Nicholas 19 Nov 98 There is an interesting paper in today's Nature called Surface-promoted replication and exponential amplification of DNA analogues
A. LUTHER, R. BRANDSCH & G. VON KIEDROWSKI (in Nature 396, 245 - 248 (1998)) report that they have designed and studied self-replicating chemical systems to identify the minimal requirements for molecular replication, to translate the principle into synthetic supramolecular systems and to derive a better understanding of the scope and limitations of self-organization processes that are believed to be relevant to the origin of life on Earth. A common problem of previous systems is product inhibition, leading to parabolic, instead of exponential, amplification (which latter is the dynamic needed for Darwinian selection). The authors describe an iterative, stepwise procedure for chemical replication which permits an exponential increase in the concentration of oligonucleotide analogues. The procedure employs the surface of a solid support: Copies are synthesized from precursor fragments by chemical ligation on immobilized templates, and then liberated and immobilized to become new templates. The process is repeated iteratively. The role of the support is to separate complementary templates which would form stable duplexes in solution. They claim that their process combines the advantages of solid-phase chemistry with chemical replication, and can be further developed for the non-enzymatic and enzymatic amplification of RNA, peptides and other templates as well as for studies of in vitro evolution and competition in artificial chemical systems. They suggest that similar processes may have played a role in the origin of life on Earth, because the earliest replication systems may have proliferated by spreading on mineral surfaces.
The figure illustrates the general scheme of the authors' procedure, which they call SPREAD (surface-promoted replication and exponential amplification of DNA analogues):
(1) A template is immobilized by an irreversible reaction with the surface of a solid support.
(2) The template binds complementary fragments from solution.
(3) The fragments are linked together by chemical ligation.
(4) The copy is released, and re-immobilized at another part of the solid support to become a template for the next cycle of steps.
Irreversible immobilization of template molecules is thus a means to overcome product inhibition.The procedure as described is highly artifical, and essentially a commercialisable process for studying molecular 'evolution'. They point out that "Solid-phase chemistry is a prerequisite for a practicable automation of the procedure, as basically pipetting and filtration steps are involved." However they speculate that "In the long run, the search for autonomous variants of SPREAD may lead to a self-sustaining chemical system capable of undergoing darwinian evolution" (italics added)
- Odessa Eliott 20 Nov 98 Thank you, Nicholas, for the summary of the article. These experiments do seem driven by the expectation of commerical applications, leading to the usual question: what company is funding the work? What surprised me was the effort to tie in the experiments to Darwinian theory. Is this de rigor for maintaining status in the academy? Surely, no parmaceutical company would care?
- Nicholas Beale 20 Nov 98 Schemes like this offer the prospect of developing lots of chemical entities which can be screened for effectiveness against targets, and you could envisage a 'darwinian' selection mechanism which helped this. Therefore it could be of great commercial interest to Pharma cos.
Nicholas Beale 22 Nov 98 Notes from Nature 19 Nov:
{a}President Clinton has expressed strong concern to the National Bioethics Advisory Commission about the implications of claims last week that researchers have created human embryonic stem cells that are part human and part cow, but he aslo asked them to review the US rules prohibting the public financing of embryo research.
{b} It turns out that in comparison with conventional high-intensity agricultural methods, 'organic' alternatives not only improve soil fertility and have fewer detrimental effects on the environment, but can also produce equivalent crop yeilds to conventional methods.
{c} A positive review of a pro-euthanasia book called Happy Endings quotes the chilling statistic that nearly 6% of all deaths in Holland are Euthanasia or Physician Assisted Suicide.
