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Origin and evolution of photosynthesis

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1 Origin and evolution of photosynthesis on Sat Mar 01, 2014 3:36 pm

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Origin and evolution of photosynthesis

http://www.genome.jp/kegg/pathway/map/map00195.html

The existence in the same organism of cyanobacterias of two conflicting metabolic systems, oxygen evolving photosynthesis and oxygen-sensitive nitrogen fixation, is a puzzling paradox. Explanations are pure guesswork.

Researchers have long been puzzled as to how the cyanobacteria could make all that oxygen without poisoning themselves. To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet? The explanations are fantasious at best

If there was a reduced atmosphere without oxygen some time back in the past ( which btw. there is no scientific evidence for, rather the oposit is the case ) then there would be no ozone layer, and if there was no ozone layer the ultraviolet radiation would penetrate the atmosphere and would destroy the amino acids as soon as they were formed. If the Cyanobacterias however would overcome that problem ( its supposed the bacterias in the early earth lived in the water, but that would draw other unsurmountable problems ), and evolve photosynthesis, they would have to evolve at the same time protective enzymes that prevented them oxygen to damage their DNA through hydroxyl radicals. So what evolutionary advantage would there be they to do this ?

Cyanobacteria are the prerequisite for complex life forms. They are said to exist already 3,5 bio years, and did not change morphologically. They do oxygenic photosynthesis, where the energy of light is used to split water molecules into oxygen, protons, and electrons. It occurs in two stages. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP and NADPH. During the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide.

They have ATP synthase nano-motors. How could ATP synthase “evolve” from something that needs ATP, manufactured by ATP synthase, to function? Absurd “chicken-egg” paradox!

In photosynthesis , 26 protein complexes and enzymes are required to go through the light and light independent reactions, a chemical process that transforms sunlight into chemical energy,  to get glucose as end product , a metabolic intermediate for cell respiration. The protein complexes are uniquely used in photosynthesis. The pathway must go all the way through, and all steps are required, otherwise glucose is not produced. Also, in the oxygen evolving complex, which splits water into electrons, protons, and CO2, if the light-induced electron transfer reactions do not go all the five steps through, no oxygen, no protons and electrons are produced, no advanced life would be possible on earth. So, photosynthesis is a interdependent system, that could not have evolved, since all parts had to be in place right from the beginning. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.

The American astronomer George Greenstein discusses this in The Symbiotic Universe, p 96:
Chlorophyll is the molecule that accomplishes photosynthesis... The mechanism of photosynthesis is initiated by the absorption of sunlight by a chlorophyll molecule. But in order for this to occur, the light must be of the right color. Light of the wrong color won't do the trick.
A good analogy is that of a television set. In order for the set to receive a given channel it must be tuned to that channel; tune it differently and the reception will not occur. It is the same with photosynthesis, the Sun functioning as the transmitter in the analogy and the chlorophyll molecule as the receiving TV set. If the molecule and the Sun are not tuned to each other-tuned in the sense of colour- photosynthesis will not occur. As it turns out, the sun's color is just right.

One might think that a certain adaptation has been at work here: the adaptation of plant life to the properties of sunlight. After all, if the Sun were a different temperature could not some other molecule, tuned to absorb light of a different colour, take the place of chlorophyll? Remarkably enough the answer is no, for within broad limits all molecules absorb light of similar colours. The absorption of light is accomplished by the excitation of electrons in molecules to higher energy states, and the same no matter what molecule you are discussing. Furthermore, light is composed of photons, packets of energy and photons of the wrong energy simply can not be absorbed… As things stand in reality, there is a good fit between the physics of stars and that of molecules. Failing this fit, however, life would have been impossible.

The harmony between stellar and molecular physics that Greenstein refers to is a harmony too extraordinary ever to be explained by chance. There was only one chance in 1025 of the Sun's providing just the right kind of light necessary for us and that there should be molecules in our world that are capable of using that light. This perfect harmony is unquestionably proof of Creation.

http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway
http://www.uncommondescent.com/intelligent-design/is-photosynthesis-irreducibly-complex/

Robert Blankenship, professor of biochemistry at Arizona State University

“The process of photosynthesis is a very complex set of interdependent metabolic pathways. How it could have evolved is a bit mysterious.”

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eigth last steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise chlorophyill is not synthesized.
Therefore, the Chlorophyill biosynthesis pathway is irreducible complex.


Evolution of photosynthetic pathways


Well, what i see, is a lot of guesswork, like probably, indicates,speculated, presumed, may explain, suggests, supposes, seem to have,

These two pathways, with the same effect on RuBisCO, evolved a number of times independently – indeed, C4 alone arose 62 times in 18 different plant families.

Well, if the evolution of just one time would be a unsurmountable problem, imagine 62 times...... why and how would it do so ??!!

So not much more than vague and superficial speculation is provided.

http://www.ps-19.org/Crea06EcoSys/index.html

According to an analysis of the cyanobacterial genome (Hasselkorn and Johnston (PNAS)) the earliest cyanobacteria already had the light & Calvin processes for photosynthesis in place. These are two very complex and subtly linked processes and involve many specialized molecules working together. These are such complex biological processes, that the complexity and early appearance on earth seems to indicate planning and design.

Biologists universally (as far as I am aware) point to the complexity and the similarity of photosynthesis among all species to imply that the process evolved only once in earth's history[FOOTNOTE: for example, Schopf p. ???; other references] -- the chance events that had to occur for photosynthesis to arise even once by natural processes are vanishingly low probability, so that assuming the same system would arise more than once defies even an evolutionist's credulity.

Evolution of photosynthesis

The biochemical capacity to use water as the source for electrons in photosynthesis evolved once, in a common ancestor of extant cyanobacteria. The geological record indicates that this transforming event took place early in Earth's history, at least 2450–2320 million years ago (Ma), and, it is speculated, much earlier.[2][3] Available evidence from geobiological studies of Archean (>2500 Ma) sedimentary rocks indicates that life existed 3500 Ma, but the question of when oxygenic photosynthesis evolved is still unanswered.

http://dippost.com/2014/03/22/wolf-ekkehard-lonnig-complex-systems-in-biology-overwhelmingly-point-to-an-intelligent-origin-of-living-beings/

Photosynthesis is a mind-blowing phenomenon that is another example of irreducible complexity which also points to an intelligent design:  “In my mutation experiments I detected hundreds of totally white seedlings where usually one individual mutation alone, most often at different sides in different plant families, stopped the entire system from functioning at all (reminds, of course of  Behe’s definition of “the removal of any one of the parts causes the system to effectively cease functioning”.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949000/

The evolutionary origin of the oxygen evolving center has long been a mystery. Several sources have been suggested, but so far no convincing evidence has been found to resolve this issue

http://www.life.illinois.edu/govindjee/Part3/31_John_Olson.pdf
http://www.ncbi.nlm.nih.gov/pubmed/23258841
http:/Timeline_of_evolutionary_history_of_life

for the last 3.6 billion years, simple cells (prokaryotes);
for the last 3.4 billion years, cyanobacteria performing photosynthesis;

When did oxygenic photosynthesis evolve?
Abstract

The atmosphere has apparently been oxygenated since the ‘Great Oxidation Event’ ca 2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event. Fluid-inclusion oils in ca 2.45 Ga sandstones contain hydrocarbon biomarkers evidently sourced from similarly ancient kerogen, preserved without subsequent contamination, and derived from organisms producing and requiring molecular oxygen. Mo and Re abundances and sulphur isotope systematics of slightly older (2.5 Ga) kerogenous shales record a transient pulse of atmospheric oxygen. As early as ca 2.7 Ga, stromatolites and biomarkers from evaporative lake sediments deficient in exogenous reducing power strongly imply that oxygen-producing cyanobacteria had already evolved. Even at ca 3.2 Ga, thick and widespread kerogenous shales are consistent with aerobic photoautrophic marine plankton, and U–Pb data from ca 3.8 Ga metasediments suggest that this metabolism could have arisen by the start of the geological record. Hence, the hypothesis that oxygenic photosynthesis evolved well before the atmosphere became permanently oxygenated seems well supported.

Photosynthesis tree
Inferences Based on the Observed Branching Order

Earliest Branching Photosynthetic Bacteria

The Genome of Heliobacterium modesticaldum, a Phototrophic Representative of the FirmicutesContaining the Simplest Photosynthetic Apparatus  1

Firmicutes (Heliobacterium) are indicated to be earliest branching photosynthetic bacteria. The ancestral nature of this group is also supported by a number of other observations:



Diagram showing a putative pathway of electron transfer based on genetic components present in H. modesticaldum. Cyclic electron transfer has not been confirmed in heliobacteria. In addition, the reduction of NAD+ by cytoplasmic ferredoxin has not been confirmed, as a gene encoding FNR was not identified in the genome. Despite this, genes encoding all 14 subunits of NADH:quinone oxidoreductase (nuoA to nuoN) were putatively identified.





   Unlike other photosynthetic bacteria, both antenna and reaction center activities are present within a single protein in Heliobacteria;
   The reaction center complex in Heliobacteria (and also green sulfur bacteria) has a simpler homodimeric structure as opposed to being heterodimeric in other photosynthetic bacteria;
   The RC in Heliobacteria contains a unique photosynthetic pigment Bchl g, which is indicated to be primitive in comparison to the pigments found in other photosynthetic organisms.
   Of the different photosynthetic bacteria, only Heliobacteria are bounded by a single unit lipid membrane (monoderm cell structure), which is indicated to be an ancestral characteristic in comparison to the cells containing both an inner and outer cell membranes (Diderm cell structure).

2. The Second Photosynthetic Bacteria

Following Heliobacteria, Chloroflexi are indicated to be the next group of photosynthetic organisms that branched off from the common ancestor. The branching of both Heliobacteria and Chloroflexi prior to Cyanobacteria provides evidence that both RC-1 and RC-2 had already evolved prior to the emergence of Cyanobacteria, which contain both of these reactions centers linked to each other.

3. Anoxygenic Photosynthesis vs Oxygenic Photosynthesis

The bacterial groups utilizing anoxygenic photosynthesis mode evolved much earlier than those capable of oxygenic photosynthesis. This is in accordance with the observation that change in atmosphere from anoxygenic to oxygenic occurred much later (between 1.5-2 billion year) after the evolution of earlier organisms. This observation indicates that the earlier prokaryotic fossils probably do not correspond to Cyanobacteria but some other groups of photosynthetic bacteria.

4. Later Branching Photosynthetic Bacteria

The later branching photosynthetic phyla which contain either one or both of these RCs could have acquired such genes from the earlier branching lineages by either direct descent or by means of lateral gene transfer.

5. Speculations About the Earliest Organism

The presence of photosynthetic ability in the earliest branching bacterial phylum indicates that photosynthesis evolved very early in evolution and it is possible that the earliest organism that evolved were photosynthetic.


Early photosynthetic systems, such as those from green and purple sulfur and green and purple nonsulfur bacteria, are thought to have been anoxygenic, using various molecules as electron donors. Green and purple sulfur bacteria are thought to have used hydrogen and sulfur as an electron donor.

http://www.fceqyn.unam.edu.ar/~celular/paginas/Articulos%20Biol%20Cel%202004/Annual%20Reviews/Review%20photosyntesis.pdf

The evolutionary path of type I

And type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits.
http://www.javeriana.edu.co/Facultades/Ciencias/neurobioquimica/libros/metabolismo/metabolismo_archivos/Evolution%20of%20Photosynthesis.pdf

One of the main reasons for interest in Chloroflexus aurantiacus is in the study of the evolution of photosynthesis. As terrestrial mammals, we are most familiar with photosynthetic plants such as trees. However, photosynthetic eukaryotes are a relatively recent evolutionary development. Photosynthesis by eukaryotic organisms can be traced back to endosymbiotic events in which non-photosynthetic eukaryotes internalized photosynthetic organisms. The chloroplasts of trees still retain their own DNA as a molecular remnant that indicated their origin as photosynthetic bacteria.

The "respiration early" hypothesis

How did photosynthesis arise in bacteria? The answer to this question is complicated by the fact that there are several types of light-harvesting energy capture systems. Chloroflexus aurantiacus has been of interest in the search for origins of the so-called type II photosynthetic reaction center. One idea is that bacteria with respiratory electron transport evolved photosynthesis by coupling a light-harvesting energy capture system to the pre-existing respiratory electron transport chain. Thus, rare organisms like Chloroflexus aurantiacus that can survive using either respiration or photosynthesis are of interest in on-going attempts to trace the evolution of photosynthesis.

The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids

Self-organizing biochemical cycles
http://www.pnas.org/content/97/23/12503.full.pdf

One could summarize the work of Ferris and colleagues by saying that montmorillonite clays catalyze the oligomerization of nucleoside -phosphorimidazolides and modify the ratio of 2 phosphodiester bonds that are formed without greatly changing the regiospecificity of the reactions. The specificity of the formose reaction is not increased by catalysis on hydroxylapatite or other minerals (23). Similar conclusions can be drawn from the work of Arrhenius and his colleagues (27), who find that a number of inorganic layer hydroxides catalyze the dimerization of glycolaldehyde phosphate and modify the ratio of threose 2,4-bisphosphates to erythrose 2,4-bisphosphates in the products, but without greatly increasing the regiospecificity of the reaction.

Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life
J. P. Ferris (2006)

https://www.rpi.edu/dept/cogsci/yesterday/chem/chem_faculty/profiles/pdfs/ferris/Joshi_Homochiral_Chem_Com_2000.pdf
https://www.academia.edu/3742566/Photosynthesis_and_the_Origin_of_Life

PHOTOSYNTHESIS AND THE ORIGIN OF LIFE

HYMAN HARTMAN
IASB, 880 Spruce St., Berkeley, CA 94707, U.S.A.
(Received 30 August, 1996)
Abstract.
The origin and evolution of photosynthesis is considered to be the key to the origin of life. This eliminates the need for a soup as the synthesis of the bioorganics are to come from the fixation of carbon dioxide and nitrogen. No soup then no RNAworld or Protein world. Cyanobacteria have been formed by the horizontal transfer of green sulfur bacterial photoreaction center genesby means of a plasmid into a purple photosynthetic bacterium. The fixation of carbon dioxide isconsidered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus) which was thenfollowed by a reductive tricarboxylic acid cycle (Chlorobium) and finally by the reductive pentosephosphate cycle (Calvin cycle). The origin of life is considered to have occurred in a hot springon the outgassing early earth. The first organisms were self-replicating iron-rich clays which fixedcarbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and theirmetabolic phenotype then evolved into the sulfide rich region of the hotspring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoesis, then the synthesis of aminoacids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acidesters by polynucleotides. Thus the origin and evolution of the genetic code is a late development and records the takeover of the clay by RNA.

Introduction

The major premise which underlies the field of either the ‘RNA world’ or the ‘Proteinoid world’ is the prior existence of a soup of monomers consisting of sugars, pyrimidine and purine bases and amino acids. In the old conundrum asto which came first the chicken (protein) or the egg (RNA), the answer is the chicken soup (of monomers). The major premise of this paper is that the soup is a hypothetical construct.  

In the absence of a soup the carbon entering the biosphere is in the form of carbon dioxide, the nitrogen is in the form of nitrogen gas, the hydrogen andoxygen enter the biosphere in the form of liquid water, the sulfur in the form of sulfide ion and the phosphate in the form of the phosphate ion.

The early atmosphere of the earth is considered to have been neutral (nitrogen and carbon dioxide). The problem arises of how oxygenic photosynthesis could have evolved under these conditions.There were abundant reducing agents such asferrous ion which made it unlikely that water would be used as an electron donor.It was thus suggested ‘that atmospheric hydrogen peroxide played a key role in inducing oxygenic photosynthesis because asperoxide increased in a localenvironment, organisms would not only be faced with a loss of reductant, but they would also be pressed to develop the biochemical apparatus (e.g., catalase) that would be ultimately be needed to protect against the products of oxygenic photosynthesis. This scenario allows for the early evolution of oxygen photosynthesis while global conditions were still anaerobic’ (McKay and Hartman, 1991).

Oxygenic photosynthesis developed in the cyanobacteria.The earliest bacterial fossils are found in the 3.5billion year old stromatolites of Western Australia. These fossil bacteria resemble cyanobacteria (Awramik, 1992).One possible conclusion from the ancient stromatolites and the bacterial fossils is that oxygenic photosynthesis was being carried out by the cyanobacteria 3.5billionyears ago.The cyanobacteria have two reaction centers; photosystem I and photosystem II. This is in contrast with the purple and the green photosynthetic bacteria which have only one reaction center. The purple bacteria have a pheophytin-quinone reaction center which is related to photosystem II. The green sulfur bacteria havea Fe-S reaction center which is related to photosystem I. ‘The simplest scenario giving rise to the linked photosystems found in oxygen-evolving organisms is that some sort of genetic fusion event took place between two bacteria, one with apheophytin-quinone reaction center and the other with an Fe-S reaction center.This produced a chimeric organism with two unlinked photosystems. Subsequently, the two photosystems were linked, and the oxygen evolving system added ’(Blankenship, 1992).

What is the origin of plastids ?
http://www.evolutionnews.org/2012/03/seeking_the_lin057151.html

Price et al. look at plastids that were supposedly derived from cyanobacteria. These plastids all contain certain features that are similar to cyanobacteria, and those organisms that contain them are therefore thought to be along the same phylogenetic lineage. They include Glaucophyta, Rhodophyta, and green algae, along with their plant descendants.

 These three lineages are postulated to form the monophyletic group Plantae (or Archaeplastida), a hypothesis that suggests the primary cyanobacterial endosymbiosis occurred exclusively in their single common ancestor.

