Darwin’s fossils freak out over ID in Brazil

_{Denyse O'Leary

June 26, 2019

Culture, Darwinism, Intelligent Design}

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Marcos Eberlin got their goat, we don’t doubt. Open access:

From the Final Remarks: Science, as a process, starts with the acceptance of our ignorance about a natural phenomenon and by seeking natural explanations for it. Hence, ignorance drives the engine of Science. Even if evolution were, hypothetically, rejected, contested by new data, scientists would have to study hard to find an alternative natural explanation that was able to explain everything that evolution explains today plus the new data that contested it.
Evolution is a fact and a well-supported scientific theory. It has endured daily and rigorous testing, and it stands as the unifying theory in biology (Rutledge and Warden, 2000). This says nothing about whether God created or did not create the world, as science is unable to distinguish a divinely guided evolution from a materialistic evolution. God may well have created the biological world through natural selection, mutation, speciation, extinction, etc. Still, evolution and Science would remain unscathed as Science is not concerned with why or who, but only with how.
Some creationists say that we must bring the evolution versus creationist debate to the classroom and claim that the opposition to the debate is anti-scientific. However, science is not about blind criticism (Meyer and El-Hani, 2013). Blind criticism is just as naïve as blind acceptance. Scientists must weigh the evidence before questioning a theory. The idea that all debates are equally scientific is misleading and it explains the sad emergence of flat-earthers and anti-vaxxers. A debate on what is the shape of our planet is not only pointless, but it is also dangerously harmful to the minds of the young students. A fruitful debate in a science class is restricted to those issues that lie within the scientific realm (Baltzley, 2016, Branch, 2016).
A recent study has suggested that science concepts, more than evolutionary basics, are critical to promoting evolution (Dunk et al., 2017). One way to reinforce these fundamentals would be the requirement of evolution and science fundaments in admission policies for biology professionals, particularly teachers (Larkin and Perry-Ryder, 2015; see Rutledge and Warden, 2000 for statistics). Claudia A.M. Russo and Thiago André, Genetics and Molecular Biology, Print version ISSN 1415-4757On-line version ISSN 1678-4685 Genet. Mol. Biol. vol.42 no.1 Ribeirão Preto Jan./Mar. 2019 Epub Feb 28, 2019 http://dx.doi.org/10.1590/1678-4685-gmb-2018-0086 More.

It’s those orchids, right? We always said, in the Uncommon Descent News virtual coffee room, it was those orchids that did in Darwin in Brazil. Oh yes, and Marcos Eberlin, of course.

See also: Jerry Coyne is already mad at Marcos Eberlin

and

Marcos Eberlin shouldn’t exist/

Comments

Darwin's Fossils. LOL! I just got it. That would be a great title for a show on cable in the year 2030. It's about a group of professors who comprise the lone holdout for the neo-Darwinist paradigm. Wishful thinking I know -- but still.hnorman42_{July 7, 2019
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BB
The only thing really open for debate is how evolution occurs. And, to be frank, other than the fine details, it is not being seriously debated by any credible scientist knowledgeable in the subject.
I don't follow that. You're saying that how it occurs is open for debate. The theory was supposed to tell us how it occurs. But you're saying here that there is some legitimate debate ("it's open for debate"). Or are you saying that the topic is debatable but nobody should debate it because we know how it occurs? So, it's not open for debate? It's open for debate by people who do not know how it occurs, but everybody else knows how it occurs therefore debate should be closed? Or, perhaps you are saying, "nobody really knows how it occurs so it should be debated"? That seems like what you're saying. If so, that is good. It is "open for legitimate, and therefore, necessary debate, because we do not know". Yes, the theory claimed to have the answer, but it does not. You follow this by saying "it is not being seriously debated by any credible scientist knowledgeable in the subject". Ok, it should be debated because we do not know how it occurs. Yes. It is necessary to debate it because the question is open. Yes. And, no credible scientists debate it. Ok. I think you've identified the problem here. I don't think we should consider those scientists to be "credible" or "knowledgeable" when they do not debate an issue that needs to be resolved. There an open and necessary debate, and they don't deal with it. Can someone point out to those scientists that they do not know how it happened, and that their theory has failed?Silver Asiatic_{July 4, 2019
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Bob O'H @39 That was bold and very good. Thank you. Yes, I think just a modest concession that does not mean more than we said, but still … It shows a lot of integrity. I appreciate it!Silver Asiatic_{July 4, 2019
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Brother Brian:
The only thing really open for debate is how evolution occurs.
