A timeline of the first life

Coroama · **#301** by **Coroama** » Dec 27, 2013 9:37 pm

Rumraket wrote:

Go and check it out if you are really interested in the evidence, instead of apologetics:
http://molbio.mgh.harvard.edu/szostakweb/publications.html.

Rather than link to a number of scientific papers, how about you quote the relevant part that shows your assertion to be true ?
I have yet to see scientific evidence how natural selection can produce coded information stored in the genome.

Explanations like these are much more convincing to me :

http://www.ucg.org/science/dna-tiny-cod ... evolution/

As Lee Strobel explains: "The data at the core of life is not disorganized, it's not simply orderly like salt crystals, but it's complex and specific information that can accomplish a bewildering task—the building of biological machines that far outstrip human technological capabilities" (p. 244).

For instance, the precision of this genetic language is such that the average mistake that is not caught turns out to be one error per 10 billion letters. If a mistake occurs in one of the most significant parts of the code, which is in the genes, it can cause a disease such as sickle-cell anemia. Yet even the best and most intelligent typist in the world couldn't come close to making only one mistake per 10 billion letters—far from it.

So to believe that the genetic code gradually evolved in Darwinian style would break all the known rules of how matter, energy and the laws of nature work. In fact, there has not been found in nature any example of one information system inside the cell gradually evolving into another functional information program.

Michael Behe, a biochemist and professor at Pennsylvania's Lehigh University, explains that genetic information is primarily an instruction manual and gives some examples.

He writes: "Consider a step-by-step list of [genetic] instructions. A mutation is a change in one of the lines of instructions. So instead of saying, "Take a 1/4-inch nut," a mutation might say, "Take a 3/8-inch nut." Or instead of "Place the round peg in the round hole," we might get "Place the round peg in the square hole" . . . What a mutation cannot do is change all the instructions in one step—say, [providing instructions] to build a fax machine instead of a radio" ( Darwin's Black Box , 1996, p. 41).

We therefore have in the genetic code an immensely complex instruction manual that has been majestically designed by a more intelligent source than human beings.

Even one of the discoverers of the genetic code, the agnostic and recently deceased Francis Crick, after decades of work on deciphering it, admitted that "an honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going"

ElDiablo · **#302** by **ElDiablo** » Dec 27, 2013 9:46 pm

Coroama wrote: But it seems a common strategy here to tap the ears , when the evidence leads in a undesired direction.

What a crock of shit.
The members here who are knocking down your lies left and right are also putting your quotemines into the proper context and demonstrating just how absolutely clueless you are about most everything you post.

Morton's Demon is lodged so fucking deep in your brain that if brain surgery was performed to remove it, you wouldn't have a neuron left.

hackenslash · **#303** by **hackenslash** » Dec 27, 2013 10:25 pm

Coroama wrote:
Bribase wrote:
But of course that's nonsense, James. Like all processes in biology the material, and the patterns it is arranged into, are the information.

Well , no.

In the same way, as the special arrangement of the letters of the alphabet constitute the information, the special arrangement of the nucloetides in the Genome constitute the information in the cell. I know, indoctrinated naturalists have a hard time to admit this, but it is very clear in all biology literature.

https://www.prote.in/en/feed/2012/11/dn ... oGXXeLQ7gE

Scientists have been looking to unlock the memory storage potential of DNA strands for a decade now. Over at Harvard it looks like they've finally cracked it with a breakthrough that allows over 700 terabytes of data to be stored on a single gram of DNA. Treating the genetic code much like the binary system traditional computer memory uses, they've successfully replicated the storage capacity of over 14,000 Bluray discs, or 151 kilograms of hard drives on a surface area smaller than the tip of your little finger.

Already dealt with this. DNA can be used for digital storage, because it is defined by a range of very specific fixed states. Do you know what a logic gate is?

Rumraket · **#304** by **Rumraket** » Dec 27, 2013 10:26 pm

Coroama wrote:
Rumraket wrote:

Go and check it out if you are really interested in the evidence, instead of apologetics:
http://molbio.mgh.harvard.edu/szostakweb/publications.html.