Unfortunately, as the authors point out, phylogenies based on other features, such as genetics, do not support the cyanobacteria- and plastid-derived phylogeny.

http://www.plantcell.org/content/25/1/4.abstract

The idea of an endosymbiotic origin of plastids has become incontrovertible, but many important aspects of plastid origins remain obscured in the mists of more than a billion years of evolutionary history

Endosymbiosis is now a well substantiated theory that explains how cells gained their great complexity and was made famous most recently by the work of the late biologist Lynn Margulis, best known for her theory on the origin of eukaryotic organelles.

In a paper "Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants" that appeared this week in the journal Science, an international team led by evolutionary biologist and Rutgers University professor Debashish Bhattacharya has shed light on the early events leading to photosynthesis, the result of the sequencing of 70 million base pair nuclear genome of the one-celled alga Cyanophora.

Thinking about the evolution of photosynthesis


There are two schools of thought concerning the origin of reaction
centers and photosynthesis. One school pictures the evolution of
reaction centers beginning in the prebiotic phase
while the other school sees reaction centers evolving later from cytochrome b
in bacteria. Two models have been put forth for the subsequent evolution
of reaction centers in proteobacteria, green filamentous (non-sulfur) bacteria,
cyanobacteria, heliobacteria and green sulfur bacteria. In the selective loss model the most recent common ancestor
of all subsequent photosynthetic systems is postulated to have contained both RC1 and RC2. The evolution of
reaction centers in proteobacteria and green filamentous bacteria resulted from the loss of RC1, while the evolution
of reaction centers in heliobacteria and green sulfur bacteria resulted from the loss of RC2. Both RC1 and RC2
were retained in the cyanobacteria. In the fusion model the most recent common ancestor is postulated to have
given rise to two lines, one containing RC1 and the other containing RC2. The RC1 line gave rise to the reaction
centers of heliobacteria and green sulfur bacteria, and the RC2 line led to the reaction centers of proteobacteria
and green filamentous bacteria. The two reaction centers of cyanobacteria were the result of a genetic fusion of
an organism containing RC1 and an organism containing RC2. The evolutionary histories of the various classes
of antenna/light-harvesting complexes appear to be completely independent. The transition from anoxygenic to
oxygenic photosynthesis took place when the cyanobacteria learned how to use water as an electron donor for
carbon dioxide reduction. Before that time hydrogen peroxide may have served as a transitional donor, and before
that, ferrous iron may have been the original source of reducing power.


This hypothesis answers the problem of how
biosynthetic pathways to complex products could have
evolved by random mutation. The pathway is built
forward with each step fulfilling a useful function,
eventually to be replaced by the next step selected for
improved utility. Olson and Pierson (1987a, b) used the Granick
hypothesis to construct a hypothetical evolutionary
history of RCs from the biosynthetic pathways of Chl
a and BChla . They proposed that protochlorophyll
a might have functioned in a primitive RC at some time
before Chla existed, and that protoporphyrin IX and
Mg protoporphyrin IX might have served as RC pig-
ments before protochlorophyll a existed. In agreement
with Mauzerall (1978), Olson (1970, 1981) had previ-
ously interpreted the biosynthetic pathway of BChl
a to indicate that Chla had appeared before BChl a
in evolutionary history.

The nature of the ancient reductase that predated the
gene duplication is not known, but typically ancient
enzymes are both less specific and less efficient than
modern enzymes (Benner 2002).

Reaction centers

The evolution of photosynthesis begins with the evo-
lution of photochemical reaction centers (RCs). Two
schools of thought exist concerning the origin of
RCs and photosynthesis. The first school pictures the
evolution of RCs/photosynthesis beginning in the pre-
biotic phase (e.g., Mauzerall 1992; Hartman 1998)
whereas the second school sees RCs and photosyn-
thesis evolving much later from anaerobic respiration
in Bacteria (eubacteria) containing DNA, electron-
transport proteins, and ATP synthase (e.g., Meyer et al.
1996; Nitschke et al. 1998). The first school envi-
sions the evolution of photosynthesis and the origin
of life to be tightly intertwined; the second school
sees the origin of photosynthesis coming much later
than the appearance of the common ancestor of all
life. According to this view photosynthesis arose in
the Bacteria after they had separated from the Archaea
(archaebacteria).

378
Figure 2.
Hypothetical history of reaction center evolution based on protein homology.
See text for details. (Reprinted with permission of Data
Trace Publishing Company. Chemtracts Biochem Mol Biol 12: 468–482, © 1999.)

all disagree with Olson and Pierson (1987a,
b) in one fundamental aspect. They propose that RC1
and RC2 evolved independently in different organ-
isms, and then were brought together in one organism
by genetic fusion to produce the cyanobacterial line
of photosynthesis with two photosystems in series.
Mathis (1990) proposed an evolutionary tree in which
genes for RC1 were transferred from a ‘heliobac-
terium’ to the genome of a ‘purple bacterium’ already
possessing genes for RC2. The resulting fusion be-
came the forerunner of the cyanobacteria. Blankenship
(1992) proposed that the ancestral RC evolved in two
directions simultaneously as shown in Figure 4. One
direction led to the evolution of RC2, and the other
direction led to RC1.


Antennas
LH1 and LH2 antenna complexes


Since both peptides are similar to helix D of subunit L
(bacterial RC2), the presumed ancient single helix or
homodimeric antenna complex may have been derived
from helix D of an ancient subunit L (Mulkidjian and
Junge 1997).

Phycobilisomes

Cyanobacteria and red algae contain supramolecu-
lar light-harvesting complexes called phycobilisomes,
that are attached to the stromal side of the photo-
synthetic membrane (Blankenship 2002). These com-
plexes can transfer excitation energy to the core
complex (CP43, CP47 and RC2) with more than
95% efficiency. The phycobilisomes consist of related
pairs of α and β phycobiliproteins (allophycocyanin,
phycocyanin and sometimes phycoerythrocyanin and
phycoerythrin). The phycobiliproteins are pigment
proteins that have evolved by multiple gene duplica-
tions and divergences from an ancestral form that
could form short rods (Grossman et al. 1995).

The most widespread source of reducing power in
late Archean and early Proterozoic (2.9–1.6 Ga) sea-
water was ferrous iron (0.1–1.0 mM) (Walker 1983),
and several authors (Olson 1978; Cohen 1984; Olson
and Pierson 1987a; Pierson and Olson 1989) proposed
that ferrous iron may have been an early electron
donor to PS II. The common ancestor of proteobacteria
and cyanobacteria might well have used Fe(OH)
+ as the principal electron donor for CO 2
fixation (Widdle et al. 1993; Ehrenreich and Widdle 1994; Heising
and Schink 1998). Because contemporary green sul-
fur bacteria utilize Fe(OH) +
rather poorly (Heising et al. 1999), one of us (Olson 2001) proposed that
the driving force for the evolution of RC2 in addi-
tion to RC1 was the necessity to utilize Fe(OH)
+ effectively for CO 2 fixation in the absence of reduced
sulfur compounds. However, some contemporary pro-
teobacteria can utilize Fe(OH) + for CO 2 fixation with
RC2 alone (Widdle et al. 1993; Ehrenreich and Widdle
1994).

Concluding remarks

This paper traces the history of thinking on how
photosynthesis originated and developed, from primit-
ive cells through anoxygenic photosynthetic bacteria,
through cyanobacteria and eventually to chloroplasts.
It is now clear that earlier attempts to reconstruct ‘the
path’ of evolutionary development were doomed to
failure. There have been many such paths that different
parts of the photosynthetic apparatus have followed,
which have not been the same in either of two classes
of organisms or even in different parts of the same
organism. Thus there is not one linear path that was
followed. The much more complex and non-linear
history that has taken place is challenging and inter-
esting to unravel, and will undoubtedly keep scientists
occupied for at least another 30 years


Captured, the moment photosynthesis changed the world

BILLIONS of years ago, a tiny cyanobacterium cracked open a water molecule - and let loose a poison that wrought death and destruction on an epic scale. The microbe had just perfected photosynthesis, ( amazing, how did it figure out that little trick ? ) a process that freed the oxygen trapped inside water and killed early Earth's anaerobic inhabitants.

Now, for the first time, geologists have found evidence of the crucial evolutionary stage just before cyanobacteria split water. The find offers a unique snapshot of the moment that made the modern world. With the advent of photosynthesis came an atmosphere dominated by oxygen and, ultimately, the diversity of life forms that we know today.

"This was the biggest change that ever occurred in the biosphere," says Kevin Redding at Arizona State University in Tempe. "The extinction caused by oxygen was probably the largest ever seen, but at the same time animal life wouldn't be possible without oxygen."

Photosynthesis uses light and a source of electrons to generate energy and power an organism. In the world as we know it, that source of electrons is water, with oxygen the waste product. But there are no signs that oxygen was being formed when photosynthesis first appeared around 3.4 billion years ago, so early photosynthesisers ( how did they come to be ? thats finally what we would like to know )  probably ( oh, so they don't know for sure ) scavenged electrons by splitting other molecules like hydrogen sulphide instead.

That had changed by about 2.4 billion years ago, when deposits of oxidised minerals tell us that oxygen was beginning to accumulate in the atmosphere. Photosynthesis as we know it had evolved.
( how do we know it evolved ?? )
To help work out how this happened, Woodward Fischer at the California Institute of Technology in Pasadena and his colleagues studied South African rocks that formed just before the 2.4-billion-year mark. Their analysis shows that although the rocks formed in the anoxic conditions that had prevailed since Earth's formation, all of the manganese in the rock was deposited in an oxidised form.

In the absence of atmospheric oxygen, manganese needs some sort of catalyst to help it oxidise - it won't react without a bit of help. The best explanation, say Fischer's team, is that a photosynthetic organism was using manganese as an electron source. That left unstable manganese ions behind, which reacted with water to form the oxides. Fischer presented the findings at the American Geophysical Union's conference in San Francisco on 6 December.

Every researcher contacted by New Scientist has hailed the significance of the study, in part because the evidence exactly matches what evolutionary theories have predicted.

A close look at today's plants and algae shows that manganese oxidation is still a vital part of photosynthesis. Within their photosynthetic structures are manganese-rich crystals that provide the electrons to drive photosynthesis. The crystals then snaffle electrons from passing water molecules to restore their deficit. It is this electron raid that cracks open water molecules and generates the oxygen we breathe.

This complicated process must have had simpler roots. In 2007, John Allen at Queen Mary, University of London, and William Martin at the University of Düsseldorf, Germany, suggested one scenario (Nature, doi.org/bs65kb).
They believe that modern photosynthesis was born when early cyanobacteria by chance floated into a watery environment rich in manganese, and quickly adapted to take advantage of the new source of electrons.

They adapted ?? How did that happen ?

Later, because manganese is a relatively scarce resource that can't be tapped indefinitely, the cyanobacteria evolved a different strategy. They incorporated manganese directly into their photosynthetic structures ( i have still not seen a explanation of how photosynthesis evolved in them )


and used it as a rechargeable battery: draining it of its electrons, but allowing its supplies to be replenished by stealing electrons from another, more plentiful source - water.

What Fischer's team has found is evidence of the initial step in this process: an anoxic environment rich in manganese that has been stripped of electrons and left in an oxidised state, almost certainly by primitive cyanobacteria. "There had to be some intermediate step in the evolutionary process," says Redding.

"This is big news," says Martin. He adds that we can expect publications in the near future that provide more evidence compatible with the theory. "But this somewhat more direct geochemical evidence is really exciting."

SO , THAT ARE ALL UNSUPPORTED CLAIMS, AD HOC EXPLANATIONS WITHOUT EXPERIMENTAL EVIDENCE WHATSOEVER, AND NEIThER DETAILED EXPLANATIONS HOW THE EVOLUTIONARY PROCESS OF PHOTOSYNTHESIS HAPPENED....

What was a simpler version of oxygen-producing photosynthesis,  and how did it evolve to what we have today?  What came first, the assembly factors of PSII, or PSII? the repair mechanism of D1 subunit, or the D1 subunit? And how was the assembly process and sequence, and repair sequence programmed? trial and error?

1) http://jb.asm.org/content/190/13/4687.full



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2 Early evolution of photosynthesis on Sat Mar 01, 2014 3:39 pm

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Early Evolution of Photosynthesis

http://reasonandscience.heavenforum.org/t1545-origin-and-evolution-of-photosynthesis#2303

When opponents of special creation asked about how photosynthesis arised, they often make a quick web search, come up with the first search result which looks like a " serious " scientific paper, which explains how photosynthesis evolved, and post it as a answer. When asked to quote the relevant part of the paper, which convinced them evolution were the best answer, commonly they don't  answer, because they did not make the effort to analise carefully the proposed evidence. That shows nicely their confirmation bias. They determined already evolution must be true, since it fits their preconceived and wished world view, so all they do, is to try to fit everything they find into their naturalistic world view, without carefully looking if the evidence is compelling. Well, the following paper is a perfect example of how methodological naturalism works, and obliges specially historical sciences to wear blinkers.  Since evolution is the only naturalistic possible explanation for the biodiversity on earth, evolution is supposed to be the answer right from the beginning, rather to start with a agnostic standpoint , and after careful examination, permitting the evidence to lead wherever it is, and  propose evolution as the best explanation if that is the outcome that fits best.

http://www.plantphysiol.org/content/154/2/434.full

Photosynthesis is the only significant solar energy storage process on Earth and is the source of all of our food and most of our energy resources. An understanding of the origin and evolution of photosynthesis rather than start with a agnostic position, they assume already evolution. Thats begging the quesion......  is therefore of substantial interest, as it may help to explain inefficiencies in the process and point the way to attempts to improve various aspects for agricultural and energy applications.

A wealth of evidence indicates that photosynthesis is an ancient process that originated not long after the origin of life and has evolved via a complex path to produce the distribution of types of photosynthetic organisms and metabolisms that are found today (Blankenship, 2002; Björn and Govindjee, 2009). Figure 1 shows an evolutionary tree of life based on small-subunit rRNA analysis. Of the three domains of life, Bacteria, Archaea, and Eukarya, chlorophyll-based photosynthesis has only been found in the bacterial and eukaryotic domains. The ability to do photosynthesis is widely distributed throughout the bacterial domain in six different phyla, with no apparent pattern of evolution. Photosynthetic phyla include the cyanobacteria, proteobacteria (purple bacteria), green sulfur bacteria (GSB), firmicutes (heliobacteria), filamentous anoxygenic phototrophs (FAPs, also often called the green nonsulfur bacteria), and acidobacteria (Raymond, 2008). In some cases (cyanobacteria and GSB), essentially all members of the phylum are phototrop2hic, while in the others, in particular the proteobacteria, the vast majority of species are not phototrophic.

Overwhelming evidence indicates that eukaryotic photosynthesis originated from endosymbiosis of cyanobacterial-like organisms, which ultimately became chloroplasts (Margulis, 1992). what evidence ?      So the evolutionary origin of photosynthesis is to be found in the bacterial domain. Significant evidence indicates that the current distribution of photosynthesis in bacteria is the result of substantial amounts of horizontal gene transfer what evidence ?    , which has shuffled the genetic information that codes for various parts of the photosynthetic apparatus, so that no one simple branching diagram can accurately represent the evolution of photosynthesis (Raymond et al., 2002). ( this actually speaks against evolution and a common ancestor ) However, there are some patterns that can be discerned from detailed analysis of the various parts of the photosynthetic apparatus, so some conclusions can be drawn. In addition, the recent explosive growth of available genomic data on all types of photosynthetic organisms promises to permit substantially more progress in unraveling this complex evolutionary process.

While we often talk about the evolution of photosynthesis as if it were a concerted process, it is more useful to consider the evolution of various photosynthetic subsystems, which have clearly had distinct evolutionary trajectories.
( or that might indicate that the whole mechanism came together all at once ? )  In this brief review we will discuss the evolution of photosynthetic pigments, reaction centers (RCs), light-harvesting (LH) antenna systems, electron transport pathways, and carbon fixation pathways. These subsystems clearly interact with each other, for example both the RCs and antenna systems utilize pigments, and the electron transport chains interact with both the RCs and the carbon fixation pathways. However, to a significant degree they can be considered as modules that can be analyzed individually.

ORIGINS OF PHOTOSYNTHESIS

We know very little about the earliest origins of photosynthesis. ( despite of this, evolution is taken as a granted fact. Nice evolution of the gaps going on here then )  There have been numerous suggestions as to where and how the process originated, but there is no direct evidence to support any of the possible origins (Olson and Blankenship, 2004). There is suggestive evidence (what they probably mean, made up, ad hoc explanations )  that photosynthetic organisms were present approximately 3.2 to 3.5 billion years ago, in the form of stromatolites, layered structures similar to forms that are produced by some modern cyanobacteria, as well as numerous microfossils that have been interpreted as arising from phototrophs (Des Marais, 2000). In all these cases, phototrophs are not certain to have been the source of the fossils, but are inferred from the morphology or geological context. There is also isotopic evidence for autotrophic carbon fixation at 3.7 to 3.8 billion years ago, although there is nothing that indicates that these organisms were photosynthetic. All of these claims for early photosynthesis are highly controversial and have engendered a great deal of spirited discussion in the literature (Buick, 2008). Evidence for the timing of the origin of oxygenic photosynthesis and the rise of oxygen in the atmosphere is discussed below. The accumulated evidence suggests that photosynthesis began early in Earth’s history, but was probably not one of the earliest metabolisms and that the earliest forms of photosynthesis were anoxygenic, with oxygenic forms arising significantly later.

PHOTOSYNTHETIC PIGMENTS

Chlorophylls are essential pigments for all phototrophic organisms. Chlorophylls are themselves the product of a long evolutionary development, and can possibly be used to help understand the evolution of other aspects of photosynthesis. Chlorophyll biosynthesis is a complex pathway with 17 or more steps (Beale, 1999). The early part of the pathway is identical to heme biosynthesis in almost all steps and has clearly been recruited from that older pathway. The later steps include the insertion of magnesium and the elaboration of the ring system and its substituents. ( there is no equivalent, its a unique pathway ) The earliest version of the pathway (and that used by most modern anoxygenic photosynthetic organisms) almost certainly was anaerobic, both not requiring and not tolerating the presence of O2.

http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eigth last steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise chlorophyill is not synthesized.
Therefore, the Chlorophyill biosynthesis pathway is irreducible complex.



