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Junk DNA turns out to have function again

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Peter M. Waterhouse & Roger P. Hellens, ” Plant biology: Coding in non-coding RNAs,” Nature (March 25, 2025)

Dominique Lauressergues, Jean-Malo Couzigou, Hélène San Clemente, Yves Martinez, Christophe Dunand, Guillaume Bécar, & Jean-Philippe Combier, “Primary transcripts of microRNAs encode regulatory peptides,” Nature (March 25, 2015)

G C S Kuhn, “‘Satellite DNA transcripts have diverse biological roles in Drosophila’,” Heredity (March 25, 2015)

Go here for simple explanation.

Nick Matzke? Darwin book burner! Where are you when we need you to dump on all this?

You used to come at half o’clock and now you come at noon.

Otherwise, Biological Information

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Comments
Joe, Regarding your criticism of Zachriel's statement,
No, but the Theory of Evolution makes many confirmed predictions…
realize that the confirmation comes before the prediction, which is made in retrospect. This makes the predictions a lot more reliable! So, for example, the presence of junk DNA is currently interpreted as evidence for Darwinian evolution, while the absence of junk DNA will also eventually be shown as evidence of evolution. Same with ring species. Pretty slick! -QQuerius
April 11, 2015
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Rocinante: "Please reference this alleged theory of evolution so we can all see what it predicts." For a theory that doesn't exist, UD (and yourself) seem to spend a lot of time and effort attacking it. Keep tilting at those windmills.lack of Focus
April 9, 2015
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Zachriel is bluffing again:
No, but the Theory of Evolution makes many confirmed predictions...
Please reference this alleged theory of evolution so we can all see what it predicts. Our bet is Zachriel won't do so because it cannot. Sweet...Joe
April 9, 2015
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DNA Joke- There isn't any evidence for a chaperone-free organism. Your imagination and wishful thinking are just that. However we all know that your position requires a chaperone-free organism to have existed so we understand your desperation.Joe
April 9, 2015
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Dr JDD: It {chaperones} does not support evolution however in and of itself. No. That can only be supported by a consilience of the evidence. Dr JDD: In support of evolution we can propose that cells and replicators pre-cursor to what we observe now existed and reproduced without chaperones, and you can rationalise that they have been lost through evolution over time but the observations that all life require chaperones in and of itself is of no evidence to support evolution: that is the crux. No, but the Theory of Evolution makes many confirmed predictions, with strong support for mechanisms of complex adaptation, so it is reasonable to hypothesize a similar process for the origin of primordial cellular mechanisms. In particular, some proteins fold without a chaperone, while extant chaperones give indication of having evolved in families. Finally, there's always going to be gaps, especially in the early history of life. That hardly implies that evolution isn't the best explanation.Zachriel
April 8, 2015
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I was not trying to mock you JDD, just offering up an analogy, in the hope that it would help you see how you are misconstruing my position
  OK, how about we accept we have both misconstrued each other’s positions (because I believe you are also misconstruing mine)? I will admit given my repetitive discussions with materialists about such subjects, they usually will say that such and such DID or MUST HAVE happened. I can perfectly accept MAY have or is an alternative theory within the confines of this discussion (not even worrying about how you get to evolve a complex protein like a chaperone in the first place). The thrust of my argument – and my position with many materialists is that regardless of whether you can test it or not, you can observe, much like materialists maintain that something has a likelihood of design, and that is a valid theory. Just as valid as abiogenesis and just as valid as the multiverse, both of which (among many other things) are considered “scientific” theories. The problem I come back to here is how most materialists will say that those theories are fine to make (despite you not really being able to test them) but design as a theory is not. That is inconsistent and hypocritical and led through necessity by a world-view.   So you must understand my position here – I am not saying chaperones are proof of design. I am saying this is a piece of evidence that can support design. It does not support evolution however in and of itself. In support of evolution we can propose that cells and replicators pre-cursor to what we observe now existed and reproduced without chaperones, and you can rationalise that they have been lost through evolution over time but the observations that all life require chaperones in and of itself is of no evidence to support evolution: that is the crux. So if new evidence emerges, i.e. that a cell/replicating organism can exist with the pre-cursor components (proteinacious components from a genetic material) but without chaperones, then this “evidence” suddenly as you say, swings away from support of design, as we know it could potentially happen without design.   This is something that virtually all materialist proponents I have encountered will not accept nor entertain. I’m not asking you/them to accept the evidence and change opinion; I am merely trying to establish it can be viewed as supportive evidence for design. (And I am incidentally not writing any of this in the vain hope that I might convince you or change your opinion – but rather for the observer who wants to hear both sides and make an informed decision without complete bias).  
