Intelligent Design, the best explanation of Origins

This is my personal virtual library, where i collect information, which leads in my view to Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


You are not connected. Please login or register

Intelligent Design, the best explanation of Origins » Photosynthesis, Protozoans,Plants and Bacterias » Chlorophyll, and what it tells us about intelligent design

Chlorophyll, and what it tells us about intelligent design

Go to page : Previous  1, 2

Go down  Message [Page 2 of 2]

26Chlorophyll, and what it tells us about intelligent design - Page 2 Empty Is photosynthesis irreducibly complex ? on Fri Apr 12, 2019 7:42 am

Admin


Admin
Is photosynthesis irreducibly complex ?

https://www.youtube.com/watch?v=ktXnLnUA8XA&t=259s

Is photosynthesis irreducibly complex ?
http://reasonandscience.catsboard.com/t1546p25-chlorophyll-and-what-it-tells-us-about-intelligent-design#6777

There is a common claim that that irreducible complexity in biology has been refuted. But has it? This video addresses this issue.

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. A good part of 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. It contains many interdependent systems composed of parts that would be useless without the presence of all the other necessary parts. In these systems, nothing works until all the necessary components are present and working. So how could someont rationally say, the individual parts, proteins and enzymes, co-factors and assembly proteins not present in the final assemblage, all happened by a series of natural events that we can call ad hoc mistake "formed in one particular moment without ability to consider any application." , to then somehow interlink in a meaningful way, to form electron transport chains, proton gradients to " feed " ATP synthase nano motors to produce ATP , and so on ? Such independent structures would have not aided survival. Consider the light harvesting complex, and the electron transport chain, that did not exist at exactly the same moment--would they ever "get together" since they would neither have any correlation to each other nor help survival separately? Repair of PSII via turnover of the damaged protein subunits is a complex process involving highly regulated reversible phosphorylation of several PSII core subunits. So it seems that photosynthesis falsifies the theory of evolution, where all small steps need to provide a survival advantage.


Chloroplast & Chlorophyll
https://www.youtube.com/watch?v=_KcLV4v6i04

A modern leaf with 70 million cells will contain about five billion chloroplasts, each containing about 600 million molecules of chlorophyll. 

Approximately 250 to 300 of them transfer the absorbed light energy through neighbouring pigments to the “special pair” chlorophylls in a reaction center. These special pair chlorophylls in photosystems I and II are the primary electron donors that drive the conversion of light into chemical energy.
 
Chlorophyll structure



Chlorophyll, and what it tells us about intelligent design - Page 2 SyS8SQ3

Since the pyrrole ring is responsible for the colour of Chlorophylls, its also called a chromophore. The basic structure is a ring made of four pyrroles, a tetrapyrrole, which is also named porphyrin. Its large inner surface area has a high cross-section suited for photon capture.  Chlorophylls are excellent light absorbers. 27s

A modern leaf with 70 million cells will contain about five billion chloroplasts, each containing about 600 million molecules of chlorophyll. Chloroplasts are organelles that conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight. 

Chlorophyll, and what it tells us about intelligent design - Page 2 WA60BU7

The tetrapyrrole system shows a high absorptivity at both the long- and short-wavelength ends of the visible spectrum of light. The middle of the light spectrum is not absorbed but reflected, which is the reason why leaves are usually green. 21s

Chlorophyll, and what it tells us about intelligent design - Page 2 PN6PcwP

How exactly do Chlorophyll pigments “capture” the energy of light? In the picture, we see two photosystems, which are surrounded by light-harvesting antennas. There, Chlorophylls are embedded, capturing photons. 17s
 
Chlorophyll, and what it tells us about intelligent design - Page 2 ZibXYDs

The photosynthesis pathway starts with light absorption which excites the chlorophyll molecule.  Then, the energy is passed from molecule to molecule until it reaches the reaction-center complex.  Here, an excited electron from the special pair of chlorophyll a molecules are transferred to the primary electron acceptor. 26s




Chlorophyll, and what it tells us about intelligent design - Page 2 JkNCnT1

When chlorophyll absorbs a photon, an electron excitation in its ring structure occurs, which moves electrons from the ground state into a higher excited state in the atoms. A sequence of alternating double and single bonds in rings, which form a system of conjugated bonds, is responsible for light absorption. 26s

Chlorophyll, and what it tells us about intelligent design - Page 2 6yNeGpH
A photon can be envisioned as a very fast-moving packet of energy. When it strikes a molecule, its energy is either lost as heat or absorbed by the electrons of the molecule, boosting those electrons into higher energy levels. Whether or not the photon’s energy is absorbed depends on how much energy it carries (defined by its wavelength) and on the chemical nature of the molecule it hits. Electrons occupy discrete energy levels in their orbits around atomic nuclei. To boost an electron into a different energy level requires just the right amount of energy, just as reaching the next rung on a ladder requires you to raise your foot just the right distance. A specific atom can, therefore, absorb only certain photons of light—namely, those that correspond to the atom’s available electron energy levels. 68s

Chlorophyll, and what it tells us about intelligent design - Page 2 NyLs3qU

Magnesium is present in the center of the ring as the central atom. If other metals instead of magnesium are used, they will competitively quench and extinguish the chlorophyll's excited state and return to the ground state. Consequently very little if any energy transfer would occur. This means that insufficient energy would reach the reaction center and the process would not continue.  Magnesium chlorophyll has a unique property which is that the absorption and emission spectra overlap exceptionally well.

That means that energy transfer to nearby molecules by the Forster (resonance) mechanism is very favourable. Magnesium chlorophyll has almost the best possible overlap of absorption and emission spectra of any molecules. All of this illustrates that photosynthesis is finely tuned, and small changes can have dramatic effects. Copper and zinc form complexes with chlorophyll, but with different affinities and functions.  80s


Chlorophyll, and what it tells us about intelligent design - Page 2 HVRVlF0

How could natural selection fix the right information in the genome to instruct the import, purification, and precise insertion of the right central atom with the required functional properties and how to insert in in the right geometric position to bear function? Each change and trial would require the change of a whole system of metal recognition and import channels in the cell membrane, finely adjusted for the right metal. 33s

Chlorophyll, and what it tells us about intelligent design - Page 2 NPikXF4

In fact, on the archaean ocean, a wide variety of trace minerals would have been available, as above mentioned science paper reports. 11s



Chlorophyll, and what it tells us about intelligent design - Page 2 4wGXJpJ

For example, the import channels for magnesium are illustrated above and radically different than import channels for Copper. 8s

Chlorophyll, and what it tells us about intelligent design - Page 2 DbhUWx5
This demonstrates that when one tiny item is changed, a much larger change on systems level has to occur. Metal metabolism, as occurs with many cellular processes, is interconnected which raises strong doubts if that are not hurdles far beyond what evolution is capable of overcoming to produce new traits and functions. 26s

Chlorophyll, and what it tells us about intelligent design - Page 2 BpG5a2t

The chlorophyll tail is a phytol hydrocarbon chain, which is attached to the pyrrole. It is not involved in light absorption but it has the essential function to anchor chlorophylls in the light-harvesting complex and provides chlorophylls with the right orientation. Without the tail, chlorophylls would have no way to anchor in the light-harvesting complex. But there is a surprising mutual benefit.  Light-harvesting complexes in plants do contain not only Chlorophyll type a, but also Chlorophyll b, and carotenoids. Chlorophyll b helps and is actually even essential for the assembly of the light harvesting complex  40s

Chlorophyll, and what it tells us about intelligent design - Page 2 Hr2JWIQ

Remarkably, Chlorophyll b's, which are produced by the Chlorophyll cycle, are required for the assembly of the Light harvesting complex. The major peripheral Light-harvesting complexes contain nearly equal numbers of Chlorophyll a and Chlorophyll b, which are held in highly specific positions. The complex is assembled via a defined pathway and the final product is stabilized by Chlorophyll b which are essential for that process. There would be no use of light harvesting antenna complexes without chlorophylls. But there would be no use for Chlorophylls either, without the right arrangement in antenna complexes! 48s



Chlorophyll, and what it tells us about intelligent design - Page 2 XhNNT73

How can evolution by gene mutations and natural selection explain its origin, if foreknowledge is required for the final function?   8s

