The Elshamah mega-thread

[Rumraket]

throw your probability number in a prebiotic scenario, where the molecules had to come together in a meaningful way to make the first self replicating cell - there was no evolution , no mutations, no natural selection yet....... all you are left with, is random chance.

Maybe there were the rules of chemistry, and the constraints of physics. So maybe it's not just random chance, maybe only a particular set of things can happen. And maybe given the right conditions, another particular thing can happen.

A drop of water rolling down a hill isn't rolling around randomly as it crisscrosses between pebbles and rocks. It's following the path of least resistance. Where it ends up depends on how the landscape looks below it. Slightly alter it's starting position and it might end up in a different place entirely.

It's the same with chemistry. What can happen depends on what is already there, how much of it there is, what the temperature and pressure is and so on. It's not just open-ended chemistry with completely random outcomes. There are physical laws governing what happens. For example, in experiments of prebiotic chemistry simulating hydrothermal vents, amino acids are often produced. But not ALL amino acids are produced, and those that are produced are not produced in equal amounts. A significant majority of them will be glycine residues, with lesser amounts of Alanine, Aspargine, Glutamine, Valine and so on.

That means the kind of peptide that will spontaneously assemble from such a mixture will at any given site be significantly more likely to have a glycine-residue, than a Alanine residue. And Alanine will be more likely than Valine and so on.

So it's not just blind random chance with an equiprobable distribution of outcomes. There is a bias that makes some outcomes more likely than others.

Here's a funny fact to consider the implications of: In phylogenetic analysis of the oldest conserved protein domains in life, there is the same relative abundance in distribution of amino acids as the one seen to result in experiments performed in prebiotic synthesis. Do you understand this statement?

 

[Elshamah]

yep. But to any just so nonsense story, no matter how much evidential support it has, just say yes. Because it supports your fantasy and wishful thinking....

Say yeah !! :lol: :lol:

No. Never just say yeah, to anything. You should always look into the evidence.

For example, when someone claims none of the enzymes in a particular pathway have any relatives anywhere else in life, you should double-check.[/quote]

Who do u wanna fool, Rumraket. ?! You are misrepresenting what i said in a grotesque way. I have never said that the enzymes in that particular pathway haven't any relatives anywhere else in life. What i said is, that these particular enzymes could not have been co-opted, because they are not being used for other duties. I backed my claim up. But since you are a bad loser, you can't admit defeat, and just change the subject and issue in question.

btw. you know well that there are many de-novo orphan genes in biology which challenge the common ancestry nonsense........

 

[Elshamah]

throw your probability number in a prebiotic scenario, where the molecules had to come together in a meaningful way to make the first self replicating cell - there was no evolution , no mutations, no natural selection yet....... all you are left with, is random chance.

Maybe there were the rules of chemistry, and the constraints of physics. So maybe it's not just random chance, maybe only a particular set of things can happen. And maybe given the right conditions, another particular thing can happen.

A drop of water rolling down a hill isn't rolling around randomly as it crisscrosses between pebbles and rocks. It's following the path of least resistance. Where it ends up depends on how the landscape looks below it. Slightly alter it's starting position and it might end up in a different place entirely.

It's the same with chemistry. What can happen depends on what is already there, how much of it there is, what the temperature and pressure is and so on. It's not just open-ended chemistry with completely random outcomes. There are physical laws governing what happens. For example, in experiments of prebiotic chemistry simulating hydrothermal vents, amino acids are often produced. But not ALL amino acids are produced, and those that are produced are not produced in equal amounts. A significant majority of them will be glycine residues, with lesser amounts of Alanine, Aspargine, Glutamine, Valine and so on.

That means the kind of peptide that will spontaneously assemble from such a mixture will at any given site be significantly more likely to have a glycine-residue, than a Alanine residue. And Alanine will be more likely than Valine and so on.

So it's not just blind random chance with an equiprobable distribution of outcomes. There is a bias that makes some outcomes more likely than others.

Here's a funny fact to consider the implications of: In phylogenetic analysis of the oldest conserved protein domains in life, there is the same relative abundance in distribution of amino acids as the one seen to result in experiments performed in prebiotic synthesis. Do you understand this statement?

Oh Yeah!! Say never no to naturalism, even if the evidence says no !! :lol: :lol:

from the book: The Logic of Chance: The Nature and Origin of Biological Evolution
By Eugene V. Koonin

The origin of replication and translation and the RNA World

http://reasonandscience.heavenforum.org/t2234-the-origin-of-replication-and-translation-and-the-rna-world

Even considering environments that could facilitate these processes, such as networks of inorganic compartments at hydrothermal vents, multiplication of the probabilities for these steps could make the emergence of the first replicators staggeringly improbable.

The ultimate enigma of the origin of life

The origin of life—or, to be more precise, the origin of the first replicator systems and the origin of translation—remains a huge enigma, and progress in solving these problems has been very modest—in the case of translation, nearly negligible. Some potentially fruitful observations and ideas exist, such as the discovery of plausible hatcheries for life, the networks of inorganic compartments at hydrothermal vents, and the chemical versatility of ribozymes that fuels the RNA World hypothesis. However, these advances remain only preliminaries, even if important ones, because they do not even come close to a coherent scenario for prebiological evolution, from the first organic molecules to the first replicator systems, and from these to bona fide biological entities in which information storage and function are partitioned between distinct classes of molecules (nucleic acids and proteins, respectively).

 

[Rumraket]

So now we know that a proteins superfamily is huge group of proteins that are related by common descent, let's go through the list you provided, taking the last one first:
(17) chlorophyll synthase.
Belongs to the: UbiA prenyltransferase family.
So it has ancestral and related enzymes. So your claim is false.

Of course it is not false. What i claimed is that the specific enzyme is only used in that pathway.

Wait. Waaaait wait wait...

Your claim now is that the specific enzyme chlorophyll synthase (the last one in the chlorophyll biosynthesis pathway) is used in no other pathway? Seriously, who the fuck would claim it was? It's called chlorophyll synthase because that's what it does.

MOST enzymes are specific and used only in one pathway. That doesn't mean they didn't evolve, or that the pathway itself couldn't evolve. Your argument is EVEN DUMBER now. You are erecting as an argument an irrelevant fact. It's like saying "the outer cell membrane isn't used to copy eukaryotic chromosomes". WHO GIVES A SHIT? Nobody says it is. What a complete irrelevancy to blather about.

Your original claim was they could not have been coopted from another pathway. That claim is false, because they WERE coopted from other pathways, BUT CHANGED. The enzyme we have now, today, is not the same enzyme that was originally coopted.

A gene duplication happened first. Then mutations happened gradually over many generations, in the duplicate. That is how the duplicate gene became the enzyme we see today, being used "only in chlorophyll biosynthesis". That's how protein superfamilies came to exist in the first place. But it still belongs to a family of enzymes that share ancestry. They are all different now, today, in their own little ways. Almost all of them only do one job, or a few in one or a few pathways. But they still evolved through duplication and subfunctionalization.

