Sunday, January 08, 2012

...then cry "Havoc!" and let loose the dogs of Philosophy

Not knowing exactly where the discussion reproduced on Marco's blog began, and unsure of where the participants in it actually agree or disagree with Prof Lennox, I will just throw out onto the aether my own thoughts about his book, 'God's Undertaker'.

I am in complete agreement with Prof Lennox wherever he is showing up the hubristic claims of the 'New Atheists'. They say things that are ridiculous and irrational and Prof Lennox does a good job of demonstrating this in his first five chapters.

Science is an instrument for making sense of the reproducible, comprehensible features of the experienced universe. To say that all features of this experienced universe are reproducible and comprehensible is a statement of faith - a defensible and rational statement of faith, but still a statement of faith. To say that nothing exists outside this experienced universe is a statement of faith that is irrational and indefensible.

The scientific worldview is not inconsistent with a belief in an omnibenevolent entity which is omniscient and omnipotent with respect to our universe. It just isn't.

The scientific worldview is not inconsistent with the definition of Good as a real feature of the universe, rather than a social construct or emergent biological epiphenomenon. Neither is the scientific worldview inconsistent with the survival in a 'location' outside the universe of the information describing a human life in its entirety; a belief in miracles; nor the active involvement in human affairs of free-willed 'macrobes' capable of masquerading as gods.

On the other hand, if 'belief in God' is conflated with 'adherence to a theistic religion', the situation becomes murkier in terms of the tension between science and religion. The scientific worldview posits a single source of authority - experience - and is antithetical in its spirit to all other sources of authority. Thus an organised religion resting on sources of authority that will in many cases appear to contradict experience - that is, all of them - will never be an entirely comfortable place for someone subscribing to a scientific worldview. Thus I have to disagree with his quotation (about 15% through) that 'vast tracts of science remain unaffected by such philosophical considerations': all of science is necessarily shot through with a spirit that is in opposition to all individual organised religions, even if it is not incompatible with theism in general.

So, where Prof Lennox is negative, I am on his side. Where he is making positive assertions, I am a little less happy. Though I have to say I didn't find anything particularly objectionable in the first five chapters.

In Chapter 6 he metaphorically wheels out his motorcycle and heads down to the aquarium when he starts talking about evolution. To me, this was because he quotes a large number of people who dissent from the 'neo-Darwinian' consensus, including Niles Eldredge of punctuated equilibrium fame, without telling us what they intend to put in its place rather than intelligent design. So, species are largely static: it makes sense that genetic change will be most rapid in small, isolated populations. So, random mutations won't cut it: but what about horizontal gene transfer? Changes in gene regulations giving major morphological changes from a minor chemical change? Some sort of Parigian neo-Lamarckism? There are a lot of possibilities, and Lennox doesn't talk about any of them because he has already written them off.

Where he talks about how unsatisfactory the current models for the origin of life are, in chapter 7, I - or more accurately, my real-world alter ego - am on pretty much the same page.

I think this just means we need to approach the question from a more fundamental direction, with simple building blocks for a metabolism, and be more open about the possibility of exogenesis. I think introducing Intelligent Design would be a terrible idea.


Consider the following syllogism, going back at least as far as the 1st century:

There is strong evidence that the universe was designed.

However, the universe is all ****ed up.

        Therefore, the designer of the universe is an ****hole.

Expressed somewhat more elegantly, this is a syllogism that has convinced a great many virtuous and intelligent people over the millennia. The problem of reconciling the existence of a good God with a ****ed-up universe is the central problem of theism. I solved this problem to my own satisfaction when I was 19, but I could not have done so if I believed biology exhibited intelligent design.

"What a book a devil's chaplain might write on the clumsy, wasteful, blundering, low, and horribly cruel work of nature!" (Charles Darwin)

The evil we see in nature can be explained as the consequence of natural selection and other natural evolutionary mechanisms: we do not see the perfect world of the divine vision, but the outcome of choices by free-willed beings that have led to a sub-optimal outcome. Extending this to a deep anthropomorphism that gives the attribute of free-will to the particles whose interactions give rise to physical law completes the process of letting God off the hook for the moral flaws of the universe.