Okay, I want you to really pay attention here, this is important: DNA would have demonstrated the possibility of starter-less cars. Has he proved that JDD was wrong to suppose that a starter deity created starter motors ex nihilo? No, he has not. Has he demonstrated that JDD’s argument “No starter-less cars today, therefore no starter-less cars ever” is fallacious. Yes, he has. It still remains possible that starter motors were created by a deity.
  You see I actually agree with you here and always have. Being able to experimentally make a starterless car would in fact swing this particular set of evidence in the balance of DNA over JDD. Of course, I have no problem with that.  
Okay, if you really need me to spell it out: from the assertion that replicators can exist without chaperones, I predict that we will be able to produce, at some future date, a replicator that replicates without chaperones. Kinda obvious, y’think?
  Well done. Sometimes you need to ask stupid questions otherwise conversations get side-tracked. Of course it is obvious. Have we done this yet? As you say, no. So my next question: What time-frame would one accept this experiment to take? What constitutes failure? 10 years? Your life-time? 1000 years? How do you know when to stop trying and that it will not be possible? After how many attempts does the alternative hypothesis (design) become more feasible? What is the null hypothesis for this experiment?  
Dichotomous thinking is a particularly popular failing amongst IDists…
  Actually, one IDist could cite the infamous idiom in relation to a materialist here: Pot, kettle, black. I could cite several examples but perhaps best to agree to disagree as this would side-track completely. I should say though that many IDists accept a lot of evolutionary principles and thinking – just not on the extrapolated and grand scale that is portrayed with virtually infinite time alluded to allow for such changes.  
You keep thinking I am making a positive claim that chaperone-less replicators did exist. I am merely pointing out your fallacy : “if X today, then X always” I fail to see the circularity in my position
  Again, please understand, I am NOT saying “If X today, then X always.” You are also misunderstanding me. I am saying all we currently can observe is X today. Now that does not necessarily MEAN X always, but with no other evidence to support X did not exist before (and given X’s vital role in ALL life as we know it), it provides a level of evidence that X may be necessary for cellular life. If that is the case (i.e. that it is necessary), it poses a problem for abiogenesis and the materialistic worldview. I am certainly not saying because “X today” this disproves abiogenesis or the materialistic account. It is a piece of evidence to consider, and the idea is that the vast majority of materialists will never acknowledge this point – they will assume and vehemently defend the notion that a cell/replicator must, nay did exist that had no “X” present.   This is where the circular argument comes in – namely, that people will argue that it is not a valid point that chaperones are needed todayfor many proteins to correctly fold because once chaperones evolved, other proteins evolved alongside them. That is a circular argument because it assumes that proteins that require aid in folding must not have existed pre-chaperone and they are only the result of post-chaperone era, which is an unproven assumption. Again, that is not me saying they definitely did not exist, I am just balancing what we can observe and what experiments to address this have so far shown (or failed to show).Dr JDD
April 8, 2015
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DATCG writes:
Chaperones were important from the beginning of time. Not just for “modern cells.”
Here, Ladies and Gentlemen, we see the fallacy in its distilled form. JDD and I were discussing pre-LUCA/peri-LUCA evolution, and along comes DATCG touting the ubiquity of chaperones in the cyanobacteria that we observe today, that is, modern cyanobacteria. DATCG is unable to wrap his brain around the idea that cyanobacteria may have descended from an ancestor that lacked chaperones. Oh dear.DNA_Jock
April 8, 2015
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Joe #82
That’s just stupid. If that were true then all deaths would be considered murders, all fires would be arsons and all rocks would be artifacts. You must be proud of your ignorance…
Consistent with design does not mean designed of course. The idea being that you could look at a death which seems pretty clearly to be from natural causes and still inferred it was designed. You may have a good reason for doing so: a particularly strong motive or a data point that just doesn't quite fit. This is the stuff of classic mystery stories. But you might just say: it could have been designed to look natural, we cannot discern the designer's motives.Jerad
April 8, 2015
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DNA_jock said... "We agree that chaperones help proteins fold faster, and that this is important in the cell. The modern cell." A 2014 paper discusses role of chaperones in cyanobacteria... Cyanobacterial heat-shock response: role and regulation of molecular chaperones.
Sustained long-term exposure to changing environmental conditions, during their three billion years of evolution, has presumably led to their adaptation to diverse ecological niches.