If it belongs to a superfamily or not, is a completely different issue.

No, it isn't for fucks sake. The fact that it belongs to a superfamily is evidence that it evolved from something else that came before it but still exists in a different form elsewhere in life. Often times in the same organism.

You even chose a wrong enzyme

There is no "wrong enzyme". I used ALL the eight last enzymes in your list and showed which relationships they belong to.

The last one, number 17, is chlorophyll synthase. It belongs to this superfamily:
http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi

UbiA family of prenyltransferases (PTases)
Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways.

So chlorophyll synthase was coopted from another biosynthetic pathway that predates it. It is an adapted version of another, older enzyme, probably still used in Heme biosynthesis.

You seem to be mindlessly spewing falsehoods as you go along now. Are you trying to save face? Just lying for the heck of it?

nice try , moving the goal posts. Nice red herring.

my claim remains true. Now go figure out my other questions..... :lol:

You're the one moving the goalposts and erecting red herrings now. Your post is total textbook projection. You are accusing me of something you are in fact guilty of yourself.

Stop posting. For your own sake.

 

[Rumraket]

Now go figure out my other questions.

But there's nothing new there. You have just copy-pasted the same crap you've said already, both in this particular thread and in the others you started on this forum. I have already debunked that shit.

Here's the main idea, again, for the 50th time:
Already been over this. Same fundamental mistake you make every time. Evolution demonstrably produces multi-component irreducibly complex structures, in fact we predict they will emerge through the evolutionary process and we have seen it happen in experiment without any guidance or design.

Irreducible complexity is not a successful argument against evolution for reasons already stated in your three other threads.

In fact we have observed the origin of an irreducibly complex pathway for the utilization of citrate under aerobic conditions in Richard Lenski's long-term evolution experiment with E coli.

A gene duplication spawned a copy of the citrate transporter in vicinity of a regulatory element that is only active under aerobic conditions. This allows the cells to use citrate when oxygen is present, which they normally cannot do.

If you remove the duplicate gene, the cell can no longer use citrate with oxygen present. If you remove the regulatory element, the citrate transporter fails to activate when oxygen is present, and the cell cannot use citrate and will die if there is no other food available. So there you go, a two-component, irreducibly complex system that requires both components to be present to work. If you remove one of the components, the system stops working. So it is irreducibly complex and it evolved.

If it is irreducibly complex it can still evolve. In fact we expect that the evolutionary process will create irreducibly complex structures. Do you understand this? If evolution is true, there should be irreducibly complex structures in living organism.</SIZE><SIZE size="150">

In response to this you have thoughtlessly claimed that Irreducible Complexity means that the structure cannot evolve by definition. As in, you simply make that up: A structure cannot evolve if it is irreducibly complex.

Then my response to that was to ask for an example of something that is, then, actually irreducibly complex. To ask for an example of a biological structure that could not evolve, by definition.

You have given no such example. You have tried by making long-winded posts full of copy-pasted materials, using existing biological structures we already know evolved, for example the chlorophyll synthesis pathway. You claimed it could not evolve because it was, according to you "irreducibly complex". But I've shown it could, so it CANNOT be irreducibly complex in the way you use the term.

The particular version of Irreducible Complexity that you use (cannot evolve by definition) is an argumentum ad ignorantiam. Because you do not know where the enzymes came from, you declare the pathway to be unevolvable.
You also made a silly mistake by claiming that even if the enzymes evolved one by one, they would have no function. But that turned out to be false as was demonstrated already back in 1965. (READ THE PAPER).

What do you have left? More copy-paste shit? Why do I need to sit here and debunk your idiotic claims time and again when they ALL SUFFER FROM THE SAME BASIC MISTAKE: YOU ARE UNABLE TO UNDERSTAND THAT THINGS DO NOT HAVE TO HAVE FUNCTIONED IN THE SAME WAY TODAY, AS THEY DID IN THE PAST.

 

[Dragan Glas]

Greetings,

Greetings,

Just to add some further comments on the "impossible odds" claims that creationists, including Elshamah, tend to trot out as "proof" that evolution can't work...

The game of chess is estimated to have 10[sup]120[/sup] possible positions.

To borrow the claims that are being made...

""The probability of randomly assembling a functional protein with complex enzymatic activity getting a position in chess is about 1 chance in 10[sup]120[/sup] per try for a protein made up of 100 amino acid residues."

Sounds impossible, doesn't it?

However, I - or anyone - has only to set up the chessboard for a game of chess to blow these "impossible odds" out the window.

Why?

Because no position in chess is "random" - the rules mean that the board can only be set up in a specific way at the start of the game; only certain moves are possible in each position; players don't move the pieces randomly - they're moved with a purpose in mind, etc.

The point being - chess isn't "random".

And it's the same with evolution - it's not "random"; everything happens within certain constraints, from mutations ("random" within the laws of chemistry) to speciation (selection of individuals according to their "fitness" resulting in a trend in the alleles passed on).

Merely calculating the maximum possible number - even if the factors were known, which they're not more often than not - is not how probabilities are calculated or work.

For the most part, the probabilities are incalculable simply because no one knows how many parameters there are.

Secondly, the path to a particular feature - such as the human eye - is both unknown and not random.

Trotting out "impossible odds" calculations is meaningless and misleading.

This has been pointed out to you before, yet you keep doing this.

You wrongly accuse Rumraket of bias, yet seem unaware of your own - does "the mote and the beam" sound familiar?

You continue to cite Behe, Meyer, et al, who simply are wrong, and have been shown to be wrong by a number of specialists in their fields.

When someone makes a false statement, as you have been doing, there are only two possibilities; either the person doesn't know what they're talking about - which casts doubt on their competence - or, they are bearing false witness - which casts doubt on their integrity.

I'm prepared to extend you the benefit of the doubt.

Kindest regards,

James

throw your probability number in a prebiotic scenario, where the molecules had to come together in a meaningful way to make the first self replicating cell - there was no evolution , no mutations, no natural selection yet....... all you are left with, is random chance.

Wrong - on all three counts, as Rumraket has - yet again - pointed out to you.

The environment existed - there's your natural selection.

The environment determines what chemical reactions can occur.

Thus, we have evolution.

And, "mutations", in the form of chemical reactions, occur all the time, even in "pre-biotic scenarios". A influx of new atoms and molecules means new reactions can occur - "mutations". It may not be mutations as the term is normally used but, nevertheless, that's the case.

Organic and biochemistry are sub-sets of chemistry, which is governed by physics.

In other words, there's no such thing as actual "random chance" within our space-time continuum.

The term is just a figure-of-speech.