Chlorophyll, and what it tells us about intelligent design - Page 2 LHhs0B0

In the photosynthesis pathway, more than 24 protein complexes which compose the system must first be synthesized and assembled in the right order and then interconnected to form a functional whole, able to start operating. 
Thylakoid membranes are like the factory floor. There the photosynthetic electron transport is carried out using some of the most sophisticated macromolecular multisubunit complexes in nature. 33s

Chlorophyll, and what it tells us about intelligent design - Page 2 RECQcB7

Recent years have seen major breakthroughs in elucidating the ultrastructure of all core constituents of these complexes, like photosystem II. They are composed of dozens of protein subunits as well as hundreds of organic and inorganic co-factors, most of which are embedded in the lipid bilayer of thylakoid membranes. 25s

Chlorophyll, and what it tells us about intelligent design - Page 2 4yyBy2X
Photosystem II is vulnerable to oxidative damage. When this occurs, it undergoes an impressive repair cycle in a multi-step process.  Specifically orchestrated degradation of photodamaged subunits are crucial steps in the repair cycle to maintain photosynthesis activity. How could such ultrasophisticated and essential repair and recycling have evolved in a gradual stepwise fashion, if, not implemented right from the start, the protein complex would soon be burned by reactive oxygen species as a response to high light and high temperature and cease its function? 50s 

Chlorophyll, and what it tells us about intelligent design - Page 2 RvaGIcV

Such sophisticated, inbuilt protection and repair mechanisms are truly awe-inspiring, surprising, and point clearly to the requirement of designed and foreplanned implementation and creation.  The biogenesis process includes the highly-ordered, step-wise assembly of proteins, lipids, pigments like chlorophyll (Chl), and carotenoids, quinones, and metal ions which to a large extent is mediated by dedicated assembly factors assisting specific steps. 40s

Chlorophyll, and what it tells us about intelligent design - Page 2 JETBQDS

Remarkably, the assembly takes place in specialized membranous compartments which are distinct from functional thylakoid membranes but involved in the synthesis and assembly of at least some photosynthetic components, especially photosystem PSII. The Illustrations show: (A) a Synechocystis cell with a biogenesis center and other relevant compartments; (B) a higher magnification view of a biogenesis center formed by the central thylakoid center  and (C) a Chlamydomonas cell with intracellular compartments. 45s

Chlorophyll, and what it tells us about intelligent design - Page 2 AowtsvX

The transfer of an enzymatic pathway and finished products from one compartment to another poses severe problems: the enzymes of the pathway acquire their targeting signals for the new compartment individually, not together, and at the same time. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. 34s

Chlorophyll, and what it tells us about intelligent design - Page 2 MndsWtp

This all is evidence that the synchronization and requirement of massive new information and precise regulation orchestrating such processes is far best explained by intelligent design.   


We will now move on to give a closer look into the biosynthesis of Chlorophyll, which impressive on its own merit. 13s

Chlorophyll, and what it tells us about intelligent design - Page 2 Ve1PX4X

We will now move on to give a closer look into the biosynthesis of Chlorophyll, which impressive on its own merit. The production of manmade solar panels requires seven highly specific steps as outlined earlier in this video.  We can draw a parallel to Chlorophyll biosynthesis, which in a similar fashion, requires seventeen consecutive manufacturing steps.  Imagine a production line in a factory. Many robots there are lined up, and raw materials are fed into the production line. The materials arrive at Robot one. It processes the first step. Then, when ready, the product moves on and is handed over to the next Robot. Next processing step. And that procedure repeats 17 times. Instead of robots, each step is performed by specific enzymes, which catalize the metabolic reactions. 58s

Chlorophyll, and what it tells us about intelligent design - Page 2 Gj1bO5P

In the end, there is a fully formed chlorophyll molecule. It is part of the larger system, namely the complete photosynthesis pathway. Chlorophyll by its own has no use unless mounted at the right place in the light-harvesting complex, in the right order. 20s

Chlorophyll, and what it tells us about intelligent design - Page 2 0XmhKb4

They are only functional when they are inserted in the light-harvesting complex, where 200 to 300 work in a joint venture, with the right distances from each other, in the right functional order, to catch photons and direct their excitation energy by Förster resonance energy transfer to the reaction center in Photosystems one and two.

 Foreplanning is absolutely essential. Individually, chlorophylls have no function.

Chlorophyll, and what it tells us about intelligent design - Page 2 DvZtLjE
Chlorophylls and the light harvesting complex form a functional unity. But the genes that produce the proteins of chlorophyll metabolism, and synthesis of the light-harvesting complex, are different and separated. 15s

Remarkably, no Light harvesting binding proteins accumulate in the absence of pigment synthesis and adjustment of the photosynthetic subunits requires a coordinated biosynthesis of apoproteins and Chlorophyll chromophores. 18s
 
Chlorophylls a and b are both required for stabilization of the apoproteins and assembly of the majority of antenna complexes in higher plants. 11s

Chlorophyll, and what it tells us about intelligent design - Page 2 KeO6acD


So there is a clear interdependence. This is a major problem for evolution. 7s

Why and how would evolution produce separately several proteins exclusively for chlorophyll synthesis, before the existence of light-harvesting complexes where they are embedded and bound to, and the regulatory instructions orchestrating the assembly of the whole complex? 21s

The binding site is precisely engineered and orchestrated, and the entire assembly of the complex depends on Chlorophylls. But more problems await for who advocates that evolution is a plausible explanation. The last eight steps of chlorophyll biosynthesis are used by specific enzymes uniquely in this pathway. 25s

Chlorophyll, and what it tells us about intelligent design - Page 2 KGgVeQe

The common cop-out that some parts could have been co-opted from somewhere else does not apply to these enzymes since they have not known multiple functions. So the whole pathway would have had to emerge from scratch. 
This is a key point of the argument in this video:21s

What good would there be for natural selection to select and produce enzymes, used in this complex manufacturing process, without all the other enzymes in place, and the whole process coordinated to get a useful end product?  18ss

Chlorophyll, and what it tells us about intelligent design - Page 2 Ulazlra

What good would there be, if the chlorophyll pathway would go only partially the way through, let's say, up to the 12th step??  11s


Chlorophyll, and what it tells us about intelligent design - Page 2 DqfcGRl



A non-functional intermediate molecule would be the product, not performing anything helping the organism to survive. 10s


Chlorophyll, and what it tells us about intelligent design - Page 2 NMjQZn2



Worse that that: It would eventually produce an intermediate product, which in the process, as waste product would produce reactive oxygen species, which would harm the cell. 14s


Chlorophyll, and what it tells us about intelligent design - Page 2 AopcO7j



What good would there be, if the chlorophyll pathway would go all the way through up to the 17th step? Chlorophyll would be produced, BUT:13s


Chlorophyll, and what it tells us about intelligent design - Page 2 MFVwWiz





What good for survival would there be for chlorophyll on its own, if not fully and correctly embedded in the photosynthesis process? none. 11s
Chlorophyll, and what it tells us about intelligent design - Page 2 4bwAyEt





What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing light is essential for the whole process. 16s


Chlorophyll, and what it tells us about intelligent design - Page 2 GdqNL6r

‘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?’ 12s


Chlorophyll, and what it tells us about intelligent design - Page 2 W0TOpxW
Blankenship notes in  Molecular mechanisms of photosynthesis: It is not conceivable that highly complex molecules such as chlorophylls were synthesized by prebiotic chemistry, given their very specific functional groups and multiple chiral centers. 19s


Chlorophyll, and what it tells us about intelligent design - Page 2 Y6XbFa2
The thing is, there's no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. 21s




Chlorophyll, and what it tells us about intelligent design - Page 2 XIaMEOo
Due to the remarkable reactivity of all tetrapyrroles, there is in living organisms a substantial danger that uncontrolled chemical reactions may occur and ultimately lead to damage of cellular and subcellular structures.  All living organisms thus need strategies to neutralize the potentially harmful tetrapyrrole compounds. 27s

In most cases, this task is achieved by tightly controlling their actual concentrations, in order for the level of free tetrapyrroles within a cell being kept to a minimum. 14s 

Chlorophyll, and what it tells us about intelligent design - Page 2 ZA8gecC

Chlorophyll triplets are harmful excited states readily reacting with molecular oxygen to yield the reactive oxygen species (ROS) singlet oxygen. 14s


