Common Descent, Common Design, and ID

_{Jonathan Bartlett

April 16, 2021

Intelligent Design}

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Mung had asked me to do a thread on common descent and common design. So, anyway, I’ll get things started by stating my own thoughts on these ideas. I intend this to be an open discussion, but I also find having a starting idea tends to help get things started.

So, as I have maintained for the last decade, I believe there is no fundamental conflict between ID and common descent. That is, it is fully possible to hold to both at the same time.

In fact, I would say that ID *potentially solves* many problems that common descent would bring. For instance, if you have gaps that are unbridgeable by a traditional Darwinian mechanism, you could posit that there was a prior source of information that the organism used to bridge the gap.

That being said, I don’t myself hold to common descent. If so, how does one explain the commonalities of organisms? The common explanation of this is “common design”. That is, since the same designer was designing these organisms, then we should expect repeated motifs to be used to solve various problems, various design ideas presented with variation, etc. The question is, is there a way to distinguish common design and common descent?

Well, to start with, common descent can actually be a mechanism for implementing common design. Therefore, inferring common design doesn’t necessarily tell you much about common descent.

Additionally problematic is that common descent actually depends on having a specific model of the origin of life. To understand this, let us say that instead of being rare, life comes about rather easily, but ALWAYS in the SAME WAY (i.e., builds the same starting organism, which we’ll call X). Therefore, if you find two X’s, there is NO WAY to tell if they are related by ancestry, despite the fact that they are identical! Let us then say that X is likely to branch to Y and then Z. Again, we could easily have two Zs that share NO common ancestors!

As you can see, inferring common descent as a definite conclusion requires a number of auxiliary hypotheses. These may or may not be reasonable, but they are there. However, *rejecting* common descent can be done with fewer.

Rejecting common descent can be done in one of two ways that I can think of:

Have a model that better fits the character space of organisms, or
Show that certain gaps are unbridgeable genetically.

#1 I believe has been done (at least on an initial basis) by Winston Ewert, with his dependency graph model. #2 is harder because, as I mentioned, in theory there could be repositories of information that help you close the gap. However, you could show that #2 *requires* information to close the gap, and then look and see if any such information repositories are known. Obviously, we might find information repositories in the future, but the question always is about what can we do with the knowledge we do have without overly-worrying about the knowledge we don’t have.

Anyway, along these lines, I think that Stephen Meyer has done a fairly good job with #2 in Darwin’s Doubt, where he discusses the origin of the phyla.

In short, ID can work inside or outside a Common Descent framework. However, ID also allows more degrees of freedom in biological thought, and many in the ID movement feel that the evidence against common descent outweighs the evidence for it. That means that many of the similarities in organisms are the results of common design and not common descent, but there is no logical contradiction in asserting both.

Those are my thoughts – what are yours?

