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The Elshamah mega-thread

arg-fallbackName="Rumraket"/>
Elshamah said:
Nothing of what you posted scratches even on the surface of my argument.
All of your arguments have been refuted in-substance.

All of them boil down to one of two main points. 1. Irreducible complexity or 2. Improbability.

All your arguments about 1. have bee refuted with a direct observation from the Long-term Evolution Experiment that irreducibly complex structures can be seen evolving in real time.

All your arguments about 2. have been refuted with the fact that you cannot calculate the odds of design.

It doesn't matter how improbable option A is if you don't know how improbable option B is. Then you cannot claim that B is more probable than A.
Elshamah said:
The last 8 steps require enzymes, that are not used in any other pathway.
Even if that was true it would be irrelevant. That just means extant chlorophyll has a long evolutionary history, with enzymes evolving one at a time to further modify an already existing molecule.

READ THE PAPER I LINKED.
Elshamah said:
I have checked.
You have checked where and how did you check it? Did you do a BLAST search, did you do structural alignments? What parameters did you use to check, what databases did you look in?

Did you just outright lie when you say you "have checked"? Yeah, you did. You haven't checked shit.
Elshamah said:
You can do the same. Check and see.
Tell me where and how you did your "checking" and I will replicate it.
Elshamah said:
So there is no reason to assume they were co-opted from somewhere else.
Even if that was true it would be irrelevant. That just means extant chlorophyll has along evolutionary history, with enzymes evolving one at a time to further modify an already existing molecule.

READ THE PAPER I LINKED.
Elshamah said:
But even IF that were the case, so what ??
Then it would simply make it all the more easy for the extant pathway to evolve, since the enzymes already existed and didn't have to evolve one by one.
Elshamah said:
Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions

http://reasonandscience.heavenforum.org/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions
That is false and the Lenski Long-term Evolution Experiment with E coli proved it.

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.
Rumraket said:
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.

Elshamah said:
Furthermore, the heme biosynthesis pathway is also irreducible complex :

The heme biosynthesis pathway is irreducible complex.
Exactly the same fundamental flaw as all your other irreducible complexity arguments. They are all functionally refuted by the observation that irreducibly complex structures are evolvable entities.
Elshamah said:
http://reasonandscience.heavenforum.org/t1322-the-amazing-hemoglobin-molecule#1859

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.
Exactly the same fundamental flaw as all your other irreducible complexity arguments. They are all functionally refuted by the observation that irreducibly complex structures are evolvable entities.
Elshamah said:
Questions:
What good would there be, if the pathway would go only up to the 7th step ? none
False, the molecule synthesized by the 7th step is functional. So is the one synthesized by the 6th step. And so on.
Elshamah said:
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.
False, Heme can carry iron without a surrounding Globin protein. Heme was already carried by globin proteins before utilization of oxygen for aerobic respiration and metabolism because oxygen came later in evolution. Heme and the globin fold most probably coevolved. As in: The biosynthesis of Heme, when it started, did not produce Heme, but a smaller subunit that was still useful for binding and carrying Iron used as a chemical catalyst. Contemporaneously with the elaboration of the Heme pathway, proteins that bind and use the Heme precursors as a cofactor in catalysis evolved. The end result of this is what we today recognize as many Hemoglobin species in different organisms. But it clearly has a long evolutionary history, and it has been functional every step of the way.
Elshamah said:
What good would there be for red bloodcells without hemoglobin, transporting oxygen to the cells in the body ? none
False. Notothenoid fish have no red blood cells and no hemoglobin, they live at temperatures so cold their blood carries so much oxygen it doesn't need hemoglobin.

https://en.wikipedia.org/wiki/Channichthyidae
Icefish blood is colorless because it lacks hemoglobin, the oxygen-binding protein in blood.[3][6] Red blood cells are usually absent and if present are rare and defunct.[7] Oxygen is dissolved in the plasma and transported throughout the body without the hemoglobin protein. The fish can live without hemoglobin because of their low metabolic rates and the high solubility of oxygen in water at the low temperatures of their environment (the solubility of a gas tends to increase as temperature decreases).[3] However, the oxygen-carrying capacity of their blood is less than 10% that of their relatives with hemoglobin.[8]

