Intelligent Design Predicted Transcription to be Proofread
Mike Gene wrote the beautiful article “Using ID to Understand the Living World”. Mike used Intelligent Design as a working hypothesis to accurately infer something about the realities of the molecular world. He declared:
“...The information flow that occurs within a cell happens at several points. DNA is used to make DNA; DNA is used to make RNA; and RNA is used to make proteins. So goes the classic formulation of the Central Dogma of molecular biology. With information flow comes the issue of fidelity - how faithful is the information transferred? Scientists have long known that proofreading mechanisms exist during DNA replication where nucleotides that are misincorporated during replication are typically removed and replaced with the correct one. Similar proofreading also occurs at the two crucial points of information flow during protein synthesis: the charging of tRNAs and the anticodon-codon interactions of mRNA and tRNA..."
"...I was thinking about proofreading and it occurred to me that an important step of information flow appeared to lack proofreading, that of transcription (where DNA is used to synthesize RNA). Now, I know a few things about transcription, but I could not recall ever hearing about proofreading being associated with RNA polymerase activity (the protein complexes that synthesize RNA). It struck me that this was a great opportunity to use ID..."
"Imagine you need to translate a book from English into German and then German into Chinese. If it was important that this translation was as accurate as possible, you would employ proofreaders at both stages. For example, it would not make much rational sense to employ proofreaders to ensure the German text was accurately translated into Chinese without also using proofreaders during the first step (the English to German translation). It defeats the purpose of carefully scrutinizing the second translation if your first is sloppy."
"Thus, using this logic, I predicted that proofreading should exist during transcription (since I strongly suspect cells, much as they are today, were originally designed by a rational agent(s)). Also, given that the degree of proofreading at the level of protein synthesis was so sophisticated, it would not make sense for a rational agent to not also ensure high fidelity at the level of RNA synthesis."
"With this hypothesis in hand, I could thus go into the lab and design experiments to determine if indeed proofreading occurs during transcription. What if I did this? Well, my prediction would have born out. As it happens, I did a literature search after coming up with this hypothesis and indeed discovered there is some good evidence of proofreading during transcription…" [see reference in original source.]
"… ID is not a sterile hypothesis. ID could have indeed led me to discover proofreading during transcription. It led Harvey to figure out how the circulatory system works. ID is a useful tool. The only reason critics deny this is because they never pick it up, which of course, renders it of no use to them. Yet just because they don't want to use it is no reason why someone else can't pick it up and see how it works."
"…without such high fidelity, autonomous cellular life might not be able to exist (or if it can, it would quickly go extinct). I think proofreading at every important step in information transfer simply underscores the importance of specificity in life processes. If transcription/translation are not proofread, this not only means you increase the likelihood of plugging non-functional cogs into the machine, but you'll might also overwhelm or overtax the chaperone/folding and proteasome/degradative systems."
"Furthermore, the need for such proof-reading might be a reflection of the wide-spread nature of irreducible complexity (IC) in the core biotic processes…"
"…Darwinian selectionist thinking cannot lead to this inference (except in an after the fact manner). Why? Darwinian selection entails only that things "work", not that they be inherently rational or sophisticated. And since I had no reason to think cells cannot work without transcriptional proofreading (prior to finding that it existed), I had no reason to think natural selection had created it…"
"…there is the overall background emphasis of specificity that comes with ID. This is in stark contrast the general emphasis on messiness that comes with Darwinian thinking. The more specified something is, the stronger the design inference. Thus, one looks for examples of extreme specificity to minimize the error of making a false design inference…"
"…What ties translation and transcription? A suspicion that we're dealing with a designed system of information flow. That is, the tie is abstract and conceptual. Thus, I have been reading up on some mechanical engineering texts that outline the process of design. Not too long ago, I finished one that describes, "Function can be described in terms of the logical flow of energy, material, or information." This has significantly colored my thinking, as I have been looking for logical flows (something I would rarely expect from the blind watchmaker). In other words, if something is designed, and the two systems are linked in a more conceptual than structural manner, one expects to find a certain logic that binds them."