And, for fun, see how many implications for the emptiness of your creationist claims you can spot in this recent research:

The weird genome of water bears (tardigrades): more than a sixth of it swiped from distantly related species

Kindest regards,

James

 

[Elshamah]

Belongs to the: UbiA prenyltransferase family.
So it has ancestral and related enzymes. So your claim is false.

Of course it is not false. What i claimed is that the specific enzyme is only used in that pathway.[/quote]
Wait. Waaaait wait wait...

Your claim now is that the specific enzyme chlorophyll synthase (the last one in the chlorophyll biosynthesis pathway) is used in no other pathway? Seriously, who the fuck would claim it was? It's called chlorophyll synthase because that's what it does.

MOST enzymes are specific and used only in one pathway. That doesn't mean they didn't evolve, or that the pathway itself couldn't evolve. Your argument is EVEN DUMBER now. You are erecting as an argument an irrelevant fact. It's like saying "the outer cell membrane isn't used to copy eukaryotic chromosomes". WHO GIVES A SHIT? Nobody says it is. What a complete irrelevancy to blather about. [/quote]

Haha. You are amusing. I mean , you REALLY are. I am saying all along that it makes no difference is certain enzymes are used in a different biological system, and could eventually have been co-opted, for the irreducible complexity argument. Behe says the same, as i quoted him. But you were insisting all along, that IF a enzyme were used in multiple systems, it could have been co-opted, and my argument of IC falls apart. When i show you that the last eight enzymes in the chlorophyll pathway are ONLY being used in that pathway, only to answer your point, you just turn around, and change your argument 180 degrees with the above. Come on, who do you think are you cheating ?

I tell you. You are cheating only yourself. God loves you, but you try to run away like a hyena bite in her ass and try to justify your unbelief. Why is that ? Probably, because you have never experienced the goodness of God. Seriously. On rational ground, you are falling short by all means, and you know it. You are intelligent enough to examine your own proposals. Its evident they fall short..... So the reason you try to press everything in your premise and wishful thinking is not the evidence. but something else. I suspect on emotinal ground... If i'd be you, i'd make a check.....

 

[Elshamah]

a new article of mine.

DNA replication, and its mind boggling nano high-technology that defies naturalistic explanations

http://reasonandscience.heavenforum.org/t1849-dna-replication-of-prokaryotes

DNA replication is the most crucial step in cellular division, a process necessary for life, and errors can cause cancer and many other diseases. Genome duplication presents a formidable enzymatic challenge, requiring the high fidelity replication of millions of bases of DNA. It is a incredible system involving a city of proteins, enzymes, and other components that are breathtaking in their complexity and efficiency.

How do you get a living cell capable of self-reproduction from a “protein compound … ready to undergo still more complex changes”? Dawkins has to admit:

“Darwin, in his ‘warm little pond’ paragraph, speculated that the key event in the origin of life might have been the spontaneous arising of a protein, but this turns out to be less promising than most of Darwin’s ideas. … But there is something that proteins are outstandingly bad at, and this Darwin overlooked. They are completely hopeless at replication. They can’t make copies of themselves. This means that the key step in the origin of life cannot have been the spontaneous arising of a protein.” (pp. 419–20)

The process of DNA replication depends on many separate protein catalysts to unwind, stabilize, copy, edit, and rewind the original DNA message. In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule. These specialized proteins include DNA polymerases, primases, helicases, topoisomerases, DNA-binding proteins, DNA ligases, and editing enzymes. DNA needs these proteins to copy the genetic information contained in DNA. But the proteins that copy the genetic information in DNA are themselves built from that information. This again poses what is, at the very least, a curiosity: the production of proteins requires DNA, but the production of DNA requires proteins.

Proponents of Darwinism are at a loss to tell us how this marvelous system began. Charles Darwin's main contribution, natural selection, does not apply until a system can reproduce all its parts. Getting a reproducible cell in a primordial soup is a giant leap, for which today's evolutionary biologists have no answer, no evidence, and no hope. It amounts to blind faith to believe that undirected, purposeless accidents somehow built the smallest, most complex, most efficient system known to man.

Several decades of experimental work have convinced us that DNA synthesis and replication actually require a plethora of proteins.

Replication of the genetic material is the single central property of living systems. Dawkins provocatively claimed that organisms are but vehicles for replicating and evolving genes, and I believe that this simple concept captures a key aspect of biological evolution. All phenotypic features of organisms—indeed, cells and organisms themselves as complex physical entities—emerge and evolve only inasmuch as they are conducive to genome replication. That is, they enhance the rate of this process, or, at least, do not impede it.

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.

It seems to me that DNA replication is interlocked, interdependent and consistent of several irreducible complex subsystems. Since evolution depends on it, it could not have emerged through evolution. Even less through random chance or physical necessity. Special creation through a incredibly intelligent powerful creator is therefor the best explanation for DNA replication.

 

[Dragan Glas]

Greetings,

No, it isn't - you've studiously ignored the linked article and paper I provided.

Kindest regards,

James

 

[Elshamah]

here goes the complete version of the above post :

DNA replication, and its mind boggling nano technology that defies naturalistic explanations

http://reasonandscience.heavenforum.org/t1849-dna-replication-of-prokaryotes


DNA replication is the most crucial step in cellular division, a process necessary for life, and errors can cause cancer and many other diseases. Genome duplication presents a formidable enzymatic challenge, requiring the high fidelity replication of millions of bases of DNA. It is a incredible system involving a city of proteins, enzymes, and other components that are breathtaking in their complexity and efficiency.

How do you get a living cell capable of self-reproduction from a “protein compound … ready to undergo still more complex changes”? Dawkins has to admit:

“Darwin, in his ‘warm little pond’ paragraph, speculated that the key event in the origin of life might have been the spontaneous arising of a protein, but this turns out to be less promising than most of Darwin’s ideas. … But there is something that proteins are outstandingly bad at, and this Darwin overlooked. They are completely hopeless at replication. They can’t make copies of themselves. This means that the key step in the origin of life cannot have been the spontaneous arising of a protein.” (pp. 419–20)

The process of DNA replication depends on many separate protein catalysts to unwind, stabilize, copy, edit, and rewind the original DNA message. In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule. These specialized proteins include DNA polymerases, primases, helicases, topoisomerases, DNA-binding proteins, DNA ligases, and editing enzymes. DNA needs these proteins to copy the genetic information contained in DNA. But the proteins that copy the genetic information in DNA are themselves built from that information. This again poses what is, at the very least, a curiosity: the production of proteins requires DNA, but the production of DNA requires proteins.

Proponents of Darwinism are at a loss to tell us how this marvelous system began. Charles Darwin's main contribution, natural selection, does not apply until a system can reproduce all its parts. Getting a reproducible cell in a primordial soup is a giant leap, for which today's evolutionary biologists have no answer, no evidence, and no hope. It amounts to blind faith to believe that undirected, purposeless accidents somehow built the smallest, most complex, most efficient system known to man.

