An ID hypothesis: Front-loaded Evolution

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Oh a quick search shoes "word salad" is the accepted spelling. You have a source that shows otherwise?

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I stand corrected.

Not true at all. Random mutations are anything but random. The mutations possible are constrained by the nature of the DNA molecules and their chemical and structural relationships to one another. Expectant mothers everywhere can rest assured that whatever horrible afflictions might plague their newborn, the child's carbon atoms being replaced by hydrogen atomsa truly random eventwill not be one of them.The physical, biological, and chemical 'laws' of the Universe are pretty much the only predetermined biases in play. And they seem quite capable of keeping things in order on their own. Of course not. There's no need to look for a designer under every rock. That'd be a foolish waste of time. What can be inferred about the nature of the supposed designer(s) based on this, and what can that add to our understanding of genesis?Jon

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There is no such thing as "a universal optimal code", that is simply another example of your making stuff up.

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I cited Freeland et al., 2000, to support the assertion that the canonical, universal genetic code is highly optimized. I am not making that up, at all.

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There is no FLE hypothesis yet other than the unsupported assertion that YOU think there is some planner or plan.

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The assertion is backed up by clues like the universal optimal genetic code.

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And as I said in the very beginning of this thread, you offered no predictions or any possible tests that would not be satisfied by pointing how well the puddle fits the water.

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Let's start with one of the FLE predictions. The FLE hypothesis predicts that genes important for the development and function of multicellular organisms will share deep homology with prokaryotic genes. How is this an example of "pointing how well the puddle fits the water"?

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Not true at all. Random mutations are anything but random. The mutations possible are constrained by the nature of the DNA molecules and their chemical and structural relationships to one another. Expectant mothers everywhere can rest assured that whatever horrible afflictions might plague their newborn, the child's carbon atoms being replaced by hydrogen atomsa truly random eventwill not be one of them.

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Are you suggesting that if FLE has not occurred, then the evolutionary trajectories were still planned? That really does not make sense. The difference between FLE trajectories and non-teleological trajectories is that the former is planned, while the latter is not. Of course, in both instances, natural laws constrain the course of evolution - but the latter is not planned.

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That'd be a foolish waste of time.

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That's more a subjective opinion, is it not?

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What can be inferred about the nature of the supposed designer(s) based on this...

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Based on this, it can be inferred that the designers are rational agents - advanced nanotechnologists who have the capability to design the genetic code such that it is optimal.

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...and what can that add to our understanding of genesis?

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Why should it add something to our understanding of Genesis? Why did an ancient text suddenly get involved in our discussion?

That is simply not a prediction, just word salad. It is no different than saying the puddle was shaped to hold the water. It is just a nonsense assertion.If you actually had read Stephen Freeland's work you would know that he has said 'that despite the continuing and widespread use of the phrase "universal genetic code", no such thing exists.'Not only is there no such thing as a universal genetic code, there is no indication that any genetic code is 'optimal' other then within the confines of that particular incident, just as the puddle is perfectly shaped to hold the water and the water fits optimally within the bounds of the puddle. In addition it is optimally placed to reflect the trees.

Hi Genomicus and welcome to EvC Forum!So, I have a couple of questions;How does this front-loading work? What is the mechanism?Can you show me an example of front-loading in a genome?Are there front-loaded genes that exist now? How would we tell?How would we differentiate between an organism whose gene had been front-loaded and one that had merely evolved?Mutate and Survive

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That is simply not a prediction, just word salad. It is no different than saying the puddle was shaped to hold the water. It is just a nonsense assertion.

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You have yet to back up your statement that it is no different than saying the puddle was shaped to hold water. How is it no different?

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If you actually had read Stephen Freeland's work you would know that he has said 'that despite the continuing and widespread use of the phrase "universal genetic code", no such thing exists.'

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That's because there are secondarily derived genetic codes. That's why in my essay I said the "nearly universal genetic code." There is indeed a nearly universal optimized genetic code. Some ciliates and other taxa use secondarily derived genetic codes. But the optimized genetic code is basal, and there is no indication it is derived. How do you account for this?

