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Proteins are defying textbooks

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We bet this isn’t the only time they have done so. 😉

Here, from U Utah Healthcare:

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a study published on Jan. 2 in Science defy textbook science, showing for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

“This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize.”

To put the new finding into perspective, it might help to think of the cell as a well-run factory. Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled.

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. More.

But what is this about “Nature is capable of more than we realize”? Does nature have a mind that has a search space for solutions?

Like a half-made car with extra horns and wheels tacked to one end, a truncated protein with an apparently random sequence of alanines and threonines looks strange, and probably doesn’t work normally. But the nonsensical sequence likely serves specific purposes. The code could signal that the partial protein must be destroyed, or it could be part of a test to see whether the ribosome is working properly. Evidence suggests that either or both of these processes could be faulty in neurodegenerative diseases such as Alzheimer’s, Amyotrophic lateral sclerosis (ALS), or Huntington’s.

“There are many interesting implications of this work and none of them would have been possible if we didn’t follow our curiosity,” says Brandman. “The primary driver of discovery has been exploring what you see, and that’s what we did. There will never be a substitute for that.”

Are these people trying to say, don’t fire us because we find evidence for design in nature?

If so, let’s hope they are not forced to yelp some fake disclaimer at a press conference.

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Comments
#269 https://uncommondescent.com/news/proteins-are-defying-textbooks/#comment-544438Dionisio
January 29, 2015
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#272 Petrushka Why do you consider it that way? Can you elaborate? Thank you.Dionisio
January 29, 2015
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It's vacuous. Does that count?Petrushka
January 29, 2015
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Open challenge to all: Does anyone dare to argue against this insightful comment? https://uncommondescent.com/intelligent-design/how-does-the-mind-arise-from-the-brain-novel-idea/#comment-544994Dionisio
January 29, 2015
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Silver Asiatic wrote:
But if I said that evolutionary biologist Shapiro was ‘lying to get attention’ you’d be outraged, right? Funny how it works that way.
This has to be one of the strangest, and most revealing, things I have ever read at UD. Before I walk you through my reaction to this statement, let me eliminate the most charitable explanation: You were being sarcastic – no, given the rest of your post, that doesn’t hold water : you genuinely expect me to be ‘outraged’ by the leveling of such an accusation at a “fellow evolutionist”. Here’s the timeline of my reaction to your statement: 1. Why would I be outraged? I agree that he’s exaggerating to get attention. 2. Wait a second, “lying”, that’s a strong word to use. Do you have evidence to support your contention that he is guilty of intentional falsehood? 3. Absent any evidence of deceit, I will give Shapiro the benefit of the doubt here. 4. I provisionally withhold agreement with the sentiment expressed. My reaction doesn’t even reach “somewhat miffed”. More like ”slightly furrowed brow”. (Here’s a hypothetical statement that would outrage me. “The CDC is lying about the safety and efficacy of vaccines”. This statement costs innocent lives, if believed. See the difference?) Trying to comprehend the point you were trying to make, the best I can manage is that the emphasis in your statement was on the word “I”, as in “But if I (Silver Asiatic, the IDist) said that [an evolutionist] was lying, you’d be outraged, right?” as in “How dare one of them bad-mouth one of us! The cheek!” Here’s the very important and very revealing thing: notice how, in step 1, I gave the statement something of a free ride, because I agreed (more or less) with the sentiments expressed. Only at step 2 did “System 2” (Kahneman) kick in, and I started to analyze the statement for veracity, even though I agreed with the overall sentiment. Simply put, you Silver Asiatic never get to step two: your mindset is stuck in “evolutionists always lie, except when they say things I agree with”. Evidence be damned. Reality be damned. The rest of your post is an impressive demonstration of this “culture wars” mindset. You assume “evolutionists” are liars and/or delusional, and you assume that I have a similar, but reversed, mindset. In SA-world, an evolutionist such as DNA_Jock will always agree with other evolutionists and must think that Richard Dawkins is awesome and always right, whatever he says.
If Dawkins cannot be considered part of the ‘evolutionary biology community’ as I said, then we’ve got an entirely different conversation
Actually, I do NOT consider Dawkins (or PZM) to be part of the ‘evolutionary biology community’. Dawkins is a writer, PZM a blogger. I have been known to refer to that pair as “arrogant dickish atheists with megaphones” at TSZ. You should visit sometime. We do have an entirely different conversation. CRD and PZM are big figures in some sad culture war that you are waging, not part of the ‘evolutionary biology community’. I just want people to keep religion out of science education, which means I am motivated to encourage people to educate themselves about biology. CRD (when in atheist mode)and PZM are actually obstacles, not allies, to me.