The starting point is still open. The extent that evolutionary processes can take a population is still open- as in what changes can genetic change actually produce? Heck we don't even know what makes a human a human beyond a baby human is born after a successful mating between a male and female human. And without that knowledge universal common descent is an untestable concept devoid of science. So there are at least a few things that are really open for debate. But Brian cannot debate them as he doesn't know anything about it.ET_{July 4, 2019
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"Evolution" has several meanings: 1. Change over time; history of nature; any sequence of events in nature 2. Changes in the frequencies of alleles in the gene pool of a population 3. Limited common descent: the idea that particular groups of organisms have descended from a common ancestor. 4. The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations. 5. Universal common descent: the idea that all organisms have descended from a single common ancestor. 6. “Blind watchmaker” thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms. It is definition 6 that ID argues against and it is definition 6 that is being taught in public schools and universities, albeit without any supporting evidence. Materialistic evolution is definition 6. What say you, Claudia?ET_{July 4, 2019
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Claudia Darwin Russo:
Materialistic evolution does make predictions for all characteristics and all organisms.
It doesn't make any predictions.
Each new genome sequenced is a test of evolutionary theory, each new phylogeny reconstructed is also a test.
Nonsense. For one there isn't any scientific theory of evolution. And for another there isn't a mechanism capable of producing eukaryotes given populations of bacteria. Endosymbiosis doesn't help.
How come the pesticide that you buy in the market works for the cockroach in your house that has never been tested in?
It has nothing to do with evolutionism- ie the claim of universal common descent via blind and mindless processes.
The definition of Evolution is change within a population over time.
That is the definition equivocators use, yes. Look, Claudia, do you have something of substance to say?ET_{July 4, 2019
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Bob O'H @ 39 SA @ 37 – I agree.
Knock me over with a feather!bornagain77_{July 4, 2019
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SA per 37:
I think you’re conceding that you’d need to rely on HGT to rescue that situation. If so, I don’t think that hurts Ewert’s findings.
Exactly! It concedes the very point under debate. Namely that genomic evidence, contrary to what Claudia was trying to claim, does not support the evolutionary scenario. The genetic evidence is severely discordant to what Darwinists originally predicted. Thus they resort to ad hoc excuses to avoid falsification of their theory.
An Enzyme's Phylogeny Reveals a Striking Case of Convergent Evolution - Jonathan M. - February 11, 2013 Excerpt: The authors attempt to account for the incongruity by positing that "the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism." They thus attribute the shared genes to horizontal gene transfer (with no offered mechanism), a proposition that has become a catch-all to explain away severe conflicts between evolutionary phylogenies.,,, "phylogenetic conflict is common, and frequently the norm rather than the exception" (Dávalos et al., 2012). Is it possible that the real reason for such striking and widespread phylogenetic discordance is that evolutionary biologists are looking at biology through the wrong lens? Could the reason that there is so much difficulty in correlating organisms to a tree be that no such tree exists? http://www.evolutionnews.org/2013/02/an_enzymes_phyl068911.html
Again, contrary to what Claudia was trying to claim, the genetic evidence is severely discordant to what Darwinists originally predicted.
'The theory makes a prediction (for amino acid and nucleotide sequence studies); we've tested it, and the prediction is falsified precisely.' Dr. Colin Patterson Senior Principal Scientific Officer in the Paleontology Department at the British Museum "Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species." (Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, "Understanding phylogenetic incongruence: lessons from phyllostomid bats," Biological Reviews of the Cambridge Philosophical Society, Vol. 87:991-1024 (2012).)
bornagain77_{July 4, 2019
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Bob O'H:
there are well known evolutionary mechanisms that would make a dependency graph structure more likely.
