Summations Only

I'm not sure I find this a compelling argument against a teleological view of biotic reality. Regarding, for instance, your automobile example: while it is true that, say, radial tires replaced bias ply tires -- if one looked at all cars during this transition from bias ply tires --> radial tires, one would find that some cars retained the older tires while newer cars had radial tires. In other words, there'd be a nested hierarchy of cars, wherein some had the new tires and others retained the older tires. It was only after this novel "trait" was fixed in the entire car "population" that (obviously) all cars had this newer innovation. In many ways, then, the human design process mimics the evolutionary "descent with modification" process; after all, the preferences of the marketplace often act as a selective force. Edited by Genomicus, : No reason given.

Right. Which is quite analogous to lateral gene transfer among prokaryotes and (less so) eukaryotes. So the argument only holds water from the perspective of so-called higher organisms, such as vertebrates and invertebrates. Otherwise, the human design process mimics the evolutionary forces of mobile genomic elements. And that is, admittedly, something that most creationists have great difficulty explaining. I was debating a creationist the other day on another online platform, and he/she/it brought up the very elementary "common design" argument that "Well, airplanes and cars both have wheels. And that's explained by a common designer!" What the typical common designer argument doesn't explain is the nested hierarchical distribution of morphological traits. That only really makes sense in the light of evolution.

Because irreducible complexity, as defined by Behe in 1996 (and later publications), isn't in and of itself a reliable indicator of rational design. Neo-Darwinian processes can account for the origin of irreducibly complex systems, through scaffolding of parts and other mechanisms. So IC cannot be taken to be in itself evidence for design; the proposition that an IC system was designed must be bolstered by other lines of evidence.So, no, pointing to IC systems doesn't in itself help your position. Edited by Genomicus, : No reason given.

I mean the totality of evolutionary mechanisms that fall under the umbrella of the modern evolutionary synthesis; these mechanisms include random mutation (beneficial, detrimental, and neutral with respect to fitness), natural and sexual selection, genetic drift, lateral gene transfer, etc. Consider the below example of a Roman arch. Remove any of the pieces, and the arch collapses. The function is eliminated. So this arch is irreducibly complex. But it was made by using a scaffold: the parts were first laid out on top of a structure in the middle. Once all the parts were in place, the scaffold was removed. Once the scaffold is removed, the structure becomes irreducibly complex. Similarly, biological structures can be rendered irreducibly complex over the course of their evolution if their parts evolve on a "scaffold" which is then eliminated by selective forces. Well, what those different forms of eyes really demonstrate is that an eye without all of its (human) parts can still function in a biological context and provide a selective advantage. So it's biological evidence that the eye is not an un-evolvable structure; this, coupled with other lines of evidence (molecular, paleontological, etc.), all work together to point to the conclusion that the eye evolved. It's called a bacterial flagellum, and is found in a variety of bacteria. So while removal of some parts of bacterial flagella in, say, gram-negative bacteria does render the system functionless as a motility system, there are systems out there (e.g., the type III secretion system) which suggest that precursor flagella could have had prior functions.In fact, during assembly, flagella do act as secretion systems -- and before the pili are assembled, the system acts as a protein channel. So all these stages have functional utility, suggesting that the IC-ness of the bacterial flagellum -- in itself -- is not evidence that it could not have evolved.Once again, this evidence that the flagellum can function in different contexts is not evidence that it DID evolve. For that, one must look to other lines of evidence. I, for one, find the arguments for the Neo-Darwinian origin of bacterial flagella suspect, based on several lines of reasoning. But it's irreducible complexity isn't something that speaks of design; Behe's irreducible complexity argument as a linchpin piece of evidence for design is fatally flawed. No, because evolutionary mechanisms can result in irreducibly complex systems.

