Wednesday, December 06, 2006

New Research Sheds Light On Photosynthesis

New Research Sheds Light On Photosynthesis, ScienceDaily, November 28, 2006. Coal, oil or natural gas: all fossil fuels

[Graphic: Photosystem II, Imperial College London]

contain the energy of sunlight, stored with the aid of photosynthesis in energy-rich chemical compounds. A researcher at the Max Planck Institute for Bioinorganic Chemistry in Mülheim on the Ruhr working with colleagues ... has shed light on an important detail in this process. The scientists have determined the structure of the complex in photosystem II, in which water is split with the energy of sunlight. This creates, in addition to molecular oxygen, protons and electrons which in principle can be combined to create hydrogen. If it were possible to copy this process, an inexhaustible source of carbon dioxide-free energy would become available (Science, November 3, 2006). The photosystem II crystal ... is smaller than the head of a pin. ...Artificial photosynthesis could provide the energy source of the future - hydrogen. To accomplish this, however, researchers must fully understand how plants and photosynthetic microorganisms split water with the energy of sunlight - only then would they be able to copy the process one day. Together with his colleagues, Dr. Johannes Messinger has now determined the precise structure of the part of the cluster containing manganese in which water is split into its component parts. Up to now it has been technically impossible to efficiently recreate this crucial step. There are four manganese, one calcium and at least five oxygen atoms linked together in the complete cluster. "The secret is in their geometric arrangement. We discussed at least 18 models for the arrangement of just the manganese and oxygen atoms," ... With their experimental and theoretical work, the scientists have put an end for now to speculation about the correct geometrical arrangement. According to their findings, the cluster is constructed of three linked rhombi. Two of the manganese and oxygen atom rhombi share an edge, so that both one manganese and one oxygen atom have three bond partners. Another manganese atom is even surrounded by four bridging oxygen atoms as the third rhombus is attached to it. "We have also calculated the distances between the individual manganese atoms," ... Previously, scientists knew that the manganese atoms were not all separated by the same distance. The international team of researchers has now found out which manganese atoms are closer and which are further apart. Messinger and his colleagues ... used a computer to compare all the theoretically possible atom arrangements with the results of the experiments and were successful. "In the end there was only one arrangement for the four manganese atoms with the bridging oxygen atoms," said Messinger. "This takes us a crucial step further." There remain only two details to be cleared up: the new findings allow for three possibilities for the orientation of the cluster in the protein of photo system II, which gives four possible positions for the calcium. The scientists in the international group developed the EXAFS (Extended X-ray Absorption Fine Structure) measurement system further for their investigations. This determines exactly the types of atoms and the distance between them and provided them with an insight that is denied crystallographers...."We now have a structural basis with which to understand the different stages of reactions in the process that uses sunlight to split water," says Messinger. "This is an important step towards developing artificial catalysts for regenerative hydrogen production." ...

Isn't "the blind watchmaker", the "blind, unconscious, automatic process which ... has no purpose in mind. ... has no mind and no mind's eye. ... does not plan for the future. ... has no vision, no foresight, no sight at all" and "which ... is the explanation for the existence and apparently purposeful form of all life" (my emphasis) and therefore photosynthesis:

"Natural selection, the blind, unconscious, automatic process which Darwin discovered, and which we now know is the explanation for the existence and apparently purposeful form of all life, has no purpose in mind. It has no mind and no mind's eye. It does not plan for the future. It has no vision, no foresight, no sight at all. If it can be said to play the role of watchmaker in nature, it is the blind watchmaker." (Dawkins, R., "The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design," W.W. Norton & Co: New York NY, 1986, p.5)

so clever to arrange into a "crystal ... smaller than the head of a pin ...four manganese, one calcium and at least five oxygen atoms linked together in" a precise "geometric arrangement ... constructed of three linked rhombi" such that "Two of the manganese and oxygen atom rhombi share an edge, so that both one manganese and one oxygen atom have three bond partners" with "Another manganese atom ... surrounded by four bridging oxygen atoms as the third rhombus is attached to it," not to mention "the calcium" and "the distance between them"!

But I wonder what survival value "1 per cent" of this arrangement was, let alone "5 ... 6", "... 7 per cent ... and so on up the gradual, continuous series":

"In a primitive world where some creatures had no eyes at all and others had lensless eyes, the ones with lensless eyes would have all sorts of advantages. And there is a continuous series of Xs, such that each tiny improvement in sharpness of image, from swimming blur to perfect human vision, plausibly increases the organism's chances of surviving. The book [Hitching, F., "The Neck of the Giraffe," Pan: London, 1982, p.103] goes on to quote Stephen Jay Gould, the noted Harvard palaeontologist, as saying: `We avoid the excellent question, What good is 5 percent of an eye? by arguing that the possessor of such an incipient structure did not use it for sight.' [Gould, S.J., "Ever Since Darwin," Penguin: London, 1978, p.107] An ancient animal with 5 per cent of an eye might indeed have used it for something other than sight, but it seems to me at least as likely that it used it for 5 per cent vision. And actually I don't think it is an excellent question. Vision that is 5 per cent as good as yours or mine is very much worth having in comparison with no vision at all. So is 1 per cent vision better than total blindness. And 6 per cent is better than 5, 7 per cent better than 6, and so on up the gradual, continuous series." (Dawkins, Ibid., p.81).

bearing in mind that the very first living organism (e.g. a minimal single cell) would have from the beginning had to have such an irreducibly complex system which is analogous to a "Rube Goldberg machine"

[Graphic: Photosynthesis Analogy, Berkeley University]

for collecting and transducing external physical (solar) or chemical energy into biological "energy-rich chemical compounds" (e.g. sugar)?

