An ID hypothesis: Front-loaded Evolution

IntroThe front-loading hypothesis is an ID hypothesis that builds on Crick and Orgel’s directed panspermia hypothesis. In 1973, in a paper published in Icarus (Directed Panspermia), Crick and Orgel proposed that the earth was intentionally seeded with unicellular life forms. Here, I will (a) describe the front-loading hypothesis, (b) provide one or two nice clues in favor of the front-loading hypothesis, and (c) list a couple of ways it can be tested.What is front-loading?The front-loading hypothesis proposes that (a) early in earth’s history, the earth (or the solar system) was intentionally seeded with unicellular life forms (i.e., directed panspermia) and (b) these life forms contained the necessary genomic information to shape future evolution, such that the course of evolution was biased in pre-determined trajectories. Thus, evolution would be biased by the genomic information designed into the first genomes on our planet. There is evidence for the notion of panspermia, which I will discuss briefly. A genomic clock based on increases in genome sizes throughout the history of life on earth suggests that life may be roughly 10 billion years old (Sharov, 2006), which would indicate that the first organisms from which all present taxa descended did not originate on earth.
Front-loading does not propose that all aspects of evolution were programmed and determined. There would be nothing stopping the blind watchmaker from taking its own unplanned courses alongside the front-loaded objectives. What might these objectives be? To use front-loading as a working hypothesis, it is assumed that multicellularity was an objective of the front-loading designers, as well as the origin of animals and plants. Further, the front-loading hypothesis proposes that the designers were rational agents; thus, poor, sloppy design in a biological system would count against the thesis that that system was designed into the first genomes.The genetic code: a clue in favor of front-loadingThe genetic code is highly optimized for error minimization (Freeland et al., 2000). This optimal genetic code is nearly universal across all taxa. Curiously, there is no phylogenetic tree consisting of less optimal codes present in basal lineages, with more optimal codes being in late-branching taxa. This is interesting because if the genetic code evolved gradually, starting with less optimal codes (there are far more sub-optimal codes than there are optimal codes) which were gradually fine-tuned to produce the universal optimal code, we might expect such a phylogenetic tree to exist. Arguing that the sub-optimal codes once did exist early in life’s history, but vanished once the optimal codes came on the scene (i.e., that they were outcompeted), looks awfully ad hoc. For starters, it is often argued by non-teleologists that flagellar genes would have non-flagellar homologs in the form of functional precursors. But if this truly is a prediction of the Darwinian/non-telic theory, then we must wonder why the Darwinian theory doesn’t predict that we should find a phylogenetic tree consisting of different genetic codes as described above. Significantly, the fact that less optimal genetic codes do exist in nature (see Freeland et al., 2000; note that these sub-optimal codes are secondarily derived — that is, they evolved from the canonical genetic code, not the other way around) is proof-of-concept that the universal optimal code can exist without causing less optimal codes to vanish from the scene. The below image illustrates a hypothetical phylogenetic tree consisting of less optimal genetic codes in deep-branching lineages. It exemplifies what could have been the case, with different codes evolving into more optimal codes.

Figure. Here, all branches on the tree are colored differently. Each different color represents a different genetic code; in this diagram, the deeper-branching lineages have sub-optimal codes. The higher you go on the tree, the more optimal the genetic code is. If such a tree existed in reality, it would be an extremely convincing piece of data against the front-loading hypothesis. That it does not exist is evidence in favor of the front-loading hypothesis.Imagine that such a phylogenetic tree did, in fact, exist. It would be convincing evidence that the extant genetic code or codes was the result of the blind watchmaker’s tinkering, gradually fine-tuning some early, sub-optimal genetic code. Yet such a tree does not exist, which is exactly what we would expect if the first life forms were designed with a highly optimized code — which follows from the front-loading hypothesis. It is evidence that the first genomes were advanced and fully optimized at the dawn of life. All of this is what we would expect if the first genomes were designed by a rational agent or agents — and this is what the front-loading hypothesis proposes. It is predicted by the front-loading hypothesis, as it is good design logic to design the first life forms with a highly optimized genetic code.Testable predictions of the front-loading hypothesisWe can test the front-loading hypothesis through several ways, two of which I will describe here:
1) The front-loading hypothesis predicts that the first genomes encoded genes that would be unnecessary (but beneficial) to early life forms, but necessary to the appearance of multicellular life forms and plants and animals. It predicts that the first organisms were not proto-cells, but highly advanced cells capable of terra-forming a hostile planet and able to shape future evolution in biased trajectories.
2) The front-loading hypothesis predicts that prokaryotic homologs of important eukaryotic/metazoan proteins will be more highly conserved in sequence identity than the average prokaryotic protein. This prediction makes sense from a rational design perspective because designing these prokaryotic homologs with functions that conserve their sequence identity will ensure that their 3D shapes will not be significantly changed by the blind watchmaker, preventing the appearance of eukaryotes (I realize that this prediction might sound a bit confusing — it’s past midnight where I am — so I’d be more than willing to elaborate on this).There are a number of things I’m interested in discussing here. I’d be interested in hearing the criticisms and objections some of you might have to my above essay or to the front-loading hypothesis. Some of you might have questions like how would future states be front-loaded? and other questions and critiques.Thoughts?P.S. Any grammatical or other errors in my essay are a reflection of the late hour, and not an indication of my education or lack thereof.ReferencesSharov, Alexei A. Genome increase as a clock for the origin and evolution of life. Biol Direct. 2006; 1:17.Freeland, SJ, et al. Early Fixation of an Optimal Genetic Code. Mol Biol Evol. (2000) 17 (4): 511-518.