Cyanobacteria exist everywhere on earth. Very diverse on land, in sea and fresh water. From very hot, dry climates to moist, or cold. From the North Pole to the Sonoran Desert.
The ability to maintain protein conformational homeostasis (folding-misfolding-refolding or aggregation-degradation) by molecular chaperones holds the key to the stress adaptability of cyanobacteria."
Chaperones were important from the beginning of time. Not just for "modern cells."DATCG
April 7, 2015
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DNA Joke:
I am always happy to acknowledge that anything is consistent with a design inference, because anything is consistent with a design inference.
That's just stupid. If that were true then all deaths would be considered murders, all fires would be arsons and all rocks would be artifacts. You must be proud of your ignorance...Joe
April 7, 2015
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JDD writes:
DNA_jock, I’m not too bothered by the mocking, but I would prefer that you did not conflate and inflate my words into something they are not saying. I have not said what you are implying, namely that because we do not see cells/replicators around or have history of them without chaperones that they did not or could not have existed…
I was not trying to mock you JDD, just offering up an analogy, in the hope that it would help you see how you are misconstruing my position. I even provided post numbers so that you could follow the analogy through our conversation. JDD has questions:
1) Could an alien visiting the earth try to create a working car without a starter motor? Do you think they could, with all the parts of cars available to them currently around in the whole world today? If they could, who would win that argument?
Yes, I think they could, but it might take a lot of work. “If they could, who would win that argument?” Okay, I want you to really pay attention here, this is important: DNA would have demonstrated the possibility of starter-less cars. Has he proved that JDD was wrong to suppose that a starter deity created starter motors ex nihilo? No, he has not. Has he demonstrated that JDD’s argument “No starter-less cars today, therefore no starter-less cars ever” is fallacious. Yes, he has. It still remains possible that starter motors were created by a deity.
2) So what testable predictions can we make from asserting that cellular life can exist (survive, replicate) without the presence of chaperones? (I repeat this because you did not answer it – you confuse my question with the thought that I have no ideas of the answers myself – far from it, but I want to hear how you would answer it, as a materialist)
Let’s be clear about the context here: you asked this question in response to my claim @72 that my position differed from the “design inference” because my position entailed testable predictions. My incredulity is my response to your asking such a mind-blowingly dumb question, as in “Really? Nothing comes to mind?” [emphasis in original] Okay, if you really need me to spell it out: from the assertion that replicators can exist without chaperones, I predict that we will be able to produce, at some future date, a replicator that replicates without chaperones. Kinda obvious, y'think?
3) What evidence would it take for you to come to a conclusion that cellular life cannot function without chaperones?
That’s a tough one I agree, and gets us into some of the definitional challenges. Challenge (1) are we restricting “chaperones” to those that consume ATP, or are we expanding the definition to include any proteins that have a modest anti-aggregation effect (such as serum albumin)? Challenge (2) the term “cellular life”: if (as I suspect) researchers are able to create a replicator that lacks “chaperones”, but they fail repeatedly to create “cellular life” and they demonstrate that they are failing because a specific, essential category of membrane protein cannot be synthesized without chaperones, then I would say that a pretty good case had been made. I think a large part of the problem is with labels that human beings feel compelled to put on things. Dichotomous thinking is a particularly popular failing amongst IDists...
I know you are committed to your materialism and the likely answer is observation of a designer or “miracle” that could be reproduced and tested, but let us play another little scenario game:
I love disappointing IDists.
Imagine that you visited another planet that had water but no life. It had the right environment to support life but life had not evolved. Now let us also assume that evolution can progress from a single celled organism to intelligent conscious beings such as humans (big assumption!). As we have the capacity to travel such distances, we had also reached a point in science where we understood the genome fully and knew a lot of DNA/RNA, protein, carbohydrate, lipid etc functionality.So much so that we designed ourselves a replicating cellular organism, one that evolution on our earth had not produced. We planted this on the distant planet, to let evolution take its course. Let’s say then 2 billion years later on that planet very intelligent life has evolved and is present. Scientists keen to understand their origins trace through fossil records and DNA evidence and archeology that they believed we evolved from a single celled organism. They have no evidence that anyone ever landed on their planet, they have not contacted any extra-terrestrial life, they think they are alone in the universe. Tell me, what evidence could they use to ascertain or differentiate between some intelligent life planting a bacteria on their planet 2bya versus abiogenesis? The fact is with this scenario, someone intelligent did plant it. But I am curious how you think you could distinguish that from it arising itself?
