In my original post (which you merely scanned, looking for things to disagree with) I called it an estimation. When I did a quick summary of my argument, some nuances got left out it, including the word “estimate”.
Glad that we are in agreement that the ateleological view does not predict what my teleological view predicts, namely that organisms ancestrally lacking an SOS response will not be found.
As I said. The ateleological view is fine either way. Unlike my teleological view, which makes more risky predictions.
Here we see the absurdity of requiring that the teleological view makes predictions that is incompatible with the ateleological view. As we have just seen, the ateleological view can accommodate any observation, both “A” and “not A”. Any predictions generated by a teleological view can therefore be ignored, as “the ateleological view can accommodate that”.
A situation has been set up in which a teleological view can only be allowed on the table if it predicts the existence of a Precambrian rabbit.
We went over this in the thread on the genetic code. At most, this method shows the existence of a bacterial LCA (Last Common Ancestor) and an archaeal LCA. And a phylogenetic three consisting of two members will always produce the same topology, by matter of sheer mathematical necessity: A—B
I’m afraid I don’t follow your point here. Could you elaborate?
The difference is that fish exist. We have a field of fish biology. This constrains the imagination when considering the transition from fish to tetrapod.
Not so with the hypothetical non-cellular world. All life on Earth is cell-dependent, including viruses. In abandoning the confines cell biology, the same imagination that is able to imagine the evolution of man-made mousetraps, step-by-darwinian-step, is free to imagine cells with RNA genomes.
Not so. The recurrent laryngeal nerve of the giraffe helps the giraffe survive, but I wouldn’t call it good design.
What are you saying here? That every structure found in extant organisms was present in the first replicator?
As a synapomorhy is defined as a shared feature derived from a common ancestor that distinguishes a clade from other clades, this is true as a matter of definition.
It certainly doesn’t help us resolve whether the ateleological view predicts that the first replicator had an SOS response system. Something you seem to disagree with, without explaining why.
You are very confused. Whether evolution is teleological or ateleological it doesn’t predict anything of the sort. Evolution is a process by which populations change genetically and physiologically, it does not predict that some particular feature should be universally shared or not. That is a matter of evidence to determine.
Your teleological view is not a model, it’s basically an assertion. Your assertion is that life was somehow designed with independent ancestry of bacteria and archaea, and that the common ancestor of bacteria had an SOS response. That’s not a prediction, that’s an assertion.
To predict this you need a model that somehow physically entails that bacteria and archaea should not share ancestry, and yet came into existence with an SOS response. Instead you just seem to have defined this to be the starting point of your view.
Also, you first wrote: “There are organisms today that have lost the SOS response. Are you saying that if an organism that was ancestrally lacking an SOS response was discovered, evolutionary biology would be in trouble?”
This I take to mean you are asking whether, if we found an organism that today has an SOS response, but had ancestors that lacked it, this would somehow be a problem for evolution? Well obviously not, since that would just imply the SOS response once upon a time did not exist but then evolved. It should be noted that the only way to determine that some organism ancestrally lacked an extant feature would be by comparative genetics, as in to see that the feature is restricted to some clade that nests within a larger clade that lacks the feature.
Strangely enough, given your later statement that you think it’s absurd that your teleological view is required to make predictions that set it apart from the ateleological view, here you seem to be confusing common descent with a particular stance on whether the evolutionary process is teleological or not.
I actually agree with you that there could be common descent of all life, and yet evolution could in principle be teleological, just as there could be independent ancestry and the independent evolution of all clades could be ateleological. Whether there is some sort of intent or goal behind evolution does not in and of itself make any predictions unless you think you know what that goal is and have a model of how this goal is supposed to be reached.
But you don’t have such a model, and have not stated what you think the purpose or goal of the evolutionary process, so it’s just not possible to derive any predictions about what we should expect to see from your teleological view.
You have merely defined a starting point for your view, and it seems it’s based entirely on the observed phylogenetic distribution of certain cellular components in bacteria and archaea. How this is supposed to be a prediction of the teleological view is anyone’s guess.
To say that evolution is ateleological is to say it’s a process without a goal or purpose, not a statement about when X evolved, or how far removed in generations we today sit from when it evolved and how many other ancestral lineages before or after X evolved, happened to go extinct.
Hey, I will admit to getting confused myself about what exactly I was arguing in my previous post, and mistakenly conflated arguing about common descent of bacteria and archaea, as opposed to arguing about whether evolution is teleological vs ateleological and what(if anything) that predicts.