But are they blind watchmaker evolutionary mechanisms and how do you know? Or are you happy to just equivocate and never back it up?ET_{July 4, 2019
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Brother Brian:
I don’t have a problem with natural selection being a huge driving force of evolution.
If it is then your position is in BIG trouble as natural selection is impotent with respect to universal common descent.
Since then we have discovered DNA, mutations, meiosis, inversions, transpositions, gene duplication, HGT, epigenetics and other sources of variation.
And still nothing that can have bacteria evolving into eukaryotes and nothing that can produce new body plans and new body parts.
In my mind, the more sources of heritable genetic/phenotypic variation we find, the more viable selection becomes as a driving force.
LoL! Natural selection is a process of elimination. You mischaracterize it by calling it selection. But we all know why evos do that. Also natural selection requires that the genetic changes be random/ happenstance. And no one has figured out a way to make that determination.
It is a long way from what Darwin envisioned, but it still comes down to differential survival/reproduction due to the variation of heritable traits in the population.
And with that mechanism you are stuck in populations of bacteria.ET_{July 4, 2019
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SA @ 37 - I agree.Bob O'H_{July 4, 2019
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BB
Since then we have discovered DNA, mutations, meiosis, inversions, transpositions, gene duplication, HGT, epigenetics and other sources of variation. In my mind, the more sources of heritable genetic/phenotypic variation we find, the more viable selection becomes as a driving force. It is a long way from what Darwin envisioned, but it still comes down to differential survival/reproduction due to the variation of heritable traits in the population.
A question we often raise here something like "what is the evolutionary origin of epigenetic relationships"? So, while proposing other sources of variation helps explain the origin of new traits (conceding that mutations cannot do it), in some cases, as with epigenetics, the new source of variation has to have an evolutionary explanation, and that only makes the situation more complex and difficult to explain.Silver Asiatic_{July 4, 2019
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Bob O'H
there are well known evolutionary mechanisms that would make a dependency graph structure more likely
I think you're conceding that you'd need to rely on HGT to rescue that situation. If so, I don't think that hurts Ewert's findings.Silver Asiatic_{July 4, 2019
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BB
But the speed with which they can become pesticide resistant does …
It seems you agree that her response was very poor. So, you decided to answer for her and correct it. I'd prefer to hear her explanation, to see how she deals with the question. It helps to see how familiar she is with the dialogue on this. In my experience, many evolutionary academics are sheltered from debate. So, they speak in generalizations and can sometimes seem very ill-informed and incapable of explaining their own view, as Claudia did here.Silver Asiatic_{July 4, 2019
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Thank you for conceding that HGT occurs. But it's not obvious how omitting an evolutionary mechanism that would lead to the pattern you find is "giving evolution every benefit of a doubt". If you don't include the evidence, it can't falsify a theory can it?Bob O'H_{July 4, 2019
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" there are well known evolutionary mechanisms" Give me a friggin break. Calling horizontal gene transfer an evolutionary mechanism certainly does not make it so. You can't even account for one piece of the intricate molecular machinery that would be involved in horizontal gene transfer. Moreover, the paper I listed stated that "Ewert specifically chose Metazoan species because “horizontal gene transfer is held to be rare amongst this clade.” Thus, somehow in the mind of a Darwinist, even giving evolution every benefit of a doubt, evidence is simply never allowed to falsify the theory. Darwinism, at least how Darwinists treat it, is NOT a falsifiable science! It is a pseudo-scientific religion for atheists.bornagain77_{July 4, 2019
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ba77 -
Bob is basically claiming that Ewert’s own bias bled over into his analysis. That claim is not true.
The second sentence is right - the claim in first sentence is false. And thank you for providing a link to a blog post that backs up my point - there are well known evolutionary mechanisms that would make a dependency graph structure more likely.Bob O'H_{July 4, 2019
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Bob is basically claiming that Ewert's own bias bled over into his analysis. That claim is not true. If anything, Ewert bent over backwards to be as fair as possible and to not let 'mechanisms we already know about' influence the results.
