It does not claim to be a model of how the very first organisms 3.8bya evolved to the LUCA 2bya.
Instead, it claims that biological life as we know it today can be traced back to a LUCA population, and the characteristics of that population can be gleaned from an understanding of the inferred genetic composition of that population.
Instead of making conclusory statements about LUCA, why don’t you try a different tack: Why not read the recommended article and its citations, then bring some questions about that reading to the forum for biologists to answer?
In my opinion, that strategy would be far more productive and far more educational. It would bring light instead of heat.
True, but it always indicates a temporal series of event, one of which is the cause (or source in this context) of the other. In this case there is something ancestral to trace back to, our microbial mother, LUCA.
Vertical descent produces a generally consistent nested hierarchy, that is, regardless of how you look at it you will generally get the same flow of relationships through time. Its similar to your family tree: DNA analysis, for example, will consistently place you as a descendant to your biological parents because you indeed descended from them.
Again, realize that a consistent nested hierarchy is a prediction of common descent and that’s what we see in datasets.
Sure and that’s due to common descent. At different levels and time points of the hierarchy we share pseudogenes, ERVs, transposons, LINES, SINES, all of which are genetic markers: these markers are great for testing common descent. All great apes, for example, have the same GULO pseudogene mutations, in the same place and with almost exactly the same mutations (exon deletions and more) . At the universal level, we see highly conserved systems spread out across all the domains of life like nearly universal metabolic pathways or the core of the ribosomes. All of these things are predictions of common descent and they pan out.
Sure, but that’s not what the data tells us. One of my favorite studies looked at this in some detail.
Another cool paper is the one below. They didn’t investigate universal common descent, but they showed how evolutionary biologists quantitatively test common descent using biological data. They directly competed special, independent creation with common descent and just like in the previous study I linked a above, common descent sealed the deal.
If there are things you don’t understand in the paper, @Chris_Falter (a statistician) and @John_Harshman (a phylogeneticist) can help out.
One more thing though. These papers demonstrate that we don’t assume common descent like you always say. Rather, they are conclusions reached after rigorous evaluation.
Its one, LUCA.
However, it is possible that there were multiple starting points prior to LUCA. We don’t just know yet.
HGT moves genes or other genomic elements across species and that can complicate phylogenetic analysis. Instead of getting this neat diagram of genes flowing down from ancestors to descendants in a tree-like manner (as Darwin naively thought), we see this web of gene transfers all across mainly prokaryotes and unicellular eukaryotes. This web, “forest”, “network” makes it a lot harder to detect the signal of common descent. When we get to multicellular organisms the signal gets a lot clearer and when we look at lifeforms together, the signal of common descent is strongest close to the tips, but diminishes as we go to deeper branching times (which is not surprising).
Everyone should notice how Bill has tried to derail the thread after showing him how scientists quantitatively test for common descent. It completely obliterates his claim that we simply assume common descent. Instead of admitting he was wrong, he has now shifted to questioning the validity of these findings simply because science proceeds by methodological naturalism (even though MN has absolutely nothing to do with scientific rigor). This demonstrates Bill is not here looking for what is right, he is here to do ID apologetics. There is no point arguing with an ID-brain-dead fellow.
In actual scientific research, a rigorous study is one that adopts the best research practices when checking if the predictions of a hypothesis are consistent with observations or doing something else. I repeat, it has nothing, absolutely nothing, to do with methodological naturalism. You are just telling us you are a complete buffoon when it comes to understanding how actual scientific research works.
If I wanted to compare the efficacy and safety of a new drug to a standard one, there are a number of factors that would make this comparative study rigorous. Double-blinding, randomization, having well-defined controls, etcetera are examples of these factors. Ditching one or more of these factors would diminish the rigor, hence, quality of the study. This is an example of how scientific research can be deemed rigorous or not.
Science proceeds via methodological naturalism because natural explanations have proven to be the best means of making sense of the natural world. However, there is nothing in principle that hinders science from considering “supernatural” explanations (whatever supernatural means). As long as these supernatural theories make verifiable predictions amenable to the methods of scientific testing, then science will have a go at it. In both papers I cited above, the “supernatural” hypothesis of separate origins was tested and its predictions did not pull through, invalidating the hypothesis; the converse was observed for common descent (did you even read both papers?).
Finally, evolution occurs in parallel, not in sequence. Get rid of that stupid strawman.
