RNA measurements may yield less insight than assumed

_{Denyse O'Leary

December 19, 2014

News, Origin Of Life}

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The majority of RNA expression differences between individuals have no connection to the abundance of a corresponding protein, report scientists from the University of Chicago and Stanford University in Science on Dec. 18. The findings point to a yet-unidentified cellular mechanism that regulates gene expression and suggest studies that rely only on RNA measurements to characterize gene function require further analysis.

“The chief assumption for studies of RNA differences is that they ultimately reflect differences in an end product, which is protein,” said senior study author Yoav Gilad, PhD, professor of human genetics at the University of Chicago. “But it turns out in most cases this may not be true.”

Interesting, when we consider the high hopes placed in RNA world.

See also: Welcome to “RNA world,” the five-star hotel of origin-of-life theories

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Comments

WD400: DNA is the closest thing to a “master molecule”, since it encodes the proteins that regulate the expression of DNA, (...)
The Selfish Gene (1976).
WD400: but biological systems are just that: systems arising from the action of many different classes of molecules and the environment.
What is the "system" under materialism? Emergent property?
WD400: There is no reason to think a single type of “decision molecule” is required, so far as I can see.
Maybe you can answer my question from post #45: "Suppose a unicellular organism. When certain proteins slide a spool along the DNA, exposing base pairs for gene expression, what is responsible for the decision to do so? The cell?"Box_{December 22, 2014
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Post-translational modification and regulation of actin. doi: 10.1016/j.ceb.2012.10.009. Many of the best-studied actin regulatory proteins use non-covalent means to modulate the properties of actin. Yet, actin is also susceptible to covalent modifications of its amino acids. Recent work is increasingly revealing that actin processing and its covalent modifications regulate important cellular events. In addition, numerous pathogens express enzymes that specifically use actin as a substrate to regulate their hosts' cells. Actin post-translational alterations have been linked to different normal and disease processes and the effects associated with metabolic and environmental stressors. Herein, we highlight specific co-translational and post-translational modifications of actin and discuss the current understanding of the role that these modifications play in regulating actin. http://www.ncbi.nlm.nih.gov/pubmed/23195437Dionisio_{December 22, 2014
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#55 wd400 I was expecting hrun0815 to respond, but it's nice to get a little help from a friend. Anyway, thank you for expressing your opinion on the given subject. :)Dionisio_{December 22, 2014
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#48 hrun0815
Since I don’t have numbered posts on my phone...
Interesting. What kind of phone is that? My Nokia Lumia 635 does show the post #s within the thread. Any idea why they don't show up on your phone? Also I use a MSFT Surface tablet, which shows the post #s fine. I'll check my wife's iPhone later to see if the post #s appear. Also will check that on her iPad. We didn't buy these gadgets. Someone gave them to us as presents on separate occasions. I don't use the Nokia Lumia as phone, but as WiFi device. My phone is a $15 ZTE Z222 flip device that works just fine and fits in my pocket very easily. :) It's kind of funny, my wife ended up with Apple gadgets and I got mine from Mr. Softy (except the flip phone). But we get along very well. :)Dionisio_{December 22, 2014
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box,
This matter goes to the heart of materialism. If one’s ambition is to reduce an organism to matter, then one has to look for material regulators with decision power – IOW decision-molecules.
Why do you think this is true? DNA is the cloest thing to a "master molecule", since it encodes the proteins that regulate the expression of DNA, but biological systems are just that: systems arising from the action of many different classes of molecules and the environment. There is no reason to think a single type of "decision molecule" is required, so far as I can see.wd400_{December 22, 2014
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Ok, what is wrong with the first statement?
Well, the fact this result relates in no way to any RNA world hypthesis is certainly a problem, don't you think. I also think it's somewhat amazing that someone could cover the "News" desk at this site for so long without picking up even the most elementary understanding of biology.
What is it that you don’t like about the second statement?
There are many known modes of post-transcriptional and post-translation regulation already known. We could, of course, stand to learn more about these important processes by it's not like we are starting from nothing.wd400_{December 22, 2014
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#40 hrun0815
the two statements are: “Interesting, when we consider the high hopes placed in RNA world.” and “The findings point to a yet-unidentified cellular mechanism that regulates gene expression…”
Ok, what is wrong with the first statement? What is it that you don't like about the second statement?Dionisio_{December 22, 2014
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"Take it easy, buddy. One step at a time. No rush. Ok?" Really? "Did you answer my 4 questions written in post #36? I don’t recall seeing your answers." In other words, before you answer a simple point that post 1 and post 3 in this thread made I will have to jump through hoops and answer your four questions? Because without an answer to your questions you don't know what I'm asking you to agree on? That seems all a bit disingenuous to me. But so be it: Since I don't have numbered posts on my phone, could you repeat the question(s) you have? I would pick just one, because generally once you start discussing a single question there is hardly any room for anything else. And maybe you can keep in mind to at some point come back to my question/points that clearly preceded yours. :)hrun0815_{December 22, 2014