Several decades of experimental work have convinced us that DNA synthesis and replication actually require a plethora of proteins.

Replication of the genetic material is the single central property of living systems. Dawkins provocatively claimed that organisms are but vehicles for replicating and evolving genes, and I believe that this simple concept captures a key aspect of biological evolution. All phenotypic features of organisms—indeed, cells and organisms themselves as complex physical entities—emerge and evolve only inasmuch as they are conducive to genome replication. That is, they enhance the rate of this process, or, at least, do not impede it.

DNA replication is an enormously complex process with many different components that interact to ensure the faithful passing down of genetic components that interact to ensure the faithful passing down of genetic information to the next generation. A large number of parts have to work together to that end. In the absence of one or more of a number of the components, DNA replication is either halted completely or significantly compromised, and the cell either dies or becomes quite sick. Many of the components of the replication machinery form conceptually discrete sub-assemblies with conceptually discrete functions.

Wiki mentions that a key feature of the DNA replication mechanism is that it is designed to replicate relatively large genomes rapidly and with high fidelity. Part of the cellular machinery devoted to DNA replication and DNA-repair. The regulation of DNA replication is a vital cellular process. It is controlled by a series of mechanisms. One point of control is by modulating the accessibility of replication machinery components ( called the replisome ) to the single origin (oriC) region on the DNA. DNA replication should take place only when a cell is about to divide. If DNA replication occurs too frequently, too many copies of the bacterial chromosome will be found in each cell. Alternatively, if DNA replication does not occur frequently enough, a daughter cell will be left without a chromosome. Therefore, cell division in bacterial cells must be coordinated with DNA replication.

In prokaryotes, the DNA is circular. Replication starts at a single origin (ori C) and is bi-directional. The region of replicating DNA associated with the single origin is called a replication bubble and consists of two replication forks moving in opposite direction around the DNA circle. During DNA replication, the two parental strands separate and each acts as a template to direct the enzyme catalysed synthesis of a new complementary daughter strand following the normal base pairing rule. At least 10 different enzymes or proteins participate in the initiation phase of replication. Three basic steps involved in DNA replication are Initiation, elongation and termination, subdivided in eight discrete steps.

http://reasonandscience.heavenforum.org/t1849-dna-replication-of-prokaryotes#4365

Initiation phase:

Step 1: Initiation begins, when DNA binds around an initiator protein complex DnaA with the goal to pull the two DNA strands apart. That creates a number of problems. First of all, the two strands like to be together - they stick to each other just as if they had tiny magnets up and down their length. In order to pull apart the DNA you have to put energy into the system. In modern cells, a protein called DnaA binds to a specific spot along the DNA, called single origin ( oriC ) and the protein proceeds to open up the double strand. The protein is a monomer, has motifs to bind to unique monomer sites, also they have motifs for protein-protein interaction, thus they can form clusters. They have hydrophobic regions for helical coiling and protein–protein interactions. Binding of the monomers to DnaA-A boxes, in ATP dependent manner (proteins have ATPase activity), leads to cooperative binding of more proteins. This clustering of proteins on DNA makes the DNA to wrap around the proteins, which induces torsional twist and it is this left handed twist that makes DNA to melt at 13-mer region and AT rich region; perhaps the negative super helical topology in this region may further facilitate the melting of the DNA. Opening or unwinding of dsDNA ( double strand DNA ) into single stranded region is an important event in initiation.

Single-strand binding protein (SSB)
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4377

The Hexameric DnaB Helicase
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4367

DnaC, and strategies for helicase recruitment and loading in bacteria
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4371

Unwinding the DNA Double Helix Requires DNA Helicases,Topoisomerases, and Single- Stranded DNA Binding Proteins
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4374

Step 2: During DNA replication, the two strands of the double helix must unwind at each replication fork to expose the single strands to the enzymes responsible for copying them. Three classes of proteins with distinct functions facilitate this unwinding process: DNA helicases, topoisomerases, and single-stranded DNA binding proteins ( SSB's). Helicase ( DnaB ) now comes along. The helicase exposes a region of single-stranded DNA that must be kept open for copying to proceed. Helicase is like a snowplow; it is a molecular machine that plows down the middle of the double helix, pushing apart the two strands. this allows the polymerase and associated proteins to travel along behind it in ease and comfort. DnaB helicase alone has no affinity for ssDNA ( single stranded DNA ) bound by SSB (single- stranded binding protein). Thus, entry of the DnaB helicase complex into the unwound oriC depends on DnaC, a additional protein factor. DnaC helps or facilitates the helicase to be loaded onto ssDNA at the replication fork in ATP dependent manner. The DnaB-DnaC complex forms a topologically open, three-tiered toroid. DnaC remodels DnaB to produce a cleft in the helicase ring suitable for DNA passage. DnaC’s fold is dispensable for DnaB loading and activation. DnaB possesses autoregulatory elements that control helicase loading and unwinding. Using energy derived from ATP hydrolysis, these proteins unwind the DNA double helix in advance of the replication fork, breaking the hydrogen bonds as they go. Helicase recruitment and loading in bacteria is a remarkable process. Following video shows how that works:

https://www.youtube.com/watch?v=YzNuLsqMqyE




There is a problem, though, with this setup. If you push apart two DNA strands they generally do not float around separately. If they are close to one another they will rapidly snap back and form a double strand again almost as soon as the helicase passes. Even if the strands are not near each other, a single strand will usually fold up and form hydrogen bonds with itself - in other words, a tangled mess. So it is not enough to push apart the two strands of DNA; there must be a way to keep the strands apart once they have been separated. In modern cells this job is done by single-strand binding proteins, or SBB's. As the helicase separates the strands of DNA, SSB's bind to the single stranded DNA and coats them. . SSB's prevent DNA from reannealing. SSB's associate to form tetramers around which the DNA is wrapped in a manner that significantly compacts the single-stranded DNA. There is another difficulty in being a double helix. The unwinding associated with DNA replication would create an intolerable amount of supercoiling and possibly tangling in the rest of the DNA. It can be illustrated with a simple example. Take two interwined shoe laces and ask a friend to hold them together at each end. Now take a pencil, insert it between the strands near one end, and start pushing it down toward the other end. As you can see, shoestrings behind the pencil become melted, in the jargon of biochemistry. The shoestrings ahead of the pencil become more and more tangled. It becomes harder and harder to push the pencil forward. Helicase and polymerase encounter the same problem with DNA. It does not matter wheter you are talking about interwined strings or interwined DNA strands. The problem of tangling is the result of the topological interconnectness of the two strands. If this problem persisted for very long in a cell, DNA replication would grind to a halt. However, the cell contains several enzymes, called topoisomerases, to take care of the difficulty. The way in which they do so can be illustrated with a enzyme called gyrase. Gyrase binds to DNA, pulls them apart and allows a separate portion of the DNA to pass through the cut. It then reseals the cut and lets go of the DNA. This action decreases the number of twists in DNA. The parental DNA is unwound by DNA helicases and SSB (travels in 5’-3’ direction), the resulting positive super-coiling (torsional stress) is relieved by topoisomerse I and II (DNA gyrase) by inducing transient single stranded breaks.Topoisomerases are amazing enzymes. In this topic, a video shows how they function :

Topoisomerase II enzymes, amazing evidence of design
http://reasonandscience.heavenforum.org/t2111-topoisomerase-ii-enzymes-amazing-evidence-of-design?highlight=topoisomerase

In modern organisms, helicase, SSB, and gyrase all are required at the replication fork. Mutants in which any of them are missing are not viable - they die.

