The Elshamah mega-thread

[Dragan Glas]

Greetings,

The improbable-odds-makes-it-impossible argument...

Given that you don't know what the odds are, simply assuming/claiming that "it's impossible" isn't a rational argument against evolution.

Kindest regards,

James

 

[Elshamah]

Greetings,

The improbable-odds-makes-it-impossible argument...

Given that you don't know what the odds are, simply assuming/claiming that "it's impossible" isn't a rational argument against evolution.

Kindest regards,

James

of course we know the odds.

Origin and evolution of the genetic code: the universal enigma
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made.

Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.

http://reasonandscience.heavenforum.org/t2001-origin-and-evolution-of-the-genetic-code-the-universal-enigma

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/

DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

Fazale Rana wrote in his book Cell's design: In 1968, Nobel laureate Francis Crick argued that the genetic code could not undergo significant evolution. His rationale is easy to understand. Any change in codon assignments would lead to changes in amino acids in every polypeptide made by the cell. This wholesale change in polypeptide sequences would result in a large number of defective proteins. Nearly any conceivable change to the genetic code would be lethal to the cell.

Even if the genetic code could change over time to yield a set of rules that allowed for the best possible error-minimization capacity, is there enough time for this process to occur? Biophysicist Hubert Yockey addressed this question. He determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the universal genetic code found in nature. The maximum time available for it to originate was estimated at 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, natural selection lacks the time necessary to find the universal genetic code.

http://www.doesgodexist.org/NovDec09/Information-Function.html

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

 

[Dragan Glas]

Greetings,

Greetings,

The improbable-odds-makes-it-impossible argument...

Given that you don't know what the odds are, simply assuming/claiming that "it's impossible" isn't a rational argument against evolution.

Kindest regards,

James

of course we know the odds.

Origin and evolution of the genetic code: the universal enigma
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293468/

In our opinion, despite extensive and, in many cases, elaborate attempts to model code optimization, ingenious theorizing along the lines of the coevolution theory, and considerable experimentation, very little definitive progress has been made.

Summarizing the state of the art in the study of the code evolution, we cannot escape considerable skepticism. It seems that the two-pronged fundamental question: “why is the genetic code the way it is and how did it come to be?”, that was asked over 50 years ago, at the dawn of molecular biology, might remain pertinent even in another 50 years. Our consolation is that we cannot think of a more fundamental problem in biology.

So, we don't know the answer yet - that doesn't mean we'll never know.

http://reasonandscience.heavenforum.org/t2001-origin-and-evolution-of-the-genetic-code-the-universal-enigma

The genetic code is nearly optimal for allowing additional information within protein-coding sequences
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1832087/

DNA sequences that code for proteins need to convey, in addition to the protein-coding information, several different signals at the same time. These “parallel codes” include binding sequences for regulatory and structural proteins, signals for splicing, and RNA secondary structure. Here, we show that the universal genetic code can efficiently carry arbitrary parallel codes much better than the vast majority of other possible genetic codes. This property is related to the identity of the stop codons. We find that the ability to support parallel codes is strongly tied to another useful property of the genetic code—minimization of the effects of frame-shift translation errors. Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information.

if we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.

Above, the science - note the last sentence, particularly the highlighted part.

And then you add the pseudo-science of creationism/ID...

Fazale Rana wrote in his book Cell's design: In 1968, Nobel laureate Francis Crick argued that the genetic code could not undergo significant evolution. His rationale is easy to understand. Any change in codon assignments would lead to changes in amino acids in every polypeptide made by the cell. This wholesale change in polypeptide sequences would result in a large number of defective proteins. Nearly any conceivable change to the genetic code would be lethal to the cell.

Even if the genetic code could change over time to yield a set of rules that allowed for the best possible error-minimization capacity, is there enough time for this process to occur? Biophysicist Hubert Yockey addressed this question. He determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the universal genetic code found in nature. The maximum time available for it to originate was estimated at 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, natural selection lacks the time necessary to find the universal genetic code.