As I wrote above, it seems to me that whether evolution is teleological or not, that does not in and of itself lead to any particular predictions about what features we should be able to discover are restricted to which clades. Evidence from comparative genetics can usually only tell us what happened and when, it can’t tell us why. If the SOS response was ancestrally lacking or not is not a prediction of any model either of us have proposed.
You can of course just declare that you think the common ancestor of bacteria had one and then rationalize that this would make sense from a teleological perspective, but you could do that at any stage of life’s evolution. If we had no evidence for life simpler than fish, you could in the same way declare that life started at fish with all the shared features of fish because it was designed to be that way in order to achieve some future goal through the evolutionary process. It’s completely ad-hoc.
There are not two members, there are two clades. The bacterial and archaeal trees contain thousands of members each, each monophyletically in their own (bacterial and archaeal) clades.
If you make a phylogenetic tree based on (say) 16S rRNA based on both baterial and archaeal species, you get some tree with a bacterial clade and an archaeal clade. And you will not find bacteria in the archaeal clade, nor will you find archaea in the bacterial clade. And in each of the two clades, there will be subclades. There will be some particular topology of branching of all the included species.
Now the question to be answered is, if we take the same species as used for the 16S rRNA tree, and do one for 23S rRNA, how will that tree look? Well it turns out it will be highly similar to the 16S rRNA tree we did. The same bacteria will most of the time be most closely related to each other in this new 23S tree, as they were in the 16S tree. And more closely related clades in the 16S tree will also be more closely related clades in the 23S tree. And so on and so forth.
Now we do a tree, using the same species, based on some ribosomal protein, or tRNA gene, or aminoacyl-tRNA-synthetase. What we will disover is ALL these trees will be very similar to each other.
This result does not obtain by mathematical necessity. There is no reason two particular bacterial species should be consistenly most closely related to each other based on trees derived from different translation system components. It is entirely possible that a tRNA gene from some other, more distantly related bacterium would work just as well in either of them.
But then why does this result obtain, if NOT by mathematical or functional necessity? Well the simplest explanation is that all the components used to infer a phylogenetic tree really did go through the same genealogical history. The trees end up like that, similar to each other to an overwhelming degree, because the trees are each constrained by a shared genealogical history.
Also remember, in that other thread I also showed another kind of evidence for common descent, which is that internal nodes in 23S rRNA trees of bacteria and archaea, which have NOT been rooted using outgroups from the “opposing clade”, still exhibit higher pairwise sequence alignment scores to members from the opposing clade, than do extant species on average.
That is to say, internal nodes in the bacterial tree (not rooted using any archaeal sequences), nevertheless is more similar to extant archaeal sequences, than extant bacterial sequences are. And the same is true for internal nodes in the archaeal tree, internal nodes are more similar to extant bacterial species sequences, than extant archaeal sequences are.
Further still, the internal nodes in both the bacterial and archaeal trees are more similar to each other(yield higher pairwise sequence alignment scores), than the nodes from the archaeal trees are to extant bacterial sequences, or the nodes from the bacterial trees are to extant archaeal sequences.
Well your argument seems to be that because the DNA replication machinery (DNA polymerases and other associated replication enzymes and proteins), and the enzymes reponsible for membrane lipid biosynthesis of bacteria and archaea are not homologous, this should cause us to consider that they might not actually share a common ancestor. Right?
So I argue against this by pulling on the evidence for the common ancestry of the bacterial and archaeal translation system.
And my point is that since the translation system is functionally, anabolically anterior to the components you used in your argument(the enzymes and proteins that carry out DNA replication, and membrane lipid biosynthesis, are each made by the translation system), the evidence for the common ancestry of the translation system is more fundamental(the fact that the translation system is the only universally shared feature of all known cellular life is pretty strong evidence for this). Also the translation system is significantly more complex(in terms of the sheer number of different components involved) than membrane lipid biosynthesis or DNA replication, so it would be less parsimonious to posit that the translation system evolved or was created twice independently, than it would be to posit that DNA polymerases and a handful of lipid-making enzymes evolved or were created twice independently.