Rather than link to a number of scientific papers, how about you quote the relevant part that shows your assertion to be true ?

I have done nothing else in this thread, but you ignore it every time and just quote some stupid creationist making a blind assertion or quotemine a scientist with some irrelevant statement about the information storage capacity of DNA or the complexity of a modern cell.

I already told you where to look in that publication list and what to look for, I trust you're not too stupid or lazy to then go and fucking read it?

Coroama wrote:I have yet to see scientific evidence how natural selection can produce coded information stored in the genome.

Explanations like these are much more convincing to me :

http://www.ucg.org/science/dna-tiny-cod ... evolution/

As Lee Strobel explains: "The data at the core of life is not disorganized, it's not simply orderly like salt crystals, but it's complex and specific information that can accomplish a bewildering task—the building of biological machines that far outstrip human technological capabilities" (p. 244).

Explanations like what? There's no explanation there, just a statement about the information carrying capacity of "life" and "biological machines". What's "convincing" about it?

You keep endlessly quoting these total irrelevancies as if they mean something or are relevant to the subject of this thread. Or as if they are relevant to the many blind assertions your creationist liars make up.

Oh my god it's so complex, see how complex that is? That is so complex, holy fuck is it complex. Irreducibly complex, Oh my oh my, so complex it is. Allakhazam - therefore god.

Also, "machines", "information", "storage capacity", "algorithmic programming", "code and language system", "memory in DNA", "error correction" and "double helix". Omg omg, so complex, sooooo so so compelx, also btw... "shannon uncertainty" - Woooo, whoa, wow! Fancy lights, gasping audience. Allakhazam - therefore god.

It is SO unbelievably stupid to see you quote this ridiculous crap over and over gain as if these terms magically changes anything.

Coroama wrote:For instance, the precision of this genetic language is such that the average mistake that is not caught turns out to be one error per 10 billion letters. If a mistake occurs in one of the most significant parts of the code, which is in the genes, it can cause a disease such as sickle-cell anemia. Yet even the best and most intelligent typist in the world couldn't come close to making only one mistake per 10 billion letters—far from it.

And yet, mistakes still happen - and they result in evolutionary change.

: Billede1.png (149.52 KiB) Viewed 1858 times

This evidence isn't going to disappear. Over 600 beneficial mutations in 50.000 generations of evolution.

Coroama wrote:So to believe that the genetic code gradually evolved in Darwinian style would break all the known rules of how matter, energy and the laws of nature work.

What rules are those specifically, that governs how "matter, energy and the laws of nature" which prevents the evolution of a genetic code? I've never heard of those "rules".

I read the assertion, but all it is is an assertion. Where is the evidence that this claim is true?

If the claim really was true, why do we have evidence that the genetic code is an evolvable entity and why do we have evidence of an evolutionary history of the translation system? Explain why there is a contradiction between the blind assertion of your claim and the available evidence.

Coroama wrote:In fact, there has not been found in nature any example of one information system inside the cell gradually evolving into another functional information program.

What the fuck does that even mean, an "information system" evolving into another "functional information program"? This is just more meaningless technobabble you throw together with words you don't even fucking understand.

Nevertheless, we have evidence that the genetic code evolved. It's still there, still not dealt with, still just being ignored by creationist quoteminers and liars for doctrine.

Coroama wrote:Michael Behe, a biochemist and professor at Pennsylvania's Lehigh University, explains that genetic information is primarily an instruction manual and gives some examples.

He writes: "Consider a step-by-step list of [genetic] instructions. A mutation is a change in one of the lines of instructions. So instead of saying, "Take a 1/4-inch nut," a mutation might say, "Take a 3/8-inch nut." Or instead of "Place the round peg in the round hole," we might get "Place the round peg in the square hole" . . . What a mutation cannot do is change all the instructions in one step—say, [providing instructions] to build a fax machine instead of a radio" ( Darwin's Black Box , 1996, p. 41).

In one step? Who the fuck says it needs to happen in one step? Oh, Michael Behe? Well then he's simply full of shit. Nice strawman Michael Behe, and how well you punch it too. :roll:

Coroama wrote:We therefore have in the genetic code an immensely complex instruction manual that has been majestically designed by a more intelligent source than human beings.

