Uncommon Descent Serving The Intelligent Design Community

Scientists’ reaction to ever more of the cell’s complexity in its own environment

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In mind-boggling detail:

For a few weeks in 2017, Wanda Kukulski found herself binge-watching an unusual kind of film: videos of the insides of cells. They were made using a technique called cryo-electron tomography (cryo-ET) that allows researchers to view the proteins in cells at high resolution. In these videos, she could see all kinds of striking things, such as the inner workings of cells and the compartments inside them, in unprecedented detail. “I was so overwhelmed by the beauty and the complexity that in the evenings I would just watch them like I would watch a documentary,” recalls Kukulski, a biochemist at the University of Bern, Switzerland.

In recent years, imaging techniques such as cryo-ET have started to enable scientists to see biological molecules in their native environments. Unlike older methods that take individual proteins out of their niches to study them, these techniques provide a holistic view of proteins and other molecules together with the cellular landscape. Although they still have limitations — some researchers say that the resolution of cryo-ET, for example, is too low for molecules to be identified with certainty — the techniques are increasing in popularity and sophistication. Researchers who turn to them are not only mesmerized by the beautiful images, but also blown away by some of the secrets that are being revealed — such as the tricks bacteria use to infect cells or how mutated proteins drive neurodegenerative diseases such as Parkinson’s.

Diana Kwon, “The secret lives of cells — as never seen before” at Nature (October 26, 2021)

No wonder panpsychism is catching on, among those who are forbidden to think in terms of design.