"…This was an analogy to highlight the relationship between specificity and logical flow among designed events. It employed "if, then" reasoning. So where did the preset "if" come from? Not from darwinian thinking, as it cannot imply these preset condition. It came from ID. If life is designed, and specificity is a common trace of design (and typically required of designed components) then conceptually, one might expect to see this theme of specificity laid out in a logical flow."
Here, Mike Gene demonstrates how Intelligent Design thinking guided his reasoning, then we can see Intelligent Design generating testable hypotheses.
One expert reader declared,
“...The information flow that occurs within a cell happens at several points. DNA is used to make DNA; DNA is used to make RNA; and RNA is used to make proteins. So goes the classic formulation of the Central Dogma of molecular biology. With information flow comes the issue of fidelity - how faithful is the information transferred? Scientists have long known that proofreading mechanisms exist during DNA replication where nucleotides that are misincorporated during replication are typically removed and replaced with the correct one. Similar proofreading also occurs at the two crucial points of information flow during protein synthesis: the charging of tRNAs and the anticodon-codon interactions of mRNA and tRNA..."
"...I was thinking about proofreading and it occurred to me that an important step of information flow appeared to lack proofreading, that of transcription (where DNA is used to synthesize RNA). Now, I know a few things about transcription, but I could not recall ever hearing about proofreading being associated with RNA polymerase activity (the protein complexes that synthesize RNA). It struck me that this was a great opportunity to use ID..."
"Imagine you need to translate a book from English into German and then German into Chinese. If it was important that this translation was as accurate as possible, you would employ proofreaders at both stages. For example, it would not make much rational sense to employ proofreaders to ensure the German text was accurately translated into Chinese without also using proofreaders during the first step (the English to German translation). It defeats the purpose of carefully scrutinizing the second translation if your first is sloppy."
"Thus, using this logic, I predicted that proofreading should exist during transcription (since I strongly suspect cells, much as they are today, were originally designed by a rational agent(s)). Also, given that the degree of proofreading at the level of protein synthesis was so sophisticated, it would not make sense for a rational agent to not also ensure high fidelity at the level of RNA synthesis."
"With this hypothesis in hand, I could thus go into the lab and design experiments to determine if indeed proofreading occurs during transcription. What if I did this? Well, my prediction would have born out. As it happens, I did a literature search after coming up with this hypothesis and indeed discovered there is some good evidence of proofreading during transcription…" [see reference in original source.]
"… ID is not a sterile hypothesis. ID could have indeed led me to discover proofreading during transcription. It led Harvey to figure out how the circulatory system works. ID is a useful tool. The only reason critics deny this is because they never pick it up, which of course, renders it of no use to them. Yet just because they don't want to use it is no reason why someone else can't pick it up and see how it works."
"…without such high fidelity, autonomous cellular life might not be able to exist (or if it can, it would quickly go extinct). I think proofreading at every important step in information transfer simply underscores the importance of specificity in life processes. If transcription/translation are not proofread, this not only means you increase the likelihood of plugging non-functional cogs into the machine, but you'll might also overwhelm or overtax the chaperone/folding and proteasome/degradative systems."
"Furthermore, the need for such proof-reading might be a reflection of the wide-spread nature of irreducible complexity (IC) in the core biotic processes…"
"…Darwinian selectionist thinking cannot lead to this inference (except in an after the fact manner). Why? Darwinian selection entails only that things "work", not that they be inherently rational or sophisticated. And since I had no reason to think cells cannot work without transcriptional proofreading (prior to finding that it existed), I had no reason to think natural selection had created it…"
"…there is the overall background emphasis of specificity that comes with ID. This is in stark contrast the general emphasis on messiness that comes with Darwinian thinking. The more specified something is, the stronger the design inference. Thus, one looks for examples of extreme specificity to minimize the error of making a false design inference…"
"…What ties translation and transcription? A suspicion that we're dealing with a designed system of information flow. That is, the tie is abstract and conceptual. Thus, I have been reading up on some mechanical engineering texts that outline the process of design. Not too long ago, I finished one that describes, "Function can be described in terms of the logical flow of energy, material, or information." This has significantly colored my thinking, as I have been looking for logical flows (something I would rarely expect from the blind watchmaker). In other words, if something is designed, and the two systems are linked in a more conceptual than structural manner, one expects to find a certain logic that binds them."