Some more observations at different milestones through the book:

7% : I agree with Prof Lennox's argument about the 'forgotten roots of science'. I made the same argument here. I am pretty sure that both of us, and C. S. Lewis as well, got the argument originally from Chesterton, who doubtless made it better than any of us.

8%: I wish people wouldn't diss Aristotle. On the page before, Lennox has been talking about the dead hand of Augustinianism keeping people's attentions focussed on the supernatural world and encouraging a symbolic, allegorical intepretation of nature. What was Augustinianism? Baptised Platonism. The dethronement of Plato by Aristotle at the time of St Thomas Aquinas was the critical moment when the tide turned. Aristotle was part of the solution, not part of the problem. Whitehead's quote about people in Europe in 1500 knowing less than Archimedes in the 3rd century BC is just bogus: if he had said 1100, sure.

11%: 'The cosmos is all there is, or was, or ever shall be' (Carl Sagan)
This is the crux of the matter for me and though I repeated myself over and over and over again when we were talking about Dawkins' 'The God Delusion' before I am still not sure I got my point across.

Let's define the 'Universe' as all there is, or was, or ever shall be.

And let's define the 'universe' as this thing that is all we can ever access by experience, which appears to obey certain rules.

Conflation of the two is not tenable.

It was not tenable to clear-thinking people at the time of Lucretius. Speaking of Plato, Aristotle, Descartes, Leibniz, Spinoza, Kant, Hegel, Locke and Berkeley, Prof Lennox says correctly 'that the universe is not self explanatory, and that it requires some explanation beyond itself, was something they accepted as fairly obvious.' After Boltzmann's formulation of the 2nd law of thermodynamics and observations of cosmic background radiation suggesting the occurrence of a 'Big Bang', the conflation of the universe with the Universe has become yet more untenable. 

12 %: I don't think the definition(s) of science offered by Lennox rigorous enough to illuminate the areas of tension and non-tension between science and religion. I would like to refer you to this monologue by my alter ego. This is just my view: there is no creed defining science that we have to sign up to when we get our degrees. But I doubt that Peirce or Feynman would find much to disagree with me about - and so there is my token argument from authority out of the way.

16 %: '...theists claim that there is someone who stands in the same relationship to the universe that Aunt Matilda stands to her cake.'

Since Aunt Matilda made the cake for her nephew's birthday, these particular theists would be good subjects for a Lovecraftian short story. "The worshippers of Pzgra claim that the end of time she will give the universe to her nephew Pthaak-Zroghoroom, who will eat it, after first blowing out the suns to the strains of music beyond human comprehension."

26%: 'Saying that the universe arises from fluctuations in a quantum vacuum simply pushes the origins question one step further back, to asking about the provenance of the quantum vacuum. More importantly, it leaves unanswered the question 'what is the origin of the laws governing such a vacuum'?

Something must be self-existent; otherwise nothing would exist. And it doubtless seems more reasonable to many people that this something be a quantum vacuum governed by certain laws, rather than God. But in essence, the problem is that the universe and everything in it are not self-existent, so we have absolutely no experience of what a self-existent thing might be like. I am pessimistic about the possibility of us ever making any meaningful stabs at figuring this out from inside the universe with our universe-bound reason. Which brings me to about 27%, and Prof Lennox's discussion of the anthropic principle.

I have never been particularly sympathetic to anthropic principle arguments.
I dislike them for two reasons: my scientific prejudice is that just as there are any number of rocky planets not so unlike ours, and our sun is nothing special, and our galaxy is nothing special, our universe ought to be nothing special. I also have a religious prejudice against the universe being somewhere where things have to balanced to 1 part in 1040 in order for us to be here: I don't like the 'author intrusion' of a Creator who would show off to that extent. It smacks of Oolon Coluphid's Babel Fish argument. I guess I have always thought,without explicitly putting it into sentences, that any amazing sensitivity of our existence to quantifiable features of the universe having certain extremely narrow quantities could be attributed to lack of knowledge and failure of imagination. That is, when we found out more about the universe and how it worked, we would find good reasons for why it was very probable that we would end up with these values, given unexciting initial conditions; and that when we thought about it more we would come up with all sorts of other ways matter could be organised so it could think, given all sorts of other specific values of these constants. Maybe I am wrong.