Shining Light on the Evolution of Photosynthesis

Chlorophyll itself, and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis.
‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’

The entire process of chlorophyll synthesis from δ-aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates. Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material. For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time.

For four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.


Triplet state chlorophyll, generated in the reaction centres when singlet (excited state) chlorophyll cannot get rid of its energy quickly enough, as may be the case when excess photon energy is coming in, lasts long enough to generate very damaging singlet oxygen , which attacks lipids, proteins, chlorophyll and DNA. Evolutionists maintain that ground-state oxygen (3O2, a triplet state biradical) was not around when photosynthesis evolved.

There is, however, considerable evidence that there has never been a time in Earth’s history when there was not significant free oxygen in the atmosphere (see Dimroth and Kimberley,32 Thaxton, Bradley and Olsen,33 Overman and Pannenberg,34 Denton35).


The evolutionists’ own analyses suggest that the last common ancestor for the bacteria and archaea already had sophisticated enzyme systems for using O2 and for disarming its reactive by-products.36 Since these organisms had already evolved by 3.5 Ga, on the evolutionists’ timescale, this also suggests something rather ominous for the absence of oxygen theory.

In the system that presently exists, a sophisticated complex of enzymes and pigments quenches the excess energy and scavenges the dangerous oxygen species generated by excess light. CuZn superoxide dismutase (in most higher plants) converts superoxide (O2-), the primary product of photoreduction of dioxygen in PSI,38 to H2O2 in the highest-known diffusion-controlled rate among enzymatic reactions. It appears that about one molecule of superoxide dismutase attaches to the surface of the membrane in the vicinity of the PSI complex, along with ascorbate peroxidase (APX). Ascorbate reduces the H2O2 generated, in a reaction catalyzed by APX. The product of this reaction, the monodehydroascorbate radical, is reduced again to ascorbate by photoreduced ferredoxin (Fd) in PSI.

The enzymes and other reducing species of this system could not evolve gradually and then microcompartmentalize over time because nothing works unless everything is in place.

This means that the first appearance of oxygen would have been lethal to the cell, whether the source of oxygen was biological or non-biological. Enzymes such as superoxide dismutase would not have been able to evolve at all. APX, for example, has only about 31–33% homology with cytochrome c peroxidase, from which it is thought to have evolved. Cells without these enzymes exposed to ground-state oxygen would simply have been destroyed before hundreds of base pair changes generated the enzymes from something else.


Natural selection is not evolution’s friend. In answer to the question, ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’


The question, ‘Why and how would evolution go about trying to produce a protein for binding pigment molecules before pigment molecules existed?’ is another major challenge for evolutionists.

If chlorophyll evolved before the antenna proteins that bind it, it would in all likelihood destroy the cell, so the proteins had to evolve first. But natural selection could not favour a ‘newly evolved’ protein which could bind chlorophyll and other pigment molecules before those crucial pigments had themselves come into existence!

Each binding site must be engineered to bind chlorophyll a or chlorophyll b only or carotene only. The carotene molecules must be present in just the right places for quenching triplet states in the chlorophylls.

Even if the pigment molecules were already around, producing just the right protein would be an extremely difficult task. It would not only have to bind pigment molecules only, but it would need to bind just the right pigments in just the right places in just the right orientation so that energy could be transferred perfectly between them, with a little lower energy at each step. Anything else would do nothing, or would transfer energy at random, and the complex would accomplish nothing at best and burn up the cell at worst.


And there is another problem for evolution. The insertion of the pigment molecules changes the conformation of the apoprotein from about 20% to about 60% α-helical content.45 So evolution would have to produce a protein with a wrong shape that would assume just the right shape by the insertion of pigment molecules in just the right positions and orientations when those pigment molecules had not yet evolved.

The energy transfer timeframe between pigment molecules in the antenna complex is between 10-15 and 10-9 seconds. The system that God engineered captures 95–99% of the photon energy for photochemistry, even though there are four other ways the energy can be lost during the slightly less than a billionth of a second the system has for capturing it.46 Humans certainly cannot begin to design systems with such efficiency, but the evolutionists are determined that chance, what Cairns-Smith47 calls ‘old fumble fingers’, can.

Our understanding of the assembly of apoproteins with their pigments is very poor, but we do know that the chloroplast encoded chlorophyll a binding proteins of PSI and PSII core complexes are inserted cotranslationally into the thylakoid.

Protein intermediates of the D1 protein have been observed due to ribosome pausing. It may be that this ribosome pausing permits cotranslational binding of chlorophyll a to the protein. This kind of controlled insertion, with synthesis of otherwise phototoxic material, is precisely what we would expect from intelligent planning and forethought, but how might ‘old fumble fingers’ hit on such a scheme?


However, all modern oxygenic photosynthetic organisms now require O2 as an oxidant at several steps in the pathway. This has been explained in terms of gene replacement of the genes coding for the enzymes at these steps, with the result that the overall pathway is unchanged but the enzymes at key steps are completely different in different groups of phototrophs (Raymond and Blankenship, 2004).

A key concept in using chlorophyll biosynthesis pathways to infer the evolution of photosynthesis is the Granick hypothesis, which states that the biosynthetic pathway of chlorophyll recapitulates the evolutionary sequence (Granick, 1965). This is an appealing idea and probably at least partly true. However, in some cases, in particular the situation of chlorophyll and bacteriochlorophyll, it has been argued that the strict version of the Granick hypothesis is misleading and other interpretations are more likely (Blankenship, 2002; Blankenship et al., 2007).

All photosynthetic organisms contain carotenoids, which are essential for photoprotection, usually also function as accessory pigments, and in many cases serve as key regulatory molecules. Carotenoids, unlike chlorophylls, are also found in many other types of organisms, so their evolutionary history may reflect many other functions in addition to photosynthesis (Sandman, 2009).

REACTION CENTERS


The RC complex is at the heart of photosynthesis; so much attention has been paid to understand the evolution of RCs. A wealth of evidence, including structural, spectroscopic, thermodynamic, and molecular sequence analysis, clearly segregates all known RCs into two types of complexes, called type I and type II (Blankenship, 2002). Anoxygenic phototrophs have just one type, either type I or II, while all oxygenic phototrophs have one of each type. The primary distinguishing feature of the two types of RCs are the early electron acceptor cofactors, which are FeS centers in type I RCs and pheophytin/quinone complexes in type II RCs. The distribution of  

Further analysis strongly suggests that all RCs have evolved from a single common ancestor and have a similar protein and cofactor structure. This is clearly seen when structural overlays of both type I and II RCs are made, showing a remarkably conserved three-dimensional protein and cofactor structure, despite only minimal residual sequence identity (Sadekar et al., 2006). These comparisons have been used to derive structure-based evolutionary trees that do not rely on sequence alignments. Figure 3 shows a schematic evolutionary tree of RCs that is derived from this sort of analysis. It proposes that the earliest RC was intermediate between type I and II (type 1.5) and that multiple gene duplications have given rise to the heterodimeric (two related yet distinct proteins that form the core of the RC) complexes that are found in most modern RCs.

Figure 1 shows an evolutionary tree of life based on small-subunit rRNA analysis. (the paper already starts , assuming evolution, therefor begging the question )

The ability to do photosynthesis is widely distributed throughout the bacterial domain in six different phyla, with no apparent pattern of evolution. how nice that they admit that [/b]

Overwhelming evidence indicates that eukaryotic photosynthesis originated from endosymbiosis of cyanobacterial-like organisms, which ultimately became chloroplasts (Margulis, 1992).   i would really like to see what kind of evidence that is.....

Significant evidence indicates that the current distribution of photosynthesis in bacteria is the result of substantial amounts of horizontal gene transfer, which has shuffled the genetic information that codes for various parts of the photosynthetic apparatus, so that no one simple branching diagram can accurately represent the evolution of photosynthesis (Raymond et al., 2002). i'd like to see how gene transfer provides increase of information......  

In addition, the recent explosive growth of available genomic data on all types of photosynthetic organisms promises to permit substantially more progress in unraveling this complex evolutionary process.     So they don't know yet, but assume evolution first hand. Thats question begging.....  

We know very little about the earliest origins of photosynthesis. There have been numerous suggestions as to where and how the process originated, but there is no direct evidence to support any of the possible origins (Olson and Blankenship, 2004).

All of these claims for early photosynthesis are highly controversial and have engendered a great deal of spirited discussion in the literature (Buick, 2008).

The accumulated evidence suggests that photosynthesis began early in Earth’s history, but was probably not one of the earliest metabolisms and that the earliest forms of photosynthesis were anoxygenic, with oxygenic forms arising significantly later. typical ad hoc ....... based on guesswork  



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3 Photosynthesis and the origin of life on Sat Mar 01, 2014 3:39 pm

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Photosynthesis and the origin of life.



Origin of Photosynthesis

http://www.macromol.uni-osnabrueck.de/Comparative_genomics.php

Structural comparison of chlorophyll-containing proteins led to a suggestion that their common ancestor was a large membrane-embedded protein with more than 10 membrane spans, supposedly protecting the primeval cells from the hazards of the UV light. It is conceivable that a purely dissipative photochemistry started still in the context of the UV-protection. The mutations causing the loss of certain porphyrin-type pigments may have led to the acquisition of redox cofactors and paved the way for a gradual transition from dissipative to productive photochemistry

The first phototrophic bacteria

The analysis of 15 complete cyanobacterial genome sequences revealed 1,054 protein families [core cyanobacterial clusters of orthologous groups of proteins (core CyOGs)] encoded in at least 14 of them. The majority of the core CyOGs are involved in central cellular functions that are shared with other bacteria; 50 core CyOGs are specific for cyanobacteria, whereas 84 are exclusively shared by cyanobacteria and plants and/or other plastid-carrying eukaryotes, such as diatoms or apicomplexans. The latter group includes 35 families of uncharacterized proteins, which could also be involved in photosynthesis. Only a few components of cyanobacterial photosynthetic machinery were found in the genomes of the anoxygenic phototrophic bacteria Chlorobium tepidum, Rhodopseudomonas palustris, Chloroflexus aurantiacus, or Heliobacillus mobilis. These observations, coupled with recent geological data on the properties of the ancient phototrophs, suggest that photosynthesis originated in the cyanobacterial lineage under the selective pressures of UV light and depletion of electron donors. We propose that the first phototrophs were anaerobic ancestors of cyanobacteria ("procyanobacteria") that conducted anoxygenic photosynthesis using a photosystem I-like reaction center, somewhat similar to the heterocysts of modern filamentous cyanobacteria. From procyanobacteria, photosynthesis spread to other phyla by way of lateral gene transfer[11].


http://www.fceqyn.unam.edu.ar/~celular/paginas/Articulos%20Biol%20Cel%202004/Annual%20Reviews/Review%20photosyntesis.pdf

Despite recent developments, there are still many unresolved key issues within
the evolution of photosynthesis, such as the precise nature of the earliest photo-
systems and how water-oxidizing capability evolved in cyanobacteria. Because
of the inherent difficulty of studying deep evolution and the presence of highly
diversified photosynthetic components, we believe that new molecular insight on
evolution of photosynthesis can only be obtained through larger sampling of pho-
tosynthesis genes in more diverse phototrophic organisms. With the increased pool
of molecular data, in particular for photosynthesis genes, and with the use of more
sophisticated phylogenetic analysis tools, a clearer picture of evolutionary history
of photosynthesis will continue to emerge



The origin and evolution of photosynthesis is considered to be the key to the origin of life. This eliminates the need for a soup as the synthesis of the bioorganics are to come from the fixation of carbon dioxide and nitrogen. No soup then no RNA world or Protein world. Cyanobacteria have been formed by the horizontal transfer of green sulfur bacterial photoreaction center genes by means of a plasmid into a purple photosynthetic bacterium. The fixation of carbon dioxide is considered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus) which was then followed by a reductive tricarboxylic acid cycle (Chlorobium) and finally by the reductive pentose phosphate cycle (Calvin cycle). The origin of life is considered to have occurred in a hot spring on the outgassing early earth. The first organisms were self-replicating iron-rich clays which fixed carbon dioxide into oxalic and other dicarboxylic acids. This system of replicating clays and their metabolic phenotype then evolved into the sulfide rich region of the hotspring acquiring the ability to fix nitrogen. Finally phosphate was incorporated into the evolving system which allowed the synthesis of nucleotides and phospholipids. If biosynthesis recapitulates biopoesis, then the synthesis of amino acids preceded the synthesis of the purine and pyrimidine bases. Furthermore the polymerization of the amino acid thioesters into polypeptides preceded the directed polymerization of amino acid esters by polynucleotides. Thus the origin and evolution of the genetic code is a late development and records the takeover of the clay by RNA.

green sulfur bacterial photoreaction center genes

http://www.c-cina.unibas.ch/publications/pdf/jmb-fmo-1.pdf

http://en.wikipedia.org/wiki/Chlorobium_tepidum

Chlorobium tepidum is an anaerobic, thermophilic green sulfur bacteria first isolated from New Zealand.[1] Cells are Gram-negative and non-motile rods of variable length. They contain bacteriochlorophyll c and chlorosomes.

Green_sulfur_bacteria

http://en.wikipedia.org/wiki/Green_sulfur_bacteria

The green sulfur bacteria are a family of obligately anaerobic photoautotrophic bacteria. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum.

photoautotrophic

http://en.wikipedia.org/wiki/Photoautotrophic

Phototrophs are the organisms that carry out photon capture to acquire energy. They use the energy from light to carry out various cellular metabolic processes. It is a common misconception that phototrophs are obligatorily photosynthetic. Many, but not all, phototrophs often photosynthesize: they anabolically convert carbon dioxide into organic material to be utilized structurally, functionally, or as a source for later catabolic processes (e.g. in the form of starches, sugars and fats). All phototrophs either use electron transport chains or direct proton pumping to establish an electro-chemical gradient which is utilized by ATP synthase, to provide the molecular energy currency for the cell.

fixation of carbon dioxide

http://en.wikipedia.org/wiki/Carbon_fixation

Carbon fixation is the conversion of inorganic carbon (carbon dioxide) to organic compounds by living organisms. The most prominent example is photosynthesis, although chemosynthesis is another form of carbon fixation that can take place in the absence of sunlight. Organisms that grow by fixing carbon are called autotrophs. Autotrophs include photoautotrophs, which synthesize organic compounds using the energy of sunlight, and lithoautotrophs, which synthesize organic compounds using the energy of inorganic oxidation.

Carbon dioxide (chemical formula CO2)

http://en.wikipedia.org/wiki/Carbon_dioxide

is a naturally occurring chemical compound composed of 2 oxygen atoms each covalently double bonded to a single carbon atom. It is a gas at standard temperature and pressure and exists in Earth's atmosphere in this state, as a trace gas at a concentration of 0.039 per cent by volume.

As part of the carbon cycle, plants, algae, and cyanobacteria use light energy to photosynthesize carbohydrate from carbon dioxide and water, with oxygen produced as a waste product.[2] However, photosynthesis cannot occur in darkness and at night some carbon dioxide is produced by plants during respiration. Carbon dioxide is produced by combustion of coal or hydrocarbons, the fermentation of sugars in beer and winemaking and by respiration of all living organisms.

carbohydrate

The term is most common in biochemistry, where it is a synonym of saccharide. The carbohydrates (saccharides) are divided into four chemical groups: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars

The fixation of carbon dioxide is considered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus)

Chloroflexus

http://en.wikipedia.org/wiki/Chloroflexus

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New study: Oxygenic photosynthesis goes back three billion years


And what does science have to say regarding the origin of Photosystem II? Here’s an excerpt from an Origins blog post titled, Seeking Microbial Missing Links by Mitch Leslie in Science magazine (April 1, 2009):

Bacteria are the Thomas Edisons of metabolism. They have “invented” myriad biochemical pathways that enable them to eke out a living from substrates as diverse as the oils on your skin, the tiny amounts of carbon monoxide in the atmosphere, and the hydrogen sulfide spewed by deep-sea volcanic vents. That metabolic diversity might include photosynthetic intermediates, scientists argue.

Researchers hope that such microbes will help them determine how early cells assembled the photosynthetic machinery, which involves more than 100 proteins working in concert to absorb light and make sugars. One of the most contentious questions in the field, as discussed in a recent Origins essay, is the origin of the photosystems, the molecular clusters that contain chlorophyll and other light-capturing proteins. Photosystems come in two flavors, I and II. Plants, algae, and primitive cyanobacteria all have both photosystems — and need both to exploit light energy. But other bacteria have only one molecular cluster — what scientists think are the ancestors of photosystem I or photosystem II. Microbial missing links might shed light on how the ancestors of today’s cyanobacteria ended up with two photosystems.

So far, researchers haven’t pinned down any of these missing links. But they take heart from a 2007 paper by microbial physiologist Donald Bryant of Pennsylvania State University, University Park, and colleagues that identified a new solar-powered bacterium… The bacterium isn’t photosynthetic. It has the “photo” part down, absorbing light energy with chlorophyll to make the ATP necessary for living. But it hasn’t mastered “synthesis.” Instead of using carbon dioxide to manufacture sugars, it depends on other bacteria for its carbon needs.


Doesn’t sound very promising, does it? Especially when you have to account for the origin of more than 100 proteins, and explain how they came to work together in concert!