Carotenoids have an essential photoprotective role in photosynthetic membranes by preventing photooxidative damage through quenching of chlorophyll singlets and triplets. They do it with an amazing efficiency of 94−97%. 19s 

Chlorophyll, and what it tells us about intelligent design - Page 2 E9Dwell

When missing, the result is high level of photodamage in high light and/or low temperature. 8s

In addition, tetrapyrrole synthesis and degradation are carefully adjusted to the cellular requirements, reflecting the different needs under varying environmental conditions. 14s

During the assembly of the photosynthetic apparatus, chlorophylls and the nuclear-encoded and plastid-encoded chlorophyll-binding proteins must interact in a highly coordinated manner. 15s

This is an all or nothing business. The evidence points to the requirement of preprogramming to coordinate the strategies of protection from day one. Programming is always tracked back to intelligent action. 16s


Chlorophyll, and what it tells us about intelligent design - Page 2 SX0Rmx2


Let's have a look at how science papers answer this question: 7s

Chlorophyll, and what it tells us about intelligent design - Page 2 K4XgSVU

Organisms generate an enormous number of metabolites; however, the mechanisms by which a new metabolic pathway is acquired are unknown.  This is a monumental admission, since metabolic pathways are used and required in basically all life forms. 21s

Chlorophyll, and what it tells us about intelligent design - Page 2 2mQGtbz

Central to the topic is the Granick hypothesis from 1965, which posits that the evolution of the chlorophyll biosynthetic pathway followed the sequential inventions of new enzymes to generate more stable products. 17s


So basically, all which is proposed, is a baseless assertion which goes back to 1965 !! There are no details, no scientific evidence that it can occur - nothing !! 14ss


Chlorophyll, and what it tells us about intelligent design - Page 2 PgzvcLi

"recruitment of genes and the evolution of orphan genes have all been suggested to contribute.". This is a blank admittance that there is no hard, compelling de facto evidence. None. Nada. Njet. Only guesswork, and baseless suggestions. 19s

Chlorophyll, and what it tells us about intelligent design - Page 2 RwNiSMb
This video has demonstrated why there is no conceivable way to get a functional metabolic pathway with several enzymes lined up by happenstance, producing purposeful products without intelligent guidance. Enzymes, in order to become functional,  must be specified in a precise manner to fold into complex 3D forms which need to be complementary with the substrates they process and act upon. This extremely remotely possible, if not impossible, unless the end goal, the " big picture" is known. Foreknowledge of the purpose is required, and what the end product will be. " Know-how" is required how to set up each enzyme, what specific synthesis step it has to perform, what its product is, which next enzyme is required to perform the next manufacturing step and so on.

There are very good reasons to be skeptic that genes would independently and blindly mutate to produce supercomplexes as seen in this video, that only bear function with other molecular machines working in a joint venture, these also supposedly products of genetic mutations, which by their own would bear no function either. On top of that, other genetic information has to orchestrate its assembly into functional working machines and all this from scratch and build in control, error detection, and repair mechanisms. I have not enough faith to believe, evolution and long periods of time have such superpowers. A blind brainless watchmaker isn't able to make a watch.

In this video, we have only scratched on the surface of photosynthesis. Much more can and should be said. That will hopefully be the case in the forthcoming videos. If you enjoyed, please subscribe to my channel, share the video, recommend, comment, and if you like, a contribution at patreon is appreciated. 






  






https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500134/
https://www.frontiersin.org/articles/10.3389/fpls.2016.01811/full
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC160907/

Investigating the bifunctionality of cyclizing and “classical” 5-aminolevulinate synthases
https://onlinelibrary.wiley.com/doi/pdf/10.1002/pro.3324

Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500134/

V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC125327/

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product
https://mmbr.asm.org/content/81/1/e00048-16

Evolutionary Relationship between Initial Enzymes of Tetrapyrrole Biosynthesis
http://sci-hub.tw/https://www.sciencedirect.com/science/article/pii/S0022283606002804?via%3Dihub

Identification of the chlE gene encoding oxygen-independent Mgprotoporphyrin IX monomethyl ester cyclase in cyanobacteria
http://sci-hub.tw/https://www.sciencedirect.com/science/article/pii/S0006291X15301789

Distribution and Origin of Oxygen-Dependent and Oxygen-Independent Forms of Mg-Protoporphyrin Monomethylester Cyclase among Phototrophic Proteobacteria
https://aem.asm.org/content/79/8/2596

Evolution of a new chlorophyll metabolic pathway driven by the dynamic changes in enzyme promiscuous activity
https://eprints.lib.hokudai.ac.jp/dspace/bitstream/2115/58225/1/PCP55-3%20593-603.pdf

The catalytic subunit of magnesium-protoporphyrin IX monomethyl ester cyclase forms a chloroplast complex to regulate chlorophyll biosynthesis in rice
http://sci-hub.tw/https://link.springer.com/article/10.1007/s11103-016-0513-4

Conserved Chloroplast Open-reading Frame ycf54 Is Required for Activity of the Magnesium Protoporphyrin Monomethylester Oxidative Cyclase in Synechocystis PCC 6803
https://ora.ox.ac.uk/objects/uuid:8318d1a6-b75f-4852-9db5-abb43e357dbc/download_file?file_format=pdf&safe_filename=Conserved.pdf&type_of_work=Journal+article

Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).
http://www.jbc.org/content/289/37/25690.full.pdf

Department of Molecular Biology and Biotechnology
Home > Molecular Biology and Biotechnology > People > Neil Hunter
https://www.sheffield.ac.uk/mbb/staff/neilhunter/neilhunter

Light Regulates Transcription of Chlorophyll Biosynthetic Genes During Chloroplast Biogenesis
http://sci-hub.tw/https://www.tandfonline.com/doi/abs/10.1080/07352689.2017.1327764?journalCode=bpts20

Circadian and Plastid Signaling Pathways Are Integrated to Ensure Correct Expression of the CBF and COR Genes during Photoperiodic Growth1
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4902621/

Rapid C8-vinyl reduction of divinyl-chlorophyllide a by BciA from Rhodobacter capsulatus
http://sci-hub.tw/https://www.sciencedirect.com/science/article/abs/pii/S1010603017309966

X-ray crystal structure of the light-independent protochlorophyllide reductase
http://sci-hub.tw/https://www.nature.com/articles/nature08950

Evolution of light-independent protochlorophyllide oxidoreductase
http://sci-hub.tw/https://link.springer.com/article/10.1007/s00709-018-1317-y

http://www.biochemj.org/content/467/2/201

Siroheme An essential component for life on earth
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835951/

Organization of energy transfer networks in photosynthesis
https://www.ks.uiuc.edu/Research/psres/



Last edited by Admin on Tue Jun 04, 2019 10:21 am; edited 112 times in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
For biochemists, chlorophyll biosynthesis provides a challenge to mechanistic understanding, because it involves compounds that are inherently unstable and reactive in the presence of oxygen and light, and yet it can take place in full sunlight in an atmosphere that is enriched in oxygen.

My comment: Consider that if there was no oxygen in the atmosphere prior to the supposed great oxygenation event, cyanobacteria, if they came to the surface, they would be killed by UV radiation. They would also have had to evolve from anoxygenic energy supply to oxygenic photosynthesis energy supply. But in that process, how and why would enzymes evolve, producing intermediate stage biochemical products, which, as being unstable, there were no protective mechanisms to deals with these compounds adequately?  

Chlorophyll, and what it tells us about intelligent design - Page 2 DI5DfGK

The paper: Cyanobacterial Evolution: Fresh Insight into Ancient Questions admits as follows:
Because of the importance of how cyanobacteria came to become masters of oxygenic photosynthesis, understanding the origins of this biological feat has perplexed scientists from different fields spanning disciplines such as biology, chemistry, geology, and paleontology. 1

Chlorophyll, and what it tells us about intelligent design - Page 2 JU0bU1O

Study of chlorophyll biosynthesis has also revealed several surprises to biochemists, including the existence of alternative routes or processes used to form certain intermediates in different types of organisms, variant mechanisms for forming intermediates under anaerobic vs aerobic conditions, and the existence of previously overlooked chlorophyll structural variants that may have important physiological roles.

