6 posts were split to a new topic: Superscripts and other fun formatting on the forum
I mean, why should we expect @Meerkat_SK5 to do any better than the reviewers who recommended the paper be published?
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The reviewers didn’t conflate the data with the extrapolation as Meerkat did, though. Also, reviewers can recommend, but the editor has the final decision.
More importantly, Meerkat’s misrepresentation is clear from the qualified statement in the abstract (emphasis added):
"Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77)…:
That’s a far cry from Meerkat’s representation of this as a certainty:
In what way, specifically, does the 2000 paper support the extrapolation that you misrepresented as a finding? Please show your math.
And is that extrapolation consistent in any way with the findings of Axe et al., Proc. Natl. Acad. Sci. USA
Vol. 93, pp. 5590-5594, May 1996? It is the same Axe, but with supervision and actual enzyme activity assays.
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As I told another user, I never pretended to be an expert in this field nor do I have a desire to be one. You either did not care to read this or did not fully absorb it into your mind. For this reason, I don’t care whether I would make mistakes or not but I care about getting the mistakes right. So I admitted that I copied and pasted from the old article I spoke of again, which I did not properly invest time in correcting because I am ultimately focused on trying to make a larger point, as a NON-expert, to get expert advice. So in one sense, it was intentional but not in the way that you suggested. There were ,of course, other reasons why I did not invest time, but this was the main reason.
Not at all, as I said before, it would just be an example of trade-offs between conflicting design goals from allegedly bad designs rather than suggest the designer is not all-powerful:
Examples:
An optimal bronchial tree may be dangerous | Nature
Glycolytic strategy as a tradeoff between energy yield and protein cost | PNAS
Do you want me to list the experiments again that I have already listed and explained in this topic and another?
I was referring to the Design Decay hypothesis that I mentioned at the start of this topic. It is supposed to explain what happened before the first cell was made, which is something that common descent does not explain.
For instance, there are three main hypothesizes on the origin of viruses with no clear explanation as to which one is correct:
- The virus-first hypothesis claims that viruses predate or coevolved with their current cellular hosts; 2. The progressive, or escape, hypothesis claims that viruses arose from genetic elements that gained the ability to move between cells; 3. the regressive, or reduction, hypothesis suggests that viruses are remnants of cellular organisms (Wessner, David R. 2010).
However, what if all three hypotheses are true? this would be the Design Decay hypothesis.
I already explained how you can tell…
The God of classical theism is generally defined as “Necessary” and “Personal”, which sums up the totality of God’s attributes. Now, here is how you test it in regards to evolution…
When the biologist chooses a particular set of natural conditions to work on, the observer has to first test and determine whether or not life can be developed within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.
The combined outcomes of these experiments would produce evidence for the hypothesis. If we apply the same procedure to a different natural condition, it would produce additional evidence for this hypothesis. This is because even though the experimenter who guides evolution within each natural condition is finite and contingent, there could not be any conscious life before simple life emerged, hence why we have to include the first experiment to support the “necessary” attribute of this common designer .
Just ask for the list of examples if you want.
Correct me if I’m wrong but Lenski’s experiment was attempting to show how millions of years of evolution in nature could eventually produce anatomic structures within a reasonable period. In essence, this would show that natural selection was the primary cause for evolution from a gradualistic mode rather than a punctuated equilibrium mode or saltation’s. So to hopefully answer your question, it needs to be repeated outcomes to show that it was a punctuated equilibrium mode of change to accurately reflect what we see in the fossil record and continue to show that natural selection was the primary cause of evolution.
In short, most theists reject the significance of Lenski’s experiment because it does not show saltations (i.e. new genetic information) nor punctuated equilibrium (i.e. repeated outcomes). This is what I meant before and was not trying to misrepresent papers or move the goalpost.
I hope you don’t mind but I am going to defer to Hugh Ross when it comes to explaining this because I think he does a much better job and it will save everyone time and energy:
"Convergence refers to the occurrence of identical, or nearly identical, anatomical, physiological, and/or genetic features in species of life that are unrelated or distantly related within an evolutionary paradigm. Both theists and nontheists offer explanations for convergence, but those explanations are radically different.