Francis Crick is a pretty smart guy (James Watson not so much). But, that jackass Dawkins was correct that this would just move the problem of abiogenesis back one step to a different world. And the Nixon-speech writer who did the ambush interview was too dumb to realize the point. To answer your hoary old chestnut of a question, it would be very difficult to distinguish between the possibilities; absent any data one way or the other, we invoke William of Ockham (post 66), and opt, provisionally, for the explanation with one fewer explanatory entities.
YET, as with most materialists, you refuse to acknowledge this is consistent with a design inference and by default use a circular argument to justify why modern cells require chaperones.
You keep thinking I am making a positive claim that chaperone-less replicators did exist. I am merely pointing out your fallacy : “if X today, then X always” I fail to see the circularity in my position. What on earth makes you think that I “refuse to acknowledge this is consistent with a design inference”? I am always happy to acknowledge that anything is consistent with a design inference, because anything is consistent with a design inference. That’s what makes it not science.DNA_Jock
April 7, 2015
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DNA_jock, I'm not too bothered by the mocking, but I would prefer that you did not conflate and inflate my words into something they are not saying. I have not said what you are implying, namely that because we do not see cells/replicators around or have history of them without chaperones that they did not or could not have existed. I also did not say that is proof they were designed. What I am arguing is based on the given evidence one cannot definitively distinguish between design and evolution here (as with much in evolutionary biology frankly) and if anything, it adds some evidence to support the possibility of design. YET, as with most materialists, you refuse to acknowledge this is consistent with a design inference and by default use a circular argument to justify why modern cells require chaperones. Now if you can produce some record of pre-chaperone life or reproduce some experiments that show replicators/cells can exist with the production of proteins but not chaperones than you have stronger evidence that this is a favourable theory (in this specific example) over a design. Some questions for you: 1) Could an alien visiting the earth try to create a working car without a starter motor? Do you think they could, with all the parts of cars available to them currently around in the whole world today? If they could, who would win that argument? 2) So what testable predictions can we make from asserting that cellular life can exist (survive, replicate) without the presence of chaperones? (I repeat this because you did not answer it - you confuse my question with the thought that I have no ideas of the answers myself - far from it, but I want to hear how you would answer it, as a materialist) 3) What evidence would it take for you to come to a conclusion that cellular life cannot function without chaperones? I know you are committed to your materialism and the likely answer is observation of a designer or "miracle" that could be reproduced and tested, but let us play another little scenario game: Imagine that you visited another planet that had water but no life. It had the right environment to support life but life had not evolved. Now let us also assume that evolution can progress from a single celled organism to intelligent conscious beings such as humans (big assumption!). As we have the capacity to travel such distances, we had also reached a point in science where we understood the genome fully and knew a lot of DNA/RNA, protein, carbohydrate, lipid etc functionality.So much so that we designed ourselves a replicating cellular organism, one that evolution on our earth had not produced. We planted this on the distant planet, to let evolution take its course. Let's say then 2 billion years later on that planet very intelligent life has evolved and is present. Scientists keen to understand their origins trace through fossil records and DNA evidence and archeology that they believed we evolved from a single celled organism. They have no evidence that anyone ever landed on their planet, they have not contacted any extra-terrestrial life, they think they are alone in the universe. Tell me, what evidence could they use to ascertain or differentiate between some intelligent life planting a bacteria on their planet 2bya versus abiogenesis? The fact is with this scenario, someone intelligent did plant it. But I am curious how you think you could distinguish that from it arising itself?Dr JDD
April 7, 2015
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Earth to DNA Joke- unguided evolution doesn't have any predictions and its entailments are: change, stasis, disease and deformities.Joe
April 7, 2015
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Z:
There is evidence that eukaryotes evolved from simpler cells.
No, there isn't any such evidence, only a need.
There is evidence that life didn’t always exist on Earth, but started in simple form soon (in millions of years) after liquid water formed.