Response to a Critic: But What About Undirected Graphs? - Andrew Jones - July 24, 2018 Excerpt: The thing is, Ewert specifically chose Metazoan species because “horizontal gene transfer is held to be rare amongst this clade.” Likewise, in Metazoa, hybridization is generally restricted to the lower taxonomic groupings such as species and genera — the twigs and leaves of the tree of life. In a realistic evolutionary model for Metazoa, we can expect to get lots of “reticulation” at lower twigs and branches, but the main trunk and branches ought to have a pretty clear tree-like form. In other words, a realistic undirected graph of Metazoa should look mostly like a regular tree. https://evolutionnews.org/2018/07/response-to-a-critic-but-what-about-undirected-graphs/
Thus, being as careful as possible to not unduly favor the design model over common descent,, Ewert still found that the design model was overwhelming favored over common descent. Favored to an overwhelming degree over common descent. As Dr. Huneter noted:
Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence. This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits. But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data.
He is a more detailed defense of the 'unbiased' nature of Ewert's paper. As the article notes "Bayesian reasoning is important in that it gives us some hope of escaping from the tyranny of fundamentalist presuppositions, whether evolutionist/naturalistic fundamentalism or creationist/biblical fundamentalism (though interestingly Thomas Bayes was a clergyman)."
The Dependency Graph Hypothesis — How It Is Inferred - Andrew Jones - July 23, 2018 Excerpt: In Bayesian Model Selection, the best model is the one that makes the data most probable. There is no point in having a simple model if it does not explain the data (if the probability of the data is zero). Likewise there is no point in having a model that is more complex (and thus even less improbable) than the data it needs to explain. That would be overfitting. The overall complexity is the probability of the model combined with the probability of the data given the model. In Ewert’s paper, there are two overarching models that we want to distinguish: the ancestry tree, and the dependency graph, but there are myriad possible sub-models, each contributing to the overall probability of the overarching model. Average Values and Bayesian Priors Unfortunately, both models (the tree of life and the dependency graph) are extremely complex, with a very large number of adjustable parameters. This might seem to make the question undecidable: We often argue that the tree of life is a terrible fit to the data, requiring numerous ad-hoc “epicycles” to make the data fit. We might further argue that a particular dependency graph is a better fit to the data. But a believer in common descent might reasonably respond that our theory is also not parsimonious; if you add enough modules you could explain literally anything, even random data. It seems that deciding between the two models can never be a rational decision; it seems it will always involve a good deal of intuition or even faith. Fortunately, however, there are ways to tame the complexity enough to get objective and meaningful answers. The main strategy for coping with the complexity is summation (or mathematical integration) over all possibilities. Ewert handles many of the parameters by integration: these include the edge probability b (the expected connectivity) of the nodes and the different propensities to add ? or lose ? genes on each of the n nodes. This may seem strange, but it is standard probabilistic reasoning. If the probability distribution of Y (for example, the actual number of gene-losses) depends on X (for example, ?), but you don’t know X, you can still calculate the probability of Y if you have the probability distribution of X. In many cases we don’t even know what the true distribution of X would be. In such cases, Ewert assumes that every possibility has an equal probability (a flat distribution) because this should introduce the least bias. This may also seem strange, but it is quite common in Bayesian reasoning, where it is called a flat prior. Although the prior distribution of X is technically a choice, and yes that choice has some influence on the result, the way Bayesian reasoning works is that the more data you add, the less the particular choice of prior matters. The important thing is to choose a prior that is not biased; a prior that allows the data to speak, if you like. Bayesian reasoning is important in that it gives us some hope of escaping from the tyranny of fundamentalist presuppositions, whether evolutionist/naturalistic fundamentalism or creationist/biblical fundamentalism (though interestingly Thomas Bayes was a clergyman). The idea is that we want to make sure that the many things we don’t know don’t stop us from making reasonable inferences using what we do know. ,,, https://evolutionnews.org/2018/07/the-dependency-graph-hypothesis-how-it-is-inferred/
bornagain77_{July 4, 2019