Theists see convergence resulting from supernatural, super-intelligent interventions by a single Creator who employs a single, optimal solution to address a common set of problems faced by organisms possessing different characteristics and living in different habitats. Nontheists conjecture that convergence occurs when unrelated species encounter identical, or nearly identical, environmental, predatory, and/or competitive selection effects. In other words, nontheists suggest that natural selection channels randomly occurring variations in unrelated species toward identical outcomes.
There are two obvious problems with the nontheistic explanation for convergence. First is the frequency with which it is observed to occur. Naturalistic models for Earth’s life predict convergence to be extremely rare. Instead, convergence is a nearly ubiquitous characteristic of Earth’s life. So far, hundreds of examples have been documented.
Second, evolutionary biologists, paleontologists, and ecologists frequently observe occurrences of convergence where the environmental, predatory, and competitive selection effects are not at all similar. A classic example is the chameleon (a reptile) and the sand lance (a fish).3 The chameleon lives in a desert while the sand lance lives on the seafloor of shallow seas. The chameleon faces very different predatory pressures than does the sand lance. Yet, both the chameleon and the sand lance possess identical eye, eyelid, and tongue mechanisms as well as designs and identical hunting strategies.
The most recently discovered example of convergence is the centralized nervous system found in all vertebrates and insects. The materialistic model asserts that the centralized nervous systems evolved from a single common ancestor.
Evidence that could be interpreted as favoring the [materialistic] model comes from the observation that all vertebrates and insects possess a nervous system consisting of a brain that is connected to a single cord of nerves that extends into the trunks of these animals. Furthermore, regulatory genes are similarly deployed during the development of the central nervous systems of these animals.
However, the new convergence discovery provides strong evidence that central nervous systems do not arise from a single common ancestor. Rather, there were multiple independent initial appearances of central nervous systems.
A research team led by marine molecular biologist José Martin-Duran found that a set of homeobox genes is expressed along the back-to-belly axis of the central nervous systems of vertebrates, flies, and one species of segmented worms. However, the team did not find this gene expression pattern in nine other bilaterian species (species with bilateral symmetry that possess a head, a tail, a back or dorsal, a belly or ventral, and a left side and right side).4 Four of the nine species were members of the xenacoelomorph phylum comprised of tiny worms that lack a through gut, gill slits, and a body cavity. The other five were members of the annelid (segmented worms), nemertea (ribbon worms), brachiopod (soft-bodied animals with shells on the upper and lower surface), platyhelminth (flatworms), and rotifer (part of the zooplankton) phyla.
The team concluded that 'the similarities in dorsoventral patterning and trunk neuroanatomies evolved independently in bilateral.'5 In a review of the paper published by Martin-Duran et al., neurobiologist Clifton Ragsdale wrote that the team’s data 'strengthen the case that the developmental and morphological similarities between bilaterian centralized nervous systems are the result of independent evolutionary events that converged on similar outcomes.'6 In other words, central nervous systems did not arise from a common ancestor through evolutionary descent. They appeared independently multiple times.
What makes this example of biological convergence especially significant is its occurrence across phyla. It is not just convergence within an order, class, or phylum. It is observed in at least eight different phyla. Biological convergence repeatedly arising in circumstances where the forces driving natural selection are vastly different strongly argues for the compelling necessity of supernatural, super-intelligent activity on the part of a personal Creator.’ [emphasis added]
Sorry, that’s far too vague to be a useful guide to a scientist.
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A question: why does not being an expert obviate the obligation to check the (original) sources you are quoting? This would appear to be common courtesy and intellectual honesty. Misquotation and quotations out of context are not uncommon, particularly in Creationist apologetics. Where you are unable to check the original source, it is better to be up front about the fact that you are taking the quote from a secondary source (saying ‘X states that Y says’, rather than ‘Y says’).
I am myself not an expert in these fields, but I feel that it places the onus of me to be extra careful, not to misrepresent material that I am unfamiliar with.
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You are wrong. About everything you said in that paragraph. Not only don’t you know what the LTEE was for, you don’t know what the punctuated equilibria theory is.
No they don’t. I suppose most creationists might, but that isn’t the same thing, is it?
Saltations are not in any way synonymous with new genetic information.
Punctuated equilibrium is not in any way synonymous with repeated outcomes. In other words, you once again have no idea what you’re talking about. This is a serious problem.
I do mind, and Ross makes several of the same mistakes you do.
No, they don’t. Creationists may see that, but those are not the same thing. Please stop equating them.
