What Makes Us Human? The Answer May Be Found in Overlooked “Junk” DNA

a reply to: cooperton

All responses = WRONG.

originally posted by: Phantom423
a reply to: cooperton

All responses = WRONG.

See how you can't specify why? It's because you're just hopelessly hoping I am wrong. But I am not. protein and dna monomers do not polymerize into chains spontaneously in water. DNA and protein polymers actually decompose spontaneously in water, this is a natural part of the decay process.

Hydrolysis is bio 101. Just admit you are wrong.

a reply to: cooperton

It's been done dozens of times - you just don't read the papers.

originally posted by: Phantom423
a reply to: cooperton

It's been done dozens of times - you just don't read the papers.

Well the last paper you sent doesn't have public access, but you can tell because they use the word "catalyst" in their abstract that they didn't actually self-polymerize. I was able to access some of the figures and they say they use "proteinaceous enzymes"... which is textbook not self-polymerization. Phantom, you need to understand this very basic thermodynamic law, protein and dna polymers decompose spontaneously in water. They do not spontaneously polymerize in water.

This makes random chance creation of dna and protein polymers extremely unfavorable in water. This is why abiogenesis is not possible without intelligence.

a reply to: cooperton

Read it again.

originally posted by: Phantom423
a reply to: cooperton

Read it again.

DNA and protein polymers decompose spontaneously in water. DNA and protein polymers do not spontaneously form in water.

It's basic biochemistry. This is why DNA/protein polymerization reactions in organisms requires catalysts.

a reply to: cooperton

Read the first line of the article.

originally posted by: Phantom423
a reply to: cooperton

Read the first line of the article.

"In vitro selection experiments show first and foremost that it is possible that functional nucleic acids can arise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove to be robust binding species and catalysts, indicating that it may have been possible to transition from even the earliest self-replicators to a nascent, RNA-catalyzed metabolism."

They're saying that oligomers (short nucleic acid chains) can sometimes serve as catalysts for polymerization. This is why they refer to them as sequences or structures, it's because they are not referring to monomers. This is not monomer polymerization. If there was access to the paper I could give you more detail. The thing is, even oligomers would not be formed in water because nucleic acids and protein monomers do not self-polymerize in water

a reply to: cooperton

Read it again.

a reply to: cooperton

One more link - and it's the last one I'm going to give you. Do your own homework for a change.



Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate
David M. Fialho, Suneesh C. Karunakaran, Katherine W. Greeson, Isaac Martínez, Gary B. Schuster, Ramanarayanan Krishnamurthy, and Nicholas V. Hud*
pubs.acs.org...

Abstract

The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive,self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.

a reply to: Phantom423

Awesome "library".

Thanks

a reply to: Annee

Thank you.

a reply to: Phantom423

You post the same nonsense and thread after thread. Time is then wasted destroying your arguments and then you vanish only to resurface again with the same nonsensical arguments that have nothing to do with the thread.

This is a side debate and cooperton has destroyed your points over and over again. At the end of the day, nothing you said refutes anything in this thread or anything I'm saying.

This is why you blindly post abstracts without any context. This is because the abstracts you post don't support what you're saying or refute anything. They're full of what ifs and blind leaps of logic. Let's look at the abstract you blindly posted.

In vitro selection experiments show first and foremost that it is possible that functional nucleic acids can arise from random sequence libraries. Indeed, even simple sequence and structural motifs can prove to be robust binding species and catalysts, indicating that it may have been possible to transition from even the earliest self-replicators to a nascent, RNA-catalyzed metabolism.

IT MAY HAVE BEEN POSSIBLE.

There's not a shred of evidence that this transition occured or this transition created the code that stores information in the sequence of a storage medium. That it also encoded the sequence with information to build machinery to decode the information or correlated information that's in the sequences(digital) with the chromosone superhelicity(analog).

Let me repeat this because this is what the thread is about. This is why your arguments always fall flat. You can't respond in any coherent way to the subject of the thread based on the abstracts you blindly post. Let me repeat:

There's not a shred of evidence that this transition occured or this transition created the code that stores information in the sequence of a storage medium. That that it also encoded the sequence with information to build machinery to decode the information or correlated information that's in the sequences(digital) with the chromosone superhelicity(analog).

Here's a paper detailing the limits to in vitro selection:

Significance
Many chemicals are valuable because they bind to other molecules. Chemical theory cannot directly design “binders.” However, we might recreate in the laboratory the Darwinian processes that nature uses to create binders. This in vitro evolution uses nucleic acids as binders, libraries of DNA/RNA to survive a selection challenge before they can have “children” (systematic evolution of ligands by exponential enrichment, SELEX). Unfortunately, with only four nucleotides, natural DNA/RNA often yields only poor binders, perhaps because they are built from only four building blocks. Synthetic biology has increased the number of DNA/RNA building blocks, with tools to sequence, PCR amplify, and clone artificially expanded genetic information systems (AEGISs). We report here the first example of a SELEX using AEGIS, producing a molecule that binds to cancer cells.

www.pnas.org...