(steps 1–6)
the initial steps  that divert general metabolic intermediates into the formation of the first cyclic tetrapyrrole, uroporphyrinogen III; 
(steps 7–9);
transformation of uroporphyrinogen III to protoporphyrin IX along the oxidative branch 
(step 10; the heme/bilin branch begins with insertion of Fe2C into protoporphyrin IX); 
the reductive branch leads from uroporphyrinogen III to siroheme, heme d1, factor F430, and corrinoids); insertion of Mg2C into protoporphyrin IX to begin the branch leading to chlorophylls 
(steps 11–14);
formation of the isocyclic ‘fifth’ ring that is present on all chlorophylls  
(step 15), 
reduction of a peripheral vinyl group to an ethyl group 
(step 16); 
followed or preceded by reduction of the macrocyclic ring system to form a chlorin, the defining oxidation state of true chlorophylls 
(step 17).
and addition of a polyisoprene alcohol to the tetrapyrrole to complete the structure of chlorophyll a






1. https://www.cell.com/current-biology/pdf/S0960-9822(14)01649-2.pdf
2. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151250#pone.0151250.ref007

View user profile http://elshamah.heavenforum.com

Admin


Admin
Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana.
https://www.ncbi.nlm.nih.gov/pubmed/27303897

View user profile http://elshamah.heavenforum.com

Admin


Admin
The enzymes that synthesize chlorophyll

Chlorophyll, and what it tells us about intelligent design - Page 2 Sm053Ss

Next processing step. And that procedure repeats 17 times. In the end, there is a fully formed chlorophyll.  The pathway must go all the way through, otherwise, chlorophyll is not synthesized.
The enzymes need to be lined up like in a factory production line.  
What good would there be, if the pathway would go only up to the 15th step? none
What good would there be, if the pathway would go all the way through the 17th step? Chlorophyll would be produced, BUT:
What good for survival would there be for chlorophyll on its own, if not fully embedded in the photosynthesis process? none.
What good would there be for a light-harvesting complex without chlorophyll? none. 
What good would there be for photosynthesis without chlorophyll in place, capturing light, and transmitting it to the photosystem? none, since capturing
light is essential for the whole process.

The structures of Heme and Chlorophyll pigments are closely related, and they share the first ten biosynthesis steps. 

Chlorophyll, and what it tells us about intelligent design - Page 2 WU30If0

‘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?’ Therefore, the Chlorophyll biosynthesis pathway is irreducibly complex.

Chlorophyll, and what it tells us about intelligent design - Page 2 Promis10

Promiscuous enzyme activity during evolution? Did you read this? Is that a Japanese way to say: "Let's fill the gap of evidence with an ad-hoc assertion, which sounds sciency " ?  Frankly speaking, this is a ridiculous claim and comes equally of throwing the towel, or giving up a rational discourse, and sticking to whatever comes in mind. 

This is confirmed by the fact that scientific papers have no evidence whatsoever how enzymatic biosynthesis pathways in general could have evolved. The quest becomes even more dramatic when it comes to the life-essential metabolic pathways essential for life, which had to emerge prior when life began. Science-based on methodological naturalism has only speculation and guesswork. 

This is a key problem for evolution:
Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words: Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system?  
A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.

Natural selection would not select allele variants, unless a huge, and just right lateral gene transfer would take place, suddenly permitting the synthesis of all seventeen highly complex enzymes used in the chlorophyll biosynthesis
pathway

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 advocates of evolution 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. Denton and Overman also cite a number of experts who suggest that there is no evidence for such a primitive soup but rather considerable evidence against it.

Life on Earth starts with an anaerobic metabolism that still nowadays persist in the form of bacteria living in oxygen-poor environments. In the early earth, nearly all oxygen was bound in compounds, like water and silicate rocks. But nearly 3 billion years ago the “invention” in nature of plant photosynthesis turned the anaerobic world into our present type of environment with aerobic life. It is clear that the introduction of oxygen into the anaerobic world obliged the organisms existing at that time to adapt since a lot of the by-products of oxygen metabolism are toxic compounds.

Chlorophyll, and what it tells us about intelligent design - Page 2 YqbD46z
Chlorophyll, and what it tells us about intelligent design - Page 2 XmvQTjI

The biosynthesis pathway of Chlorophyll

Chlorophyll, and what it tells us about intelligent design - Page 2 3BPRazC

Since cyanobacteria emerged first in the evolutionary timeline, their pathway on the left in which we will give a closer look. 

Steps involving more than two enzymes are shown by two arrows. 
Two separated arrows indicate that the two enzymes are distinct, and two overlapped arrows indicate that two enzymes are isoforms.  A protein isoform, or "protein variant" is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences.
Enzymes that have an essential role under aerobic conditions are shown in red. 
Enzymes that operate mainly under microoxic conditions and the transcription of the genes encoding these upregulated enzymes are shown in blue. 
Enzymes that require oxygen for catalysis are shown by “O2” in the red background, and 
enzymes that are inactivated by oxygen are shown by red “x-O2” symbols.

There are at least four enzymatic steps that require oxygen for catalysis. On the other hand, there are also oxygen-sensitive enzymes that are readily inactivated by oxygen in this biosynthetic pathway. These enzymes may be inactivated under aerobic conditions. Thus, to cope with the circumstances of various oxygen levels, cyanobacteria have an elaborate mechanism involving two enzymes that catalyze the same reaction. One enzyme functions under aerobic conditions and the other under anaerobic/microoxic conditions. ( microxic = with very small amounts of oxygen in the atmosphere  )The expression of genes encoding these enzymes is mainly controlled at the transcriptional level in response to cellular oxygen tension.

Comment:  If the atmosphere was anaerobic, without oxygen, before oxygenic photosynthesis brought the atmosphere to levels as today by the great oxygenation event, of about 20% oxygen, why would cyanobacteria evolve enzymes that only function in aerobic conditions?   Did Cyanobacteria have foresight, and know that once oxygenic photosynthesis evolved by themselves and the atmosphere would become aerobic, these enzymes that only work in aerobic conditions would be required? Evidently, that makes no sense whatsoever. And on top of that, the use of either aerobic or anaerobic enzymes is regulated by transcription factors !! How did that regulation emerge? Truth is, the existence of both enzymes, one adapted for aerobic conditions, and the other for anaerobic conditions, and both regulated to adapt the various conditions had to exist from day one. It seems that the atmosphere was always aerobic, but there are ecological niches, where oxygen is low or even non-extant, and cyanobacteria, which occupy all ecological systems on earth, were created to be able to adapt to all kind of atmospheric conditions.

There are  37 cyanobacterial representative species. The aerobic-type enzymes are ubiquitously conserved in all species. In contrast, the anaerobic/microoxic-type enzymes are missing in about half of these species, and some anaerobic enzymes, in only two species.

The first stage 

The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: 

(1) condensation of succinyl CoA and glycine (C4 pathway) using  ALA synthase, or 

(2) decarboxylation of glutamate (C5 pathway) via three different enzymes:

glutamyl-tRNA synthetase to charge a tRNA with glutamate, 
glutamyl-tRNA reductase to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and 
GSA aminotransferase to catalyse a transamination reaction to produce ALA.

Chlorophyll, and what it tells us about intelligent design - Page 2 3287tJu

5-aminolevulinic acid  (ALA) can be considered to be the first universal, committed tetrapyrrole precursor.which is made either via the C4 or Shemin pathway or by the C5 Beale pathway

Route 1: the C4 or Shemin pathway 

Chlorophyll, and what it tells us about intelligent design - Page 2 2s2o5Os

Remarkably, this pathway shares the same first ten steps with the pathway of heme biosynthesis.

The Shemin pathway is used by eukaryotes that do not contain plastids (e.g., animals, yeasts, fungi) and members of the subgroup of purple bacteria, to form ALA. 

ALA is synthesized in the one-step condensation of succinyl-CoA and glycine catalyzed by ALA synthase .

Chlorophyll, and what it tells us about intelligent design - Page 2 GygPXbH

The ALA synthase enzyme 

Chlorophyll, and what it tells us about intelligent design - Page 2 QBJLLl5

succinyl CoA and glycine and produces ALA by a condensation reaction ( condensation reactions are the same that bind amino acids together by amide bonds to form protein polypeptide chains ) accompanied by the liberation of Coenzyme A and CO2.