Permutations don't count - what you need to know are the viable combinations.

These determine which work, and which don't.

Thus any claims to "impossible odds" fall flat on their face.

http://www.doesgodexist.org/NovDec09/Information-Function.html

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

And, again, the nonsensical probabilities being calculated and trotted out as "fact". :roll:

Kindest regards,

James

 

[Rumraket]

No. In fact trial and error is even how designers work. Evolution is an extremely powerful designer that can design things more complicated and more intricate than any human team of engineers ever will.

baseless assertion based on wishful thinking and blatant ignorance of the subject. Not even worth to refute...... :roll:

That's it? This is your reponse? :lol:

 

[Rumraket]

And, as has been asked throughout numerous threads, it is up to creationists to show what stops the same biochemical reactions underlying micro-evolution from occurring resulting in new species.

What natural "barrier" stops speciation?


James

James,

speciation is a proven fact. change above species is not.

Speciation IS change above the species level. That's literally what it means.

 

[Rumraket]

It's just religion, not science - as the judge in the Dover trial ruled.

Kindest regards,

James

James

when you have scientific evidence that macro evolution is a viable mechanism for biodiversity, let me know.

http://www.talkorigins.org/faqs/comdesc/

29+ Evidences for Macroevolution

The Scientific Case for Common Descent

Version 2.89
Copyright © 1999-2012 by Douglas Theobald, Ph.D.
Last modified
Permission is granted to copy and print these pages in total for non-profit personal, educational, research, or critical purposes.​

Introduction

Evolution, the overarching concept that unifies the biological sciences, in fact embraces a plurality of theories and hypotheses. In evolutionary debates one is apt to hear evolution roughly parceled between the terms "microevolution" and "macroevolution". Microevolution, or change beneath the species level, may be thought of as relatively small scale change in the functional and genetic constituencies of populations of organisms. That this occurs and has been observed is generally undisputed by critics of evolution. What is vigorously challenged, however, is macroevolution. Macroevolution is evolution on the "grand scale" resulting in the origin of higher taxa. In evolutionary theory, macroevolution involves common ancestry, descent with modification, speciation, the genealogical relatedness of all life, transformation of species, and large scale functional and structural changes of populations through time, all at or above the species level (Freeman and Herron 2004; Futuyma 1998; Ridley 1993).

Universal common descent is a general descriptive theory concerning the genetic origins of living organisms (though not the ultimate origin of life). The theory specifically postulates that all of the earth's known biota are genealogically related, much in the same way that siblings or cousins are related to one another. Thus, universal common ancestry entails the transformation of one species into another and, consequently, macroevolutionary history and processes involving the origin of higher taxa. Because it is so well supported scientifically, common descent is often called the "fact of evolution" by biologists. For these reasons, proponents of special creation are especially hostile to the macroevolutionary foundation of the biological sciences.

This article directly addresses the scientific evidence in favor of common descent and macroevolution. This article is specifically intended for those who are scientifically minded but, for one reason or another, have come to believe that macroevolutionary theory explains little, makes few or no testable predictions, is unfalsifiable, or has not been scientifically demonstrated.

There you go.

 

[Elshamah]

ahm

Rumraket

running away from the other thread at Skeptical Zone ??

Well, you have not answered to this.....

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function, and no survival advantage of the organism would be provided. Natural selection could not operate to favor a system with anything less than all seventeen enzymes being present, functioning and processing all intermediate products to get the final product. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? And even if everything were in place correctly, and chlorophyll were synthesized correctly, so what ? Unless chlorophyll AND all other proteins and protein complexes were fully in place, fully evolved and functional, correctly interlocked and working in a interdependent manner, photosynthesis would not happen. But even if photosynthesis would happen, so what ? Why would the organism chose such a extremely complex mechanism, if it was surviving just fine previously ? Furthermore, you do not just need the right enzymes. For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or / and evolution, since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there’s no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it’s not that it doesn’t function as well – it doesn’t function at all!