A more recent paper by James P. Allen et al., titled, Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers (PNAS February 14, 2012 vol. 109 no. 7 2314-2318) argues that the complex manganese-calcium cluster needed to perform the reactions that oxidize water could have been built up gradually:

These results provide insight into the evolution from anaerobic to oxygenic photosynthesis. The core cofactors and subunits of photosystem II and the bacterial reaction center have similar three-dimensional structures (4, 23), with the D1 and D2 subunits of photosystem II and the L and M subunits of bacterial reaction centers being derived from a common ancestor. The evolutionary transition from primitive anaerobic phototrophs to organisms capable of oxygenic photosynthesis is thought to have triggered the great oxidation event approximately 2.4 Gyr [2400 million years - VJT] ago, in which molecular oxygen emerged as a significant constituent of Earth’s atmosphere (24–29). This transition would have required the development of a highly oxidizing complex with a Mn [manganese - VJT] cluster capable of water oxidation. Creation of a highly oxidizing protein complex could have been achieved through a combination of altered interactions between the bacteriochlorophyll dimer and the surrounding protein as well as the incorporation of more highly oxidizing tetrapyrroles, such as chlorophyll d (29–31)…

where did the various proteins that make up Photosystem II come from in the first place?

Regarding proteins, all we are told is that two proteins at the core of photosystem II, called D1 and D2, are homologous, and that they’re similar to “the L and M subunits of bacterial reaction centers,” suggesting a common ancestry. I have grown very wary of claims like these, so I decided to do a little fishing. I came across a paper by Jyoti Sharma et al. Primary Structure Characterization of the Photosystem II D1 and D2 Subunits (Journal of Biological Chemistry, 1997, 272:33158-33166, doi: 10.1074/jbc.272.52.33158). On page 33161, Figure 3 shows the protein sequence of the D1 subunit in photosystem II. On page 33164, Figure 6 shows the protein sequence of the D2 subunit in photosystem II. I would invite the reader to flip backwards and forwards between the two pages, examining the two proteins carefully. Despite the existence of broad similarities between the two proteins, there are also a large number of differences. That’s important, because recent research by Douglas and Ann Gauger (see this video) suggests that there’s a limit to how many mutations a protein can undergo, even to achieve a slight functional modification. David Klinghoffer summarizes their findings:

To get one protein (A) to do the job of another (B), not a completely novel protein just a slight but functional modification, Axe working together with Ann Gauger found that it would take at the very least seven or more mutations. That doesn’t sound so bad, but what would it mean in the real world of a bacterial population? Axe gives the bottom line, a distressing one for Darwinian theorists:

It turns out once you get above the number six [changes] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.

So let’s say you’re looking at a transition between two proteins that needs eight or nine steps. You’re out of luck, buddy, because six is the most that unguided evolution can do. This by itself would seem to present a devastating rebuke to any Darwinian account of how proteins, the fundamental structures of all cellular life, came to be as they are.


So much for Photosystem II. What about Photosystem I? Photosystem I

is believed to have appeared earlier in the history of life on Earth than Photosystem II, since a photosystem very similar to it is present in purple and green bacteria, while Photosystem II is unique to cyanobacteria, plants and algae. So you might be thinking that Photosystem I is nice and simple, right? Wrong!

According to Wikipedia, most scientists believe that Photosystem I found in plants, algae and cyanobacteria is derived from an analogous photosystem found in green-sulfur bacteria. But even if they were right, the photosystem found in green-sulfur bacteria is formidably complex, as we saw above, and we still have to account for where it comes from.


Finally, it was pointed out above that in plants, algae and cyanobacteria, the second, light-independent stage of photosynthesis produces sugars by a process known as the Calvin cycle. Here’s what it looks like:

Now I hope readers can see why many scientists were inclined to believe (until recently) that the dazzlingly complex process we call oxygenic photosynthesis (which occurs in plants, algae and cyanobacteria) may have taken two billion years to evolve (see for instance this paper). The work of Dr. Sean Crowe and his team strongly suggests that this complex form of photosynthesis may have appeared very early in the history of life on Earth. And as we’ve seen, even the simpler versions of photosynthesis require complexes of several kinds of proteins to work properly – proteins whose evolution cannot be accounted for by natural selection, as the pioneering work of Dr. Douglas Axe has shown. I’ll just quote one paragraph from his paper,

The Case Against a Darwinian Origin of Protein Folds, in BioComplexity 2010(1):1-12. doi:10.5048/BIO-C.2010.1:

Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin. (p. 11)

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Shining Light on the Evolution of Photosynthesis

Biochemical sequences necessary for the evolution of photosynthesis would have required the evolution of a set of sophisticated enzymes that generated a series of useless intermediates. In the series of enzymes necessary for the manufacture of chlorophyll, these intermediates would have been lethal to the cell before the next enzyme in the series evolved to pick up and modify phototoxic material and insert it into apoproteins. Evidence is presented that: a) the appearance of ground state oxygen would have been lethal to the cell well before oxygen-disarming complexes evolved; b) probability would have eliminated any chance for the evolution of genes for complex enzymes from analogous proteins; c) any junk protein production would have been a death sentence; d) the ATP* synthase motor could not possibly have evolved in a stepwise fashion, and e) the rubisco complex could not and would not have evolved.

* Items marked with an asterisk, the first time they are mentioned, are defined in a glossary at the end of the article.

If we define science as the assumption of naturalism, that matter and energy are all that ever has been or will be, then photosynthesis must of course have evolved, since the only reasonable alternative, that it was designed by intelligence, falls outside our definition of ‘science’. So, by definition, the fabulously complex systems of photosynthesis have arisen by accident. But man’s way of defining words has no jurisdiction in the dominion of objective reality. Truth is sublimely indifferent to our definition of words, even to our definition of science. The thesis of this paper is that evolution would not have been capable of generating the process of photosynthesis as it exists in cyanobacteria, green algae and higher plants, and that it must therefore have been intelligently designed. (For those who are familiar with the intricacies of the photosynthetic system and The Calvin Cycle, please jump ahead to Problem areas for evolution.)

How photosynthesis works: the basics

Eukaryotic photosynthetic organisms have their photosynthetic mechanism isolated in organelles called chloroplasts. A Chlorella green algae cell has one large chloroplast. A modern leaf with 70 million cells will contain about five billion chloroplasts, each containing about 600 million molecules of chlorophyll. Generally speaking, about 250 to 300 chlorophyll molecules per chloroplast will be involved in the transfer of absorbed light energy through neighbouring pigments to a ‘special pair’ of chlorophylls in the reaction centre of their particular photosystem*.

The chloroplast is surrounded (usually) by two lipid, that is fatty, bilayers. In the green algae and higher plants, chlorophyll is bound to proteins on the internal membranes of the chloroplasts, called lamellae, which are the site of the light reactions* of photosynthesis. The carbon reduction reactions, which ultimately produce sugar from CO2, are catalyzed by water-soluble enzymes that are found in the liquid called stroma, the region of the chloroplast outside the thylakoids.Most of the internal chloroplast membranes are closely associated with each other in what are called grana lamellae, which are membrane pouches (thylakoids) stacked like coins, while some membrane sacks are in isolated strands out in the stroma, called stroma lamellae (Figure 1). The parts of the photosynthetic proteins that are inserted in the thylakoid membranes must be mostly hydrophobic (repelling water); the parts that protrude into the lumen* or out into the stroma need to be generally hydrophilic (attracting water).
Figure 2

Photosynthetic bacteria and eukaryotes collect light energy for photosynthesis in structures called light-harvesting antenna complexes. There are two kinds of reaction centres (RCII and RCI) in the photosystems of eukaryotic photosynthetic organisms that contain chlorophyll a and b, and each has its own kinds of antenna protein complexes. The geometry of the light-harvesting complex proteins of photosystem II (PSII) has been determined. The complex is a transmembrane pigment protein complex, with three α helices* that cross the membrane. About 15 chlorophyll a and b molecules are associated with the complex, along with several carotenoids (see Figure 2). The two long carotenoids form an X in the centre of the complex.3 When too much energy is coming through PSII (the first photosystem to be utilized) for PSI to handle, LHCII complexes can migrate in the membrane to the aid of PSI.4 These antenna complexes are clustered around the reaction centres in the thylakoid membranes and transfer electron excitation energy to the centre complex. The antenna complexes of reaction centre I (RCI) are actually part of the reaction centre complex.5

Light energy is captured by pigment molecules in the antenna complexes when photons strike electrons in their conjugated double bonds (alternating single and double bonds). Certain pigments absorb photons at just certain wavelengths. Pigment molecules in antenna complexes, as a general rule, pass their energy along to pigments absorbing at a somewhat lower energy (longer wavelengths) level at each step. Carotenoid pigments can pass their excitation energy to chlorophyll b, which passes its energy to chlorophyll a, which absorbs maximally at 670 nm, and then to the first reaction centre (RCII) pair of chlorophylls, which absorb at 680 nm. The system captures between 95 and 99% of photon energy for use in photochemistry (electron transfer, see Figure 3), sacrificing a tiny amount of energy at each step so that energy transfer is irreversible.6

When a photon is absorbed by a pigment molecule, an electron jumps up from a lower energy orbital, where it is paired with another electron of opposite spin, to a higher energy orbital, leaving both electrons unpaired7 (see Figure 4). This excitation energy is not passed along to the reaction centre by electron transfer, but rather, we think, by resonance transfer,8 like the energy transfer from one tuning fork to another when one is struck and properly placed near the other. This energy transfer is purely a physical process, whereas electron transfer involves chemical changes in molecules.

The last step of the sequence is the excitation of an electron in one of a special pair of chlorophylls (P680) in reaction centre II. The excited electron from this pair is transferred to a molecule called pheophytin, which is a chlorophyll-like molecule in which two protons replace the magnesium in the centre of the (modified) tetrapyrrole molecule. The lightning-fast reactions that follow the reduction of P680 in RCII prevent the loss of the energy harnessed as heat. The electron lost to pheophytin is replaced in the P680 chlorophyll pair from a tyrosine residue (Y) in the reaction centre protein, which in turn derives it from water in a system of four precisely arranged manganese atoms, which are successively oxidized to higher and higher states by light in a process not well understood.9 This system becomes the most powerful oxidizing agent in any known biological system, capable of splitting water molecules to draw off electrons.10

Pheophytin transfers its newly acquired electron to a plastoquinone and this electron is quickly passed to a second plastoquinone (Figure 5). The second quinone picks up two protons from the stroma after it has received two electrons in succession from the first, and then dissociates and carries the electrons to the cytochrome b6f complex where it is oxidized, dumping its two protons into the lumen of the thylakoid and passing its electrons to the cytochrome complex. One of its two electrons is passed through an iron sulfur protein to a cytochrome f and to plastocyanin, on the lumen side, as shown in Figure 3, and one is passed through two cytochrome b molecules to re-reduce an oxidized plastoquinone. This plastoquinone picks up two more protons from the stroma and the process is repeated with two more protons being transferred from the stroma to the lumen. The electron coming through the Rieske iron-sulfur protein and cytochrome f is ferried by plastocyanin to photosystem I (PSI), where it reduces the special chlorophyll pair (P700) of reaction centre I (RCI). This new electron is re-energized by light energy in RCI, and passes to a chlorophyll a (labelled A0 in Figure 611), then to a vitamin K1 (a quinone, labelled A1), and then to a series of iron-sulfur-containing protein complexes to ferredoxin, which can reduce NADP+ to NADPH* via ferredoxin-NADP reductase.12

PSII produces extremely strong oxidizing agents that can pull electrons out of water, but it is not capable of reducing NADP+ to NADPH. PSI produces extremely strong reducing agents that ultimately do the job of reducing ferredoxin and NADP+. Neither system does anything meaningful apart from the other, which is to say, nothing works unless everything works. The whole sequence of events, labelled the Z scheme by Hill and Bendall13 (Figure 6), results in the production of the high energy NADPH molecule. This energy can be utilized in the reduction and regeneration reactions of the Calvin cycle (Figure 7), where CO2 is incorporated into organic molecules and built into triose (three carbon) sugars.

The other energy-accumulating activity resulting from these processes is the accumulation of protons in the lumen of the thylakoids. These protons accumulate as water is split in PSII, and the protons are left in the lumen, and as hydroquinone (the reduced plastoquinone) is oxidized at the cytochrome b6f complex. Protons accumulating in the lumen are channelled back into the stroma through an enzyme complex called ATP synthase (see Figure Cool. The CF0 complex of ATP synthase forms a channel through the membrane. The binding sites for ADP and inorganic phosphate and for ATP appear to be on the 3α and 3β subunits of the CF1 complex, alternating like slices of an orange. Evidence seems to support a model in which the asymmetric χ protein rotates within the αβ subunits from the energy of protons entering and exiting at nonaligned sites in the CF0 complex. It appears that the configuration of the β subunit changes so that ADP and inorganic phosphate are bound, then the subunits close, binding the substrates together so that ATP is formed, and then the subunits open out again and ATP is released.14

One ATP is generated for about every four protons that pass through the complex.15 ATP and NADPH generated by the light reactions are utilized in the reduction reactions of the Calvin cycle.
Figure 7

Figure 7. Three stages of the Calvin cycle. 1) In the carboxylation reaction, CO2 is covalently linked to the number two carbon of Ribulose-1,5-bisphate (RUBP). 2) In the reduction reactions, carbohydrate is formed from the 3-phosphoglycerate (PGA) molecules using the energy of ATP and NADPH. 3) In the regeneration reactions, five sixths of the triose sugars are recombined in the simplest possible sets to reproduce RUBP. Two molecules of NADPH and two of ATP are used in the reduction of 3-phosphoglycerate for every CO2 fixed, and one ATP is used in the regeneration reactions for a total of 2 NADPH and 3 ATP’s per carbon fixed.

The Calvin cycle


One sixth of this triose phosphate is used either to produce starch in the chloroplast, or is exported from the chloroplast to be used in the production of sucrose. The remaining five sixths is used in regenerating the molecule (RUBP) the plant uses to capture CO2. What we see in these regeneration reactions is the simplest way of generating sets of five from sets of three, keeping the number of carbon atoms in each molecule as small as possible, except that one-carbon compounds are not allowed.19


The assembly of complex molecules involves a series of enzymes that must react in a proper sequence, very often producing intermediates that are useless to the cell until the final product is formed. Evolutionists imagine that these enzymes evolve randomly, often from a duplicate gene, and that the succession of steps in the synthesis, at least often, represents the succession of steps in the historical evolution of the process (the Granick hypothesis). But forces of natural selection could not operate to favour an organism which had ‘evolved’ a series of enzymes which merely produced useless intermediates until it somehow got around to making the end product. The Calvin cycle requires eleven different enzymes, all of which are coded by nuclear DNA and targeted precisely to the chloroplast, where the coding sequence is clipped off at just the right place by a nuclear-encoded protease. In reality, as described in the preceding paragraph, none of the enzymes can be missing if the Calvin cycle is to function. It is true that many of these enzymes are ubiquitous in living systems because every living cell needs to generate ribulose phosphates for the production of RNA, but evolutionists cannot solve the problem by merely pushing it back in time.



The assembly of chlorophyll takes seventeen enzymes. Natural selection could not operate to favour a system with anything less than all seventeen being present and functioning. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? Some evolutionists argue that the assumed primeval organic soup had many of the simpler chemicals, and that only as they were used up did it become necessary to generate the earlier enzymes in the pathway. In The Mystery of Life’s Origin: Reassessing Current Theories, the authors set forth the good basic chemistry that demonstrates that there could never have been an organic soup, and present some of the evidence out there in the world indicating that there never was.22 Denton23 and Overman24 also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Chlorophyll itself, and many of the intermediates along its pathway of synthesis can form triplet states, which would destroy surrounding lipids by a free radical cascade apart from the context of the enzymes that manufacture them and the apoproteins into which they are inserted at the conclusion of their synthesis.25 According to Asada26 ‘triplet excited pigments are physiologically equivalent to the active oxygens’, and according to Sandmann and Scheer, chlorophyll triplets ‘are already highly toxic by themselves … .’27 The entire process of chlorophyll synthesis from δ-aminolevulinic acid to protoporphyrin IX is apparently tightly coupled to avoid leakage of intermediates.28 Almost all of the enzymes of chlorophyll biosynthesis are involved in handling phototoxic material.29 For many of these enzymes, if they are not there when their substrate is manufactured, the cell will be destroyed by their substrate on the loose in the wrong place at the wrong time. Apel30 has cited four of the enzymes of chlorophyll biosynthesis for which this has been proven to be the case. This is a significant problem for evolutionists, who need time for these enzymes to evolve successively. Each time a new enzyme evolved it would have produced a new phototoxin until the next enzyme evolved.

Triplet state chlorophyll, generated in the reaction centres when singlet (excited state) chlorophyll cannot get rid of its energy quickly enough, as may be the case when excess photon energy is coming in, lasts long enough to generate very damaging singlet oxygen (1O2), which attacks lipids, proteins, chlorophyll and DNA.31 Evolutionists maintain that ground-state oxygen (3O2, a triplet state biradical) was not around when photosynthesis evolved. There is, however, considerable evidence that there has never been a time in Earth’s history when there was not significant free oxygen in the atmosphere (see Dimroth and Kimberley,32 Thaxton, Bradley and Olsen,33 Overman and Pannenberg,34 Denton35). The evolutionists’ own analyses suggest that the last common ancestor for the bacteria and archaea already had sophisticated enzyme systems for using O2 and for disarming its reactive by-products.36 Since these organisms had already evolved by 3.5 Ga, on the evolutionists’ timescale,37 this also suggests something rather ominous for the absence of oxygen theory.

In the system that presently exists, a sophisticated complex of enzymes and pigments quenches the excess energy and scavenges the dangerous oxygen species generated by excess light. CuZn superoxide dismutase (in most higher plants) converts superoxide (O2-), the primary product of photoreduction of dioxygen in PSI,38 to H2O2 in the highest-known diffusion-controlled rate among enzymatic reactions.39 It appears that about one molecule of superoxide dismutase attaches to the surface of the membrane in the vicinity of the PSI complex, along with ascorbate peroxidase (APX). Ascorbate reduces the H2O2 generated, in a reaction catalyzed by APX. The product of this reaction, the monodehydroascorbate radical, is reduced again to ascorbate by photoreduced ferredoxin (Fd) in PSI.40 The enzymes and other reducing species of this system could not evolve gradually and then microcompartmentalize over time because nothing works unless everything is in place. This means that the first appearance of oxygen would have been lethal to the cell, whether the source of oxygen was biological or non-biological. Enzymes such as superoxide dismutase would not have been able to evolve at all. APX, for example, has only about 31–33% homology with cytochrome c peroxidase, from which it is thought to have evolved.41 Cells without these enzymes exposed to ground-state oxygen would simply have been destroyed before hundreds of base pair changes generated the enzymes from something else.