To compensate for the loss of hemoglobin, they have larger blood vessels (including capillaries), greater blood volumes (four times that of other fish), bigger hearts, and greater cardiac outputs (fivefold greater) compared to other fish.[3] Their hearts lack coronary arteries and the ventricle muscles are very spongy, enabling them to absorb oxygen directly from the blood they pump.[9] Their hearts, large blood vessels and low-viscosity (RBC free) blood are specialized to carry out very high flow rates at low pressures.[10] This helps to reduce the problems caused by the lack of hemoglobin. In the past, their scaleless skin had been widely thought to help absorb oxygen. However, current analysis has shown that the amount of oxygen absorbed by the skin is much less than that absorbed through the gills.[9] The little extra oxygen absorbed by the skin may play a part in supplementing the oxygen supply to the heart[9] which receives venous blood from the skin and body before pumping it to the gills.

Hemoglobin[edit]
Channichthyidae are the only known vertebrates to lack hemoglobin as adults. Although they do not manufacture hemoglobin, remnants of hemoglobin genes can be found in their genome. The hemoglobin protein is made of two subunits (alpha and beta). In 15 of the 16 icefish species, the beta subunit gene has been completely deleted and the alpha subunit gene has been partially deleted.[11] In only one of the icefish species, Neopagetopsis ionah, there is a more complete, but still nonfunctional hemoglobin gene.
[12]

Elshamah said:
, 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.
Diametrically opposite to demonstrable fact. Hemoglobin is not required for oxygen transport. It helps under many circumstances, but there are other ways to do it. Your argument is therefore ineffective.
Elshamah's copy-pasta said:
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.
I read the very first sentence of that and realized you didn't write it yourself. You copy-pasted this shit from here, but now pass it off as if you wrote it yourself.

The huge irony here is that the very thing you copy-paste from contains the sentence I highlighted in red.

Porphyrins are all biologically useful molecules, but are simultaneously the precursors for Heme and Chlorophyll. Which rams a freight-train through the idiotic assertion that none of the precursors of Heme or Chlorophyll would be useful.

What's it like to be CONSTANTLY WRONG?
Elshamah said:
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 ?
Globins are used for many things besides carrying Heme. Globins are a SUPERFAMILY of proteins that all share the overall Globin fold. They have many many different roles and functions in all of biology. As I already wrote above, they probably coevolved side by side. The precursors of Heme coevolved with the precursos of the Globin fold and both became gradually more complex with time.
Elshamah said:
Yes, i copy/paste from my virtual library, but these are MY arguments.
.. from ignorance. Deliberate ignorance. First you ask a question, then you make a blind declaration that is contrary to demonstrable fact. This can only happen because you allow yourself to make the claim before checking if you are right.

Now, those enzymes you said you checked whether had any homologoues. Where did you check and how did you check?
 
arg-fallbackName="SpecialFrog"/>
Elshamah, various people have pointed out that your "virtual library" is full of plagiarized text from other sources so even your claim that your copypasta is your own text is questionable.
 
arg-fallbackName="DutchLiam84"/>
Elshamah said:
Yes, i copy/paste from my virtual library, but these are MY arguments.
Seriously dude? Almost everything I've checked on your website was word for word copy/pasted from other sources and in many cases you neglect to mention the original source or acknowledge that it's a quote from someone else. Or do you think you're the only one whose heard of "google"? Why do you feel the need to lie about this? As I've said before, in any academic setting you would be nailed to a fuckin cross for this kind of unethical behavior! Get it, nailed to a cross....yeah, you get it!
 
arg-fallbackName="Elshamah"/>
Rumraket said:
[

All your arguments about 1. have bee refuted with a direct observation from the Long-term Evolution Experiment that irreducibly complex structures can be seen evolving in real time.