{d} A probable fragment of the meteorite which wiped out the Dinosaurs has been found. {see in this context Prof Conway Morris' remarks on are we alone?}
Steven Carr 9 Nov 98 Science, by definition, involves the view that we can only study material objects when doing science (I include energy as material of course). I can't recall my lecturers at Cambridge slipping God into their physics lectures. I'm sure that many believed in God, but science cannot study the workings of God. Nicholas Beale 9 Nov 98a Mathematicians don't study material objects, and it's very hard in practice to draw the line between Maths and Science. I'd be interested to know what 'definition' of science you are using. Remember what is written over the doors of the Cavendish. Steven Carr 9 Nov 98a Science is the study of publicly available evidence. Nicholas Beale 10 Nov 98 So historians, lawyers, pure mathematicians, Literary Critics and Biblical Scholars are all doing science?? (and BTW even if this 'definition' were correct I don't see how it follows that "Science, by definition, involves the view that we can only study material objects when doing science") Steven Carr 10 Nov 98 Historians, yes when they are disussing the evidence.
Lawyers - sometimes, although they sometimes try to ensure evidence is not publically available. I woudn't say they were good scientists, as they give a partial view.
Pure mathematicians - yes. Why ever not?
Literary Critics - No, if they say Shakespeare is a 'better' writer than Hardy. There is no publicaly available evidence which everybody, can in principle, agree shows Shakespeare to be better than Hardy.
Biblical scholars can be said to be doing science if they are discussing evidence, but not if eg, they say that monotheism is morally better than polytheism.
I'm using science in very general terms, to mean evidence that can be examined by others. Science is always restricted to material objects.
{b} Suppose you had a video of the crucifixion. What evidence on this video would show that an atonement was taking place? What would you examine to see if it was or was not happening?Nicholas Beale 10 Nov 98a {a}Pure Mathematicians are clearly not studying material objects. Nor is the notion of 'publicly available' as simple as you suggest.
{a3} Consider eg 'Shakespeare is a better writer than Hardy'. There is a great deal of publicly available evidence that could be examined to support this view. Although a determined sceptic could try to maintain the contrary, the evidence (both by looking at their work, and the work of experts in the field, and citations) is overwhelming: at least as overwhelming as the evidence that Evolution is a better theory than Special Creation.
{b} If you had a video of the experiment at CERN what evidence would you examine to show that the discovery of the W and Z particles was taking place? You would need to know a great deal of background information. It would always be conceivable that the whole thing was a sham. But you would probably say: I have good reason to believe that this is a properly set up experiment and that W and Z particles would produce phenomena like this and look - here are the phenomena.
{b1}Similarly, if I had a video of the Crucifixion I would say: I have good reason to believe that this is the Son of God and the Atonement would produce phenomena like this and look - here they are. (If indeed the events described in Luke are shown on the Video this would be rather more convincing than a set of tracks in a bubble chamber). No single piece of evidence on its own proves anything, but evidence becomes cumulatively conclusive in the presence of well-motivated theory.Steven Carr 10 Nov 98a {a}It depends what you mean by material. AsFar As I Know, triangles do not have supernatural powers. Remember, I am a constructivist when it comes to maths.
{a1} I notice you don't attempt a definition of science.
{a2} Suppose a mathematician had a divine revelation that the Riemman hypothesis is true. Would you expect other mathematicians to accept that? Mathematicians work on publicly available evidence.
{a3} Really? Surely it is a matter of taste whether or not you consider Shakespeare to be better than Hardy. What publicly available metric determines that a play is better than a novel or short story? It is like comparing apples and oranges. Some people find apples tastier, some oranges. I prefer short stories to plays. While I agree personally that S. is a better writer than H., better is a personal, not a public term.
{b}The ontological status of fundamental particles 'predicted' by our theories is very interesting. I for one don't believe W and Z are fundamental.
{b1} Really? What phenomena would you examine? Chemical composition of the blood? Tone of voice of Jesus as he said 'My God, my God why have you forsaken me'? The exact depth of the darkness?
What phenomena could be looked at? Next you'll be telling me you can get physical evidence of Jesus in the transubstantiation.
The atonement at the Crucifixion is a belief that its adherents do not belief can be detected by looking at the writing on the cross or examining the vinegar Jesus was given.
{b2}Are you saying an eclipse of the sun is a phenomenon associated with an atonement? Will an atonement take place next year on August 11th?