Comments
But there is no strong evidence that it didn’t occur.
Yes, there is extremely strong evidence it didn’t occur. That’s why ID is the more intellectually superior and intellectually honest position. The statement above is an example of the begging the question fallacy.jerry
October 30, 2021
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Some unknown naturalistic processes did something isn’t a real convincing narrative for a mechanistic position. But then again, you are hooked on the failed DNA model.
Good thing no one is saying that then.
Are you daft? That is all you have.
Guess we’ll just have to disagree on that then.
What I said is a fact. Only fools disagree with facts.
Guess we’ll just have to disagree on that then.
No one cares. You can't refute what I posted. That is all that matters.
Well, obviously, no one can exhibit a complete, plausible, step-by -step narrative.
Science is about EVIDENCE, not narratives.
But there is no strong evidence that it didn’t occur.
There isn't any evidence that it did or could occur. You lose.ET
October 30, 2021
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JVL @45
… is there any other kind of evidence that would convince you that evolution proceeded via unguided processes?
Good question. For me, to be open to the concept of unguided evolution, first and foremost a tendency by blind matter to spontaneously form simple systems [such as mobile phones & airplanes] has to be demonstrated. After that I may be somewhat open to the idea that blind matter also has the tendency to form inordinately complex systems, such as organisms.Origenes
October 30, 2021
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ET: Some unknown naturalistic processes did something isn’t a real convincing narrative for a mechanistic position. But then again, you are hooked on the failed DNA model. Good thing no one is saying that then. You talk about fossil evidence without understanding that you don’t have anything capable of producing the organisms that were fossilized. If you did then we wouldn’t be having this chat. Guess we'll just have to disagree on that then. Yes, the genetic evidence is the strongest evidence for a Common Design. And it refutes unguided evolution/ evolution by means of blind and mindless processes. Guess we'll just have to disagree on that then. Please tell us how to model the idea that blind and mindless processes produced the genes required for developmental biology. How can that claim be tested? Well, obviously, no one can exhibit a complete, plausible, step-by -step narrative. Yet! But there is no strong evidence that it didn't occur. In fact, the evidence is slowly accumulating which makes it more and more sure.JVL
October 30, 2021
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Jerry: JVL has not read the two references I left for him. In these links it essentially says there is no genetic information supporting macro evolution. I disagree but if we lay that aside . . . is there any other kind of evidence that would convince you that evolution proceeded via unguided processes?JVL
October 30, 2021
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Origenes: What do you mean by “the genetic evidence”? The evidence in the genomes of extant and extinct (when it can be accessed) lifeforms. Endogenous retroviruses are just one particular example.JVL
October 30, 2021
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Bornagain77: Yet his claimed ‘strongest’ evidence for Darwinism evaporates into thin air and has, in fact, been falsified as an evidence for common descent, turned on its its head, and been shown to support the intelligent design model. (in overwhelming fashion I might add) Other views are available. Just out of curiosity: what kind of evidence would you accept as strongly supportive of evolution via unguided processes? Not genetic . . . fossils? Morphological? Geographic distributions? Anything?JVL
October 30, 2021
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That Seversky does not know for a fact that the universe is chosen, a creation, means he doesn't really understand anything. Same as if you don't know the fact that people make choices, then you don't really have any understanding of human beings. The creationist conceptual scheme stops social darwinist pseudoscience. That is the main contribution of creationism to science. Apart from that, intelligent design science will come to fruition, at the same time that we have the technology to look directly inside of people's imagination. That is when we would have a better understanding of the decisionmaking processes by which things are created.mohammadnursyamsu
October 30, 2021
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Bornagain77 @18 and ET @34, Nicely summarized. Devastating to the tired drivel being put forward all the time. Seekers @ 40, Exactly! I can't believe he keeps repeating the lie that ID is the same as Creationism and that somehow they "undermine confidence in science" despite having the difference explained to him numerous times by different people, and that the track record of ID has been demonstrably better than Darwinism! He's only fooling himself or being a troll or a bot. What a complete waste of time for everyone!
If not then i find it rather peculiar “participating” in something you have no willingness to learn about or debate.
Bingo! -QQuerius
October 29, 2021
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Seversky,@39 You state, “ ID/creationism’s sustained campaign to undermine confidence in science, is exactly what they want.” Given such a statement I find it prudent to ask, why are you here? What use to you is your participation (reluctant to name it that) here? You have made it obvious you have no use for ID/creationist science, so why stick around? To troll? Surely you have more pressing things that would require your attention. Or are you simply a bot? If not then i find it rather peculiar “participating” in something you have no willingness to learn about or debate.Seekers
October 29, 2021
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JVL/11
How can you model an undefined, unobserved, unlimited being who can act without leaving a trace violating physical laws which work 99.999 . . . . % of the time?
Precisely. Such a being would render the whole scientific enterprise futile which, given ID/creationism's sustained campaign to undermine confidence in science, is exactly what they want.Seversky
October 29, 2021
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Bornagain77/19
And please note that Lenski did not respond to Minnich’s work as a scientist who is falsified by experimental evidence should have done, i.e. by humbly admitting that he was wrong. No, Lenski responded with hostility and ad hominem towards Minnich. Which is the exact opposite reaction that any responsible scientists, who is more concerned with the truth than with his reputation, should have had when shown to be wrong by experimental evidence itself.
Once again, you fail to provide a link to Lenski and Blount's response to Minnich's critique but, for anyone interested in seeing if BA77's characterization is fair and balanced, it is here:
On the Evolution of Citrate Use