Well, the removal of a scaffold is precisely the same as the elimination of functional redundancy. And there are plenty of biological systems chock-full with functionally redundant parts; and if those parts are lost over time, the system will become irreducibly complex. Here's for starters if you want an actual biological example:(1) Some bacteria have a molecular machine known as the ExbB-ExbD system. Basically, this little machine is part of a system that allows the bacteria cells to transport iron ions across their cell membranes.(2) Now, in cyanobacteria, there are three sets of ExbB-ExbD systems. If you eliminate one of them, the cell doesn't die. If you eliminate both of them, the cell doesn't die. Only if you eliminate all 3 sets of ExbB-ExbD machines will the cell die.(3) So here we see functional redundancy in the cyanobacteria iron uptake system.(4) Thus, the cyanobacteria iron uptake system could become irreducibly complex by elimination of the two redundant ExbB-ExbD systems. No rational designer needed. What the different eye morphologies show, in fact, is that eyes across the animal kingdom don't have to have a certain number or types of parts. In other words, the human eye's irreducible complexity doesn't mean the eye is un-evolvable, because we know that light-detecting systems in animals can have fewer parts. This is not imposing an evolutionary (or design) interpretation on biology; it is simply stating the observation that animal eyes can use different parts and don't have to have all parts in the human eye in order to be of use to an organism. But I didn't say the eye was not un-evolvable "because evolutionary theory says so." I said that the eye was not un-evolvable because there's a large number of eye types, which use different biological parts, among animals -- and this shows that eye functionality across animals is flexible and doesn't have to have a certain number and types of parts to function. This, in turn, means that the eye could have evolved, as there isn't a lack of a selective pathway for the origin of eyes in mammals. Well, we can't observe atoms directly, but I am very, very certain that you subscribe to some form of atomic theory. But you could always surprise me, you know. Well, cells need to build molecular machines (the molecular machines don't just pop out of nowhere, of course). So cells build flagella, step-by-step, starting with a protein channel, then creating a secretion system -- and this process of assembly ends up as a flagellum. Kinda like how humans assemble houses, cells follow a genetic blueprint that tells them how to assemble the flagellum part-by-part. These patterns go beyond mere suggestiveness; the totality of these patterns all lead to the incontrovertible conclusion of common descent. Like, there's some stuff that can't be explained any other way -- and more importantly, is perfectly explained by the common ancestry perspective. When everything is taken into consideration, then, the common ancestry explanation for the origin of species is as rock-solid as the atomic theory of matter. The question of irreducible complexity is not whether IC systems are ironclad pieces of evidence for evolution; the question of IC is whether or not Neo-Darwinian processes can account for their origin. I have rather extensively supported the argument that Neo-Darwinian mechanisms can explain the origin of IC systems; second, rational design is not implicated by irreducible complexity because such evolutionary mechanisms can explain IC systems. No, I've said that evolutionary mechanisms are very adequate for explaining the origin of IC systems. My critique of the Neo-Darwinian perspective for the origin of early-branching molecular machines like flagella has little to do with irreducible complexity. That's not the point. Evolutionary mechanisms can yield irreducibly complex systems, so why point to IC systems as hallmarks of design, when you can just as easily point to non-IC systems and claim this as evidence of design? You were the one who brought up IC systems as evidence of design because evolution could not explain them; but evolutionary mechanisms can, in fact, result in IC systems, so this is the fatal flaw in Behe's argument. Umm, evolutionary hypotheses can be tested, replicated, and demonstrated just as much as the predictions of the atomic theory of matter can be demonstrated, replicated, and tested. Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.

What the freak is a "Soley"?Edited by Genomicus, : No reason given.

Okay, let me get this straight. You have this idea (the "braking system") that flies in the face of what we actually know about genetics, then you complain to herebdragons about not being able to understand his technical prose. I.e., you know next to nothing about genetics, you admit as much, and yet you have the intellectual audacity to propose an idea regarding genetics? Seriously?

That wasn't my point, Faith, and I suspect you know that. No, the point is that it's absolutely not intellectually honest to whine to herebdragon (and others) that you can't understand the technical genetics/biology prose...when at the same time you're proposing an idea regarding genetics without having a grasp of genetics and molecular biology beyond a high school level.Since you don't know scratch about genetics, and you admit as much, whatever gives you the notion that your particular idea is in any way valid? Why would you even propose such an idea with nothing more than an extremely rudimentary understanding of genetics? That's not intellectually honest.To you, this is gibberish:"Why would you expect simple sequence repeats to be informative as to population structure? Why would you expect basic housekeeping genes, such as Ribosomal RNA and cytochrome C, to be highly conserved across unrelated species and yet show patterns of differences that can be grouped into a nested hierarchy - and one that largely matches predictions based on morphology (which both of the genes mentioned have little to no direct effect on morphology). Why would there not be just 1, or at least a very small number, of each of these highly conserved housekeeping genes that is used across all species? Why does each species or group of species get their own unique sequence that is just a little bit different from their closest relatives?"To people who actually freakin' know about genetics and molecular biology, this reads as easily as Dr. Seuss. So tell me: how is it intellectually honest to propose an idea about genetics without knowing a thing about genetics, based on your own admission?Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.Edited by Genomicus, : No reason given.