This is word salad (to borrow from John Harshman). It makes no sense and I bet you don’t understand what you wrote here. For example, how can you say we should “compare [the] alternative of LUCA to multiple origins” when the alternative to LUCA is multiple origins by default. In one of those papers I cited, a key prediction of separate origins, non-coalescence at the oldest time points possible, failed to bear out; instead the further one went back in time the more the sequences coalesced validating common descent; that’s how science works Bill!
Are you aware that Behe accepts common descent? If Behe’s “design detection process” failed to convince him to reject the common descent of man and apes, then why should it convince us?
More importantly, Behe has no design detection process. In his interview with Dr Dan, he was asked to provide a criteria for quantifying the extent irreducible complexity must reach before it can be deemed impossible for evolution to catch up to. Behe gave nothing! Yes, nothing after 20 long years of rambling about ICity. We have seen ICity evolve before our very eyes in the Lenski LTEE and other places and with the same mechanisms that guide evolutionary change in general. We have no need for the dead ideas parroted by the ID crew and its legion of brain-dead followers.
We’re not talking about a mere “claim.” We’re talking about a robust theory that makes predictions, many of which involve mathematics that you clearly refuse to engage with, even the simplest ones.
That alternative model has suffered strong rejection following a handful of empirical tests. There aren’t multiple starting points, but one.
So you choose to propose magic as the source of genes instead of having to do the research into potential natural mechanisms. ID is indeed the death of science.
More importantly, gene families are mostly created by gene duplication events followed by some divergence. Remember Joe Thornton? Someone in his lab reconstructed the evolutionary history of the hemoglobin (a member of the globin gene family) using ancestral sequence reconstruction, beautifully demonstrating sufficiency of natural mechanisms (gene duplication in this case) to account for the origin of gene families.
We can explain the origin of genes through a variety of mechanisms, most of which have been demonstrated in realtime . Why don’t you examine this evidence instead of pretending it doesn’t exist.
That’s why its called population genetics. Hematology exists because a substance called blood exists, parasitology exists because organisms called parasites exists. Sometimes I wonder why the more reasonable ID people who participate on the forum don’t come in to correct you.
Ewert tested his model. He literally described that in his paper.
If by common design you mean separate origins, then this (the part of your comment I bolded) has been done. Genes and gene families have been used to test separate origins vs common descent. I don’t need to remind you who the winner was:
Let’s not forget you asked for genes and gene families to be used for testing separate origins vs common descent and that’s exactly what happened here and boy-o-boy did special origins take a beating . Who wants to bet Bill is going to shift the goalposts now, @Chris_Falter?
Winston used methodological naturalism, so kindly throw away his paper and its results.
No. Sequence change is brought about mutations (and recombination). Mutations are continually generating variation and when selection shows up due to some environmental pressure, organisms with adaptive mutations will contribute more progeny to the next generation.
Yes, but in the meantime mutations increase genetic diversity.
No one says so.
Now you think neutral theory is the dominant paradigm . You are a clown indeed. Stop with the strawman please.
How is that in any way a problem? You invoke these numbers but you don’t even attempt to do a calculation that indicates this should be considered problematic numbers.
Bill what are “searches”? Above you speak about fixed mutations, and now you mention “10^8 searches”? What is that?
You have already been cited papers that show novel enzyme functions evolved in less than 3000 bacterial generations. In some cases a few weeks to a few months is all it took for the bacteria to sample the sequence space in the vicinity of their existing enzymes and find mutants that conferred novel functions.
There is no capacity for this to happen in the LTEE, as there are no compounds in the media that wild-type E coli has not been exposed to before. It already has enzymes that can metabolize literally everything they encounter in the growth medium. The experiment was intentionally designed with maximum simplicity in mind to answer questions about the repeatability of evolution, and the long-term adaptability, not to answer questions about the evolution of novelty or under what conditions bacteria evolve new functions or greater complexity.
There have been other such experiments done, though on much shorter timescales than the LTEE. Again, you’ve been cited some of them, where (for example) novel enzymatic functions evolved within weeks or months.
Organisms with slower generation times have higher mutation rates and bigger genomes, and they do things like meiosis and sex(homologous recombination).
In a way it is unfortunate, though understandable, that so much attention has been devoted to the evolution of the ability to metabolize citrate in one of the strains, as that has often obscured the more fundamental findings of the experiment.
If virtually all functional proteins have alpha helices and beta sheets, can you then see why another functional protein may be a short distance in sequence space from another?
Textbook natural selection in an asexual population. It is well recognized that multiple competing beneficial mutations co-exist at any given instance of time in the LTEE (by a phenomenon known as clonal interference), partly facilitated by the daily recurrence of phases of exponential competitive growth, followed by population bottlenecking, and generally speaking the beneficial mutations with stronger effect eventually win out in the long term.