Those who follow the long-term evolution experiment (LTEE) with E. coli know that the most dramatic change we have observed to date is the origin of the new ability to grow on citrate. It’s dramatic for several reasons including the fact (external to the LTEE) that E. coli has been historically defined as a species based in part on its inability to grow on citrate in oxic environments and the fact (internal to the LTEE) that it was so difficult for the bacteria to evolve this ability that only one of the populations did so, and that it took over 30,000 generations even though an abundance of citrate has been present in the medium throughout the LTEE. Even after 64,000 generations, only the Ara–3 population has evolved that new ability. Zachary Blount, formerly a graduate student and now a postdoc in my lab, has spent the last decade studying the evolution of this population and its new ability. His two first-authored papers in PNAS (2008) and Nature (2012) demonstrated, respectively, that (i) the origin of the ability to grow on citrate in the LTEE was contingent on one or more “potentiating” mutations that happened before the “actualizing” mutation that conferred the new function first appeared, and (ii) the actualizing mutation was a physical rearrangement of the DNA that brought together a structural gene, citT, that encodes a transporter and a previously unconnected regulatory region to generate a new module that caused the phenotypic transition to Cit+. These papers presented and discussed much more than these two points, of course, but they are the key findings. More recently, Zack was a coauthor on a paper in eLife (2015) by Erik Quandt, Jeff Barrick, and others that identified two mutations in the gene for citrate synthase—one that potentiated the evolution of citrate utilization, and another that subsequently refined that new function. So we were keenly interested when we saw a new paper titled “Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA” by Dustin Van Hofwegen, Carolyn Hovde, and Scott Minnich. The paper is posted online as an accepted manuscript by the Journal of Bacteriology. What follows here are some overall impressions of their paper that Zack and I put together. We may follow these impressions later with some further analysis and comments. * * * * * Let’s begin by saying that it’s great to see other groups working on interesting systems and problems like the evolution of citrate utilization in E. coli. Moreover, the actual science that was done and reported looks fine and interesting, though we have a few quibbles with some details that we will overlook for now. By and large, the work confirms many of the findings that were reported in our papers cited above:
For further reading, here is Larry Moran's blog post on their reply
An Intelligent Design Creationist disputes the evolution of citrate utilization in the LTEE ... Lenski responds
Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon. The pathway to this event is complex and requires multiple mutations [see On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment and Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source]. Intelligent Design Creationists are not happy about this experiment because it not only shows evolution in action but it also illustrates features of the process that ID proponents don't understand; features like drift, neutral alleles, and contingency that expose the ignorance of the average creationist. However, there are a few ID proponents who actually understand evolution so they are forced to come up with other kinds of criticism to soften the impact of the results coming out of the Lenksi lab. ...
Seversky
October 29, 2021
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Bornagain77/18
At 9 Seversky pulls Douglas Theobald’s old “29+ Evidences for Macroevolution” out of cold storage and pretends like it has not already been addressed
A Critique of “29 Evidences for Macroevolution ” By Ashby L. Camp Excerpt: In “29 Evidences for Macroevolution,” Douglas Theobald sets forth the evidence that he believes proves scientifically that all living organisms descended from “one original living species.” He does so by listing what he claims are 29 potentially falsifiable predictions of the hypothesis of universal common ancestry and presenting the evidence that he believes confirms each of those predictions.,,
And, as usual, you completely fail to mention that Theobald wrote a response to Camp's critique:
29+ Evidences for Macroevolution
A Response to Ashby Camp's "Critique"
Anti-evolutionist Ashby Camp has penned a critique of these "29 Evidences of Macroevolution," which can be found posted at TrueOrigin. Camp's critique is well-written, very thorough, and quite lengthy (the criticism is longer than the original article). Although I intend to address Camp's concerns in totality, currently I can only devote a limited amount of time to this effort. In the meantime, this partial response will suffice. I would like to thank Camp for his congenial criticism. It has given me the impetus to rework and expand the "29 Evidences," and the result is a more comprehensive, clearer, and stronger article. My response has been two-fold. First, I have incorporated new material into the original essay that specifically addresses many of Camp's points, and thus much of his response is now superfluous. Second, in the following sections I rebut the more egregious errors found in Camp's criticism, especially ones that would interrupt the flow and thrust of the original article if they were included there. In the following response, Camp's words are indented in grey boxes, set apart from mine. Material that Camp has quoted in his criticism is also in the grey boxes, surrounded by quotes, and followed by the pertinent external reference. Mr. Camp's critique is error-ridden in various ways, and is primarily characterized by: Straw man arguments Red herrings Self-contradictions Equivocation Two wrongs make a right Fallacies of accident and converse accident Ignoratio elenchi Naive theological assumptions Insufficient knowledge of basic biology, molecular biology, biochemistry and genetics Misunderstanding of the scientific method Forwarding of untestable competing "hypotheses" Mischaracterization of evolutionary theory Misleading mis-quotes Fallacies of accent Distortion of scientific controversies Arguments from authority False analogies The repeated use of these errors and others in Camp's "Critique" will be abundantly clear in the following rebuttal.
Yet, there was a small problem with Theobald’s claim. As Casey Luskin noted, “The problem is that Theobald didn’t test universal common ancestry against “creationism.”
The not-so-small problem is that there is no testable hypothesis of creationism or intelligent design against which to compare anything else.
In the following article Dr. Cornelius Hunter explains just how badly the common decent model was falsified when the test was run properly by Dr. Ewert.,,, Dr. Hunter stated, “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!”
Why don't you explain to us all - in layman's terms - what a dependency graph model is and how it can be applied to evolution.Seversky
October 29, 2021
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Yes, the genetic evidence is the strongest evidence for a Common Design. And it refutes unguided evolution/ evolution by means of blind and mindless processes. Please tell us how to model the idea that blind and mindless processes produced the genes required for developmental biology. How can that claim be tested?ET
October 29, 2021
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Earth to JVL: Some unknown naturalistic processes did something isn't a real convincing narrative for a mechanistic position. But then again, you are hooked on the failed DNA model. You talk about fossil evidence without understanding that you don't have anything capable of producing the organisms that were fossilized. If you did then we wouldn't be having this chat.ET
October 29, 2021