That is true enough, but that’s also the evidence that shows has been through a long process of change of seemingly “fundamental” functions. What I’m arguing for here is that analyzing the history of life gives historical precedent for thinking none of the things we see are actually fundamentally required for life. It would be difficult to imagine how I could survive without arms, legs, and eyes. Yet worms exist! Going back far enough we lose more and more of these seemingly critical functions, yet persist as a form of life. That should cause us to to seriously consider that we could go back so far all the apparently shared attributes of life as we know it, had some time in the past where even they did not exist, or had a different form.
It is an observation that the species in a clade share these features. What I am trying to emphasize is the tree-like structure of shared features, and how different shared features appear at different parts of the tree.
First of all, when I’m talking about the “ateleological view”, I’m talking about the ateleological view of the origin of life, not about evolution.
Second of all, one’s view of the origin of life does lead to different expectations for its subsequent evolution.
Consider the first replicator. Not the last universal common ancestor (LUCA), but the first unit capable of replicating itself in a way that makes it subject to darwinian selection. The ateleological view requires that this be as simple as possible. The reason for this is easy to understand: The simpler the first replicator, the less is required of raw chance and the more can be put into the hands of natural selection, the blind watchmaker.
This is why ID critics sneer at probability calculations for the random assembly of a cell. They don’t envision the first life consisting of a cell, but of something far simpler, like a self-replicating RNA molecule.
From this, two things follow:
1. None of the structures found in extant life existed in the first replicator
2. For every structure X, every extant organism with structure X ultimately descends from an organism without structure X
The second statement follows from the first and should be considered an utterly non-controversial statement about conventional evolutionary biology: Every organism with eyes ultimately descend from an organism without eyes. The same goes for feathers, brains, and SOS response systems.
Now, from this we cannot conclude that those originally X-less organisms have any X-less ancestors alive today. So the ateleological view is fine whether they are alive today or not. But we can conclude that they must once have existed.
This means that in claiming that they never existed and will therefore never be found, one is making a risky prediction, in contrast to, for example, “predicting” that the moon will turn out not to be made of cheese.
Now, as to how this prediction is generated:
I don’t claim to have a model. In fact, I’ve repeatedly referred to my views as a “conjecture”.
More to the point, any prediction is an assertion about what will or will not be found. And the prediction follows naturally from how I think about design. As I wrote earlier in the thread:
Expecting that engineers want their designs to be robust and able to overcome the challenges of the environment isn’t an ad hoc expectation. It flows naturally from what we could term “good design” principles.
But let’s see what this teleological perspective leads us to expect. Remember, I’m only suggesting that the original population of cells was designed. That means that if a particular structure found in extant life was designed, it would have been present in an ur-state in the first cells, from which it has diversified and become modified by evolution. For example, antifreeze proteins that evolved in the Antarctic notothenioids 10-14 million years ago would be a poor candidate for design.
This means that I would expect the phylogenetic distribution of the machinery required for regulated mutagenesis, such as the SOS response, to show that the system traces back to an ur-state in the first bacteria. And indeed, both recA and lexA, which play key roles in the regulation of the SOS response, are practically universal in bacteria. And those bacterial groups which lack them are thought to have secondarily lost them. This points to the existence of an original SOS response core, which evolution has then unfolded into the systems we see today.
Can you clarify what you mean by “physically entail” and how it relates to design thinking? When an engineer investigates an unknown piece of technology and expects that an electricity-consuming part is connected to an electricity-generating part, is that something that is physically entailed?
I’m talking about the archaeal LCA and the bacterial LCA, as reconstructed from your 16s rRNA and 23s rRNA comparison. The observed pattern is also consistent with an originally designed ur-archaea and ur-bacteria with identical translation systems, from which extant life has diverged.
The cell consists of a number of circular, chicken-and-egg like processes. So the ribosome may be functionally prior to DNA replication and membrane lipid biosynthesis, but it is itself dependent on upstream DNA sequences to encode its constituent molecules, chaperones to fold those molecules, and a cellular architechture enclosed by a membrane. Which are again dependent on the translation machinery.
From the ateleological perspective, common descent is indeed the most parsimonious explanation for the universality of the translation machinery, as it is unlikely that blind, natural processes would have produced the same machinery twice.
Not so from the teleological perspective, in which designers can reuse their designs. Which reasons might a designer have for reusing the translation system? For one thing, reusing the translation system also means reusing the genetic code, which enables life to take advantage of horisontal genetic transfer.