Not nontheists: scientists. The two are not at all the same thing. And the outcomes are quite unlikely to be identical, though they may be similar. Think of bird wings and bat wings and pterodactyl wings.
Just not true at all. Whatever do you mean, and how do you quantify it?
Hundreds out of how many possible examples? I’d say those are a tiny percentage of all traits in different species. Many more similarities are due to homology rather than convergence.
I’d be very surprised if this were true. Can you cite your source? Or are you still quoting Ross? That both are ambush predators concentrating on much smaller prey is enough of a similarity in niche. Do chameleons even have eyelids? Do any fish have them? I had thought not.
Possibly, but I’m dubious. Multiple losses may be more parsimonious.
I see no logical reason why that should be true. Hugh Ross is a much better astronomer than he is a biologist. Or so I assume. I’ve been told he’s a pretty good astronomer.
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Expert advice: stop citing articles you haven’t read.
If you have to quote via a secondary source (e.g. because the original source is no longer available) then do so explicitly.
For example Yockey (1981) as quoted by Luskin here
That way, it’s immediately obvious that any misrepresentation is probably Luskin’s not yours, and we point out to you that Luskin and co. are untrustworthy, rather than pointing out to everyone else that you are untrustworthy.
Of course if you had done this after the first time it was pointed out to you, you might have some credibility left. It may be too late now.
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You’re wrong.
You have far more E, coli in your own gut than Lenski uses in his study Do you expect them to have started growing legs, wings and ears by the time you hit middle age?
I doubt many serious evolutionary biologists consider saltation of the sort you describe there as a likely mechanism. You don’t seem to understand what PE is. And neither of those is what the LTEE was trying to understand.
Only partly correct. Genomic convergence also occurs just by chance.
Does it? Why?
“Hundreds.” Out of how many trillions of physical features of the many millions of species that have existed on earth? It seems it is an understatement to say convergence is rare if Ross is correct.
I’ll let someone else handle the rest of the nonsense in Ross’s screed.
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You’re wrong.
The goals were to study the dynamics of evolutionary change, the repeatability of evolution, and the interaction between genomic and phenotypic changes.
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[quote=“Meerkat_SK5, post:89, topic:13625”]
I suspected you knew next to nothing about Lenski’s LTEE, but your above comment is good evidence that is the case. The questions Lenski LTEE has explored are given in the quote below. I advise you read the entire source article to update yourself and possibly prevent you from spewing nonsensical claims about it.
https://www.nature.com/articles/ismej201769
Rubbish again. Natural selection is not the primary cause of evolution. In some cases it dominates, in others it plays a lesser role or might have a fairly equal influence on evolutionary change.
Bull crap. The fossil record indicates evolution can run slowly over millions of years (whale evolution, for example) and that it can be rapid as well.
There is no link between repeated evolutionary outcomes and punctuated equilibrium. Punctuated equilibrium is just a mode of evolutionary change.
Saltations are not new genetic information, neither is punctuated equilibrium linked to repeated outcomes. You just don’t know what you are saying.
Praise God then for the murder of millions of people infected with HIV. Convergent evolution has helped the virus persist within human populations, inflicting a lot of pain, discomfort and death on many people infected with it:
https://mbio.asm.org/content/11/4/e00782-20
The current coronavirus pandemic is also fueled by convergent evolution. Your God is a true mastermind of evil:
We have empirical evidence that this happens. Its not a suggestion. And its not just natural selection alone that acts on existing genetic variation.
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As I tell you, your level of expertise has nothing to do with your repeated citations of things you’ve never bothered to read.
I’m not seeing that.
And then you claimed that 2 papers “found” something that was a mere extrapolation from only one of them.
And I am speaking to that larger point. As an expert, I advise you to never cite papers you haven’t read yourself.
I don’t see how any of that is a response to my question about Axe’s laughable extrapolation that you presented as data.
If Axe’s extrapolation is correct, how do you explain the existence of beta-lactamase abzymes?
Only if you are:
- not employing hearsay and
- the experiments are consistent with your hypothesis.
I know. It still makes no sense.
Is your assumption that the first life was cellular valid?
Hypotheses (not “hypothesizes”) do not make claims. Hypotheses do not make suggestions. Hypotheses make empirical predictions. This basic understanding is missing from everything you have written.
