My articles

" Tetrapods evolved " . Really ?  

https://reasonandscience.catsboard.com/t2219-the-evolution-of-tetrapods

Recently i saw following youtube video :



I thought how much brainpower was required to program and make these robots. In the natural world, according to proponents of naturalism, the required coordination and invention of new limbs were due just too random natural processes. That made me have a closer look at what mainstream scientific papers have to say about the subject. How did the first limbs of tetrapods emerge? What mechanism is required to grow body parts like legs, and how do proponents of evolution explain the rise of tetrapods?

According to proponents of evolution, tetrapods arose from a lineage of fish. This kind of dramatic change over time is called macroevolution.
The transition from life in water to life on land would have necessitated dramatic structural changes of the whole body to withstand the increased effects of gravity, amongst other new requirements.
Many aspects of tetrapod origins remain elusive. Its supposed evolution has generated great interest, but the earliest phases of their history are poorly understood. Recent studies have questioned long-accepted hypotheses about the origin of the pentadactyl limb, the phylogeny of tetrapods, and the environment in which the first tetrapods lived.
The ‘earliest’ known tetrapods with feet and legs are now thought to have been aquatic animals; proponents of evolution, therefore, argue that feet and legs evolved in a shallow water environment and were only later co-opted for use on the land.

Most discussions of the topic concentrate to elucidate if the fossil record permits to find transitional forms that permit infer water to land transition. Not only are there huge gaps, but the idea bears big problems conceptually, and as a whole.

http://reasonandscience.heavenforum.org/t1808-transition-from-water-to-land-dilemma?highlight=land

Moreover, as Behe explained nicely: In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as the rise of tetrapods must include how the transition occurred on a molecular explanation. It is no longer sufficient for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.

So rather than stick to anatomy comparisons of fossils that might bear some similarity that could be interpreted as intermediates and evolution of tetrapod limbs from fish fins, let us try to elucidate how significant the functional and morphological shift was it in terms of the underlying genetic mechanisms. The fossil record provides insight into supposed morphological changes. However, to understand the underlying mechanisms, we must peer into the gene regulatory networks of living vertebrates.

Do new anatomical structures arise de novo, or do they evolve from pre-existing structures? Advances in developmental genetics, paleontology, and evolutionary developmental biology have recently supposedly shed light on the origins of the structures that most intrigued Charles Darwin, including tetrapod limbs. According to proponents of evolution, structures arose by the modification of pre-existing genetic regulatory circuits.

The genetic program instructs how to make new structures, but that program must be precisely programmed, and the genetic regulatory circuits need also to be programmed. That is, two separate programs need to emerge, that is 1. the program which defines the physical form and structure, and 2. the program which instructs where to find the genetic information in the genome, and when to express is during development, that is in the right sequence. That are different layers of information, which must exist fully developed in order to make the new anatomical parts in question. 

The instructions that control when and where a gene is expressed are written in the sequence of DNA bases located in the regulatory region of the gene. These instructions are written in a language that is often called the ‘gene regulatory code’. This code is read and interpreted by proteins called transcription factors that bind to specific sequences of DNA (or ‘DNA words’) and increase or decrease gene expression. Changes in gene expression between species could, therefore, be due to changes in the transcription factors and/or changes in the instructions within the regulatory regions of specific genes.

In order for communication to happen, 1. The sequence of DNA bases located in the regulatory region of the gene is required, and 2. transcription factors that read the code. If one or both is missing, communication fails, the gene that has to be expressed, cannot be encountered, and the whole procedure of gene expression fails. This is an irreducibly complex system. The gene regulatory code could not arise in a stepwise manner either since if that were the case, the code has only the right significance if fully developed.  That's an example par excellence of intelligent design.

https://reasonandscience.catsboard.com/t2220-shannons-theory-of-information

During vertebrate limb development, Hoxd genes are transcribed in two temporal phases; an early wave controls growth and polarity up to the forearm and a late wave patterns the digits. In this issue of Developmental Cell, Tarchini and Duboule (2006) report that two opposite regulatory modules direct early collinear expression of Hoxd genes.

Question: how could natural mechanisms have programmed and directed the right temporal phases of gene transcription of the right genes,  and early wave control? Furthermore, the limbs develop at the right place, the right coordinates and positional information is required, they could develop anywhere on the body. Did natural mechanisms find out about the right place by trial and error? There were myriads of positions possible to add the limb. How could the right and precise coordination of axial position be achieved by mutations? 

The problem is that nature has too many options and without design couldn’t sort them all out. Natural mechanisms are too unspecific to determine any particular outcome. Mutation and natural selection could theoretically form a new complex morphological feature like a  leg or a limb with the right size and form , and arrange to find out the right body location to grow them , but it could  also produce all kinds of other new body forms, and grow and attach them anywhere on the body, most of which have no biological advantage or are most probably deleterious to the organism. Natural mechanisms have no constraints, they could produce any kind of novelty. Its however that kind of freedom that makes it extremely unlikely that mere natural developments provide new specific evolutionary arrangements that are advantageous to the organism.  Nature would have to arrange almost a infinite number of trials and errors until getting a new positive  arrangement. Since that would become a highly  unlikely event, design is a better explanation. 

Going over through several mainstream scientific papers, i have not come across one of them, that were able to provide a detailed description how exactly the morphological transition could have occurred through evolution.

Some biologists have also envisioned special mutations in regulatory homeobox or "Hox" genes, where simple mutations might be able to make large developmental changes in an organism which might case a radically different phenotype. However, manipulating "Hox" genes does little to solve the problem of generating novel functional biostructures, for making large changes in phenotype are rarely beneficial. Hox gene mutations may be a more simple mechanism for generating large change, but they also do not escape the problem of the "hopeful monster":"The drawback for scientists is that nature's shrewd economy conceals enormous complexity. Researchers are finding evidence that the Hox genes and the non-Hox homeobox genes are not independent agents but members of vast genetic networks that connect hundreds, perhaps thousands, of other genes. Change one component, and myriad others will change as well--and not necessarily for the better. Thus dreams of tinkering with nature's toolbox to bring to life what scientists call a "hopeful monster"- such as a fish with feet--are likely to remain elusive."Furthermore, many biologists forget when invoking Hox gene mutations that Hox genes can only re-arrange parts which are already there--they cannot create truly novel structures.

Casey Luskin : Hox mutations will never create new "body part genes", and thus cannot add truly new phenotypic functions into the genome, and at best we are left with the quandaries associated with "pre-adaptation". The majority of evolutionary change must take place through evolving new "body part genes", which Hox mutations cannot do. One reviewer in Nature recognizes this fact:"Schwartz ignores the fact that homeobox genes are selector genes. They can do nothing if the genes regulated by them are not there. It is these genes that specify in detail the adaptive structure of the organs. To be sure, turning on a homeobox gene at the wrong place can result in the appearance of an ectopic organ, but only if the genes for that organ are present in the same individual. It is totally wrong to imply that an eye could be produced by a macromutation when no eye was ever present in the lineage before.


Darwins doubt, pg.239

WHAT ABOUT HOX GENES? Hox (or homeotic) genes regulate the expression of other protein-coding genes during the process of animal development. Some biologists have likened them to the conductor of an orchestra who plays the role of coordinating the contributions of the players. And because Hox genes affect so many other genes, many evo-devo advocates think that mutations in these genes can generate large- scale changes in form.

But can mutations in Hox genes transform one form of animal life—one body plan—into another? There are several reasons to doubt that they can.
First, precisely because Hox genes coordinate the expression of so many other different genes, experimentally generated mutations in Hox genes have proven harmful.  in fruit flies "most mutations in homeotic [Hox] genes cause fatal birth defects." In other cases, the resulting Hox mutant phenotype, while viable in the short term, is nonetheless markedly less fit than the wild type. For example, by mutating a Hox gene in a fruit fly, biologists have produced the dramatic Antennapedia mutant, a hapless fly with legs growing out of its head  where the antennae should be.  

https://reasonandscience.catsboard.com/t2077-hox-genes

The irreducibly complex ATP Synthase nanomachine, amazing evidence of design

http://reasonandscience.heavenforum.org/t1439-the-irreducibly-complex-atp-synthase-nanomachine-amazing-evidence-of-design

Structural Biochemistry/The Evolution of Membranes
https://en.wikibooks.org/wiki/Structural_Biochemistry/The_Evolution_of_Membranes
F- and A/V- type ATPases are membrane-embedded proteins and were feasibly present in the LUCA (last universal common ancestor) due to their omnipresence in modern cellular life. 11

A critically important macromolecule—arguably “second in importance only to DNA”—is ATP. ATP is an abbreviation for adenosine triphosphate, a complex molecule that contains the nucleoside adenosine and a tail consisting of three phosphates. As far as known, all organisms from the simplest bacteria to humans use ATP as their primary energy currency. In each of the approximately one hundred trillion human cells is about one billion ATP molecules.
Without ATP, life as we understand it could not exist. All the books in the largest library in the world may not be able to contain the information needed to understand and construct the estimated 100,000 complex macromolecule machines used in humans.  Anything less than an entire ATP molecule will not function and a manufacturing plant which is less then complete cannot produce a functioning ATP. Dr. Jerry Bergman
New X-ray crystallographic studies have revealed the working of adenosine triphosphate synthase, the basis of energy transport in all living organisms.
ATP captures the chemical energy released by the combustion of nutrients and transfers it to reactions that require energy, e.g. the building up of cell components, muscle contraction, transmission of nerve messages and many other functions. ATP synthase molecules located within mitochondria stick out on the mitochondria, attached to their inner surfaces in mushroom-like clusters. When food is broken down or metabolized for energy, the last stages of the process occur within the mitochondria.

ATP synthase is an irreducibly complex motor—a proton-driven motor divided into rotor and stator portions. Protons can flow freely through the CF0 complex without the CF1 complex, so that if it would have emerged 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.  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, which is equally impossible for proponents of evolution to explain.  10


ATP synthatse is a irreducible complex molecular motor par excelence. Disconnect one of its components, disturb one of its forms, replace some of your AA position,  and the system loses function altogether. Try to build it slowly, step by step, by mindless unguided processes, where would  the energy come from to build it, if it is the energy provider of life? Remember though that the energy that produces ATP synthase is essential to life, virtually for all forms of life. And unless the proton gradient is in place, ATPsynthase would be useless. 

“Various forms of this ingenious device are found in all forms of life.”

Thus, your statement, “But some anaerobic bacteria do not contain the enzyme ATP synthase” is apparently incorrect. If any bacterium is discovered without it, I would like to know about it.