Your argument is with fellow evolutionist Shapiro – not me. You’re making it clear that I can’t trust what evolutionists have to say. I guess I have to run their comments by you to get the right interpretation?
No, try using your own brain to assess the accuracy of statements on a case by case basis. Sometimes scientists say things that are wrong. Learn to be more skeptical of those statements that you agree with, and less quick to dismiss as lies or delusions those statements that you disagree with. Stop being so lazy and engage System 2, for crying out loud!
. I only posted a link to [Shapiro] because he’s an evolutionist and I know you won’t care about what IDers have to say.
Completely and utterly wrong. This is a textbook example of your Culture Wars bias. You are projecting. I am almost always interested in what IDers have to say, but I do expect them to be willing to support their claims. My discussions with gpuccio bear this out, I believe. When Radioaction writes
There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.
You think this supports your strawman
the real version of evolutionary theory – the one that has no weaknesses and which offers precise and accurate predictions with each new finding in the data. [snip] …I might say that your version of evolutionary theory could be considered a strawman as well, especially if you’re proposing it as highly certain and irrefutable.
It doesn’t. Note the qualifiers in Radioaction's statement. You write
You’re claiming that my views were fictional.
No. I claim you are arguing against a fictional adversary. As evidenced by your continuing efforts to ascribe to me views that I do not hold.
Ok, you’re denying that evolutionists (I didn’t limit it to biology researchers) claim that their theory is essentially complete and explains the origin of the entire biosphere on earth.
But I DID limit it to biology researchers. And even the atheist culture warriors that you love to hate don’t make that claim, since it encompasses OOL.
Am I supposed to believe that evolutionary biologist Shapiro just imagined the notion that fellow-evolutionists overstate claims for their theory?
I am quite willing to accept that people on all sides have, on occasion, overstated their claims. You should try it out sometime. But your TGTKtM is still a fictional adversary.
You see my posts as agenda-driven but I hope you don’t ignore the bias that is evident in your own views.
I am on the look-out for bias in my own views. I am fortunate to have had training that is extremely helpful in this regard. You, on the other hand, may well be the poster-child for confirmation bias.DNA_Jock
January 27, 2015
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OT Disclaimer: I'm not paid by the moderators or this site admin for luring in more commenters into any discussion thread. However, it's kind of fun to watch how some interlocutors react to different types of comments. :)Dionisio
January 27, 2015
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#265 DNA_Jock Is that the best you can do? Really? Ran out of arguments? BTW, what about #264? :)Dionisio
January 27, 2015
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#263 Aurelio Smith Are you implying that in your post #101 you were barking up the wrong tree? Are you implying that your post #101 was a regrettable knee-jerk reaction? Is that why you did not respond to post #115? https://uncommondescent.com/news/proteins-are-defying-textbooks/#comment-541499 If that's the case, maybe it's understandable. :)Dionisio
January 27, 2015
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DNA_Jock
I cannot find any support for Shapiro’s claim that Dawkins said any such thing, although it does sound like the kind of thing that he would say, if he as trying to get an audience’s attention…
But if I said that evolutionary biologist Shapiro was 'lying to get attention' you'd be outraged, right? :-) Funny how it works that way.
Anyway, Dawkins isn’t a researcher, so quoting him with attribution (were you able to) still wouldn’t meet my request @216.
Yes, but your request didn't meet what I posted. If Dawkins cannot be considered part of the 'evolutionary biology community' as I said, then we've got an entirely different conversation.
The “facts are all on my side” quote is Shapiro quote-mining Coyne. Shapiro is in fact whining about the beat-down Coyne gave him for some rather silly statements Shapiro made, such as
Your argument is with fellow evolutionist Shapiro - not me. You're making it clear that I can't trust what evolutionists have to say. I guess I have to run their comments by you to get the right interpretation?
I would be quite interested in trying to understand what triggers skepticism in you, although I think I already know the answer…
You've already claimed that I shouldn't trust what Shapiro says. I only posted a link to him because he's an evolutionist and I know you won't care about what IDers have to say. Shapiro merely supported what I have seen in discussion blogs for years -- claims about how 'there are no weaknesses' in evolutionary theory are very common. I don't need Shapiro to support that. Here's one of 'you guys' right on this very thread:
Radioaction There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.
But my original point remains. You were arguing with ME, and you repeatedly attributed to me views that I do not hold. Not that I’m surprised, it’s par for the course here.
You're claiming that my views were fictional. I posted an article from Shapiro that was written for the specific purpose of putting aside notions that evolutionary theory is complete. You then claim that Shapiro wrote that for manipulative (getting attention) or vindictive (against a beat-down) motives. So, he can't be trusted. I said:
Ok, you’re denying that evolutionists (I didn’t limit it to biology researchers) claim that their theory is essentially complete and explains the origin of the entire biosphere on earth.