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We were speaking in another thread about the law, and I will interject here that that advice is as good in the law as it is in science: never cite any source you have not read and UNDERSTOOD. I doubt there is any worthwhile field of study in which this is not just as true.
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If my approach bothers you and others that much, then, I will just say [ask for source] whenever you want justification for a particular claim I made and will take extra time to make sure the source is consistent with the claim. But, I gotta say, we are making a lot of progress going about this way and I am learning a lot in the process as well. I feel we are really close to creating an alternative model of evolution that can be understood and used by scientists.
Alright, let me put it to you this way then, if Lenski’s experiment is not producing results similar to what we see from an engineer, such as the study below, then it does not count as evidence against the common design theory, which was my overall point:
" The success of this exercise is particularly relevant to the field of molecular evolution, where the degree to which mutations are nonadditive has been debated at length. Some believe that recent work in developing protein mutant libraries supports the hypothesis that nonadditivity is the rule rather than the exception, and occurs much more often than believed previously (Zaccolo and Gherardi, 1999). Others have put forth both theoretical and experimental evidence suggesting that, though frequent nonadditivity of mutations is still a possibility in these contexts, its existence is not yet supported well (Drummond et al , 2005). Since the method of Yoshikuni et al identifies only additive mutations, the success of the method implies that the space of well‐behaved, additive mutations is big enough for engineering potent changes in activity (see Figure 1 ). The natural prevalence of nonadditivity in mutations may still be a point of debate, but it might be irrelevant to the protein engineer if the case of γ‐humulene synthase is representative of nature as a whole."
Like what? or did you already mentioned them in the post?
Don’t forget. I merely referenced Hugh Ross’s description of the universal common design predictions versus common descent to help you understand and respond to what you said earlier here…
“Spark plugs in different cars are identical, as one would expect from re-use of parts, while parts in different species are non-identical in precisely the nested hierarchy we expect from common descent. And in fact species re-use parts in cases where it makes no engineering sense, as when whales make flippers and bats make wings from the same five-digit hand. But it makes perfect sense from the perspective of common descent. And again, how does this relate to “Evolution by Divine Intelligence”?”
Were you able to understand what we would expect from a universal common design model that is different from common descent? Or do you feel like the explanation is still missing something that I did not go over on this topic?
For instance, do you agree with this statement from Stephen J. Gould’s Wonderful Life?
“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.”
RTB’s point, which is my point as well, is that “Gould’s metaphor of ‘replaying life’s tape’ asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different. The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, ‘repeatable’ evolution is inconsistent with the mechanism available to bring about biological change.”
Then, this would be a common design prediction, which we can potentially confirm in the future, that is different than common descent.
Unfortunately, I can’t find the source on this from what he said. So never mind, I guess.
Tell me if this is specific enough…
Thaxton et al. (1984) established these criteria for the amount of observer interference acceptable for attempts to prove that unguided material processes produced life:
Degree of investigator interference
- Selected chemicals, isolated from other soup ingredients
- Selected wavelengths of UV, heat, isolated from other energy sources
- Spark, shock waves, isolated from other energy sources
- Concentrated solutions where reactions depend on concentrated conditions (e.g., HCN polymerization)
- Traps
- Photosensitization
Threshold of illegitimate interference
- Concentrated solutions where law of mass action is validly extrapolated +
- “Synthesis in the Whole”: dilute solutions mixed together
As shown in the outline, the demarcation line between legitimate and illegitimate interference is between 2) and 3). Any situation higher than 3) (i.e. 2) and 1)) would be illegitimate because the experimenter is deviating from plausible prebiotic conditions, and there is no analogy between the techniques and reliably plausible prebiotic conditions (Thaxton 1984 p.99-110; Jekel 1985). These same criteria can also be applied to biological evolution experiments because the main difference between chemical evolution and biological evolution is that chemical evolution can produce new characteristics and abilities without depending on reproduction or a self-replicating molecule.
I quoted the wrong thing somehow. Here is what I was referring to…
Not at all, as I said before, it would just be an example of trade-offs between conflicting design goals from allegedly bad designs rather than suggest the designer is not all-powerful:
Examples:
An optimal bronchial tree may be dangerous | Nature
Glycolytic strategy as a tradeoff between energy yield and protein cost | PNAS
I will just show you rather than tell…
The God of classical theism is generally defined as “Necessary” and “Personal”, which sums up the totality of God’s attributes. Now, here is how you test it in regards to evolution…
When the scientist chooses a particular set of natural conditions to work on, the observer has to first test and determine whether or not life can be developed within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.