In sum, all life depends on ATPase, but not all life depends on it for ATP production. Anaerobic bacteria use it to maintain pH balance instead. So ATPase must have been present in the very first cell. No known natural process could have built it up piece-by-piece, as you have suggested, because without the entire apparatus, there is no living cell and therefore no evolution, even in theory.

Since evolution by natural selection requires reproduction, and since reproduction requires life, which requires ATPase, the enzyme is therefore a prerequisite for evolution. But with evolution out of order until ATPase ‘appears’, evolution is not even in the running as a model to explain the origin of the molecular motor.

At least five of the below mentioned parts are ESSENTIAL and IRREDUCIBLE. Take away one , and ATP synthase ceases to function. Neither could any of the sub parts simply be co-opted from anywhere else. That would be the same as to say, in order to make a motor function, and a cylinder is missing, go search and find any cylinder nearby , co-opt it, and solved is the problem. The thing is that cylinders come in all size, specification, materials etc. And there is no goal oriented search of parts that fit through evolution Evolution has no forsight. Furthermore, there must be the information how and when and where to mount the parts, at the exact place, in the right sequence.  Thats a far fetch for a mindless  tinkerer to be able to achieve. 

1.The nucleotide binding stator subunits (“cylinders”) :  The electrostatic interaction of these rotor and stator charges is essential for torque generation
2.The central stalk (“crankshaft”) : The torsional elasticity of the central stalk and the bending and stretching elasticity of the peripheral stalk create an elastic coupling between Fo and F1. Is is essential.
3, The A/V rotor subunit (“adapter”) ; It is not used in all ATP synthase motors, and can therefore be reduced.
4. The Rotor ring (“turbine”) ;  A ring of 8–15 identical c-subunits is essential for ion-translocation by the rotary electromotor of the ubiquitous FOF1-
ATPase.
5.The Jon channel forming subunit ; Subunit a harbors the ion channel that provides access to the binding site on the c11 ring in the middle of the membrane from the periplasmic surface . The channel is essential for the operation of the enzyme, because mutants in which the channel is blocked are completely inactive in both the ATP synthesis and/or coupled ATP hydrolysis mode
6. The peripheral stalk (“pushrod”) ; The peripheral stalk of F-ATPases is an essential component of these enzymes. It extends from the membrane distal point of the F1 catalytic domain along the surface of the F1 domain with subunit a in the membrane domain.
7 - 11 do not exist in all atp synthase motors, and can therefore be reduced. 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC27776/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3846802/
4. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043045
5. http://onlinelibrary.wiley.com/doi/10.1046/j.1432-1033.2002.03264.x/pdf
6. https://www.ncbi.nlm.nih.gov/pubmed/16697972

There are at least 5 subunit parts essential to mantain the basice function of the ATP synthase motor.

If the substrates like crude oil  required to make gasoline are not provided at the correct refinery place at the Oil industrial plant, the refinery process cannot happen. Same happens inside the cell.  In order for mitochondria to function, shuttling of ADP, ATP, phosphates and other substrates is essential. That process  does not catch mutch attention, but  is actually life essential for eukaryotic cells to function. We need the right charge of ADP and ATP, the electrochemical gradient inside the inner membrane,  the ADP/ATP carrier proteins that drive the substrates around, and carrier proteins that shuttle the phosphate that is required along with ADP for ATP synthesis to the right place at atp synthase motors, ready to be used , to be added to ADP to make ATP. That seems a ingeniously precise  orchestrated process requiring several indispensable parts. ATP synthase is a prime example of intelligent design, and should be able to convince even the most skeptic that intelligent design is the best explanation for its origin . 

The amazing design of the DNA packaging motor

http://reasonandscience.heavenforum.org/t2134-the-amazing-design-of-bacteriophage-viruses-and-its-dna-packaging-motor

The argument from the DNA’s molecular motor
1. There is a “very fast and powerful molecular motor” that crams the viral DNA tightly into the capsid with the help of five moving parts.
2. The parts of the motor move in sequence like the pistons in a car's engine, progressively drawing the genetic material into the virus's head, or capsid.
3. The motor is needed to insert DNA into the capsid of the T4 virus, which is called a bacteriophage because it infects bacteria.
4. The T4 molecular motor is the strongest yet discovered in viruses and proportionately twice as powerful as an automotive engine. The motors generate 20 times the force produced by the protein myosin, one of the two proteins responsible for the contraction and strength of muscles.
5. Even viruses, which are not even alive by the scientific definition of being able to reproduce independently, show incredible design.
6. If design is what we observe, then there must be a designer.
7. God exists.


According to the United Nations, 2015 is the International Year of Light as well as the International Year of Soils. But, for the marine microbial ecologist Forest Rohwer, 2015 is also the Year of the Phage.  Phages, more formally known as bacteriophages, are viruses that infect bacteria. They are easily as ubiquitous, universal, and essential to life on Earth as light and soil, and yet they are largely unknown. 

“The thing that even most biologists don’t get—let alone most of the rest of the world—is that phages are the most diverse things on the planet, and there are more of them than anything else, and we really don’t have a clue” Phages possess a wide array of forms and functions. They are all incredibly small; at just a few nanometres across, they lie on the border of measurability between quantum and classical physics, all but impossible to see without a scanning electron microscope.

Viruses look incredibly well designed. Some bacteriophages look like lunar landing capsules, legs and all.

Viruses are tiny particles that can’t reproduce on their own, but hijack the machinery of truly living cells. But they still have genetic material, long strands of DNA (or sometimes RNA) enclosed in a protein sheath. They are biologically inert until they enter into host cells. Then they start to propagate using host cellular resources. The infected cell produces multiple copies of the virus, then often bursts to release the new viruses so the cycle can repeat. One of the most common types is the bacteriophage (or simply ‘phage’) which infects bacteria. It consists of an infectious tailpiece made of protein, and a head capsule (capsid) made of protein and containing DNA packaged at such high pressure that when released, the pressure forces the DNA into the infected host cell.

How does the virus manage to assemble this long information molecule at high pressure inside such a small package, especially when the negatively charged phosphate groups repel each other? It has a special packaging motor, more powerful than any molecular motor yet discovered, even those in muscles.  ‘The genome is about 1,000 timeslonger than the diameter of the virus. It is the equivalent of reeling in and packing 100 mts of fishing line into a coffee cup, but the virus is able to package its DNA in under five minutes.
Force 
A surprising finding  is that the phage packaging motor generates enormous force in order to package DNA. Forces as high as ∼60 pN were measured in phages ϕ29, λ, and T4, thus making the packaging motor one of the strongest force generating biological motors reported to date.  The force is 20–25 times that of myosin, 10 times that of kinesin, or >2 times that of RNA polymerase. Such high forces seem to be essential to pack the viral DNA against the enormous electrostatic repulsive forces (and bending and entropic energies) to confine a highly negatively charged DNA polymer within a limited volume of the capsid

Velocity
The phage packaging motors show high rates of packaging as well as high processivity. The T4 motor can achieve rates as high as ∼2000 bp/sec, the highest recorded to date. 

Power
Phage packaging motors generate enormous power, with the T4 motor being the fastest and the most powerful. Even with a high external load force of 40 pN, the T4 motor can translocate DNA at a remarkable speed of ∼380 bp/sec. This is equivalent to a power of 15,200 pN/bp/s, or 5.2 × 10−18 W. Scaling up the nanoscale T4 packaging motor to a macromotor, the motor power density is approximately twice that of a typical automobile engine

The sequence of steps in the head morphogenesis  is as follows:

(i) assembly of the packaging motor on a nascent (unexpanded) empty prohead (Figure A)
(ii) expansion of the capsid after about 10%–25% of the genome is packaged (Figure B)
(iii) packaging until the head is full
(iv) cutting of DNA and dissociation of the motor (Figure C)
(v) assembly of neck proteins to seal the packaged heads (Figure D)

Question : How could natural forces and chemical reactions have come up with such a elaborated mechanism ? 

In a specially interesting scientific paper from last year scientists report that  The 30° tilt of the subunits matches perfectly with the 30° transitions that the dsDNA helix exhibits during revolution (360° ÷ 12 = 30°). 

Question : how did this precise and finely tuned arrangement emerge ? trial and error ?

In each step of revolution that moves the dsDNA to the next subunit, the dsDNA physically moves to a second point on the channel wall, keeping a 30° angle between the two segments of the DNA strand . This structural arrangement enables the dsDNA to touch each of the 12 connector subunits in 12 discrete steps of 30° transitions for each helical pitch . Nature has created and evolved  a clever machine   that advances dsDNA in a single direction while avoiding the difficulties associated with rotation, such as DNA supercoiling, as seen in many other processes.

Question : how did this precise and finely tuned arrangement emerge ? trial and error ? since when can  be clever be assigned to something that is not intelligent ?? Should the author of the article not rather honor the inventor of this amazing nano machinery, namely the creator ??

The dramatic divergence of bacteriophage genomes is an obstacle that frequently prevents the detection of homology between proteins and, thus, the determination of phylogenetic links between phages.

Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. 

Convergence, of course,is a common feature of design. It’s also precisely the opposite of “divergence”, which is supposed to be a hallmark of evolution.

Even viruses, which are not even alive by the definition of being able to reproduce independently, show incredible design.  They are too well designed to be accidents. 

Proponents of naturalism have to believe in miracles – that super-efficient, compact, powerful motors like this just appeared, arose or emerged (favorite Darwinian miracle-words) from nowhere.

The large packaging subunit gp17 but not the small subunit gp16 exhibited an ATPase activity. 2 Although gp16 lacked ATPase activity, it enhanced the gp17-associated ATPase activity by >50-fold. The gp16 enhancement was specific and was due to an increased catalytic rate for ATP hydrolysis. A phosphorylated gp17 was demonstrated under conditions of low catalytic rates but not under high catalytic rates in the presence of gp16. The data are consistent with the hypothesis that a weak ATPase is transformed into a translocating ATPase of high catalytic capacity after assembly of the packaging machine. The nonstructural terminase complex, constituted by one small subunit and one large subunit, is a key component of the DNA-packaging machine 

So both subunits are required for proper functioning of the molecular motor. These subunits do not have any use unless duly embedded in this nano motor. A irreducible complex system must have at least two subunits, who could not have emerged through evolutionary steps. This seems to be the case in this amazing molecular machine as well. Further evidence is the fact that no protein homology exists between different Phages, which is another indication that they are designed and created separately.