You should have learned by now that ic and evolution exclude each other. If a system can evolve, its not ic.
All your arguments about 2. have been refuted with the fact that you cannot calculate the odds of design.

that is not required. things specially in the post we are discussing have been portrayed very clearly. But you derail to issues that are not central to the problem, ignore the relevant issues, and sing victory. What is the matter with you ? You are intelligent enough to understand my arguments....
It doesn't matter how improbable option A is if you don't know how improbable option B is. Then you cannot claim that B is more probable than A.

The probability that ic systems can evolve is ZERO.

I give you a example.

http://reasonandscience.heavenforum.org/t2231-protein-protein-interactions-evidence-of-design#4387

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose. And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result. But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function. But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much. And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites. Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.

Even if that was true it would be irrelevant. That just means extant chlorophyll has a long evolutionary history, with enzymes evolving one at a time to further modify an already existing molecule.

LOL. And you know that how exactly ??
READ THE PAPER I LINKED.

quote where it explains how enzymes could evolve, that would have no function, unless everything is in place, fully connected to exercise a specific function.
Did you just outright lie when you say you "have checked"? Yeah, you did. You haven't checked shit.

Look, kid. I have no patience to argue with the rest of your drivel, if you throw the lie canard.

Deal with what i have posted up to now.
 
arg-fallbackName="Mr_Wilford"/>
DutchLiam84 said:
Elshamah said:
Yes, i copy/paste from my virtual library, but these are MY arguments.
Seriously dude? Almost everything I've checked on your website was word for word copy/pasted from other sources and in many cases you neglect to mention the original source or acknowledge that it's a quote from someone else. Or do you think you're the only one whose heard of "google"? Why do you feel the need to lie about this? As I've said before, in any academic setting you would be nailed to a fuckin cross for this kind of unethical behavior! Get it, nailed to a cross....yeah, you get it!

You nailed it!
 
arg-fallbackName="Elshamah"/>
SpecialFrog said:
Elshamah, various people have pointed out that your "virtual library" is full of plagiarized text from other sources so even your claim that your copypasta is your own text is questionable.

Well, check the text in green. That are my inferences upon the evidence provided and posted. And if you like or do not like that i copy paste scientific articles, which serve as the premise and scientific evidence, upon which i draw my conclusions, is your problem, not mine.
 
arg-fallbackName="Dragan Glas"/>
Greetings,
Elshamah said:
SpecialFrog said:
Elshamah, various people have pointed out that your "virtual library" is full of plagiarized text from other sources so even your claim that your copypasta is your own text is questionable.

Well, check the text in green. That are my inferences upon the evidence provided and posted. And if you like or do not like that i copy paste scientific articles, which serve as the premise and scientific evidence, upon which i draw my conclusions, is your problem, not mine.
The problem is that you're including sentences, etc, from articles within what purports to be your own thoughts as if they're your own - this, as SpecialFrog and Rumraket have pointed out, is plagiarism.

That's what those here dislike.

That's on top of the fact that your religiously-inspired claims are baseless and have been shown to be wrong.

Kindest regards,

James
 
arg-fallbackName="Mr_Wilford"/>
Redefining irreducible complexity. Why am I not surprised? This thread is amusing to lurk
 
arg-fallbackName="Rumraket"/>
Elshamah said:
Rumraket said:
All your arguments about 1. have bee refuted with a direct observation from the Long-term Evolution Experiment that irreducibly complex structures can be seen evolving in real time.
You should have learned by now that ic and evolution exclude each other. If a system can evolve, its not ic.
Then there are no IC systems known. Your definition is begging the question.
Elshamah said:
Rumraket said:
Even if that was true it would be irrelevant. That just means extant chlorophyll has a long evolutionary history, with enzymes evolving one at a time to further modify an already existing molecule.
LOL. And you know that how exactly ??
READ THE PAPER I LINKED.
Elshamah said:
Rumraket said:
READ THE PAPER I LINKED.
quote where it explains how enzymes could evolve, that would have no function, unless everything is in place, fully connected to exercise a specific function.
The enzymes did not evolve and be functionless for fucks sake, nobody suggests this is what happened. Apparently you didn't understand what I wrote. Or you can't read very well. Which one is it?