 

[SpecialFrog]

Elshamah, this alleged problem evolution has been addressed multiple times. Why are you unwilling to attempt to engage with any of the responses?

 

[Elshamah]

Elshamah, this alleged problem evolution has been addressed multiple times. Why are you unwilling to attempt to engage with any of the responses?

post the responses here . I don't know them.

 

[Rumraket]

ahm

Rumraket

running away from the other thread at Skeptical Zone ??

Well, you have not answered to this.....

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function, and no survival advantage of the organism would be provided. Natural selection could not operate to favor a system with anything less than all seventeen enzymes being present, functioning and processing all intermediate products to get the final product. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? And even if everything were in place correctly, and chlorophyll were synthesized correctly, so what ? Unless chlorophyll AND all other proteins and protein complexes were fully in place, fully evolved and functional, correctly interlocked and working in a interdependent manner, photosynthesis would not happen. But even if photosynthesis would happen, so what ? Why would the organism chose such a extremely complex mechanism, if it was surviving just fine previously ? Furthermore, you do not just need the right enzymes. For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or / and evolution, since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there’s no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it’s not that it doesn’t function as well – it doesn’t function at all!

I'm sorry I don't have time to write out detailed responses to all your copy-paste.

You see the inequality in our modus operandi here don't you? You copy-paste shit off your website and I have to read your copy-paste, think about what it says and then compose a reponse and type it out in a way you can understand. Naturally I cannot devote as much time to debunking your irrelevant blather as would be required when all you have to do is just copy-paste shit time and again.

In this particular case, your "response" about chlorophyll is functionally refuted by the very fucking post you are responding to. But since you are responding with crap that has already been refuted in substance, the reason you are making this post is because you didn't understand how or why it has been refuted. Which means I now have to spend a lot of time going into depth and cutting it all into little pieces you can understand.

And what will you do when I do that? You will copy-paste even more irrelevant blather, with no further substance than the shit you have already copy-pasted. This is not a discussion or a debate, this is just "I have all this shit you need to debunk, and every time you debunk something I will just move on to copy-paste another wall of text".

It's frankly idiotic and childish. You are a child, your religion has made you behave like a child. You don't invenst any mental effort into this, there is no attempt to understand or to criticize by using your thoughts and forming arguments. You are only doing this so you can "prove" god is required to explain life. You are not equipped to explore whether that is actually true. You come here with a conclusion already in mind seeking to make "converts", you don't come here to actually test your own beliefs.

 

[Rumraket]

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function

False. There is absolutely no reason to think the intermediate steps in the biosynthesis of chlorophyll are without function. This is just something you assume. We know it to be diametrically opposite to demonstrable fact. The precursors to "chlorophyll" in all it's forms, are all also functional photoreactive molecules.

In fact most chlorophyll belongs to a class of molecules called Porphyrins, ALL OF WHICH have functions in biology. A subclass of the Porphyrins is Chlorins where we find Chlorophyll. Chlorophyll exists in 11 different types, so you're claiming that there's just "chlorophyll" and that there's no way the biosynthesis of "chlorophyll" can produce a functional product without getting all the way to the last step in... what pathway in particular? What chlorophyll producing species are you talking about? There are many different ones, and they all produce multiple different chlorophylls. And they're all functional.

And they're all functional every step of the way, from the entry into the chlorophyll pathway at the conversion of the first porphyrin.

, and no survival advantage of the organism would be provided.

It took me 20 fucking seconds on google to refute your claim. With a reference from 1965. In other words, your idiotic copy-pasted bullshit has been known to be false for FIFTY YEARS.