Here's more from your abstract:

Simple binding species and catalysts could have evolved into other structures and functions. As replicating sequences grew longer, new, more complex functions or faster catalytic activities could have been accessed. Some activities may have been isolated in sequence space, but others could have been approached along large, interconnected neutral networks. As the number, type, and length of ribozymes increased, RNA genomes would have evolved and eventually there would have been no area in a fitness landscape that would have been inaccessible.

www.sciencedirect.com...

The whole paper is a fantasy of what if's that don't have anything to do with this thread. This is why you just blindly posted an abstract without any context as how it pertains to this thread or the questions I posed.

To go from simple binding species and catalysts into other structures and functions is a fantasy. It explains nothing about how information was encoded in a sequence of a storage medium or how non coding regions evolved separately to regulate the expression of coding regions and how this information was correlated through a natural interpretation of evolution.

As the other paper noted:

Chemical theory cannot directly design “binders.” However, we might recreate in the laboratory the Darwinian processes that nature uses to create binders...Unfortunately, with only four nucleotides, natural DNA/RNA often yields only poor binders, perhaps because they are built from only four building blocks. Synthetic biology has increased the number of DNA/RNA building blocks

This is why Phantom blindly posts abstracts without any context. This is because the papers don't refute anthing that's being said and the papers admit to mostly wishful thinking. They have to DESIGN these experiments in the lab because naturally they yield poor results and simple sequences that are meaningless. They need to use their intelligence to DESIGN synthetic DNA to make more complex structures. Let me repeat this because it clearly shows why your argument falls flat over and over again.

Chemical theory cannot directly design “binders.” However, we might recreate in the laboratory the Darwinian processes that nature uses to create binders...Unfortunately, with only four nucleotides, natural DNA/RNA often yields only poor binders, perhaps because they are built from only four building blocks. Synthetic biology has increased the number of DNA/RNA building blocks

Here's some questions:

How did self assembly encode the sequence of a unique storage medium like DNA with information, encode the instructions to build the machinery to decode this information and encode non coding sequences with information that regulates the expression of coding regions?

Also, DON'T BLINDLY POST AN ABSTRACT. If you post an Abstract explain in your own words how the abstract relates to the thread. You have a habit of running to Google and then blindly posting an Abstract that has nothing to do with the thread.

It get's worse for you. Tell me how parts evolved separately through a random, natural process that are the right size, shape and come together to carry out different tasks. Here's a video showing how all the parts of ATP Synthase works together.



If you believe in a natural interpretation of evolution, you have to explain how all of the right parts that are the right size and shape and come together at the right angles did so naturally and randomly.

Also, this doesn't explain how a code evolved and why nature needed a code. Why does nature need to transcribe and translate information to specify the arrangments of amino acids on a polypeptide chain? That's intelligent design. Naturally, these amino acids should form these complex sequences without the need of a code, transcription, translation, error correcting and more.

As always, your arguments and the blindy posting of abstracts leads nowhere.

a reply to: neoholographic

Then why are you responding? You might consider doing your homework, too!

originally posted by: Phantom423


Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate

Yeah like Neo said, this is getting old. Amino acid monomers are different than depsipeptides. The problem the scientific community is ignoring is the fact that amino acid monomers do not self-polymerize in an aqueous solution. Without this self-assembly of amino acids, you will get no Oligomers, polymers, or pepsipeptides to begin with.


I don't know how to explain it any simpler. You're either gaslighting, being obtuse, or you have been faking your biological credentials for some time now.

a reply to: cooperton

Nah those are exaggerated numbers. Chimpanzees have 100 million more DNA nucleotides in their genome than humans, so how could they have only 35 million total differences? They selectively choose wording that makes there appear to be more similarities in order to fit their theory.

No they dont you are misuderstanding something again. The DNA sequence that can be directly compared between the two genomes is almost 99 percent identical. When DNA insertions and deletions are taken into account, humans and chimps still share 96 percent of their sequence. At the protein level, 29 percent of genes code for the same amino sequences in chimps and humans. In fact, the typical human protein has accumulated just one unique change since chimps and humans diverged from a common ancestor about 6 million years ago.

originally posted by: Phantom423
a reply to: cooperton

All responses = WRONG.

i agree he seems very confused about genetics.