Researchers: Genetic code emerging in an RNA world faces “insuperable problems”

Quoting myself @ 17 "I am a farmer and not a chemist … concerning origin of sugars I was parroting Dr James Tour who is very knowledgeable but not infallible . I do stand corrected but it hardly makes a difference to the insurmountability of the problem." I erroneously misinterpreted Dr James Tour. He makes synthetic sugars in the lab and he describes how difficult it is to do. Requires many purification steps etc otherwise impurities react with the sugars as they are being produced. He states that in nature it would be impossible to produce the pure sugars found in DNA and RNA. Therefore he poses the question .... what is the origin of the sugars in a prebiotic world? Johnnyfarmer

OLV @15 Thanks Johnnyfarmer

PeterA Ok thanks I went back to 11 which I must have read over and not taken so seriously..... but now I got it !!!! "All the Kings Horses and all the Kings men are conspicuously absent" No free lunch but there is free sugar for the coffee as long as there is some agent there to pour and stir it in. Johnnyfarmer

Johnnyfarmer, Once you got the sugar and other ingredients ready to use, then read comment posted @11. There’s no free lunch. :) PeterA

Yo Brian @ 16 OK you scored one. Sugars and sugar related molecules have been created in laboratory under conditions which might mimic those which produced sugars and related molecules naturally aside from biology (photosynthesis). Your link also refers to amino acids discovered in asteroids. So mixture of sugars and amino acids possibly existed in pre-biotic world. As with amino acids, sugars also exist as optical isomers and so you have the yet unsolved problem of isolating them naturally aside of a laboratory. You have the linking of amino acids by peptide bond without a ribosome to also solve. If you would be able to link amino acids together via peptide bond to create a protein then how do you replicate that protein ? I am a farmer and not a chemist ... concerning origin of sugars I was parroting Dr James Tour who is very knowledgeable but not infallible . I do stand corrected but it hardly makes a difference to the insurmountability of the problem. Johnnyfarmer

Johnny

Thanks for the link…. went there and had communion …. grape Kool Aid

You asked where the ribose in RNA could have come from if there was no previous life, and a ten second google search provided the link I provided earlier. The link below is to the actual research paper. If you have criticisms of the actual research, I am open to it. After all, I know very little about it. But if your response is no better than that at 14, I think this conversation has run its course. http://science.sciencemag.org/content/352/6282/208 Brother Brian

Over 3 years ago in this website a professor argued that scientists already know how morphogen gradients form. However, recent papers seem to indicate the opposite. How can that be? Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis DOI 10.15252/msb.20188355 Molecular Systems Biology (2018) 14, e8355 Lucia Durrieu, Daniel Kirrmaier, Tatjana Schneidt, Ilia Kats, Sarada Raghavan, Lars Hufnagel, Timothy E Saunders, Michael Knop

Embryogenesis relies on instructions provided by spatially organized signaling molecules known as morphogens. Understanding the principles behind morphogen distribution and how cells interpret locally this information remains a major challenge in developmental biology.

Acquisition of different cell fates at specific spatial and temporal locations is an essential process driving development. The necessary information is provided locally by morphogens (Wolpert, 1969; Lander, 2011). Understanding morphogen gradient formation requires systematic measurement of the morphogen abundance, mobility, and distribution using temporally resolved methods. However, the technical challenges associated with this undertaking are high, leading to significant discussions on how to best assess the principles and mechanisms (Ribes & Briscoe, 2009; Rogers & Schier, 2011; Muller et al, 2013) that have resulted in a plethora of models for the formation of morphogen gradients.

The classic view of Bcd gradient formation is that the protein is synthesized in the anterior pole of the Drosophila blastoderm and forms a long range gradient through diffusion, with the gradient shape adapted by protein degradation However, several other models involving alternative mechanisms for Bcd production and distribution have been proposed, all of which are capable of producing an exponential?like concentration profile, as further outlined below

Efforts to distinguish experimentally the different mechanisms of gradient formation have been hindered by uncertainties associated with the measurements of the relevant parameters: local production rates of Bcd; Bcd mobility and transport; and Bcd degradation.

Finally, the extent of the region where Bcd protein is produced is unclear

Altogether, these debates regarding nearly every aspect of Bcd gradient formation argue for the need of more incisive tools to investigate this paradigmatic problem.