That's why Shapiro wrote the article. The quotes from Dawkins or Coyne were illustrative. Am I supposed to believe that evolutionary biologist Shapiro just imagined the notion that fellow-evolutionists overstate claims for their theory? That's very hard to believe. You see my posts as agenda-driven but I hope you don't ignore the bias that is evident in your own views.Silver Asiatic
January 27, 2015
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Dionisio writes @261
DNA_Jock FYI – in case you didn’t notice it, as I wrote in my post #251, your post #250 failed to respond my previous posts, including my post #243. Did you run out of arguments?
LOL. Your post 243 refers back to 234, which refers to 209, 187, 190. All answered in my 198. FYI, your 231 is word salad. The incoherence continues.DNA_Jock
January 27, 2015
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AVS, DNA_Jock, and your party comrades: Please, note that there's more of the same bitter medicine, enough to treat your condition that makes you criticize how others quote and highlight text in their posts. :) Here's the link (serve yourselves): https://uncommondescent.com/intelligent-design/mystery-at-the-heart-of-life/#comment-544014 :)Dionisio
January 27, 2015
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Radioaction Did you see my post #240 in reference to your post #237? Don't you have anything to comment on that?Dionisio
January 27, 2015
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DNA_Jock FYI - in case you didn't notice it, as I wrote in my post #251, your post #250 failed to respond my previous posts, including my post #243. Did you run out of arguments?Dionisio
January 27, 2015
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To rebut my contention that he is arguing with a fictional adversary, Silver Asiatic @257 offers up the following:
DNA_Jock 216 You claimed that I was arguing against a ‘fictional adversary’ and wanted some references. The following article by evolutionary biologist, James Shapiro offers some insights that might help: http://www.huffingtonpost.com/.....25133.html – Richard Dawkins began his lecture by saying, “I will not only explain that Darwin had the right answer, but I will show that he had the only possible right answer.” – conventional evolutionists make absolutist statements like “all the facts are on my side.”
Couple of problems here. I cannot find any support for Shapiro's claim that Dawkins said any such thing, although it does sound like the kind of thing that he would say, if he as trying to get an audience's attention... Anyway, Dawkins isn't a researcher, so quoting him with attribution (were you able to) still wouldn't meet my request @216. The "facts are all on my side" quote is Shapiro quote-mining Coyne. Shapiro is in fact whining about the beat-down Coyne gave him for some rather silly statements Shapiro made, such as
The second problem is that Darwin understood only “numerous, successive, slight modifications” as the sources of inherited change. His neo-Darwinian followers have modified this position to assert that all mutations occur randomly. They insist there is no biological input into the change process. For them, the genome determines organism characteristics. They think of it as a read-only memory (ROM), which only changes by accident.
and
Three remarkable things about somatic hypermutation and CSR are explicitly excluded from the prevailing philosophy of genetic change. First, they are adaptive and purposeful genome changes. Second, they are functionally targeted. Third, for CSR, targeting involves intercellular signals that depend on how other cells in the immune system perceive a particular infection.
claiming that somatic hypermutation is somehow anti-Darwinian. So when, in this context, Coyne says, "the facts are all on my side", he is stating a simple fact, not making an "absolutist statement", which would look more like this:
...the real version of evolutionary theory – the one that has no weaknesses and which offers precise and accurate predictions with each new finding in the data.
Also, if you believe Shapiro when he makes these uncorroborated claims about what Dawkins said, do you also believe him when he writes, in the Huffpo article you linked to,
5. The newly discovered processes of genome change do indeed have the potential to generate "irreducibly complex" new functions. Such complex evolutionary inventions are at the center of the Intelligent Design critique of neo-Darwinian explanations, which are based exclusively on random genetic accidents and natural selection. Doubling the whole genome, distributing copies of mobile elements to different sites, and incorporating similar domains in different proteins provide the necessary raw materials for generating complex interactive networks in cells.