Question : Had not all three parts , the SSB binding proteins, the topoisomerase, and the helicase and the DnaC loading proteins not have to be there all at once, otherwise, nothing goes ? They might exercise their function but their own, but then they would not replicate DNA or have function in a bigger picture. Its evident that they had to come together to provide a functional whole. What we see here are highly coordinated , goal oriented tasks with specific movements designed to provide a specific outcome. Auto-regulation and control that seems required beside constant energy supply through ATP enhances the difficulty to make the whole mechanism work in the right manner. All this is awe inspiring and evidences the wise guidance and intelligence required to make all this happening in the right way.

Step 3: The enzyme DNA primase (primase, an RNA polymerase) attaches to the DNA and synthesizes a short RNA primer to initiate synthesis of the leading strand of the first replication fork.

Elongation phase :

Step 4: In the elongation fase, DNA polymerase III extends the RNA primer made by primase.

DNA Polymerase
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4375

DNA polymerase possesses separate catalytic sites for polymerization and degradation of nucleic acid strands. All DNA polymerases make DNA in 5’-3’ direction . A ring-shaped sliding clamp protein encircles the DNA double helix and binds to DNA polymerase, thereby allowing the DNA polymerase to slide along the DNA while remaining firmly attached to it. Most enzymes work by colliding with their substrate, catalyzing a reaction and dissociating from the product. If that were the case with DNA polymerase, then it would bind to DNA, add a nucleotide to the new chain that was being made, and then fall off of the chain. Then ,put the next nucleotide onto the growing end, bind it and catalyze the addition. This same cycle would have to repeat itself a very large number of times to complete a new DNA chain. Polymerases however catalyze the addition of a nucleotide but do not fall off the DNA. Rather, they stay bound to it, until the next nucleotide comes in, and then they catalyze its addition to the chain. and they again stay bound. If it were not so, the replication process would be very slow. In the cell, polymerases stay on the DNA until their job is completed, which might be only after millions of nucleotides have been joined. This velocity is only possible because of clamp proteins. These have a ring shape. The ring can be opened up. These clamp proteins are joined to the DNA polymerase in a intricate way, through a clamp loader protein, which has a remarkable shape similar to a human hand. It takes the clamp, like a hand with five fingers would grab it, opens it up becoming like a doughnut shape,where the whole hole in the middle is big enough to accommodate the DNA, and then, when it is on the DNA, it positions it in a precise manner on the DNA polymerase, where it stays bound until it reaches the end of its polymerizing job. Through this ingenious process, the clamp stabilizes the DNA, making it possible to increase the speed of polymerization dramatically. They can be seen here:

The sliding clamp and clamp loader
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4376

Question : How would and could natural , unguided processes have figured out 1. the requirement of high-speed of polymerization ? How could they have figured out the right configuration and process to do so ? how could natural processes have emerged with the right proteins incrementally, with the hand-shaped clamp loader, and the precisely fitting clamp , enabling the fast process ?? Even the most intelligent scientists are still not able to imagine how this process is engineered ? Furthermore, the process requires molecular energy in the form of ATP, and everything must fit together, and be functional. Without the clamp loader protein, the clamp could not be positioned to the polymerase enzyme, and processivity would not rise to the required speed. The whole process must also be regulated and controlled. How could that regulation have been programmed ? Trial and error ?

Several Proteins Are Required for DNA Replication at the Replication Fork
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4398

The various proteins involved in DNA replication are all closely associated in one large complex, called a replisome.
Leading strand synthesis: On the template strand with 3’-5’ orientation, new DNA is made continuously in 5’-3’ direction towards the replication fork. The new strand that is continuously synthesized in 5’-3’ direction is the leading strand.
Lagging strand synthesis: In the lagging strand, the synthesis of DNA also elongates in a 5ʹ to 3ʹ manner, but it does so in the direction away from the replication fork. In the lagging strand, RNA primers must repeatedly initiate the synthesis of short segments of DNA; thus, the synthesis has to be discontinuous.

The Primase (DnaG) enzyme, and the primosome complex
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4379

The length of these fragments in bacteria is typically 1000 to 2000 nucleotides. In eukaryotes, the fragments are shorter—100 to 200 nucleotides. Each fragment contains a short RNA primer at the 5ʹ end, which is made by primase. The remainder of the fragment is a strand of DNA made by DNA polymerase III. The DNA fragments made in this manner are known as Okazaki fragments. To complete the synthesis of Okazaki fragments within the lagging strand, three additional events must occur: removal of the RNA primers, synthesis of DNA in the area where the primers have been removed, and the covalent attachment of adjacent fragments of DNA. In E. coli, the RNA primers are removed by the action of DNA polymerase I. This enzyme has a 5ʹ to 3ʹ exonuclease activity, which means that DNA polymerase I digests away the RNA primers in a 5ʹ to 3ʹ direction, leaving a vacant area. DNA polymerase I then synthesizes DNA to fill in this region. It uses the 3ʹ end of an adjacent Okazaki fragment as a primer. , DNA polymerase I would remove the RNA primer from the first Okazaki fragment and then synthesize DNA in the vacant region by attaching nucleotides to the 3ʹ end of the second Okazaki fragment. After the gap has been completely filled in, a covalent bond is still missing between the last nucleotide added by DNA polymerase I and the adjacent DNA strand that had been previously made by DNA polymerase III. To the left of the origin, the top strand is made continuously, whereas to the right of the origin it is made in Okazaki fragments. By comparison, the synthesis of the bottom strand is just the opposite. To the left of the origin it is made in Okazaki fragments and to the right of the origin the synthesis is continuous. Finally the two ends of the fragment have to be joined together; this is the job of an enzyme called DNA ligase. After the completion of one Okazaki fragment , the equipment has to be released, the clamp has to let go, and a new clamp has to be loaded at the beginning of the next fragment. Clearly the formation and control of the replication fork is an enormously complex process.