Evolution of Heme and Chlorophyll

Scroll down to the section entitled: "Elaboration of the photochemical function" and read from there. After you are done, you can go and delete this idiotc copy-pasta from your "library" of quotemines and never speak about it again.
Let me post the section here so everyone can see how stupid one would have to be to copy-paste the shit you did:

 

[Rumraket]

Edit: Was missing a page.

 

[Rumraket]

So let us attempt to evolve a bicycle into a motorcycle by the gradual accumulation of mutations. Suppose that a factory produced bicycles, but that occasionally there was a mistake in manufacture. Let us further suppose that if the mistake led to an improvement in the bicycle, then the friends and neighbors of the lucky buyer would demand similar bikes, and the factory would retool to make the mutation a permanent feature. So, like biological mutations, successful mechanical mutations would reproduce and spread. If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle. So if the factory mistakenly increased the size of a nut or decreased the diameter of a bolt, or added an extra wheel onto the front axle or left off the rear tire, or put a pedal on the handlebars or added extra spokes, and if any of these slight changes improved the bike ride, then the improvement would immediately be noticed by the buying public and the mutated bikes would, in true Darwinian fashion, dominate the market. Given these conditions, can we evolve a bicycle into a motorcycle? We can move in the right direction by making the seat more comfortable in small steps, the wheels bigger, and even (assuming our customers prefer the «biker» look) imitating the overall shape in various ways. But a motorcycle depends on a source of fuel, and a bicycle has nothing that can be slightly modified to become a gasoline tank. And what part of the bicycle could be duplicated to begin building a motor? Even if a lucky accident brought a lawnmower engine from a neighboring factory into the bicycle factory, the motor would have to be mounted on the bike and be connected in the right way to the drive chain. How could this be done step-by-step from bicycle parts? A factory that made bicycles simply could not produce a motorcycle by natural selection acting on variation—by «numerous, successive, slight modifications»—and in fact there is no example in history of a complex change in a product occurring in this manner.

How lucky we are that nobody ever proposed the motorcycle evolved from the bicycle.

Gears, wheels and handlebars aren't molecules. They do not have any of the same properties of electromagnetic attraction or repulsion, they don't catalyze chemical reactions, they do not have structural affinities and can randomly bind together in complex ways simply by altering their shape. Random chunks of plastic and metal doesn't stick together in the same way molecules do. A lump of plastic of some particular shape or composition will not chemicall alter a piece of metal next to it in the same way a biological catalyst will modify a substrate.

There is nothing in this utterly shite analogy that has any relevance to biology or biochemistry, which is why it fails as an analogy. It is superficial in it's treatment of how organisms function, drawing only an analogy between the idea that they are made of "multiple parts that fit together". But beyond this superficial similarity there is nothing left of commonality between them.

 

[Rumraket]

The development of new functions is the only thing important for evolution.

No it isn't. The only thing important for evolution is reproductive success, which can happen entirely without "development of new functions".

What is a "new" function anyway? How different from function A must function B be, before we can label it new? No IDcreationist have ever answered this question in a substantive way.

I predict you won't be the first.

 

[Rumraket]

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

This line of argument is unfathomably dumb. You cannot calculate the "probabilistic resource" of the universe by measuring the number of elementary particle interactions, what a supremely stupid line of thought.

Let's prove it by physical example: The szostak lab produced a library of 6 x 10^12 proteins each containing 80 contiguous random amino acids.

What is the probability that they got the specific set of 6x10^12 proteins of 80 random amino acids in length that they got?

It is one in 20 (amino acid alphabet size) ^ (80 (sequence lengths) * 6x10^12 (total number of proteins of 80 length)) = 10^(10^14.79552854685122)

So they got a result with a probability of 1 in [sub]10[/sub]10[sup]14.79552854685122[/sup]


The probability of this event was so small you could not type the decimal value if you wrote a million digits on every elementary particle in the known universe.

In other words, if the bullshit math you copy-pasted was right the result attained from the Szostak lab's experiment should have been impossible. Literally impossible.

 

[Rumraket]

Yet, the simplest known free-living organism, Mycoplasma genitalium, has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451.