More precisely, the scientific method is not concerned with determining whether or not something is “natural”. To my mind, “methodological naturalism” is best understood as the assumption that everything we observe and measure operates according to fundamental laws and principles that are never violated. So if we observe something that violates what we thought was an inviolable law, it means we must abandon or change our understanding of that law. We don’t have the option of saying “Oh, something supernatural did that, so it doesn’t count.”
This does not mean that the existence of the supernatural is ruled our or discounted. It just has to be accommodated within the methodology described above, if it exists.
This would appear to be an obvious strawman. The real “objection” would appear to be not that “we cannot observe its direct action”, but we don’t even have a hypothesised mechanism for this action – making it impossible to test for the existence of this interaction even indirectly.
Lacking even a hypothetical mechanism for how this (purely hypothetical) mind acts on the target that it is supposed to “arrange parts”, this claim (I wouldn’t even call it a hypothesis), is clearly utterly useless for science and is a very weak argument against a set of mechanisms that have been hypothesised, observed, tested, and studied in great detail.
A useful analogy might be the claim that it is fairies (or the Earth’s magnetic field, if you wish for a non-supernatural hypothesis), rather than internal combustion, that make car engines work. You don’t need to directly observe fairies (or the Earth’s magnetic field) doing this to test this hypothesis, but you do need a hypothesis of how the fairies (or the Earth’s magnetic field) do it. Otherwise you’d have no idea what indirect observations would tend to confirm or disconfirm the presence of their action.
That’s true. It is primarily interested in vetting the validity of created hypotheses. These hypotheses could be about supernatural or natural events.
True.
True. If the global flood hypothesis turned out to be right, it would defy a lot of things we know about the laws of nature, but that doesn’t mean scientists would throw their hands up in the air and say God did it. Instead, they would create new hypotheses to explain observations and go ahead to see if they hold up.
This is the counter argument but I find it deficient for several reasons. We understand what evolution is and we can create predictive models of how it works as its function can be empirically demonstrated.
We do know to quite some detail how both human and digital minds work and we know both are capable of iterative improvement by trial and error, in a similar fashion to evolution, to generate both concepts and physical constructs.
Proposing untestable and unobservable minds as a mechanistic explanation for an observation that evolution more than satisfactorily explains by itself just because one is a-priori decided a mind must be the reason does not have scientific precedent. I therefore think that hypothesising minds is both poor unnecessary and poor science.
Also, having a mind as a mechanistic explanation is very useful for science as it provides a strong counter argument to help with rigor for evaluating a hypothesis. I think exploring the possibility of a separate ancestry hypothesis has already been refuted by observable genetic data, and as such would be a total waste of time.
Without repeating myself, you keep asserting the minds hypothesis without rigorous empirical support beyond God said so in the man-made human redacted bible assembled by fallible humans blinded by both motive and culture, and keep asserting that nested hierarchy is consistent with a hypothesis that is consistent with anything and hence useless as a hypothesis.
Even if the universe was created, independent creation of “fully formed animals” is inconsistent with the data. You have no explanation for consilience of independent phylogenies.
You’re welcome to give a model of separate ancestry that has the same predictive and explanatory power as common descent. Be careful to show that it actually predicts something, for example about the fossil record.
Substitution biases, consilience of independent phylogenies in everything from the sequences of shared similar genes, comparative anatomy, to embryology and molecular functions. You have no explanation for ANY of this. You have no explanation for why scientists can experimentally reconstruct ancestral genes and show their functions are consistent with expectations given what we know from geology and the fossil record.
What you have are complaints about the very method of science itself (parsimony and falsification are out the window with your methods), and you have appeals to gaps and appeals to ignorance.
Diametrically opposite to demonstrable fact. Every piece of “new sequence data” further confirms already accepted models and hypotheses about evolution and universal common descent. Particularly the endosymbiotic theory for the origin of the mitochondrion during eukaryogenesis, and members of lokiarchaea as closest extant relatives to the ancestors of the endosymbiotic host. Simpler antecedents of many previously unique eukaryotic systems and molecules have been found in the lokiarchaeota.
You don’t know anything about the field and you are talking out of your rear end and you should be embarrassed about it.
I suppose I would be wasting my time if I tried to again explain why that scenario (assuming by “animals” you meant life forms) is fully compatible with the LUCA model. Right?
. You are a clown indeed. Stop with the strawman please.