Of course, if one starts with a faulty premise, one can derive any conclusion one wants. Unfortunately, the evidence is that the genetic code evolved.

Coroama wrote:Even one of the discoverers of the genetic code, the agnostic and recently deceased Francis Crick, after decades of work on deciphering it, admitted that "an honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going"

Oh look, the same irrelevant quote all over again. Notice the word "almost". Also, nobody here claims we know the origin of life, so that quote truly is still completely irrelevant.

The evidence that the genetic code evolved is still there, waiting for you to deal with it.

Coroama · **#305** by **Coroama** » Dec 28, 2013 4:05 am

Rumraket wrote:

The evidence that the genetic code evolved is still there, waiting for you to deal with it.

Despite your assertion you did, i am still waiting to see the relevant part of your papers , that present evidence without a doubt, that its possible. Where is it ? I hope you won't come up with funny papers that call for a frozen fucking accident.....

ElDiablo · **#306** by **ElDiablo** » Dec 28, 2013 4:09 am

Coroama wrote:
Rumraket wrote:

The evidence that the genetic code evolved is still there, waiting for you to deal with it.

Despite your assertion you did, i am still waiting to see the relevant part of your papers , that present evidence without a doubt, that its possible. Where is it ? I hope you won't come up with funny papers that call for a frozen fucking accident.....

This is hilarious coming from someone who accepts this as an explanation for the origin of life -> "let there be..."
Your world is upside down and backwards.

Rumraket · **#307** by **Rumraket** » Dec 28, 2013 9:38 am

Coroama wrote:
Rumraket wrote:

The evidence that the genetic code evolved is still there, waiting for you to deal with it.

Despite your assertion you did, i am still waiting to see the relevant part of your papers , that present evidence without a doubt, that its possible. Where is it ? I hope you won't come up with funny papers that call for a frozen fucking accident.....

Have anyone ever demonstrated instantaneous magical creation? No. Has anyone ever demonstrated the supernatural? No.
Has any observed phenomenon ever turned out to have a supernatural explanation so far? No.

Have we seen evolution in action? Yes. All the mechanisms of evolution are observed facts. And then there's evidence of an evolutionary history of the genetic code. You just sitting there and declaring blindly in your religiously motivated denial that this evidence has not been shown to you isn't going to make that evidence go away. Go back and read the paper you keep pretending doesn't exist.

By the way, can you explain what is meant by a frozen accident specifically with respect to the genetic code? What is a "frozen accident" about the code? Do you even understand what is meant by that term? Of course you don't. :roll:

Coroama · **#308** by **Coroama** » Dec 28, 2013 12:44 pm

Rumraket wrote:
Have anyone ever demonstrated instantaneous magical creation? No. Has anyone ever demonstrated the supernatural? No.
Has any observed phenomenon ever turned out to have a supernatural explanation so far? No.

Argument from incredulity. We can infere God's existence based on creation, and his revealed word, the bible.

And then there's evidence of an evolutionary history of the genetic code.

Thats what you are supposed to present .......

You just sitting there and declaring blindly in your religiously motivated denial that this evidence has not been shown to you isn't going to make that evidence go away. Go back and read the paper you keep pretending doesn't exist.

how about you present the BEST paper you have safed that you think has the most convincing arguments and shows in powerful way, that the dna code has evolved ? maibe you quote mine the relevant part, and we'll have a close look at it.

By the way, can you explain what is meant by a frozen accident specifically with respect to the genetic code? What is a "frozen accident" about the code? Do you even understand what is meant by that term? Of course you don't.

Since you do understand, please elucidate me. :thumbup:

Rumraket · **#309** by **Rumraket** » Dec 28, 2013 1:14 pm

Coroama wrote:
Rumraket wrote:
Have anyone ever demonstrated instantaneous magical creation? No. Has anyone ever demonstrated the supernatural? No.
Has any observed phenomenon ever turned out to have a supernatural explanation so far? No.

Argument from incredulity.

When there's no evidence, incredulity is justified. We should not believe that for which there is no evidence, and against which we actually have evidence.