I would be quite interested in trying to understand what triggers skepticism in you, although I think I already know the answer... But my original point remains. You were arguing with ME, and you repeatedly attributed to me views that I do not hold. Not that I'm surprised, it's par for the course here.DNA_Jock
January 26, 2015
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Silver, as I said, I enjoy talking about biology and I enjoy arguing. I don’t really care what you think about me. You are correct, there is no threat to the theory and time spent here by everyone is futile and wasted. Silver Asiatic: “First of all, I don’t give credence to any and all authors statements. I wouldn’t be surprised if they’re lying or delusional – I expect that from the evolutionary biology community.” “Statements that include conditional or speculative phrases like “might have evolved” or “may have emerged” or “could have developed” I usually consider to be lies and/or delusions. And that’s what most of evolutionary science is, in my opinion.” Apparently you forgot? It’s not “a very precise definition of strategy?” Move the goalposts much? They are making the claim that evolution produced these varying regulation strategies seen in different histidine kinases. I am not misrepresenting the paper, just saying it in words I was hoping you’d understand. Evolution doesn’t optimize? Are you kidding me? Evolution certainly does optimize and fine-tune. Just take a look at the fin-tuning of organisms to their environment. Whether it’s teleological language or not, it is a description of what happens over the course of evolution. Once again the ID argument relies on word-play. No it’s not that mutations “can supposedly” do things. Certain mutations DO these things. You’re requirement that science figure out exactly how “one thing evolves from another” by recreating evolution in a lab, is childish. There was no contradiction. We may not entirely understand how evolution works, but it is quite obvious that it is occurring. If you’re going to make statements like “evolution isn’t a theory,” then this conversation certainly is futile and a waste. Good day.Radioaction
January 26, 2015
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Radioaction
Why shouldn’t I defend it when it comes under fire?
When you defend something from a non-existent threat, I recognize something in your motivation. If I defend my house against non-existent beings (predatory unicorns) it says something about me. If I spend time going to blogs about topics I think are unsubstantial (wizards who make magic potions) - then that says more about me than the topic.
Especially from people that don’t know what they are talking about.
There's no threat to your theory from people who are ignorant of it.
Promoting evolution among the skeptics here is pointless; there is nothing that will change your minds.
I would guess that you don't really believe that. But anyway, it would make your time spent here seem more futile and wasted. Spending time on a blog that nobody cares about, among people who are ignorant and incapable of changing their minds ... it certainly makes me wonder about you.
You know, things like “all evolutionists are liars/delusional.”
No, I don't know that. Please show me where you can find that quoted text.
The “strategy” in this case is the way in which each histidine kinase is regulated. They state that evolution has come up with diverse mechanisms of regulation of HKs and give a couple examples that are very different.
I wouldn't call that a very precise definition of a strategy. They also do not state that "evolution has come up" with these mechanisms. You're misrepresenting the paper. That's been the topic under discussion.
Each regulatory system is optimized for that specific system through the course of evolution;
That's an undemonstrated assertion. You're missing a very signficant point also - evolution does not 'optimize' anything. Optimization refers to a value which is invisbile to evolution. If there are optimizations, then evolution works towards 'what is better' and is therefore directional.
basically evolution is constantly fine-tuning selected new functions.
You might want to read the link I offered from Ann Gauger. You're using teleological language to describe evolution. "Fine-tuning" is something that can only be measured against a reference point. It's also a perfect example of design language. Mutatation, selection, drift and whatever other unintelligent mechanisms you have cannot 'fine-tune' things. Again, that's teleological language of directed evolution.
Direct evidence is given when they talk about HK853 which has one form of activity that relies on the interface between two domains. This activity can be altered by mutations at this interface and results in a change in the reaction catalyzed by the enzyme.
No direct evidence of evolution is given. Mutations 'can' supposedly do things. But what 'did' they do?
It is the evolutionary biologists that focus on evolutionary questions and publications in that field focus much more heavily on providing the direct evidence you choose to ignore.
As I said, there is zero direct evidence that those mechanisms evolved at all. Direct, observed evidence is watching in a lab as one thing evolves from another. You have none of that in this case.
There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.