Route 2: C5 Beale pathway

Chlorophyll, and what it tells us about intelligent design - Page 2 L6B0R5t
Plants, algae, and most groups of bacteria, including cyanobacteria, form ALA by the C5 Beale pathway. The amino acid L-Glutamate is converted to Aminolevulinic acid (ALA) in three steps, via three different enzymes:


Glutamyl-tRNA synthetase (GluRS)
Glutamyl-tRNA reductase (GluTR)
Glutamate-1-semialdehyde aminotransferase (GSAM)


Chlorophyll, and what it tells us about intelligent design - Page 2 CzMD5o0

In phase one, tRNA is charged with glutamate by a Aminoacyl tRNA synthetase. Its name is Glutamyl-tRNA synthetase, to form glutamyl-tRNA.

https://www.youtube.com/watch?v=1GdTTCRw1sw&t=17s



Glutamyl-tRNA is reduced to glutamate-1-semialdehyde (GSA) by glutamyl-tRNA reductase (HemA). Then, GSA is isomerized to ALA by Glutamate-1-semialdehyde aminotransferase (GSAM)  . At physiological pH, GSA is a very unstable amino aldehyde that easily degrades generating toxic products within the cells.




Phase 1. Glutamate—tRNA ligase  catalyzes  L-Glutamate  into L-Glutamyl-tRNA(Glu)



Glutamyl-tRNA synthetase has been studied in connection with its role in protein synthesis. Like all aminoacyl-tRNA synthetases, the enzyme requires the cognate amino acid and tRNA as substrates, and the reaction requires the
energy of ATP hydrolysis. There is no evidence to suggest that the glutamyl-tRNA synthetase that charges tRNAGlu for ALA biosynthesis differs from the one involved in protein synthesis. 

Phase 2. Glutamyl-tRNA reductase (GluTR) to reduce L-Glutamyl-tRNA(Glu) to L-glutamate-semialdehyde (GSA)



Reduction of the glutamate carboxyl group Glutamyl-tRNA reductase is the least well-understood enzyme of the five-carbon ALA biosynthetic pathway, owing to its instability in vitro, low cellular abundance, and the need to provide a relatively unstable aminoacyl-tRNA substrate. The enzyme requires NADPH as the source of the reductant for converting the tRNA-ligated carboxyl group of glutamate to an aldehyde. An unresolved question is whether the glutamyl moiety is transferred from the tRNA to the enzyme and becomes covalently attached to the enzyme during the course of the reaction. Another question concerns the structure of the reaction product. Although most workers have assumed that the product is free L-glutamate-semialdehyde (GSA)  or its hydration product (hemiacetal), Jordan et al. (1993) have proposed that the product is the cyclic ester formed from the -carboxyl group and the hydrated aldehyde group. The cyclic structure does not contain free aldehyde or carboxylic acid functions, and is more compatible with some previously reported properties of the chemically synthesized product (stability in aqueous solution, heat stability) than the free or hydrated -aminoaldehyde. It seems probable that in solution, GSA occurs as an equilibrium mixture of the free aldehyde, hydrated form, and cyclic compound, analogously to aldose sugars.














Phase 3. Glutamate-1-semialdehyde aminotransferase (GSAM) to catalyse a transamination reaction to produce 5- aminolevulinic acid (ALA)



Activation of glutamate by ligation to form glutamyl-tRNA. Next, the activated glutamate is reduced at C-1 to form GSA. Finally, the amino group at C-2 of GSA is replaced by one at C-1, yielding ALA. The only known role of GSA is as a tetrapyrrole precursor, and therefore GSA formation can be considered to be the first committed step of the tetrapyrrole pathway in cyanobacteria. GSA supplies all of the C and N atoms of the tetrapyrrole nucleus.

This is a remarkable observation.  The only known role of GSA is as a tetrapyrrole precursor means GSA has no function by its own. How could its biosynthesis be explained by evolution, if its solely role is to be an intermediate product in the path to the final product, which requires further biosynthesis steps ? 

The pathway is a sequence of three steps for ALA formation as follows: (a) activation of the C1 of glutamate in a step requiring ATP and Mg2+; (b) reduction of the activated carboxyl group by NADPH to form glutamate 1-semialdehyde (GSA); and (c) transamination of GSA to form ALA. the activated form of glutamate is the tRNA adduct, glutamyl-tRNAglu.




Tetrapyrroles are large macrocyclic compounds. The end-product, uroporphyrinogen III

The synthesis of 5-aminoaevulinic acid in plastids, cyanobacteria, and many eubacteria proceeds by reduction of glutamate. the difference in redox potentials between a carboxylate and an aldehyde is so high that a reduction of a carboxyl group by NADPH is only possible when this carboxyl group has been previously activated (e.g., as a thioester or as a mixed phosphoric acid anhydride. In the plastid 5-aminoaevulinic acid synthesis, glutamate is activated in a very unusual way by a covalent linkage to a transfer RNA (tRNA) (Fig. 10.22). This tRNA for glutamate is encoded in the plastid genome and is involved in the plastids in the synthesis of 5-aminoaevulinic acid as well as in protein biosynthesis. As in protein biosynthesis (see Fig. 21.1), the linkage of the carboxyl group of glutamate to tRNA is accompanied by consumption of ATP. During reduction of glutamate tRNA by glutamate tRNA reductase, tRNA is liberated and in this way the reaction becomes irreversible. The glutamate 1-semi-aldehyde thus formed is converted to 5-aminoaevulinic acid by an aminotransferase with pyridoxal phosphate as a prosthetic group. This reaction proceeds according to the same mechanism as the aminotransferase reaction shown in Figure 7.4, the only difference being that the amino group (as amino donor) and the keto group (as amino acceptor) is present in the same molecule. Two molecules of 5-aminoaevulinic acid condense to form porphobilinogen. The open-chain tetrapyrrole hydroxymethylbilan is synthesized from four molecules of porphobilinogen via hydroxymethylbilan synthase. The enzyme contains a dipyrrole as cofactor. After the exchange of the two side chains on ring d the closure of the tetrapyrrole ring produces uroporphyrinogen III. Subsequently, protoporphyrin IX is formed by reaction with a decarboxylase and two oxidases (not shown in detail). Magnesium is incorporated into the tetrapyrrole ring by magnesium chelatase and the resultant Mg-protoporphyrin IX is converted by three more enzymes to protochlorophyllide. The tetrapyrrole ring of protochlorophyllide contains the same number of double bonds as protoporphyrin IX. The reduction of one double bond in ring d by NADPH yields chlorophyllide. Protochlorophyllide oxido-reductase, which catalyzes this reaction, is only active when protochlorophyllide is activated by absorption of light. The transfer of a pyrophosphate activated phytyl chain to protochlorophyllide via a prenyl transferase (chlorophyll synthetase, completes the synthesis of chlorophyll. The light dependence of the protochlorophyllide reductase allows a developing shoot to green only when it reaches the light. Also, the synthesis of the chlorophyll binding proteins of the light harvesting complexes is light-dependent. The exceptions are some gymnosperms (e.g., pine), in which protochlorophyllide reduction as well as the synthesis of chlorophyll binding proteins also progresses during darkness. Unprotected and unbound porphyrins may lead to photochemical cell damage. It is therefore important that intermediates of chlorophyll biosynthesis do not accumulate. To prevent this, the synthesis of 5-aminoaevulinic acid is light-dependent, but the mechanism of this regulation is not yet fully understood. Moreover, 5-aminoaevulinic acid synthesis is subject to feedback inhibition by chlorophyllide. The end products protochlorophyllide and chlorophyllide inhibit magnesium chelatase (Fig. 10.24). Moreover, intermediates of chlorophyll synthesis control the synthesis of light harvesting proteins (section 2.4) via the regulation of gene expression.

The porphyrin ring with its conjugated double bonds is assembled in the chloroplast from eight molecules of 5-aminolevulinic acid, a highly reactive nonprotein amino acid (5-amino, 4-keto pentanoic acid).