Comments

From the OP:
Rejecting common descent can be done in one of two ways that I can think of: Have a model that better fits the character space of organisms, or Show that certain gaps are unbridgeable genetically.
ok, but how does the theory of "common design" do either of these? If it does not, should ID proponents perhaps be willing to say, ok, we should take a step back? I was hoping for a fleshed-out theory of common design. One at least worthy of competing against the theory of common descent. I have not seen one. But I very much appreciate the OP and the opportunity to discuss. Common Design needs to explain the pattern if it ever hopes to compete with Common Descent. And it needs to have a mechanism other than inheritance from a common ancestor!Mung_{April 17, 2021
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Gordon Davisson:
Just invoking common design doesn’t work as an alternative explanation, because what needs to be explained isn’t just that organisms are similar, it’s the pattern of similarities and differences.
Exactly so. And "Common Design" has no explanation of that pattern. Or at least none that I have seen. So once again, I think that johnnyb deserves a great deal of credit for being willing to broach this subject.Mung_{April 17, 2021
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kf@11:
Mung, Mung, calling Mung . . .
I'd be happy to give you my phone number!Mung_{April 17, 2021
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From the OP:
Well, to start with, common descent can actually be a mechanism for implementing common design. Therefore, inferring common design doesn’t necessarily tell you much about common descent.
Yes! But you say that you do not hold to common descent. So by what mechanism does one species come to share the same "design" as another species, if not by inheritance? Common Descent easily explains Common Design. It's still not clear how Common Design explains anything that can't also be explained by Common Descent, much less that it offers a better explanation. Common Design seeks to explain the same things that are attributed to Common Descent. It's offered as an alternative to Common Descent. Can "Common Design" accomplish this? In order to do so, it must explian what common descent cannot. It most appeal to something other than the mechanism of inheritance. If not, why not?Mung_{April 17, 2021
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I suppose Mung is trying to claim that the genetic code is universal and is therefore proof of universal common descent. There are a few holes in his theory. First, it turns out that the genetic code in not universal,
Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011 Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal:?"The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10)?OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 19 variants of the genetic code).?Simple counting question: does "one or two" equal 19? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two. http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html Universal Genetic Code? No! - January 18, 2016 Excerpt: “To date, the National Center for Biotechnology Information (NCBI), which houses all published DNA sequences (as well as RNA and protein sequences), currently acknowledges nineteen different coding languages for DNA… “,,, This was a shock to me. As an impressionable young student at the University of Rochester, I was taught quite definitively that there is only one code for DNA, and it is universal. This, of course, is often cited as evidence for evolution.,,, In the end, it seems to me that this wide variation in the genetic code deals a serious blow to the entire hypothesis of common ancestry, at least the way it is currently constructed. Perhaps that’s why I hadn’t heard about it until reading Dr. Rossiter’s excellent book. http://blog.drwile.com/?p=14280 The Genetic Codes http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c podcast 2017 - Brian Miller interviews Paul Nelson on universal common ancestry. Listen in as Nelson describes how common descent predicts one – and only one – genetic code. Yet, this is not what we find. https://www.podomatic.com/podcasts/intelligentdesign/episodes/2017-04-10T14_52_38-07_00
Secondly, alternative splicing patterns and/or codes are species specific. i.e. Where we find the greatest differences between humans, chimps, kangaroos, dolphins, etc.. etc.. is not in the DNA sequences but is in the ‘species-specific’ alternative splicing patterns and/or codes between the different species. As the following article states, “The alternative splicing patterns are very different even between humans and chimpanzees,”
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F
In fact, “Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, and,,, As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes,, collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification.”
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing – 2016 In Brief Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013). http://iakouchevalab.ucsd.edu/publications/Yang_Cell_OMIM_2016.pdf
To say that the preceding findings present a problem for the 'bottom up' gene-centric view of Darwinists is to make a severe understatement. This finding is a straight-up empirical falsification of their foundational ''bottom up' gene-centric assumption.bornagain77_{April 17, 2021
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The denial of Agent causality as an adequate causal explanation is science's biggest blind spot. Indeed, it's biggest insanity.