This is a incredible animation of T4 bacteriophage Virus assembly: 





Virus has powerful mini-motor to pack up its DNA 4



How does the virus manage to assemble this long information molecule at high pressure inside such a small package, especially when the negatively charged phosphate groups repel each other? It has a special packaging motor, more powerful than any molecular motor yet discovered, even those in muscles.  ‘The genome is about 1,000 timeslonger than the diameter of the virus. It is the equivalent of reeling in and packing 100 mts of fishing line into a coffee cup, but the virus is able to package its DNA in under five minutes.. Researchers   analysed the bacteriophage T4—a virus that infects E. coli bacteria, the type that inhabit human intestines.  This motor exerts a force of > 60 piconewtons. This sounds small (6 × 10–11 N), but for its size, it’s twice as powerful as a car engine. So the motor, a terminase enzyme complex, ‘can capture and begin packaging a target DNA molecule within a few seconds.’








Viral DNA packaging motors are among the most powerful molecular motors known. 

1 Single-molecule studies show that the packaging motor is fast and powerful. 2

DNA packaging into a viral capsid is a complex process consisting of initiation, elongation, and termination. It involves orchestrated coordination and sequential action of multiple proteins 1


Force 8
Velocity
The phage packaging motors show high rates of packaging as well as high processivity. The T4 motor can achieve rates as high as ∼2000 bp/sec, the highest recorded to date. 

Power
Phage packaging motors generate enormous power, with the T4 motor being the fastest and the most powerful. Even with a high external load force of 40 pN, the T4 motor can translocate DNA at a remarkable speed of ∼380 bp/sec. This is equivalent to a power of 15,200 pN/bp/s, or 5.2 × 10−18 W. Scaling up the nanoscale T4 packaging motor to a macromotor, the motor power density is approximately twice that of a typical automobile engine

Large dsDNA bacteriophages and herpesviruses encode a powerful ATP-driven DNA-translocating machine that encapsidates a viral genome into a preformed capsid shell or prohead. 







Study reveals structure of DNA packaging motor in virus 
7

an elongated prohead that serves as the virus shell
a doughnut-shaped connector that is positioned at the entrance to the virus shell and feeds DNA into the shell 
a novel ribonucleic acid (RNA)-enzyme complex that converts chemical energy to mechanical energy needed for packaging.

This motor system appears to be novel mechanistically.

Did God make pathogenic viruses?  6 
 
 
1) http://www.pnas.org/content/111/42/15096.short
2) http://cel.webofknowledge.com/InboundService.do?SID=2DypYOwSdUP2rHMIiEw&product=CEL&UT=WOS%3A000261767000027&SrcApp=Highwire&Init=Yes&action=retrieve&SrcAuth=Highwire&Func=Frame&customersID=Highwire&IsProductCode=Yes&mode=FullRecord
3) http://www.ncbi.nlm.nih.gov/pubmed/22297528
4) https://creation.com/images/pdfs/tj/j22_1/j22_1_15-16.pdf
6) http://creation.com/did-god-make-pathogenic-viruses
7) http://www.purdue.edu/uns/html4ever/001206.Rossmann.DNAmotor.html
8 )  http://teaguesterling.com/dna/motor-protein.pdf
9)   http://www.newyorker.com/tech/elements/phage-killer-viral-dark-matter
10 ) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109452/

The Argument of the Original Replicator

https://reasonandscience.catsboard.com/t1849-dna-replication-of-prokaryotes

The Argument of the Original Replicator
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place,  fully functional and working properly, otherwise the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function by their own. They have only function interconnected in the working whole. 
The individual parts must be readily available on the construction site of the rna replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design. 

According to mainstream scientific papers, the following twenty protein and protein complexes are essential for prokaryotic DNA replication. Each one mentioned below. They cannot be reduced. If one is missing, DNA replication cannot occur: 

Pre-replication complex  Formation of the pre-RC is required for DNA replication to occur
DnaA The crucial component in the initiation process is the DnaA protein
DiaA this novel protein plays an important role in regulating the initiation of chromosomal replication via direct interactions with the DnaA initiator.
DAM methylase  It’s gene expression requires full methylation of GATC at its promoter region. 
DnaB helicase Helicases are essential enzymes for DNA replication, a fundamental process in all living organisms.
DnaC Loading of the DnaB helicase is the key step in replication initiation.  DnaC is essential for replication in vitro and in vivo. 
HU-proteins  HU protein is required for proper synchrony of replication initiation
SSB Single-stranded binding proteins  Single-stranded DNA binding proteins are essential for the sequestration and processing of single-stranded DNA. 6
SSBs from the OB domain family play an essential role in the maintenance of genome stability, functioning in DNA replication, the repair of damaged DNA, the activation of cell cycle checkpoints, and in telomere maintenance. SSB proteins play an essential role in DNA metabolism by protecting single-stranded DNA and by mediating several important protein–protein interactions. 7
Hexameric DNA helicases DNA helicases are essential during DNA replication because they separate double-stranded DNA into single strands allowing each strand to be copied.
DNA polymerase I and III DNA polymerase 3 is essential for the replication of the leading and the lagging strands whereas DNA polymerase 1 is essential for removing of the RNA primers from the fragments and replacing it with the required nucleotides. 
DnaG Primases  They are essential for the initiation of such phenomena because DNA polymerases are incapable of de novo synthesis and can only elongate existing strands 
Topoisomerases  are essential in the separation of entangled daughter strands during replication. This function is believed to be performed by topoisomerase II in eukaryotes and by topoisomerase IV in prokaryotes. Failure to separate these strands leads to cell death. 
Sliding clamp and clamp loader the clamp loader is a crucial aspect of the DNA replication machinery.  Sliding clamps are DNA-tracking platforms that are essential for processive DNA replication in all living organisms 
Primase (DnaG) Primases are essential RNA polymerases required for the initiation of DNA replication, lagging strand synthesis and replication restart.  They are essential for the initiation of such phenomena because DNA polymerases are incapable of de novo synthesis and can only elongate existing strands. 
RTP-Ter complex Ter sequences would not seem to be essential, but they may prevent overreplication by one fork in the event that the other is delayed or halted by an encounter with DNA damage or some other obstacle
Ribonuclease H  RNase H1 plays essential roles in generating and clearing RNAs that act as primers of DNA replication. 
Replication restart primosome Replication restart primosome is a complex dynamic system that is essential for bacterial survival. 
DNA repair: 
RecQ helicase  In prokaryotes RecQ is necessary for plasmid recombination and DNA repair from UV-light, free radicals, and alkylating agents. 
RecJ nuclease the repair machinery must be designed to act on a variety of heterogeneous DNA break sites.

I do not know of any scientific paper  that explains in a detailed manner how DNA replication de novo or any of its parts might have emerged in a naturalistic manner, without involving intelligence. The systems responsible for DNAreplication are well beyond the explanatory power of unguided natural processes without guiding intelligence involved. Indeed, machinery of the complexity and sophistication of that described above is, is in my view best explained through a intelligent designer.

Precisely BECAUSE WE KNOW that each of the described and mentioned parts is indispensable, it had to arise all at once. We know of intelligence being able to project, plan and make such a motor-like system based on lots of information , and it could not have emerged through evolution ( even less so because evolution depends on dna replication being in place ) we can infer rationally design as the best explanation. Chance is no reasonable option to explain the origin of DNAreplication since the individual parts would have no function by their own, and there is no reason why matter aleatory-like would group itself in such highly organized and complex machine-like system.

1) http://www.weizmann.ac.il/plants/Milo/images/MolMachinesSize120116Clean.pdf
2) http://cshperspectives.cshlp.org/content/5/10/a010116.full
3) https://en.wikipedia.org/wiki/Control_of_chromosome_duplication
4) http://www.biochem.umd.edu/biochem/kahn/molmachines/replication/Dna%20C%20protein.htm
5) http://www.nature.com/nsmb/journal/v15/n1/full/nsmb1356.html
6) http://www.biomedcentral.com/1471-2199/14/9
7) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632105/
8 ) Meyer, signature of the cell, page 111
9 ) http://journal.frontiersin.org/article/10.3389/fmicb.2014.00735/full#F1
10 ) http://creationsafaris.com/epoi_c08.htm
11) http://creationsafaris.com/ar_srds.htm
12) http://www.ncbi.nlm.nih.gov/books/NBK6360/
13) from the book: The Logic of Chance: The Nature and Origin of Biological Evolution By Eugene V. Koonin, page 266
14) https://www-als.lbl.gov/index.php/science-highlights/science-highlights/669-structures-of-clamp-loader-complexes-are-key-to-dna-replication.html
15) http://www.nature.com/nature/journal/v429/n6993/full/nature02585.html
16) http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.604184

Amazing molecular assembly lines and non ribosomal amino-acid chain formation pathways come to light

https://reasonandscience.catsboard.com/t2445-new-amazing-molecular-assembly-lines-and-non-ribosomal-amino-acid-chain-formation-pathways-come-to-light

If you thought there is only one way to make polypeptide amino-acid chains by the well-known process  DNA => RNA polymerase => mRNA => Ribosome + tRNA =>>  amino-acid polypeptides, you did not hear until now ( as me ) about NRPS, or Nonribosomal peptide synthetases. Well, you might ask, how do they work and what do they produce? Maybe i should start and explain first, how i came to know about them. The best way to learn about molecular biology is to get curious, ask questions, and dig deep until it reaches the bottom. Follow the evidence like Sherlock Holmes.

I was starting to read the book A privileged Planet, and on page 201,  Gonzales writes: The strong nuclear force is responsible for holding protons and neutrons together in the nuclei of atoms. In such close quarters, it is strong enough to overcome the electromagnetic force and bind the otherwise repulsive, positively charged protons together. It is as short-range as it is strong, extending no farther than atomic nuclei. But despite its short-range, changing the strong nuclear force would have many wide-ranging consequences, most of them detrimental to life.  The periodic table of the elements would look different with a changed strong nuclear force. If it were weaker, there would be fewer stable chemical elements. The more complex organisms require about twenty-seven chemical elements, iodine being the heaviest (with an atomic number of 53). Instead of ninety-two naturally occurring elements, a universe with a strong force weaker by 50 percent would have contained only about twenty to thirty. This would eliminate the life-essential elements of iron and molybdenum. 

Molybdenum, life-essential? Hmm, yes, of course. I read about Molybdenum required in nitrogenase enzymes in cyanobacteria. So my next question was: What are the life-essential elements for life? Here the list:

Essential elements and building blocks for the origin of life
http://reasonandscience.heavenforum.org/t2437-essential-elements-and-building-blocks-for-the-origin-of-life

So, i went on, and gave closer attention to Molybdenum.  I remembered that the amazing nitrogenase enzyme which works as a molecular sledge-hammer, breaks the molecular triple bond of nitrogen, and transforms nitrogen gas into ammonia, essential for the makeup of living things, and it uses in its active site as co-factor molybdenum.