1. Glutamyl-tRNA synthetase
Glutamyl-tRNA (Glu-tRNA), formed by Glu-tRNA synthetase (GluRS), is a substrate for protein biosynthesis and tetrapyrrole formation by the C5 pathway. In this route Glu-tRNA is transformed to δ-aminolevulinic acid, the universal precursor of tetrapyrroles (e.g., heme and chlorophyll) by the action of Glu-tRNA reductase (GluTR) and glutamate semialdehyde aminotransferase.



Last edited by Admin on Mon May 13, 2019 4:21 pm; edited 1 time in total

View user profile http://elshamah.heavenforum.com

Admin


Admin
In our example of solar panel production, if one of the robots of the production line ceases to work for some reason, the whole fabrication ceases, and the completion of the finished solar panels cannot be accomplished. That means, a tiny mal connection of one of the robots in the production line of the solar panel might stop the production of the solar panel, and the finished photovoltaic system cannot be produced. Nobody would project a solar panel without visualizing the higher end upfront, in the project and development stage, and based on the requirement, specify the complex functional form, shape and materials which will be useful to perform the required task. And the whole production line and each robot the right placement and sequence where each robot will be placed must be planned and implemented as well. Everything has to be projected with a higher end goal in mind.

In each moment of cell life, billions of molecules are transformed into different ones through reactions that are accelerated (catalyzed) by the so-called enzymes, most of which are represented by proteins. Even though these proteins might interact with a plethora of different molecules during their chaotic trip within the cell, they bind only to specific molecules representing their substrate, and transform it into another and different molecules called product (of the reaction). Overall, this is not true for all enzymes; each enzyme interacts with one substrate giving rise to a specific product. Hence, in each moment of cell life billions of substrates are transformed into billions of products by billions of enzyme molecules. These reactions are extremely fast, and we can imagine the cell as a viscous environment where these reactions occur in an ordered (and only apparently chaotic) fashion. The whole body of these reactions is called metabolism, a circular “entity” in the sense that molecules can be destroyed (catabolism) to obtain energy and “bricks” that are required to construct other different molecules

 Nobody would project a solar panel without visualizing the higher end upfront, in the project and development stage, and based on the requirement, specify the complex shape of the solar panel. And the whole production line and each robot the right placement and sequence where each robot will be placed must be planned and implemented as well. Everything has to be projected with a higher end goal in mind. And there is an interdependence. If one of the robots ceases to work for some reason, the whole fabrication ceases, and the completion of the finished solar panel cannot be accomplished. That means, a tiny mal connection of one of the robots in the production line of the door might stop the production of the door, and the finished solar panel cannot be produced.




The argument of irreducible complexity is obvious and clear.

View user profile http://elshamah.heavenforum.com

Admin


Admin
Chlorophyll, and what it tells us about intelligent design - Page 2 LksDJWM
The metabolic pathways to form Chlorophyll molecules is subdivided into two steps: The first consists of ten steps where the branch point is between chlorophyll and heme synthesis. And the second consists in seven steps where the end product is Chlorophyll a

Chlorophyll, and what it tells us about intelligent design - Page 2 PgxaQ5X
 
We can further subdivide Chlorophyll biosynthesis in four distinct sections.(1) The synthesis of protoporphyrin IX from the first committed precursor, 5-aminolevulinic acid (ALA). Since protoporphyrin IX is the common precursor for Chl and protoheme, this section is called “common pathway”. In the common pathway, two molecules of ALA are condensed to form the monopyrrole, porphobilinogen, which are then sequentially polymerized linearly and subsequently to form the cyclic tetrapyrrole, called uroporphyrinogen III. The pathway is branched at this step to form siroheme which is called (“siroheme branch”). Siroheme is by the way life essential, and had to be synthesized prior life began.

Chlorophyll, and what it tells us about intelligent design - Page 2 XtIdLc6

The insertion of Magnesium (Mg2+) into protoporphyrin IX for Chlorophyll a biosynthesis is called “the Magnesium branch”. Later, we will give a closer look at these biosynthesis steps. Now i am giving just an overview.

Chlorophyll, and what it tells us about intelligent design - Page 2 WU30If0

The biosynthesis pathway of Chlorophyll

Chlorophyll, and what it tells us about intelligent design - Page 2 3BPRazC

Cyanobacteria emerged first in the evolutionary narrative, the pathway on the left demonstrates the pathway to metabolize chlorophyll molecules of cyanobacterias, so we will give a closer look. 

Steps involving more than two enzymes are shown by two arrows. 
Two separated arrows indicate that the two enzymes are distinct, and two overlapped arrows indicate that two enzymes are isoforms.  A protein isoform, or "protein variant" is a member of a set of highly similar proteins that originate from a single gene or gene family and are the result of genetic differences.
Enzymes that have an essential role under aerobic conditions are shown in red. 
Enzymes that operate mainly under microoxic conditions and the transcription of the genes encoding these upregulated enzymes are shown in blue. 
Enzymes that require oxygen for catalysis are shown by “O2” in the red background, and 
enzymes that are inactivated by oxygen are shown by red “x-O2” symbols.

There are at least four enzymatic steps that require oxygen for catalysis. On the other hand, there are also oxygen-sensitive enzymes that are readily inactivated by oxygen in this biosynthetic pathway. These enzymes may be inactivated under aerobic conditions. Thus, to cope with the circumstances of various oxygen levels, cyanobacteria have an elaborate mechanism involving two enzymes that catalyze the same reaction. One enzyme functions under aerobic conditions and the other under anaerobic/microoxic conditions. ( microxic = with very small amounts of oxygen in the atmosphere  )The expression of genes encoding these enzymes is mainly controlled at the transcriptional level in response to cellular oxygen tension.

Comment: If the atmosphere was anaerobic, without oxygen, before oxygenic photosynthesis brought the atmosphere to levels as today by the great oxygenation event, of about 20% oxygen, why would cyanobacteria evolve enzymes that only function in aerobic conditions?   Did Cyanobacteria have foresight, and know that once oxygenic photosynthesis evolved by themselves and the atmosphere would become aerobic, these enzymes that only work in aerobic conditions would be required? Evidently, that makes no sense whatsoever. And on top of that, the use of either aerobic or anaerobic enzymes is regulated by transcription factors !! How did that regulation emerge? Truth is, the existence of both enzymes, one adapted for aerobic conditions, and the other for anaerobic conditions, and both regulated to adapt the various conditions had to exist from day one. It seems that the atmosphere was always aerobic, but there are ecological niches, where oxygen is low or even non-extant, and cyanobacteria, which occupy all ecological systems on earth, were created to be able to adapt to all kind of atmospheric conditions.

There are  37 cyanobacterial representative species. The aerobic-type enzymes are ubiquitously conserved in all species. In contrast, the anaerobic/microoxic-type enzymes are missing in about half of these species, and some anaerobic enzymes, in only two species.

On the diagram of the Chlorophyll biosynthesis pathway, you see many double arrows. This has an amazing meaning.

Organisms like cyanobacteria, supposedly existed as anaerobes in a reduced atmosphere without oxygen, and according to the evolutionary narrative, bacteria, which were doing non-oxygenic photosynthesis, evolved the oxygen-evolving complex which is responsible for the production of oxygen, and oxygenated the atmosphere, giving room for the evolution of multicellular organisms which use respiration to get enough energy.

The two arrows means, in the Chlorophyll synthesis pathway, there are enzymes that function in an anoxic environment, and as well enzymes that require oxygen to function. Photosynthetic organisms populate all environments, from the oceans to the Sahara desert. In environments without oxygen supply, and with oxygen supply. So these organisms can adapt to any environment, and use either one enzyme that is oxygen sensitive or the other which requires it.  

Now imagine there was no oxygen in the archean epoch, and only oxygen sensitive enzymes in the pathway to make chlorophylls. As soon as these bacterias would have evolved oxygenic photosynthesis , the oxygen would mute these enzymes and kill their enzymatic activity.

Not only that. Oxygen is also sensitive to nitrogenase enzymes, which fix nitrogen, another essential process to fuel the supply of ammonia, which is essential for all life forms, to produce the basic building blocks of life, amino acids, dna, rna etc.

So the evolution of oxygenic photosynthesis would have brought unsurmountable problems, which - voilá - according to the evolutionary narrative, the evolution of oxygen-depending enzymes solved. Since there are oxygen dependent enzymes that do the same reaction, but in a completely different route, they use oxygen, permit the production of light capturing cholorophylls, and photosynthesis can continue. And of course, the oxygen sensitive at the same time, evolved protection mechanisms in order not to be killed.