A Professor's Journey out of Nihilism: Why I am not an Atheist - University of Wyoming - J. Budziszewski Excerpt page12: "There were two great holes in the argument about the irrelevance of God. The first is that in order to attack free will, I supposed that I understood cause and effect; I supposed causation to be less mysterious than volition. If anything, it is the other way around. I can perceive a logical connection between premises and valid conclusions. I can perceive at least a rational connection between my willing to do something and my doing it. But between the apple and the earth, I can perceive no connection at all. Why does the apple fall? We don't know. "But there is gravity," you say. No, "gravity" is merely the name of the phenomenon, not its explanation. "But there are laws of gravity," you say. No, the "laws" are not its explanation either; they are merely a more precise description of the thing to be explained, which remains as mysterious as before. For just this reason, philosophers of science are shy of the term "laws"; they prefer "lawlike regularities." To call the equations of gravity "laws" and speak of the apple as "obeying" them is to speak as though, like the traffic laws, the "laws" of gravity are addressed to rational agents capable of conforming their wills to the command. This is cheating, because it makes mechanical causality (the more opaque of the two phenomena) seem like volition (the less). In my own way of thinking the cheating was even graver, because I attacked the less opaque in the name of the more. The other hole in my reasoning was cruder. If my imprisonment in a blind causality made my reasoning so unreliable that I couldn't trust my beliefs, then by the same token I shouldn't have trusted my beliefs about imprisonment in a blind causality. But in that case I had no business denying free will in the first place." http://www.undergroundthomist.org/sites/default/files/WhyIAmNotAnAtheist.pdf
bornagain77_{April 17, 2021
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kf@29 Do you see, in anything that I have written, any denial of what you say? I have the utmost respect for you. How is the common code passed on from one generation to the next? Is it not by the mechanism of inheritance? I'm not talking the Darwinian mechanism's ability to generate the things you talk about . The code is passed on from one generation to the next. That it is present in the descendants of the ancestors is easily explained by common descent. To say that the presence of this code in all these different species is not because they share a common ancestor, but rather due to "common design" requires some explanation. Do the proponents of "common design" have a better explanation of why this code appears in so many species, in the pattern of distribution, in which it appears, that does not resort to a religious explanation?Mung_{April 17, 2021
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The mechanism for common design is a mind that created the design. What mechanism do we use to create thoughts? It's the immaterial power of intelligence. As for how the design is implemented in nature, it's through various singularities. As the big bang is a singularity (what mechanism caused it?), so is the creation of planet earth (finely tuned) the emergence of life on earth, the emergence of mammalian life, the emergence of human life. Same mechanism as the big bang. Designed in mind, then implemented.Silver Asiatic_{April 17, 2021
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From the OP:
In fact, I would say that ID *potentially solves* many problems that common descent would bring. For instance, if you have gaps that are unbridgeable by a traditional Darwinian mechanism, you could posit that there was a prior source of information that the organism used to bridge the gap.
I propose that these are not problems that Common Descent would bring. They are problems that the Darwinian mechanism would bring. That intelligent design can solve the problem is not an argument against CD. That the organism had at its disposal a prior source of information indicates that that could be passed on to descendants is not a counter to common descent, but an acceptance of it, as a mechanism to pass on favorable "information.". This is a question that advocates of Common Design need to address if Common Design is supposed to be an alternative to Common Descent. To accept Common Descent is not to accept the Darwinian mechanism, which suggests that the presence of these features that can be passed on from one generation to the next is entirely unrelated to any future outcome.Mung_{April 17, 2021
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The fossil record, from the Cambrian explosion onward, does not support universal common descent. But instead reveals a 'top-down' pattern of disparity preceding diversity. Which is exactly the opposite pattern that Charles Darwin predicted with his 'bottom-up' diversity preceding disparity model.
Scientific study turns understanding about evolution on its head – July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,, Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,, http://phys.org/news/2013-07-scientific-evolution.html
As well, the supposed evidence for universal common descent, via genetic comparisons, was refuted by Winston Ewert.
The Dependency Graph of Life - Winston Ewert - 2018 Abstract The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency graph. We evaluate several predictions made by this model about both biological and synthetic data, finding them to be fulfilled. https://bio-complexity.org/ojs/index.php/main/article/view/109