The Nitrogenase enzyme,  the molecular sledgehammer  
With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism, but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue.
http://reasonandscience.heavenforum.org/t1585-nitrogenase#2406

So my next question was: How are the MOLYBDENUM COFACTORs synthesized, the essential active sites for nitrogenase function that contain molybdenum?

So this lead me to following research:

Molybdenum, essential for life
http://reasonandscience.heavenforum.org/t2430-molybdenum-essential-for-life

So i discovered, that for the starting point of molybdenum co-factor maturation ( or biosynthesis ), Iron-Sulfur ( FE/S) clusters are used. They were not unknown to me. I studied about them some time ago:

Biosynthesis of Iron-sulfur clusters, basic building blocks for life  
http://reasonandscience.heavenforum.org/t2285-iron-sulfur-clusters-basic-building-blocks-for-life

So, i asked myself: In order to make FE/S clusters, the cell needs the uptake of Iron and Sulfur. How does that happen in the cell ? Here we go:

Sulfur essential for life
http://reasonandscience.heavenforum.org/t2433-sulfur-essential-for-life

Iron Uptake and Homeostasis in Cells
http://reasonandscience.heavenforum.org/t2443-iron-uptake-and-homeostasis-in-prokaryotic-microorganisms

And here comes the amazing part: 

Iron Bioavailability
Although iron is one of the most abundant elements on Earth, the environment is usually oxygenated, non-acidic, and aqueous. Under these conditions, extracellular iron is predominantly found in the poorly soluble ferric (Fe3+) state. One way that organisms such as yeast improve iron bioavailability is by acidifying the local environment.  By lowering the pH of the surrounding environment, organisms facilitate solubilization and uptake of iron. ATP-driven proton transporters move H+ ions from the cytosol across the plasma membrane to control the pH at the cell surface.

Question: Had this system not have to emerge fully setup right from the beginning in order to facilitate and make Iron uptake into the cell even possible ?

Uptake of Iron by micro-organisms like Bacteria and fungi
Many microorganisms, including some fungi, also secrete low molecular weight compounds known as siderophores into their surroundings, which form high-affinity (~10−33 M) complexes with ferric iron to make it bioavailable for uptake. Transporters on the cell surface then recapture the Fe3+-siderophores complexes.  Many microorganisms, including some fungi, also secrete low molecular weight compounds known as siderophores into their surroundings, which form high-affinity (~10−33 M) complexes with ferric iron to make it bioavailable for uptake. Transporters on the cell surface then recapture the Fe3+-siderophores complexes.

Wow... now comes the most fascinating part. To make these siderophores, incredible assembly lines in the cell are used: 

Its remarkable, how Nature magazine describes in the article Enzymes line up for assembly ,  how non-ribosomal peptide synthetase (NRPS) work ( we are back at the starting point of this article ) :

Nearly 100 years ago, Henry Ford demonstrated the full strength of economist Adam Smith’s insights into productivity and the division of labour when he established the first moving assembly line. By shuttling partially constructed cars mechanically from one worker to the next, each performing a single specific task, Ford’s assembly line could issue a new Model T every three minutes. This manufacturing method provided the foundation of modern mass production. But nature employed much the same approach for constructing molecules long before humans existed to ponder questions of economy and efficiency.  Walsh and colleagues identify a previously unrecognized link in one such biological assembly line — an enzyme that could some day be exploited by chemists to modify complex, naturally occurring compounds. The enzymes that form the polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) families are responsible for the biosynthesis of many useful compounds, including the antibiotics erythromycin and vancomycin, and the antitumour drug epothilone. These multi-subunit enzymes are the molecular equivalents of moving assembly lines: growing substrate molecules are handed, bucket-brigade style, from one specialized catalytic site to the next, with each site performing a specific and predictable function. The PKS assembly line starts by recruiting The PKS assembly line starts by recruiting small building-blocks (such as acetate and propionate molecules, which contain ‘acyl’ chemical groups) onto carrier proteins. The building-blocks are then bonded together in reactions catalysed by a ‘ketosynthase’ region of the PKS. The resulting substrate may then be chemically tailored by various other enzyme domains, before being passed on to another ketosynthase for a further round of extension and modification. The cycle is repeated until the finished molecule is finally offloaded. The various catalytic domains may exist as discrete enzymes (as in type II PKS), or be connected end to end, like beads on a string (as in type I PKS), but in both cases the biosynthetic strategy remains the same. The NRPS cycle is very similar to that of PKS enzymes, except that it uses amino acids as building-blocks. Thus, amino acids become bound to peptidyl carrier proteins (PCPs); PCP-bound amino acids are joined together with amide bonds to form peptides, in catalytic sites known as condensation domains; tailoring regions may then modify the newly formed peptide before passing it along for further cycles of extension and tailoring; and finally, the finished product is cleaved from the enzyme. The PKS and NRPS enzymes each produce very different products, but the logic they use is strikingly similar — so similar, in fact, that they can easily cooperate to construct hybrid PKS–NRPS products such as epothilone.





this assembly line, together with non-ribosomal codes, produces siderophores, essential for the uptake of iron in bacterias. Iron, essential for the synthesis of FE/S clusters. FE/S clusters, essential for the formation of Molybdenum cofactors.  All the above-described cell processes must exist prior to life began, in order to produce Molybdenum co-factors, essential for various life-essential processes.

Minerals containing molybdenum are key in assembling atoms into life-forming molecules. The researcher points out that boron minerals help carbohydrate rings to form from pre-biotic chemicals, and then molybdenum takes that intermediate molecule and rearranges it to form ribose, and hence RNA. Chromium, molybdenum, selenium, and vanadium, for example, are essential for building proteins, and proteins serve as life’s molecular “factories.”

The scientific evidence exposed points to the requirement of 1. finely tuned fundamental forces to make the higher elements, like Molybdenum 2. Molecular assembly lines and biosynthesis pathways fully set up right from the beginning, 3. Interdependence and irreducible processes all along inside the cell, and all these processes had to emerge all at once, intelligently created, fully setup,  with an initial injection of instructional complex information.  A cell membrane to host siderophores, ABC transporters, membrane proteins for the sensing and intake of the substrates,  mechanisms for homeostasis control, etc. if you have an automobile, and you lose the key to turn it on, it will not function. What was the key for the event of the moment of transition from non-life to life ? All cellular compartments, essential proteins, and molecular machines, replication process, and mechanism, the ability of sensing and recognition of the environment, organization, information, regulation, nutrition uptake, cell wall, metabolism had to be there, or there would not be the first go. If just a tiny part of the machinery to make siderophores for the uptake of iron was not there, no iron would have been disposed to the cell, no FE/S cluster formation, no Molybden cluster formation, no proteins that use it in their active site could emerge, no life....just a tiny part missing, no life. How could someone with even a superficial understanding of how life and cells work, argue that chemical evolution and the stepwise, down-up process could produce life? A stepwise, gradual origin of these processes is impossible, and would equal to a miracle. 

At following article from Nature magazine about the origin of life:

Opinion: Studies on the origin of life — the end of the beginning

they write:

The transition of a system from the inanimate state to the animate is envisioned as an increase in ‘aliveness’ over time.

Haha !! Thats the same as to ask a woman : are you pregnant ?
She: I am in a phase of increase of non-pregnancy to pregnancy.....

We (and others) prefer to consider this transition as a series of steps, rather than a single step, following the prelude of prebiotic chemistry1. Equilibrium is death, which means some sort of coupling of energy dissipation to maintain the system continuously out of equilibrium throughout the transition is envisaged, but when we first started contemplating this, we could not see a way in which this might be achieved, hence the somewhat nebulous picture. Also shown is the necessity–contingency boundary beyond which material limitations prevent full exploration of the sequence space of macromolecules assembled from different monomeric building blocks; therefore, chemical determinism can no longer be relied on as a source of innovation, and further improvements have to be chanced upon instead.

http://www.nature.com/articles/s41570-016-0012?WT.feed_name=subjects_biosynthesis

The article is interesting so far as it illustrates the difficulties that OOL ( origin of life ) researchers face, and the status quo after a century of research is as follows:

Clearly, we are not yet even at the beginning of the end of our quest to understand it, but the end of the beginning is offering up some very tantalizing clues about the origin of life.

chemist Wilhelm Huck, professor at Radboud University Nijmegen :

A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity,"

The cell protein trash grinder looks 100% designed to me. And it had to exist fully developed prior life began. its essential for Cell homeostasis

Substrate Recognition and Degradation by a AAA+ Protease
The recognition step is mediated by binding of a peptide tag (brown) on the protein substrate to a AAA+ ATPase (blue). In subsequent steps, the protein is unfolded, translocated into a compartmental peptidase (magenta), and degraded. Peptide fragments are shown diffusing out of the peptidase, but active participation of the ATPase may be required for exit of large fragments.

http://reasonandscience.heavenforum.org/t2447-homeostasis-in-cells-and-origin-of-life-scenarios#5216

The  essential signaling pathways for animal development

https://reasonandscience.catsboard.com/t2351-the-essential-signaling-pathways-for-animal-development

Cell signaling is arguably the most important characteristic of multicellular organisms.  Without cell signaling, the different cells in the body of a plant or animal could not communicate with each other, and they could not coordinate their actions. Such coordination is essential: first, to build a complex body composed of thousands or millions of cells and second, for the correct performance of such a body in everyday life, whether acquiring nutrients, excreting toxins, or dealing with hostile or friendly interactions from other organisms. This coordination is corroborated by the many problems and diseases (such as developmental abnormalities and cancers) that arise from malfunction of the cellular machinery that deals with cell signaling and communication. Thus, the study of such cell signaling machinery is receiving a great deal of attention by biological and medical research. At the most basic level, any cell signaling process must involve a signal, synthesized or otherwise, generated by the sending cell and some kind of system to receive that signal and respond to it in the receiving cell.

Less attention than this issue deserves,  has been given in the evolution/ID debate to elucidate  how cell signal transduction pathways function, what mechanisms, kind of molecules and proteins  are involved,, in what organisms they first emerged, and how these extremely complex and multifaceted  pathways could have possibly emerged, and what causes explain best their origins.  

If macroevolution involves changing morphological features, then the altering of signal transduction pathways becomes critical for any discussion of large scale evolution.

Signalling pathways are  complex networks of interactions. Surprisingly, only a few classes of signalling pathways are sufficient to pattern a wide variety of cells, tissues and morphologies. The specificity of these pathways is based on the history of the cell (referred to as the ‘cell’s competence’), the intensity of the signal and the cross-regulatory interactions with other signalling cascades.