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Not only is there no such thing as a universal genetic code, there is no indication that any genetic code is 'optimal' other then within the confines of that particular incident...

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Other than within the confines of that particular incident? What incident are you speaking of? The work of Freeland et al. show that the canonical genetic code is highly optimized for error minimization. Why is there no phylogenetic tree consisting of sub-optimal codes in basal lineages, gradually leading to more optimal codes? What do you think is the best explanation for this phenomenon?

Hello Genomicus,Welcome to EvC I would note that Crick and Orgel have since rejected their views expressed in the 1973 paper as overly pessimistic - see Anticipating an RNA World. How do you intend to test this hypothesis? The trouble with this prediction is that it does not, in fact, differ from the predictions of conventional theory. If a protein exists with homologes in Bacteria, Archaea and Eukarya* then it must have be strongly conserved, otherwise it wouldn't exist in all three domains. Such strongly conserved proteins will trivially be more highly conserved in sequence identity than other proteins. Interestingly, the 3D shape of proteins is much more highly conserved than sequence identity. I'm not really sure how your justification follows, either.* - It seems to me that Bacteria and Archaea are sufficiently distinct that they should be separately addressed in this kind of deep time discussion.Edited by Mr Jack, : No reason given.

Is it that you can't read or that you refuse to read?You did read that the very source you are using says that there is no universal genetic code?And that particular incident refers to any particular incident you select, just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.Your use of the term 'optimal' is just word salad, nonsense; as absurd as all of the Intelligent Design crap.

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Hi Genomicus and welcome to EvC Forum!

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Thanks!

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How does this front-loading work? What is the mechanism?

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There are several mechanisms that could potentially be used. For example, if we wanted to front-load molecular machine X, we could design molecular machine Y into the first genomes. Molecular machine Y would have molecular machine X embedded within it. Further, molecular machine Y would be more complex (i.e., having more components) than molecular machine X. Subsequent deletion of several components in molecular machine Y would unveil molecular machine X. Possibly, we might have a real example of this in the biological world. Within the bacterial flagellum, an export system seems to be embedded. Deletion of the cap and hook proteins, and the motor proteins, would result in a protein export system that could mediate interactions between prokaryotes and eukaryotes.Another way to front-load a biological system would be simply to make the appearance of that biological system much more probable. Suppose we wanted to front-load blood. In this case, we would endow the first life forms with homologs of hemoglobin, which would carry out an important function so that they don't decay over time as a result of natural selection and genetic drift. So, if the first life forms had homologs of hemoglobin, the blind watchmaker wouldn't have to tinker around, eventually happening to "land" on hemoglobin. The homologs of hemoglobin would already be in place.

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Can you show me an example of front-loading in a genome?

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By this do you mean an example of a genome that was front-loaded?

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Are there front-loaded genes that exist now? How would we tell?

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According to the front-loading hypothesis, genes that are important to multicellular life were front-loaded. Thus, Pax-6 genes, which are important in developmental pathways, would have been front-loaded from homologs in bacteria. Genes for brain development and brain function would be front-loaded. Blood would be front-loaded, if we're front-loading animals. How can we tell? In the first place, deep homology of these genes with prokaryotic genes would be indicative that they were front-loaded; if these prokaryotic homologs were fairly well-conserved in sequence identity, this would strengthen the hypothesis of front-loading further.

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How would we differentiate between an organism whose gene had been front-loaded and one that had merely evolved?

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You'd have to look at the broad biological context of the gene; determine its prokaryotic homolog and check their level of sequence conservation.

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You did read that the very source you are using says that there is no universal genetic code?

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There is no truly universal genetic code. There is, however, a nearly universal genetic code, which happens to be highly optimized. How do you account for this?

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And that particular incident refers to any particular incident you select, just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.

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I really have no idea where you're going with "incidents" or what you mean by "incidents." The nearly universal genetic code is highly optimized for error minimization, as supported by the scientific literature. Do you think they've messed up badly?