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ba77 - I'm amused at a claim that Bayesian methods aren't based on any "subjective judgement call". The one thing that makes Bayesian methods Bayesian in that they explicitly incorporate subjectivity. Also, Ewert's paper has an important disclaimer:
Critics will be quick to point out that there are a variety of mechanisms to explain deviations from the hierarchical pattern, such as incomplete lineage sorting, gene flow, horizontal gene transfer, convergent evolution, and gene resurrection. These mechanisms occur in nature, but are not included in this model. Recall that we are testing predictions about whether a particular dataset will more closely fit a tree or the dependency graph. Mechanisms which produce deviations from the tree are not relevant to that prediction
IOW a dependency graph will be favoured even without design, because of mechanisms that we already know about.Bob O'H_{July 4, 2019
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BB. you are severely confused. First and foremost I appealed to the evidence itself. You yourself were the one who disparaged my sources, i.e. "Darwin’s God and YouTube videos aren’t exactly credible sources." In response, I listed a few of the sources. Eugene V. Koonin, Didier Raoult and Eric Bapteste, etc.. etc... (And could have listed many more of the same caliber). All of them, contrary to what you tried to imply about my sources, are highly credible sources for genomic evidence. Moreover, if anything, they are biased towards Darwinian presuppositions, not Design presuppositions. Which makes their critique all the more devastating. An argument from authority would have been to say something like, "so and so says Design is true therefore Design must be true", without any appeal to the evidence whatsoever. I did not do that, I appealed directly to the evidence itself first and foremost, Moreover, my supposed 'authorities' are themselves of the evolutionary mindset and are biased against Design being true. And yet, even though they themselves are biased against design, they are the ones who are adamantly claiming that the evidence itself does not match Darwinian predictions. The truth is that you yourself do not like what they have found in the evidence and therefore you just threw anything on the wall that you could think of to try to avoid accepting the evidence as it is. Moreover, Ewert's paper "wasn’t based on any kind of subjective judgement call. Dr. Ewert used Bayesian model selection, which is an unbiased, mathematical interpretation of the quality of a model’s fit to the data."
Please understand that the decision as to which model fit each scenario wasn’t based on any kind of subjective judgement call. Dr. Ewert used Bayesian model selection, which is an unbiased, mathematical interpretation of the quality of a model’s fit to the data. In all cases Dr. Ewert analyzed, Bayesian model selection indicated that the fit was decisive. An evolutionary tree decisively fit the simulated evolutionary scenarios, and a dependency graph decisively fit the computer programs as well as the nine real biological datasets. ,,, Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent.
So BB, perhaps you now want to argue that Bayesian model selection is "arguing for authority"? I would not put it past you to try to do so. After all, you already resort to Ad Hominem when you disparage me personally as "BS77" instead of ever honestly addressing any of the evidence that I present (as you currently are doing). You said this debate "will be very informative and educational." And I guess so far it is "informative and educational.". Right off the bat we learn that you yourself are severely biased in how you are willing to interpret the data. And we also learn that you will ignore evidence at the drop of a hat, with any flimsy and self-refuting excuse that you can find, if the evidence does not fit your desired narrative. Thanks for teaching unbiased observers that lesson about your personal character.bornagain77_{July 4, 2019
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BB
Combining a Gish gallop fallacy and...
Debasing someone who is no longer with us is completely inappropriate. And repeatedly referring to BA77 as BS77 is just childish. I understand why you do it, but doing so just lowers you to his level. I think that you are better than that.Ed George_{July 3, 2019
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BS77
BB, perhaps you should check my sources a little more carefully???
Combining a Gish gallop fallacy and an argument from authority fallacy at the same time. I am impressed. But, no thanks. I have better things to do with my time. However, if you are willing to make a concise argument, in your own words, I will respond to it. Until then, I will continue to follow my own advice and ignore you.Brother Brian_{July 3, 2019
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AaronS1978
My objections are normally against strict natural selection that somehow managed to create everything we see and know.