Natural selection is not evolution’s friend. In answer to the question, ‘Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?’

The question, ‘Why and how would evolution go about trying to produce a protein for binding pigment molecules before pigment molecules existed?’ is another major challenge for evolutionists.

If chlorophyll evolved before the antenna proteins that bind it, it would in all likelihood destroy the cell, so the proteins had to evolve first. But natural selection could not favour a ‘newly evolved’ protein which could bind chlorophyll and other pigment molecules before those crucial pigments had themselves come into existence! Each binding site must be engineered to bind chlorophyll a or chlorophyll b only or carotene only. The carotene molecules must be present in just the right places for quenching triplet states in the chlorophylls. Even if the pigment molecules were already around, producing just the right protein would be an extremely difficult task. It would not only have to bind pigment molecules only, but it would need to bind just the right pigments in just the right places in just the right orientation so that energy could be transferred perfectly between them, with a little lower energy at each step. Anything else would do nothing, or would transfer energy at random, and the complex would accomplish nothing at best and burn up the cell at worst.

And there is another problem for evolution. The insertion of the pigment molecules changes the conformation of the apoprotein from about 20% to about 60% α-helical content.45 So evolution would have to produce a protein with a wrong shape that would assume just the right shape by the insertion of pigment molecules in just the right positions and orientations when those pigment molecules had not yet evolved.

The energy transfer timeframe between pigment molecules in the antenna complex is between 10-15 and 10-9 seconds. The system that God engineered captures 95–99% of the photon energy for photochemistry, even though there are four other ways the energy can be lost during the slightly less than a billionth of a second the system has for capturing it.46 Humans certainly cannot begin to design systems with such efficiency, but the evolutionists are determined that chance, what Cairns-Smith47 calls ‘old fumble fingers’, can.

Our understanding of the assembly of apoproteins with their pigments is very poor, but we do know that the chloroplast encoded chlorophyll a binding proteins of PSI and PSII core complexes are inserted cotranslationally into the thylakoid. Protein intermediates of the D1 protein have been observed due to ribosome pausing. It may be that this ribosome pausing permits cotranslational binding of chlorophyll a to the protein.48 This kind of controlled insertion, with synthesis of otherwise phototoxic material, is precisely what we would expect from intelligent planning and forethought, but how might ‘old fumble fingers’47 hit on such a scheme?

ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions as described and illustrated earlier in this paper (Figure Cool. Protons can flow freely through the CF0 complex without the CF1 complex, so that if it evolved first, a pH gradient could not have been established within the thylakoids. The δ and critical χ protein subunits of the CF1 complex are synthesized in the cytosol and imported into the chloroplast in everything from Chlorella to Eugenia in the plant kingdom.49 All of the parts must be shipped to the right location, and all must be the right size and shape, down to the very tiniest detail. Using a factory assembly line as an analogy, after all the otherwise useless and meaningless parts have been manufactured in different locations and shipped in to a central location, they are then assembled, and, if all goes as intended, they fit together perfectly to produce something useful. But the whole process has been carefully designed to function in that way. The whole complex must be manufactured and assembled in just one certain way, or nothing works at all. Since nothing works until everything works, there is no series of intermediates that natural selection could have followed gently up the back slope of mount impossible. The little proton-driven motor known as ATP synthase consists of eight different subunits, totalling more than 20 polypeptide* chains, and is an order of magnitude smaller than the bacterial flagellar motor,50 which is equally impossible for evolutionists to explain.

Evolution cannot account for the assembly and activation of rubisco. All attempts to reconstitute a 16-unit rubisco from any source have failed, so the assembly of rubisco must be studied in the chloroplast extracts.51 The eight large (L) subunits of rubisco are coded by the chloroplast DNA, and the eight small (S) subunits by nuclear DNA. The S subunit of rubisco is synthesized on free cytosolic polyribosomes* and maintained even during synthesis in an unfolded state by chaperones* of the Hsp70 class and their protein partners.52 When the small unit is brought to the import complex of the chloroplast, the fourteen-polypeptide chloroplast Cpn60 chaperonin protein associates with IAP100 (protein) of the import complex and can also associate with mature imported small subunits. The chloroplast Cpn60 chaperone is similar to the E. coli GroEl protein.53 After the unfolded precursor protein enters the stromal space, it binds briefly to a stromal Hsp70 chaperone protein and the N terminal targeting sequence is cleaved.54

The large subunits of the rubisco enzyme are produced by the DNA and machinery of the chloroplast itself and stored complexed to a Cpn60 chaperonin.55,56 This chaperone protein keeps the large subunit protein from folding incorrectly, and therefore becoming useless,57 and is also necessary for the proper binding of the eight large subunits; without it they will form a useless clump.58 In many plants, the large subunits are chemically modified by specialized enzymes59 before they bind to the chaperonin protein. There is strong evidence that chloroplast Cpn60, Cpn21 and Hsp70 also participate in the assembly of the sixteen-unit rubisco complex.60 After a soluble L8 core is formed with the assistance of the chaperonin proteins, tetramers (four-part complexes) of small subunits bind to the top and bottom of the complex to form the complete enzyme.61 There are almost certainly other chaperones and chaperone-like polypeptides or lipo-proteins involved that are not yet characterized.

How do evolutionists explain how natural selection would have favoured a protein complex the function of which was to prevent a still-useless rubisco small subunit from folding outside the chloroplast? Before it evolved a way to get the protein inside, there would be no benefit from keeping it unfolded outside. How could blind chance ‘know’ it needed to cause large subunit polypeptides to fold ‘correctly’ and to keep them from clumping? It could not ‘anticipate’ the ‘correct’ conformation before the protein became useful. And evolution would need to be clever indeed to chemically modify something not yet useful so that it could be folded ‘correctly’ when even the ‘correctly’ folded polypeptide would not yet become useful.

Only a designer would know why it would be necessary to produce a specialized protease, target it to the chloroplast, and program it to clip off the targeting sequence of the small subunit at just the right place. And what about the assembly of a collection of meaningless rubisco parts in just one certain way? In order to design a sophisticated set of tools to make something else useful in the future that had, as yet, no function, evolution (as ‘designer’) would have had to have detailed knowledge of the future usefulness of the protein it was so cleverly engineering. If evolution managed to generate any one of these chaperone protein complexes (and it would not), it would still be useless for generating rubisco unless all the other chaperones were also present. Without any one of them, the sixteen-unit complex could not be generated.

But let us assume the impossible, that evolution succeeded in producing the rubisco enzyme complex, and that random chance happened to generate a new, otherwise useless, enzyme to create its substrate, RUBP. The perfect and complete rubisco sixteen-unit protein complex would then bind tightly to RUBP and do nothing.

In the real world, far away from the never-never land of evolution, another enzyme is needed to separate rubisco from RUBP. Once the rubisco complex is produced, a protein activase uses ATP energy to separate it from RUBP, to which it is tightly bound in its inactive (dark conditions) form. Apparently, the hydrolysis of ATP changes the configuration of the activase protein so that it can bind to rubisco and cause it to release its RUBP. The rubisco must then be carbamylated on the ε-NH2 group of just a certain lysine amino acid residue, and then it must pick up a Mg2+ ion on that carbamyl group* to form the active rubisco site.62 The amide group starts out as NH3+, which must become NH2 before the CO2 can be added, and another proton is lost when the COO- actually attaches, so that these steps are stimulated by low H+ concentration and high Mg2+. Light lowers the H+ concentration of the stroma by a process we have discussed, and raises the Mg2+ also. However, no RUBP can be detected in photosynthetic tissue at night, signifying that it is actually phosphoribulokinase that disrupts the cycle at night.63 What all of this implies is that even if evolution managed the impossible task of generating the rubisco enzyme, the entire system as it presently stands would be needed to turn it on in the light and off in the dark.

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6 Re: Origin and evolution of photosynthesis on Sat Mar 01, 2014 5:11 pm

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The evolution of photosynthesis…again?

Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. ( how do they know ? ) To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.

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7 Ancient soils provide early whiff of oxygen on Tue Mar 04, 2014 7:08 am

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Ancient soils provide early whiff of oxygen

Oxygen may have been accumulating in Earth's atmosphere hundreds of millions of years earlier than we thought.
An international team has made the claim in Nature magazine after studying the oldest soils on Earth.
The researchers say elements in the three-billion-year-old material show evidence for oxidative weathering.
This is some 700 million years before the Great Oxidation Event when other geological data points to a dramatic rise in free O2 in the atmosphere.
If confirmed, it is a significant observation because it suggests the ability of ancient lifeforms to produce oxygen may also have got going earlier than previously recognised.
"Oxygenic photosynthesis is a very complicated metabolism and it makes sense that the evolution of such a metabolism would take perhaps two billion years - that we might not see its manifestation until the Great Oxidation Event. But now that we see oxygen much earlier in the atmosphere, it tells us that even really complex metabolisms can evolve very fast," said team-member Dr Sean Crowe from the University of British Columbia, Canada.
The group looked at remnant soils, dated to about 2.95 billion years ago, which have subsequently become locked up in rocks in what is now Kwazulu-Natal Province, South Africa.
In particular, the researchers studied the ratios of different types, or isotopes, of chromium atoms that were present in the palaeosoils.
Subtle chemistry
These isotopes are very sensitive to reactions involving oxygen, with the heavier form of the atom, chromium-53, becoming slightly more soluble when oxidised than the lighter chromium-52 type.
Marine sediments Marine sediments in Kwazulu-Natal show a very slight enrichment in chromium 53
It means that, over time, soils that have been oxidised should become depleted in chromium-53 as rain water washes away these atoms; and, conversely, sea sediments, where the products of weathering eventually end up, should become enriched in chromium-53.
The team made precisely this observation in Kwazulu-Natal, in rocks that represented both ends of the process - the soils and the sea sediments.
The conclusion is that the ancient soils would have been exposed to an atmosphere that contained 0.03% of the oxygen it does now; about one-10,000th of the present level.
"This is considerably more than people had estimated," said team-member Prof Michael Bau, from Jacobs University, Bremen, Germany.
"There is some evidence also for a whiff of oxygen at around 2.6-2.7 billion years ago based on molybdenum isotope systems. But the important point about these older whiffs is that they probably represent episodic increases, and it is not until 2.3-2.4 billion years ago that we see an irreversible oxygenation of the atmosphere," he told BBC News.
This was the Great Oxidation Event, which coincided with a big rearrangement of the Earth's continents, creating vast shallow-water shelf environments where photosynthetic cyanobacteria could really flourish.
Protective layer
It was a very significant moment in the story of Earth because some of the abundant oxygen would then have been converted in the atmosphere into ozone.
This three-atom oxygen molecule filters damaging ultraviolet light from the Sun, and would have enabled many new classes of life to emerge.
The team, which includes co-workers at the universities of Copenhagen and Johannesburg, wishes to test its findings further on rocks from other parts of the world.
This is not straight-forward, however, as three-billion-year-old rocks are extremely rare - certainly, those that have also not undergone significant alteration. But the scientists hope to find suitable material to work on in Greenland and Australia.
"One of the key aspects of all this is the sensitivity now of techniques such as the chromium isotopes, which allow us to probe very low levels of oxygen. And I'm sure continued technological advances will eventually enable us to look for even lower levels of oxygen, even earlier in time," said Dr Crowe.



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8 Re: Origin and evolution of photosynthesis on Fri Mar 07, 2014 8:23 pm

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Evolutionary relationships among photosynthetic bacteria



Evolutionary Relationships Among Photosynthetic Bacteria

Origin of Photosynthesis

this key fundamental innovation which either directly or indirectly sustains all eukaryotic organisms, originated within the prokaryotes.

Within prokaryotes, photosynthetic capability is present within five major groups of bacteria:

Firmicutes or the low G+C Gram-positive bacteria (Heliobacterium),
Chloroflexi or Green nonsulfur bacteria,
Chlorobi or Greensulfur bacteria,
Proteobacteria and,
Cyanobacteria.


Of these only Cyanobacteria, which contains two different reaction centers (RC) RC-1 and RC-2 (or PS I and PS II) linked to each other, are capable of carrying out oxygenic photosynthesis. All other photosynthetic bacteria carry out only anoxygenic photosynthesis and contain a single reaction center. Of these Heliobacteria and Chlorobi contain Fe-S type of reaction centers (RC-1) whereas Chloroflexi and Proteobacteria have a pheophytin-quinone type of reaction center (RC-2). The similarities of these RCs in component parts and the mechanisms of charge transfer indicate that they have evolved from a common ancestor. To understand the origin of photosynthesis and which of these reaction centers first evolved, it is essential to understand the branching order of different photosynthetic phyla from a common ancestor, which is not resolved by traditional phylogenetic means. However, based upon the signature sequence approach the branching orders of different bacteria phyla can now be reliably deducted (see diagram on above)

1. Earliest Branching Photosynthetic Bacteria

Firmicutes (Heliobacterium) are indicated to be earliest branching photosynthetic bacteria. The ancestral nature of this group is also supported by a number of other observations:

Unlike other photosynthetic bacteria, both antenna and reaction center activities are present within a single protein in Heliobacteria;
The reaction center complex in Heliobacteria (and also green sulfur bacteria) has a simpler homodimeric structure as opposed to being heterodimeric in other photosynthetic bacteria;
The RC in Heliobacteria contains a unique photosynthetic pigment Bchl g, which is indicated to be primitive in comparison to the pigments found in other photosynthetic organisms.
Of the different photosynthetic bacteria, only Heliobacteria are bounded by a single unit lipid membrane (monoderm cell structure), which is indicated to be an ancestral characteristic in comparison to the cells containing both an inner and outer cell membranes (Diderm cell structure).

2. The Second Photosynthetic Bacteria


Following Heliobacteria, Chloroflexi are indicated to be the next group of photosynthetic organisms that branched off from the common ancestor. The branching of both Heliobacteria and Chloroflexi prior to Cyanobacteria provides evidence that both RC-1 and RC-2 had already evolved prior to the emergence of Cyanobacteria, which contain both of these reactions centers linked to each other.

3. Anoxygenic Photosynthesis vs Oxygenic Photosynthesis

The bacterial groups utilizing anoxygenic photosynthesis mode evolved much earlier than those capable of oxygenic photosynthesis. This is in accordance with the observation that change in atmosphere from anoxygenic to oxygenic occurred much later (between 1.5-2 billion year) after the evolution of earlier organisms. This observation indicates that the earlier prokaryotic fossils probably do not correspond to Cyanobacteria but some other groups of photosynthetic bacteria.

4. Later Branching Photosynthetic Bacteria

The later branching photosynthetic phyla which contain either one or both of these RCs could have acquired such genes from the earlier branching lineages by either direct descent or by means of lateral gene transfer.

5. Speculations About the Earliest Organism

The presence of photosynthetic ability in the earliest branching bacterial phylum indicates that photosynthesis evolved very early in evolution and it is possible that the earliest organism that evolved were photosynthetic.

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Palaeoproterozoic ice houses and the evolution of oxygen-mediating enzymes: the case for a late origin of photosystem II

Abstract


Two major geological problems regarding the origin of oxygenic photosynthesis are (i) identifying a source of oxygen pre-dating the biological oxygen production and capable of driving the evolution of oxygen tolerance, and (ii) determining when oxygenic photosynthesis evolved.
One solution to the first problem is the accumulation of photochemically produced Hydrogen peroxide H2O2 at the surface of the glaciers and its subsequent incorporation into ice. Melting at the glacier base would release H2O2, which interacts with seawater to produce O2 in an environment shielded from the lethal levels of ultraviolet radiation needed to produce H2O2. Answers to the second problem are controversial and range from 3.8 to 2.2 Gyr ago. A sceptical view, based on the metals that have the redox potentials close to oxygen, argues for the late end of the range. The preponderance of geological evidence suggests little or no oxygen in the Late Archaean atmosphere (less than 1 ppm). The main piece of evidence for an earlier evolution of oxygenic photosynthesis comes from  Lipid biomarkers. Recent work, however, has shown that 2-methylhopanes, once thought to be unique biomarkers for cyanobacteria, are also produced anaerobically in significant quantities by at least two strains of anoxygenic phototrophs. Sterane biomarkers provide the strongest evidence for a date 2.7 Gyr ago or above, and could also be explained by the common evolutionary pattern of replacing anaerobic enzymes with oxygen-dependent ones. Although no anaerobic sterol synthesis pathway has been identified in the modern biosphere, enzymes that perform the necessary chemistry do exist. This analysis suggests that oxygenic photosynthesis could have evolved close in geological time to the Makganyene Snowball Earth Event and argues for a causal link between the two.

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10 Re: Origin and evolution of photosynthesis on Sat Mar 08, 2014 11:44 am

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Evolution of the oxygen evolving complex

On the purely intellectual front, Sauer and Yachandra have investigated the evolutionary origin of the manganese complex. "It's fascinating that there's been no improvement in the system in over 2.5 billion years," says Sauer. "Photosynthetic bacteria used the same complex. Where did it come from?"

Clusters resembling the oxygen-evolving complex occur in tunnel-structured manganese oxide minerals, found near sites of active chemistry like underwater thermal vents. Hollandite, for example, exhibits 18 different configurations of manganese (blue) and oxygen (red) compatible with the manganese clusters of photosystem II. Primitive organisms could have used mineral clusters to aid photosynthesis.