Dr. Cornelius Hunter gives us a glimpse of just how badly the universal common descent model failed:
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/
bornagain77_{April 17, 2021
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Mung, I think we can see a common basic architecture of life, use of a common code with dialects etc. That architecture exhibits features and information rich, functionally specific complexity vastly beyond what blind chance and mechanical necessity could account for. I allude to 500 - 1000 bits of FSCO/I. We know that design can account for that degree of complexity. KFkairosfocus_{April 17, 2021
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Common descent assumes that evolution has explained the emergence of new body types at the Cambrian explosion and I don't think that's the case. It also proposes a continuity between animal and human on the basis of mutations - so human rationality, intentionality, consciousness, free will, moral conscience, and spiritual aspirations are reducible to physical modifications via mutations and selection. The supposed creative power of mutations is far from adequate for producing such - even if it was possible in theory (given those are immaterial aspects that separate human from chimp). Michael Behe shows that mutations cannot produce the kinds of innovations needed - the waiting time is prohibitive and mutations that confer benefits are almost always degradations of existing function. There's nothing that shows that mutations can build new body plans or create the vast number of differences between something like human and chimp, for example.Silver Asiatic_{April 17, 2021
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From the OP:
So, as I have maintained for the last decade, I believe there is no fundamental conflict between ID and common descent. That is, it is fully possible to hold to both at the same time.
I agree with you that there is no fundamental conflict between ID and common descent. If by common descent you mean universal common descent then perhaps you could indicate that by including UCD in parenthesis. I don't think there is any fundamental conflict between ID and UCD either, but also I accept that many within ID would disagree. I'm sure that many others within ID also agree that there is no fundamental conflict. So why then, do so many arguments for ID involve the denial of common descent? What is "the argument from Common Design" other than a way to present "an argument for ID" that seeks to offer an alternative to Common Descent? The sole reason for "Common Design," imo, is to challenge CD.Mung_{April 17, 2021
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Actually the supposed human-chimp DNA similarity, as well as the fossil record, has been severely distorted by Darwinists, Sept. 2020 - Refutation of Human Evolution: Fossil Record and Genetics https://uncommondescent.com/intelligent-design/debunking-another-claim-that-an-alleged-pillar-of-human-exceptionalism-has-fallen/#comment-713398bornagain77_{April 17, 2021
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ET@22:
Without a mechanism Common Descent isn’t an explanation, it’s just a story.
You failed to mention the mechanism for Common Design. Did the OP offer a mechanism for Common Design, or did I miss that as well? So from where I sit, there is no mechanism for Common Design either. Should I say then, that since Common Design also has no mechanism, that it too is just a story? The well-known mechanism for common descent is inheritance,. Reproduction. It's how you got here. It's how I got here. So I'm going to assume that you are talking about something entirely different. Now, the funny thing is, that the mechanism of Common Design is also inheritance. (Speaking from a software development point of view.) But accepting inheritance as the mechanism for both common design and common descent seems to defeat the purpose of "the argument from common design."Mung_{April 17, 2021
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If DNA does NOT determine biological form then changes to DNA cannot account for the anatomical and physiological differences observed between chimps and humans, for example. And the paper "On the Problem of Biological Form" is evidence against the claim that DNA determines biological form. How can it? DNA just codes for RNAs. It doesn't say how mRNA is processed. It doesn't say how the polypeptide will fold into a functional shape. And it doesn't direct the protein or tell proteins how to assemble. DNA is no more than the encoding for the raw materials. Mess with it randomly and you get genetic diseases and deformities. Common Descent without Intelligent Design falters at the transition from prokaryotes to eukaryotes. And from single-celled eukaryotes to metazoans and developmental biology.ET_{April 17, 2021
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Gordon, thank you for your comments.
3. Intelligent design without common descent
Evey ID model, or model of ID, that I am aware of, accepts common descent. You and your siblings descended from the same parents. Some within ID may even accept that all felines descended from a common ancestor. What is not clear is why. Do they rely on the same evidence as other scientists? Do they rely on the same reasoning as scientists who accept common ancestry? So given such provisional acceptance within ID of at least some common descent, how really, do we tell what common design explains better than common descent? This is a point that I have never seen any proponent of "common design" over "common descent" explain.Mung_{April 17, 2021
