting bits, are inaccessible to our tinkering.
As I grew older, I grew to lust after the secret and paradoxical wisdom of the physicists, the world of Schrödinger’s cat and Lorenz’s butterfly and the modest goal of the Theory of Everything. Here again, I was driven by the desire to know what was going on. Once upon a time physics was a science where you could do things.
But now, alas, they have mostly been done. Now you need obscene amounts of money to do experiments and whatever result you get can be explained by the theoreticians. Is that falsifiability?
Actually, I must be honest. I cannot discount physics. I am a failed physicist. Somewhere among the ordinary differential equations I got lost, and fell off the mathematical billycart. When I say that the great achievements of what we call ‘Modern Physics’ ended in the 1930s, and that since then it is chemistry and its biological metastases that have transformed the world, you must discount it as sour grapes. Likewise, when I proclaim: ‘physics has given we chemists our tools, and now its job is done.’ Sour grapes.
Essentially, chemistry drew me in because it let me play with liquid nitrogen and fire.
If you actually want to do something, chemistry is the only science worth considering. With physics, we can control things, but we can rarely see them or even imagine them. We can see the subjects of the historical sciences everywhere, but cannot control them. Chemistry is the science of things we can both see and control.
Chemistry is called by some of its practitioners the ‘Central Science’, a term that I have always found naff. It is the ‘Human-Sized Science’.
A few more facts about chemistry:
Chemists are allowed to:
(a) Appropriate any part of physics they like and call it ‘physical chemistry’
(b) Invade and subvert any ‘softer’ science they like and turn it into chemistry.
It is no coincidence that so many Deans, Pro-Vice Chancellors, Vice Chancellors and Prime Ministers (e.g., Margaret Thatcher) have been chemists. Those whose job it is to manipulate matter naturally want to manipulate it wherever they find it.
When I was young, I never gave chemistry a second thought. I loved the grand sweep of biological evolution, with its single unifying idea and its endless ramifications, every twig on life’s branch subjected to a neat exegesis by my idol, Stephen Jay Gould. I loved the vastness of space, the unimaginably gigantic and inhuman universe subjected to the breathless exposition of Carl Sagan. I was brought up in an atmosphere suffused with geology, and I cannot remember ever not knowing that I lived on a thin chunk of crust moving inexorably towards Asia. These, the descriptive sciences, the historical sciences, were where I lived. I wanted to know where I was; I wanted to know where I was going.
But...
It is not enough to know. If you actually want to do something, all of these sciences have serious flaws. You cannot crash galaxies together to see what will happen. You cannot evolve your own species of toothed whale. You cannot smear an archipelago onto the Pacific coast of North America. You can only watch, and collect data, and hope for a ‘natural laboratory’ which will test whatever hypothesis you have developed. The essential bits of the historical sciences, the most interesting bits, are inaccessible to our tinkering.
As I grew older, I grew to lust after the secret and paradoxical wisdom of the physicists, the world of Schrödinger’s cat and Lorenz’s butterfly and the modest goal of the Theory of Everything. Here again, I was driven by the desire to know what was going on. Once upon a time physics was a science where you could do things.
But now, alas, they have mostly been done. Now you need obscene amounts of money to do experiments and whatever result you get can be explained by the theoreticians. Is that falsifiability?
Actually, I must be honest. I cannot discount physics. I am a failed physicist. Somewhere among the ordinary differential equations I got lost, and fell off the mathematical billycart. When I say that the great achievements of what we call ‘Modern Physics’ ended in the 1930s, and that since then it is chemistry and its biological metastases that have transformed the world, you must discount it as sour grapes. Likewise, when I proclaim: ‘physics has given we chemists our tools, and now its job is done.’ Sour grapes.
Essentially, chemistry drew me in because it let me play with liquid nitrogen and fire.
If you actually want to do something, chemistry is the only science worth considering. With physics, we can control things, but we can rarely see them or even imagine them. We can see the subjects of the historical sciences everywhere, but cannot control them. Chemistry is the science of things we can both see and control.
