A Tour of Directed Mutations

_{Jonathan Bartlett

November 23, 2021

Intelligent Design}

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Many people think that directed mutations don’t exist. This video explores both the theory behind directed mutations (what is meant by “directed”, how is selection involved, etc.) as well as the mechanics and specifics of many different types of directed mutations. It’s a lot to take in but well worth your time.

Comments

Mutations may be the stuff of variation and a change in allele frequency over time, but they cannot be the mechanism for universal common descent.ET_{November 24, 2021
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yes, but not minimized
I disagree. For Evolution it should be minimized. For genetics it should take front and center. The point I am making is that ID cares little about genetics even though it is important and directed adaptation may exist. It an interesting aspect of genetics that certain changes seem ordained by built in tendencies. The point of ID is that certain aspects of nature point to an intelligence and various aspects of biology are front and center for that. Namely, the existence of information processing systems. But these information processing systems are only relevant for genetics not Evolution. The current thinking of evolutionary biology is that these information processing systems is what led to macro evolution. They beg the question on how they arose but also completely miss the mechanism for macro evolution. In other words they are begging a second question, they are assuming micro evolution or changes in DNA is what leads to macro evolution. By making DNA important. ID is just affirming this begging the question. No reason to avoid the investigation of DNA changes just not emphasize its importance to Evolution. The interesting thing is that with all this built in information processing no recent Evolution has taken place. One would think more would happen. Aside: if at some future time it looks like changes in DNA could lead to Evolution, then ID could just affirm that finding. But in the mean time, current science is committing what they accuse ID of doing, preventing an investigation into the real causes of Evolution. ID should take the lead.jerry_{November 24, 2021
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Jerry - Excellent points all around. However, I don't think that looking at DNA should be minimized. Recognized as one part of the puzzle, yes, but not minimized. I agree that the current DNA-centric view of the organism is faulty. However, the informational question is essentially the same whether it is stored in DNA or some other medium. The one area where informational measures may not be sufficient for explanation would be for any spiritual aspect of the organism (i.e., vitalism-ish considerations).johnnyb_{November 24, 2021
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This discussion is irrelevant to the Evolution debate. It is a debate over how certain mutations happen to DNA. It’s a theory of adaptation not Evolution. No one ever has demonstrated that DNA has anything to do with Evolution. Yes, micro evolution but not macro evolution. It’s making the same flawed argument that a zillion micro evolution events add up to macro evolution. The basic mistake is that adaptation is what leads to new species. Adaptation leads to a temporary more fit species. Directed or not, it’s irrelevant to Evolution but possibly very important to genetics and adaptation. Jonathan Wells and Stephen Blume and others point to other processes that must be changed for macro evolution to happen and true Evolution to occur. These other processes require new DNA but the new DNA is not sufficient for any major changes to happen. Aside: this site and ID will progress and not run in circles till it abandons or minimizes anything to do with DNA. Admit that Darwin made a great insightful breakthrough but it had nothing to do with Evolution. It will embarrass those in science who will be forced to eventually agree.jerry_{November 24, 2021
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Hoosfoos - You are correct that there is a path (under the assumption that there is a LUCA). There's actually innumerable paths, all almost equally likely. That makes the problem that we can no longer infer what the path actually is.johnnyb_{November 23, 2021
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johnnyb@6, If LUCA has all the information, then this a path of devolution to each of the organisms.hoosfoos_{November 23, 2021
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Hoosfoos - You could use the concept of information to measure phylogenetic **distance**, but it potentially prevents you from being able to infer lines of ancestry. Basically, if the LUCA has all the information, then any particular instance can occur by selective deletion. So, if you have organism 1 that has information pieces [A, B], organism 2 has information pieces [B, Q], and organism 3 has information pieces [J, L, M], the ancestry could look like this: Lineage of organism 1: LUCA: ABQJLMNOP -> ABQOP -> AB Lineage of organism 2: LUCA: ABQJLMNOP -> BQJLM -> BQ Lineage of organism 3: LUCA: ABQJLMNOP -> BQJLM -> JLM Thus, while a phylogenetic analysis might show a shorter *distance* between 1 and 2, it doesn't imply the ancestry. Here, organism 2 and 3 shared ancestry, but had *no* shared genetics. Evolution by deletion/specialization means that traditional phylogenetic analysis doesn't actually imply much of anything about ancestry.johnnyb_{November 23, 2021
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Could this information box concept be applied to phylogenetic trees to measure the distance in bits between apparent ancestors? Choose ribosmal RNA for example. If the ancestor inference is correct, then the source of information to make the change needs to be identified. How much time is available for the change? Is this within reach of Darwin? Or, is this a case of evolution of the gaps?hoosfoos_{November 23, 2021