Despite the bewildering number of cell types and patterns found in the animal kingdom, only a few signalling pathways are required to generate them.  One clear conclusion to be drawn from all these studies is that there is a rather limited number of signalling pathways to generate the remarkable variety and complexity of form and function that we see today, both across phyla and within the individuals of a given species. Understanding how these pathways have emerged and function can thus illuminate the origin of morphological diversity, as well as the molecular and cellular basis of development and disease. Amongst the central canon of developmental signalling pathways are the :

Hedgehog (Hh)
Wingless related (Wnt)
Transforming growth factor-β (TGF-β)
Receptor tyrosine kinase (RTK)
Notch
Janus kinase (JAK)/signal transducer  
Activators of transcription (STAT) protein kinases
Nuclear hormone pathways
Bone morphogenetic proteins (BMP)
Epidermal growth factor receptors (EGFR)
Fibroblast growth factors (FGF)

Hedgehog
The  conserved Hedgehog (Hh) pathway is essential for normal embryonic development and plays critical roles in adult tissue maintenance, renewal and regeneration.  The Hedgehog (Hh) family of proteins control cell growth, survival, and fate, and pattern almost every aspect of the vertebrate body plan. The Hh gradient is shaped by several proteins that are specifically required for Hh processing, secretion, and transport through tissues. The primary cilium is crucial for mammalian Hedgehog signaling

Wnt signaling pathway
The Wnt signaling pathway is an ancient and evolutionarily conserved pathway that regulates crucial aspects of cell fate determination, cell migration, cell polarity, neural patterning and organogenesis during embryonic development.

Transforming growth factor-β (TGF-β)
Transforming growth factor-β (TGF-β) superfamily signaling plays a critical role in the regulation of cell growth, differentiation, and development in a wide range of biological systems.

Receptor tyrosine kinase
Tyrosine phosphorylation is an essential element of signal transduction in multicellular animals.

Notch
Notch signaling is an evolutionarily conserved pathway in multicellular organisms that regulates cell-fate determination during development and maintains adult tissue homeostasis.

JAK/STAT
Cell-cell signaling represents an essential hallmark of multicellular organisms, which necessarily require a means of communicating between different cell populations, particularly immune cells. Cytokine receptor signaling through the Janus kinase/Signal Transducer and Activator of Transcription/Suppressor of Cytokine Signaling (CytoR/JAK/STAT/SOCS) pathway embodies one important paradigm by which this is achieved.

Bone morphogenetic proteins (BMP)
Bone Morphogenetic Proteins (BMPs) are a group of signaling molecules that belongs to the Transforming Growth Factor-β (TGF-β) superfamily of proteins. Initially discovered for their ability to induce bone formation, BMPs are now known to play crucial roles in all organ systems. BMPs are important in embryogenesis and development, and also in maintenance of adult tissue homeostasis.

Since all seven signal transduction pathways are essential for multicellular development  : is it feasable to suppose that they were all co-opted or borrowed from uncellular organisms ? If so, they still need the information to direct new body plan development. Where did this information come from ?

Wanna Build a Cell? A DVD Player Might Be Easier 1
https://reasonandscience.catsboard.com/t2404-wanna-build-a-cell-a-dvd-player-might-be-easier

THE AMAZING HEMOGLOBIN MOLECULE

http://reasonandscience.heavenforum.org/t1322-the-amazing-hemoglobin-molecule#1859

The argument by hemoglobin
1. The hemoglobin is a protein made of 564 amino acids.
2. The hemoglobin’s three dimensional structure; the amino acid sequence and the 4 iron atoms in the central region of the hemoglobin are all together enabling the special function of the hemoglobin - the transfer of the oxygen.
3. An alteration of any part of this structure of hemoglobin would cause inability to execute its duty of carrying oxygen.
4. Conclusively, such a structure is a proof of perfect design.
5. Behind a design there is an intelligent designer.
6. That designer is God.

Technological Ingenuity in Red Blood Cells 1

Each mm3 (= 1 ul = 1 microliter) of our blood contains five million red blood cells; so there are 150 million of them in each drop of blood. These highly specialized cells perform functions vital to life.
• Throughout their 120-day lifetime, while circulating through the lungs, they are refueled with oxygen 175,000 times, while simultaneously offloading carbon dioxide, the waste product of oxidation.
• Red blood cells are so tiny that they can squeeze through narrow capillaries to reach every part of the body.
• Our body produces two million new red cells every second and each cell is rich in hemoglobin, a remarkably complex chemical compound.

Hemoglobin is used for transporting oxygen, even during development of the embryo. Up to about the third month of pregnancy, the embryo's oxygen needs are distinctly different from those in the ensuing fetal stage, which are different again from the needs of the infant and adult. All three stages— embryo, fetus and adult—require the production of chemically different forms of hemoglobin. Shortly before birth, for example, the body's 'factories' start switching to top production mode of the third (adult) type of hemoglobin. These three types of hemoglobin could not have arisen by trial-and-error evolutionary processes because none of the other mutant forms of the hemoglobin molecule could carry enough oxygen and would thus be deadly. Even if the right forms of hemoglobin were to somehow arise to supply the first two stages, but without the genetic coding to produce the third form, the outcome would still be certain death. Each of these three stages of our development requires fundamentally different DNA coding to produce each of the three different hemoglobin molecules.
Further, each set of different DNA coding, and its biomachinery that synthesizes the hemoglobin molecules must be switched on and off at the right point in time. Where did such a complex system of information-controlled machinery come from? All conceivable evolutionary explanations fail miserably because any partially completed transitional stage required by evolution would not permit the organism to survive. The whole complex of
information and machinery must be present and functional from the start. This concept of 'irreducible complexity' also applies to the immune system and to the flagellum that many bacteria use to propel themselves. In each case, the organisms 'on the way' to their completed state would not have been able to survive. A more obvious explanation is that this information-controlled machinery was initially complete—something only possible if a wise Creator conceived and made everything fully functional in the beginning.

The heme biosynthesis pathway is irreducible complex.

Heme biosynthesis is a complex pathway with 8 highly specific steps, of which 6 steps are used by specific enzymes uniquely in this pathway.
The pathway must go all the way through, otherwise heme is not synthesized.
Therefore, the heme biosynthesis pathway is irreducible complex.

Questions: 
What good would there be, if the pathway would go only up to the 7th step ? none
What good would there be, if the pathway would go all the way through the 8th step ? Heme would be produced , BUT :
What good for survival would there be for Heme by its own, if not fully embedded in the globin proteins? none.
What good would there be for red bloodcells without hemoglobin, transporting oxygen to the cells in the body ? none, transporting oxygen is essential for the whole process. I conclude therefore that the heme biosynthesis pathway is irreducible complex, and could not have evolved upon mutation and natural selection.

I mentioned that some enzymes have to be imported into the mitochondrion. These enzymes contain special protein sequences called targeting signals that direct them to the right place. So the next question: is globin targeted to the mitochondrion? No - it is synthesised on ribosomes, attached to the Golgi apparatus in the cytoplasm and it stays there. Some of the haem made in the mitochondrion is used by mitochondrial proteins called cytochromes, but the rest is exported back outside where it can attach to the globin protein. Have a look at these Wikipedia pages: heme and porphyrin, for some more details. Porphyrins, by the way, are intermediates in haem synthesis that also have the tetrapyrrole structure.

Researchers have done experiments in which they synthesised globin protein chains to see at what point the haem attached. It can attach when about 80-90 amino acids have emerged from the ribosome - in other words, it attaches to the "nascent chain" as the protein is being synthesised. One of the mysteries that we don't fully understand is how the haemoglobin assembles itself properly - so as it has 2 alpha chains and 2 beta chains each with a haemoglobin attached.

Question : for what reason would evolution try to assemble the heme to the globin ? what survival advantage would there be provided by a globin without the heme ? and what advantage of the heme without the globin ?

Animals with 'Lamps'

https://reasonandscience.catsboard.com/t2061p50-my-articles#5236

From the energy viewpoint, there is a most remarkable phenomenon exhibited by many sea animals and some land animals (e.g., glow-worms and fireflies), namely, bioluminescence (Latin lumen = light). 2 These animals can emit light of various colors (red, yellow, green, blue, or violet) and in different signal sequences. Our technological attempts at generating light look extremely amateurish in terms of energy efficiency when compared with bioluminescence. A standard electric light bulb converts only 3 to 4 percent of the energy consumed into light, and the efficiency of a fluorescent tube is only about 10%. Because our lights tend to generate more heat than light, our lamps perhaps more closely resemble ovens than lights.

The Creator's bioluminescent systems work with a 'cold light' that has an efficiency up to 95%. No man-made light source has even approached this efficiency. This involves the oxidation of certain fluorescent substances (luciferins) by an enzyme called luciferase.There are three fundamentally different types of luciferin, namely that of bacteria, that of fireflies, and that of Cypridina (clam-like creatures). American biochemist Professor W. D. McElroy, was able to quantify the efficiency of this type of light production. It was found that each quantum of energy transported to the light organ in the form of ATP1was converted to light. The number of oxidized luciferin molecules is exactly equal to the number of emitted light quanta. All the light emitted by a firefly is indeed 'cold' light, which means that there is no loss of energy as heat. Here we are confronted with lamps operating at nearly 100% efficiency where the incoming energy is almost completely converted into light. The Creator has equipped many types of bacteria, microorganisms, insects, and especially deepsea fish with this method of illumination.

THE FIREFLY 
Here is another ID hypothesis, one of my own. It’s the Firefly.

This one is within the Scientific Theory of Irreducible Complexity. This time the irreducible complexity is observed in the firefly. In order for the illumination to occur, the following are needed:

1. Abdominal trachea. Keep in mind of what purpose this organ (complex in its own rite) serves the organism when this oxygen intake mechanism has NOTHING to do with the beetle’s need for breathing.
2. Organic Compound, luciferin. It’s challenging enough of a question to explain why the beetle’s metabolism is producing this complex compound in the first place, but just the mere fact that the compound is complex creates a problem explaining as to why NS would select to manufacturer the compound.
3. Enzyme luciferase. How did NS have the intelligence to go shopping for this enzyme, as if it were an item to go pick up at the local pharmacy?
4. Processing call bioluminescence. The firefly beetle can do nothing with these ingredients unless if there is a complex organ, like a carburetor or fuel injector that mixes the to substances together in the right quantities and ration for light illumination.
5. Light-emitting organ on the lower abdomen. And finally, even if there is electricity, you still need to harness it, which means you need a light bulb, which is yet another complex organ necessary.