"…This was an analogy to highlight the relationship between specificity and logical flow among designed events. It employed "if, then" reasoning. So where did the preset "if" come from? Not from darwinian thinking, as it cannot imply these preset condition. It came from ID. If life is designed, and specificity is a common trace of design (and typically required of designed components) then conceptually, one might expect to see this theme of specificity laid out in a logical flow."
"Nothing in Darwinian theory led anyone to suspect that the RNA polymerase was proofreading; it is not even discussed in the 2004 edition of the Lodish et al, "Molecular Biology of the Cell".
Here, Mike Gene demonstrates how Intelligent Design thinking guided his reasoning, then we can see Intelligent Design generating testable hypotheses.
One expert reader declared,
"...[In] loss of vitamin D signaling, or, under non physiological conditions, where there is overexpression of so-called dominant negative forms of proteins (this occurs during some oncogenic viral infections, and in cancer)... since different classes of transcription factors recruit common cofactors (and ultimately the same RNA polymerase), dominant negative proteins can disrupt transcription controlled by several signal transduction pathways."
"Thank God for proofreading I'd say."
[His quote:] "For many [ID proponents] the main motive is not the foreseen spiritual implications but simply the denuding of what they believe is a contemptible flow of misinformation." -- Thomas Woodward, Doubts About Darwinism
posted by fdocc | 2:48 PM
3 Comments:
I find it interesting to note that his inference is exactly what a scientist does every day, Darwinian or otherwise. He simply made a prediction from prior experience. It happens that humans prior experience involves design of complex systems such as translating between languages.
He did not infer proofreading based on the system being designed, rather that his observation was that he had never seen a system work without proofreading at every step. Coincidentally his only experience was human and thus a product of design.
Now, knowing that it is true that proofreading occurs could it be that the system could not have worked without that proofreading? No one will know without getting into the lab, but even proving this false does not prove design to be the mode by which it was designed.
Thus his argument is simply another way to think about our way of producing logical hypotheses, namely that we work from our experience and observations. Scientists do this every day but it doesn't prove anything about ID. I would hope he would do this for the sake of ID calling themselves science. He's not using ID, he's using the scientific method.
It really shows how science ends up at a single, concrete conclusion for a test despite the ideaological background from which the hypothesis was made. Science is robust because of this.
Further, if a system cannot work without certain steps in the process, yet it works, does that prove design. NO! It simply is an obsevation upon which to test why it does work and how it might have come about. The challenge for ID'ers has been to make a workable test by which they can stake their claims.
Possibly ID needs to think about what it is they are talking about. Are they talking about a way to view the world or a way to explain it? If we approach science from an ID perspective we can still do science if we are willing to read the information wherever it leads. If we want a theory to explain the origins of life it needs to hold up logically to the scientific method. As yet it really hasn't held up as well as darwinistic theory.
I would agree that there is some scientific dogma that needs to be gotten rid of, but ID doesn't really have many answers yet to my eyes. It does do a good job of pointing out areas in which to research and a smart graduate student could find some mediagenic and very well funded research by following the trail left by the ID arguments.
Jens,
Your comments are bright. However, we need to realize that Intelligent Design is a new "metatheory", as Jonathan Wells describes it, which is able to embrace all the practical and useful research rejected or deliberately distorted, until now, by a current dominance of the Darwinian thinking in biology. You may want to see one example of "ID thinking", in sharp contrast to the currently held views of a 'Darwinian Conservatism' in biology. Next, the ID framework is applied to "The Crayfish Variation":
http://fdocc.blogspot.com/2005/10/crayfish-variation.html
MikeGene could have found this "prediction" after the fact. The literature abounded with references to transcriptional proofreading before MikeGene made his "prediction"...
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