Historical arguments can be useful, but one should be mindful that other historical arguments, based on other narratives, can be made. For example, I might tell the story of how we once thought that all that was fundamentally required for life was a blob a protoplasm. Later, it was thought that viruses could represent a precellular stage of life. Now, we know that all life depends on a complex set of molecular machinery, and that even noncellular parasites need a cell to reproduce.
Not really, no. You are confusing the view that life’s origin and evolution is ateleological(as in not for some purpose) with some sort of philosophical principle that we should prefer more likely over less likely explanations.
Life’s origin and evolution not happening for some purpose has no implications for the degree to which life’s origin is or must be likely or unlikely, simple or complex. Some might even say that if life is not for some purpose, but just some random fluke, it is more reasonable to think it’s origin would appear to have been unlikely. It’s not an argument I would buy myself, but I can still see where they’re going with that.
Even so I would generally agree with you that, given a choice, we should prefer more likely over less likely explanations. The opposite seems to be irrational.
This is why ID critics sneer at probability calculations for the random assembly of a cell. They don’t envision the first life consisting of a cell, but of something far simpler, like a self-replicating RNA molecule.
Not exactly. Rather ID critics (such as myself) sneer at probability calculations for an originating process that simply isn’t known or understood. It is senseless to try to calculate the odds of some event or process we don’t even know what was.
From this, two things follow:
1. None of the structures found in extant life existed in the first replicator
2. For every structure X, every extant organism with structure X ultimately descends from an organism without structure X
Perhaps with the exception of RNA (if that was the first self-replicator) I agree those do follow from the idea that life began as some bare self-replicating molecule from which everything else descends and subsequently evolved.
The second statement follows from the first and should be considered an utterly non-controversial statement about conventional evolutionary biology: Every organism with eyes ultimately descend from an organism without eyes. The same goes for feathers, brains, and SOS response systems.
Now, from this we cannot conclude that those originally X-less organisms have any X-less ancestors alive today.
From that alone, no.
So the ateleological view is fine whether they are alive today or not. But we can conclude that they must once have existed .
Based merely on the idea that life did not originate and evolve for some purpose, no. Because that statement doesn’t have any obvious entailments, you’d need additional premises and auxiliary hypotheses to derive predictions about what earlier life should have been like. Perhaps combined with models about how different kinds of pre-biological chemistry and physics could work, or with a model about how the evolutionary process is likely to unfold, could you derive genuine predictions about earlier stages of life.
Now, as to how this prediction is generated: (…)
I don’t claim to have a model. In fact, I’ve repeatedly referred to my views as a “conjecture”.
More to the point, any prediction is an assertion about what will or will not be found. And the prediction follows naturally from how I think about design. As I wrote earlier in the thread:
I agree with that, but that doesn’t get you to predicting the existence of an SOS response in particular. An SOS response might be one way to enhance a capacity to overcome the challenges of changing environments(bacteria still do mutate and evolve without having a mechanism to elevate the rate of mutation), but it is not the only way, and there are many organisms that don’t have one. Now, you can certainly rationalize that the SOS response was one such mechanism designed to enhance the capacity to meet and overcome environmental challenges by facilitating evolutionary change. Which is what you seem to be doing. You don’t predict it, you rationalize it. I don’t think it’s a bad rationalization, as it does makes sense to me, but I think we should be clear that this is what it is.
But let’s see what this teleological perspective leads us to expect. Remember, I’m only suggesting that the original population of cells was designed. That means that if a particular structure found in extant life was designed, it would have been present in an ur-state in the first cells, from which it has diversified and become modified by evolution. For example, antifreeze proteins that evolved in the Antarctic notothenioids 10-14 million years ago would be a poor candidate for design.
This means that I would expect the phylogenetic distribution of the machinery required for regulated mutagenesis, such as the SOS response, to show that the system traces back to an ur-state in the first bacteria.
If you think the SOS response was designed and put into the first bacterium, yes. But then that isn’t a prediction (that it would be present in the first bacterium), it’s a premise. An assumption.
And indeed, both recA and lexA, which play key roles in the regulation of the SOS response, are practically universal in bacteria. And those bacterial groups which lack them are thought to have secondarily lost them. This points to the existence of an original SOS response core, which evolution has then unfolded into the systems we see today.
This isn’t a prediction. You speak of this as a prediction, but it’s sort of your opening premise. You begin with the premise that the SOS response was designed to be present in the first bacterium, and then you “predict” it will be present in the last common ancestor of all bacteria. Not really a prediction I’m afraid.