I am told I have been typing too long, so I will call this part one, and return to the anthropic principle real soon now...


Marco said...

Well to answer the first sentence. Nathanael read this book a while back, and agrees with it in general. His brother Winston Inabox has been convinced to read it, and although he hates it is reviewing it for discussion on his Facebook wall as he goes. I have worked out how to "cut and paste" roughly by taking a screenshot of the relevant pages. At this stage there has been a thread on Galileo, where me and Winston more or less agree that Lennox had somewhat misrepresented what actually happened in relation to the conflict of church and science. The second thread is regarding the requirement of faith in science. I believe there is a requirement for faith, and that it is the New Atheists that are misrepresenting this requirement, while Winston is adamant that it is Lennox playing semantics.

Marco said...

I don't understand what your objection to FaceBook is, it would really be good to have you there, even if you block absolutely everything you object about it.

Dr Clam said...

I guess as far as Lennox's treatment of Galileo goes, I am with Nathanael (I presume) in asserting that there is no significant misrepresentation there. I also don't see any great interest or benefit in arguing about it.

So far as the second thread goes... as you know... I am with you 102%.

It is probably cowardice keeping me away from FaceBook. Cowardice, and a lack of human empathy manifesting as irritability. (Speaking of cowardice, I still haven't sent that email to start that argument I asked you about in Twitter.)

Marco said...

Indeed. You got me interested even though I have absolutely no information on what the argument was about.

As for empathy - I have decided that it is entirely unnecessary on FaceBook. It appears just like a blog that more of your friends would actually read. It is still irritating that the most mundane of things go viral, and really amazing stuff gets ignored.

Marco said...

Oh. By the way - I reread that absolutely excellent trio of posts about show me the metabolism. I have had this hunch swirling around in the back of my mind about how metabolism and reproduction co-evolved. The basis of my hunch is based on what dna is like and that what it is like can tell you about where it originated. A bit like the slit in a human zygote (embryo?) can lead you to believe that we evolved from creatures that had gills knowing nothing else.
I wondered if you know of any sources of information about the physical chemical properties of dna (principally mitochondrial dna) and in particular the energy transfers within the chemical structure when subjected to sporadic high level radiation doses. My hunch is that the dna acted both as a store of energy *AND* a store of genetic information in its raw form. The source of energy would be the strong ionising radiation, which would be stored in the chemical bases of the dna, and when shielded from the radiation would use this energy to assemble its helical or even substructures relevant to the organic molecules involved.

Marco said...

...something something Asimov something something radioactive decay something something left hand molecules something something why not 50-50 left and right something something donkey.

Dr Clam said...

You got me interested even though I have absolutely no information on what the argument was about.

I'm not sure which argument you are talking about here?

I wondered if you know of any sources of information about the physical chemical properties of dna (principally mitochondrial dna)...

I'm glad you like the 'Show me the Metabolism' posts :D I haven't had a look yet for information on the properties of DNA but I expect you can do as well as I hunting facts in cyberspace. I think you are on to something in that there is very likely to be a connection between the adoption of DNA and metabolism, since ATP and GTP are 'energy currency' in living systems - but I think the adaptation of a metabolic process to reproduction would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate and (therefore) existing in an environment shielded from ionising radiation.

Dr Clam said...

Re Facebook, nobody read my stuff there either. The "Global Warming Is a Myth" essay was up there for years with no comments :(

Marco said...