I don’t have a problem with natural selection being a huge driving force of evolution. What I think is still poorly understood is the source of genetic variation that selection can work on. In Darwin’s day nobody knew about DNA and mutations. Since then we have discovered DNA, mutations, meiosis, inversions, transpositions, gene duplication, HGT, epigenetics and other sources of variation. In my mind, the more sources of heritable genetic/phenotypic variation we find, the more viable selection becomes as a driving force. It is a long way from what Darwin envisioned, but it still comes down to differential survival/reproduction due to the variation of heritable traits in the population.Brother Brian_{July 3, 2019
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Here is a paper from last year:
This Could Be One of the Most Important Scientific Papers of the Decade - July 23, 2018 Excerpt: Now we come to Dr. Ewert’s main test. He looked at nine different databases that group genes into families and then indicate which animals in the database have which gene families. For example, one of the nine databases (Uni-Ref-50) contains more than 1.8 million gene families and 242 animal species that each possess some of those gene families. In each case, a dependency graph fit the data better than an evolutionary tree. This is a very significant result. Using simulated genetic datasets, a comparison between dependency graphs and evolutionary trees was able to distinguish between multiple evolutionary scenarios and a design scenario. When that comparison was done with nine different real genetic datasets, the result in each case indicated design, not evolution. Please understand that the decision as to which model fit each scenario wasn’t based on any kind of subjective judgement call. Dr. Ewert used Bayesian model selection, which is an unbiased, mathematical interpretation of the quality of a model’s fit to the data. In all cases Dr. Ewert analyzed, Bayesian model selection indicated that the fit was decisive. An evolutionary tree decisively fit the simulated evolutionary scenarios, and a dependency graph decisively fit the computer programs as well as the nine real biological datasets. http://blog.drwile.com/this-could-be-one-of-the-most-important-scientific-papers-of-the-decade/ Bayesian model selection http://alumni.media.mit.edu/~tpminka/statlearn/demo/ New Paper by Winston Ewert Demonstrates Superiority of Design Model - Cornelius Hunter - July 20, 2018 Excerpt: Ewert’s three types of data are: (i) sample computer software, (ii) simulated species data generated from evolutionary/common descent computer algorithms, and (iii) actual, real species data. Ewert’s three models are: (i) a null model which entails no relationships between any species, (ii) an evolutionary/common descent model, and (iii) a dependency graph model. Ewert’s results are a Copernican Revolution moment. First, for the sample computer software data, not surprisingly the null model performed poorly. Computer software is highly organized, and there are relationships between different computer programs, and how they draw from foundational software libraries. But comparing the common descent and dependency graph models, the latter performs far better at modeling the software “species.” In other words, the design and development of computer software is far better described and modeled by a dependency graph than by a common descent tree. Second, for the simulated species data generated with a common descent algorithm, it is not surprising that the common descent model was far superior to the dependency graph. That would be true by definition, and serves to validate Ewert’s approach. Common descent is the best model for the data generated by a common descent process. Third, for the actual, real species data, the dependency graph model is astronomically superior compared to the common descent model. Where It Counts Let me repeat that in case the point did not sink in. Where it counted, common descent failed compared to the dependency graph model. The other data types served as useful checks, but for the data that mattered — the actual, real, biological species data — the results were unambiguous. Ewert amassed a total of nine massive genetic databases. In every single one, without exception, the dependency graph model surpassed common descent. Darwin could never have even dreamt of a test on such a massive scale. Darwin also could never have dreamt of the sheer magnitude of the failure of his theory. Because you see, Ewert’s results do not reveal two competitive models with one model edging out the other. We are not talking about a few decimal points difference. For one of the data sets (HomoloGene), the dependency graph model was superior to common descent by a factor of 10,064. The comparison of the two models yielded a preference for the dependency graph model of greater than ten thousand. Ten thousand is a big number. But it gets worse, much worse. Ewert used Bayesian model selection which compares the probability of the data set given the hypothetical models. In other words, given the model (dependency graph or common descent), what is the probability of this particular data set? Bayesian model selection compares the two models by dividing these two conditional