Wrong again- you conflate a need with evidence.Joe
April 7, 2015
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Some time later: JDD "Did you know that starter motors are delivered to car factories by vehicles that have starter motors? The inference to best explanation is that there exists a starter motor deity that created starter motors." DNA "Oh Cthulhu! You have got to be kidding me."DNA_Jock
April 7, 2015
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What the heck, I'll try an analogy, imperfect as they are. Two aliens, JDD and DNA, arrive on earth, unaware of the history of the internal combustion engine. JDD (59) “Given that all cars have starter motors, what evidence do you have that cars could exist without starter motors?” DNA (60) “Well, as you yourself put it, plenty of internal combustion engines do not require starter motors. It seems to be a common Centaurian fallacy that ‘just because X is essential today, X was always essential’” JDD (62) “You`re confusing science with fantasy. Although snow blowers, lawn mowers, chain saws and outboard engines do not need starter motors, all cars do. You say it is a common Centaurian fallacy to say that just because things are this way now means they couldn’t have been differently before but it is an equal fallacy to say they must have been different before otherwise they do not fit in with your worldview. I certainly would not argue with the sentiment that things we see now are probably much different to a long time ago, but if you actually take that argument for what it is and extend your own argument, you suddenly support YECs who will say that perhaps radioactive isotopes had different decay rates in the past hence the apparent very old ages. After all, just because something appears a certain way/rate now does not mean it always was!” DNA (66) “We agree that most internal combustion engines do not require starters, we agree that things we see now are probably much different to a long time ago. We agree that modern cars have starter motors. But earlier cars could have been much worse. If better cars came along they would replace the crummy cars. Centaurians fail to appreciate the importance of this fact.” JDD (70) "Not at all. I and many fellow Centaurians completely understand this argument and the importance of it. But we do not observe anywhere any cars without starter motors" DNA (72) "Say what? You just did it again!" JDD (73) “Oh I understand the concept, I just don't accept it. You are arguing thus: 1) All cars have starter motors. 2) Therefore there must have been a time when cars did not have starter motors and could get by without. What testable predictions can we make from asserting that cars could exist that lacked starter motors? ” DNA "Really?DNA_Jock
April 6, 2015
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Dr JDD, Try reading what I actually wrote, rather than what you think I wrote. Specifically, the words "could" and "importance" in the passage in question. Your strawman is showing:
1) We see all organisms with protein class X present and necessry for life 2) Therefore there must However, there may have been a time when cellular organisms replicators did not have protein class X and could survive without
Similarly:
So what testable predictions can we make from asserting that cellular life can exist (survive, replicate) without the presence of chaperones?:
Really? Nothing comes to mind? Contrast that with
The design inference predicts there are complex ordering to the molecular level of the cell that are not observed to spontaneously come into existence yet are necessary to life.
As written, it isn't a prediction. Critically, it is not an entailment. Rather it is a time-qualified observation which happens to be the primary motivation for ID. Primary outside of theology, that is.DNA_Jock
April 6, 2015
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Dr JDD: 1) We see all organisms with protein class X present and necessry for life 2) Therefore there must have been a time when cellular organisms did not have protein class X and could survive without What evolutionary biologists see is evidence that complex adaptations have evolved over the history of life, both on the molecular and morphological levels. There is evidence that eukaryotes evolved from simpler cells. There is evidence that life didn't always exist on Earth, but started in simple form soon (in millions of years) after liquid water formed. There is molecular evidence that extant cellular processes evolved from simpler processes. The evidence from the other end is more tenuous. We have nucleic acids that can self-catalyze. We observe lipids forming into micelles that can grow and divide.Zachriel
April 6, 2015
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Substrate x is converted to substrate y in a system where you can only detect enzyme A. What can you scientifically say about that observation? Can you say "enzyme A requires a co-factor for catalysing y-->x" ? That is analagous to saying "we do not observe something therefore we have no experimental or direct evidence for it" which is what science works on, not extrapolations or speculations.
You say “Not at all”, but you cannot even finish the paragraph without repeating the error. Dammit, I need a new meter.
Sorry but you really do not get this do you. You are equating the understanding of a concept/idea with the acceptance. You are saying because I do not accept your concept in this particular case I have made an error and/or do not understand your point. That is a completely ludicrous way to view theories and is self-validating therefore is non-falsifiable. You can understand Freud's theories completely. You can even accept 90% of them. But just because you reject some of his theories on psychology does not mean you do not understand them. How in the world is this science? Can anyone help me??: 1) We see all organisms with protein class X present and necessry for life 2) Therefore there must have been a time when cellular organisms did not have protein class X and could survive without If you take out the assumptions of abiogenesis and a materialists worldview that is what your argument here boils down to. So what testable predictions can we make from asserting that cellular life can exist (survive, replicate) without the presence of chaperones? The design inference predicts there are complex ordering to the molecular level of the cell that are not observed to spontaneously come into existence yet are necessary to life. Tell me, have you or anyone else ever observed directly the coming into existence through random processes of chaperones? Tell me how the design inference has failed to predict such complexity? What would you expect from a design based cell?Dr JDD
April 6, 2015
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Early replicators could have been horrendously inefficient and extremely slow (to fold their proteins, for instance), but if there were able to propagate better than their lame-ass cousins, they would do just fine. Every single ID proponent that I have read fails to appreciate the importance of this fact.