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Without a mechanism Common Descent isn't an explanation, it's just a story. The mechanisms determine patterns. So we don't have any idea what would be conserved during the innumerable transitions and why. And that is because evolutionary biologists still don't even know what determines biological form. Common design is an observed occurrence with human and animal designs. Automobiles exemplify a common design. PCs exemplify a common design. Building codes all but ensure houses will have some fundamental similarities. The point being is we have quite a bit of experience with common design in engineering and technology. It is true that the two concepts are not mutually exclusive but there still is the problem of the missing mechanism for Common Descent.ET_{April 17, 2021
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Jonathan, thank you for the OP. My primary interest is not in a critique of Common Descent, but in understanding and evaluating whether "Common Design" presents any credible scientific alternative to Common Descent. It is not uncommon, in my experience, to encounter claims that that something, never quite clearly defined, called "common design" can explain the same things that common descent explains. Is this position substantive? Instead of arguing for common descent should I be arguing for common design? Are the two mutually incompatible? Is it really an either/or scenario? I think not, but I could be mistaken. As such, I question the wisdom of trying to set the two positions against each other, as if one is true, the other must be false. To reason that if Common Design is true, then Common Descent must be false, requires some heavy lifting which, again in my opinion, has not yet been done. Some might say that they are only saying that Common Design is a better explanation. It's not that Common Descent is false, but that there is a better explanation. But how are we to decide which of the two is the better explanation for the data? I'm not even sure that the two positions agree on the data they are trying to explain! Anyways, thanks again. I've not read the OP in it's entirety, or the thread, but I will do so with great interest and let you know my thoughts.Mung_{April 17, 2021
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Johnnyb @ 18: Thanks, I'll try to get a chance to watch the debate, but I'm not sure when I'll get around to it. In the meantime, I have a couple of comments. First, I think you're somewhat undercutting your argument that ID and common ancestry are compatible. If evidence that the mechanisms of evolution are inadequate counts against common ancestry, then necessarily evidence for common ancestry also counts for the adequacy of evolutionary mechanisms. But let's separate the two questions again. Go back to my various combos of ID and/or common ancestry. You reject combo #1 (common descent without intelligent input), and I assume also #4 (which I just realized I garbled -- it should be neither ID or common descent). That means you're down to #2 (ID + common descent) and #3 (ID without common descent). Can you give me any evidence at all that favors #3 over #2? Can you explain any of the genetic evidence in my last comment in terms of combo #3? If not, why not just go ahead and accept common ancestry? (I don't want to get distracted by what I consider a tangent, but just for the record: I disagree about the adequacy of evolutionary mechanisms to produce the diversity of life on Earth. I don't claim we can prove that they're sufficient, but I also haven't seen an argument I found convincing that they aren't sufficient. And that's exactly what I'd expect if, in fact, they are what produced all the variations we see.)Gordon Davisson_{April 17, 2021
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Jerry @ 15:
Let’s assume that any species, say species A is different from all other species in some or many functional genetic/epigenetic molecular sequences but at least one. Where did these novel functional genetic/epigenetic molecular sequences come from? [...] What should be researchable is how many of these partial non functional sequences exist in similar but different species? If UCD by natural means was the mechanism of evolution for changes in life forms then there should be a plethora of these similar but not functional sequences all over life. (Davisson option 1 above) But do we see them? [...] All this is easily researched with the tools available today.
Although I disagree with some of the details, I agree with your basic point. This can be researched, and has been researched, and we do see them. The actual scientific literature on this is extensive, technical, and I'm not that familiar with it. But for a simple example, look at Vincent Torley's post here from a few years back, "Double Debunking: Glenn Williamson On Human-Chimp DNA Similarity And Genes Unique To Human Beings". The second debunking is what's relevant here: Dr. Cornelius Hunter found a paper that found 60 new protein-coding genes that originated de novo on the human lineage since divergence from chimps. But in correspondence with Torley, Glenn Williamson identified very closely similar (but non-protein-coding) sequences in the chimpanzee genome, and Torley was able to replicate his results:
I’ve had a look at the output, and even to my untutored eye, it’s obvious that any claims that these “de novo” genes are not found in the DNA of chimps and other apes are flat-out wrong. They have virtually identical counterparts on the chimpanzee and orangutan genomes, even if these are non-protein coding.