I'll ignore the contradiction in that sentence and point you to the thread on Susan Mazur's book on UD's front page. In any case, you're totally convinced by evolutionary theory and are willing to claim that 'there are no serious problems with it'. I can point out, simply, that the theory cannot even define or explain what the mechanisms of evolutionary change are or to what degree they function in nature. To that extent, it's not a theory. A theory cannot say 'there might be mechanisms that caused XYZ to evolve'. It has to say precisely what those mechanisms are and how they caused something to evolve. The mutation/selection notion is becoming more discredited. Again, see the 'third way of evolution' threads and/or the one I just referenced.Silver Asiatic
January 26, 2015
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DNA_Jock 216 You claimed that I was arguing against a 'fictional adversary' and wanted some references. The following article by evolutionary biologist, James Shapiro offers some insights that might help: http://www.huffingtonpost.com/james-a-shapiro/evolution-debate_b_1425133.html -- Richard Dawkins began his lecture by saying, "I will not only explain that Darwin had the right answer, but I will show that he had the only possible right answer." -- conventional evolutionists make absolutist statements like "all the facts are on my side."Silver Asiatic
January 26, 2015
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Why shouldn’t I defend it when it comes under fire? Especially from people that don’t know what they are talking about. Promoting evolution among the skeptics here is pointless; there is nothing that will change your minds. You know, things like “all evolutionists are liars/delusional.” I just like to argue and talk about biology. The “strategy” in this case is the way in which each histidine kinase is regulated. They state that evolution has come up with diverse mechanisms of regulation of HKs and give a couple examples that are very different. Each regulatory system is optimized for that specific system through the course of evolution; basically evolution is constantly fine-tuning selected new functions. Direct evidence is given when they talk about HK853 which has one form of activity that relies on the interface between two domains. This activity can be altered by mutations at this interface and results in a change in the reaction catalyzed by the enzyme. This is direct evidence that mutations can alter the regulation “strategy” of these proteins and that each strategy is likely to be unique and optimized for each protein and its function, over the course of evolution as shown by the two examples given. Anything I skipped is right there in the papers and what I have already said. I fear that you simply do not understand how research works. It’s not that there is an unwillingness to explore, to ask why, or what. “Run ahead on unquestioned assumptions” couldn’t be further from the truth. Biologists take tiny incremental steps to figure out the answer to a very specific question and then relate their findings to the existing body of knowledge. Publications on cellular biology focus on their main question and often relate it to evolutionary findings as in the examples I have given. It is the evolutionary biologists that focus on evolutionary questions and publications in that field focus much more heavily on providing the direct evidence you choose to ignore. Criticism of evolutionary claims from the ID community is of little importance. The majority of the ID community have no clue what they are talking about, as shown on PaV’s latest posted which I commented on. It is also redundant. There is plenty of criticism within evolutionary biology, along with every other field, as researchers continually disagree on interpretations of evidence and validity. What isn’t criticized in any of these fields is the mention of evolutionary ideas as in the paper I have cited. This is because there is no uncertainty within these fields as to whether or not evolution has occurred. There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.Radioaction
January 24, 2015
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We might be able to help those with some intellectual integrity. It occurred to me yesterday, when you commended me for pointing out that mind/body dualism had been CONCLUSIVELY proven, that maybe some of you boffins should keep a 'running' log on this site of what has now been EMPIRICALLY established, CONCLUSIVELY, but which the atheists' religious beliefs will not countenance, a priori; fearful of 'letting God's foot in the door'. You could keep one log for positive, empirically-proven findings, simply proving them completely wrong, and another log for their empirically DISPROVEN findings - although the latter I suppose could not fit into all the pages of all the books in the Library of Congress. But might not the first 'have legs'? What do you think? Don't consider my feelings. I've the hide of a rhinoceros. I seem to remember seeing a similar compilation by Cornelius Hunter, exposing the glaring obstacles to a sound belief in evolution.Axel
January 24, 2015
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Axel
Rationality, in the here and now, never took root among atheists, because they see themselves, not as insanely deluded numpties, but as temporarily- unrecognised geniuses, just waiting for their promissory notes to become cashable.
Another great point. Rationality leads to some uncomfortable truths, whereas the belief that one is a genius who stands above and beyond the rest of humanity can't afford to be challenged by such things. Yes, they're waiting for their promissory notes - excellent. Every bit of new data is filtered and adapted to support their investment. I guess delusional is not the right word for many - it's actually euphemistic. If there's an inner, conscious decision and commitment to a belief system, then it shouldn't be excused as merely a mistaken understanding. At the same time, not all are liars. I guess its fair to say some are delusional, some are lying, some are open to correction and some are willfully mistaken.Silver Asiatic
January 24, 2015
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Axel
ROFL. Silver Fox , you’re a cruel *******! And you just get meaner ‘n’ meaner!
I smiled at your comment (thank you!), but I hope its the strength of the argument that is getting meaner and not my personal disposition. :-)Silver Asiatic
January 24, 2015
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Radioaction 249 That was a long reply. I always keep in mind that, given the overwhelming support in the biological community for modern Darwinian theory, that evolutionists (like yourself) on this blog should not be defending the theory against ID, which according to you, has nothing substantive to offer. Instead of defending, you should (I think) try to promote evolution among skeptics like myself. Otherwise, why bother to post on a site devoted to a 'substanceless' idea like ID? So, in all of that response, I notice quite clearly what you avoided. It's this - and I even said "most importantly":
But most importantly: What is a ‘strategy’ in this case? You’re claiming there’s evidence that a “strategy” evolved. Again, what is a “strategy”? Then beyond that, what is an “optimized strategy”? What does “optimized” mean and how did evolution do it? What evidence is there that this happened — admitting you have zero direct evidence?