Not at all. I and MANY other ID proponents completely understand this argument and the importance of it...We do not observe anywhere horribly inefficient cellular organisms...
You say "Not at all", but you cannot even finish the paragraph without repeating the error. Dammit, I need a new meter. You ask:
How is this any different or more “scientific” than the design inference?
Because it entails testable predictions, unlike the "design inference" which does not, pace Wells.DNA_Jock
April 6, 2015
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Joe @64: Sorry, I do not know if this is why genetic engineering has failed as such. In the industry I am in it is certainly known that drugs and products can and will fail due to simple folding problems or modification problems, stability, aggregation, etc, etc. Many factors influence this and you can have the best biologic in the world but if it is not "druggable" then there is no point. And this is in a highly controlled and externally manipulated environment.Dr JDD
April 6, 2015
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DNA_Jock,
You are arguing that, based on the 20 – 30% of extant proteins that do require chaperones, a rudimentary protein synthesizing organism would absolutely require chaperones. It just doesn`t follow
No I am not arguing that at all, not exclusively as you put it. Where did I write that? You are putting words in my mouth. My conclusion from that line of reasoning was: we could assume at best case 10% of cytosolic proteins require chaperones, etc. that is not insignificant I am saying if 20-30% of proteins absolutely require chaperones (hypothetically as I do not know of a solid reference for this) there is a good chance some really important proteins cannot just “fold correctly”. That is observable evidence, based on what we see around us and can test and measure. What we can also test and measure is that in any organism if you rid the cell of chaperones, even archaea who have 3 I believe, it is lethal to the organism. That we can observe. Now with archaea I believe there is just 1 that is necessary, but that still makes the point either: - The simplest of cells have evolved to rely on chaperones from a pre-chaperone era where they did not rely on them for life - Cellular life cannot survive and reproduce without the aid of protein folding molecular machinery So my point is not that all life “absolutely require chaperones” (please show me where I have implicitly stated that?), my point that to make the claim that there “must have been” a pre-chaperone era is unscientific as it is not founded on evidence that is testable and observable but mere speculative fantasy. I’m with Joe @68 on this one – you are extrapolating which is a sin in science, yet most of Darwinian evolution is extrapolating in a similar way. So please do tell me, what evidence do we have that simpler cells could exist without chaperones, given that no cellular organism today can be rid of all their chaperones? How do you arrive to such a conclusion that a cell must have existed without these proteins? There are a lot of scientists who would look at such evidence as certain complex functionally specific necessary proteins present in all life, and make a different conclusion to you – that is, they may even accept UCD but from a design perspective because the machinery necessary for life is absolutely necessary and complex and therefore as we have no observable evidence of anything less complicated maintaining “life” and we know something so complicated and organised could not just spontaneously appear in such ordered fashion, this is seen as strong evidence for external tinkering as opposed to dust to molecules to molecular machines. So my point is it is fine to invoke the “mysteries of nature” just undergoing abiogenesis to a horribly inefficient route until it magically produced efficient cellular machines (and then left no trace of its predecessors) but you cannot pretend that this is any more scientific than invoking a designer. And THIS is my criticism (note, I am not saying you are 100% wrong which you fail to grasp. I am not saying this is proof of a designer) – you speak as most materialists do in “must have” and “just so story” terms. There must have been a cellular predecessor that could operate and function without such machinery, its just we have no trace of it, we never will know what it looked like, and it was lost to evolution. But it must have existed (otherwise I have to call into question my whole world view...). How is this any different or more “scientific” than the design inference? Secondly, I am certainly not saying the laws of physics have changed. I am making a principle point – the fact that the data does not fully support your position therefore you invoke an alternative explanation which cannot be proven or tested nor observed (abiogenesis and “early” cellular life) and call this scientific fact – only to support your worldview. This is just as bad (often worse) than the YEC who says the rates of radioisotope decay may have been different at “creation” than they are now.
Early replicators could have been horrendously inefficient and extremely slow (to fold their proteins, for instance), but if there were able to propagate better than their lame-ass cousins, they would do just fine. Every single ID proponent that I have read fails to appreciate the importance of this fact.