There was an organism without chlorophyll, but with Heme. This organism randomly evolves new enzymes here and there by standard means (duplication and sub/neo-functionalization as has been directly observed happening many time and we can prove happened in the past using Ancestral Sequence Reconstruction). Some of these enzymes modify Porphyrins (the precursors of Heme and Chlorophyll) such that they alter it's properties in useful ways. This happens multiple times, in useful ways making them retained by natural selection, giving additional steps to the pathway to Chlorophyll.

READ THE PAPER I LINKED.
READ THE PAPER I LINKED.
READ THE PAPER I LINKED.
Elshamah said:
Rumraket said:
Elsamah: "The last 8 steps require enzymes, that are not used in any other pathway. I have checked."

You have checked where and how did you check it? Did you do a BLAST search, did you do structural alignments? What parameters did you use to check, what databases did you look in?

Did you just outright lie when you say you "have checked"? Yeah, you did. You haven't checked shit.
Look, kid. I have no patience to argue with the rest of your drivel, if you throw the lie canard.
Awww boo-hoo. Stop crying and answer my questions.

Where did you check? What did you check? How did you check it? Prove that you did so. I don't believe you checked anything, I believe you are lying when you say you have checked. Prove me wrong if you can.
 
arg-fallbackName="Dragan Glas"/>
Greetings,
Elshamah said:
The probability that ic systems can evolve is ZERO.

I give you a example.

http://reasonandscience.heavenforum.org/t2231-protein-protein-interactions-evidence-of-design#4387

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose. And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result. But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function. But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much. And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites. Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.
Still citing Behe in support of ID - even though he couldn't defend it in court.

Interestingly, Wiki has on article on Behe's The Edge Of Evolution.

And here's a review by NCSE.
What is perhaps most remarkable about The Edge of Evolution is how much Behe now concedes to the evidence that supports Darwinian evolution. He not only accepts that life has existed on earth for billions of years, but that it has evolved over time. He now agrees with the Darwinian notion that all life on the planet "descended with modification from one stage to another." He even acknowledges that natural selection is the obvious mechanism by which adaptive gene variants spread through a population. It is difficult to imagine his core audience being receptive to this revised position. But at this point, Behe is stuck between the need to establish a semblance of scientific credibility and the desire to forward his distinctly unscientific creationist ideas.
It seems Behe's own beliefs in ID/creationism are failing - perhaps his son has finally gotten through to him.

The review makes very interesting reading. ;)

How does that sit with your notion about ID/creationism being the explanation for life on Earth, Elshamah!?

And, just for fun, here's another article on Behe's supposedly problematic protein-protein interactions.

Kindest regards,

James
 
arg-fallbackName="Elshamah"/>
Rumraket said:
Then there are no IC systems known. Your definition is begging the question.

haha.

READ THE PAPER I LINKED.

quote the relevant part which you think substantiates your assertions, and we'll see.
The enzymes did not evolve and be functionless for fucks sake, nobody suggests this is what happened. Apparently you didn't understand what I wrote. Or you can't read very well. Which one is it?

So how about you give a example of what any of the last eight enzymes did prior being used in chlorophyll synthesis ?
There was an organism without chlorophyll, but with Heme.

Heme does not use ANY of the last eight enzymes in the pathway......

This organism randomly evolves new enzymes here and there by standard means (duplication and sub/neo-functionalization as has been directly observed happening many time and we can prove happened in the past using Ancestral Sequence Reconstruction). Some of these enzymes modify Porphyrins (the precursors of Heme and Chlorophyll) such that they alter it's properties in useful ways. This happens multiple times, in useful ways making them retained by natural selection, giving additional steps to the pathway to Chlorophyll.