Step 5: After DNA synthesis by DNA pol III, DNA polymerase I uses its 5’-3’ exonuclease activity to remove the RNA primer and fills the gaps with new DNA. In the next step, finally DNA ligase joins the ends of the DNA fragments together. As the replisome moves along the DNA in the direction of the replication fork, it must accommodate the fact that DNA is being synthesized in opposite directions along the template on the two stands. Picture above provides a schematic model illustrating how this might be accomplished by folding the lagging strand template into a loop.Creating such a loop allows the DNA polymerase molecules on both the leading and lagging strands to move in the same physical direction, even though the two template strands are oriented with opposite polarity. The replisome faces special challenges as it makes new DNA at rates that can approach 1,000 nucleotides per second. Unlike the machines that make proteins and RNA, which work relatively sluggishly and in a linear fashion, the replisome must simultaneously copy two strands of DNA that are aligned in opposite directions (5ʹ to 3ʹ and 3ʹ to 5ʹ). Replisome chemistry obeys two rules.


Questions: How did they arise with that cabability to " obey two rules " ? Suppose a primitive polymerase were duplicated and somehow started to replicate the second strand in the opposite direction while remaining attached to the first strand - how could that change have been directed , and why should that feat have happened randomly ?




The DNA polymerase holoenzyme alone would not be able to duplicate the long DNA faithfully. Tests have shown that Polymerase III alone gets stuck. Furthermore, Polymerase III is not a simple enzyme. Its rather three enzymes in one. Beside replicating DNA, it can also degrade DNA in two different ways. It does so by three different, discrete regions of the molecule. The exonuclease activity plays a critical role in replication. It allows the enzyme to proofread the new DNA and cut out any mistakes it has made. Although the polymerase reads the sequence of the old DNA to produce a new DNA, it turns out that simple base bairing allows about one mistake per thousand base pairs copied. Proofreading reduces errors to about one mistake in a million base pairs. The question is if wheter a proofreading exonuclease and other DNA repair mechanisms had to be present in the very first cell.

Eigen’s theory revealed the existence of the fundamental limit on the fidelity of replication (the Eigen threshold): If the product of the error (mutation) rate and the information capacity (genome size) is below the Eigen threshold, there will be stable inheritance and hence evolution; however, if it is above the threshold, the mutational meltdown and extinction become inevitable (Eigen, 1971). The Eigen threshold lies somewhere between 1 and 10 mutations per round of replication (Tejero, et al., 2011) regardless of the exact value, staying above the threshold fidelity is required for sustainable replication and so is a prerequisite for the start of biological evolution. Indeed, the very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded (Penny, 2005). The crucial question in the study of the origin of life is how the Darwin-Eigen cycle started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses with the replication fidelity of only about 10^3 and viroids that replicate with the lowest fidelity among the known replicons (about 10^2; Gago, et al., 2009), replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual.

DNA damage and repair
http://reasonandscience.heavenforum.org/t2043-dna-repair?highlight=dna+repair
http://reasonandscience.heavenforum.org/t1849p30-dna-replication-of-prokaryotes#4401

Replication forks may stall frequently and require some form of repair to allow completion of chromosomal duplication. Failure to solve these replicative problems comes at a high price, with the consequences being genome instability, cell death and, in higher organisms, cancer. Replication fork repair and hence reloading of DnaB may be needed away from oriC at any point within the chromosome and at any stage during chromosomal duplication. The potentially catastrophic effects of uncontrolled initiation of chromosomal duplication on genome stability suggests that replication restart must be regulated as tightly as DnaA-directed replication initiation at oriC. This implies reloading of DnaB must occur only on ssDNA at repaired forks or D-loops rather than onto other regions of ssDNA, such as those created by blocks to lagging strand synthesis.Thus an alternative replication initiator protein, PriA helicase, is utilized during replication restart to reload DnaB back onto the chromosome

Question: Could the first cell, with its required complement of genes coded for by DNA, have successfully reproduced for a significant number of generations without a proofreading function ? A further question is how the function of synthesis of the lagging strand could have arisen, and the machinery to do so. That is, the Primosome, and the function of Polymerase I to remove the short peaces of RNA that the cell uses to prime replication, allowing the polymerase III function to fill the gap. These functions all require precise regulation, and coordinated functional machine-like steps. These are all complex, advanced functions and had to be present right from the beginning. How could this complex machinery have emerged in a gradual manner ? the Primosome had to be fully functional, otherwise polymerisation could not have started, since a prime sequence is required.

Step 6: Finally DNA ligase joins the ends of the DNA fragments together.

Termination phase:

Termination of DNA replication
http://reasonandscience.heavenforum.org/t1849p15-dna-replication-of-prokaryotes#4399

Step 7: The two replication forks meet ~ 180 degree opposite to ori C, as DNA is circular in prokaryotes. Around this region there are several terminator sites which arrest the movement of forks by binding to the tus gene product, an inhibitor of helicase (Dna B).
Step 8: Once replication is complete, the two double stranded circular DNA molecules (daughter strands) remain interlinked. Topoisomerase II makes double stranded cuts to unlink these molecules.

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 DNA replication 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 DNA replication 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.

 

[Dragan Glas]

Greetings,

Still doesn't change what I said in my previous post.

And, as has been explained elsewhere, chemistry is sufficient to accomplish everything you've claimed requires an intelligence.

Kindest regards,

James

 

[Elshamah]

Greetings,

Still doesn't change what I said in my previous post.

And, as has been explained elsewhere, chemistry is sufficient to accomplish everything you've claimed requires an intelligence.

Kindest regards,

James

nice confession of blind faith.

 

[Rumraket]

here goes the complete version of the above post :

DNA replication, and its mind boggling nano technology that defies naturalistic explanations

Nice mindless copy-paste.

Anyway, why did you dispense with the word "high" in the title? You wrote it earlier and it sounded much more profound when you called it "nano high-technology". I also think you should use the word "complex" and "complexity" more often. You know, spice it up a little with some thick technical jargon from the computer and engineering sciences. Oh, ALGORITHM. You can almost feel the Jesus when you say it. A-L-G-O-R-I-T-H-M. oOOOHHhh, praise the LORD!

I suggest a new title:
The mindboggling algorithmic sequence complexity of the irreducible DNA-replication nano-machinery defies naturalistic explanation.

If you really want to make it baffling you can take some hints from the papers of young Earth creationist and retired veterinarian Davil L Abel. You can find them on pubmed I think. It will totally blow your mind.

 

[Rumraket]

Wait. Waaaait wait wait...

Your claim now is that the specific enzyme chlorophyll synthase (the last one in the chlorophyll biosynthesis pathway) is used in no other pathway? Seriously, who the fuck would claim it was? It's called chlorophyll synthase because that's what it does.

MOST enzymes are specific and used only in one pathway. That doesn't mean they didn't evolve, or that the pathway itself couldn't evolve. Your argument is EVEN DUMBER now. You are erecting as an argument an irrelevant fact. It's like saying "the outer cell membrane isn't used to copy eukaryotic chromosomes". WHO GIVES A SHIT? Nobody says it is. What a complete irrelevancy to blather about.