Lots of questions and issues which you skipped entirely. This is merely from one paper. You're claiming evidence supports that 'optimized strategies' might have evolved. But even on the theoretical level there are lots of problems with this. Yes, I think that evolutionary claims like that are delusional. It's a delusion because there's an unwillingness to explore the underlying meaning of what is said. There's an unwillingness to ask 'why' evolution does the things that is claimed for it. Why does evolution create regulartory systems. What does a 'strategy' in cell function mean and how and why, precisely, did evolution create a strategy? Biologists don't ask these questions. They run ahead simply on unquestioned assumptions. Some biologists have noted recently that ID plays an important role at least as a critical voice against evolutionary claims. In closing, I think you've fair-minded about the issue. I understand your bias - you're defending a theory you believe in. I think that blinds you to some very serious problems with the theory, but you're not as hardened in your position as many others we encounter. For that, again, I commend you. And with that, I apologize for a harsh tone in some of what I said. Years of battling with people who are quick to ridicule ID and are very quick with personal insults have shaped my attitude for the worse, unfortunately.Silver Asiatic
January 24, 2015
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#250 DNA_Jock You're wrong again. You think that you have responded, but you have not. Try again, if you really want to. After all, deep inside, you may not be interested in responding my questions. At least that's the perception one gets after reading your posts. It's up to you, but definitely you have not responded. Whatever you think you responded may not qualify as a serious response. However, you're not obligated to respond. You know that. Think about it. BTW, the post #s directly or indirectly referenced in my posts are valid for AVS and for you.Dionisio
January 23, 2015
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Dionisio, You keep referring me back to your post #209, and "the posts referenced therein". But post 209 reads
#205 AVS First read carefully post # 204 and then come back with more questions. BTW, are you also a paid cover agent working for the admin of this site, pretending to be stubbornly unpleasant, so that the discussions turn senseless, but heated enough to attract the attention of trashy talk show audiences, thus increasing the site traffic? Or you do all that voluntarily? Is your constant foul language included in your contract? Or is it part of your party line?
204 (which is likewise addressed to AVS) references some of your earlier posts, which I had responded to @198. Frankly, you're getting quite incoherent.DNA_Jock
January 23, 2015
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No. “Might have evolved,” and every variation of this statement is not ambiguous. These statements are made in published research when there is evidence to back it up. There can be evidence that one protein may have evolved from another protein, just as there can be evidence that one protein did not evolve from another protein. “Might have evolved” and “unlikely to have evolved” (or some variation) would be used in these cases respectively. These statements are not subjective because to my knowledge, each time claims like these are made in published research, evidential support is provided. What I said was “I don’t determine precisely how strong or weak the evidence is.” “Precisely” is the key word. I can judge the strength of an argument just fine, but there is not an objective way to “precisely” measure how strong an argument is. The question is, does the argument convince you? Obviously you, along with many of your friends here, require an inordinate amount of evidence to be convinced of anything that disagrees with your personal beliefs. The only “direct evidence” you guys would be willing to accept is a stepwise walkthrough of every tiny step in evolution and until provided with this, you convince yourself that the entire field of evolutionary biology is nothing but a pile of “lies/delusions.” This is despite the massive body of work in the field of evolutionary biology, along with the evidence from every other field of biology that supports it. You choose to ignore all this because of a few examples of fraud (the UD favorite of which is over 100 years old). As I said, you will find fraud in every field or research. I note that you did not answer my question about whether or not you think design research is immune to this. I’ll give you a hint: it’s not. You were asked exactly that. Earlier you were asked for “a paper that has one of these lies and/or delusions.” We are still waiting for said paper. It would be great if the subject of the paper was on some form of cellular biology if you can manage it. Whether there is a bias or not against intelligent design doesn’t matter. There is bias against anything that shifts paradigms in science. If a new finding or idea really is better than what’s currently accepted, it will eventually find its way to the table. Just look at the original opposition to the chemiosmotic model. Intelligent design has had a while to make their case, and have failed time and time again. They have their own little research institute, researchers, and funding; surely if they had something of substance we would have seen it by now, no? I did not make a mistake, don’t worry. “You guys ” included you and axel, the same as AVS said earlier. DNAJock didn’t seem to have any issue understanding this. Maybe it’s your ability to evaluate what’s written that we should be worried about. There is evidence supporting all of the claims I cited from the papers. I briefly mentioned this evidence and how it was presented. Feel free to read about it for yourself and decide its strength. Your problem is that “Evolutionary interpretations get less weight (from me) than mere facts about observations.” Do interpretations of data in cellular biology get less weight from you as well? How about any other field of science, for that matter. They are all based on interpretation of data and it is up to the