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#40 hrun0815 Sorry, I didn't notice you wrote to me in a post you initially addressed to Box. Kind of confusing. Please, can you address me on separate posts? I'll appreciate it.Dionisio_{December 22, 2014
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hrun0815 @41 I’m certainly happy to try and answer questions you might have.
Why didn’t you answer the easy questions written for you in my post #36? I've repeated the question about the questions you didn't answer in post #36, in order to increase the probabilities that you see it. :) Let's see, maybe this time you won't skip it. :)Dionisio_{December 22, 2014
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hrun0815 @41 I’m certainly happy to try and answer questions you might have.
Why didn’t you answer the easy questions written for you in my post #36?Dionisio_{December 22, 2014
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41 hrun0815 I’m certainly happy to try and answer questions you might have.
Why didn’t you answer the easy questions written for you in my post #36?Dionisio_{December 22, 2014
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@41 hrun0815 I’m certainly happy to try and answer questions you might have.
Why didn’t you answer the easy questions written for you in my post #36?Dionisio_{December 22, 2014
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#41 hrun0815 I’m certainly happy to try and answer questions you might have.
Why didn’t you answer the easy questions written for you in my post #36?Dionisio_{December 22, 2014
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#41 hrun0815 I’m certainly happy to try and answer questions you might have.
Why didn't you answer the easy questions written for you in my post #36?Dionisio_{December 22, 2014
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hrun0815: As for what materialists believe it look for- I’m not sure there is a single answer. But for the current scientific endeavor it is pretty clear that scientists are looking how large ensembles of molecules, each acting according to rules of physical chemistry, (…)
If you mean “only according to rules of physical chemistry” then yours is a statement of faith. One could argue that at the moment of death molecules start acting (only) according to rules of physical chemistry and notably according to the second law, which informs us that things tend to descend into chaos.
hrun0815: (...) end up ‘making decisions’ on a larger level (e.g. as organelles, cells, organs, or organisms).
Suppose a unicellular organism. When certain proteins slide a spool along the DNA, exposing base pairs for gene expression, what is responsible for the decision to do so? The cell?
hrun0815: That, taken to the point, is the very essence of Systems Biology that many ID supporters appear to be pretty find of.
Indeed, but the vast majority of ID supporters is aware of the fact that information cannot make decisions.Box_{December 22, 2014
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#43 hrun0815 Take it easy, buddy. One step at a time. No rush. Ok? Before I agree on anything, I want to understand exactly what it is I'm agreeing on. Did you answer my 4 questions written in post #36? I don't recall seeing your answers. :)Dionisio_{December 22, 2014
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Dionisio, just to reply to this real quick: "That’s why they point to obscure issues related to the OP." If you find the point that phys.org is a terrible source for science information or the point that News takes something terrible and makes it even worse an obscure issue then so be it. I don't know how to actually have a serious discussion if you are talking with somebody who can't even agree on this relatively simple matter. Do you agree? Do you, Box? And why would you not be willing or able to clarify this point with a even a single word before moving on?hrun0815_{December 22, 2014
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Box, of course no materialist would not look for 'a decision molecule'. If there was such a molecule how would you propose or could make a decision. Now a non-materialist could simply posit that the molecule has a soul or that some non-material entity acts by manipulation this magical molecule, but I guess that is not a commonly held view. As for what materialists believe it look for- I'm not sure there is a single answer. But for the current scientific endeavor it is pretty clear that scientists are looking how large ensembles of molecules, each acting according to rules of physical chemistry, end up 'making decisions' on a larger level (e.g. as organelles, cells, organs, or organisms). That, taken to the point, is the very essence of Systems Biology that many ID supporters appear to be pretty find of.hrun0815_{December 22, 2014
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Dionisio, I'm certainly happy to try and answer questions you might have. I'd suggest to start small: pick one or two questions, ideally not something that requires chapters or whole books to answer, and if you want something concrete try to stick with factual questions rather than those that require philosophical musings.hrun0815_{December 22, 2014
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Box, if you consider the point of my post that you initially commented on 'some unrelated matter', then indeed it is probably pointless to continue. Dionisio, the two statements are: "Interesting, when we consider the high hopes placed in RNA world." and "The findings point to a yet-unidentified cellular mechanism that regulates gene expression..."hrun0815_{December 22, 2014