probabilities. The so-called Bayes factor is the quotient yielded by this division. The problem is that the common descent model is so incredibly inferior to the dependency graph model that the Bayes factor cannot be typed out. In other words, the probability of the data set, given the dependency graph model, is so much greater than the probability of the data set given the common descent model, that we cannot type the quotient of their division. Instead, Ewert reports the logarithm of the number. Remember logarithms? Remember how 2 really means 100, 3 means 1,000, and so forth? Unbelievably, the 10,064 value is the logarithm (base value of 2) of the quotient! In other words, the probability of the data on the dependency graph model is so much greater than that given the common descent model, we need logarithms even to type it out. If you tried to type out the plain number, you would have to type a 1 followed by more than 3,000 zeros. That’s the ratio of how probable the data are on these two models! By using a base value of 2 in the logarithm we express the Bayes factor in bits. So the conditional probability for the dependency graph model has a 10,064 advantage over that of common descent. 10,064 bits is far, far from the range in which one might actually consider the lesser model. See, for example, the Bayes factor Wikipedia page, which explains that a Bayes factor of 3.3 bits provides “substantial” evidence for a model, 5.0 bits provides “strong” evidence, and 6.6 bits provides “decisive” evidence. This is ridiculous. 6.6 bits is considered to provide “decisive” evidence, and when the dependency graph model case is compared to comment descent case, we get 10,064 bits. But It Gets Worse The problem with all of this is that the Bayes factor of 10,064 bits for the HomoloGene data set is the very best case for common descent. For the other eight data sets, the Bayes factors range from 40,967 to 515,450. In other words, while 6.6 bits would be considered to provide “decisive” evidence for the dependency graph model, the actual, real, biological data provide Bayes factors of 10,064 on up to 515,450. We have known for a long time that common descent has failed hard. In Ewert’s new paper, we now have detailed, quantitative results demonstrating this. And Ewert provides a new model, with a far superior fit to the data. https://evolutionnews.org/2018/07/new-paper-by-winston-ewert-demonstrates-superiority-of-design-model/
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BB, perhaps you should check my sources a little more carefully???
Eugene V. Koonin Senior Investigator National Center for Biotechnology Information (NCBI) National Library of Medicine (NLM) National Institutes of Health (NIH) Bldg. 38A, Room 5N503 8600 Rockville Pike Bethesda, MD 20894, USA Didier Raoult - most cited microbiologist in Europe Eric Bapteste Institut de Biologie Paris Seine; Department of evolutionary biology; University Pierre et Marie Curie Bapteste owns a PhD in evolutionary biology and a PhD in philosophy of biology. He is Directeur de Recherche at the CNRS. Kevin J. Peterson Academic Appointments Professor of Biological Sciences Professor in the Ecology, Evolution, Ecosystems and Society Graduate Program Adjunct Professor of Earth Sciences Noah A Rosenberg - Stanford University James H Degnan University of New Mexico | UNM · Department of Mathematics & Statistics etc.. etc... etc...
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So I read that definition and I immediately responded exactly the same way, this is something that’s really not debatable, because it’s so broad and nobody honestly is going to disagree with that I agree with the fact that the real debate is whether it happened the way it did, whether it used natural selection viva Darwinian method or other methods or mixture of them. Much like in the thread about hybridization. For me I was debating what honestly was more prevalent. My objections are normally against strict natural selection that somehow managed to create everything we see and know. An over emphasis of Darwinian evolution. I don’t think natural selection is the star of the show, I honestly believe life is the real star it is far more intelligent than we gave it credit for, And I see intelligent design supports my view better then Darwinian natural selection evolution.AaronS1978_{July 3, 2019
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VB
“The definition of Evolution is change within a population over time.” I’m down with that but this is hardly controversial is it?
No rational being would deny this. I don’t think Ms. Russo said this in an attempt to be controversial. The only thing really open for debate is how evolution occurs. And, to be frank, other than the fine details, it is not being seriously debated by any credible scientist knowledgeable in the subject.Brother Brian_{July 3, 2019
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BS77
It failed.
Except for the thousands and thousands of concrete examples published in the literature. Darwin’s God and YouTube videos aren’t exactly credible sources.Brother Brian_{July 3, 2019
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per CDR at 7:
Each new genome sequenced is a test of evolutionary theory, each new phylogeny reconstructed is also a test.