The problem with the firefly is that the benefit, in this case to emanate light for mate attraction purposes, would not be reached until ALL FIVE components have been naturally selected for. That is not how NS operates in real life nature because as already noted, NS selects blindly without foresight or planning. That’s the whole point of ID. ID is not an attempt to insert the God of the Bible although too often the case too many ID proponents do. It is very much legitimate science to probe into this “foresight” characteristic of NS, and why scientist attribute or impute design intelligence to NS. That’s really what ID as a science explores, among other things. If organic chemistry drives chemistry students to madness keeping track of the hydrogen and carbon compounds, then how does NS have the ability perform biochemical engineering?

The test in this model here is to show how removing just one component of the list of five items renders the other four useful for NS to select for. If scientists can show that the other four properties are useful to NS without the other, then the hypothesis that the glowing engine of a firefly is falsified, and that it is not irreducibly complex, and NS remains the best explanation.

I have not yet come across material that was damaging to the IC hypothesis yet. I will not ever throw in the towel on IC until Michael Behe does, and it appears he stands behind it as much today, if not more so, than ever before.

The best-known examples are the fireflies and the glowworms (Lampyris and Phausis). Most of the subtropical and tropical lampiryds differ from the mid- European species in that they can emit deliberate sequences of flashes. In experiments with the pyralis firefly (Photinus pyralis), it was found that the flying male emitted 0. 06-second flashes at intervals of 5.7 seconds, and the female on the ground replied after exactly 2.1 seconds with the same rhythm. These flashing signals serve as communication between prospective mates. There also are insects with 'lamps' that emit different colors, like the Brazilian railroad worm (Phrixothrix). This larva from the beetle family of snail predators (Drilidae) normally carries two orange-red lights in front. At the approach of danger, two rows of11 greenish lanterns are switched on, one row on each side. This resemblance to a train approaching in the dark gives this larva its apt name, 'railroad worm'.

Glycolysis, Gluconeogenesis, and Glucose, part 2.  

http://reasonandscience.heavenforum.org/t1796-glycolysis#5157

I just answered at Laurence A. Morans blog :

https://sandwalk.blogspot.com.br/2017/02/trying-to-educate-creationist-otangelo.html?showComment=1486414817560#c5538064323536634305

The whole issue of this topic is if  a prebiotic world  had the  the basic building blocks for life. Before even there were ANY cells and organisms, a pre - requirement for life to start was the existence of matter to build proteins, lipids, carbohydrates ( sugars, glucose ), nucleic acids ,  and small molecules, ions, water, metals etc. Larry made a fool of himself by asserting that Glycogen was a possible energy source for metabolism, since it requires the synthesis through the complex cellular machinery ( which was not there, and its origin we try to explain ) . Since i pointed that out, he rather than admitting his grotesque mistake, tried to attack me and camouflage with name calling, hoping that nobody would observe. Unfortunately, it back fired.

According to your story, Larry, first there was Gluconeogenesis in some bacterial cells, and - two or three new enzymes arose to replace and make it to an efficient glycolysis pathway after millions of years of evolution. You admitted of not knowing how this transition or replacement could have happened naturally ( humm.. genetic drift ?! ) . Further, you have not explained how Gluconeogenesis emerged in the first place. You failed to mention that a parallel initial precursor Glycolysis pathway would have been necessary, and you did not explain how it could have emerged either. This precursor system of Glycolysis had to be in place to synthesize the products required in a hypothetical proto cell ( supposed there were other complex chemical cellular reactions required already, somehow through natural pressure/self assembly of chemicals ( humm, did they have a inborn drive to become alive and start self replication , somehow ??! ....).

As i have mentioned at my library, there is a HUDGE UNBRIDGEABLE GAP between unspecified metal catalysts performing glucose or similar substrate production, as the paper " The widespread role of non-enzymatic reactions in cellular metabolism " asserts - , and parallel another identical system ( convergence development already at this stage ? - amazing !! ) as precursor of Glycolysis, to a transition to the highly complex specific enzymes required in both pathways. How could unguided , random chemical reactions provide a compelling explanation to that question ? Both pathways, Gluconeogenesis, and Glycolysis, use about ten highly specified complex enzymes, each exercising very different tasks. Since there was no evolution at this stage, the emergence would have had to happen by random chance. There was no energy to form polypeptide assemblage and interlinking without these enzymes. Lets assume that the average size of each enzime was 500 amino acids. In some miraculous way, they would have had to be all selected to be only left handed, the 20 different amino acids used for life would have had to be selected amongst many others, ( how they were available, amongst fixed nitrogen etc etc. is another story ) and then assemble in the right sequence through peptide bonds . There is a hudge gap that has to be filled between " modern " polypeptide formation through ribosomes, mRNA, and tRNA's, and supposed primordial amino chain formations without this advanced machinery. How could the gap be closed ? Not only are prebiotic mechanisms unlikely, but the transition would have required the emergence of a prebiotic specific mechanism and afterwards transition from one mechanism to the other extant today.

Laurent Boiteau Prebiotic Chemistry: From Simple Amphiphiles to Protocell Models, page 3:
Spontaneous self-assembly occurs when certain compounds associate through noncovalent hydrogen bonds, electrostatic forces, and nonpolar interactions that stabilize orderly arrangements of small and large molecules.  The argument that chemical reactions in a primordial soup would not act upon pure chance, and that  chemistry is not a matter of "random chance and coincidence , finds its refutation by the fact that the information stored in DNA is not constrained by chemistry. Yockey shows that the rules of any communication system are not derivable from the laws of physics.  He continues : “there is nothing in the physicochemical world that remotely resembles reactions being determined by a sequence and codes between sequences.” In other words, nothing in nonliving physics or chemistry obeys symbolic instructions. So, to find functional enzymes in sequence space is not determined by chemical reactions.

A short protein molecule of 150 amino acids, the probability of building a 150 amino acids chain in which all linkages are peptide linkages would be roughly 1 chance in 10^45.
Lets assume a average size of each enzyme in both pathways  of about 500 amino acids. That would result in the possibility to get all these enzymes after one of  10^10000 trial and error attempts. That is ten with 10.000 zeroes. If we add the odds to get the right interlinking of the enzymes to get a functional  metabolic network, the picture  becomes even  less remotely possible. It should be evident that chance is not a capable mechanism to come up with just one of the several metabolic pathways required for a first organism.

http://www.doesgodexist.org/NovDec09/Information-Function.html
Literature from those who posture in favor of creation abounds with examples of the tremendous odds against chance producing a meaningful code. For instance, the estimated number of elementary particles in the universe is 10^80. The most rapid events occur at an amazing 10^45 per second. Thirty billion years contains only 10^18 seconds. By totaling those, we find that the maximum elementary particle events in 30 billion years could only be 10^143. Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

The requirement of various interdependent and irreducible complex organs and systems to make blood.

http://reasonandscience.heavenforum.org/t2295-hematopoiesis-the-mystery-of-blood-cell-and-vascular-formation#4866

Little attention has been given to the evolutionary origin of blood. Hematopoiesis is the description of how blood cellular components form. Blood is a fluid  that circulates through the cardiovascular system.  Blood and the developing blood cells and their precursors are produced  in the bone marrow through pluripotential Hematopoietic stem cells (HSCs)  which give rise to all   ten different type of blood cells through the process of haematopoiesis  These blood cells are: macrophages , neutrophils, basophils, eosinophils, erythrocytes, dendritic cells, platelets, T cells, B cells, and natural killer cells.

Bruce Alberts and his colleagues noted: “Blood contains many types of cells with very different functions, ranging from the transport of oxygen to the production of antibodies. Some of these cells function entirely within the vascular system, while others use the vascular system only as a means of transport and perform their function elsewhere (1994, p. 1161).


The process of developing the diverse blood cell repertoire from stem and progenitor cells termed hematopoiesis has been subject to considerable investigation. However, key steps in the complex process of hematopoiesis,
including hematopoietic stem cell generation during embryogenesis, hematopoietic stem, and progenitor cell expansion to accommodate physiological and pathological requirements, and mechanisms that ensure hematopoietic
stem and progenitor cell phenotypic integrity remain incompletely understood.

Recent studies indicate that hematopoietic stem cells (HSCs) also have the potential to differentiate into multiple non–blood cell lineages and contribute to the cellular regeneration of various tissues and multiple organs. 

Blood is a bodily fluid in animals that delivers necessary substances such as nutrients and oxygen to the cells and transports metabolic waste products away from those same cells. In vertebrates, it is composed of blood cells suspended in blood plasma. Plasma, which constitutes 55% of blood fluid, is mostly water, and contains dissipated proteins, glucose, mineral ions, hormones, carbon dioxide (plasma being the main medium for excretory product transportation), and blood cells themselves. Albumin is the main protein in plasma, and it functions to regulate the colloidal osmotic pressure of blood. According to H.Glicksman, the regulation of blood pressure requires a irreducible complex system . 
 The blood cells are mainly red blood cells, white blood cells  and platelets. The most abundant cells in vertebrate blood are red blood cells. These contain hemoglobin, an iron-containing protein, which facilitates oxygen transport by reversibly binding to this respiratory gas and greatly increasing its solubility in blood. In contrast, carbon dioxide is almost entirely transported extracellularly dissolved in plasma as bicarbonate ion. 

The bone marrow, which is the flexible tissue in the interior of bones, forms a suitable environment for stem cell survival, growth and development. It is composed of stromal cells and a microvascular network. Bones are an amazing example of design, present in all vertebrates. They have a huge advantage over man-made girders, in that they are constantly rebuilding and redesigning themselves to cope with changing stress directions.12 This involves a fine balance of the activity of bone-depositing cells (osteoblasts) and bone resorbing cells (osteoclasts).  It’s been recently shown that thyroid-stimulating hormone (TSH), best known for what its name says—stimulating the production of hormones in the thyroid gland—has an important role. It oversees both types of cells—without it, bones have osteoporosis in some parts (too little bone, so very weak), and are too dense in other patches. So both are essential. For bone formation, over 24 different proteins, cells, Vitamins, transcription factors etc. are required. So, we can confidently say, the production of blood requires a hudge number of different body parts, which are essential. Blood by its own has no function. The vascular system without blood has no function. Bones require a vascular system, which by their own are required to make blood. The vertebrate body is a hudge irreducible complex sytem, that could not have emerged gradually. Each multicellular organism had to emerge fully, in its interdependent form.   


Hemopoiesis (hematopoiesis) includes both erythropoiesis and leukopoiesis (development of red and white blood cells, respectively), as well as thrombopoiesis (development of platelets.