Blind assertion and pseudo scientific claim, based on wishful biased thinking and bad science. Who do you think you can delude with your nonsense beside yourself ?

You have checked where and how did you check it? Did you do a BLAST search, did you do structural alignments? What parameters did you use to check, what databases did you look in?

Check by yourself if you do not believe me.
Did you just outright lie when you say you "have checked"? Yeah, you did.

Keeping with false acusations ? Prove me wrong. Go ahead.

But even If ..... lets suppose they had other functions, So what ??

Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions

A Response to Sharon Begley's Wall Street Journal Column
Michael J. Behe
Discovery Institute

http://reasonandscience.heavenforum.org/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions

In a recent column in the Wall Street Journal (February 13, 2004, Science Journal, page B1, "Evolution Critics Come Under Fire for Flaws In 'Intelligent Design'") science writer Sharon Begley repeated some false claims about the concept of irreducible complexity (IC) that have been made by Darwinists, in particular by Kenneth Miller, a professor of biology at Brown University. After giving a serviceable description in her column of why I argue that a mousetrap is IC, Begley added the Darwinist poison pill to the concept. The key misleading assertion in the article is the following: "Moreover, the individual parts of complex structures supposedly serve no function." In other words, opponents of design want to assert that if the individual parts of a putatively IC structure can be used for anything at all other than their role in the system under consideration, then the system itself is not IC. So, for example, Kenneth Miller has seriously argued that a part of a mousetrap could be used as a paperweight, so not even a mousetrap is IC. Now, anything that has mass could be used as a paperweight. Thus by Miller's tendentious reasoning any part of any system at all has a separate "function". Presto! There is no such thing as irreducible complexity.

That's what often happens when people who are adamantly opposed to an idea publicize their own definitions of its key terms—the terms are manipulated to wage a PR battle. The evident purpose of Miller and others is to make the concept of IC so brittle that it easily crumbles. However, they are building a straw man. I never wrote that individual parts of an IC system couldn't be used for any other purpose. (That would be silly—who would ever claim that a part of a mousetrap couldn't be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin's Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention.

In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn't form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system.

Darwin's Black Box, page 66.

The reason why a separate function for the individual parts does not solve the problem of IC is because IC is concerned with the function of the system:

By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.

Darwin's Black Box, page 39.


The system can have its own function, different from any of the parts. Any individual function of a part does not explain the separate function of the system.

Miller applies his crackerjack reasoning not only to the mousetrap, but also to the bacterial flagellum—the extremely sophisticated, ultra complex biological outboard motor that bacteria use to swim, which I had discussed in Darwin's Black Box and which has becoming something of a poster child for intelligent design. No wonder, since anyone looking at a drawing of the flagellum immediately apprehends the design. Since the flagellum is such an embarrassment to the Darwinian project, Miller tries to distract attention from its manifest design by pointing out that parts of the structure can have functions other than propulsion. In particular, some parts of the flagellum act as a protein pump, allowing the flagellum to aid in its own construction—a level of complexity that was unsuspected until relatively recently.

Miller's argument is that since a subset of the proteins of the flagellum can have a function of their own, then the flagellum is not IC and Darwinian evolution could produce it. That's it! He doesn't show how natural selection could do so; he doesn't cite experiments showing that such a thing is possible; he doesn't give a theoretical model. He just points to the greater-than-expected complexity of the flagellum (which Darwinists did not predict or expect) and declares that Darwinian processes could produce it. This is clearly not a fellow who wants to look into the topic too closely.

In fact, the function of a pump has essentially nothing to do with the function of the system to act as a rotary propulsion device, anymore than the ability of parts of a mousetrap to act as paperweights has to do with the trap function. And the existence of the ability to pump proteins tells us nil about how the rotary propulsion function might come to be in a Darwinian fashion. For example, suppose that the same parts of the flagellum that were unexpectedly discovered to act as a protein pump were instead unexpectedly discovered to be, say, a chemical factory for synthesizing membrane lipids. Would that alternative discovery affect Kenneth Miller's reasoning at all? Not in the least. His reasoning would still be simply that a part of the flagellum had a separate function. But how would a lipid-making factory explain rotary propulsion? In the same way that protein pumping explains it—it doesn't explain it at all.