It failed
“The genomic revolution did more than simply allow credible reconstruction of the gene sets of ancestral life forms. Much more dramatically, it effectively overturned the central metaphor of evolutionary biology (and, arguably, of all biology), the Tree of Life (TOL), by showing that evolutionary trajectories of individual genes are irreconcilably different. Whether the TOL can or should be salvaged—and, if so, in what form—remains a matter of intense debate that is one of the important themes of this book.” Koonin, Eugene V. (2011-06-23). The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 76-80). Pearson Education (USA). Kindle Edition. A New Model for Evolution: A Rhizome – Didier Raoult – May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html Sweeping gene survey reveals new facets of evolution – May 28, 2018 Excerpt: Darwin perplexed,,, And yet—another unexpected finding from the study—species have very clear genetic boundaries, and there’s nothing much in between. “If individuals are stars, then species are galaxies,” said Thaler. “They are compact clusters in the vastness of empty sequence space.” The absence of “in-between” species is something that also perplexed Darwin, he said. https://phys.org/news/2018-05-gene-survey-reveals-facets-evolution.html Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php Toward a Consensus: An Open Letter to BioLogos on the Genetic Evidence - Cornelius Hunter - May 27, 2016 Excerpt: One of Venema's basic points (see here and here) is that the genomes of different species are what we would expect if they evolved.,,, What Does the Evidence Say? For starters, phylogenetic incongruence is rampant in evolutionary studies. Genetic sequence data do not fall into the expected evolutionary pattern. Conflicts exist at all levels of the evolutionary tree and throughout both morphological and molecular traits.,,, As one evolutionist explained, "The tree of life is being politely buried.",,, http://www.evolutionnews.org/2016/05/toward_a_consen102879.html Reviewing The Evolution Revolution, the NCSE Offers Uninformed Criticism that Misses the Point - Lee M. Spetner - January 13, 2016 Excerpt: Some researchers in the life sciences, who are not necessarily knowledgeable about evolution (including Levin), think that the various trees based on different biological systems or on protein- and DNA-sequence data yield the same tree. Life scientists once thought that trees based on anatomy and on the molecular sequences of proteins and DNA would be the same, but they were wrong (Nichols 2001; Degnan and Rosenberg 2006; Degnan and Rosenberg 2009; Heled and Drummond 2010; Rosenberg and Degnan 2010). They thought at least there would be consistency among the trees based on the DNA sequences of different genes, but again they were wrong. They then hoped that if they used the whole genome instead of individual genes, the data might average out and things would be better. In fact, it only made matters worse (Jeffroy et al. 2006; Dávalos et al. 2012). All this is discussed in my book. Levin is mistaken about what he calls the "cornerstone" of the evidence for common descent. He criticizes my rejection of common descent. I reject common descent because it is based on only circumstantial evidence. The drawback to circumstantial evidence is that it needs a valid theory to connect the evidence with the conclusion, and evolutionary theory is invalid, as I explain at length in my first chapter. There is thus no valid evidence for common descent -- and certainly not what Levin calls its "cornerstone." http://www.evolutionnews.org/2016/01/reviewing_the_e102281.html Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885 UCEs - Another Big Failure (For Darwinism) - Cornelius Hunter Dec. 20, 2012 Prediction Evolution predicts that more distant species should have greater differences in their genomes. Evolutionists were astonished to discover these highly similar DNA sequences in such distant species. In fact, across the different species some of these sequences are 100% identical. Species that are supposed to have been evolving independently for 80 million years were certainly not expected to have identical DNA segments. “I about fell off my chair,” remarked one evolutionist. [1],,, Reaction “It can’t be true” was one evolutionist’s reaction to the UCE findings in recent years. [6] The findings falsify predictions of evolution, but they are true and they have been verified independently.,,, http://darwins-god.blogspot.com/2012/12/uces-see-somethingsay-something.html Finally, a 2009 article in New Scientist titled, "Why Darwin was wrong about the tree of life," states: "For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. etc.. etc.. etc..
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