Magic violates the laws of physics.

Coroama wrote:We can infere God's existence based on creation,

All of "creation" (what a fatuos, question-begging term) testifies that magic does not exist and is most probably nothing but a fantasy, a physical impossibility.

Upon completion of a thorough search, absense of evidence is evidence of absense. The evidence is as close to conclusive as it is possible to get.

Coroama wrote:and his revealed word, the bible.

The bible isn't evidence, the bible contains claims. It would take actual direct, empirical demonstration to justify believing the crap it says.

Extraordinary claims require extraordinary evidence, it says so in my old book isn't fucking evidence of anything.

Coroama wrote:
Rumraket wrote:And then there's evidence of an evolutionary history of the genetic code.

Thats what you are supposed to present .......

Here it is for the tenth fucking time:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072225

Go INTO THE FUCKING PAPER AND READ ABOUT IT. Structural phylogenomics, they resurrect he evolutionary history of key aspects of the translation system from the structures of the proteins and RNA's that work to achieve translation and protein synthesis. The entire history of the code is tied in with the interaction between the tRNA's and the aaRS active sites. This IS the code itself. They show which codons arose first, which amino acids they coded for, what the structures did before they became part of the modern translation system.

The evolutionary accretion of structure is the process by which molecules add parts such as substructures or structural modules (domains) to their molecular makeup. The process can take millions of years and is usually driven by improvements in biological function and stability [5.6]. Timelines that describe the gradual appearance of domain structures in evolution have shown that the editing and anticodon-binding domains of aaRSs are late additions to the central catalytic role of their aminoacylation domains [6], [7]. In these timelines, the relative ages of domains at three different levels of the structural hierarchy defined by the STRUCTURAL CLASSIFICATION OF PROTEINS [8], fold (F), fold superfamily (FSF), and fold family (FF), are derived from phylogenomic trees reconstructed from a census of domain structure in hundreds of fully sequenced genomes (reviewed in [5]). The phylogenomic strategy, which is summarized in Figure 1A, reconstructs history with high predictive power. The ages of protein domains explain known patterns of structural change [9] and organismal diversification [10], early evolution of molecular functions [11], links between geochemistry and metallome evolution [12], and the definition of a molecular clock that matches fossil and geochemical records [13], [14]. For example, the age of single-domain enzymes established that aerobic metabolism appeared ~2.9 billion years (Gy) ago [13] and that Mn catalase was the most likely culprit of planet oxygenation [14], findings that align with inferences from geology and geochemistry [15]. Domain history is also compatible with studies of physical clustering of genes in genomes [16], links between ancient sequence motifs in loops and domain structures [17], conservation of loop motifs [18] and an analysis of gene birth, transfer, duplication and loss in gene families across evolutionary history [19]. Network connectivity in these studies suggest that a central metabolic core that includes nucleotide/phosphate binding functions typical of ABC transporters and nucleotide interconversion reactions, is more ancient that rings of gene neighbors and clusters of ancient motifs organized around aaRSs and even more ancient than a gene expansion enriched in electron-transport and respiratory functions that occurred ~2.9–3.3 Gy ago. The emergence of the most ancient functions in timelines of domains suggests that the first proteins were most likely hydrolase and transferase enzymes involved in nucleotide interconversion, storage and recycling of chemical energy through high energy phosphate transfer [20]. These enzymes harbor the P-loop containing nucleoside triphosphate (NTP) hydrolase fold (c.37), specifically the ABC transporter ATPase domain-like and the extended and tandem AAA-ATPase domain FFs [7], confirming previous inferences at other levels of the structural hierarchy [5], [9], [20]. Remarkably, the evolutionary age of domains correlates with the age of associated molecular functions inferred directly from hundreds of thousands of terminal ontological terms of molecular functions and biological processes [11]. These studies suggest again that metabolism preceded translation and showed that the oldest proteins had ATPase, GTPase, and helicase activities. We note that the primordial ATPase FFs have the potential to use the energy of nucleotide binding and hydrolysis for mechanical work, which is generally used to move polypeptides and nucleotides [21]. The fact that enzymatic catalysis precedes aminoacylation, and aminoacylation precedes RNA recognition congruently in retrodictive and nomothetic analyses of structural, functional and genomic data is remarkable and has implications for this study – congruence should be considered the most powerful statement of evolutionary biology.