Haha. You are amusing. I mean , you REALLY are. I am saying all along that it makes no difference is certain enzymes are used in a different biological system, and could eventually have been co-opted, for the irreducible complexity argument.

Who cares that this is what you say? You can say it fifty trillion times that doesn't make it true. I have explained why it makes all the difference and you have said nothing that rebuts my explanation.

Behe says the same, as i quoted him.

Then all that means is that you have copied an already refuted argument from Michael Behe. Congratulations.

But you were insisting all along, that IF a enzyme were used in multiple systems, it could have been co-opted, and my argument of IC falls apart.

No. I'm saying that if we can detect homolgous enzymes in other systems, and those systems predate the origin of chlorophyll, then we know the chlorophyll synthesizing enzymes WERE coopted from other, already existing, systems.

That is what we find, so we know they evolved by cooptation.

When i show you that the last eight enzymes in the chlorophyll pathway are ONLY being used in that pathway, only to answer your point, you just turn around, and change your argument 180 degrees with the above.

No. My argument has been the same from the beginning: It doesn't matter that the enzymes don't have DIRECT COPIES, what we are searching for is HOMOLOGOUS enzymes.

For fucks sake man. These enzymes belong to well-characterised protein superfamilies. They are just mutated versions of enzymes that already existed elsewhere in the cells. They got duplicated, then they mutated so they catalyzed slightly different reactions, those reactions turned out to be useful, and now the result is they are part of the chlorophyll biosynthesis pathway.

Nothing has changed with my argument. They were all useful and functional every step of the way.

Come on, who do you think are you cheating ?

Nobody, because I'm not trying to cheat anyone.

I tell you. You are cheating only yourself. God loves you, but you try to run away like a hyena bite in her ass and try to justify your unbelief. Why is that ? Probably, because you have never experienced the goodness of God. Seriously. On rational ground, you are falling short by all means, and you know it. You are intelligent enough to examine your own proposals. Its evident they fall short..... So the reason you try to press everything in your premise and wishful thinking is not the evidence. but something else. I suspect on emotinal ground... If i'd be you, i'd make a check.....

Bla bla bla bla Jesus bla bla bla it feels so good bla bla bla you just hate god and want to sin bla bla bla you're fooling yourself bla bla bla god really loves you bla bla bla bla.

Thanks man. Thank you so much, I don't know how I could have lived without this irrelevant religionutter rant.

 

[Elshamah]

here goes the complete version of the above post :

DNA replication, and its mind boggling nano technology that defies naturalistic explanations

Nice mindless copy-paste.

Call it however you want. Do you think i would suck my premises from my finger ? You are correct...... i did not. I took it from mainstream scientific papers. Thats how i make sure the premise, the evidence of the scientific facts, are correct.

Anyway, why did you dispense with the word "high" in the title? You wrote it earlier and it sounded much more profound when you called it "nano high-technology". I also think you should use the word "complex" and "complexity" more often. You know, spice it up a little with some thick technical jargon from the computer and engineering sciences. Oh, ALGORITHM. You can almost feel the Jesus when you say it. A-L-G-O-R-I-T-H-M. oOOOHHhh, praise the LORD!

I suggest a new title:
The mindboggling algorithmic sequence complexity of the irreducible DNA-replication nano-machinery defies naturalistic explanation.

If you really want to make it baffling you can take some hints from the papers of young Earth creationist and retired veterinarian Davil L Abel. You can find them on pubmed I think. It will totally blow your mind

the cell is indeed a " high-tech" nano factory of the highest advancement and complexity. I wrote about this.

information , biosynthesis , analogy with human programming, engeneering, and factory robotic assembly lines

http://reasonandscience.heavenforum.org/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines

The best and most advanced result that intelligent and capable minds, thousands and hundred thousands of the most brilliant and inventive man and woman from all over the globe have been able to come up with after over one hundred years of technologic advance and progress, of what is considered one of the greatest innovations of the 20th century , is the construction of complex factories with fully automated assembly lines which use programmed roboters in the manufacturing, assembly, quality control and packing process of the most diverse products, in the most economic, efficient and effective way possible, integrating different facilities and systems, and using advanced statistical methods of quality control, making from cell phones, to cars, to power plants etc., but the constant intervention of intelligent brain power is required to get the whole process done, and obtain the final products. The distribution of the products is also based on complex distribution networks and companies, which all require hudge efforts of constant human intervention and brainpower.

Amazingly, the highest degree of manufacturing performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement and intelligence of production automatization ( at our scale = 100 ) we find in proceedings adopted by each cell, analogous to our factory , and biosynthesis pathways and processes in biology. A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. If just one of the enzymes is not present or otherwise not functioning then the entire process doesn’t work. We now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.Cells adopt highest advanced Mass-Craft production techniques , which yeald products with the ability of high adaptability to the environment ( micro evolution ) while being produced with high efficiency of production, advanced error checking mechanisms, low energy consumption and automatization, and so being generally being far far more advanced, complex, better structured and organized in every aspect, than the most advanced robotic assembly facility ever created by man. Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . I advocate that this fact is strong evidence of a planning, super intelligent mind, which conceptualized and created life right from scratch.

Considerations of the planning of the layout of a assembly line facility.

Important considerations for a high economic, effective and proper material flow are required and must be considered, thought and brought in when planning the concepts and layout design of a new factory assembly line, as for example maximal flexibility in the line for demand and supply fluctuation, planning deep enough to answer all possible aspects of a new line to get max efficiency afterwards. There should be simple material delivery routes and pathways throughout the facility that connect the processes. Also, there needs to be a plan for flexbility and changes, since volumes and demand are variable. Awareness of the many factors involved right in the planning process of the factory is key. Right-sized equipment and facilities must be planned and considered as well. All equipment and facilities should be designed to the demand rate or takt timeProjects and facility designs that do not take these considerations in account, start out great, but quickly bog down in unresolved issues, lack of consensus, confusion and delay.

 

[Dragan Glas]

Greetings,

Here's another article/paper for you, Elshamah:

Looking back 3.8 billion years into the root of the 'Tree of Life'

Have you read the other article/paper that I linked above? Are you going to let us know what you think of its implications for your claims?

Kindest regards,

James

 

[Dragan Glas]

Greetings,

Simple physical mechanism for assembly and disassembly of structures inside cells

Scientists say face mites evolved alongside humans since the dawn of human origins

Kindest regards,

James

 

[thenexttodie]

Greetings,

Here's another article/paper for you, Elshamah:

Looking back 3.8 billion years into the root of the 'Tree of Life'

Have you read the other article/paper that I linked above? Are you going to let us know what you think of its implications for your claims?

Kindest regards,

James

Pure conjecture. From the article,

" Like rings in the trunk of a tree, the ribosome contains components that functioned early on in its history. The center of the trunk records the tree's youth, and successive rings represent each year of the tree's life, with the outermost layer recording the present. Just as the core of a tree's trunk remains unchanged over time, all modern ribosomes contain a common core dating back 3.8 billion years. This common core is the same in all living organisms, including humans.