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Wouldn't this be true, though, no matter what? Wouldn't the form of the genetic material always create a predisposition simply by virtue of being one thing as opposed to another?

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Yes. The difference here, of course, is that one evolutionary trajectory is planned, while the other is simply the result of contingency.

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Well I guess it depends on what aspects you're talking about. In a general sense, evolution is simply part of the natural operation of the world to which all reproducing lifeforms are subject.

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What I meant was that front-loading does not propose that all taxa were front-loaded, or even most.

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Well, there are a lot of examples of poor, sloppy design in the living world.

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Yes, and that'd be evidence that those particular biological systems are the result of the blind watchmaker's tinkering. Note, however, that any supposed poor design must be thoroughly analyzed before concluding that no rational designer would have done it that way.

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Why?

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Precisely because a phylogenetic tree consisting of sub-optimal codes in basal lineages is not what we would expect under front-loading; we would expect a universal optimal genetic code (or several optimal genetic codes), not a phylogenetic tree of genetic codes like I describe above. I guess it's not quite accurate to say "that it does not exist is evidence in favor of the front-loading hypothesis." Better would be: that there is a universal optimal genetic code, instead of a phylogenetic tree of genetic codes (as I describe above), is evidence in favor of the front-loading hypothesis? Why? Because it is expected under the FLE model. We'd predict that the first designed genomes were highly optimized such that when complex life forms do appear on the scene, they don't have to cope with a sub-optimal code, which could even lead to their extinction.

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The con is that an assumption is slipped in just as the carny magician slips the coin onto the four year old's ear with the intent of amazing the kid when he pulls a whole dime out of the tykes ear.

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And what is that assumption that is slipped in?

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The model is to intentionally misuse language so that some intent is implied and then to amaze the audience by pulling "intent" out of thin air.

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I'd like to you to present evidence to support the above statement. Thanks.

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If you look at the so called first prediction is not a prediction at all but instead simply a distortion of what the evidence actually shows. It implies some intent yet never offers any evidence of either intent or some critter that might have intent. It simply uses charged words to misdirect the audience attention.

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How is the first prediction a distortion of what the evidence actually shows? And what do you mean by a "critter that has intent"? That doesn't seem very relevant to the front-loading hypothesis.

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The second is pretty much the same. It is NOT a prediction at all but just a jumble of words meant to seem scientific but in reality only an attempt to hide the fact that the carny conman is trying to insert intent without the crowd noticing that the only intent is his intent to insert intent.

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You're going to have to back up the statement that the second prediction is "just a jumble of words" that is, in reality, only an attempt to be devious.

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I did present the evidence, I quoted your word salad.

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Huh? I think you mean "word-salad"? I know you claimed that I was doing some word-salad, but your evidence for that is where?

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I also told you what the assumption was, that there was some intent.

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All scientific hypotheses are based on an initial "assumption," that is, the premise. For example, Darwinian theory "assumes" that common descent has occurred; evidence is then found to support that idea. The FLE model proposes that the course of evolution was planned to some degree and that the earth was seeded with advanced unicellular organisms; evidence could then be found to support that proposal.

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They imply that there was some intent to include things that would be needed in the future.

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Of course that's what they imply because I was describing the front-loading hypothesis, a teleological hypothesis. I wasn't saying that those statements were necessarily true; I was saying that that is what the FLE model proposes.

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Wrong again, common descent is not an assertion but rather a conclusion based on the evidence.

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And similarly, the FLE hypothesis has been advanced based on various clues that has been provided by the world of life.

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Yes, you seem to begin with a conclusion and then look for evidence that can be twisted to support your conclusion.

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Actually, I begin with looking for the best explanation for various observations, like the universality of the genetic code. What is the best explanation for the observation of the universal optimal genetic code? In my brief essay, I explained why the non-teleological position does not explain the observation that there is a universal optimal code, found from the deepest branching taxa to later-branching lineages. Front-loading explains this observation nicely, without any ad hoc rationalizations. Thus, this is a clue to support the FLE hypothesis. I then listed two ways we could test the model; if we tested these predictions, and found them to be confirmed, the case for FLE would be strengthened.

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...no one has ever presented any evidence that there has been any plan or any planner...

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Did you read my essay? There, I provided a clue in the form of the genetic code that suggests FLE has occurred. You have yet to respond to this.

