How does nature evolve instructions to stop and start?

originally posted by: Phantom423
a reply to: cooperton

The ribosome self assembles from various components. This article describes the machinery. As I said in my previous post, ribosomes are very ancient molecules. The ribosome evolved to fit into the DNA world where codons carried the stop/start signals. If a self assembled ribosome started reading the codon, then that was a leap in evolution.

arxiv.org...

Their mentioning of "self-assembly" in this paper is referring to their production via the transcription-translation machinery (polymerase and ribosomes)

"The transcription-translation machinery has a dual role to synthesize the proteome, and to synthesize copies of itself. Two key players in this process, RNA-polymerases and ribosomes, self-replicate by jointly producing their sub-components which subsequently self-assemble to new RNA-polymerases and ribosomes..."

This is a well known synchronization of RNA-polymerase and ribosomes, it allows a max-efficiency reproduction of the proteome (all the necessary proteins of a cell) by lining up multiple ribosomes along multiple RNA-polymerases:



The ribosomes and RNA-polymerase proteins are still created by the conventional transcription-translation method. I will save you time, you are not going to find any paper that finds the spontaneous creation of the polypeptide sequence of either ribosomal subunit. It is impossible. The E. coli ribosome has 7,459 amino acids, which is a sequence of over 22,377 DNA nucleotide monomers.... This stuff cannot form by random chance. It requires a meticulous factory-like process as shown in the picture above. Remember, without ribosomes there can be no protein synthesis, and without protein synthesis there can be no ribosomes. Do you understand this dilemma?

a reply to: cooperton

Remember, without ribosomes there can be no protein synthesis, and without protein synthesis there can be no ribosomes. Do you understand this dilemma?

If ribosomes existed in the RNA world and moved to the DNA world, why would they suddenly disappear? There's no point in time where the ribosome did not exist. There's no dilemna - it's just evolution at work. The ribosome increased its functionality by evolution. It can't be more obvious. But if you disagree, you can always go into the lab and design an experiment to prove your hypothesis. Right now the literature if fairly clear that the ribosome has been in existence since the RNA world. Again, there's no point in time where the ribosome didn't exist.

This is probably one of the best examples of evolution at work that I've seen in a long time.

In any case, when you design and execute an experiment to prove your point, let me know.

originally posted by: Phantom423
There's no point in time where the ribosome did not exist.

Faith-based.

it's just evolution at work.

"not sure how, but we know evolution definitely did it". Let's call it evolutionism of the gaps

The ribosome increased its functionality by evolution.

What is the mechanism for this? How could the 7,000+ amino acid monomers have self-assembled themselves in the right order to make a ribosome? Even if this miracle did occur, and evolution miraculously created a ribosome without transcription or translation, the ribosome still is useless unless there is something to make an mRNA strand.

Do you understand this? You can't just say ribosomes were always existent. You are assuming evolution must be true, a logical fallacy, and then forcing a fantasy RNA world into the equation to fill in the insurmountable gaps.

But if you disagree, you can always go into the lab and design an experiment to prove your hypothesis.

It is not my responsibility to prove a negative. There is no empirical evidence that a 7,000+ amino acid chain can form spontaneously. It is laughably absurd, and defies science entirely. You can only make up theoretical fairy tales, because science is of no help in proving the deranged evolutionary theory.

originally posted by: Phantom423

originally posted by: cooperton

originally posted by: Phantom423

How does a polypeptide chain read a codon? Please provide an example. Thanks

The ribosome (a polypeptide) reads the codons to orchestrate translation of mRNA into a peptide chain. When it reaches a stop codon it stops the amino acid amalgamation. This is basic biology.

The ribosome is an ancient molecule of the RNA world. It was self replicating and didn't require codons (as far as I know).

In view of the DNA-RNA-protein team impasse, some researchers have offered “the RNA world” theory. Instead of asserting that DNA, RNA, and proteins originated simultaneously to produce life, they say that RNA by itself was the first spark of life. Is this theory sound?

In the 1980’s, researchers discovered in their laboratory that RNA molecules could act as their own enzymes by snipping themselves in two and splicing themselves back together. So it was speculated that RNA might have been the first self-replicating molecule. It is theorized that in time, these RNA molecules learned to form cell membranes and that finally, the RNA organism gave rise to DNA. “The apostles of the RNA world,” writes Phil Cohen in New Scientist, “believe that their theory should be taken, if not as gospel, then as the nearest thing to truth.”

Not all scientists, though, accept this scenario. Skeptics, observes Cohen, “argued that it was too great a leap from showing that two RNA molecules partook in a bit of self mutilation in a test tube, to claiming that RNA was capable of running a cell single-handed and triggering the emergence of life on Earth.”

And researchers have never located a piece of RNA that can replicate itself from scratch. There is also the issue of where RNA came from in the first place. Though “the RNA world” theory appears in many textbooks, most of it, says researcher Gary Olsen, “is speculative optimism.”

I tend to use the term “wishful thinking” more often.

A bit of background on Philip Cohen from his profile page on PNAS.org:

He is widely cited in biology and biochemistry, was knighted in 1998, and received the Royal Medal for his work on protein phosphorylation in 2008.

a reply to: cooperton

I'm not assuming anything. It's obvious that if ribosomes existed in the RNA world that they evolved to fit into the DNA world. If there's a gap in the timeline, point to a research paper or something that says that a gap exists. Right now, the research shows that ribosomes evolved from the RNA world into the DNA world. Unless some other evidence shows up, then that's the current hypothesis. I don't see a problem here. If you can demonstrate that this isn't the case, then do it. It doesn't matter to me one way or the other. The science is pragmatic - whatever the evidence shows, that's the current knowledge. When a new discovery is made and confirmed, then that's the current knowledge. This is not rocket science. It's just logic.