How does the Bcd gradient form? an mRNA gradient plays only a limited role in Bcd protein gradient formation. Changes in protein levels can be caused by regulation of their synthesis or their degradation. Bcd production is reduced during cycle 14, probably due to degradation of its mRNA or cellularization. The underlying mechanisms driving the time dependence in the kinetic parameters could be due to a number of (potentially inter?related) factors. the embryo must be interpreting a dynamic gradient at all times. more complicated modes of interpretation—likely via spatial and temporal integration through the downstream gap gene network—are essential for reliable interpretation of the Bcd concentration gradient into precise positional information understanding of developmental patterning requires access to both spatial and temporal information

  OLV

Bro Brian Thanks for the link.... went there and had communion .... grape Kool Aid Johnnyfarmer

Well OOL studies have come a long way since the old days... back then cells were pulverized and the contents then analyzed in an effort to comprehend cellular life. Imagine someone given a computer and in effort to comprehend how it functions he grinds it up and analyzes the powder in a lab !!! In the early days efforts to re-create life consisted of mixing the elements found in the earth and shake and bake them hoping to mimic the conditions which accidentally produced life. If you were given a computer and you wanted to learn how it functions the obvious approach is to reverse engineer. And that is the approach which has been used more recently (maybe last 40 years) to comprehend the cell . Would anyone knowing how a computer functions attempt to re-create a computer by mixing raw elements in powder form and then shake and bake ? So today we are on our way to fairly well comprehending how cells function and we have arrived here via reverse engineering. We no longer attempt to grossly produce life by crude shake and bake methods. We have sophisticated labs and techniques and yet have not come even close to re-creating life. IMO the creator did not give us the ability to create life ....for if we could we would be like God and He would be very jealous !!! And if we do not have the ability to create life, then science fails in it's fundamental premise and endeavor ..... that is to prove the physical world can be comprehended in terms of chance and necessity. Johnnyfarmer

Es58 @1: Interesting point. PeterA

Brother Brian @8: Ok, you got the sugar, then what do you do with it? Pour it in the tea or coffee? Wake up and smell the flowers? Did you ever meet Mother Goose? Did you hear about Humpty Dumpty? Do you know what happened to it? Well, OOL is like Humpty Dumpty after the fall, but much worse, because all the king’s horses and all the king’s men are conspicuously absent. Really bizarre. :) Wake up and smell the flowers! PeterA

Johnnyfarmer @6, Good contribution. Thanks PeterA

Even given all of the components and energy they still need to get a replicating RNA or a sustained replication, somehow. That would be the first step. Next comes Spiegelman's Monster and the fact that nature prefers the simplest solutions. ET

Johnny

Some of the issues …. where did the penta sugar backbone come from? The sugar carbohydrates to assemble the backbone …where did these sugars originate ? Were they the product of photosynthesis? (obviously not !)

Apparently biology isn't the only way that sugars can be formed. https://www.sciencenewsforstudents.org/article/key-sugar-life-earth-could-have-formed-space Brother Brian

Start with the phrase: "A quick brown fox jumped over the lazy dog". Copy it over and over again. Each time introduce random changes, including duplications of all type (letters, letter sequences, words, entire sentence(s)) recombination, insertions, deletions- whatever you can program. If the evolutionists are right, given enough time/ generations and especially with the proper fitness function, you may have reproduced much of everything that has ever been written. (HT- David Berlinski who had the starting point as the "Don Quixote") ET

Well I never post here but always lurking. Some of the issues .... where did the penta sugar backbone come from? The sugar carbohydrates to assemble the backbone ...where did these sugars originate ? Were they the product of photosynthesis? (obviously not !) And RNA being even less stable than DNA ...were there repair mechanisms and if not then what would be the consequences. And finally how would RNA be replicated? Magic I guess !! Otherwise just another common self replicating molecule ??? The most ever read thread here at UD by James Tour: https://uncommondescent.com/origin-of-life/chemist-james-tour-writes-an-open-letter-to-his-c Johnnyfarmer

This is true- there isn't any way to go from a RNA World to coded biology. There is a huge disconnect between the two. But that may be moot because nature doesn't even seem to be capable of producing replicating RNAs ET

Vmahuna, That logical conclusion is unacceptable to the academic establishment. Sorry. Try something else that excludes conscious design, even if it doesn’t make sense. PeterA

OK, so as I understand what the summary is trying to say is that they have no explanation for HOW RNA came into existence, but once you HAVE RNA, RNA works just fine. I think this confirms that RNA was well designed. vmahuna

“the situation is so awkward that we cannot even present a clear definition of life in any textbooks of biology,” What Does “the RNA World” Mean to “the Origin of Life”? Wentao Ma Life (Basel). 2017 Dec; 7(4): 49. doi: 10.3390/life7040049 This paper is so scientifically poor that it could have been written by a robot. It’s very discouraging to see a paper with so much nonsense published in a supposedly serious journal. Has it been cited? PeterA

No problem: Dawkins next book title will be climbing Mount insuperable:-) es58