So the person who has only a high school level understanding of genetics says that her idea only requires a high school level understanding of genetics. Which, of course, isn't something you're in a position to say since...well, you only have a rudimentary understanding of genetics. And this also means you aren't in a position to assess if your idea is valid or not; which means proposing such an idea based on an elementary knowledge of genetics isn't intellectually honest.I mean, I could easily refute your idea but then you'd probably complain about a "snow job." Right?

Which is an easy way to make any position irrefutable, right? "I can't understand you, bruh. This stuff's too technical for me, so even though I'm the one who proposed this idea in this field, I'm not going to defend it because I can't understand the language of the field this idea relates to."Yeah, really nice intellectual honesty right there, huh?

Says the person wholly untrained in a technical scientific field...Gee whiz, there's just no limit to the ignorant comments you'll make, is there?For starters: it's really hard to explain to a layperson what the Riemann hypothesis is all about. In order to properly grasp the extent and meaning of the Riemann hypothesis, one must first have an understanding of mathematics well beyond the high school level.You know next to nothing about genetics, so it is wholly intellectually dishonest to pretend you're in a position to properly assess if your view is accurate. And there are plenty of free resources to get a firmer understanding of genetics, so your excuses appear to boil down to: "I simply don't want to understand this stuff on a more granular, precise level."

Wut? You really didn't grasp why I brought up the Riemann hypothesis, do you? What I said was that it is very difficult to explain to a layperson the meaning and extent of the Riemann hypothesis, without resorting to apparently mystifying mathematical terms. That the Riemann hypothesis has not been proven has absolutely nothing to do with my point, and I fear for your deeper, more nuanced verbal comprehension skills.I could have just easily brought up the Brumer—Stark conjecture or the Poincar conjecture. The point here is that contrary to your assertion that 'pretty much anything can be explained in simple English,' there are a multitude of scientific, engineering, and mathematical concepts that cannot be reduced to simple English explanations. One first needs a background in these fields; you lack the requisite background in genetics in order to properly assess the validity of your idea. Honestly, I thought you had a high school understanding of genetics, but you do not seem to understand the Hardy—Weinberg principle, which is high school level stuff.

Umm, not irrelevant since it proves that your statement that just about anything can be reduced to a simple English statement is categorically incorrect in the science, engineering, and mathematics disciplines. Right, because the test of an idea's validity is whether it can be easily refuted in terms someone with only high school level understanding of the subject can comprehend. Such intellectual dishonesty.Why do you think it's intellectually honest to propose ideas in fields you know next to nothing about? Why don't you, instead, actually take the time and effort to learn the field? I can supply a list of introductory links that'd be a good start; MIT's OCW is great for starters.

Duplicate post. Edited by Genomicus, : No reason given.