I am not sure of the "endpoint" of evolution I am trying to get to here, but in subjective terms, I am looking for an environment and system whereby the building blocks upon which DNA is built on are "reproducing". In this sense I am looking at the neucleotides and related molecules. I am trying to think of an environment ( possibly a common environment in the stretch of space that predates our solar system) where an energy source applied to a molecule (neucleotide like) would cause neighbouring molecules to arrange themselves into a neucleotide without destroying the original neucleotide and when that is complete, the process would repeat with both neucleotide type molecules. The environment in which this happens would of course be completely different to the environment for the next step, which would, however require an abundance of neucleotide bases being available from the previous step. This process should be still apparent somewhere in the galaxy, or be able to be simulated from what we know about the pre-sol era in this stretch of space.

Marco said...

Woohoo. Look what I found casually looking for information about the chemistry of neucleotides!!!! From Wikipedia: Neucleotides

In August 2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting nucleobases (such as adenine, guanine, xanthine, hypoxanthine, purine, 2,6-diaminopurine, and 6,8-diaminopurine) may have been formed extraterrestrially in outer space.

This is looking closer and closer to the origin of metabolism/life. Outer space.

Marco said...


"In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water. This provides a plausible mechanism for their synthesis in the asteroid parent bodies, and supports the notion that they are extraterrestrial," says Callahan.

I wish I knew a chemist somewhere, that would set up an experiment for his honours students, to demonstrate that these neucleotides use a rudimentary "metabolism", using energy to reproduce themselves in conditions like on an asteroid...

Dr Clam said...

That's not metabolism, that's just catalysis. In segueing from nucleic acids to nucleobases you have lost the nugget of gold in your original hunch.

Like I said: ...There is very likely to be a connection between the adoption of DNA and metabolism, since ATP and GTP are 'energy currency' in living systems - but I think the adaptation of a metabolic process to reproduction would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate

Marco said...

Ok. So I get that the endpoint we are getting towards is nucleic acid. But I do want to explore whether some forms of catalysis are like reproduction. Ie. if seeded with a base, does this multiply the number of bases you end up with? And can this reproduction be "powered" ie, energy is absorbed and catalyses the process, but then excess heat just radiates away, doesn't reverse the process. Can this plausibly match your energy graph for metabolism? Also, as far as I understand, chemical bases are recycled more than created within the nucleus, so for more complex chains to evolve a requirement is a high population of bases.

Marco said...

ATP and GTP are similar chemically to the neucleotide bases, and they are used for energy in all sorts of ways within living cells. Before there was something complex and delicate (which I assume involves membranes of the type you talk about in your metabolism posts) I am postulating there was something less complex and hardy to hostile environments including radiation, and capable of using all sorts of energy (from a sun, or from radioactive decay of some elements)to the sole purpose of powering the generation of the building blocks of neucleic chemistry, including energising the future energy currency. I am postulating that these building blocks were subject to selection and inheritance in a very basic way, that in the environment of colliding asteroids of various sizes with fairly high radiation,there was a survival of the fittest happening. Thus whereas the elements concerned may have been expected to form random combinations of molecules, a large chunk of them formed these bases and are spread through all the asteroids in varying concentrations. Once you have the assumption of high concentrations of this soup of bases, then you can look at how these could be polymerised into more complex compounds, that could separately be subject to reproduction and rudimentary metabolism, selection, mutation and inheritance.

Dr Clam said...

Okay, let me rephrase that: 'I think anything containing nucleobases remotely susceptible to inheritance and selection would have happened a long way along the process of 'protobiotic evolution' in a system that was already complicated and delicate.'

Complicated and delicate meaning it has to not be in an environment bombarded by radiation, but down in the sea-bottom mud on a planet or deep in the interior of a big dirty snowball.

'Subject to selection and inheritance in a very basic way' presupposes sugars and phosphates and reactions that would produce them all as intermediates and a way to separate the 'system' from the 'surroundings' - in fact, all the interesting things that we want to explain. Replication is not something that happens with nucleobases by themselves. To paraphrase something I said long ago: looking at nucleic acids and proteins and trying to work out the origin of life is like looking at smartphones and sattelites and trying to work out the invention of the telegraph. You can't get there from here!