To predict that, you’d need a model of the designing and originating process. Analogously to how a chemical non-design account for life’s origin would have to start with some initial conditions and chemicals, and then from there the laws of physics operating from those initial conditions leads to some particular molecules or structures coming into existence.
So you’d need to somehow model the designer and show that, given such and such a designer with these capacities and these desires, this particular structure would be expected to come into existence.
I’m not sure whether you mean to ask if the engineer’s expectations of the designed components are physical entailments(he can’t help but expect this because he is physically determined to do so?), or do you mean an electricity consuming part must of it’s own nature necessarily be physically hooked up to an electricity generating part?
In either case, the answer is no. I don’t think the engineer necessarily HAS to expect such a connection(some devices come without batteries), nor do I think such a connection follows automatically from the laws of physics(there is no physical law that says the batteries MUST be there, though if you ask me I think there should be).
Now if the engineer is investigating a device that is actively consuming electricity, then yes I think it is physically entailed that the device is hooked up to something that generates electricity. Not because that would be good design(It’d be even better design to have an actively running device that consumes electricity without the need to have it generated anywhere, I’d be really impressed by such a design), but because the laws of physics says there must be such a device(you can’t have a consuming device running without a generating one).
Okay, but then that’s completely meaningless as a response to my argument, since nobody would infer trees with only two members, and nobody would consider the results of such a “tree” to be evidence for anything at all. What matters here are the consilience of the trees containing many dusins, if not hundreds of species of bacteria and archaea, as inferred from different translation system components.
Note though, I’m only invoking this argument as evidence for common descent of bacteria and archaea. Not as evidence for whether life’s origin and evolution is or is not teleological.
The observed pattern is also consistent with an originally designed ur-archaea and ur-bacteria with identical translation systems, from which extant life has diverged.
Sure, but then that’s observationally indistinguishable from common descent. And why then think there was independent ancestry of bacteria and archaea if their shared components exhibit ancestral convergence? Could you then not also invoke the same argument for independent ancestry of clades at much “lower” taxonomic ranks? Primates exhibit ancestral convergence to, for example, a rodent common ancestor, because they were actually designed to use identical ancestral genes from which they both subsequently diverged independently?
Not anabolically. It is true that the recurrent production of new ribosomes when the old ones degrade in daughter cells following binary fission is dependent on the reliable replication of the DNA that encodes ribosomal components. But in any living cell, the enzymes that carry out DNA and phospholipid biosynthesis are made by the translation system.
If you think about it you can see that going back through trillions of cell divisions to the very first cell, there could never have been a cell replication event where the daughter cell did not inherit fully intact, still-functioning ribosomes.
But there could have been cells that continued to function which did not inherit intact still-functioning lipid-biosynthesizing or DNA-replicating enzymes. If the cell inherited ribosomes (and the requisite transcriptional machinery for expressing other relevant genes), it could rebuild it’s DNA replicating machinery and membrane lipid biosynthesis from the ground-up. It could not do so if it only inherited DNA replicating machinery and lipid making enzymes, because then it could never translate any protein coding genes.
Logically I agree that would explain ancestral convergence in trees from independent clades. But you have now fine-tuned the teleological view to be compatible with the same evidence as one would expect from common descent: Consilience of independent phylogenies, ancestral covergence of internal nodes in independent clades.
But why re-use the translation system, but have different DNA replication machineries and lipid biosynthesizing enzymes? There doesn’t seem to be any obvious adaptive or functional reason for it. Where we find hyperthermophilic archaea, we find hyperthermophilic bacteria. This rationalization can be applied at any taxonomic level. Why have some shared components, but independently evolve others?
That is still thought by many.
Now, we know that all life depends on a complex set of molecular machinery, and that even noncellular parasites need a cell to reproduce.
We don’t know that all life depends on this. Life as we know it uses a complex set of molecular machinery to accomplish various tasks, but we don’t actually know that all life that could exist requires these systems for it’s existence. This problem is partially definitional of course. If you define life to be cellular and having the capacity to internally biosynthesize all it’s constituents from simple inorganic precursors picked up from the environment, then sure that would probably require these components.
But are simpler forms of life without these systems possible? To pick just one example, life today uses complex enzymes like topoisomerases and helicases to unwind and separate DNA strands so they can be replicated by DNA polymerases. But a mere temperature cycle can accomplish the same unwinding and strand separation as these two complex classes of enzymes.