The combined outcomes of these experiments would produce evidence for the hypothesis. If we apply the same procedure to a different natural condition, it would produce additional evidence for this hypothesis. This is because even though the experimenter who guides evolution within each natural condition is finite and contingent, there could not be any conscious life before simple life emerged, hence why we have to include the first experiment to support the “necessary” attribute of this common designer .
ORIGIN OF LIFE
Whenever unguided chemical processes under atmospheric conditions were left to themselves without any interference, they did not produce the desired results. Rather, the living state would always subside and turn into “useless networks of RNA sequences” as demonstrated by Szostak and Bartel (1993) where more than half of the pool of RNA molecules precipitated when incubated. They were able to solve this problem by tying the molecules onto a substrate to make sure the pool of RNA molecules do not diffuse and form intermolecular reactions, and, thus, safely incubated. Although this is an unlikely occurrence within the primordial soup, this was apparently the prevailing inclination within in vitro selection experiments under atmospheric conditions:
“…After all, it is not easy to see what replaced the flasks, pipettes and stir bars of a chemistry lab during prebiotic evolution, let alone the hands of the chemist who performed the manipulations. (And yes, most of us are not comfortable with the idea of divine intervention in this context.)”
COMPLEXITY OF LIFE
Phage-assisted continuous evolution (with the apt acronym “PACE”) is a microbial experiment where molecules from E.coli drift through a provocatively named “lagoon” filled with bacteriophages. Each phage contains a copy of the gene of interest (GOI) that will undergo directed evolution. To successfully infect E. coli, the phage requires a protein called pIII (just ask). To force the GOI to evolve, researchers substitute the phage gene for pIII into the bacteria, linking its expression to the activity of the GOI. Thus, phage containing more active versions of the GOI will generate more pIII and will be more infectious, spreading more copies of that version of the GOI as they infect more hosts. Eventually, only the most successful mutant version(s) of the GOI will be left. However, the phages that are lacking the functional pIII protein are rapidly lost under continuous culture conditions because they have no ability to propagate (just ask).
DIVERSITY OF LIFE
[This one probably does not apply but I included it anyways just to hear your thoughts]
"Effects of small population size and reduced genetic variation on the viability of wild animal populations remain controversial. During a 35-year study of a remnant population of greater prairie chickens, population size decreased from 2000 individuals in 1962 to fewer than 50 by 1994. Concurrently, both fitness, as measured by fertility and hatching rates of eggs, and genetic diversity declined significantly. Conservation measures initiated in 1992 with translocations of birds from large, genetically diverse populations restored egg viability. Thus, sufficient genetic resources appear to be critical for maintaining populations of greater prairie chickens."
Tracking the long-term decline and recovery of an isolated population - PubMed (nih.gov)
I’m not seeing the relevance of this.
It is almost as if you imagine that there are materialists out there attempting to disprove your God. It is nonsense.
Scientists have this thing called “curiosity”? They run experiments on various scenarios, because they are curious to find out what will happen. When they do these kinds of experiments, they are exploring. They aren’t trying to prove anything, they are just exploring and hoping to learn something useful.
If their explorations resulted in clear evidence of intelligent design, I would expect them to publish that.
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How did Thaxton et al. establish them, precisely? Wouldn’t a more accurate verb be “proposed”?
Do you not realize that citing the literature involves more than a name and a year?
As nothing in science is ever considered to be formally proven, this phrase is nonsense scientifically.
So why aren’t you responding to my questions about your citations of Axe?
I don’t see any “design goal” that would be satisfied by using a ribozyme at the center of protein synthesis. Do you?
Neither of those cases has anything to do with the fact that a ribozyme remains at the center of protein synthesis. Evolutionary theory explains it quite well; so well, in fact, that every IDcreationist who claims to address it resorts to misrepresenting the evidence itself.
You’re not showing anything relevant to your assumption.
False. This ridiculous straw man is not even close to the way in which real scientists test real abiogenesis hypotheses. Have you even read any of the relevant primary literature?
Are you aware that what you cited is a mere comment, and not the primary literature?
Did you read the paper, or just the abstract?
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