Do you have anything other than mindless fucking quote mines and empty handed dismissals of an entire fucking branch of science of which you are terminally, manifestly and obviously entirely clueless?

Coroama wrote:
Rumraket wrote:You just sitting there and declaring blindly in your religiously motivated denial that this evidence has not been shown to you isn't going to make that evidence go away. Go back and read the paper you keep pretending doesn't exist.

how about you present the BEST paper you have safed that you think has the most convincing arguments and shows in powerful way, that the dna code has evolved ? maibe you quote mine the relevant part, and we'll have a close look at it.

You're asking me to quotemine? Do you even know what the fucking term means? :picard:

Coroama wrote:
Rumraket wrote:By the way, can you explain what is meant by a frozen accident specifically with respect to the genetic code? What is a "frozen accident" about the code? Do you even understand what is meant by that term? Of course you don't.

Since you do understand, please elucidate me.

Thank you for confirming that you do not. No, I cannot be bothered personally undertaking your education. My job here is done, you don't know shit about the subject. All faith and know-nothing. Good luck with your life. :roll:

Coroama · **#310** by **Coroama** » Dec 28, 2013 2:50 pm

Rumraket wrote:
Here it is for the tenth fucking time:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072225

that paper again ??

:lol:

I answered already , but you simply ignored the critic :

http://www.evolutionnews.org/2013/10/on ... 78441.html

Results reveal that genetics arose ( how do they know ?? they just assert it !! ) through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness [i]were likely internalized into the emerging genetic system with the early rise of modern protein structure.[/i]

Thats nothing else that typical GUESSWORK, typical sciencie fiction fantasy packed in intelligent looking words.

But as long as non thinking evolution indoctrinated atheists bite it, everything is ok. :crazy:

as evolutionnews continues :

Needless to say, this tale of "emergence of codon specificities" and "archaic synthetases" requires heavy doses of imagination -

just haveing a look at your first sentence :

5.6]. Timelines that describe the gradual appearance of domain structures in evolution have shown that the editing and anticodon-binding domains of aaRSs are late additions to the central catalytic role of their aminoacylation domains [6],

what timelines are that ??

ElDiablo · **#311** by **ElDiablo** » Dec 28, 2013 3:05 pm

Coroama wrote:
Rumraket wrote:
Have anyone ever demonstrated instantaneous magical creation? No. Has anyone ever demonstrated the supernatural? No.
Has any observed phenomenon ever turned out to have a supernatural explanation so far? No.

We can infere God's existence based on creation, and his revealed word, the bible.

In other words, the answer is no, you have no evidence, and that hearsay is sufficient for you to believe that your god exists.
:thumbup:

Rumraket · **#312** by **Rumraket** » Dec 28, 2013 4:26 pm

Coroama wrote:
Rumraket wrote:
Here it is for the tenth fucking time:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072225

that paper again ??

Yes, because you haven't actually dealt with it. You go on to still not deal with it here below, you just mindlessly quote an empty handed dismissal of the key findings of the paper expressed in the abstract. What fucking kind of response is that?

Coroama wrote:

I answered already , but you simply ignored the critic :

I didn't ignore it, I expressly stated what was the key flaw of their criticism: They don't offer one.

The findings of the paper are simply dismissed with a factually incorrect blind assertion. One which you are all too happy to gobble up.

Coroama wrote:http://www.evolutionnews.org/2013/10/on_the_origin_o_4078441.html

Results reveal that genetics arose ( how do they know ?? they just assert it !! )

That's what the fucking structural phylogenomics reveal for fucks sake. That is THE evidence. If the events did not take place, the evidence would not fucking imply it. Why don't you get this? What is hard to comprehend?

They use the structures of the proteins and RNA's of the translation system, from hundreds of genomes spread over the diversity of life, to build a timeline of the evolution of these very proteins and RNA's. When doing this, what they get is the evolutionary history of the code. This is molecular forensics, they reconstruct the past. The evidence is right there, before us, in the genomes of extant living organisms.