The irreducible complexity of the flagellum remains unaltered and unexplained by any unintelligent process, despite Darwinian smoke-blowing and obscurantism.

I have pointed all this out to Ken Miller on several occasions, most recently at a debate in 2002 at the American Museum of Natural History. But he has not modified his story at all.

As much as some Darwinists might wish, there is no quick fix solution to the problem of irreducible complexity. If they want to show their theory can account for it (good luck!), then they'll have to do so by relevant experiments and detailed model building—not by wordplay and sleight-of-hand.
 
arg-fallbackName="Dragan Glas"/>
Greetings,

Read the review of Behe's book.

You're quoting out-of-date material - he's changed his position.

Kindest regards,

James
 
arg-fallbackName="Rumraket"/>
Elshamah said:
quote the relevant part which you think substantiates your assertions, and we'll see.
I already did.

We already have seen, it is not something "we shall see". I posted the whole section in pictures. Read it through. The entire thing.
Elshamah said:
Rumraket said:
The enzymes did not evolve and be functionless for fucks sake, nobody suggests this is what happened. Apparently you didn't understand what I wrote. Or you can't read very well. Which one is it?
So how about you give a example of what any of the last eight enzymes did prior being used in chlorophyll synthesis ?
They don't have to have been involved in anything other than chlorophyll synthesis. They could have arisen de novo with one or two at first, then the rest arisen by duplication.
Elshamah said:
Rumraket said:
There was an organism without chlorophyll, but with Heme.
Heme does not use ANY of the last eight enzymes in the pathway......
I don't claim it did. You are not understanding anything I write. The biosynthesis of chlorophyll splits off from the biosynthesis of heme at porphyrin. The "unique" enzymes in the chlorophyll pathway (and I don't believe you have checked whether they are without any homologoues, how did you check this? Tell me) arose independently and acted on porphyrin, not Heme.
Elshamah said:
Rumraket said:
This organism randomly evolves new enzymes here and there by standard means (duplication and sub/neo-functionalization as has been directly observed happening many time and we can prove happened in the past using Ancestral Sequence Reconstruction). Some of these enzymes modify Porphyrins (the precursors of Heme and Chlorophyll) such that they alter it's properties in useful ways. This happens multiple times, in useful ways making them retained by natural selection, giving additional steps to the pathway to Chlorophyll.
Blind assertion and pseudo scientific claim, based on wishful biased thinking and bad science. Who do you think you can delude with your nonsense beside yourself ?
There is no rebuttal here, just mindless posturing and blind dismissal. Well done, what a powerful "argument" you have here.
Elshamah said:
Rumraket said:
You have checked where and how did you check it? Did you do a BLAST search, did you do structural alignments? What parameters did you use to check, what databases did you look in?
Check by yourself if you do not believe me.
Where? How did you check?
Elshamah said:
Rumraket said:
Did you just outright lie when you say you "have checked"? Yeah, you did.
Keeping with false acusations ?
You say they are false. Okay, then tell me how you checked it.
Elshamah said:
But even If ..... lets suppose they had other functions, So what ??
Then it makes their evolution all the more probable since gene duplication is one of the most frequent types of mutations to happen.
Elshamah said:
Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions

A Response to Sharon Begley's Wall Street Journal Column
Michael J. Behe
Discovery Institute

http://reasonandscience.heavenforum.org/t1572-irreducible-complexity-is-an-obstacle-to-darwinism-even-if-parts-of-a-system-have-other-functions

... bla bla irrelevant copy-paste from Michael Behe...
All this crap is completely irrelevant because individual enzymes are not irreducibly complex, neither in Behe's new sense or in your horribly mangled version.