Macrophages are essential components of the innate immune system. They are a type of white blood cell that engulfs and digests cellular debris, foreign substances, microbes, cancer cells, and anything else that does not have the types of proteins specific of healthy body cells on its surface in a process called phagocytosis.2 
Dendritic cells are needed to control B and T lymphocytesm, and capture and process antigens, express lymphocyte co-stimulatory molecules, migrate to lymphoid organs and secrete cytokines to initiate immune responses.  3
Neutrophils  are a required type of immune cell that is one of the first cell types to travel to the site of an infection. Neutrophils help fight infection by ingesting microorganisms and releasing enzymes that kill the microorganisms. A neutrophil is a type of white blood cell,
Basophils contain anticoagulant heparin, which prevents blood from clotting too quickly. They also contain the vasodilator histamine, which promotes blood flow to tissues.
Eosinophils effector functions include production of: cationic granule proteins and their release by degranulation, the production of reactive oxygen species such as hypobromite, superoxide, and peroxide, production of lipid mediators like the eicosanoids, enzymes, such as elastase. growth factors such as TGF beta, VEGF, and PDGF. etc.... 
Red blood cells ( erythrocytes ) are the most common type of blood cell and essential for the vertebrate organism's  delivering oxygen (O2) to the body tissues—via blood flow through the circulatory system 6
Platelets  are a essential component of blood whose function (along with the coagulation factors) is to stop bleeding by clumping and clotting blood vessel injuries 7
T cells are essential for human immunity. 8
B cells  are a type of white blood cell that makes antibodies. B lymphocytes are part of the immune system and develop from stem cells in the bone marrow. Primary B-cell immunodeficiencies (B-PID) constitute a heterogeneous group of immunodeficiencies characterized by defective production of antigen-specific antibodies and predisposition to recurrent and severe infections9 
Natural killer cells are a type of immune cell that has granules (small particles) with enzymes that can kill tumor cells or cells infected with a virus. A natural killer cell is a type of white blood cell. Also called NK cell and NK-LGL. They  are part of the innate immune defense against infection and cancer, and are especially useful in combating certain viral pathogens9

1) https://en.wikipedia.org/wiki/Hematopoietic_stem_cell
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956013/
3) http://www.ncbi.nlm.nih.gov/pubmed/9521319
4) http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0022058/
5) https://en.wikipedia.org/wiki/Basophil
6) https://en.wikipedia.org/wiki/Red_blood_cell
7) https://en.wikipedia.org/wiki/Platelet
8  http://www.tcells.org/beginners/tcells/
9) http://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0022043/
10) https://en.wikipedia.org/wiki/Blood
11) http://www.evolutionnews.org/2015/09/controlling_blo099611.html
12) http://creation.com/bone-building-perfect-protein-osteocalcin#r1
13) http://reasonandscience.heavenforum.org/t2296-origin-and-development-of-bones-osteogenesis?highlight=bones

The oxygen evolving complex (OEC) of photosystem II is irreducible complex. 

http://reasonandscience.heavenforum.org/t1583-the-oxygen-evolving-complex-oec-of-photosystem-ii-is-irreducible-complex

"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)

Deep in the thylakoid membrane, the key process that produces breathable oxygen in the Earth’s atmosphere takes place, namely, the splitting of water molecules and the subsequent release of molecular oxygen. Without the OEC, no advanced life on earth would be possible.  This process, which occurs in the oxygen-evolving complex (OEC) of the intricately arranged multiprotein and pigment complex known as photosystem II (PSII), is driven by the strong electrochemical potential generated from the capture and conversion of visible light to chemical energy. First, chlorophyll molecules in PSII absorb photons and lose electrons. These electrons are then passed through an electron transport chain, creating redox potential strong enough to oxidize water, which leads to the evolution of molecular oxygen and the release of protons into the thylakoid lumen. This proton gradient is a major contributor to the proton motive force (PMF), which is used to biosynthesize ATP from ADP via ATP synthase. 

The OEC contains an inorganic, flexible Mn4CaO5 cluster resembling a distorted chair, which is bound to a pocket formed by six amino acids from the D1 core subunit protein and one amino acid from the light-harvesting protein CP43 . The Mn4CaO5 cluster is stabilized, at least in part, by the PsBO subunits of the OEC. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ). Maintenance of the highly dynamic Mn4CaO5 cluster also requires the delivery of a constant supply of the proper levels of Mn2+ and Ca2+. 

The functional features of PSII in all oxygenic photosynthetic organisms are remarkably similar. The mechanism of water oxidation has remained virtually unchanged between  green plants and cyanobacteria, and is similar in all higher plants. Studies on PSII from plants, algae, and cyanobacteria have revealed several PSII proteins that collectively regulate the unique redox environment of this inorganic catalytic center 12

Mainstream scientific papers quoted and cited below state that each of the extrinsic proteins, (PsbO, PsbP, PsbQ and PsbR)  of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient, and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster, and D1 protein subunit of PSII are also indispensable, and irreducible.


Laurence A. Moran claims at his blog : We have a pretty good idea how photosynthesis (sensu stricto) evolved because there are plenty of simple examples in bacteria. In my textbook, I describe a probable evolutionary pathway to the complex pathway seen in cyanobacteria and plants. That idea has been around for decades.

http://sandwalk.blogspot.com.br/2017/02/scientists-confused-about.html#more

Larry, would you mind to EXPLAIN , and not just ASSERT, how photosynthesis evolved ?

Why do you not start and explain how oxygenic photosynthesis evolved from anoxigenic photosynthesis? Since as far as i know, there is no known shorter or simpler process than the one we know of.

Just claim, ah, there is anoxygenic photosynthesis , and there is oxygenic photosynthesis, so one must have evolved from the other is the typical just so story which won't cut the cake.

To refresh your memory, last time you posted about this subject:

http://sandwalk.blogspot.com.br/2016/04/fun-and-games-with-otangelo-grasso.html

i pointed out that :

The oxygen evolving complex (OEC) of photosystem II is irreducible complex.

http://reasonandscience.heavenforum.org/t1583-the-oxygen-evolving-complex-oec-of-photosystem-ii-is-irreducible-complex

the central ( core ) part that produces oxygen in photosynthesis is the oxygen evolving complex.

Without the OEC, no advanced life on earth would be possible.

Mainstream scientific papers quoted and cited below state that each of the extrinsic proteins, (PsbO, PsbP, PsbQ and PsbR) of plants are ESSENTIAL, and each was tested upon mutated form, and the mechanism was found inefficient, and compromising the OEC function. Furthermore, a water network around the Mn4CaO5 cluster, and D1 protein subunit of PSII are also indispensable, and irreducible.

Larry, in order to make a credible case, you need to dive. Snorkel on the surface of shallow waters and scream how amazing evolution is will not cut the cake. you need to check what is below and check the details......

Cyanobacteria

http://reasonandscience.heavenforum.org/t1551-cyanobacteria

The main source for food and oxygen are cyanobacteria and chloroplasts that do photosynthesis. Cyanobacteria are essential for the nitrogen cycle, and so to transform nitrogen in the atmosphere into useful form for organisms to make the basic building blocks for life. The end product of photosynthesis is glucose, - needed as food source for almost all life forms. For a proponent that life took millions of years to emerge gradually and biodiversity as well, and so cyanobacteria and chloroplasts, that came hundreds of millions of years after life started, that is a hudge problem. No oxygen in the atmosphere, and UV radiation would kill the organisms. Nor could they emerge without a adequate food source. Looking everything in that perspective, it makes a lot of sense to believe God created everything in six days. And created the atmosphere with oxygen , and the nitrogen cycle fully setup, and plants and animals like cyanobacteria, essential in the food chain and nitrogen cycle. That would solve the - problem of nutrition, - the problem of UV radiation - and the problem of the nitrogen source required for life.

Where did Glucose come from in a prebiotic world ?

http://reasonandscience.heavenforum.org/t2419-where-did-glucose-come-from-in-a-prebiotic-world

Glucose is a ubiquitous fuel in biology. It is used as an energy source in most organisms, from bacteria to humans, through either aerobic respiration, anaerobic respiration, or fermentation. Sugar phosphates are however constituents of many molecules, such as RNA, DNA, ATP and lipids, which are inevitably connected with the emergence of life. It is the fundamental role of sugar phosphates, and the virtual universality of their few metabolic interconversion sequences, that places their origin to the very early stages in the history of  life. Glucose is used by Glycolysis,  which is  the most universal pathway in all energy metabolism, occurring in almost every living cell.  The glycolytic pathway is multifunctional. Thus it provides the cell with energy  (ATP)] from glucose catabolism - the process that breaks down molecules into smaller units.  Glucose is the human body's key source of energy. Through glycolysis and later in the reactions of the citric acid cycle and oxidative phosphorylation, glucose is oxidized to eventually form CO2 and water, yielding energy mostly in the form of ATP.
The ultimate origin of  Glucose - sugars is a huge problem for those who believe in life from non-life without requiring a creator.  In order to provide credible explanations of how life emerged, a crucial question must be answered : Where did Glucose come from in a prebiotic  earth ?
The source of glucose and other sugars used in metabolic processes would have to lie in an energy-collecting process. Without some means to create such sugar, limitations of food supply for metabolic processes would make the origin of life probably impossible.

Following are the  possible explanations:

Gluconeogenesis is a reverse process to glycolysis, which produces Glucose.
Nonenzymatic reactions that would be precursor mechanisms to glyconeogenesis,  leading to the biosynthesis of glucose
Metabolic networks are largely composed of intermediate substrates that are not characterized by long‐time stability, at least when considering geological environments and timescales.  In addition, large sugar phosphates are not frequently generated in experiments that address scenarios of primordial carbon fixation.
A paper reports that Fe(II) was broadly available before oxygenation of the early Earth, implying a scenario for the first glycolytic enzymes being simple iron-binding RNA or oligopeptide molecules, which would have possessed the potential of enhancing many reactions now found in central metabolism.

Did you read that carefully ? DIGEST IT !! This is a ridiculous pseudoscientific  festival of just so made up fairy tale stories based on wishful thinking.  We shall believe that unspecified metal catalysts where somehow ( HOW ??!! ) transformed miraculously and bridged a hudge gap from unspecified chemical reactions  into the highly complex specific enzymes, highly regulated by other complex mechanisms,  required in these pathways. If such baseless assertions would have been made in ANY other discipline of science, the authors would have been ridiculed. Not so in biochemistry, where any fantastic story is PLAUSIBLE, and is swallowed as serious science.