The only real problem here is that you don't understand any of this evidence, and the people at the intelligent design webpage are propagandists getting paid to lie to people like you. They don't even have any answer for this evidence, they simply ignore it and dismiss the paper with a single fucking sentence. All they do is pick out one single fucking sentence of the abstract, which is the RESULT of compiling the evidence. The evidence itself is not IN the abstract, it is in the MATERIALS AND METHODS and Supplementary Information part of the paper.

Coroama wrote: through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness [i]were likely internalized into the emerging genetic system with the early rise of modern protein structure.[/i]

Thats nothing else that typical GUESSWORK

No, that is the CONCLUSION distilled down into a few sentences of the ABSTRACT of the paper. The actual evidence itself is in the METHODS and supplementary information to the paper. This is where you find the data from the structural phylogenetic inference. All this data is being compiled and the results thereof presented in the main body of the paper itself. Go and fucking read it.

Coroama wrote:, typical sciencie fiction fantasy packed in intelligent looking words.

It's a demonstrable fact that the genetic code evolved, that the central elements of the translation system have divergent ages and show evolutionary relationships to even older RNA and protein structures that served different functions. The evidence is right there in the paper, compiled and distilled into a description of what this evidence implies.

Coroama wrote:But as long as non thinking evolution indoctrinated atheists bite it, everything is ok.

This is so incredibly ironic to read, since you are the one who blindly believes the utterances of committed doctrinalists who fool you with a simplistic bait and switch. They simply pick out a few short sentences from the abstract (which is really just a short resume of the key findings of the paper, not the actual evidence itself), then dismiss them out of hand. They never actually deal with the structural phylogenomics evidence. They pretend it doesn't even exist. After having done the bait by dismissing the entire paper on no basis other than a blind assertion, they pull the switch by starting to blather about a completely different paper that is totally unrelated to the evolution of the translation system.

And it worked, you fell for it, all too keen to gobble it up. Bait and switch.

Coroama wrote:as evolutionnews continues :

Needless to say, this tale of "emergence of codon specificities" and "archaic synthetases" requires heavy doses of imagination -

This is it. This is their criticism. A blind fucking assertion that doesn't actually deal with the evidence. An empty dismissal of a few key terms mentioned in the ABSTRACT of the fucking paper. The main findings, the structural phylogenomics, the implied evolutionary history, the HARD EMPIRICAL EVIDENCE IN THE FUCKING PAPER ITSELF is never touched. Never mentioned. Never thought of or dealt with. All hand-waved away with a simplistic claim that the conclusion of a colossal phylogenomic investigation is "imagination".

And you just believe it on the claim alone. No thoughts on why or how, no mention of the evidence of the paper. No attempt to understand why the abstract says what it does. Nothing but blind belief in a single short claim that dismisses the entire paper out of hand.

Handwaving. That is all you have. Handwaving and blind belief in magic.

Coroama wrote:just haveing a look at your first sentence :

Coroama wrote:5.6]. Timelines that describe the gradual appearance of domain structures in evolution have shown that the editing and anticodon-binding domains of aaRSs are late additions to the central catalytic role of their aminoacylation domains [6],

what timelines are that ??

READ THE FUCKING PAPER. TIMELINES INFERRED FROM STRUCTURAL PHYLOGENOMICS. GO IN TO THE MAIN BODY OF THE PAPER AND READ THE FUCKING MATERIALS AND METHODS AND SUPPLEMENTARY INFORMATION SECTION.