Not at all. I and MANY other ID proponents completely understand this argument and the importance of it. We just do not accept that it can account for abiogenesis and the appearance of complex molecular machineries. Especially when the basic requirements for cellular life in what we can observe involve many components efficiently balanced. We do not observe anywhere horribly inefficient cellular organisms. You claim that is because they no longer exist as they were selected out but that makes your claim non-observable therefore speculation at best and pseudoscience at worst. The only evidence you have that there were “highly inefficient cellular organisms” is because you have an a priori commitment to materialism, not because of any scientific observations or experimental evidence. And that is something I have never heard a materialist ever acknowledge in these discussions.Dr JDD
April 6, 2015
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This is just a note of appreciation for those of you with informed and well-thought-out replies. Incidentally, I've learned the hard way on several occasions to compose my longer posts in an external editor and then cut-and-paste it in. -QQuerius
April 5, 2015
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DNA Joke:
Early replicators could have been horrendously inefficient and extremely slow (to fold their proteins, for instance), but if there were able to propagate better than their lame-ass cousins, they would do just fine. Every single ID proponent that I have read fails to appreciate the importance of this fact.
You don't have any evidence for these alleged early replicators that were horrendously inefficient and extremely slow (to fold their proteins, for instance) . You don't have any evidence for a chaperone-free cell. You can't get from simple replicators to those which produce proteins. Every single evo proponent I have read fails to appreciate the importance of these facts.Joe
April 5, 2015
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Chapter XIII "What Teaches Proteins Their Shapes?" Dr Sermonti discusses prions and how they rearrange a host protein's spatial shape just by contact. He discusses the failures of genetic engineering too. He says:
Proteins transferred from one kingdom to another through biological smuggling did, indeed, form in their new environment, but they often failed to function. The amino acids making up the proteins duly placed themselves in the proper sequence, but they failed to take up the spatial configuration necessary to make the proteins as active as they were in the donor species. Instead they formed glutinous masses, the equivalent of a dish of overcooked spaghetti. page 129
Enter chaperones...Joe
April 5, 2015
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Dr JDD, You seem to be arguing against a strawman of your own construction. We agree that many extant proteins do not require molecular aides for folding (you put the proportion at 70 – 80%). You are arguing that, based on the 20 – 30% of extant proteins that do require chaperones, a rudimentary protein synthesizing organism would absolutely require chaperones. It just doesn`t follow. We agree that “things we see now are probably much different to a long time ago”, but you conflate my position with a denial of uniformitarianism - “radioactive isotopes had different decay rates in the past”. Really? There`s no reason to think that the laws of physics and chemistry have changed during life on earth, but every reason to think that the circumstances (e.g. oxygen levels, predation) have changed. We agree that chaperones help proteins fold faster, and that this is important in the cell. The modern cell. Early replicators could have been horrendously inefficient and extremely slow (to fold their proteins, for instance), but if there were able to propagate better than their lame-ass cousins, they would do just fine. Every single ID proponent that I have read fails to appreciate the importance of this fact.
So it is fine for you to have your opinion on what we cannot observe and cannot test (that a cellular organism could exist without chaperones) but it is not based upon experimental science and is assumption and deduction to fit with your world view – no different to how one might conclude there needed to be a designer as all life have proteins needed to correctly produce other proteins necessary for life.
Paging William of Ockham, William of Ockham … P.S. would you set Joe straight on his “Why is a fly not a Horse?” rubbish. He`s not going to believe me…DNA_Jock
April 5, 2015
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Gpuccio asks
Again, I would appreciate examples of generic isolated alpha helices which are naturally selected because they confer a reproductive advantage in a biological system. Again, it’s your theory, not mine. You have to show the supporting facts.
At the risk of running afoul of all those qualifiers in there - “generic” “isolated” “naturally selected” “reproductive advantage” “ biological system” – I`ll offer up Ma & Ptashne PMID:3115591 Giniger & Ptashne PMID: 3317067 With the note that there’s a wrinkle, but I`ll let you figure that out for yourself…
gp: Again, homology can detect recombination.
DNAJ This is rather misleading. Yes, by looking at DNA sequences, we can detect the recent recombination of relatively large fragments. But, as I went to considerable lengths to explain to you, the absence of detectable homology DOES NOT preclude common ancestry.