{b3} Apart from the small detail of Luke or Acts never saying that Jesus died 'for sin' or 'for us' or 'for you' or 'for the world' (and chopping statements like that out of Mark or Isaiah 53 when he used Mark or Isaiah 53), I'm surprised by your claim. I had no idea Christians claimed that atonement for sin was something which could be physically examined and which produced physical phenomena.Nicholas Beale 10 Nov 98b {a} 'Material' = composed of matter/energy. Clearly a mathematical object like the number 1000^(1000^1000)+1 is not 'material' - there are not enough particles in the universe.
{a2} Mathematicians don't care where they get their ideas from - the issue is whether they can then provide a convincing proof. See eg Fermat's Last Theorem for a rather extreme description of the process.
{a3} So it's a personal decision whether Evolution is a better theory than Special Creation?
{b} Whether or not W and Z are fundamental, almost all scientists would accept that the experiments performed at CERN confirmed their existence.
{b1} As I'm sure you undertand, Christians believe in the reality of the Incarnation: Jesus was physically present on earth and His life was as phyisical as yours or mine. In much the same way as, given a deep undertsanding of the underlying theory, the tracks in the bubble chamber are convincing evidence for the W and Z particles, the physical events of Jesus' death and resurrection are convincing evidence of the atonement (and much else besides). Although chemical analyses are in one way beside the point, in principle you would expect to be able to analyse Jesus' blood and find that it is real blood (and if it were fake blood coming from his side this would be strong evidence that the whole thing was a put up job) just as in principle you should be able to check chemically that the materials used in the CERN experiment are what they claim to be. Are you really telling me that if you had reliable scientific evidence that the Crucifixion and post-Resurrection appearances happened substantially as described in the Bible, you would not be a Christian?
{b2} Come off it! Would you say that every time people cheered at CERN a W or Z had been discovered?
{b3} The Atonement can no more be physically examined than the Dirac Equation, but like the Dirac Equation it has physical consequnces.Steven Carr 11 Nov 98 {a} But this number can be constructed. Can an object which can be made be described as non-material? I think I have a much wider defintion of 'material' than you do? I tend to regard 'non-material' as 'something which cannot be examined.'.
{a1} I notice that you still don't {attempt a definition of science}
{a2} A mathematician who had a revelation from God that the Riemann Hypothesis was true would not be accepted by other mathematicians, unless he could also provide evidence.
{a3} Better as in fitting more of the facts and allowing predictions to be made.(Special Creation isn't even a theory.) Not better as in appealing more to people's personal tastes.
{b1} You can analyse any crucified person and find it is real blood. So your physical criteria for an atonement is that if a crucified person has real blood, then all of humanity's sin is atoned? Surely lots of people with real blood have been crucified.
As you say chemical analyses are in one way beside the point, I take it you agree that analysis of the physical phenomena surrounding the crucifixion are just as pointless to establishing Christian belief in Jesus's atoning death on the cross, as a physical analysis of the bread and wine is pointless to establishing Christian belief in the transubstantiation (or disproving it for that matter). I had asked about the crucifixion and not the post-Resurrection appearances. Seeing somebody rise from the dead would be publically available evidence that somebody had risen from the dead. Seeing somebody crucified is not the same kind of evidence that that person's death atoned for all sin ever committed by any person, as the evidence of seeing somebody rise from the dead is evidence that somebody rose from the dead.
So you would state that eg if the saints did not rise from their graves or their was no earthquake or if the Temple curtain had not been torn at the exact moment that Jesus breathed his last, then the atonement could not have happened? I imagine not.
{b2} What physical consequences are essential to the atonement and could have been captured on video, and which are inessential?
Could a video capture the fact that someone is the Son of God?
I wonder why Luke never says Jesus died 'for sin', and why he dropped Mark 10:45.
- Steven Carr 12 Nov 98 {accidentally not posted until 19 Nov - sorry} The current issue of Astronomy quotes John Polkinghorne as saying at the Conference on Science and the Spiritual Quest at Berkeley in June 'Science is very successful because it has limited itself to a small but very interesting objective' and the author goes on to say that this objective is 'the description of physical reality.'
Nicholas Beale 14 Nov 98
{a} Ah - so conscience, and feelings, and intentions are all material.