Evolutionary accretion of domains in aaRS enzymes. A. One of nine most parsimonious phylogenomic tree reconstructions describing the history of the aaRS protein domains analyzed in this study. Terminal leaves are colored according to aaRS class (class I, blue leaves; class II, coral red leaves) and indexed with aaRS domains labeled with concise classification strings (ccs). The tree matches the corresponding subtree in the global tree of FFs described in the next panel. B. Optimal most parsimonious phylogenomic tree of FFs [177,864 steps; ensemble consistency index (CI) = 0.030; ensemble retention index (RI) = 0.749; g1 = −0.070] reconstructed from an analysis of the proteomes of 420 free-living organisms. Terminal leaves are not labeled in the tree since they would not be legible. The Venn diagram shows occurrence of FFs in the three superkingdoms. C. Evolutionary timeline of domain innovation. Domain ages (arrowheads) are mapped along a timeline of FF domain appearance derived from the global phylogenetic tree of FFs. For reference, the timeline is indexed with landmarks derived from domain history [6], [7]. Dashed black lines indicate aaRS history prior to the appearance of the first accessory domain in the structure. The three epochs of the protein world, ‘architectural diversification’, ‘organismal specification’ and ‘superkingdom diversification’ are shaded in green, salmon and yellow, respectively, and are divided into six phases (shade hues) according to Wang et al. [10]. A molecular clock of domain structures places the relative timeline in a geological time scale in billions of years (Gy) [13]. Evolutionary landmark accretion events are indicated with encircled numbers: (1) Catalytic domains have structures with Rossmann-like α/β/α-layered topologies with a central β-sheet flanked by α-helices [53], [101], [102] and can be summarized by the idealized form structure I31 of a periodic table of structures [103]. SerRS, LeuRS, ProRS, LysRS and MetRS structures harbor the most ancient pre-transfer and post-transfer editing functions [2], [27]. The SerRS, LysRS, and MetRS enzymes lack distinct editing domains and probably hydrolyze misactivated amino acids in the active site of the catalytic domain [104]–[106]. Pretransfer editing at the active site has been detected in LeuRS [107] and ProRS [108]. TyrRS lacks internal editing functions [109] but contains a short connecting segment that is homologous to the CP1 editing domain of LeuRS, which harbors species-specific acceptor helix recognition properties [110]. (2) The first editing domain (CP1) has proof reading hydrolase activities that avoid misactivation of Val at frequencies of 1/200. Val mimics the hydrophobic qualities of cognate Ileu and fits in the catalytic pocket of the IleRS enzyme [111]. Similarly, Thr is misactivated by ValRS since both Thr and Val have similar physical and chemical properties and the same barrel structure provides hydrolytic activities. (3) The earliest trans-editing function is provided by D-Tyr-tRNATyr deacetylase (DTD). The enzyme hydrolyzes D-Tyr-tRNATyr (also D-Trp, D-Ser, D-Asp and D-Glu charged tRNAs) in TyrRSs, which lack internal editing functions [109]. (4) Class IIa anticodon-binding domains of ProRS, GlyRS, ThrRS, HisRS and AlaRS are the first to appear and were closely followed by class Ia (LeuRS, IleuRS, CysRS, MetRS, ValRS and ArgRS) and Ib (GlnRS) anticodon-binding domains. (5) Accretion of aaRS domains, which decorate and enhance the discrimination against non-cognate substrates [112], continues throughout the timeline in parallel with that of ribosomal protein domains. In general, amino acid sieving functions of editing domains appear before recognition of identity elements in the anticodon arm of tRNA by anticodon-binding domains. Accretion encompasses over 2.6 Gy of evolution.

Coroama · **#313** by **Coroama** » Dec 28, 2013 5:02 pm

Rumraket wrote:
TIMELINES INFERRED FROM STRUCTURAL PHYLOGENOMICS. GO IN TO THE MAIN BODY OF THE PAPER AND READ THE FUCKING MATERIALS AND METHODS AND SUPPLEMENTARY INFORMATION SECTION.

Don't i say, its always the same blabla pseudo scientific guesswork.... which you take as granted truth. Of course.

http://www.evolutionnews.org/2012/03/st ... 57501.html

Unfortunately, while the authors suggest co-option, they do not have a model system on which to base the prior function of these mechanical parts, which makes this highly speculative

Overall, the authors appeal to co-option and co-evolution and justify this using phylogenetic homology studies. They contend as many in the ID camp do that "the de novo appearance of complex functions is highly unlikely. Similarly, it is highly unlikely that a multi-component molecular complex harboring several functional processes needed for modern translation could emerge in a single or only a few events of evolutionary novelty." Their explanation, however, is that a simpler system was performing a different function, and then was recruited into the complex protein translation machine.