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#38 Dionisio, For some reason, I also tend to believe that hrun0815 is a materialist. If that is indeed the case, then he said something very untypical:
hrun0815: Of course we do not expect to find a ‘decision mole Ike’ [decision-molecule] and the very notion is indeed absurd. I’ve never heard of any scientist looking for it either. Have you? [my emphasis]
This matter goes to the heart of materialism. If one's ambition is to reduce an organism to matter, then one has to look for material regulators with decision power - IOW decision-molecules. Now hrun0815 tells me that "of course" there is no such thing and that scientists never looked for such a thing. Moreover he states that the very notion is "absurd". I can easily agree with his statement that the notion of a decision-molecule is absurd, but only because I'm no materialist. The question is: how can a materialist hold that the notion of a decision-molecule is absurd? If molecules are not making the decisions, then what is behind the steering wheel?Box_{December 22, 2014
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#37 Box
I’m interested to read your view on the matter. However if you insist on agreement on some unrelated matter, then discussion ends here.
Perhaps your discussion with your interlocutor ended before it could start. Any attempt to have a meaningful discussion between two irreconcilable worldview positions fails before it starts, unless both parties are really interested in having a serious discussion, where the ultimate goal is to find the truth about the discussed subject. Obviously that's not what is happening in this case. Your interlocutor along with his comrades and fellow travelers don't seem interested in any serious discussion. Their motivations are not clear, but they don't seem to be serious. That's why they point to obscure issues related to the OP.Dionisio_{December 22, 2014
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hrun0815, I don't wish to opine on phys.org or the alleged methods by news.
hrun0815: If we agree on that then we could go on and discuss what scientists are looking for.
I'm interested to read your view on the matter. However if you insist on agreement on some unrelated matter, then discussion ends here.Box_{December 22, 2014
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#35 hrun0815 Please, can you point to the exact statement(s) that you don't like in the OP? Can you quote it (them)? Thanks. Did you read the reports that were referenced in previous posts in this thread? They seem to confirm what the OP indicated. Do you see it differently? I have very specific questions to ask the scientists who worked on the referenced reports. Do you want to try answering my questions? Are you qualified to answer them? I'll give you a hint. See the text in bold characters in my previous posts. Some of my questions might be related to the bold text. Wanna try? :)Dionisio_{December 22, 2014
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Box, before we go on could we get back to the original point of my post? Do you agree that if you rely on poor science aggregators like Phys.org or worse still on the mangled science comments of News, then you will be badly misinformed (like both WD400 and my original post point out)? Do you agree that if you actually want to take anything away from this you'll have to go to the original article and actually read it? If we agree on that then we could go on and discuss what scientists are looking for. (I presume you meant 'they' or 'the scientists' rather than 'we' in your last post.)hrun0815_{December 22, 2014
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#33 Box
what are we looking for?
Interesting question. It seems like science researchers are trying to figure out how things work in biology, so we can have better medical treatments and more effective health maintenance plans. However, it also seems like the ultimate answers keep eluding the researchers. As they answer some of the outstanding questions, new ones pop up. Kind of like a never ending story. Like the Energizer bunny, it just keeps going, and going... :) But in the meantime the research reports shed light on the elaborate systems they try to describe. And guess what? They look more interesting than before the reports were published. New unknowns appear. Perhaps that's one of the reasons why we read so many times words like 'unexpected', 'surprising', etc. in some of those reports. Then we ask what did they expect? No idea. Now, that's really cool. Isn't it? :) Perhaps that's why some folks didn't like the OP in this thread. It made them feel itchy. But that's their problem, not yours. :) We look forward, with much anticipation, to reading newer reports coming out of research. We ain't seen nothing yet. This party is just starting. The fun part is still ahead. Enjoy it! :)Dionisio_{December 22, 2014
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hrun0815: Of course we do not expect to find a ‘decision mole Ike’ and the very notion is indeed absurd. I’ve never heard of any scientist looking for it either. Have you?
There was a time that the DNA-molecule was a likely candidate. Scientists aren't exactly trying to show that 'everything is interconnected', right? They want to find 'the regulator', don't they? If there are no molecules with decision-power, and if the very notion is indeed absurd, then, pray tell, what are we looking for?Box_{December 22, 2014
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Ahh, Box, the silly 'you can't explain ultimate causes so how dare you point out that some statement is stupid'? I ask again: What result of the paper suggests there is a as-of-yet unidentified mechanism of regulation of gene expression? And by the way: Of course we do not expect to find a 'decision mole Ike' and the very notion is indeed absurd. I've never heard of any scientist looking for it either. Have you?hrun0815_{December 22, 2014
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Got enough yet? :)Dionisio_{December 21, 2014
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