Marco said...

I am a little confused just trying to piece together the latest NASA discovery of neucleobases on all the meteorites they tested. This is measured in parts per billion, but compared to the places they landed, that is high enough and of the type that would indicate that they originated from the parent asteroids they came from. This matches another study which indicates that the chemistry of a lot of asteroids including cyanide, water and ammonia, could very plausibly have generated these bases. From what you sort of were telling me, if some neucleobases were in the mix, they would catalyze reactions that would generate more neucleobases of some kind. Thus I'm surmising, that if a chunk of asteroid from a collision, landed on another asteroid, bringing some neucleobases with it, that it would "seed" the virgin asteroid, catalysing the formation of neucleobases that may not have otherwise formed. Let us just consider this part of the puzzle first. If this is what happened, are they "reproducing?. Now if they survived on a relatively small chunk of asteroid subject to sporadic ionizing radiation, and were still in a chemical form that could "seed" other systems to catalyze their reaction, while other candidate molecules wouldn't, would that make them more likely to catalyze the reactions that they catalyze, than other reactions ? Would this not be a rudimentary form of selection? If the end product of the reaction they catalyse is also a nucleotide base, would that not be a form of inheritance? I'm not playing semantics here, and Ithe next step is not going to be of the exact nature of this step, but is this very,very, very basic selection and inheritance.

Marco said...

Oh. And if this is found to be a supremely primitive form of reproduction, the supremely primitive metabolism, is the energy exchanges which enable the molecules to reproduce.

Dr Clam said...

From what you sort of were telling me, if some nucleobases were in the mix, they would catalyze reactions that would generate more nucleobases of some kind.

Er, no. This is what you sort of told me, and I have been saying isn't going to happen...

Marco said...

Is there a plausible explanation for them to be on all the meteorites?

Dr Clam said...

Plausible explanation: The meteorites are remnants of the original molecular cloud from which the solar system condensed, in which hydrogen cyanide, ammonia, and water were generally distributed, and hence nucleobases ended up being generally distributed too.

In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water.

Marco said...

I guess what I am trying to say is that in a "physical chemistry" sense, reproduction looks a lot like catalysis. And it wouldn't even matter if the mass production of a relatively complex molecule was just due to the nature of the conditions. My assumption is that nature builds on complexity only if natural selection can be made to bear on it- even if is nothing like natural selection as we know it. Clearly, in a physical chemical sense, self catalysis, or a cycle of catalysis is the only way that "inheritance" can come into it. Whether, as you say, the reactions wouldn't happen that way in space, and the source of energy might be something like geothermal underwater chemistry or whatever. But I strongly believe the building blocks of DNA would have to evolve, but in a completely different way than how it does that now, and in an environment common pre-earth.

Dr Clam said...

...something something Asimov something something radioactive decay something something left hand molecules something something why not 50-50 left and right something something donkey.

Is this the kind of thing you are looking for?

Marco said...

Yes. It is. Ever since I read one of your Asimov books on science, I felt this chiral chemistry bizzo was of absolute dreadful importance in the "physical chemistry" part of the origin of life, even though I couldn't quite put my finger on exactly what it means. My first guess was that the weak force must in some way be the energy source for the synthesising metabolism that I kind of described in terms of solely physical chemistry component reactions. It's not metabolism as we know it. The "inside" is the complex molecule itself. Energy transfers are radiative rather than selective chemistry going through membranes - you get the drift - This is just the Guess/hunch part of science, which is the most important. However, I need to structure my hunch in a way that is testable - which will take some doing.

Dr Clam said...

I found this great quote from a random person in the interwebz:
"I felt real anger and indignation when the definition of ‘universe’ was changed (arbitrarily in my opinion) from ‘everything that exists’ to ‘everything that exists within our segment of space-time’. To me this was intellectual laziness on the part of the astrophysicists who didn’t want to have to say that the ‘universe’ didn’t necessarily begin at the big bang but rather the portion of the universe that we exist in and the only portion that we currently have the ability to observe began at the big bang." (