It's true what I wrote. Enzymes can evolve gradually by gene duplication from other enzymes.

Enzyme A gets duplicated so you now have A and A1. A1 undergoes a mutation that slightly changes it so it catalyzes a slightly different reaction. A1 then undergoes further mutations and so on. Happens all the time, I have already brought the papers that prove this in this very thread.

Here it is again:
Rumraket said:
Okay, but.. how does this even happen then. How do these enzymes change so much through evolution?
Well, new studies have shed some light on that too and it's mostly by gene-duplication:
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001446
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene Duplication
Karin Voordeckers equal contributor, Chris A. Brown equal contributor, Kevin Vanneste, Elisa van der Zande, Arnout Voet, Steven Maere mail, Kevin J. Verstrepen
Abstract

Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.
It turns out the oldest reconstructed proteins are functionally promiscous. That means they catalyze many different reactions(by accepting many different substrates) at the same time, though at sub-optimal reaction-rates compared to their faster and later evolved descendants:
Author Summary

Darwin's theory of evolution is one of gradual change, yet evolution sometimes takes remarkable leaps. Such evolutionary innovations are often linked to gene duplication through one of three basic scenarios: an extra copy can increase protein levels, different ancestral subfunctions can be split over the copies and evolve distinct regulation, or one of the duplicates can develop a novel function. Although there are numerous examples for all these trajectories, the underlying molecular mechanisms remain obscure, mostly because the preduplication genes and proteins no longer exist. Here, we study a family of fungal metabolic enzymes that hydrolyze disaccharides, and that all originated from the same ancestral gene through repeated duplications. By resurrecting the ancient genes and proteins using high-confidence predictions from many fungal genome sequences available, we show that the very first preduplication enzyme was promiscuous, preferring maltose-like substrates but also showing trace activity towards isomaltose-like sugars. After duplication, specific mutations near the active site of one copy optimized the minor activity at the expense of the major ancestral activity, while the other copy further specialized in maltose and lost the minor activity. Together, our results reveal how the three basic trajectories for gene duplicates cannot be separated easily, but instead intertwine into a complex evolutionary path that leads to innovation.

A great figure that shows this:
fetchObject.action

Figure 2. Duplication events and changes in specificity and activity in evolution of S. cerevisiae MalS enzymes.
The hydrolytic activity of all seven present-day alleles of Mal and Ima enzymes as well as key ancestral (anc) versions of these enzymes was measured for different α-glucosides. The width of the colored bands corresponds to kcat/Km of the enzyme for a specific substrate. Specific values can be found in Table S2. Note that in the case of present-day Ima5, we were not able to obtain active purified protein. Here, the width of the colored (open) bands represents relative enzyme activity in crude extracts derived from a yeast strain overexpressing IMA5 compared to an ima5 deletion mutant. While these values are a proxy for the relative activity of Ima5 towards each substrate, they can therefore not be directly compared to the other parts of the figure. For ancMalS and ancMal-Ima, activity is shown for the variant with the highest confidence (279G for ancMalS and 279A for ancMal-Ima). Activity for all variants can be found in Table S2.
doi:10.1371/journal.pbio.1001446.g002
As you can see, the original ancestral enzyme has low substrate specificity and is functionally promiscous(it catalyzes reactions from all the different substrates(colors), but at a low reaction rate(the thickness of the bars). Subsequently it gets duplicated, and daughter enzymes acquire novel mutations that change the substrate specificity, vastly increasing the reaction-rates for a smaller subset of substrates, sometimes losing functionality entirely for specific substrates.

There you go.

Now tell me how you "checked" there are no related enzymes to the ones in the Chlorophyll pathway. Tell me how you checked that.
 
arg-fallbackName="Rumraket"/>
What is wrong with the paper I just linked?

They elucidate the sequences of enzymes that no longer exist in any organism on Earth, using statistics about how evolution happens at the genetic level, and reconstruct them in the laboratory. Then they test them and find out not only THAT they work, but HOW they work and that they work in a DIFFERENT WAY than the modern versions.