Now, there's a caveat here: it's not clear if these novel genes are actually functional. Protein-coding doesn't mean it's functional any more than non-protein-coding means it's junk. Identifying function (or lack therof) is hard. And under standard evolutionary theory, it wouldn't be surprising to see junk sequences acquiring mutations that made them get translated into protein, but that protein not do anything useful (at least, not at first). But even with that caveat, this seems like a pretty clear match to the common-ancestry prediction. As I said, I'm not that familiar with the actual scientific research on this, but I took a quick look and found "Origin of Primate Orphan Genes: A Comparative Genomics Approach" by Toll-Riera et al, in Molecular Biology and Evolution, Volume 26, Issue 3, March 2009, Pages 603–612. They looked at human protein-coding genes that had homologs in the chimp and rhesus (monkey) genomes, but not in various non-primate genomes (including mice, rats, cattle, chickens, frogs, and more distantly -- um, related -- species). Since these proteins are found in a range of organisms, it's much more likely they have functions, and several of those they looked at had known functions. They found 270 primate-only genes, and compared those sequences to corresponding non-primate genome sections to try to infer how they'd originated. They found that 66 of the genes (24%) were mutated duplicates of other genes (which aren't terribly relevant for our purposes), 142 (53%) were made by transposable elements ("jumping genes", which can move/copy themselves around the genome, and stir things up as a result), 15 (5.5%) originated "de novo" from noncoding regions (like the ones Torley looked at), and 47 (17%) had unknown origins. Now, I suppose you could cocentrate on those 47 that they didn't identify an evolutionary origin for, but if you want to make that case you need to examine them in much more detail. Just because Toll-Riera didn't identify how they originated doesn't mean there's no evolutionary way they could have originated, just that it wasn't clear using their methods. But what about the 175 they did identify corresponding sequences for, and the 60 that Williamson and Torley did? Can these be explained without common ancestry? I don't see any way to do it (and that includes Ewert's dependency graph model). Actually, I'll go even further than that, and argue that these similarities don't even fit some of the ID+common ancestry mechanisms. For instance, it's pretty clearly inconsistent with the "toolbox theory" (which I'd call front-loading via the initial ancestor's genome) mentioned by AaronS1978 @ 3 and Johnnyb @ 4. On the other hand, it seems completely consistent with ID via directed selection, where the designer would gradually "nudge" genomes toward distant goals.Gordon Davisson_{April 17, 2021
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Gordon - I appreciate the comments. The main sticking point seems to be whether or not there exist sufficient information repositories necessary to bridge the gaps and do the changes. If there aren't, then there's not much room for large-scale evolution to get off the ground. This is something that I've found that proponents of common descent often miss - common descent requires not *just* a pattern of similarity and difference, but a *mechanism* to accomplish it. Speaking of which a great debate which puts this question in full view, in my opinion, is the Nelson/Velasco debate. It's great, and I encourage everyone to watch it: https://www.youtube.com/watch?v=Ni0E6rWa-QE Velasco completely punts on the efficacy of the mechanism to accomplish the changes. He acts like it isn't even needed. Now, there is another possibility you could be referring to, and that is common descent, but with an entity (such as God) making highly specific changes along the way. Historically, that has been considered special creation not evolution. I'm not a real stickler on terminology, but I thought I'd point out that many people who consider themselves to be old earth special creationists hold to this view. If God is infusing specific information at specific places, then merely the fact that this new information is infused in someone's specific offspring may or may not be true, but it doesn't seem causally significant. If it is a material evolution, then we would need to recover the starting "toolbox" (as Aaron calls it) in order to have reason to think that the gaps could be bridged. Personally, I've always thought that the tree of life, in general, is evidence against common descent (though, again, speaking of a non-teleological common descent). The reason is that if it were mere branch-points, you wouldn't have these highly distinct systems. That is, there wouldn't be a "mamallian" template or a "reptilian" template. While there are some organisms that exhibit cross-class characteristics, the fact that we can put so many into a general box rather than a continuum seems to me to indicate that descent with modification is not the appropriate model. A great book on this, by the way, is Louis Agassiz's "Essay on Classification". It's a bit out of date on the specifics and the terminology, but the ideas are pretty timeless.johnnyb_{April 17, 2021