After all, evolution is an amazing process, capable of the most demanding adaptations. Isnt it ?

So the evolution of oxygenic photosynthesis - for no reason - which rather than helping the survival, would have killed the organism, by horizontal gene transfer, for unknown reasons, produced the oxygen evolving complex, oxygenic photosynthesis, and as well enzymes that work depending on oxygen rather than an anoxic environment, and at the same time, did split cyanobacteria cells into two types, and produced heterocysts, which protect nitrogenase enzymes from oxygen.

There is more:
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.

Nick Lane describes the dilemma in the book Oxygen, the molecule that made the world:
Before cells could commit to oxygenic photosynthesis, they must have learned to deal with its toxic waste, or they would surely have been killed, as modern anaerobes are today. But how could they adapt to oxygen if they were not yet producing it? An oxygen holocaust, followed by the emergence of a new world order, is the obvious answer; but we have seen that there is no geological evidence to favor such a catastrophic history. In terms of the traditional account of life on our planet, the difficulty and investment required to split water and produce oxygen is a Darwinian paradox.

If there was a reduced atmosphere without oxygen some time back in the past ( which is btw quite controversial ) 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 ?  

Of course, evolution has to be significantly elastic in order to accomodante all these challenges, but hey, no matter what, its a fact after all. So who are we to question it?

But i, as a YEC, believe, God knew the essential ecological role of cyanobacterias and plants, and equipped them with the toolkit to adapt from the beginning to all environments.

Voilá. Occams Razor well applied. The simplest explanation is often the best.

View user profile http://elshamah.heavenforum.com

Admin


Admin
Spectroscopic properties of chlorophylls

Chlorophyll, and what it tells us about intelligent design - Page 2 WA60BU7

In photosynthesis of a green plant, light is collected primarily by chlorophylls, pigments that absorb light at a wavelength below 480 nm and between 550 and 700 nm. When white sunlight falls on a chlorophyll layer, the
green light with a wavelength between 480 and 550 nm is not absorbed but is reflected. This is why plant chlorophylls and whole leaves appear green.

Chlorophyll, and what it tells us about intelligent design - Page 2 WeQ8qwM

There are several chlorophyll molecule variants. Chlorophyll-a is the central photosynthesis pigment. 


Chlorophyll, and what it tells us about intelligent design - Page 2 RTHlh4V
Chlorophyll b is identical to chlorophyll a except at the C-7 position, a formyl group replaces the methyl group.  In a wide range of the visible spectrum of light, chlorophyll -a does not absorb it. This non-absorbing region is named the “green window.” The absorption gap is narrowed by the light absorption of chlorophyll-b, with its first maximum at a higher wavelength than chlorophyll -a and the second maximum at a lower wavelength. As shown in the picture, the light energy absorbed by chlorophyll b (chl-b) can be transferred very efficiently to chl-a. In this way, chl-b enhances the plant’s efficiency for utilizing sunlight energy. The structure of chlorophylls has remained remarkably unchanged in the deep past. 


Bu why does chlorophyll have this dip in the area where the sun emits the most energy?  The answer is that by this, chlorophyll makes better use of the range of light that it does absorb. It does so with high efficiency. Plants and most other photosynthetic organisms achieve far higher overall photon capture rates with chlorophyll than it would be the case with any other pigments

Leaf colour is fine-tuned on the solar spectra to avoid strand direct solar radiation 
Terrestrial green plants are fine-tuned to spectral dynamics of incident solar radiation and PAR absorption ( Photosynthetically active radiation ) is increased in various structural hierarchies.

Chlorophyll, and what it tells us about intelligent design - Page 2 9aQYAKY

If leaves were black, plants would absorb all wavelengths of visible light. What would be the consequence? Well, the amount of thermal stress this would plants under would probably cause cells to rupture. Cell walls are already under a lot of pressure as it is; additional heat could cause rupture in the short term, or water loss in the long-term. There are some plants with dark leaves, but they occupy ecological niches where sunlight irradiation is low, and they cannot survive in the canopy of trees.

Chlorophyll, and what it tells us about intelligent design - Page 2 AJpidBa

A sequence of alternating double and single bonds in rings, which form a system of conjugated bonds, is responsible for light absorption. Differences in the structure of these pigments result in certain variations in their absorption spectra.


 
Chlorophyll structure

Chlorophyll, and what it tells us about intelligent design - Page 2 Chloro10


The basic structure is a ring made of four pyrroles, a tetrapyrrole, which is also named porphyrin. Manganese Mg is present in the center of the ring as the central atom. Chlorophylls are excellent light absorbers. At ring d a  phytol. Phytol chain is attached. It consists of a long branched hydrocarbon chain. The phytol chain is not involved in light absorption, but it anchors the chlorophyll molecule in the thylakoid membrane and provides it with the right orientation. Remarkably, if just this phytol chain were not extant, chlorophyll could not be anchored in the light-harvesting complex, light could not be absorbed, photosynthesis could not occur, and no higher, more advanced and complex life forms could exist. Isn't that remarkable and amazing ?! 

The tetrapyrrole ring not only is a constituent of chlorophyll but is also employed in a variety of other biological functions.  With Copper as the center atom, it forms cobalamin (vitamin B12), which is one of the most complex Vitamins known, and life essential. With Iron instead of Manganese, as the central atom, the tetrapyrrole ring forms the basic structure of hemes, used in haemoglobin, which stores and transports oxygen in the blood of aerobic organisms.

Chlorophylls are embedded in Light-harvesting complexes

Chlorophyll, and what it tells us about intelligent design - Page 2 Z7HoXCo
All chlorophyll-based photosynthetic organisms contain light-gathering antenna systems. These systems function to absorb light and transfer the energy in the light to a trap, which quenches or deactivates the excited state. In most cases, the trap is the reaction center itself, and the excited state is quenched by photochemistry with energy storage. In some cases, however, the quenching is by some other process, such as fluorescence or internal conversion.


Chlorophyll, and what it tells us about intelligent design - Page 2 Y4V5vRN

The antenna pigments are arranged in well-defined, three-dimensional structures, so that only a few energy transfer steps are required to connect any two pigments in the array.


How exactly do Chlorophyll pigments “capture” the energy of light? 
The photosynthesis pathway starts with light absorption  which excites the chlorophyll molecule
When chlorophyll absorbs a photon, an electron excitation in its ring structure occurs, which moves electrons from the ground state into a higher excited state in the atoms. A sequence of alternating double and single bonds in rings, which form a system of conjugated bonds, is responsible for light absorption.





Chlorophyll, and what it tells us about intelligent design - Page 2 6yNeGpH
A photon can be envisioned as a very fast-moving packet of energy. When it strikes a molecule, its energy is either lost as heat or absorbed by the electrons of the molecule, boosting those electrons into higher energy levels. Whether or not the photon’s energy is absorbed depends on how much energy it carries (defined by its wavelength) and on the chemical nature of the molecule it hits. Electrons occupy discrete energy levels in their orbits around atomic nuclei. To boost an electron into a different energy level requires just the right amount of energy, just as reaching the next rung on a ladder requires you to raise your foot just the right distance. A specific atom can, therefore, absorb only certain photons of light—namely, those that correspond to the atom’s available electron energy levels.

As a result, each molecule has a characteristic absorption spectrum, the range and efficiency of photons it is capable of absorbing. Chlorophyll pigment molecules are good absorbers of light in the visible range. There are only two general types used in green plant photosynthesis: carotenoids and chlorophylls. Chlorophylls absorb photons within narrow energy ranges. Two kinds of chlorophyll in plants, chlorophylls a and b, preferentially absorb violet-blue and red light. Neither of these pigments absorbs photons with wavelengths between about 500 and 600 nanometers, and light of these wavelengths is, therefore, reflected by plants. 

When these photons are subsequently absorbed by the pigment in our eyes, we perceive them as green. Chlorophyll a is the main photosynthetic pigment and is the only pigment that can act directly to convert light energy to chemical energy.  
 
This higher energy state then can be transferred by electromagnetic interactions to its nearby adjacent pigment, moving from one molecule to another.