Chemistry is called by some of its practitioners the ‘Central Science’, a term that I have always found naff. It is the ‘Human-Sized Science’.
A few more facts about chemistry:
Chemists are allowed to:
(a) Appropriate any part of physics they like and call it ‘physical chemistry’
(b) Invade and subvert any ‘softer’ science they like and turn it into chemistry.
It is no coincidence that so many Deans, Pro-Vice Chancellors, Vice Chancellors and Prime Ministers (e.g., Margaret Thatcher) have been chemists. Those whose job it is to manipulate matter naturally want to manipulate it wherever they find it.
Monday, April 16, 2007
An especially egregious example...
...of something that greatly irritates Marco is the language used in this popular science article.
The thing that greatly irritates Marco- and me too, for that matter- is the pervasive image of evolution as a 'ladder' leading step by step to 'more highly evolved' beings. Nothing can be 'more highly evolved' in general. A species can be 'better adapted' for circumstances X, Y, or Z; but circumstances are subject to review (by climate change, giant asteroids, motorways, etc.).
One thing that confuses me is the relationship between population size and genetic change mentioned in the extract below. It seems counterintuitive. Perhaps a real biologist could help? :)
The thing that greatly irritates Marco- and me too, for that matter- is the pervasive image of evolution as a 'ladder' leading step by step to 'more highly evolved' beings. Nothing can be 'more highly evolved' in general. A species can be 'better adapted' for circumstances X, Y, or Z; but circumstances are subject to review (by climate change, giant asteroids, motorways, etc.).
One thing that confuses me is the relationship between population size and genetic change mentioned in the extract below. It seems counterintuitive. Perhaps a real biologist could help? :)
Zhang's team found that 233 chimp genes, compared with only 154 human ones, have been changed by selection since chimps and humans split from their common ancestor about 6 million years ago.
The result makes sense, he says, because until relatively recently the human population has been smaller than that of chimps, leaving us more vulnerable to random fluctuations in gene frequencies. This prevents natural selection from having as strong an effect overall.
Saturday, April 14, 2007
Thursday, April 12, 2007
The Electrochromic Effect
We are very coy and subtle folks, sometimes, we scientists. The other day I was skimming through 'Molecules and Radiation' by Jeffrey Steinfeld while preparing some lectures and came across this sentence:
Other spectroscopists who did not like Stark?
Why should other spectroscopists not like Stark?
My curiosity was piqued, and it did not take long for me to discover why.
The electrochromic effect it is!
"The Hamiltonian for the interaction of an atom with a static electric field [called the Stark effect after its discoverer, Johannes Stark (1874-1957); also called the electrochromic effect by other spectroscopists who did not like Stark] is just the electric-dipole interaction:"
Other spectroscopists who did not like Stark?
Why should other spectroscopists not like Stark?
My curiosity was piqued, and it did not take long for me to discover why.
The electrochromic effect it is!
Friday, April 6, 2007
Twitch, twitch, twitch, twitch...
When will the world listen to reason?
I get the feeling it'll be a long time.
When will the truth come into season?
I get the feeling it'll be a long time.
- The Offspring
I can't take much more of this kind of thing, I really can't. I will burst a blood vessel somewhere. This unwarranted hyperbole about climate change is going to harm the reputation of science for generations. I used to think that the collective insanity of the early 20th century was caused by mass heavy metal poisoning of urban populations and we would see saner arguments and saner policies as we moved into the 21st century. But it appears I was sadly mistaken.
If we are worried about people in the poorest regions of the Earth suffering 'malnutrition, disease, and increased untimely death rates because of heat waves, floods, storms, fires and droughts', then the logical thing to do is to bring them to a standard of living so that they will suffer as little as we in the developed world do from heat waves, floods, storms, etc.
If we are worried about the alkalinisation of the oceans, we should take a deep breath and acquaint ourselves with how flimsy the evidence for this particular doomsday scenario is.