"The ribosome recorded its history," said Williams. "It accreted and got bigger and bigger over time. But the older parts were continually frozen after they accreted, just like the rings of a tree. As long as that tree lives, the inner rings will not change. The very core of the ribosome is older than biology, produced by evolutionary processes that we still don't understand very well."

^^^=conjecture

"By taking ribosomes from a number of species - humans, yeast, various bacteria and archaea - and looking at the outer portions that are variable, we saw that there were very specific rules governing how they change," said Williams. "We took those rules and applied them to the common core, which allowed us to see all the way back to the first pieces of RNA.

Dragan Glas, You are giving links to articles which assume the very ideas which Eishamah is disputing.

 

[Dragan Glas]

Greetings,

Greetings,

Here's another article/paper for you, Elshamah:

Looking back 3.8 billion years into the root of the 'Tree of Life'

Have you read the other article/paper that I linked above? Are you going to let us know what you think of its implications for your claims?

Kindest regards,

James

Pure conjecture. From the article,

" Like rings in the trunk of a tree, the ribosome contains components that functioned early on in its history. The center of the trunk records the tree's youth, and successive rings represent each year of the tree's life, with the outermost layer recording the present. Just as the core of a tree's trunk remains unchanged over time, all modern ribosomes contain a common core dating back 3.8 billion years. This common core is the same in all living organisms, including humans.

"The ribosome recorded its history," said Williams. "It accreted and got bigger and bigger over time. But the older parts were continually frozen after they accreted, just like the rings of a tree. As long as that tree lives, the inner rings will not change. The very core of the ribosome is older than biology, produced by evolutionary processes that we still don't understand very well."

Not conjecture...

Some clues along the way helped. For instance, though RNA is now responsible for creating proteins, the very earliest life had no proteins. By looking for regions of the ribosome that contain no proteins, the researchers could determine that those elements existed before the advent of proteins. "Once the ribosome gained a certain capability, that changed its nature," Williams said.

While the ribosomal core is the same across species, what's added on top differs. Humans have the largest ribosome, encompassing some 7,000 nucleotides representing dramatic growth from the hundred or so base pairs at the beginning.

"What we're talking about is going from short oligomers, short pieces of RNA, to the biology we see today," said Williams. "The increase in size and complexity is mind-boggling."

The researchers obtained their ribosomes from structure and sequence databases that have been produced to help scientists identify new species. Ribosomes can be crystallized, which reveals their three dimensional structures.

Kindest regards,

James

 

[Elshamah]

Factory and machine planning and design, and what it tells us about cell factories and molecular machines

http://reasonandscience.heavenforum.org/t2245-factory-and-machine-planning-and-design-and-what-it-tells-us-about-cell-factories-and-molecular-machines

Some steps to consider in regard of factory planning, design and operation

All text in red requires INTELLIGENCE :

Choosing Manufacturing and Factory location
Selecting Morphology of Factory Types
Factory planning
Factory design
Information management within factory planning and design
Factory layout planning
Equipment supply
Process planning
Production Planning and Control
establishing various internal and external Communication networks
Establishing Quantity and Variant Flexibility
The planning of either a rigid or flexible volume concept depending of what is required
Establishing Networking and Cooperation
Establishing Modular organization
Size and internal factory space organization, compartmentalization and layout
Planning of recycling Economy
Waste management
Controlled factory implosion programming

All these procedures and operational steps are required and implemented in human factories, and so in biological cells which operate like factories. It takes a lot of faith to believe, human factories require intelligence, but cells, far more complex and elaborated, do not require intelligence to make them, and intelligent programming to work in a self sustaining and self replicating manner, and to self disctruct, when required.

Molecular machines:

The most complex molecular machines are proteins found within cells. 1 These include motor proteins, such as myosin, which is responsible for muscle contraction, kinesin, which moves cargo inside cells away from the nucleus along microtubules, and dynein, which produces the axonemal beating of motile cilia and flagella. These proteins and their nanoscale dynamics are far more complex than any molecular machines that have yet been artificially constructed.

Probably the most significant biological machine known is the ribosome. Other important examples include ciliary mobility. A high-level-abstraction summary is that, "n effect, the [motile cilium] is a nanomachine composed of perhaps over 600 proteins in molecular complexes, many of which also function independently as nanomachines." Flexible linker domains allow the connecting protein domains to recruit their binding partners and induce long-range allostery via protein domain dynamics.

Engineering design process

The engineering design process is a methodical series of steps that engineers use in creating functional products and processes. 2

All text in red requires INTELLIGENCE

locating information and research
feasibility study
evaluation and analysis of the potential of a proposed project
process of decision making. Outlines and analyses alternatives or methods of achieving the desired outcome
feasibility report is generated
determine whether the engineer's project can proceed into the design phase
the project needs to be based on an achievable idea
concept study (conceptualization, conceptual engineering
project planning
solutions must be identified
ideation, the mental process by which ideas are generated
morphological chart - independent design characteristics are listed in a chart, and different engineering solutions are proposed for each solution. Normally, a preliminary sketch and short report accompany the morphological chart.
the engineer imagines him or herself as the item and asks, "What would I do if I were the system?"
Synthesis is the process of taking the element of the concept and arranging them in the proper way.
Synthesis creative process is present in every design.
thinking of different ideas, typically as part of a small group, and adopting these ideas in some form as a solution to the problem
Establishing design requirements is one of the most important elements in the design process
feasibility analysis
Some design requirements include hardware and software parameters, maintainability, availability, and testability
the overall system configuration is defined, and schematics, diagrams, and layouts of the project will provide early project configuration.
detailed design and optimization
the preliminary design focuses on creating the general framework to build the project on.
further elaborate each aspect of the project by complete description through solid modeling,drawings as well as specifications.
Some of the said specifications include:
Operating parameters
Operating and nonoperating environmental stimuli
Test requirements
External dimensions
Maintenance and testability provisions
Materials requirements
Reliability requirements
External surface treatment
Design life
considering packaging requirements and implant them
External marking
production planning and tool design
planning how to mass-produce the project and which tools should be used in the manufacturing of the part.
selecting the material, selection of the production processes, determination of the sequence of operations, and selection of tools, such as jigs, fixtures, metal cutting and metal forming tools.
start of manufactoring
the machines must be inspected regularly to make sure that they do not break down and slow production

Someone can object and say, that human invented machines do nor replicate, and therefor the comparison is invalid. Fact is however, that replication adds further complexity , since humans have not been able to construct self replicating machines in large scale. This is imho what every living cell is able and programmed to do. In order to so so, extremely complex celluar mechanisms are required, like DNA replication.

1) https://en.wikipedia.org/wiki/Molecular_machine
2) https://en.wikipedia.org/wiki/Engineering_design_process