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I also think common design explains things like genetic hotspots and synteny. Common descent is very good at explaining variation, but not innovation. When I went though my patent examination, one of the things that were central to being awarded a patent was the "obviousness" criterion. If something is so obvious as to warrant rejection because it offers no novelty in part of the inventor, then no award is given. In other words, mere slight modification is not considered an innovation and, therefore, not an "invention". The problem-solving analysis tool (TRIZ) developed by Russian inventor, Genrich Altshuller, had something similar to what Behe termed Irriducible Complexity to explain the need for a design hypothesis to explain innovation; that is, an inventive solution to unresolved problems in which improving one parameter impacts negatively on another (what Altshuller termed "technical contradictions") requires a radical (saltation) change. It needs to make major adjustments that require foresight, planning, and ingenuity. Of course, the inventor recognized the similarities in inventive design patterns and natural patterns and even came up with his "Laws of evolution" thesis, but the point is that the patterns do not support "gradual" innovation, but rather, abrupt appearance of novel features. More on this: https://triz-journal.com/trends-patterns-evolution-product-innovation/Mario A. Lopez_{April 17, 2021
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buffalo
Common descent is obvious.
Children are descendants of their parents, true.Silver Asiatic_{April 17, 2021
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This is all interesting but there is a simple definitive approach/path to settle this. That is the origin of functional genetic/epigenetic molecular sequences. Let’s assume that any species, say species A is different from all other species in some or many functional genetic/epigenetic molecular sequences but at least one. Where did these novel functional genetic/epigenetic molecular sequences come from? If one accepts UCD then they must either be in the ancestor or some have developed independently after separating from the ancestral gene pool. Now it is possible that those that differ could have entered whole through some event such as HGT or viruses. But evolutionary theory postulates that most such sequences developed inside the gene pool and must have done so gradually over a long time and during this time was not functional. If the latter, then at some point the sequences became functional in some of the gene pool while similar sequences remained non functional in other parts of the gene pool. And a new species arose. This new species would be very similar to others from the same original gene pool. What should be researchable is how many of these partial non functional sequences exist in similar but different species? If UCD by natural means was the mechanism of evolution for changes in life forms then there should be a plethora of these similar but not functional sequences all over life. (Davisson option 1 above) But do we see them? It no, then evolution by a gradual mechanism did not happen. Gould tried to explain away the absence of gradualism in the fossil record by the punctuated equilibrium mechanism which is actually a form of gradualism. It just says the sudden addition was due to the slow accumulation of changes taking place somewhere in the genome which suddenly became functional. (For example, in the so called junk DNA). All this is easily researched with the tools available today. Then there is the Grants observation that new bird species take 32 million years to form. If this in general holds for all new species formation, we will need a much older universe to explain all the varieties of species in the history of life.jerry_{April 17, 2021
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Buffalo that is correct. (i will also check your blog, i also run a blog at https://www.stuffhappens.info)martin_r_{April 17, 2021
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Universal common descent is the issue. Common descent is obvious.buffalo_{April 17, 2021
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Gordon D: "whales are actually much closer to the hippo than to the sharks!" 2021 update from Sciencedaily: "Aquatic skin adaptations of whales and hippos evolved independently" ""Our latest findings contradict the current dogma in the field -- that relatives of the amphibious hippo might have been part of the transition as mammals re-entered life in the water."" "The work suggests that their last common ancestor was likely a land-dwelling mammal, uprooting current thinking that the skin came fine-tuned for life in the water from a shared amphibious ancestor." here we go again: "...latest findings contradict the current dogma...." "...uprooting current thinking...." https://www.sciencedaily.com/releases/2021/04/210401112857.htmmartin_r_{April 17, 2021
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Mung, Mung, calling Mung . . .kairosfocus_{April 17, 2021
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Gordon Davisson, i have no formal education in biology, i am mechanical engineer, i graduated from technical university (Europe),... but i do lots of biology study. Have you noticed my post on viruses? During my biology study, I figured out pretty quick, that Darwinists have no idea where viruses comes from, but they do teach, that the evolution is a fact... and that the common descent is a fact... Of course, first i had to learn more about viruses... i was confused, because it was clear, that viruses are a fully different system - not made of cells... I was pretty shocked, that the most abundant biological entity on Earth does not fit evolutionary theory. Is it not absurd ? Gordon, do you understand what the following means? (From virology.ws) "While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins." Could you explain with your own words what the above means?martin_r_{April 17, 2021
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