By the way, the math there is wrong.

The odds of producing a 347 amino acid protein is 1 in 20[sup]347[/sup], which is roughly 1 in 2.037×10[sup]390[/sup].

One wonders how the hell the numbnut you got that shit from could ever get a power of 451. He's wrong by sixty orders of magnitude.

One wonders why you'd copy-paste incorrect math you could have double-check yourself. You didn't do that, you just believed it.

 

[Rumraket]

Another study by Axe and Ann Gauger found that merely converting one enzyme into a closely related enzyme -- the kind of conversion that evolutionists claim can easily happen -- would require a minimum of seven simultaneous changes,6exceeding the probabilistic resources available for evolution over the Earth's history. This data implies that many biochemical features are so complex that they would require many mutations before providing any advantage to an organism, and would thus be beyond the "edge" of what Darwinian evolution can do.

Axe and Gauger?

You mean the two people employed to be liars for doctrine, by deliberately NOT properly testing evolutionary postulates, and never actually searching for design at all? Their entire research output has been nothing but attempts to falsify "neo-Darwinism" by deliberately constructing strawmen of the process of evolution, then declaring something along the lines that evolution is not up to the job when their deceptive strawman is knocked down.

Case in point, let's take a loot at the work of Discovery institute bioengineers Douglax Axe and Ann Gauger, who in their ironic attempt to disprove evolution, end up disproving design and confirming evolution (as we shall see when we take a hard look at what they actually did, and how the research SHOULD have been done).

This is a "paper" from Doug Axe and Ann Gauger of the BioLogic-institute:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K. Gauger, Douglas D. Axe

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

The great irony here is that Axe and Gauger inadvertently test one of the popular (and very ad-hoc) design-postulates, but deliberately ignore the evolutionary postulate.

They don't do ancestral sequence reconstruction and try to infer the most probable ancestral sequence using phylogenetic maximum likelyhood trees (as evolutionary biologists would have them do). Instead, they do what many design-proponents postulate their designer did, they take one sequence (Kbl2) and try to directly convert it into another distantly related structural homologue (BioF2), mutation by mutation.

They discover that doing this BREAKS THE FUCKING ENZYME. It stops working. Seemingly affirming the many claims of the creationists and ID proponents, that mutations invariably destroy function, that there are too large distances of nonfunctionality between isolated "islands" of function in the conceptual phenotypical space of protein functions.

But this is not what evolution postulates took place, this is NOT what is done with ancestral sequence reconstruction. Here both sequences (actually more, you need 3 orthologues sequences or more to do ancestral sequence reconstruction) evolved from a different common acestor to both of them, they did not change directly one into the other. There was a long history of divergence from a common ancestor, that took a totally different evolutionary route than the direct conversion Axe and Gauger is attempting, and the result of which they deceptively use to insinuate falsifies evolution. This is DELIBERATE INCOMPETENCE, they're PAID to be liars.

I made a nice little drawing for you:

¨
These people simply cannot be trusted to accurately report or even test the facts of the matter. It's all part of an elaborate ruse to produce religious converts. Stop deluding yourself.

There are hundreds of excellent publications by actual competent evolutionary biologists and biochemists, utilizing ancestral sequence reconstruction to test ancient versions of extant proteins, and they all CURIOUSLY find functional intermediates, contrary to Axe and Gauger's deceptive pretensions.

But when actual ancestral sequence reconstruction methods are used, functional sequences ARE found. As demonstrated aptly in all the papers I linked earlier. Therefore we have good reason to think the extant homologous proteins actually DID evolve FROM these resurrected by phylogenetic inference-sequences, and were NOT created through simple mutational change from one into the other.

What makes the results of these kinds of ancestor reconstructions even more robust is when they use resurrected nodes to further infer even more distantly related ancestral sequences. It would be absurd to postulate that you can keep inferring ancestors from already inferred ancestors and still get functional protein products if the reconstructed evolutionary relationship didn't actually take place.