{a1} Yes - it's not straightforward at all. I don't rule things out 'by definition' either.
{a2} A theologian who claimed he had a revelation from God would not be accepted by other theologians unless he could also provide evidence, either.
{a3} That's not what people mean when the say Shakespeare is better than Hardy either.
{b1} One of the few ways in which people can avoid the overwhelming evidence that the crucifixion and resurrection provide for the truth of the Christian Faith is to argue that Jesus did not die on the Cross. A hypothetical chemical analysis of His blood (esp after His side was pierced) would clearly be germane to this.
{b2} My criteria for 'an atonement' are that Jesus, Son of God, dies on a cross. Clearly physical evidence is easier for some parts of this than others. Understanding that Jesus is the Son of God is a deep insight - deeper even than the Dirac Equation - but it's no more completely disjoint from the world of physical experience than other deep insights are.Steven Carr 14 Nov 98 {a2} Do you accept the account of the visions of Paul in 2 Corinthians 12? Surely this claim would not be accepted unless you can also provide evidence? Surely people never give physical evidence that they have had revelations from God? Nicholas Beale 14 Nov 98a Paul's point is that the 'super-apostles' in Corinth who said they had visions did not have a monopoly in this area. Paul certainly provides a lot of evidence that he is trustworthy guide to the truth (although not infalliable). I don't say physical evidence (although stigmata may be in that category) but few Christians would doubt that St Francis had revelations from God, for example. The evidence is complex, but includes the soundness of his teaching and the blessedness of his work. Odessa Eliott 12 Nov 98
I joined this discussion after reading a note in another discussion reporting that there was a very good "science and religion" discussion group available from The Star Course's Web site.
I am puzzled by the notes that have been posted, since I joined. It appears to me that there is much confusion about what "science" is - which seems very odd, in a group that is supposed to be discussing science. Now I'm wondering just how "religion" is defined?Fr Gregory Hallam 12 Nov 98 Odessa ...
"Religion" is how a sociologist describes faith. "Science!" exclaims the layman as he peers into the lab. Polkinghorne sees beyond the lab. Feuerbach et. al. get stuck in culture. I am a very occasional contributor here. It seems to me that the ever processing circles which we all dance round each other arise from a failure to go to the heart of the matter. Rarely do we citique our OWN assumptions but, rather feel a need to defend them "to the death." A dialogue of the deaf? That doesn't mean of course that the enterprise is worthless. Perhaps we should all have more imagination ... a very dangerous thing!
Fr Gregory Hallam St. Aidan's Orthodox Church, Manchester, UKOdessa Eliott 13 Nov 98 Your observation is cogent, especially for those engaged professionally in various fields of both "hard" and "soft" science. Philosophers classically set out their assumptions as they wrote. So did theologians.
In this regard, we should consider Nicholas' point about "friends of science" not using the word "objective" in a naive way.
It has been my experience, that science-bashers are more prone to using "objective" in a naive way ... "naive" because after denying any "scientist" can be objective, they then deny the relativism underlying their own statements. But, then, I suppose that's true of most modern relativists?
How "objective" can a "scientist" be?
My example will be in zoology, the only science in which I have a smattering of "hands on" experience (as well as academic knowledge). Carefully cutting up a preserved frog was not my idea of a "fun" afternoon, so I must confess that I had a definite bias against the entire process. I also had a sheet of paper telling me what I should look for, when I managed to get the skin neatly folded back. Well, I felt somewhat better about the project when I was able to discover everything on the list. So then I began to appreciate "zoology" again... my self-confidence
having been lifted a few notches. :)
I submit that the above is a fairly widespread reaction to entry-level work in any laboratory. I also submit that there proably always will be X number of individuals who eagerly look forward to learning how to dissect animals and the organs of animals, and who (more likely than not) go on to be gifted surgeons. They were "biased" in favor of zoology all along, we might say.
PS My other laboratory experience was as a human guinea pig (earning pocket money) in J. B. Rhyne's parapsychology laboratory at Duke. What I learned from my experiences in eyelid blinking: Pavlov was right!