Gp Why these strange limitations? The sequences in ATP syntase have remained almost the same for about 4 billion years. The Helix-loop-helix domain in human myc shows clearly detectable homology with the same domain in the mxl-3 protein in C. Elegans…
Thanks to selection; you are making my point for me. After the recombination event, selection may preserve or destroy the homology signal. Remember, your argument was that IF recombination had occurred, THEN we would certainly be able to detect it. My point was “sometimes, sometimes not”. It is you, gpuccio, who is making the claim that [protein X] has no homolog that I can detect, therefore she leapt fully formed from her father`s forehead. I, DNAJ, am merely making the observation, “it ain`t necessarily so”.
As a lot of conserved sequences or anyway of recurrent motifs, some of them very short, are well known, you can certainly show the relevant role of those sequences and motifs in building up long and complex functional proteins by recombination and natural selection
and
My point is simple. If recombination of functional modules were really a fundamental component in protein evolution, as many on your side have bben affirming, then we shopuld be able, in the general case, to recognize the functional modules which have been recombined, and therefore be able to analyze the role of recombination according to facts.
I know. Isn`t titin a great example: it`s a huge protein, and most of it is obviously the result of recombination events – in this case duplications of the Ig-domain. But as to it being the “general case” :
While it can be true that in some cases we would miss the sequence homology, that would be the exception, and not the rule.
Well that would depend on whether selection preserves or destroys the homology. Care to support your assertion here?DNA_Jock
April 5, 2015
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Dr JDD:
HOWEVER, just because you can fold without a chaperone is not necessarily enough in the context of a cell, in particular a dynamic cell. Folding in vitro without molecular aids is quite inefficient and takes much much longer without chaperones.this is not a moot point and is important in the cell.
I read that the main reason genetic engineering has been so limited has been due to the foreign proteins not folding properly, if they folded at all. Insulin being one of the few victories. Dr Giuseppe Sermonti talks about it in "Why Is A Fly Not A Horse?". How can that be checked? (He was an editor for a peer-reviewed journal and a working geneticist for many years so he had access to that information.)Joe
April 4, 2015
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gpuccio:
Who is Joe Gallien?
The person who cannot find the reference for his claim that proteins do not grow like stalagmites and stalactites because that would tend to bury the active site or make docking difficult to impossible. I didn't make it up, I just can't find it.Joe
April 4, 2015
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DNA_jock, This discussion takes me to the fundamental place that most origins discussions end up - confusing experimental science and scientific fantasy. We can experimentally show that a lot of proteins do not "need" chaperones or other proteins to fold, however although it is hard to find a reference as you say the numbers I have read say 20-30% do absolutely require molecular aides for folding. Given that virtually all membrane proteins will require help and they maybe make up ~10% of proteins in mammals we could assume at best case 10% of cytosolic proteins require chaperones, etc. that is not insignificant, however the point firstly to address is "need" chaperones. What constitutes needing? Like I have said and you acknowledge aggregation is a problem and it is a fair point that purity does impact on this due to as you correctly say more hydrophobic interactions and novel interactions. We see this in production of our proteins that purity helps with less precipitation usually but you do need certain salts nd other buffers in the right concentrations. HOWEVER, just because you can fold without a chaperone is not necessarily enough in the context of a cell, in particular a dynamic cell. Folding in vitro without molecular aids is quite inefficient and takes much much longer without chaperones.this is not a moot point and is important in the cell. Now you could argue similar to as you have that pre-chaperone era that organisms were less fussy about the time to fold a protein so could "get by" without. But this is my first point. The only thing you can scientifically say is that not all proteins require chaperones to fold but all cellular life possess chaperones and have as far back as we have information for. When you state that there "was a time when chaperones were not needed" that is a fantasy argument as it is assuming that there must have been because of the assumption abiogenesis and UCD from abiogenesis. There is nothing to support this (abiogenesis) scientifically but rather it is a just so story and is no different to someone saying archaea, prokaryotes and eukaryotes were intelligently designed with chaperones and evolved from these points respectively. You say it is a common fallacy of ID to say that just because things are this way now means they couldn't have been diffently before but it is an equal fallacy to say they must have been different before otherwise they do not fit in with your worldview. I certainly would not argue with the sentiment that things we see now are probably much different to a long time ago, but if you actually take that argument for what it is and extend your own argument, you suddenly support YECs who will say that perhaps radioactive isotopes had different decay rates in the past hence the apparent very old ages. After all, just because something appears a certain way/rate now does not mean it always was! So it is fine for you to have your opinion on what we cannot observe and cannot test (that a cellular organism could exist without chaperones) but it is not based upon experimental science and is assumption and deduction to fit with your world view - no different to how one might conclude there needed to be a designer as all life have proteins needed to correctly produce other proteins necessary for life.Dr JDD
April 4, 2015
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