 

[Elshamah]

ahm

Rumraket

running away from the other thread at Skeptical Zone ??

Well, you have not answered to this.....

Chlorophyll biosynthesis is a complex pathway with 17 highly specific steps, of which eight last steps are used by specific enzymes uniquely in this pathway.

Even if we find in the sequence space the right steps to make the enzymes required to permit the synthesis of the products of these intermediate steps, so what ? the intermediate products would have no function, and no survival advantage of the organism would be provided. Natural selection could not operate to favor a system with anything less than all seventeen enzymes being present, functioning and processing all intermediate products to get the final product. What evolutionary process could possibly produce complex sophisticated enzymes that generate nothing useful until the whole process is complete? And even if everything were in place correctly, and chlorophyll were synthesized correctly, so what ? Unless chlorophyll AND all other proteins and protein complexes were fully in place, fully evolved and functional, correctly interlocked and working in a interdependent manner, photosynthesis would not happen. But even if photosynthesis would happen, so what ? Why would the organism chose such a extremely complex mechanism, if it was surviving just fine previously ? Furthermore, you do not just need the right enzymes. For the assembly of a biological system of multiple parts, following steps must be explained : the origin of the genome information to produce all subunits and assembly cofactors. Parts availability, synchronization, manufacturing and assembly coordination through genetic information, and interface compatibility. The individual parts must precisely fit together. All these steps are better explained through a super intelligent and powerful designer, rather than mindless natural processes by chance, or / and evolution, since we observe all the time minds capabilities producing machines and factories, producing machines and end products.

everything *has* to be in place at once or else an organism has no survival advantage. The thing is, there’s no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. The necessity for the parts of the system to be in place all at once is simply evidence of creation. Photosynthesis missing one piece (like chlorophylls) is like a car missing just one piece of the drive train (such as a differential); it’s not that it doesn’t function as well – it doesn’t function at all!

I'm sorry I don't have time to write out detailed responses to all your copy-paste.

You see the inequality in our modus operandi here don't you? You copy-paste shit off your website and I have to read your copy-paste, think about what it says and then compose a reponse and type it out in a way you can understand. Naturally I cannot devote as much time to debunking your irrelevant blather as would be required when all you have to do is just copy-paste shit time and again.

In this particular case, your "response" about chlorophyll is functionally refuted by the very fucking post you are responding to. But since you are responding with crap that has already been refuted in substance, the reason you are making this post is because you didn't understand how or why it has been refuted. Which means I now have to spend a lot of time going into depth and cutting it all into little pieces you can understand.

And what will you do when I do that? You will copy-paste even more irrelevant blather, with no further substance than the shit you have already copy-pasted. This is not a discussion or a debate, this is just "I have all this shit you need to debunk, and every time you debunk something I will just move on to copy-paste another wall of text".

It's frankly idiotic and childish. You are a child, your religion has made you behave like a child. You don't invenst any mental effort into this, there is no attempt to understand or to criticize by using your thoughts and forming arguments. You are only doing this so you can "prove" god is required to explain life. You are not equipped to explore whether that is actually true. You come here with a conclusion already in mind seeking to make "converts", you don't come here to actually test your own beliefs.

Nothing of what you posted scratches even on the surface of my argument. The last 8 steps require enzymes, that are not used in any other pathway. I have checked. You can do the same. Check and see. So there is no reason to assume they were co-opted from somewhere else.

But even IF that were the case, so what ??

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

Furthermore, the heme biosynthesis pathway is also irreducible complex :

The heme biosynthesis pathway is irreducible complex.

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.


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

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

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

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

Yes, i copy/paste from my virtual library, but these are MY arguments.

And, come on , Rumraket, you have been able to stop behaving like a teenager on the schoolyard........ it would be better if you keep behaving like a adult.