It's a great example of how evolution works.

a reply to: whereislogic

That type of mish-mash is exactly why you never learn anything. Why not take a break and do a literature search on the topics. You would be amazed how wrong you are on so many points.

a reply to: whereislogic

That's a nice review. But I can't comment on it as I haven't read the papers you refer to. But I do think it's a mistake to construct a world view based on your own bias. The other side has something to say as well.

The DNA scenario of not assembling "from scratch" isn't correct. Nor is it correct that it's not self replicating. That's all over the literature. Take the time to research.

a reply to: Phantom423
I don't tend to fall for twisted marketing storylines with misleading misapplications of terms such as “self-assembly” (or “self-organization” or “self replicating”). Or storylines such as the one from Dawkins and how he uses the term “from scratch” in his story about the evolution of the eye (9:20 - 12:50):

originally posted by: Phantom423
a reply to: whereislogic
You would be amazed how wrong you are on so many points.

You thought you were sending me an article on ribosomes self-assembling from scratch but it actually proved my point that it requires transcription and translation. Just step down from the pedestal. You're incapable of giving a reasonable retort to the problem I address.

It's obvious that if ribosomes existed in the RNA world that they evolved to fit into the DNA world.

You're basis for this assertion is that evolution must absolutely be fact. So therefore, you suppose that this idea must also be absolutely fact. Your religion is a house of cards based on no real empirical evidence. Show evidence that ribosomes can form without protein translation and I will concede, otherwise you should realize that your theory is not based in observable science.

a reply to: cooperton

Get a grip. I know exactly what the article is about. When you find a gap in time where ribosomes did not exist, let me know. The only problem here is that you can't put the pieces of the puzzle together. Go to Google Scholar and do a genuine literature search on the subject. When you find that gap, I'll send you a bottle of Veuve Clicquot.

a reply to: neoholographic

Here is a paper on the evolutionary biology of intron exon structures in Eukaryotic genes

it helps when looking to have a good search term, I searched the evolutionary biology of intron and exons in organisms

Evolution of the Intron Exon structure in Eukaryotic Genes

However as a starting point it would be better to enquire as to how genes came into being in the first place

Origin and evolution of the genetic code : the universal enigma

At present we simply don't understand enough to answer this question , and we may well never know the answer in our lifetime !

but whoever discovers the reason will be a nobel prize winner for sure!

Here are a couple more

Origin and Evolution of DNA and DNA replicating Machinaries

and this

The emergence of DNA in an RNA world

I would think that if DNA was "made" then the approach would be similar to how humans would create a self replicating nanomachine
first it would need a language in which to operate (ATGC) , then it would need a CPU and an operating system
what are the biological equivalents of this ? CPU would be the cell nucleus , operating system is the DNA , RNA ?

A suggestion posted earlier made a lot of sense to me but it was completely ignored in the scuffle. Why exactly are members coming here to a conspiracy forum for their college level biology lessons? That's not what this website is about? Are there certified teachers lurking around just waiting for the chance to kill some free time by educating randoms on the internet? Is the local community college closed for the week? I'm confused about your choice in resources here.

originally posted by: cooperton

originally posted by: Phantom423
There's no point in time where the ribosome did not exist.

Faith-based.

it's just evolution at work.

"not sure how, but we know evolution definitely did it". Let's call it evolutionism of the gaps

The ribosome increased its functionality by evolution.

What is the mechanism for this? How could the 7,000+ amino acid monomers have self-assembled themselves in the right order to make a ribosome? Even if this miracle did occur, and evolution miraculously created a ribosome without transcription or translation, the ribosome still is useless unless there is something to make an mRNA strand.

Do you understand this? You can't just say ribosomes were always existent. You are assuming evolution must be true, a logical fallacy, and then forcing a fantasy RNA world into the equation to fill in the insurmountable gaps.

But if you disagree, you can always go into the lab and design an experiment to prove your hypothesis.

It is not my responsibility to prove a negative. There is no empirical evidence that a 7,000+ amino acid chain can form spontaneously. It is laughably absurd, and defies science entirely. You can only make up theoretical fairy tales, because science is of no help in proving the deranged evolutionary theory.

What phantom posted makes a lot more sense than saying some mysterious supernatural force with unmeasurable properties is probably responsible for these events because reasons. Phantom is at least trying, and their scholarly skill is apparent.

if DNA has been manufactured , then look for the signature or makers mark!

if they have an ego like humans do then they would seek to let others know that they created it !

are there any tell tale markers in the human genome ?

Just a thought

a reply to: sapien82

I understand your point, but that paper was written 10 years ago - 2009. Much has happened since then. If you use Google Scholar, I suggest you click on a more recent time frame - since 2015 for instance - which is on the upper left of the page.
It's good to have an historical perspective, but if you're looking for the most recent discoveries, it makes more sense to read the most recent research.

Summary of this thread: I don't know how it can happen, therefor it's false!

originally posted by: Barcs
Summary of this thread: I don't know how it can happen, therefor it's false!

Summary of your posts: "I don't know how evolution can happen, but it still must be true."

originally posted by: cooperton

originally posted by: Barcs
Summary of this thread: I don't know how it can happen, therefor it's false!

Summary of your posts: "I don't know how evolution can happen, but it still must be true."

See my previous post. If you can do better then maybe you should share.