This thread was titled "The Science in Creationism," by a creationist no less. Nonetheless, there has been no demonstration that creationism qualifies as a properly constructed scientific theory or hypothesis. What instead has been attempted is a re-defining of what "science" is and the predictable attacks on the theory of common ancestry.Since Dawn's incoherent posts -- which lay waste to rather elementary rules of grammar and verbal logic -- appear to make manifest the poor state of education in much of the U.S., I will direct most of this summation to my various exchanges with Faith.First, there is the consistent presumption that the appearance of design is in itself evidence for rational design. However, the appearance of design is merely an observation; it cannot be evidence of anything in particular since both teleological and non-telic processes can produce structures and systems that look designed.The example of irreducible complexity was raised by Faith; yet I dismantled this argument thusly:(1) First, there are -- in principle -- natural processes which can produce irreducibly complex systems without the presence of agency. For example, a river can eventually bore a hole through rock and produce an arch. An arch, if functioning as a bridge, is irreducibly complex (remove a chunk of the arch and the whole thing collapses) -- yet natural, non-telic processes produce arches all the time.(2) Within biology itself, there are many examples of systems that can easily become irreducibly complex through the elimination of functional redundancy. I pointed to the ExbB-ExbD system in cyanobacteria (Message 358) as just such a system that could rather easily become irreducibly complex without the intervention of agency.Thus we see that irreducible complexity can not only be created by Neo-Darwinian evolution, but also that this can occur despite the fact that irreducibly complex systems "look designed." This, in turn, means that the mere appearance of design is not evidence for agency; it is, instead, simply an observation.We have also seen, throughout this thread, a prominent theme: Faith doesn't at all have a strong background in genetics and molecular and cell biology. This is an important point, because it is representative of the overall intellectual laziness that is prominent among those who deny various scientifically supported theories (such as anti-vaxxers, GMOs-are-horrible-horrible-things proponents, etc.).In short, despite the fact the Faith only has a high school understanding of the relevant biological disciplines, Faith has chosen to outright deny the scientific strength of the modern evolutionary synthesis. But Faith does this from a position of ignorance, not knowledge; she could not understand herebdragon's example of cytochrome c and why it refutes the common design argument for molecular nested hierarchies -- despite the fact that all the terms used by herebdragons are rather rudimentary (electron transport chain? That's basic stuff I learned in high school). So despite being an active participant on this forum for several years (AFAIK), Faith has apparently not done much in the way of real learning of biology, instead trusting in her elementary understanding of the most basic biology.At this point, I could go on and on about the nature of scientific inquiry, what constitutes scientific evidence, and why the evidence for common descent rivals the evidence for the atomic theory of matter or germ theory. But here I will take a different approach.I have no particular ideological attachment to accepting common descent or rejecting creationism. Indeed, I openly acknowledge that there are parts of the biotic world which may be better explained by agency.So why do I accept common descent? The enormous mountain of evidence in its favor aside, it's really simple really. When it comes to genomics research, creationism would leave me absolutely blind. On the other hand, the theory of common descent continues to hold tremendous explanatory power. I will provide a brief example here. Most of this will likely go over your head, Faith; I trust you have the intellectual fortitude to read up on the relevant disciplines -- as I am not an educator, and you're not a high school student anymore.Without getting too technical, if a given phylogeny of a prokaryotic protein does not match the consensus phylogeny of bacteria phyla (based on rRNA and highly conserved proteins), there are two main explanations from the perspective of common descent: (1) that these proteins were horizontally transferred and thus their phylogeny is a reflection of horizontal transfer rather than vertical descent; (2) that there were gene duplications and subsequent losses, leading to a scenario wherein the protein tree does not wholly match the species tree.We can test these two competing evolutionary models using a variety of bioinformatic approaches. One way to test the validity of the horizontal gene transfer model is to compare the G+C content of the genes under consideration with the genomes from which they are thought to have been transferred from. If the G+C content matches, then this would indicate they originally came from the genome of some other bacterial clade. On the other hand, if the G+C content does not match, then the gene duplication + loss scenario becomes much more likely.So the common descent model offers these two competing hypotheses, and a way to test these hypotheses. I've done (and published) research on prokaryotic flagellar and other systems; and over the course of this research, I have tested the horizontal gene transfer model against the gene duplication + loss scenario. In this particular line of research, the G+C content of the genes hypothesized to have been horizontally transferred match the G+C content of their "host" genomes to a statistically significant degree -- exactly what would be predicted under the HGT model.Now, creationism would leave me absolutely blind. This is not because I am operating under a common descent paradigm; it is, rather, because creationism has no workable model. Creationism attributes molecular similarity to "common design." How, then, am I to account for gene similarities that do NOT match most hierarchies of gene similarities? I cannot invoke horizontal gene transfer, as that would imply evolutionary descent, as would the gene duplication + loss model. What, then, am I to do?On the one hand, I have a working theory that leads to two competing alternatives; I can rigorously test these alternatives against each other, with the predictions of one of the models being perfectly confirmed.On the other hand, if I invoked creationism, I would be at a loss for an explanation. I could not make any predictions regarding G+C content; and if the G+C content of the genes match the G+C content of some other "host" genomes, I could not make sense of this, either, under the creationism model.All of this is my way of shining light on why exactly I reject creationism; it's not because I have an ideological bent towards rejecting creationism. Rather it is because it is horrible as an explanatory framework for the biological world; meanwhile, common descent continues to make sense of everything from protein sequence data to disease prediction to vaccine development. It simply works. And that's science.