SpecialFrog
New Member
Rumraket, I read these posts and found them insightful even if Elshamah is unlikely to do so.
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All of your arguments have been refuted in-substance.Elshamah said:Nothing of what you posted scratches even on the surface of my argument.
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.Elshamah said:The last 8 steps require enzymes, that are not used in any other pathway.
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?Elshamah said:I have checked.
Tell me where and how you did your "checking" and I will replicate it.Elshamah said:You can do the same. Check and see.
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.Elshamah said:So there is no reason to assume they were co-opted from somewhere else.
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:But even IF that were the case, so what ??
That is false and the Lenski Long-term Evolution Experiment with E coli proved it.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
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.
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: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.
False, the molecule synthesized by the 7th step is functional. So is the one synthesized by the 6th step. And so on.Elshamah said:Questions:
What good would there be, if the pathway would go only up to the 7th step ? 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, 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. 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.Elshamah said:What good would there be for red bloodcells without hemoglobin, transporting oxygen to the cells in the body ? none
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]
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 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.
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.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.
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: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 ?
.. 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.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!Elshamah said:Yes, i copy/paste from my virtual library, but these are MY arguments.
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.
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.
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.
Did you just outright lie when you say you "have checked"? Yeah, you did. You haven't checked shit.
DutchLiam84 said: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!Elshamah said:Yes, i copy/paste from my virtual library, but these are MY arguments.
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.
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.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.
:lol: I actually lol-ed.itsdemtitans said:You nailed it!
Then there are no IC systems known. Your definition is begging the question.Elshamah said:You should have learned by now that ic and evolution exclude each other. If a system can evolve, its not ic.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.
READ THE PAPER I LINKED.Elshamah said:LOL. And you know that how exactly ??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.
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?Elshamah said: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.Rumraket said:READ THE PAPER I LINKED.
Awww boo-hoo. Stop crying and answer my questions.Elshamah said:Look, kid. I have no patience to argue with the rest of your drivel, if you throw the lie canard.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.
Still citing Behe in support of ID - even though he couldn't defend it in court.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.
It seems Behe's own beliefs in ID/creationism are failing - perhaps his son has finally gotten through to him.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.
Rumraket said:Then there are no IC systems known. Your definition is begging the question.
READ THE PAPER I LINKED.
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.
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.
My statement stands uncontested.Elshamah said:haha.Rumraket said:Then there are no IC systems known. Your definition is begging the question.
Rumraket said:My statement stands uncontested.
I already did.Elshamah said:quote the relevant part which you think substantiates your assertions, and we'll see.
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:So how about you give a example of what any of the last eight enzymes did prior being used in chlorophyll synthesis ?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?
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:Heme does not use ANY of the last eight enzymes in the pathway......Rumraket said:There was an organism without chlorophyll, but with Heme.
There is no rebuttal here, just mindless posturing and blind dismissal. Well done, what a powerful "argument" you have here.Elshamah said: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 ?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.
Where? How did you check?Elshamah said:Check by yourself if you do not believe me.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?
You say they are false. Okay, then tell me how you checked it.Elshamah said:Keeping with false acusations ?Rumraket said:Did you just outright lie when you say you "have checked"? Yeah, you did.
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:But even If ..... lets suppose they had other functions, So what ??
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.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...
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
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: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.
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:
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.
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
Rumraket said:They could have arisen de novo with one or two at first, then the rest arisen by duplication.
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.