 

[Mr_Wilford]

To make an analogy of this thread:

Elshamah claims pebbles cannot be formed by natural processes.

When shown theyve been observed to, he simply comes back with "Yeah well, you can explain the pebble but how can you explain this boulder?? Checkmate evilutionaughts."

He commits the same fallacy, just ups the scale of the object

 

[Mr_Wilford]

Another study by Axe and Ann Gauger found that merely converting one enzyme into a closely related enzyme -- the kind of conversion that evolutionists claim can easily happen -- would require a minimum of seven simultaneous changes,6exceeding the probabilistic resources available for evolution over the Earth's history. This data implies that many biochemical features are so complex that they would require many mutations before providing any advantage to an organism, and would thus be beyond the "edge" of what Darwinian evolution can do.

Axe and Gauger?

You mean the two people employed to be liars for doctrine, by deliberately NOT properly testing evolutionary postulates, and never actually searching for design at all? Their entire research output has been nothing but attempts to falsify "neo-Darwinism" by deliberately constructing strawmen of the process of evolution, then declaring something along the lines that evolution is not up to the job when their deceptive strawman is knocked down.

Case in point, let's take a loot at the work of Discovery institute bioengineers Douglax Axe and Ann Gauger, who in their ironic attempt to disprove evolution, end up disproving design and confirming evolution (as we shall see when we take a hard look at what they actually did, and how the research SHOULD have been done).

This is a "paper" from Doug Axe and Ann Gauger of the BioLogic-institute:
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K. Gauger, Douglas D. Axe

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs--the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations--transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

The great irony here is that Axe and Gauger inadvertently test one of the popular (and very ad-hoc) design-postulates, but deliberately ignore the evolutionary postulate.

They don't do ancestral sequence reconstruction and try to infer the most probable ancestral sequence using phylogenetic maximum likelyhood trees (as evolutionary biologists would have them do). Instead, they do what many design-proponents postulate their designer did, they take one sequence (Kbl2) and try to directly convert it into another distantly related structural homologue (BioF2), mutation by mutation.

They discover that doing this BREAKS THE FUCKING ENZYME. It stops working. Seemingly affirming the many claims of the creationists and ID proponents, that mutations invariably destroy function, that there are too large distances of nonfunctionality between isolated "islands" of function in the conceptual phenotypical space of protein functions.

But this is not what evolution postulates took place, this is NOT what is done with ancestral sequence reconstruction. Here both sequences (actually more, you need 3 orthologues sequences or more to do ancestral sequence reconstruction) evolved from a different common acestor to both of them, they did not change directly one into the other. There was a long history of divergence from a common ancestor, that took a totally different evolutionary route than the direct conversion Axe and Gauger is attempting, and the result of which they deceptively use to insinuate falsifies evolution. This is DELIBERATE INCOMPETENCE, they're PAID to be liars.

I made a nice little drawing for you:

¨
These people simply cannot be trusted to accurately report or even test the facts of the matter. It's all part of an elaborate ruse to produce religious converts. Stop deluding yourself.

There are hundreds of excellent publications by actual competent evolutionary biologists and biochemists, utilizing ancestral sequence reconstruction to test ancient versions of extant proteins, and they all CURIOUSLY find functional intermediates, contrary to Axe and Gauger's deceptive pretensions.

But when actual ancestral sequence reconstruction methods are used, functional sequences ARE found. As demonstrated aptly in all the papers I linked earlier. Therefore we have good reason to think the extant homologous proteins actually DID evolve FROM these resurrected by phylogenetic inference-sequences, and were NOT created through simple mutational change from one into the other.

What makes the results of these kinds of ancestor reconstructions even more robust is when they use resurrected nodes to further infer even more distantly related ancestral sequences. It would be absurd to postulate that you can keep inferring ancestors from already inferred ancestors and still get functional protein products if the reconstructed evolutionary relationship didn't actually take place.

So their "common design" idea was just blown out of the water?