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Doug Theobald's 29+ evidences for macroevolution is pure fiction. The first clue is he starts out saying the evidence is there regardless of the mechanism. Yet mechanisms determine patterns and most of his evidence pertains to patterns. He also chokes on nested hierarchies. Transitional forms are the exact types of organisms one would expect with universal common descent. And they are also the exact type of organisms which prevent descent with modification from producing a nested hierarchy! 1- There aren't any known naturalistic mechanisms capable of producing eukaryotes given starting populations of prokaryotes. 2- There aren't any known naturalistic mechanisms capable of producing metazoans given starting populations of prokaryotes and single-cell eukaryotes. 3-The DNA model is a complete FAILURE with respect to being able to produce the diversity of life. 4- DNA's scope is very, very limited 5- Evolutionary biologists don't know what determines biological form.ET
October 29, 2021
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the genetic evidence
JVL has not read the two references I left for him. In these links it essentially says there is no genetic information supporting macro evolution.jerry
October 29, 2021
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JVL:
I find the genetic evidence the strongest and possibly able to make the case on its own.
What do you mean by "the genetic evidence"?Origenes
October 29, 2021
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JVL, claims to "find the genetic evidence the strongest". Yet his claimed 'strongest' evidence for Darwinism evaporates into thin air and has, in fact, been falsified as an evidence for common descent, turned on its its head, and been shown to support the intelligent design model. (in overwhelming fashion I might add) https://uncommondescent.com/intelligent-design/some-at-your-fingertips-stats-on-human-chimp-similarity/#comment-739134bornagain77
October 29, 2021
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Seekers: Just out of curiosity, what evidences convinced you of macro-evolution(or not, if that’s the case) Good question! It was not a single piece of evidence but multiple bits of evidence in multiple areas. So, it wasn't just fossils or genetics, it was the sum total of fossils and genetics and morphology and bio-geography. And not individual cases in those areas but, again, a large collection of individual cases in each area. At one point I came to the realisation that there was so much evidence that the case was still strong even if you took away a whole class of examples. Some people think that the fossil evidence is inconclusive; I can forgo all fossils and still come to the conclusion that evolutionary theory is correct. I suppose I find the genetic evidence the strongest and possibly able to make the case on its own. Fortunately that's not the case; all the threads come together and point to the same conclusion. That's just my personal view, obviously. But that's what you asked for.JVL
October 29, 2021
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Jerry: No evolutionary biologist on the planet has addressed my concerns. Otherwise they would have won the Nobel Prize. I believe you. If you could just say, specifically, what those concerns are then I might either be able to address them or go away and leave you alone. Clearly you have a line that no one has been able to cross. If you could just draw that line in the sand so we could all see it we might get somewhere.JVL
October 29, 2021
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JVL, Just out of curiosity, what evidences convinced you of macro-evolution(or not, if that’s the case)Seekers
October 29, 2021
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If I had a better idea of what you were looking for then I might be able to address your concerns a bit better.
No evolutionary biologist on the planet has addressed my concerns. They are the same for anyone who understands the issues. Otherwise they would have won the Nobel Prize. https://uncommondescent.com/intelligent-design/do-nylon-eating-bacteria-show-that-new-functional-information-is-easy-to-evolve/jerry
October 29, 2021
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Jerry: TMS If you can't be specific about what you'd like to see then I don't understand how you expect anyone to provide it to you. Let's say I show you a sequence of fossils which I say shows the evolution of . . . the otter. Just to pick something. Let's say I have a sequence of 10 fossils spanning 10 million years or so. Is your objection that: you don't know what the specific mutations were to create that sequence? Is your objection that: there are gaps and no proof that those gaps were filled by intermediate species? Is your objection that: we don't know that the mutations which brought about those forms were unguided? If I had a better idea of what you were looking for then I might be able to address your concerns a bit better.JVL
October 29, 2021
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Sigh.
TMS https://uncommondescent.com/darwinism/pope-on-evolution/#comment-523744jerry
October 29, 2021
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Jerry: It would be in every text book on biology and evolution there is. But there are none in these text books. Sigh. I think there are such examples in textbooks but you don't. What I am really asking is: What evidence of macro evolution would you find convincing? I don't want to waste your time with examples you don't find convincing so if you could give me some idea of what you would find convincing that would be helpful.JVL
October 29, 2021
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What would an example of macro evolution by naturalistic means look like?
It would be part of the Nobel prize nominating letter for the individual who discovered it. It would be in every text book on biology and evolution there is. But there are no examples in these text books nor nominating letters.jerry
October 29, 2021
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Querius: Certainly they will simply dismiss (or more likely, not read) the stunning content in the article in Nature. Umm . . . there's nothing to dismiss. I don't understand. This is great technology, cutting-edge stuff.JVL
October 29, 2021
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Methodological naturalism does not exclude any explanations a priori. The door is open to any who can step over the threshold. That threshold is that if you want your pet explanation to be considered, be it God or gravity, you need to provide good reasons for doing so. As CD pointed out, just complaining you’re not being treated fairly doesn’t cut it. Where’s your evidence that compels ID as a conclusion?
You really are a piece of work, Sev. Read this entire website from beginning to now. There are terabytes of evidence that you ignore on a daily basis. Good grief.AnimatedDust
October 29, 2021
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Martin_r, The video is indeed amazing! Also, you might want to check into the incredible speed at which DNA is rewound. I'd also note that the detractors here continue to make their assertions regardless that they have been repeatedly and thoroughly refuted! Seekers makes a good point regarding trolls and bots. I'd also note that Chuckdarwin hasn't responded to his being corrected on his misunderstanding something as basic to botany as transpiration. Certainly they will simply dismiss (or more likely, not read) the stunning content in the article in Nature. -QQuerius
October 29, 2021
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