And, as ID theorist Neil Broom, an Associate Professor in the Department of Chemical and Materials Engineering at the University of Auckland, outlines, "the reaction center of photosystem II" is just a part of "photosynthesis" which ... is the biological equivalent of `Russian nesting dolls' ... machinery ... literally made up of systems within systems" which "modern science has been" highly successful "in providing a detailed understanding, at a molecular level" of such "physical and chemical processes that are utilized in the living world" but in the "example of the plant's photosynthetic machinery, we find that modern mechanistic science is strangely silent on how this sophisticated biological system might have originated" (my emphasis)!:

"But for now let's consider the familiar example of photosynthesis. This is just one of the many truly remarkable life-supporting innovations that lie at the heart of the living world. The immensely sophisticated living machinery that is used to carry out photosynthesis in the plant world is the biological equivalent of `Russian nesting dolls.' This machinery is literally made up of systems within systems, starting at the level of the plant leaf ... and extending right down to the subatomic world of the electron. So let me try to explain it in a little more detail. Photosynthesis takes place in seemingly insignificant microscopic bodies called chloroplasts ... that are present in the cells within the interior of the leaf and that account for its green color. Within these chloroplasts there are special membranes stacked in parallel layers known as grana and visible only at very high magnification under the electron microscope .... Embedded within these membranes is the very heart of the photosynthetic machinery - complex clusters of pigmented molecules that are able to collect sunlight. These light-harvesting units consist of a special chlorophyll molecule termed the `reaction center,' surrounded by several hundred `antenna' pigment molecules that include both chlorophyll and carotenoid molecules. [Graphic: Photosystem antennae linked to reaction centre, Prof. Ed Klekowski, University of Massachusetts] Collectively this combination of specialized light-reacting molecules is known as a `photosystem' .... The chlorophylls absorb the light of red and blue wavelengths while reflecting the green portion of the spectrum, whereas the carotenoid molecules absorb the blue and green wavelengths and reflect the yellow, orange and red. Sunlight is absorbed by the layer of antenna pigment This oxygen is released into the atmosphere while the hydrogen ions or protons pass into the fluid space enclosed by the tiny membrane surfaces ... Let us now follow the journey of an electron that has left the reaction center of photosystem II .... After its reception by an acceptor molecule, it is passed down a voltage `staircase,' or gradient of precisely arranged molecules called the electron transport system, ending up in the positively charged reaction center of photosystem I where it makes up for the electron deficit also created by the excitation process. The original electron that was excited from photosystem I is received by its own acceptor molecule and then passes down another electron transport system. The energy given up by the electron in its passage down this `staircase' is used to form an energy-transacting molecule biologists abbreviate as NADPH, which drives important energy-storing reactions elsewhere in the cell. The action of both photosystems produces a buildup of protons with a higher concentration on one side of the special membranes in the grana than on the other. It is this proton gradient that is used to power the production of another important energy-transacting molecule called ATP .... Both molecules, NADPH and ATP, although they cannot be stored in the cell's energy bank, are used by the cell to produce energy-rich sugars that can be transported as required to different parts of the cellular factory, or stored as starch. ... This vastly incomplete description of just some of the principal mechanisms known to be involved in photosynthesis serves to illustrate just how successful modern science has been in providing a detailed understanding, at a molecular level, of the physical and chemical processes that are utilized in the living world. ... Continuing with our example of the plant's photosynthetic machinery, we find that modern mechanistic science is strangely silent on how this sophisticated biological system might have originated. Textbooks typically describe the chloroplast as having evolved from some simpler organism employing a metabolic system that might have been able to produce the first oxygen from an oxygenless early earth atmosphere. Apart from rather vague comments like these, there is little serious discussion of the chloroplast's origin. Photosynthesis is in fact the ultimate energy source of almost all living things known to us today, and its origin is just part of the much more fundamental question of how life began in the first place. ... I would suggest that any attempt to provide an explanation for the existence of a biological system such as the chloroplast based on the impersonal material laws of nature is doomed to failure." (Broom, N., "How Blind is the Watchmaker?: Nature's Design & the Limits of Naturalistic Science," [1998], InterVarsity Press: Downers Grove IL, Second Edition, 2001, pp.35-39).

Stephen E. Jones, BSc (Biol).

Genesis 21:1-7. 1Now the LORD was gracious to Sarah as he had said, and the LORD did for Sarah what he had promised. 2Sarah became pregnant and bore a son to Abraham in his old age, at the very time God had promised him. 3Abraham gave the name Isaac to the son Sarah bore him. 4When his son Isaac was eight days old, Abraham circumcised him, as God commanded him. 5Abraham was a hundred years old when his son Isaac was born to him. 6Sarah said, "God has brought me laughter, and everyone who hears about this will laugh with me." 7And she added, "Who would have said to Abraham that Sarah would nurse children? Yet I have borne him a son in his old age."

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