If we are worried about coastlines disappearing, we should get rid of those dams upstream and regenerate those coastal swamps we have cleared. And we should move people away from that dangerous big blue thing which is always going to twitch and kill people, no matter what the climate does.
If parts of the planet become too hot or too cold for traditional crops, then we should switch to different crops, shouldn't we? We do this kind of thing all the time.
I can't imagine any possible scenario where Bangladesh would run out of drinking water. Very dry poor countries with high population densities survive by economising on all the other things we do with water besides drink it. Very dry rich countries don't care, because if they want more water, they just build more desalination plants.
If we are worried about extinctions, we should address the primary cause of biodiversity loss- the dangerous fragmentation of habitats. We can move people out of marginal regions to amalgamate little reserves into big reserves. The little reserve is always vulnerable. If global climate change means your preferred habitat shifts a hundred metres uphill, in a large enough reserve you move a hundred metres uphill. Conversely, if a minor local event means your preferred habitat shifts a hundred metres uphill, in a reserve that is too small you're not going to be able to move.
Coincidentally, I just came back from holidaying on the seaside at a house with very little in the way of reading matter. There were three copies of the Readers' Digest there, the oldest from August 1974. This magazine had an article about the alarming drop in global temperatures of 0.5 C since 1940 and forecasts of the dire effects to come...
Thursday, April 5, 2007
In the beginning was the Metabolism
Being some comments on ‘The Origins of Order: Self-Organization and Selection in Evolution’, by Stuart A. Kauffman.
If I was arguing with one of the people Marco sometimes has to contend with- those who find the transition monkey --> man as implausible as the transition unlife --> life- then an exposition of how a ‘primordial protoplasmic globule’ (PPG) might have unfolded into the bewildering variety of life we know on Earth today might be of value. In the 19th century, or in the darker corners of the 21st century, a layman might suppose a PPG simple enough to have arisen spontaneously. For such a layman, an exposition of the pageant of evolution might seem to be a complete materialist description of the history of life, and might well shake their worldview to its foundations.
To the biologist, this pageant is far from a complete description. The biologist knows the complexity of the prokaryote, the PPG, and finds the unfolding of its descendants almost trivial. The PPG is not the simple explanation: it is the complicated thing that needs to be explained.
In a similar way, to the chemist, the unfolding of Kauffman’s ‘complex system of catalytic polymers’ (CSCP) to give rise to something recognisable as life seems almost trivial. The CSCP is the complicated thing that needs to be explained. Kauffman’s statement: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a complex system of catalytic polymers and the molecules on which they act’ should become: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a vastly improbable complex system of catalytic polymers and the molecules on which they act’.
I will now try to justify this assertion by considering the requirements a CSCP needs to have in order to be relevant to the origin of life.
Firstly, the CSCP must be secured from the overwhelming tendency for matter and energy to become more randomly distributed in the universe. This has one easy part and one hard part.
The easy part is the barrier to separate the system from the surroundings: something to draw a surface around the CSCP and keep it together. Kauffman mentions vesicles and protein coacervates as possible CSCP microcontainers for the early terrestrial environment, and plenty of other possibilities have been canvassed.
The hard part is whatever reaction allows the CSCP to increase the disorder of its surroundings in order to persist in time. The molecules making up the CSCP cannot be just any old polymers we happen to be fond of. They must be- if the system is to persist in time- intermediates in a spontaneous chemical reaction. This is whatever reaction converts energy-rich ‘food’ into energy-poor ‘waste’. The requirements of this net of reactions also make the easy part less easy: the low molecular weight intermediates have to stay in, not just the polymers. The ‘food’ has to get in. The ‘waste’ has to get out. Some selectivity is therefore required in the barrier separating the system from the surroundings.
Secondly, not just any thermodynamically favourable driving reaction will do. It would be preferable for this central driving reaction to proceed relatively slowly, so there plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways- because a great deal of complexification of the net of reactions must take place before we arrive at a CSCP. Before a CSCP can form, all of its constituent parts must be present as intermediates in a net of thermodynamically favourable reactions.