They believe the answer may lie in the rocks. They examined manganese oxide minerals with x-ray spectroscopy and found that many contain crystalline structures corresponding to possible configurations of the PSII manganese cluster. Indeed, a single representative mineral, hollandite, exhibits a complete set of the manganese cluster's possible geometric arrangements.

Such minerals are found near deep-sea vents and on the ocean floor, and in soils, rock varnishes, and weathered outcrops. Primitive bacteria could have adapted the machinery in the rocks to help oxidize water, eventually stumbling upon a way to encode genes for manganese oxide structures in their own genomes. Just by surveying the numerous mineral structures, Sauer and Yachandra found several new candidates for the manganese cluster in PSII.

The history of the evolution of plants is fascinating in itself, but understanding the way the oxygen-evolving complex works will have practical applications as well. "You can isolate PSII from a bunch of spinach, put it in water, turn on a light, and get oxygen," says Yachandra. "We still don't know how to do that on the lab bench using synthetic catalysts."

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11 Re: Origin and evolution of photosynthesis on Sat Mar 08, 2014 12:48 pm

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A possible evolutionary origin for the Mn4 cluster of the photosynthetic water oxidation complex

The photosynthetic water oxidation complex consists of a cluster of four Mn atoms bridged by O atoms, associated with Ca22 and Cl_,and incorporated into protein.The structure is similar in higher plants and algae, as well as in cyanobacteria of more ancient lineage,dating back more than2.5billion years ago on Earth. It has been proposed that the proto-enzyme derived from a component of a natural early marine manganese precipitate that contained a CaMn4O9 cluster. A variety of MnO2 minerals are found in nature. Three major classes are spinels, sheet-like layered structures, and three-dimensional networks that contain parallel tunnels. These relatively open structures readily incorporate cations (Na2, Li2, Mg22, Ca22, Ba22, H2, and even Mn22) and water. The minerals have different ratios of Mn(III) and Mn(IV) octahedrally coordi-nated to oxygens. Using x-ray spectroscopy we compare the chemical structures of Mn in the minerals with what is known about the arrangement in the water oxidation complex to define the parameters of a structural model for the photosynthetic catalytic site. This comparison provides for the structural model a set of candidate Mn4 clusters—some previously proposed and considered and others entirely novel.

In the presence of good reductants, such as sulfide, sulfur, dihydrogen, and prebiotic organic compounds, the precursors of microbial life as we know it on Earth somehow appeared.

As the available reductants, such as Fe21, dihydrogen, and sulfide_sulfur_thisulfate, gradually decreased or disappeared in local environments owing to photo-oxidation, water became the most available reductant for carbon fixation, and oxygenic photosynthesis as we know it today evolved.

Conclusion


The hypothesis of Russell and Hall that the origin of the photosynthetic water oxidation complex may be reflected in the structure of manganese minerals§ provides an intriguing adjunct to the growing picture of how life on Earth evolved. We know that the photosynthetic water oxidation complex is not formed by direct incorporation of such a preformed cluster in present-day organisms. The evolution of the modern complex, however, presumably began in the absence of the refined PS II protein binding site and fully developed mechanism for photo-oxidizing Mn21 during its incorporation. It is well known that solid MnO2 exhibits pronounced ‘‘catalase’’ activity in its ability to increase the rate of decomposition of H2O2 into H2O and O2 by many orders of magnitude. A primitive organism that succeeded in the task of oxidizing water to H2O2 could then make use of a CaMn4 cluster to complete the


Sauer and Yachandra


conversion to O2. There is no evidence that free H2O2 is produced by PS II in present-day photosynthesis, but a bound peroxide link in one of the intermediate S-states is a possi-bility. It is also possible that the further conversion of H2O2 to O2 was especially valuable in a symbiotic relation with another primitive organism that depended on respiration. The hypoth-esis has also considerably enlarged our repertoire of possible Mn4 clusters. We will benefit from these ideas during the interval of uncertainty until a high-resolution structure of the water oxidation complex is available.


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Cyanobacterial photosynthesis in the oceans: the origins and significance of divergent light-harvesting strategies



http://www.darwinismrefuted.com/origin_of_plants_03.html

http://m.harunyahya.com/tr/Books/986/The-Miracle-Of-Creation-In-Plants/chapter/2556/The-Imaginary-Scenario-of-Plant-Evolution

Another problem facing evolutionist scientists who expect bacteria to produce their own food is the difficulty of the endeavour. In the preceding sections we stressed that photosynthesis depends upon very complex systems. And of all the processes known in the world, this is really the most complicated, its general outlines having been only partly uncovered in our day; many of its stages are still a mystery to man.

Prof. Dr. Ali Demirsoy, Kalitim ve Evrim (Inheritance and Evolution), Ankara, Metek

This is what evolutionist scientists expect of a dying bacteria: that it should by itself develop this process - a process which has not been artificially reproduced even in reactors with the most highly developed technology. One of the most striking admissions that such a complicated event as photosynthesis could not have evolved over time is again made by
Photosynthesis is a rather complicated event, and it seems impossible for it to emerge in an organelle inside a cell, because it is impossible for all the stages to have come about at once, and it is meaningless for them to have emerged separately.



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The structure of photosystem I and evolution of photosynthesis

The function of these primordial chlorophyll–protein complexesandthewaythatthereactioncentersevolvedfromthem is arguable. It was suggested that the ancestral chlorophyll– protein complexes were evolved for the protection of the primordial organisms against UV damage.(20) In addition to the protection of the proteins and DNA from UV damages, the chlorophyll–protein complexes had to develop protective mechanisms against their own excited states.(21,22) Thus it was suggested that to prevent damage by the excited chlorophylls, some of them were established as chlorophyll-dimers (which are called ‘‘red traps’’ since their absorption peakisshiftedtolowerenergy).Aslongasthetwochlorophylls in the dimers were kept in an environment that did not allow oxidation–reduction reactions, the excitation in these traps preferentially decayed as singlets.(21,22) This prevented the formation of long-lived damaging triplets.(23,24) By letting the chlorophylls in one of these dimers get close enough, and by evolving the environment of this chlorophyll-dimer to promote electron transfer from it, a primordial reaction center was formed from the ancient chlorophyll–protein complex. For an unknownmechanisticreason,thechlorophylldimercapableof oxidation–reduction activity evolved from a homodimeric protein, with each monomer donating one chlorophyll mole-cule.(21,25–27) Now beinga productive entityofconvertinglight to chemical energy, it had to be protected from its own photochemical activity.

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14 Re: Origin and evolution of photosynthesis on Fri Mar 14, 2014 5:41 pm

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Origin of photosynthesis

In a recent Nature article, the origin of photosynthesis is discussed and begins with the term invention. “The invention of oxygenic photosynthesis was a small step for a bacterium, but a giant leap for biology and geochemistry” (emphasis added).1 I think two terms need to be considered more closely—invention and small. An invention, according to Webster’s Online Dictionary2 is, “the creation of something in the mind, a creation resulting from study and experimentation.” The terms in italics would all seem to indicate a conscious intelligence that does not apply to bacteria. Most people are familiar with the definition of small. Considering that photosynthesis involves approximately “100 proteins that are highly ordered” (according to the article), I think small is a major understatement.

The authors also go on to say, “Biologists agree that cyanobacteria invented the art of making oxygen, but when and how this came about remain uncertain” (emphasis added). Certainly the authors do not believe that bacteria consciously invented photosynthesis. So, what evolutionary mechanisms might be responsible for bacteria being able to “invent” photosynthesis? From the article, it appears like a bunch of “just-so” stories.
Photosynthesis in plants and bacteria

There are two basic types of photosynthesis—oxygenic, in which oxygen is produced, and anoxygenic, in which oxygen is not produced. Oxygenic is carried out by plants and cyanobacteria. Anoxygenic is carried out by various types of green and purple bacteria. Oxygenic involves two photosystems which convert light to energy molecules, which are then used to make sugars. A photosystem is a cluster of pigments like chlorophyll that absorbs light. Anoxygenic involves only one photosystem which accomplishes the same thing. The photosystems of the two basic types of photosynthesis are different in structure and composition but accomplish a similar goal.

A need for time

A big question for evolutionists is when oxygen appeared on the earth. Oxygen is needed by animals, humans, and plants to make the energy molecule ATP. The appearance of oxygen on earth is very important because it is needed for the development of larger organisms (than bacteria) that have greater energy requirements. (Think what happens when you overdo your exercise routine and your muscles start burning. This is because you have run out of oxygen and are producing lactic acid as a byproduct of ATP production.) The article indicates that the only known significant source of oxygen is photosynthesis and that geochemical evidence places the appearance of oxygen (and thus, cyanobacteria) at 2.3 billion years ago. The article cites other work claiming that cyanobacteria could have been around at 3.4 billion years ago. The authors go on to say, “This range [3.4 billion to 2.3 billion years ago] is admittedly rather imprecise, but it is something. Of course, absence of evidence is not evidence of absence, and other authors suggest that O2 could have been produced as early as 4.0 billion years ago, but was rapidly consumed.” By moving the appearance of cyanobacteria and oxygen back almost 2 billion years, they have given evolution 2 billion more years to perform molecules-to-man evolution. However, as stated in many other articles on this website—no matter how much time is given the mechanisms of evolution—mutation and natural selection will never result in a microbe becoming a microbiologist.

From one photosystem to two

Green and purple bacteria (containing only one photosystem similar to either one or the other of the photosystems found in cyanobacteria and plants) are believed to be the ancestors of cyanobacteria. Two questions arise—how did both the photosystems arise and how did both photosystems get into one bacteria? No mechanism is provided for how the photosystems came into existence, just that “these genes arose” for one photosystem. It is then proposed that a “simple duplication” of the genes encoding one photosystem occurred, followed by mutation leading to the formation of another photosystem. What is needed is new information to form another photosystem, not duplication of already present genes followed by mutation. This will only lead to the loss of information.

The article proposes that lateral gene transfer (a DNA-swapping mechanism in bacteria) then occurred, and both photosystems ended up in the same bacterium. A good question to pose here is what is the selection pressure to keep both photosystems in a bacterium if one is sufficient? For both photosystems to be kept, a functional relationship between the two would have to form that would give the bacterium an advantage over other bacteria. So, what is the mechanism proposed to form this new functional relationship? “It would have only been a small step away from the cyanobacterial state of oxygenic photosynthesis, provided that it underwent the right mutation [...] and provided that this happened in the right environmental setting at the right time.” The improbability of this is enormous considering that mutations and natural selection, which decrease genetic information, are the only mechanisms that evolution can use.

Evolution—a faith based system

Towards the end of the article, the authors continue with inferences to some form of natural intelligence embedded in nature. They use the term “fine-tuning” to describe the process that would have occurred to allow the photosystems to gain the ability to produce oxygen. This would be the final step in going from anoxygenic photosynthesis in green and purple bacteria to oxygenic photosynthesis in cyanobacteria. Again, who or what is doing the fine-tuning and why? Evolution can’t do this—it has no goal in mind. One of their final statements is this, “The best evidence for this evolutionary scheme would be the discovery of a modern-day protocyanobacterium. Although it is possible that all protocyanobacterial lineages have died out, we prefer to think that the missing link is still out there” (emphasis added). So, their best evidence for the origin and evolution of photosynthesis is faith in an organism which may not exist. I prefer to put my faith in the Word of the living God who says, “‘Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds.’ And it was so.” (Genesis 1:11, NIV)

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The PsbP Protein Is Required for Photosystem II Complex Assembly/Stability and Photoautotrophy in Arabidopsis thaliana


Abstract

Interfering RNA was used to suppress the expression of the genes At1g06680 and At2g30790 in Arabidopsis thaliana, which encode the PsbP-1 and PsbP-2 proteins, respectively, of photosystem II (PS II). A phenotypic series of transgenic plants was recovered that expressed intermediate and low amounts of PsbP. Chlorophyll fluorescence induction and QA– decay kinetics analyses were performed. Decreasing amounts of expressed PsbP protein led to the progressive loss of variable fluorescence and a marked decrease in the fluorescence quantum yield (FV/FM). This was primarily due to the loss of the J to I transition. Analysis of the fast fluorescence rise kinetics indicated no significant change in the number of PS IIβ centers present in the mutants. Analysis of QA– decay kinetics in the absence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea indicated a defect in electron transfer from QA– to QB, whereas experiments performed in the presence of this herbicide indicated that charge recombination between QA– and the oxygen-evolving complex was seriously retarded in the plants that expressed low amounts of the PsbP protein. These results demonstrate that the amount of functional PS II reaction centers is compromised in the plants that exhibited intermediate and low amounts of the PsbP protein. Plants that lacked detectable PsbP were unable to survive in the absence of sucrose, indicating that the PsbP protein is required for photoautotrophy. Immunological analysis of the PS II protein complement indicated that significant losses of the CP47 and D2 proteins, and intermediate losses of the CP43 and D1 proteins, occurred in the absence of the PsbP protein. This demonstrates that the extrinsic protein PsbP is required for PS II core assembly/stability.

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Release and Reactive-Oxygen-Mediated Damage of the Oxygen-Evolving Complex Subunits of PSII during Photoinhibition

Under photoinhibitory illumination of spinach PSII membranes, the oxygen-evolving complex subunits, OEC33, 24 and 18, were released from PSII. The liberated OEC33 and also OEC24 to a lesser extent were subsequently damaged and then exhibited smeared bands in SDS/urea-PAGE. Once deteriorated, OEC33 could not bind to PSII. The effects of scavengers and chelating reagents on the damage indicated that hydroxyl radicals generated from superoxide in the presence of metal ions were responsible for the damage. These results suggest that, like the D1 protein of the PSII reaction center complex, OEC subunits suffer oxidative damage and turnover under illumination.

Oxygen-evolving complex (OEC) subunits are extrinsic proteins that are associated with the intrinsic core part of PSII at the lumenal surface, and participate in the oxygen-evolving reaction catalyzed by the Mn cluster.

The three OEC subunits from higher plants have Mr of 33, 24 and 18 kDa and are designated OEC33, 24 and 18, respectively. Among the three subunits, OEC33 plays a central role in oxygen evolution, and stabilizes the catalytic Mn cluster. It helps the functional binding to PSII of OEC24 and 18, which are involved in the retention of Ca2+ and Cl–, essential cofactors for oxygen evolution (. In addition, OEC33 protects the PSII core complex from damage caused by donor-side photoinhibition of PSII . In accordance with the role in PSII, OEC33 has a highly flexible structure, which enables the protein to shield the lumenal surface of PSII. Structural modeling supported this conclusion and suggested that OEC33 has two β-sheet-enriched domains connected by a hinge structure, which makes the overall conformation quite extended and flexible

Among the supramolecular complexes in the thylakoid membrane, PSII has an intriguing feature in that it undergoes disassembly and reassembly under illumination even under the optimum conditions for plant growth. This is called the photoinhibition and repair cycle of PSII

Although the photodamage and subsequent degradation of the D1 protein of the PSII reaction center complex have been intensively studied , information on damage to the OEC subunits under illumination is quite limited. A previous in vitro study using inside-out thylakoid vesicles demonstrated that the OEC subunits and Mn are released from PSII in parallel with the loss of the D1 protein under strong illumination that causes photoinhibition of PSII . It is unclear, however, whether the OEC subunits suffer some damage and are replaced by intact forms under such illumination in vivo.

In the present study, we investigated the effects of photoinhibitory illumination on the OEC subunits using isolated PSII membranes from spinach. It was demonstrated that each of the three subunits is released from PSII under strong illumination and that the released subunits, particularly OEC33, suffer oxidative damage mediated by hydroxyl radicals generated under the illumination. The mechanisms of photodamage to the OEC subunits, together with the role of the reservoir pool of the OEC subunits in the lumen, are discussed.



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The Psb27 Protein Facilitates Manganese Cluster Assembly in Photosystem II*

Photosystem II (PSII) is a large membrane protein complex that uses light energy to convert water to molecular oxygen. This enzyme undergoes an intricate assembly process to ensure accurate and efficient positioning of its many components. It has been proposed that the Psb27 protein, a lumenal extrinsic subunit, serves as a PSII assembly factor. Using a psb27 genetic deletion strain (Δpsb27) of the cyanobacterium Synechocystis sp. PCC 6803, we have defined the role of the Psb27 protein in PSII biogenesis. While the Psb27 protein was not essential for photosynthetic activity, various PSII assembly assays revealed that the Δpsb27 mutant was defective in integration of the Mn4Ca1Clx cluster, the catalytic core of the oxygen-evolving machinery within the PSII complex. The other lumenal extrinsic proteins (PsbO, PsbU, PsbV, and PsbQ) are key components of the fully assembled PSII complex and are important for the water oxidation reaction, but we propose that the Psb27 protein has a distinct function separate from these subunits. We show that the Psb27 protein facilitates Mn4Ca1Clx cluster assembly in PSII at least in part by preventing the premature association of the other extrinsic proteins. Thus, we propose an exchange of lumenal subunits and cofactors during PSII assembly, in that the Psb27 protein is replaced by the other extrinsic proteins upon assembly of the Mn4Ca1Clx cluster. Furthermore, we show that the Psb27 protein provides a selective advantage for cyanobacterial cells under conditions such as nutrient deprivation where Mn4Ca1Clx cluster assembly efficiency is critical for survival.


The electron transfer reactions through PSII require precise positioning of its redox active cofactors. Proper assembly of the numerous PSII components is essential, and the PSII biogenesis pathway entails an ordered assembly of the constituent proteins and cofactors


How did evolution find out the correct sequence of assembling of the constituent proteins and cofactors? trial and error?

Moreover, PSII assembly occurs frequently because this enzyme continually undergoes a cycle of damage and repair.

How did natural selection find out the mechanisms of repair? trial and error? how did PSII evolve the proteins and cofactors after the complex or partial subunits were damaged?