The question that follows is what exactly did the recruiting? What provokes recruitment to another system? The authors labeled this time of recruitment the "first major transition" but their explanation of the transition is a little cloudy.

They seem to answer the question of "motivation to recruitment" by appealing to co-evolution. The RNA and ribosome proteins are co-dependent such that as one evolves, the other does too and somehow it reached a point where a "major transition" occurs.

There are many striking features of this study, such as the authors' acknowledgement of the deficiency of ribozymes to account for the "chicken-and-egg" problem with protein synthesis, and their recognition of the improbable evolution of RNA apart from the ribosomal protein in view of the fact that the relevant functions are so intimately intertwined.

While these results show a relationship and even a correlation between tRNA and the ribosome, it is still unclear what exactly promoted recruitment, what attracted the tRNA to the proto-ribosome, or why co-option must be the conclusion. Could this not also be a case of an irreducibly complex machine?

:whistle:

It's a demonstrable fact that the genetic code evolved,

Its not. Try harder...... :popcorn:

Rumraket · **#314** by **Rumraket** » Dec 28, 2013 5:12 pm

That's another paper. :picard:

Seriously, do you ever, EVER question anything you read on those sites?

So in desperation you went to search for some kind of response to the paper, you didn't bother really reading what you found, you just latched on to the fact that it was coauthored by one of the same guys, and you hurried back to copy-paste the "response" from the nearest propaganda outlet. A response to an entirely different paper.

Brilliant. We could get no better confirmation that you don't even fucking read the stuff before you, it's all "must find copy-paste source", "must find copy-paste source".

:rofl:

Regina · **#315** by **Regina** » Dec 28, 2013 5:22 pm

Rumraket wrote:That's another paper.

Seriously, do you ever, EVER question anything you read on those sites?

So in desperation you went to search for some kind of response to the paper, you didn't bother really reading what you found, you just latched on to the fact that it was coauthored by one of the same guys, and you hurried back to copy-paste the "response" from the nearest propaganda outlet. A response to an entirely different paper.

Brilliant. We could get no better confirmation that you don't even fucking read the stuff before you, it's all "must find copy-paste source", "must find copy-paste source".

That's how he ends up on advertising agencies' sites. :grin:

Coroama · **#316** by **Coroama** » Dec 28, 2013 6:04 pm

Rumraket wrote: back to copy-paste the "response" from the A response to an entirely different paper.

what ??

Rumraket · **#317** by **Rumraket** » Dec 28, 2013 6:26 pm

Coroama wrote:
Rumraket wrote: back to copy-paste the "response" from the A response to an entirely different paper.

what ??

Calilasseia · **#318** by **Calilasseia** » Dec 28, 2013 6:42 pm

Rumraket wrote:
Coroama wrote:
Rumraket wrote: back to copy-paste the "response" from the A response to an entirely different paper.

what ??

Indeed, he can't even be bothered to read any of the apologetics he's copy-pasting to determine if it's horseshit. He just assumes that because it's written by another ideological stormtrooper for creationist doctrine, it purportedly "must be right", regardless of how wrong it's shown to be upon proper critical analysis. If anyone needs any evidence of the brain-rotting effects of supernaturalism, this modus operandi provides said evidence in quantity. As if the fact that creationists can't actually be bothered to read the entire paper when said paper is presented to them, and only bother with scientific papers in order to skim through them for duplicitous quote mines, wasn't evidence enough.

All he has here, quite literally, is "my mythology is right because my mythology says so, along with these other people who make shit up to prop up the mythology".

Valsregen · **#319** by **Valsregen** » Dec 28, 2013 8:30 pm

Rumraket wrote:
Coroama wrote:
Rumraket wrote: back to copy-paste the "response" from the A response to an entirely different paper.

what ??

He sure got you there racket. Get checkmated. :roll:

Valsregen · **#320** by **Valsregen** » Dec 28, 2013 8:31 pm

Actually. I hope God exists so he can punish Coroama for his stupidity.

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