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Doubter - I feel like you did not watch the whole video (understandable, since it is quite long). "Is your ultimate point that ID is invalid and that all of life must have evolved by some process not involving outside intelligence?" This would be exactly the opposite of my ultimate point. Towards the end I get to Dembski's "Displacement Theorem". He points out that you can, indeed move design back indefinitely, but that the design gets *bigger*, not smaller, if you do so. Remember, I said my hypothesized box of information had *MORE* information in it than is in the current implementation of the flagellum, not less. However, you are incorrect that there *couldn't* be such a box of information. Let me give you a very specific example. The installer on for your computer's operating system. That was a single program that had a minimal function. However, out of that single program came hundreds of distinct programs. How? Because the installer has sufficient *information* to build them. They did not arise by random mutation and natural selection. However, that doesn't mean that every installation is identical, either. The installer may have chosen to install or not install a driver based on your hardware. It could have decided to change a configuration file, etc. But the installer works BECAUSE OF prior information that it has. The information on the installer is actually *more* than the information that gets installed (though it may be compressed more). As I said, the design gets BIGGER when you move back in time, not smaller. No one would suggest that because an installer exists there is no need for design or ID. Quite the opposite. If there is a repository of information, you have to account for *both* the information and how it is deployed. However, an examination of a computer will not necessarily tell us about the *history* of the software. Did the all of the software components come from a single installer program, or were there separate installations? You can't tell that from just looking at the programs that exist on the computer. What you can do is describe how much information the installer had to contain to produce them, and then look around and see if any available program has that quantity of information around.johnnyb_{November 23, 2021
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I think that the mechanisms outlined in the video by themselves could not evolve something like the flagellum. Then you suggest subsidiary hypotheses that if added might still enable the intricate structure like the flagellum to have evolved. For instance:
...there could be a “box” of information somewhere which held, say, information on how multipart structures should be joined together, information on how assembly steps need to be sequenced, and information on how different shapes correspond to different environmental conditions.
The basic problem with this is in part that this would still not supply the essential quality or capability of conscious intelligence needed to choose which information items out of those already existing somehow in this hypothesized "reservoir", and when in the exact sequence required. Secondly, it would just be kicking the can down the road so to speak in that some sort of an outside conscious intelligence would still have been required to so providentially store all the necessary information files for later use (I guess some form of "front-loading"). Is your ultimate point that ID is invalid and that all of life must have evolved by some process not involving outside intelligence?doubter_{November 23, 2021
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Doubter - I don't disagree with you. The main thing, however, is we have to recognize how much we don't know about biology. I don't think there's any evidence that these systems had any real precursors. However, there is nothing illogical about positing such precursors, ****provided that they have sufficient information to close the gap****. So, for instance, there could be a "box" of information somewhere which held, say, information on how multipart structures should be joined together, information on how assembly steps need to be sequenced, and information on how different shapes correspond to different environmental conditions. This would be a LOT of information. More information, indeed, than we currently know about for the flagellar system itself. But it might be there somewhere. My point is that the question is not so much "did this evolve" but "how could it have evolved". You have to answer the latter question **before** you answer the former question. If you know the requirements of the evolution of X, and you know the capabilities of the thing Y that is evolving, you can then deduce whether or not Y can evolve X. Everyone (on pretty much all sides) is trying to argue the other way around. They are trying to say ahead-of-time whether or not it can evolve, and then after-the-fact trying to figure out a mechanism which achieves or prevents it. If we know the *requirements* of such an evolution, we can then use that to check and see if there are valid precursors which match the requirements.johnnyb_{November 23, 2021
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It seems to me that the mechanisms outlined in this video are interesting but don't even begin to explain the intelligent design process which seems to have been required in what has been termed macroevolution. These mechanisms for cellular self-directedness are all short-range in both time and spacial extent - they are limited to a directedness aimed at the immediate needs of the cell and of the organism. These mechanisms outlined in the video don't have any sort of the long-range foresight and insight into a future requirement, and the capability for creative invention of the coordinated structures that would fulfill it, that are needed for the invention and building of the many intricate irreducibly complex biological machines found in the cell and in multicellular animal bodies. These contain many interlinked parts with such cellular organ systems as the bacterial flagellum. Or with other this time multicellular examples from Behe, such as the blood clotting system. The flagellum was a future complicated structure needed by the bacterial cell for food gathering and toxicity avoidance, the achievement of which required a large number of coordinated working together specialized individual proteins and molecular machines. Irreducibly complex means that the machine that is the goal, that certainly will be selected for if it is designed and built (and it's assembly system is also at the same time designed and built), can't work and can't be advantageous in selection, and may even be deleterious, until it is entirely finished and all parts are working together as envisaged by the designer intelligence. The selection process can't work until the whole thing is built. Just the tip of this iceberg: the ATP-powered rotor motor won't give the cell any advantage until the whip-like rod is also assembled, and the two have to be exactly fitted to each other, and it goes on. Just the motor without the associated subassemblies will just consume extra material and energy that will be expensive to the cell without any selective advantage, and in fact may be deleterious and be selected against. Just the molecular motor by itself doesn't contain anything that would allow the prediction of the need also for a rod and whip assembly. This prediction requires conscious intelligence. The bottom line is that whatever designs the intricate biological machine (unlike the relatively simple mechanisms outlined in the video) has to have true intelligence, that has so far in our experience only been exhibited by man.doubter_{November 23, 2021
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