As a consequence of its normal function, the D1 membrane protein of PSII is irreversibly damaged and must be replaced with a newly synthesized copy. During this repair cycle, the complex is at least partially disassembled as the damaged D1 protein is proteolytically removed. Key events in the reassembly pathway include  the integration of a newly translated precursor D1 protein (pD1) with a C-terminal amino acid extension, cleavage of the pD1 protein extension by the CtpA protease to yield the mature D1 protein, assembly of the catalytic Mn4Ca1Clx cluster, and binding of a number of extrinsic proteins on the lumenal side of the complex.

It seems that this repair cycle mechanism is essential and  integral part of the function of PSII. How did this repair cycle evolve? How could PSII survive without the repair cycle mechanism fully in place and functioning?



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18 Re: Origin and evolution of photosynthesis on Sat Mar 15, 2014 6:33 pm

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http://www.javeriana.edu.co/Facultades/Ciencias/neurobioquimica/libros/metabolismo/metabolismo_archivos/Evolution%20of%20Photosynthesis.pdf

In the case of oxygenic photosynthesis, the two types of reaction centres are both needed and work in series. In photosystem II, water can serve as the ultimate electron donor. However, the Em of the ultimate electron acceptor at the acceptorside, QB ,is too positive to be able to reduce NAD or NADP without having additional driving force (such as a proton gradient). In contrast, oxidized photosystem I-type reaction centres are rather weak oxidants and cannot oxidize water but can oxidize electron carriers that ultimately received their electrons from photosystem II.

The important questions that are still open are what the ancestral reaction centre may have looked like, what its origin may have been, and what could have been the selection pressure for two types of reaction centres to develop.

However,the primary structure of the purple bacterial reaction centre is far removed from that of photosystems II and I, particularly in terms of the antenna system. Therefore, if purple bacteria are indeed evolutionarily ancient, one or several links between these organisms and those containing photosystem I-type reaction centres or photosystem II either are no longer extant or have not yet been discovered.


Even a heliobacterial homodimeric reaction centre has 11 membrane-spanning regions per subunit,and it is unlikely that such a complex structure would have formed spontaneously

the sequence similarities between single membrane-spanning helices of different reactioncentre complexes are weak,it is impossible at this point to develop an unequivocal evolutionary scheme of the formation of photosynthetic reaction centres.


http://www.queenmaryphotosynthesis.org/krauss/photosystems/page19/page19.html

shifting the redox potentials of Chl in two different types of photosynthetic reaction centres in opposite directions, about +300 mV in P680 and about −400 mV in P700 with respect to Chla in organic solvent [1., 8. and 9.••], was one of the central achievements required for the evolution of oxygenic photosynthesis, as it made it possible to bridge the free energy gap for the strongly endergonic reduction of NADP+ by water.


From one photosystem to two

Green and purple bacteria (containing only one photosystem similar to either one or the other of the photosystems found in cyanobacteria and plants) are believed to be the ancestors of cyanobacteria. Two questions arise—how did both the photosystems arise and how did both photosystems get into one bacteria? No mechanism is provided for how the photosystems came into existence, just that “these genes arose” for one photosystem. It is then proposed that a “simple duplication” of the genes encoding one photosystem occurred, followed by mutation leading to the formation of another photosystem. What is needed is new information to form another photosystem, not duplication of already present genes followed by mutation. This will only lead to the loss of information.

The article proposes that lateral gene transfer (a DNA-swapping mechanism in bacteria) then occurred, and both photosystems ended up in the same bacterium. A good question to pose here is what is the selection pressure to keep both photosystems in a bacterium if one is sufficient? For both photosystems to be kept, a functional relationship between the two would have to form that would give the bacterium an advantage over other bacteria. So, what is the mechanism proposed to form this new functional relationship? “It would have only been a small step away from the cyanobacterial state of oxygenic photosynthesis, provided that it underwent the right mutation [...] and provided that this happened in the right environmental setting at the right time.” The improbability of this is enormous considering that mutations and natural selection, which decrease genetic information, are the only mechanisms that evolution can use.

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19 evolution of photosystem II and nitrogenase on Mon Mar 17, 2014 2:03 pm

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Evolution of photosystem II and nitrogenase

The existence in the same organism of cyanobacterias of two conflicting metabolic systems, oxygen evolving photosynthesis and oxygen-sensitive nitrogen fixation, is  a puzzling paradox. How to explain it ? 7)

Researchers have long been puzzled as to how the cyanobacteria could make all that oxygen without poisoning themselves. To avoid their DNA getting wrecked by a hydroxyl radical that naturally occurs in the production of oxygen, the cyanobacteria would have had to evolve protective enzymes. But how could natural selection have led the cyanobacteria to evolve these enzymes if the need for them didn’t even exist yet?  The explanations are fantasious at best 8

Nitrogenase is one of the most metabolically expensive processes in biology

The nitrogenase enzyme seems to be irreducible complex

http://www.ebi.ac.uk/interpro/entry/IPR000392

Nitrogen fixing bacteria possess a nitrogenase enzyme complex that catalyses the reduction of molecular nitrogen to ammonia [PMID: 2672439, PMID: 6327620, ]. The nitrogenase enzyme complex consists of two components:

Component I is nitrogenase MoFe protein or dinitrogenase, which contains 2 molecules each of 2 non-identical subunits.
Component II is nitrogenase Fe protein or dinitrogenase reductase, which is a homodimer. The monomer is encoded by the nifH gene [PMID: 6327620].

the subunits are unique , and cannot be used in other proteins :

http://www.biologie.uni-halle.de/microbiology/general-mibi/sawers/basem_soboh/

The active site of [NiFe]-hydrogenase has one carbon monoxide and two cyanide ligands coordinated to the iron atom, a feature that is to date unique in biology.

Since the nitrongenase enzyme is composed of two subunits, set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic it can be considered irreducible complex.

Biosynthesis and evolution of the Nitrogenase enzyme :

http://www.annualreviews.org/doi/full/10.1146/annurev.micro.62.081307.162737

It is accepted that FeMo-co is assembled separately in the cells and is finally incorporated into a FeMo-co-deficient apo-MoFe protein.

How could this process be result of evolutionary mechanisms ? The nitrogenase enzyme functions only, if fully assembled .

When synthesized, the nitrogenase components are not immediately competent for nitrogen fixation. Rather, they become mature by the actions of several nif and non-nif gene products to achieve catalytic competency.

How did evolutionary mechanisms forsee the necessity of maturing  and evolve  several gene products for doing so  ?

How happened the alleged transition from a reduced atmoshpere, to a atmosphere with oxygen ? Its acknowledged there are many unresolved issues 3)

   So a date and a culprit can be fixed for what scientists refer to as the Great Oxidation Event, but mysteries remain. What occurred 2.45 billion years ago that enabled cyanobacteria to take over? What were oxygen levels at that time? Why did it take another one billion years—dubbed the "boring billion" by scientists—for oxygen levels to rise high enough to enable the evolution of animals?

   Most important, how did the amount of atmospheric oxygen reach its present level? "It's not that easy why it should balance at 21 percent rather than 10 or 40 percent," notes geoscientist James Kasting of Pennsylvania State University. "We don't understand the modern oxygen control system that well."

What evolutionary reasons could exist for chemoautrophic bacterias to evolve photosynthesis ? Specially, as splitting of water is such a extremely complex and energy consuming mechanism ?  Science has no answer .

"Of all the biochemical inventions in the history of life, the machinery to oxidize water — photosystem II — using sunlight is surely one of the grandest." (Sessions, A. et al, 2009)

Photosystem II "is one of nature's most complicated enzymes — complicated partly because it involves a four-electron oxidation process resulting in four intermediate states and the concurrent chemistry of O-O bond formation."

to see the protein in 3D:

http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=99538

Fact is, the various protein complexes used in the light and dark reactions of photosynthesis  are IC, but the  Z-Scheme , together with the Calvin cycle, is  a interdependent system ;  removing ATPase, no ATP can be generated, and the whole function will be compromised. If the thylakoide membrane is not fully formed, no proton gradient can be formed, and ATP will not be generated.

Biosynthesis of Chlorophyll uses 17 enzymes in the pathway , and probably most proteins involved in photosynthesis, are also a IC. If one of the enzymes in the pathway is missing, the final product cannot be synthesized.
How could it be product of evolution ? And what function would Chlorophyll a have, if not employd in the whole photosyntesis system ?
I have tracked the biosynthesis pathway of Chlorophill a.

http://reasonandscience.heavenforum.org/t1546-chlorophyll-biosynthesis-pathway

The enzymes in the last eight steps, from Protoporphyrin IX, to Chlorophyllide a, are unique and exclusively used in the Chlorophyll biosynthesis pathway.
So fantasious explanations as from Miller will not do it - co-opting parts from other biological systems. That  fairy tale pseudo scientific idea of copying, modifying, and combining together preexisting parts , already operating in other systems.......  Borrowing parts from other biological systems and assemble them to a chlorophyll molecule with a new function , perfectly ordered, with perfect fits, and new functions,with the help of saint time , how could they do the miracle ?
Researching scientific papers about evolution of photosynthesis, i encountered this explanation :
However, all modern oxygenic photosynthetic organisms now require O2 as an oxidant at several steps in the pathway. This has been explained in terms of gene replacement of the genes coding for the enzymes at these steps, with the result that the overall pathway is unchanged but the enzymes at key steps are completely different in different groups of phototrophs (Raymond and Blankenship, 2004).
Gene replacement. Cool. So evolution selects to " replace " the genes just for fun,  as a capriche of nature, without any apparent reasons,  and the job gets done. Amazing.....
Plants, algae and cyanobacteria grow because of their ability to use sunlight to extract electrons from water. This vital reaction is catalysed by the Photosystem II (PSII) complex, a large multisubunit pigment protein complex embedded in the thylakoid membrane. Recent results show that assembly of PSII occurs in defined regions of the membrane system.
Nano roboters ( the assembly factor proteins ) build the nano machines ( proteins, enzymes etc. ), like the PSII subunit, the oxygen evolving complex, ( which splits water utilizing energy from the sun to split O2 into protons, electrons and oxygen ) ,beside  a large number of proteins, pigments, lipids and ions, in a highly coordenated and extremely precise, step-wise fashion. It  proceeds through a number of distinct assembly intermediates.   Associated with these assembly complexes are proteins that are not found in the final functional PSII complex.
So these proteins work like roboters in a assembly line, mounting the protein complex.
Structural information and possible functions are beginning to emerge for several of these ‘assembly’ factors, notably Ycf48/Hcf136, Psb27 and Psb28.  4)

All these units are assembled together :

- 17 intrinsic  sub-units
-   3 extrinsic sub-units
-    cofactors
-  35 chlorophylls
-  2   pheophytins
- 11 β-carotenes
- > 20 lipids
- plastoquinones
- 2 heme irons
- 1 non-heme iron
- 4 manganese atoms,
- 4 calcium atoms
- 3 Cl- ions per monomer

How could these assembly factors ( nano roboters ) be result of evolution ? there is no function  in a intermediate stage of evolution for them. And they become only functional, when used to build the protein complexes. They do not have a final function of their own. How could they forsee, what final function they would have to get ? How could they know, once fully synthesized , where to take the subunit parts, and how to mount them in the right order, at the right place ?

Oxygenic photosynthesis produces various radicals and active oxygen species with harmful effects on photosystem II (PSII). Such photodamage occurs at all light intensities. Damaged PSII centres, however, do not usually accumulate in the thylakoid membrane due to a rapid and efficient repair mechanism. 5)

PSII has a more oxidized redox potential compared to PSI; therefore, in case of excess of light, PSII is damaged first. If PSII is not repaired, a phenomenon called photoinhibithion occurs , causing a decrease of photosynthesis and thus a decrease of
growth. To keep PSII homeostasis, assembly and repair mechanisms maintain to certain level the amount of functional PSII in the thylakoids.6)

Unless the repair mechanism would have not been in place right from the beginning, PSII probably would not be able to function in order to sustain life of the plant or bacterium for enough time. How could it evolve separately ?  
The excellent design  of PSII gives protection to most of the protein components and the damage is most often targeted only to the reaction centre D1 protein. Repair of PSII via turnover of the damaged protein subunits is a complex process involving (i) highly regulated reversible phosphorylation of several PSII core sub units. Photosynthetic water splitting involves highly oxidative chemistry, which is accomplished by a unique PSII complex. PSII converts light energy into chemical form using water as a source of electrons and liberating molecular oxygen as a side product. Light is a harmful substrate for the water-splitting PSII complex, exposing its protein subunits to structural damage.

A number of protective systems exist in the thylakoid membrane and surrounding stroma to dissipate excess light energy and to scavenge various radicals and active oxygen species.

to make the assembly of a photosystem, external enzymes which make not part of the complex, are required, to assemble to protein subunits in the right order, into the right place. That must happen in a extremely precise and accurate order. What function would these co factors have by their own ? none. That indeed falsifies the ToE very much in its tenets , and in its core assertions.

How could this regulation be result of evolution ? unless the regulation mechanism were not fully in place and working, it would have no function


3) http://www.scientificamerican.com/article/origin-of-oxygen-in-atmosphere/
4) http://aob.oxfordjournals.org/content/106/1/1.full
5) http://jxb.oxfordjournals.org/conten...1/347.abstract
6) http://www.diva-portal.org/smash/get/diva2:556757/FULLTEXT01.pdf
7) http://mmbr.asm.org/content/56/2/340.full.pdf
8 ) http://www.universetoday.com/1002/how-did-early-bacteria-survive-poisonous-oxygen/

http://www.alga.cz/userfiles/media/file/sobotka/COPB_komenda_2012.pdf



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20 Re: Origin and evolution of photosynthesis on Wed Mar 19, 2014 2:46 pm

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http://www.psi.cz/ftp/ola/Molecular%20Mechanisms%20of%20Photosynthesis.pdf

Another apparent paradox is the discovery that enzyme systems that either use O2,
such as various oxidases,or protect against its reactive by-products,such as superoxide or
hydrogen peroxide, are found widely distributed throughout the tree of life. This suggests
that these enzyme systems were present in the last common ancestor, which we
earlier argued was not even photosynthetic, let alone oxygenic. So the ability to use or
protect against oxygen appears on the surface to have been present prior to the ability to
make oxygen (Castresana and Saraste, 1995; Castresana and Moreira, 1999).

Isnt that not rather evidence that oxygen was present right from the beginning in the atmosphere  ?


There are two possible explanations for this apparent paradox. First, low levels of O2 and other reactive
oxygen species were almost certainly produced on the early Earth by nonbiological
processes, so even the earliest cells may have needed protection from these toxic species.


"almost certainly" indicates guesswork, right ?!!



Second, the ability to use and cope with oxygen species is such a huge advantage for any
life form that early enzyme systems that developed in response to the advent
of oxygenic photosynthesis may have been very widely disseminated by lateral gene
transfer.


All known existing photosynthetic organisms are highly sophisticated cells, far removed from the first forms.

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21 Re: Origin and evolution of photosynthesis on Thu Mar 20, 2014 12:57 pm

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Spinach, Or The Search For The Secret Of Life As We Know It

Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems.

Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers

One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere.


TRANSITION TO OXYGENIC PHOTOSYNTHESIS

Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis.

http://www.fceqyn.unam.edu.ar/~celular/paginas/Articulos%20Biol%20Cel%202004/Annual%20Reviews/Review%20photosyntesis.pdf

The evolutionary path of type I

and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits

http://www.sciencedirect.com/science/article/pii/S0960982209011890

While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved.

http://www.pnas.org/content/early/2013/06/20/1305530110

The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown.


Chlorophyll Biosynthesis Gene Evolution Indicates Photosystem Gene Duplication, Not Photosystem Merger, at the Origin of Oxygenic Photosynthesis

An open question regarding the evolution of photosynthesis is how cyanobacteria came to possess the two reaction center (RC) types, Type I reaction center (RCI) and Type II reaction center (RCII).

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22 Is Photosynthesis Irreducibly Complex? on Wed Apr 02, 2014 9:40 am

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Is Photosynthesis Irreducibly Complex?

From Nature this week. “Knowing how plants and bacteria harvest light for photosynthesis so efficiently could provide a clean solution to mankind’s energy requirements. The secret, it seems, may be the coherent application of quantum principles. Roseanne J. Sension doi:10.1038/446740a Full TextÂÂ

Photosynthesis provides the primary energy source for almost all life on Earth. One of its remarkable features is the efficiency with which energy is transferred within the light harvesting complexes comprising the photosynthetic apparatus. Suspicions that quantum trickery might be involved in the energy transfer processes at the core of photosynthesis are now confirmed by a new spectroscopic study. The study reveals electronic quantum beats characteristic of wavelike energy motion within the bacteriochlorophyll complex from the green sulphur bacterium Chlorobium tepidum. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer.
ÂÂ
Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke ‘hopping’ of excited-state populations along discrete energy levels 1, 2. Spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex 6, 10. Here we obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems Gregory S. Engel et al Nature 446, 782-786 (12 April 2007) | doi:10.1038/nature05678″

Conclusion? Obviously this is a brilliant piece of design by someone who even knows how quantum mechanics works. Well not exactly …
Photosynthesis Analysis Shows Work Of Ancient Genetic EngineeringÂÂ

Science Daily 2002 — The development of the biochemical process of photosynthesis is one of nature’s most important events, but how did it actually happen? This is a question that molecular biology has first posed, and now perhaps answered.
“The process of photosynthesis is a very complex set of interdependent metabolic pathways,” said Robert Blankenship, professor of biochemistry at Arizona State University. “How it could have evolved is a bit mysterious.”

Photosynthesis is one of the most important chemical processes ever developed by life — a chemical process that transforms sunlight into chemical energy, ultimately powering virtually all the living things and allowing them to dominate the earth. The evolution of aerobic photosynthesis in bacteria is also the most likely reason for the development of an oxygen-rich atmosphere that transformed the chemistry of the Earth billions of years ago, further triggering the evolution of complex life. After decades of research, biochemists now understand that this critical biological process depends on some very elaborate and rapid chemistry involving a series of enormously large and complex molecules a set of complex molecular systems all working together.
“We know that the process evolved in bacteria, probably before 2.5 billion years ago, but the history of photosynthesis’s development is very hard to trace,” said Blankenship.