A paper from Nature magazines reported that Carbonaceous meteorites were a source of sugar-related organic compounds for the early Earth. They claimed :
Sugars, sugar alcohols and sugar acids are vital to all known lifeforms - they are components of nucleic acids (RNA, DNA), cell membranes and also act as energy sources. But there has hitherto been no conclusive evidence for the existence of polyols in meteorites, leaving a gap in our understanding of the origins of biologically important organic compounds on Earth.
Analyses of water extracts indicate that extraterrestrial processes including photolysis and formaldehyde chemistry could account for the observed compounds. We conclude from this that polyols were present on the early Earth and therefore at least available for incorporation into the ®rst forms of life.
Just because something COULD HAVE happened on the early earth, they conclude IT DID happen. The logical fallacy is evident.

1. Natural pro­cesses tend to produce gunk with little relevance to life.
2. The amounts of these chemicals were tiny—far too low to contribute to biological processes.
3. Chemical reactions would have somehow to select the useful compounds amongst   contaminated gunk.
4. Sugars are very unstable, and easily decompose or react with other chemicals.
5. Living things require homochiral sugars, i.e. with the same ‘handedness’, but these ones would not have been.
6. There is no plausible method of making the sugar ribose join to some of the essential building blocks needed to make DNA or RNA, let alone into RNA or DNA themselves
7. Even DNA or RNA by themselves would not be life, since it’s not enough to just join the bases (‘letters’) together, but the se­quence of the letters must consitute meaningful information.
8. Even this letter sequence would be meaningless without elaborate decoding machinery to translate this into amino acid sequences.

Chemisynthesis is employed by organisms that live in the environment around deep-sea volcanic vents, where hot, hydrogen sulfide-rich waters pour out of newly formed ocean crust.  Such waters, compared to the colder, sulfide-poor adjacent regions, have an abundant supply of free energy. This term refers to a source of energy that can be utilized readily to do some form of work, such as sustain biological processes, or can be stored in high-energy phosphate bonds. One readily available means to extract energy from the vents is to combine hydrogen sulfide with oxygen to form sulfur dioxide with production of energy. Such a process is possible in an ocean that has free oxygen available, but would not work on the primitive, pre-oxygen-rich Earth. Other biochemical cycles that use sulfur but not oxygen are conducted by some prokaryotic organisms, but these capture much less energy than the oxygendriven cycles. As with fermentation, chemisynthesis without free oxygen was the hallmark of a rather sluggish primitive biota.

Further problems:

There would have had to exist a cell membrane, dividing the outside from the inside of the proto-cell, to protect the chemical reactions, and complex gates regulating the compound entrance into the cell. That is another serious problem for origin of life research:

even in the simplest cells, the membrane is a biological device of a staggering complexity that carries diverse protein complexes mediating energy-dependent – and tightly regulated - import and export of metabolites and polymers  Remarkably, even the author of the book: Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV. asks the readers:
Hence a chicken and egg paradox: a lipid membrane would be useless without membrane proteins but how could membrane proteins have evolved in the absence of functional membranes?

The book Origins of Life on the Earth and in the Cosmos tries to solve the ridde as follows :
Membrane-enclosed cells came into being some time after the first ribozymes and definitely before the advent of translation systems.  It is highly likely that these primitive living systems were sequestered in some way, possibly by adhering to clay surfaces. It is also likely that the first fatty acids used to make cellular membranes were made under conditions that would have been too harsh to share with living systems that are far more delicate. In view of this we must ask how the first membranes made contact with the early membrane- free living systems. How could life exist without membranes ?
Then we must consider how the early living systems became enclosed by these membranes and how the membranes of these most primitive cells evolved. True. Big questions, isnt it?
The encapsulation of the living systems into the liposomes was probably a simple process that required no more than one or two dry–wet cycles.

The pseudo-scientific just so stories are remarkable, aren't they ?! The conclusion  is that naturalistic explanations do not suffice to answer the relevant question in a satisfying manner, where Glucose came from, adding to all other unbridgeable problems of origin of life research, and thus giving proponents of intelligent design good reasons to infer intelligent design as the better explanation.

Biosynthesis o Amino Acids

http://reasonandscience.heavenforum.org/t1397-biosynthesis-o-amino-acids

Could the oxygen and nitrogen cicle be explained by naturalistic means ? The reason for the abundance of oxygen in the atmosphere is the presence of a very large number of organisms which produce oxygen as a byproduct of their metabolism. Cyanobacteria or blue-green algae became the first microbes to produce oxygen by photosynthesis. They are one of the oldest bacteria that live on earth, said to exist perhaps as long  as 3.5 billion years. And their capabilities are nothing more than astounding.  No cianobacteria, no oxygen, no higher life forms. These cianobacterias have incredibly sophisticated enzyme proteins and metabolic pathways, like the electron transport chains, ATP synthase motors, circadian clock, the photosynthetic light reactions, carbon concentration mechanism, and transcriptional regulation , they produce binded nitrogen through nitrogenase, a highly sophisticated mechanism to bind nitrogen, used as a nutrient for plant and animal growth.

The Nitrogen cycle is a lot more complex than the carbon cycle. Nitrogen is a very important element. It makes up almost 80% of our atmosphere, and it is an important component of proteins and DNA, both of which are the building blocks of animals and plants. Therefore without nitrogen we would lose one of the most important elements on this planet, along with oxygen, hydrogen and carbon. There are a number of stages to the nitrogen cycle, which involve breaking down and building up nitrogen and it’s various compounds.There is no real starting point for the nitrogen cycle. It is an endless cycle. Potential gaps in the system cannot be reasonably bypassed by inorganic nature alone. It must have a degree of specificity that in all probability could not have been produced by chance.

A given function or step in the system may be found in several different unrelated organisms. The removal of any one of the individual biological steps will resort in the loss of function of the system. The data suggest that the nitrogen cycle may be irreducibly interdependent based on the above criteria. No proposed neo-Darwinian mechanisms can explain the origin of such a system.The ultimate source of nitrogen for the biosynthesis of amino acids is atmospheric nitrogen (N2), a nearly inert gas. Its needed by all living things to build proteins and nucleic acids. This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things?

To be metabolically useful, atmospheric nitrogen must be reduced. It must be converted to a useful form. Without "fixed" nitrogen, plants, and therefore animals, could not exist as we know them. This process, known as nitrogen fixation, occurs through lightening, but most  in certain types of bacteria, namely cianobacteria. Even though nitrogen is one of the most prominent chemical elements in living systems, N2 is almost unreactive (and very stable) because of its triple bond (N≡N). This bond is extremely difficult to break because the three chemical bonds need to be separated and bonded to different compounds. Nitrogenase is the only family of enzymes capable of breaking this bond (i.e., it carries out nitrogen fixation). Nitrogenase is a very complex enzyme system. Nitrogenase genes are distributed throughout the prokaryotic kingdom, including representatives of the Archaea as well as the Eubacteria and Cyanobacteria.With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision.

In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism, but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’ If one merely substitutes the name of God for the word 'nature', the real picture emerges.These proteins use a collection of metal ions as the electron carriers that are responsible for the reduction of N2 to NH3. All organisms can then use this reduced nitrogen (NH3) to make amino acids. In humans, reduced nitrogen enters the physiological system in dietary sources containing amino acids. One thing is certain—that matter obeying existing laws of chemistry could not have created, on its own, such a masterpiece of chemical engineering.Without cyanobacteria - no fixed nitrogen is available.Without fixed nitrogen, no DNA, no amino-acids, no protein can be synthesised. Without DNA, no amino-acids,protein, or cyanobacteria are possible. So thats a interdependent system.

How Cellular Enzymatic and Metabolic networks  point to design

http://reasonandscience.heavenforum.org/t2371-how-cellular-enzymatic-and-metabolic-networks-point-to-design


The argument of a intelligent designer required to setup the Metabolic Networks for the origin of life 

Observation: The existence of metabolic pathways is crucial for molecular and cellular function.  Although bacterial genomes differ vastly in their sizes and gene repertoires, no matter how small, they must contain all the information to allow the cell to perform many essential (housekeeping) functions that give the cell the ability to maintain metabolic homeostasis, reproduce, and evolve, the three main properties of living cells. Gil et al. (2004)  In fact, metabolism is one of the most conserved cellular processes. By integrating data from comparative genomics and large-scale deletion studies, the paper "Structural analyses of a hypothetical minimal metabolism"   proposes a minimal gene set comprising 206 protein-coding genes for a hypothetical minimal cell. The paper lists 50 enzymes/proteins required to create a metabolic network implemented by a hypothetical minimal genome for the hypothetical minimal cell. The  50 enzymes/proteins , and the metabolic network, must be fully implemented to permit a cell to keep its basic functions.
  
Hypothesis (Prediction): The origin of biological irreducible metabolic pathways which also require regulation and and which are structured like a cascade, similar to electronic circuit boards,  are best explained by the creative action of an intelligent agent.

Experiment: Experimental investigations of metabolic networks  indicate that they are  full of nodes with enzymes/proteins, detectors, on/off switches, dimmer switches, relay switches, feedback loops etc.  that require for their synthesis information rich, language-based codes stored in DNA . Hierarchical structures have been proved to be best suited for capturing most of the features of metabolic networks (Ravasz et al, 2002). It has been found that metabolites can only be synthesized if carbon, nitrogen, phosphor, and sulfur and the basic building blocks generated from them in central metabolism are available.

 This implies that regulatory networks gear metabolic activities to the availability of these basic resources.  So one metabolic circuit depends on the product of other products, coming from other, central metabolic pathways, one depending from the other, like in a casacade.  Further noteworthy is that Feedback loops have been found to be required to regulate metabolic flux, and the activities of many or all of the enzymes in a pathway.  In many cases, metabolic pathways are highly branched, in which case it is often necessary to alter fluxes through part of the network while leaving them unaltered or decreasing them in other parts of the network (Curien et al., 2009). These are interconnected in a functional way, resulting in a living cell. The biological metabolic networks  are  exquisitely integrated, so the significant alterations in  inevitably damage or destroys the funcion. Changes in flux often require changes in the activities of multiple enzymes in a metabolic sequence. Synthesis of one metabolite typically requires the operation of many pathways.

Conclusion:   Regardless of its initial complexity, self-maintaining chemical-based metabolic life could not have emerged in the absence of a genetic replicating mechanism insuring the maintenance, stability, and diversification of its components. In the absence of any hereditary mechanisms, autotrophic reaction chains would have come and gone without leaving any direct descendants able to resurrect the process. Life as we know it consists of both chemistry and information.   If metabolic life ever did exist on the early Earth, to convert it to life as we know it would have required the emergence of some type of information system under conditions that are favorable for the survival and maintenance of genetic informational molecules. ( Ribas de Pouplana, Ph.D.)