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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.

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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?

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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?

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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.

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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.

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Naturally a high quality genetic code is advantageous. But to argue that the sub-optimal genetic codes disappeared from the scene as a result of the appearance of the highly optimized code is ad hoc. Also note that there might actually be an advantage for prokaryotes to have a sub-optimal genetic code: radical mutations would be more frequent, and this could possibly accelerate evolution. You wouldn't have to go through multiple amino acid substitutions to get to a radically different amino acid. I.e., if you take a look at the PAM1 substitution matrix, there is a 0% probability that an alanine --> tryptophan substitution will occur. So, in order to get alanine to change into tryptophan, it'd have to be like this, for example: alanine --> arginine --> tryptophan. The canonical genetic code, then, is a good system for complex organisms, where radical substitutions will be very likely deleterious. But for bacteria, a sub-optimal genetic code, where radical mutations are far more frequent, this might just be a selective advantage.In response to the argument that HGT results in a selective advantage for a shared genetic code, I could just as easily respond that HGT reduces the selective advantage for a shared genetic code: horizontally transferred genes can be deleterious if the genes are translated and are incompatible with the genes in the original genome. An important point to realize about HGT is that selfish, mobile elements can be transferred laterally, and so can genes incompatible with the original genome - which means that HGT can be deleterious.

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Living prokaryotes are not ancient throwbacks, they do not represent the vestiges of an ancient world...

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While basal lineages are certainly not ancient, in a way they do represent vestiges of an ancient world. Thus, the observation that flagellar genes have been found in deeper-branching bacteria has been used as an argument by various investigators that the bacterial flagellum is more ancient than the type III secretion system.

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Welcome to EvC...

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Thanks - I saw your later message before I saw this one, so I'm replying to this one now.

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How do you intend to test this hypothesis?

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We could identify genes important to the development and function of multicellular organisms, and BLAST them against prokaryote genomes, and see if we get any significant hits.

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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.

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If a protein exists with homologs in all domains of life, then it does not follow from conventional theory that it must also be highly conserved in sequence identity - not any more so than the average protein. For example, actin has a homolog in prokaryotes: MreB. What does conventional theory say about MreB's degree of sequence conservation, in contrast with other prokaryotic proteins (and without knowing the function of MreB)?

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Interestingly, the 3D shape of proteins is much more highly conserved than sequence identity. I'm not really sure how your justification follows, either.

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Yes, but it is sequence identity that, in a large part, determines the tertiary structure of the protein. Thus, ensuring that the sequence identity is well conserved ensures that the basic 3D shape of the protein will be well preserved, which prevents the blind watchmaker from getting in the way of the front-loading objectives by significantly altering the protein's 3D shape.

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Okay, so we now know that you admit that there is no universal genetic code.

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I already stated that in my first post here, in my essay. I said the "nearly universal genetic code."That said, I really have little interest in continuing a discussion with you. I'd prefer to spend my time (and I haven't got too much of it) discussing biological origins with the likes of MrJack or DWIII, and not with those of you who seem to be fond of making snide remarks (e.g., "It also smells, more than a little, of a convoluted Christian apologetic, wherein humans are the result of front-loading by the Christian god").Cheerios!

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Panspermia, of course, pushes the problem one level deeper.

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Although Crick and Orgel abandoned directed panspermia later in their life, this particular quote from their paper is as relevant as ever:
It has also been argued that "infective" theories of the origins of terrestrial life should be rejected because they do no more than transfer the problem of origins to another planet. This view is mistaken; the historical facts are important in their own right. For all we know there may be other types of planet on which the origin of life a6 initio is greatly more probable than on our own. For example, such a planet may possess a mineral, or compound, of crucial catalytic importance, which is rare on Earth.

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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?

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No it would not necessarily follow. The front-loading designers may have evolved through non-teleological mechanisms. That's not a problem for front-loading since front-loading isn't so much about finding gaps in the non-teleological theory than in presenting positive evidence in favor of teleology. Also, from a philosophical point of view (I'm no philosopher, so I may very well be cut to shreds here): life might have no historic origin. If the universe is infinite, as many believe, life may also be infinite. I like to think, however, that it is not, 'cause then there'd be a good reason to pursure OoL research.

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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?

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Complex life forms probably couldn't survive the early, hostile earth. Bacteria are by far the more "survivable" organisms.

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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.

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Quite right, but we can still identify ancient systems over more recent systems based on phylogenetic analyses, for example. In other words, if deep-branching organisms (e.g., Firmicutes) had less optimal codes, while later-branching lineages had more optimal genetic codes, this would be a good chunk of evidence against the FLE hypothesis.

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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.

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Yea - but that it is possible that competing codes once existed isn't evidence that they did. There's no phylogenetic evidence whatsoever for the view that the canonical, optimized genetic code evolved gradually from sub-optimal codes.Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.Edited by Genomicus, : Lots of typos -.-