In a paper in the November 22 2002 issue of Science, Blankenship and colleagues partially unravel this mystery through an analysis of the genomes of five bacteria representing the basic groups of photosynthetic bacteria and the complete range of known photosynthetic processes.

The analysis revealed clear evidence that photosynthesis did not evolve through a linear path of steady change and growing complexity but through a merging of evolutionary lines that brought together independently evolving chemical systems — the swapping of blocks of genetic material among bacterial species known as horizontal gene transfer.

“We found that the photosynthesis-related genes in these organisms have not had all the same pathway of evolution. It’s clear evidence for horizontal gene transfer,” said Blankenship.

Blankenship performed a mathematical analysis of the set of shared genes to determine possible evolutionary relationships between them, but they arrived at different results depending on which genes were tested
“We did a kind of tree analysis of all 188 genes to determine what the best evolutionary tree was. We found that a fraction of the genes supported each of the different possible arrangements of the tree. It’s clear that the genes themselves have different evolutionary histories,” Blankenship said.

Blankenship argues that different pieces of the system evolved separately in different organisms, perhaps to serve purposes different from their current function in the photosynthesis. Brought together either by fusion of two different bacteria or by the “recruitment” of blocks of genes, the new combination of genes resulted in a new combined system.

“This kind of evolution in bacteria is kind of like what happens at a junk dealer,” said Blankenship.

“Bits and pieces of whatever there is out in the yard get hauled back and welded together and made into this new thing. All these metabolic pathways get borrowed and bent a bit and changed.”

Blankenship points out that nature’s way of creating useful and complicated chemical systems through horizontal gene transfer also points to how human-directed biodesign might co-opt the process.

“This work gives us some insights into how complex metabolic pathways originated and evolved, so this might give some ideas about how to engineer new pathways into microorganisms,” he said. “These organisms could be designed to carry out new types of chemistry that may benefit mankind, such as multi-step synthesis of drugs.”

How exactly did all those different organisms, who donated parts of the photosynthesetic process, get their energy while they were doing all that evolving of the components of the Irreducibly Complex looking system ready to be put together by the Blind Watchmaker?

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Spinach, Or The Search For The Secret Of Life As We Know It

Deep in the heart of this nest of proteins lies the manganese cluster, whose precise arrangement of atoms remains one of biology's outstanding problems.


Light-driven oxygen production from superoxide by Mn-binding bacterial reaction centers

One of the outstanding questions concerning the early Earth is how ancient phototrophs made the evolutionary transition from anoxygenic to oxygenic photosynthesis, which resulted in a substantial increase in the amount of oxygen in the atmosphere.



TRANSITION TO OXYGENIC PHOTOSYNTHESIS

Perhaps the most widely discussed yet poorly understood event in the evolution of photosynthesis is the invention of the ability to use water as an electron donor, producing O2 as a waste product and giving rise to what is now called oxygenic photosynthesis.


http://www.fceqyn.unam.edu.ar/~celular/paginas/Articulos%20Biol%20Cel%202004/Annual%20Reviews/Review%20photosyntesis.pdf

The evolutionary path of type I

and type II reaction center apoproteins is still unresolved owing to the fact that a unified evolutionary tree cannot be generated for these divergent reaction center subunits


http://www.sciencedirect.com/science/article/pii/S0960982209011890

While the rise of oxygen has been the subject of considerable attention by Earth scientists, several important aspects of this problem remain unresolved.

http://www.pnas.org/content/early/2013/06/20/1305530110

The emergence of oxygen-producing (oxygenic) photosynthesis fundamentally transformed our planet; however, the processes that led to the evolution of biological water splitting have remained largely unknown.

http://astrobiology.nasa.gov/media/txp_files/Blankenship%20Santander%20Astrobiology%203013%20part%202.pptx.pdf

Evolutionary origins of oxygen evolution center and linked photosystems are important unsolved problems.

To understand the origin and early evolution of photosynthesis, we need to consider mechanisms and evolution of all these subsystems and processes:

Pigments ( Chls , carotenoids, bilins )

Reaction centers (including O2  Evolution Center)

Antenna complexes

Electron transfer pathways

Carbon fixation pathways

Photoprotection mechanisms

Integration into cellular metabolism

No single branching diagram can represent the complex path of evolution of photosynthesis.



The following diagram shows how helpless science is to explain through evolution the origin of photosynthesis



The evolution of PS2 proteins has been partially by gene recruitment and partially by gene duplication, but most of the proteins are orphans, with no known source.

Origin and Evolution of Photosynthesis- Remaining Challenges

Nature of the earliest PS systems not known

Significance of gene duplications in RC evolution not understood

Evolutionary origin of the oxygen evolving complex not known

No good understanding of how two photosystems were linked in series

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24 The Biophysics of Photosynthesis on Tue Jun 27, 2017 8:42 pm

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The Biophysics of Photosynthesis, page 421

Geochemists tend to believe that the early Earth atmosphere was rather slightly oxidizing or neutral than reducing. It is likely that consensus has emerged that a start of life needed a constant generation of thermodynamic disequilibria and highly reducing conditions for the synthetic reactions. Deep-sea hydrothermal vents that were common through Hadean and Archean time had provided such thermodynamic disequilibria and those reducing conditions on the global scale. Given high concentrations of CO2, the reactive conditions at the alkaline hydrothermal vents were conducive to the origin of chemoautotrophic life. Alternatively, the hypothesis of the terrestrial origin of life emphasizes on a local start of heterotrophic life boosted by thermodynamic disequilibria provided by terrestrial geothermal ponds or similar environments and enhanced by the UV-driven photochemical synthesis
of the organic compounds that fed the heterotrophic protocells.

When life had started is fundamental question as development of the genetic code would need time. It is suggested that the components of the protocells such as metabolic blocks, compartmentalized membrane systems, or RNA-based coding and translation could have been evolved in the pre-LUCA communities, natural reactive habitats such as proposed for the deep-sea hydrothermal vents or the geothermal ponds. This means that the pre-LUCA development could have started earlier in the Hadean (~4.3 Ga). Unfortunately, the timing of this is compromised by uncertainty with the degree of impacts from the heavy meteorite bombardment, which is thought to be characteristic of this time. It is possible that life had emerged several times but it was intermittently sterilized on the surface. Within the framework of the terrestrial origin of life emergence of primitive photosynthesis could have occurred not long after the origin of life. The primordial photosynthetic components that were supposedly synthesized at the pre-LUCA stage could have been integrated into the simple heterotrophic protocells. In this case the evolution of the tetrapyrrole pathways would mirror the evolution of photosynthesis, and the early start of photosynthesis would favor the Granick hypothesis. The early photoheterotrophic organisms could diverge into mixotrophs in the ocean depending on the source of electron donors for photosynthesis. Recent discoveries of non-photosynthetic heterotrophic and photoheterotrophic species in Chlorobi family  would support a scenario of the photoheterotrophic life later turned mixotrophic and strictly autotrophic.

However, widely accepted hypothesis of the Late Heavy Bombardment (4.2–3.8 Ga) would imply that only hyperthermophiles had chances to survive through the bottleneck of the bombardment. The discovery of endolithic and subsurface habitats of both terrestrial and marine microorganisms living off the rock geochemistry as deep as 3 km would support this idea. This is also supported by recent modeling studies concluding that the Earth habitable zone could not have been destroyed even by the harshest impacts  giving preference to the seafloor and the oceanic deep crust primordial habitats and excluding the terrestrial habitats. Thus, the deep-rooted hyperthermophilic chemoautotrophic survivors of Eubacteria could possibly give rise to the photosynthetic lineages when they encountered light in the photic zone. The photosynthesis in the photic zone could have appeared after the end of the bombardment around 3.8 Ga and could have settled in shallow water habitats by 3.4 Ga as evidenced by microfossil records of the diverse microbial life including shallow water anoxygenic photosynthesis.

We do not know what type of metabolism the photosynthetic ancestors possessed. Based on the properties of extant chemoautotrophs this could be as primitive as the reductive acetyl-CoA pathway, the reductive TCA pathway, or a combination of both. As photosynthesis is generally considered to be a complex process the recruitment of the ancestor’s available systems for new light-driven generation of the reducing power for the CO2 reduction would be evolutionarily justified. For the same reason, the BChl biosynthetic pathway could have been built based on recruitment of the available ancient pathways and the enzymes and their adjustment to the synthesis of Mg- or Zn-containing Chls, Bchls, or both. Should we consider the connection of the PSI with metabolism primeval? Iron–sulfur centers in the PSI possibly descended from the primordial iron–sulfur clusters or primitive ferredoxins that catalytically mediated the reduction of CO2 in the microporous compartments of the alkaline hydrothermal vents. The PSI is a major producer of the light-generated reducing power for the carbon fixation and other metabolic pathways through a series of Fe–S-containing proteins, which are shared by many metabolic networks. The ancient bacteria possessing proto-reaction centers would immediately benefit from the new source of energy by outgrowing their competitors and surviving by natural selection.

Finally, current uncertainty in the origin of photosynthesis is determined by the fact that the competing hypotheses provide alternative explanations and have different levels of conclusive evidence or experimental testing. Future discoveries of new photosynthetic phyla, improved quality of genome-wide phylogenetic analysis, experiments on simulation of the primordial conditions, and directed evolution will inevitably lead to a synthesis of unified concept of the evolution of photosynthesis.

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25 Evidence of design of photosynthesis is growing on Sat Jul 29, 2017 10:20 pm

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Origin Of Photosynthesis In A Sun-loving Bacteria 1

With today's solar panels limited by their efficiency (currently, more than 80 percent of available solar energy is lost as heat), scientists have been looking into nature as inspiration to better understanding the way photosynthetic plants and bacteria capture sunlight.

"Nature's invention of photosynthesis is the single most important energy conversion process driving the biosphere, and photosynthesis forever changed the Earth's atmosphere," said Raimund Fromme, an associate research professor at the ASU Biodesign Institute's Center for Applied Structural Biology and in the School of Molecular Sciences.

Life's solar panels, which scientists call photosystems, are used by plants, algae and photosynthetic bacteria as an incredibly efficient system for capturing almost every available photon of light to grow and thrive, filling almost every nook and cranny on earth.

"To truly and fully understand photosynthesis, one has to follow the process of converting light into chemical energy," said Fromme. "This is one of the fastest chemical reactions ever studied, which is part of what makes it so hard to study and understand."

The timescales of photosynthesis turn a bolt of lightning into a snail-like pace by comparison. Photosynthesis reactions occur at the scale of picoseconds, which is one-trillionth of a second. A picosecond is to one second as one second is to 37,000 years.


Using X-ray light at the Advanced Light Source in Berkeley, CA, and a beamline at Advanced Photon Source at Argonne National Lab, IL., Fromme's group has now visualized the heliobacteria reaction centers for the very first time at near-atomic, 2.2-angstrom resolution (an angstrom is the width of a hydrogen atom). They found an almost perfect symmetry in the heliobacter RC (shown by the mirror image pattern of the main protein motifs, indicated by cylinders (top image) and a close up of the exact placement of individual reaction center atoms (bottom).

At the heart of photosynthesis is a reaction center; it's an elaborate complex of pigments and proteins that turn light into electrons to power the cell.

Chlorophyll is the pigment that makes plants green. In plants, chlorophyll captures the sun's energy and uses it to make sugars out of carbon dioxide from the air and water.

anoxygenic phototrophic bacteria, such as Heliobacterium modesticaldum, use a single RC to drive a cyclic electron transfer (ET) pathway that creates a proton-motive force across the membrane, which is used to drive energy production and metabolism by ATP synthesis.

At this point "a thrilling discovery on unchartered territory began, as each new chlorophyll was cheered," Fromme remembered, and "proved everyone's initial prediction on the heliobacteria's RC was wrong."

They found an almost perfect symmetry in the heliobacter RC.

The core polypeptide dimer and two small subunits coordinate 54 (bacterio)chlorophylls and 2 carotenoids that capture and transfer energy to the core at the reaction center, which performs charge separation, stabilization and electron transfer it consists of 6 (bacterio)chlorophylls and an iron-sulfur cluster; unlike other reaction centers, it lacks a bound quinone.

A reaction centre is laid out in such a way that it captures the energy of a photon using pigment molecules and turns it into a usable form. Once the light energy has been absorbed directly by the pigment molecules, or passed to them by resonance transfer from antenna pigments, they release two electrons into an electron transport chain. 2

Function and Regulation of Antenna Systems 3

The vast majority of the pigments in a photosynthetic organism are not chemically active, but function primarily as an antenna (1,4). The photosynthetic antenna system is organized to collect and deliver excited state energy by means of excitation transfer to the reaction center complexes where photochemistry takes place. The antenna system increases the effective cross section of photon absorption by increasing the number of pigments associated with each photochemical complex. The intensity of sunlight is sufficiently dilute so that any given chlorophyll molecule only absorbs at most a few photons per second. By incorporating many pigments into a single unit, the biosynthetically expensive reaction center and electron transport chain can be used to maximum efficiency. A remarkable variety of antenna complexes have been identified from various classes of photosynthetic organisms. There seems to be little doubt that there have been multiple evolutionary origins of antenna complexes, as there is no common structural theme evident.

So basically, there is no common ancestor, but the convergent evolution of the same function. So, when there is a similarity, evolution is inferred. When there is no similarity as in this case, evolution is also inferred.....

Antenna systems are often viewed as being "on" all the time, with the regulation of photosynthesis in response to different conditions taking place primarily in the reaction centers and carbon metabolism enzymes. Clearly, this is not the case, and the modern view is of a much more actively regulated system at all stages of energy storage. The advantages of "directional signals" or "volume controls" to regulate either the distribution between the photosystems or the number of excitations delivered by the entire antenna network are easy to appreciate.

One of the most interesting and important of these regulatory mechanisms is the phenomenon of "nonphotochemical quenching" (qN) of chlorophyll excited states in chloroplasts (7). During periods of high irradiance such as midday, or under certain stress conditions, a substantial fraction of the excited state energy is dissipated by quenching before it is ever transferred to the reaction center. The basic idea is that it is much easier and safer for cells to dispose of this energy before it initiates the photochemical processes in reaction centers than it is for them to try to repair the substantial photooxidative damage that can result from excess light. This process is now thought to be a major regulatory mechanism and understanding it is likely to have great economic significance.

So how did this regulatory system emerge? trial and error? If the regulation was not in place, then photooxidative damage would occur. If repair mechanisms were not in place right from the start, the system would be damaged by high solar radiation, and the plant would die. Had both, the regulation, AND repair mechanisms not have to be in place right from the start ?

All the antenna systems share both high quantum efficiency and two structural characteristics: first, they have very densely packed chromophores (e.g., the antenna of Photosystem I has a chlorophyll concentration of about 0.9 M.11) This dense packing, required for the effective absorption of sunlight, produces strong interactions between the component molecules, modifying their electronic and dynamic properties and introducing new functions significantly different from their components. In other words, they exhibit emergent properties. Second, most, if not all, antenna systems contain carotenoid molecules, which serve as both secondary light harvesters and photoprotective agents.  4

This is remarkable. It means, a density and packing less than the actual system of chlorophyll concentration, the function is lost. This obviously means a gradual stepwise evolutionary rise of the antenna complex with chlorophylls capturing photons is not possible. It's an either as is, or no function - situation. This disproves evolution as capable mechanism to explain the origin of the antenna system of photosynthesis.

In light-harvesting organisms, these conditions lead to a general architecture of pigment–protein complexes where large, dense arrays of chromophores serve as antennae, or the sites of initial absorption events.2,3 The excitation then migrates quickly, without losses from relaxation to the ground state, to a location, the reaction center, where a photochemical reaction traps the excitation and initiates an electron transfer chain that converts the light energy to usable chemical energy. Once the excitation reaches the reaction center, it must be converted irreversibly into chemical energy. Charge separation must be ultrafast with little or no back flow of charge, while metal-based catalysts must be made from earth-abundant materials to allow plants to flourish across the planet

A model of the Photosystem II (PSII) supercomplex, and a sample trajectory, is shown in Fig. 1



Dynamics of light harvesting
Speed is essential to efficient light harvesting. As noted above, at low light levels, energy transfer processes in photosynthetic organisms can show a >90% quantum efficiency, which is defined as the percentage of absorbed photons that undergo charge separation at the reaction center. Fig. 1 presents a sample trajectory of excitation energy through a model of the photosynthetic apparatus. This translocation of the excitation must be achieved before the energy is lost through fluorescence or nonradiative relaxation. If excitation movement is modelled via a classical random walk, in an antenna of 250 Chls each energy transfer step must take 100 fs for >90% of excitations to reach the reaction center, given a Chl fluorescence lifetime of 2 ns. The ultrashort energy transfer timescale raises the question of whether mechanisms beyond that envisaged in standard F€orster theory are utilized in photosynthesis. The short answer is yes. Nature uses God created  a variety of sophisticated methods to achieve the necessary speed and directionality of energy flow. One such method that has gathered much recent attention is the use of intrinsically quantum mechanical phenomena to optimize energy flow.

Coherence most likely arose as a byproduct of the packing density required to optimally absorb sunlight.

Most likely, there would never have been the first go, if the packing density were not right from the start......



1. http://astrobiology.com/2017/07/origin-of-photosynthesis-in-a-sun-loving-bacteria.html
2. http://www.assignmentpoint.com/science/chemistry/introduction-of-photosynthetic-reaction-centre.html
3. http://deisenhofer.checknobel.com/1.htm
4. http://pubs.rsc.org.sci-hub.bz/en/content/articlelanding/2012/fd/c1fd00078k/unauth#!divAbstract

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