I believe this set of requirements allowing a CSCP to persist in space and time are very difficult to meet. Nothing approaching them has ever been observed, except in two common instances: living systems, and systems we have designed. The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.
Kauffman, understandably invigorated by the Central Dogma1 of molecular biology like so many in the last half century, is chiefly concerned with reproduction as the defining feature of life. He makes only a superficial discussion of metabolism that does not consider its central thermodynamic requirements. But ultimately, metabolism is what is most important. Without petrol, the most splendidly engineered automobile will just sit there. Without a plausible metabolism, the most elegant net of autocatalytic reactions is an empty exercise in symbol manipulation.
I don’t intend this as an argument in favour of intelligent design2, still less of Intelligent Design3. My main aim is to defend a strongly held view that both the ‘RNA world’ and the ‘Protein world’ are historically late phenomena, and that the critical events for the origin of life lie much deeper. We are trying to reconstruct the invention of the telegraph, knowing only the mobile phone: Which came first, we argue, the handset, or the system of towers dotting the landscape? It is an unquestion. We have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, as one phase of pre-DNA-life succeeded another. At each stage, we have destroyed our history more effectively than any Red Guards, as we cannibalised previous stages for chemical substrates. Perhaps there have been shifts in pre-DNA evolution radical enough that unassimilated chemical traces of previous stages remain, somewhere. Perhaps we will be lucky, and find somewhere out there traces of pre-DNA intelligent designers. But as far as the ultimate origin of life is concerned, it is useless to try and work backwards. We need to work forwards, by considering the necessary requirements for a CSCP to arise and where and how such a system might realistically arise.
If I was arguing with one of the people Marco sometimes has to contend with- those who find the transition monkey --> man as implausible as the transition unlife --> life- then an exposition of how a ‘primordial protoplasmic globule’ (PPG) might have unfolded into the bewildering variety of life we know on Earth today might be of value. In the 19th century, or in the darker corners of the 21st century, a layman might suppose a PPG simple enough to have arisen spontaneously. For such a layman, an exposition of the pageant of evolution might seem to be a complete materialist description of the history of life, and might well shake their worldview to its foundations.
To the biologist, this pageant is far from a complete description. The biologist knows the complexity of the prokaryote, the PPG, and finds the unfolding of its descendants almost trivial. The PPG is not the simple explanation: it is the complicated thing that needs to be explained.
In a similar way, to the chemist, the unfolding of Kauffman’s ‘complex system of catalytic polymers’ (CSCP) to give rise to something recognisable as life seems almost trivial. The CSCP is the complicated thing that needs to be explained. Kauffman’s statement: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a complex system of catalytic polymers and the molecules on which they act’ should become: ‘the origin of life, rather than being vastly improbable, is instead an expected collective property of a vastly improbable complex system of catalytic polymers and the molecules on which they act’.
I will now try to justify this assertion by considering the requirements a CSCP needs to have in order to be relevant to the origin of life.
Firstly, the CSCP must be secured from the overwhelming tendency for matter and energy to become more randomly distributed in the universe. This has one easy part and one hard part.
The easy part is the barrier to separate the system from the surroundings: something to draw a surface around the CSCP and keep it together. Kauffman mentions vesicles and protein coacervates as possible CSCP microcontainers for the early terrestrial environment, and plenty of other possibilities have been canvassed.
The hard part is whatever reaction allows the CSCP to increase the disorder of its surroundings in order to persist in time. The molecules making up the CSCP cannot be just any old polymers we happen to be fond of. They must be- if the system is to persist in time- intermediates in a spontaneous chemical reaction. This is whatever reaction converts energy-rich ‘food’ into energy-poor ‘waste’. The requirements of this net of reactions also make the easy part less easy: the low molecular weight intermediates have to stay in, not just the polymers. The ‘food’ has to get in. The ‘waste’ has to get out. Some selectivity is therefore required in the barrier separating the system from the surroundings.