reader to decide on their validity. You, I will assume, decide that evolutionary interpretations are invalid simply because it disagrees with your personal belief system. The requirements for evidence-based claims are just as strict in evolutionary biology as they are in cellular biology and any other scientific field. “Yes, show me the observed evidence. Repeat it in a lab. Demonstrate that this evolved from that.” Open an evolutionary biology book, open a journal dedicated to evolutionary research, it’s all there, you just choose to get your information on evolution from websites like UD. “If I say the evidence is so weak that it does not exist, you have no real basis to counter that.” I can show you the paper (as I have), tell you about the evidence in the paper that supports the claims (as I have), point you in the direction of other literature that supports these claims (as I have), and your response is that the evidence does not exist. That’s your choice. The bottom line is this: We are light years beyond Darwin’s original idea. The basics he outlined still hold true and are the basis of the theory of evolution, but since his publications the theory itself has evolved based on the vast amount of information coming out of every field in biology. You can be skeptical all you want of specific claims that one protein “might have evolved” from another protein, but to believe that every scientist who makes these claims is lying/delusional or that the entire field of evolutionary biology is made up of lies/delusions? Now that’s delusional.Radioaction
January 23, 2015
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'“There may be evolution selection” means that “there may not be evolutionary selection”. What is the precise likelihood that there “may not be”? On what basis can it be determined that one or the other is more or less likely?' ROFL. Silver Fox , you're a cruel *******! And you just get meaner 'n' meaner!Axel
January 23, 2015
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Yes, indeed, oh wily Silver Fox, considering that the monitoring equipment the patients were hooked up to, would have been as sophisticated as one might expect, and others, leading-edge. Plus they were subject to more rudimentary procedures such as the fitting of blindfolds and ear plugs. I watch those videos a lot. Absolutely fascinating, particularly the pitch of the emotional body language, and the sometimes wry humour. That's the weird thing, though. They seem unable to distinguish between gratuitous, open-ended speculation, conjecture, work-a-day evidence for practical purposes, and conclusive evidence. They remind me of John Steinbeck's words: "Socialism never took root in America because the poor see themselves not as an exploited proletariat but as temporarily embarrassed millionaires." Rationality, in the here and now, never took root among atheists, because they see themselves, not as insanely deluded numpties, but as temporarily- unrecognised geniuses, just waiting for their promissory notes to become cashable.Axel
January 23, 2015
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Axel
Evidence relating to ‘out of body experiences’, and hence mind/body dualism is conclusive, so, if none of them have the gumption to look for a place to start, that should serve admirably.
Fascinating point regarding evidence.Silver Asiatic
January 23, 2015
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Radioaction
Alright, went to google scholar, as you said. Over 1 million hits. Many of them have the phrase or a version of it in the title of the paper, and the author(s) subsequently explain the evidence behind their claims within the paper.
First of all, I commend you for actually pursuing my suggestion and doing this research. You've noted those examples (and "could have evolved" is another one giving a million plus hits). I'll mention below, "might have evolved" is ambiguous. What about "might not have evolved"? These are subjective interpretations and as you state, you have no means to weigh them for strength or weakness.
Papers with these phrases within the text also provided evidence of their claims by either directly giving the evidence or citing specific papers that provide the evidence.
There's no direct evidence that any of those things evolved. It's speculative. It's based on assumptions which are also unobserved (common descent).
I did not read the links because what you were asked for was a single specific paper that uses one of those phrases and does not support it with evidence.
I wasn't asked that. So again, should I question your ability to evaluate what is written. Can you evaluate the quality of evolutionary speculations? Can you accurately evaluate the strength or weakness of evidence in this regard?
I cannot find those phrases in any of your provided links.
From the scientist in the second link I posted:
In a 2008 issue of Scientific American Mind the writer Chip Walter argued, citing British zoologist Desmond Morris, that kissing may have originated from the primate behavior of pre-chewing food and passing it to the kids.
If you're not willing to understand that 'may have originated' is the same in biology as 'might have evolved' then we won't be able to continue. Now that I showed you what you claimed didn't exist, you could try to tell me how strong the evidence is that kissing 'may have originated' in the ancient past through that practice.
As for fraud in science, you will find it in small amounts in every field of research unfortunately.
There is fraud in evolutionary biology, yes. But more than that, there is a bias against intelligent design as indicated in one of the links I provided. There is also a systemic attempt at manipulation by use of language.
There’s no need to be uncivil, I was simply lumping you and Axel together, since you both sounded so sure of yourselves.
I'd call a failure to admit a mistake as a form of uncivility, myself. You made a mistake.
Biologic insights from structures of two-component proteins. 2009. Gao & Stock. In this paper they use the phrase “might have evolved,” twice. Both times they back the claim with a comparison among a number of phosphatase and kinase proteins and cite a paper that also supports their claims.