Chlorophyll, and what it tells us about intelligent design - Page 2 CFnf2e5


Remarkably, the higher energy state can result in four different reactions. It can result in a process known as fluorescence. It can from its higher energy state simply return into its ground state, and convert the excitation energy into heat, or transfer the energy to another molecule. This excited state is inherently unstable, and for that reason, any process that captures its energy must be extremely rapid. The photochemical reactions of photosynthesis are among the fastest known chemical reactions.  This extreme speed is necessary for photochemistry to compete with three other possible reactions of the excited state. 

Chlorophyll, and what it tells us about intelligent design - Page 2 GbhCpw2

An extremely rapid transfer of that excitation energy through the light-harvesting antenna occurs in picoseconds, to a specific chlorophyll pair in the reaction center of an enormously large super multisubunit protein-pigment complex called photosystem. Oxygenic photosynthesis uses two photosystem supercomplexes, Photosystem II and Photosytem I. (  photosystem II comes first in the pathway. )

Chlorophyll, and what it tells us about intelligent design - Page 2 EX4FiMF

This process is a high quantum efficiency resonance energy transfer. The distance from the donor pigment molecule to the acceptor molecule plays a crucial role in regards to the efficiency by which this energy transfer occurs. Light-harvesting complexes have their pigments specifically positioned to optimize these rates. The antenna pigments are arranged in well-defined, three-dimensional structures, so that only a few energy transfer steps are required to connect any two pigments in the array. A staggeringly high efficiency of approximately 95-99% is achieved when the energy of photons absorbed by the pigments is transferred to the reaction center and then is used in photochemistry.If chlorophylls would be arranged so that the energy had to diffuse along a linear, or one-dimensional, array of chlorophyll pigments, then the concept of energy transfer in photosynthesis would not be feasible. One-dimensional diffusion is very inefficient because many, many transfers are required to move the excitation from one point in the array to another.


Chlorophyll, and what it tells us about intelligent design - Page 2 Reacti10

Chlorophyll, and what it tells us about intelligent design - Page 2 8qpcsRk
A photon – a particle of light  collides with an electron in a leaf outside your window. The electron, given a serious kick by this energy boost, starts to bounce around, a little like a pinball. It makes its way through a tiny part of the leaf’s cell, and passes on its extra energy to a molecule that can act as an energy currency to fuel the plant. 

One-dimensional and three-dimensional antenna organization models.
In the one-dimensional model, excitation must be transferred by many steps before encountering a trap where photochemistry takes place. In the three-dimensional model, the trap is always no more than a few energy transfer steps from any of the pigments in the antenna complex.

Question: How could the right arrangement have emerged in a gradual, stepwise, evolutionary fashion, if only the arrangement in well-defined, three-dimensional structures, where only a few energy transfer steps are required to connect any two pigments in the array is feasible? 

Chlorophyll, and what it tells us about intelligent design - Page 2 Light_15

Observe that electrons are not transferred from one chlorophyll pigments in the antenna, to the adjacent ones. Only the energy of the excited state of the electron is moved on until reaching the special chlorophyll pair in the reaction center. The special chlorophyll pairs are named P680 in Photosystem I, and P700 in Photosystem II.  

The absorbed energy of the photon in this special chlorophyll pair performs a process called charge separation.  In this process, an electron is removed from that special chlorophyll pair, and this highly energized electron is donated to a carrier protein called Plastoquinone, to start a journey in the electron transport chain. During these electron transport reactions, adenine triphosphate (ATP) which is the energy provider in living cells, is produced by a proton gradient and is later consumed in carbon reductions, which will produce Glucose as the end product.

That special chlorophyll pair in the reaction center of the photosystem, alone, would not be able to collect enough energy through sunlight to be able to eject that electron to start the electron transfer. For that reason, there is this antenna light-harvesting complex which hosts in average 200 to 300 chlorophyll molecules per each photosystem. These surround the special chlorophyll pair in the reaction center to focus, deliver and transmit efficiently enough energy using before mentioned resonance energy transfer, more specifically named Förster resonance energy transfer. Chlorophyll thus acts as a large light-collecting antenna and it is at the reaction centers that the photochemical event occurs.

If every chlorophyll had associated with it the entire electron transfer chain and enzymatic complement needed to finish the job of photosynthesis, then these expensive components would sit idle most of the time, only occasionally springing into action when a photon is absorbed. This would obviously be wasteful, and ultimately such an arrangement would be unworkable. It is as if a factory were to have a number of expensive manufacturing machines sitting idle most of the time while a key raw material is being brought in at a slow pace. It makes more sense to buy only a few expensive machines and somehow to improve the delivery system of raw materials. This is what antennas do for photosynthetic organisms.

My comment: Did you observe the language employed? " It makes more sense". This is teleology. Goal orientation. Why would unguided evolutionary mechanisms produce chlorophylls wherein an inadequate arrangement and chaotic position would be of no use at all? - but only, in a workable arrangement? This is once again a formidable example where only intelligent setup explains rationally the setup of the biological system in question. 

Only by the accumulating of the energy from all these chlorophylls, the charge separation occurs in this special chlorophyll pair can occur,  enough to eject an electron from one atom to the plastoquinone carrier molecule, which starts the journey of the electron in the electron transport chain.

Chlorophyll, and what it tells us about intelligent design - Page 2 WiO0SZo


Light-harvesting antennae do not contain only chlorophylls, but also other molecules, additional accessory pigments such as carotenoids which have a crucial,  role in photosynthesis: photoprotection through destruction of reactive oxygen species that arise as byproducts of photoexcitation, and chlorophyll biosynthesis. 

When a chlorophyll pigment absorbs a photon,  the energy of the photon excites electrons and transfers them to a higher energy level, which results in an excited state of the chromophore molecule. The energy is absorbed only in discrete quanta, resulting in discrete excitation states.


Photosynthesis is comprised of a series of redox reactions. An oxidation-reduction (redox) reaction is a type of chemical reaction that involves a transfer of electrons between two species. It is any chemical reaction in which the oxidation number of a molecule, atom, or ion changes by gaining or losing an electron.

The oxidation state of an element corresponds to the number of electrons, that an atom loses, gains, or appears to use when joining with other atoms in compounds. The chemical species from which the electron is stripped is being oxidized, while the chemical species to which the electron is added is being reduced.

Redox reactions are vital to photosynthesis in which light produces NADPH, which acts as the reducing molecule for CO2 fixation via the Calvin cycle.  

Biological energy is frequently stored and released by means of redox reactions. Photosynthesis involves the reduction of carbon dioxide which occurs in the light-independent reactions, in the second phase of photosynthesis, into glucose sugars and the oxidation of water into molecular oxygen in the light-dependent reactions, right in the beginning.  

The reverse reaction, respiration in mitochondria in eukaryotic cells, oxidizes glucose sugars ( produced through photosynthesis ) to produce carbon dioxide and water. As intermediate steps, the reduced carbon compounds are used to reduce nicotinamide adenine dinucleotide (NAD+) to NADH, which then contributes to the creation of a proton gradient, which drives the synthesis of adenosine triphosphate (ATP) and is maintained by the reduction of oxygen.

When the photosynthetic apparatus is light saturated,  the intense absorptions and the long-lived excited states render both Chls and their tetrapyrrole toxic, generating highly toxic reactive oxygen species. Biosynthesis and degradation of Chls are therefore tightly controlled and co-regulated with the other parts of the photosynthetic apparatus.


rattlesnakes have infrared detectors that give them “heat pictures” of their surroundings. To our eyes, both the male and female Indian luna moths are light green and indistinguishable from each other, but the luna moths themselves perceive the ultraviolet range of light. Therefore, to them, the female looks quite different from the male. Other creatures have difficulty seeing the moths when they rest on green leaves, but luna moths are not camouflaged to one another; rather, they see each other as brilliantly colored. Bees can also detect ultraviolet light. In fact, many flowers have beautiful patterns that bees can see to guide them to the flower. These attractive and intricate patterns are totally hidden from human perception. 


https://www.ncbi.nlm.nih.gov/pubmed/27023791/

View user profile http://elshamah.heavenforum.com

Sponsored content


Back to top  Message [Page 2 of 2]

Go to page : Previous  1, 2

Permissions in this forum:
You cannot reply to topics in this forum