Secondly, not just any thermodynamically favourable driving reaction will do. It would be preferable for this central driving reaction to proceed relatively slowly, so there plenty of intermediate molecules around. This reaction must also have many steps, with many intermediates capable of being transformed in various ways- because a great deal of complexification of the net of reactions must take place before we arrive at a CSCP. Before a CSCP can form, all of its constituent parts must be present as intermediates in a net of thermodynamically favourable reactions.
I believe this set of requirements allowing a CSCP to persist in space and time are very difficult to meet. Nothing approaching them has ever been observed, except in two common instances: living systems, and systems we have designed. The question of how systems meeting these requirements can spontaneously arise is the key question for the origin of life.
Kauffman, understandably invigorated by the Central Dogma1 of molecular biology like so many in the last half century, is chiefly concerned with reproduction as the defining feature of life. He makes only a superficial discussion of metabolism that does not consider its central thermodynamic requirements. But ultimately, metabolism is what is most important. Without petrol, the most splendidly engineered automobile will just sit there. Without a plausible metabolism, the most elegant net of autocatalytic reactions is an empty exercise in symbol manipulation.
I don’t intend this as an argument in favour of intelligent design2, still less of Intelligent Design3. My main aim is to defend a strongly held view that both the ‘RNA world’ and the ‘Protein world’ are historically late phenomena, and that the critical events for the origin of life lie much deeper. We are trying to reconstruct the invention of the telegraph, knowing only the mobile phone: Which came first, we argue, the handset, or the system of towers dotting the landscape? It is an unquestion. We have pulled ourselves up by our own bootstraps, as one phase of pre-biotic evolution succeeded another, as one phase of pre-DNA-life succeeded another. At each stage, we have destroyed our history more effectively than any Red Guards, as we cannibalised previous stages for chemical substrates. Perhaps there have been shifts in pre-DNA evolution radical enough that unassimilated chemical traces of previous stages remain, somewhere. Perhaps we will be lucky, and find somewhere out there traces of pre-DNA intelligent designers. But as far as the ultimate origin of life is concerned, it is useless to try and work backwards. We need to work forwards, by considering the necessary requirements for a CSCP to arise and where and how such a system might realistically arise.
1: I hate this term, 'Central Dogma'. Similarly, when Kauffman describes his theory as 'heretical'. This quasi-religious language makes scientific discussions sound very silly to outsiders, I am sure.
2: Defined as manipulation by, for instance, Jumba Jootika, vide infra...
3: Defined as manipulation directly by God.
Tuesday, March 27, 2007
Such things are sent to try us
The magazine of our professional association, Chemistry in Australia, has just published an article by a creationist chemist, John Ashton. Perhaps this is an experiment to see how many people are actually reading the magazine. Well before the magazine appeared in my pigeonhole I was being cc'ed messages from fellow chemists who rightly saw this as a very dumb thing for Chemistry in Australia to do. The perilous aspect of this is not that we should be publishing unscientific articles that aren't at all about chemistry (though that bugs me) or that some chemists are silly (though hardly any, of course), but that getting non-refereed articles into publications with scientific-sounding names is apparently a favourite creationist tactic.
I am peeved by John Ashton's attempt to drag Francis Collins into the fray as a supporter. In an entirely sensible address on science and faith, the Christian director of the National Genome Project has this to say about creationist views:
I am peeved by John Ashton's attempt to drag Francis Collins into the fray as a supporter. In an entirely sensible address on science and faith, the Christian director of the National Genome Project has this to say about creationist views:
'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?'
Sunday, March 25, 2007
Bearing fruit in keeping with repentance
I have confirmed that our Bachelor of Health Sciences (Homeoapthic Medicine) was discontinued last year, as I thought, and this link will soon be inactive. Hurrah!
The Funneled Web currently has an article about other universities that have not yet seen the error of their ways.
The Funneled Web currently has an article about other universities that have not yet seen the error of their ways.
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