From that paper: "Certainly, HKs might have evolved diverse strategies optimized for individual systems to regulate kinase/phosphatase activities. " You, apparently, think there is evidence supporting this. You cannot give the precise strength or weakness of the evidence, that much is known. But most importantly: What is a 'strategy' in this case? You're claiming there's evidence that a "strategy" evolved. Again, what is a "strategy"? Then beyond that, what is an "optimized strategy"? What does "optimized" mean and how did evolution do it? What evidence is there that this happened -- admitting you have zero direct evidence?
Molecular dynamics simulations of biomolecules. 2002. Karplus & McCammon. In this paper they talk about how “there may be evolutionary selection for dynamics” in protein function. They back this claim in a section about the dynamics of acetylcholinesterase and its function.
"There may be evolution selection" means that "there may not be evolutionary selection". What is the precise likelihood that there "may not be"? On what basis can it be determined that one or the other is more or less likely?
I don’t determine “precisely” how strong or weak the evidence is behind these claims;
Very good. Of course you can't. Even the researchers cannot do this. The evidence could be very weak. The evidence could be based on the assumption that 'similarity means ancestry', which is a standard evolutionary assumption - which could be entirely false (and is false in cases of convergent evolution). So, with no means of weighing the evidence, the evidence may in fact be zero. Speculations on zero evidence, without admitting that it "may not have evolved" is what I call a delusion or lie. You've exposed several case of that already,
it is a matter of reading the evidence and thinking about it. Does it make sense? Does it agree with what is known? Do any cited references further the claims?
This is a subjective interpretation of data. It can render evidence meaningless. It can claim not to actually see evidence, or claim evidence is so weak as to not exist. It can claim that evidence is very strong, based on personal interpretation. When we're talking personal, subjective interpretation - here's where bias, lies and fraud play a part.
Do you know of a better way to determine the quality of an argument?
Yes, show me the observed evidence. Repeat it in a lab. Demonstrate that "this evolved from that". Don't use personal bias to claim "might have evolved" when it could be more likely that it "did not evolve". Would you say, two apples plus Two apples "might equal four apples"?
I’m still waiting on a single paper from you. I honestly wouldn’t be surprised if they are out there, there is a wide spectrum of researchers, some good, some not so much. I just thought you had a paper or two in mind when you originally spoke about these phrases with such certainty.
You showed me papers that gave zero direct evidence that anything evolved. You then said you couldn't tell precisely how strong or weak the evidence that you found in the papers actually was. If I say the evidence is so weak that it does not exist, you have no real basis to counter that.Silver Asiatic
January 23, 2015
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Alright, went to google scholar, as you said. Over 1 million hits. Many of them have the phrase or a version of it in the title of the paper, and the author(s) subsequently explain the evidence behind their claims within the paper. Papers with these phrases within the text also provided evidence of their claims by either directly giving the evidence or citing specific papers that provide the evidence. I did not read the links because what you were asked for was a single specific paper that uses one of those phrases and does not support it with evidence. I cannot find those phrases in any of your provided links. As for fraud in science, you will find it in small amounts in every field of research unfortunately. Do you think Intelligent Design research is immune to this? Everyone is entitled to their own opinion, but supplementing opinion with evidence certainly adds more weight to said opinion. There’s no need to be uncivil, I was simply lumping you and Axel together, since you both sounded so sure of yourselves. As I said, I would be interested in reading a paper that makes such claims without evidence, particularly one within cellular biology. Feel free to produce one if you are as sure of yourself as you appear. Here are some examples of papers that use phrases you don’t like, and also back them up with evidence: Biologic insights from structures of two-component proteins. 2009. Gao & Stock. In this paper they use the phrase “might have evolved,” twice. Both times they back the claim with a comparison among a number of phosphatase and kinase proteins and cite a paper that also supports their claims. Molecular dynamics simulations of biomolecules. 2002. Karplus & McCammon. In this paper they talk about how “there may be evolutionary selection for dynamics” in protein function. They back this claim in a section about the dynamics of acetylcholinesterase and its function. Structural symmetry and protein function. 2000. Goodsell & Olson. In this paper they make the claim that a specific interleukin “may have evolved” in a certain manner and they talk about the evidence behind this as well as citing the specific paper that some of these concepts originated from. I don’t determine “precisely” how strong or weak the evidence is behind these claims; it is a matter of reading the evidence and thinking about it. Does it make sense? Does it agree with what is known? Do any cited references further the claims? Do you know of a better way to determine the quality of an argument? Sure, it is possible that I have little experience, although I have presented scientific papers above that both, make the claims we have been talking about and support them with evidence. I’m still waiting on a single paper from you. I honestly wouldn’t be surprised if they are out there, there is a wide spectrum of researchers, some good, some not so much. I just thought you had a paper or two in mind when you originally spoke about these phrases with such certainty.Radioaction
January 23, 2015
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