How is this possible, how could they get this result, if evolution didn't produce the modern enzymes? You claim functional proteins are very rare, but then how can they use statistics that assume the evolutionary process and just so happen to produce functional proteins that no longer exist, and which are clear ancestral versions of extant enzymes?

Explain it. Explain how this result is possible if evolution is false and if functional proteins really are astronomically rare in protein sequence space. Enough of your brainless copy-paste bullshit, EXPLAIN IT.
 
arg-fallbackName="Elshamah"/>
Rumraket said:
They could have arisen de novo with one or two at first, then the rest arisen by duplication.

There you go. Are you not tired to come up with just so pseudo scientific explanations based on wishful thinking ?

http://reasonandscience.heavenforum.org/t2062-proteins-how-they-provide-striking-evidence-of-design#4272

If you ask a proponent of evolution how a protein evolved, you will likely hear the standard answer: via gene duplication and subsequent divergence. In other words, the protein arose from a different type of protein that was pre existing. The gene for that protein duplicated, and then mutated until landing on a new protein that was helpful. And of course this story must have repeated itself thousands of times to create the many different proteins in biology.

It is an unlikely, just-so, story, for viable protein sequences are hard to find. If the different types of proteins each have their own tiny slivers of sequence space as science is suggesting, then gene duplication and divergence, alone, doesn’t stand a chance.

What would be needed are long trails of intermediate, functional, proteins connecting the different types of proteins. These proteins would not only need to be functional, their particular function would have to be useful at the time.

And why would the known proteins just happen to be fortuitously connected by these trails? Science gives us no reason to think such a lucky circumstance is built into the protein world. So either there are no such trails, which means evolution has a problem, or there are such trails which means someone has monkeyed with the fundamentals of protein chemistry.

And we have not yet even addressed the problem of how the first proteins evolved. Remember the proponents of evolutions standard explanation for how proteins evolved is by gene duplication and subsequent divergence. But that requires the pre existence of other types of proteins. In other words, the question of how proteins evolve in the first place has been swept under the rug.

The problem of how evolution could create a new type of protein from an existing protein, via gene duplication and subsequent divergence, as difficult as it is, pales in comparison to how evolution was supposed to have created new proteins from scratch. Proponents of evolution speak of an initial world where RNA molecules do the work of proteins. But even this heroic story doesn’t magically make the problem of protein evolution go away. Whether there were RNA precursors or not, there is a substantial difficulty in explaining how the first proteins could have evolved.
 
arg-fallbackName="Rumraket"/>
I now went ahead and checked myself what you claim to have checked, which is whether any of the "last 8 enzymes" in the "unique" chlorophyll biosynthesis pathway, truly are unique.

The first enzyme I decided to check was Protochlorophyllide reductase.

This is what I found: http://www.ncbi.nlm.nih.gov/pubmed/10811655
Reconstitution of light-independent protochlorophyllide reductase from purified bchl and BchN-BchB subunits. In vitro confirmation of nitrogenase-like features of a bacteriochlorophyll biosynthesis enzyme.

Fujita Y1, Bauer CE.
Abstract

Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to green (form chlorophyll) in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. However, unlike the well characterized features of nitrogenase, there has been no previous biochemical characterization of dark protochlorophyllide reductase. In this study, we report the first reproducible demonstration of dark protochlorophyllide reductase activity from purified protein subunits that were isolated from the purple nonsulfur photosynthetic bacterium Rhodobacter capsulatus. Two of the three subunits (Bchl and BchN) were expressed in R. capsulatus as S tag fusion proteins that facilitated affinity purification. The third subunit (BchB) was co-purified with the BchN protein indicating that BchN and BchB proteins form a tight complex. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. The similarity of dark protochlorophyllide reductase to nitrogenase is discussed.

LOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOL.

LOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOL.

LOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOL.

You didn't check shit. I rest my case.
 
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