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...just as every puddle is optimized for the water it holds and the water it holds is optimally designed to fit the puddle it's in.

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The analogy is entirely irrelevant, I'm afraid. Water fits into puddles "optimally" as a result of natural laws. Water flows downhill; thus, if water is flowing along, and a hole is in its path, it will fill up the hole as a result of gravity. It will fit the shape of the hole as a result of the chemical properties of the water. Things are different for the genetic code. There are no natural/chemical/physical laws that say that it must be optimal. The analogy does not hold.Edited by Genomicus, : No reason given.

Because the selective advantage of a high quality genetic code is high, and the nature of horizontal gene transfer means that there is an advantage in a shared genetic code.Living prokaryotes are not ancient throwbacks, they do not represent the vestiges of an ancient world - they are extremely highly evolved organisms.

Okay, so we now know that you admit that there is no universal genetic code.Now let's try to deal with your optimized bullshit.What makes you think the genetic code is any more optimized than the water is to fill the puddle or the puddle is to fit the water?

Panspermia, of course, pushes the problem one level deeper. Would it necessarily follow that the propagators themselves (of which you talk of) originated by way of earlier directed panspermiatic projects? Where does the chain end, if it ever ends? And what's so special about multicellularity, then? The vast bulk (by mass) of life on Earth has been, and currently remains, unicellular (bacteria in particular). If multicellularity (and therefore plants and animals and fungi) was a legitimate goal, why not have started off with it immediately? Unfortunately, constructing phylogenic trees requires the existence of intact genetic material, which by and large is not preserved over billions of years; and thus is necessarily limited to currently-living species. That the various extant alternative genetic codes are derivative from the "universal" code is quite uncontroversial, given that they seem more likely to have arisen via extreme genetic bottlenecks. Unfortunately, this says little to nothing about the actual origins of the universal code itself, except that it shows that even something as hard-wired as the universal genetic code is subject to a possibility of some change under the right circumstances. It is probably reasonable to infer that all known extant life forms one clade with its last common ancestor having had that particular code, but it does not preclude the past existence of other contemporaneous (and currently extinct) clades which had competing codes.

Merely using the phrase "molecular machine" does nothing to establish a mechanism. It is clearly a place-holder term that is standing in for an actual specific mechanism.Am I to assume that you are doing this because you cannot name a specific mechanism? How exactly is that supposed to be achieved? How does the genome "know" which elements are to be deleted and which are to be retained? The problem with this is that it sounds very much like an evolutionary origin for the flagellum. It sounds like it would be equally compatible with the regular Theory of evolution. So to follow on from that, can you show me that any such example has indeed occurred? Can you show me a front-loaded gene that has been taken up? And can explain how you differentiate it form one that merely evolved? No, I mean a gene that has been front-loaded but has not yet been, shall we say, "activated"? In other words, can you show me any allele that has been front-loaded but is not yet actively expressed in any extant organism? Why choose multi-cellular life? It seems a bit random, was it picked out of a hat? Why not hypothesise that life was front-loaded to produce Archaea? Or bacteria?Of course, I might hazard a guess. It's because the organisms that ID lobbyists really want to think have been front-loaded are humans. Because we're special. After all, Jesus does love us... Once again, this is indistinguishable from the consensus ToE, where the common ancestry of leads to homologous genes. In fact, a shared evolutionary heritage is pretty much part of the definition of a homologous gene. This seems to be another instance of this idea being unfalsifiable.
Are you saying that it is impossible for a non-front-loaded sequence to be highly conserved? I don't think it is.So given that independently evolved sequences can be just as highly conserved, I fail to see how this can differentiate evolved systems form front-loaded ones. But again, that tells us nothing. It only tells us that the sequence is highly conserved. It does not tell us whether the conservation is due to front-loading or whether it is due to it simply being a useful and thus evolutionarily successful sequence.It sounds to me like your hypothesis is lacking an actual mechanism, is based upon circular logic and assuming the consequent. It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god.Mutate and SurviveEdited by Granny Magda, : No reason given.