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

originally posted by: cooperton

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.

I suggest you read this then we can discuss

a reply to: dragonridr

There are more than a few threads on this board discussing the same topic. I've uploaded a variety of papers explaining the biochemistry of amino acid/peptide polymerization. It's a useless conversation when people are hell-bent on doing science ass-ways backwards.

I've posted this illustration previously. I'll post it again. It's a self-evident explanation as to how the science works.




www.ncbi.nlm.nih.gov...

originally posted by: Phantom423

www.ncbi.nlm.nih.gov...

This paper still doesn't show an example of peptide bonds forming spontaneously in water. The bonds formed when it was dissolved in an acid. 120mM of malic acid (which they used in the experiment) gives you a pH of 2... that's equivalent to battery acid haha.

They let the samples be exposed to water for 30 minutes, and then dehydrated them again. They do it for such a short time because they know that amino acid bonds break down spontaneously in water, so they could not have them in there for long. It's so quick that some of their pepsipeptides were "fragmented" when they were testing their structures (the test involves temporary dissolution in water). They were essentially doing lab-grade chemical synthesis reactions, and then splashing it briefly with water to say "look, prebiotic conditions!".

Also, amino acid polymers in human beings are comprised of specific C1-N2 bonds, which is ensured by peptidyl transferase in the ribosome which facilitates proper bonding at that specific point. This would not be possible in a primordial soup scenario. Enzymes also degrade spontaneously when exposed to uv light. Beyond the secondary structure, You would also need more enzymes to chaperone the proper folding into the tertiary and quaternary structure which are necessary for proper function.

Amino acid polymerization is one of countless requirements needed to get the first lifeform created from scratch. The fact that you need lab-grade acids to polymerize amino acids goes to show how difficult it is to make even the most rudimentary polymer.

Given enough time and enough opportunities every possible permutation can be realized. Only the fittest survive.

I never believed there was such a thing as junk DNA, just DNA we didn't understand yet. Hell, we don't even know what an appendix does.

originally posted by: dragonridr
The DNA sequence that can be directly compared between the two genomes is almost 99 percent identical.

well duh, of course regions of the genome that are comparable will be comparable haha. You see how this is such a misleading statement to say 99% of the genome is similar? You see it in headlines and people take it as gospel.

When in actuality the human genome has up to 150,000,000 less DNA nucleotides than chimpanzees (it was a bigger difference than I remembered): human genome count chimpanzee genome length. This alone means they can at max be 95.8% similar, assuming all coding is identical.

of the remaining genome, a genetic analysis found:

"Approximately 306 Mb (9.91%) of the human sequence did not align to the chimpanzee sequence" source

This means 9.91% of the human sequence did not align with the chimpanzee genome. So now the max similarity can be about 86%. Now is where we get the deceptively highlighted statistic that about 98% of the remainder is similar. so 98% x 86% equals a total of about 84% of the genomes that is similar. Yet you never see this percentage in any headlines, you have to dig through the raw data to find it.

Thanks for sending me down this rabbit hole, gonna post about it because people need to know how deceptive the (un)scientific journalism is.

a reply to: cooperton

You're a lousy chemist.

originally posted by: Phantom423
a reply to: cooperton

You're a lousy chemist.

wow it's like you can't actually discuss science so you just resort to insult and erroneous tangents

a reply to: cooperton

You don't understand laboratory chemistry -

originally posted by: cooperton
wow it's like you can't actually discuss science so you just resort to insult and erroneous tangents

Knowledgeable people find it hard to discuss science with people who make up their own and then insist it's real because they are not informed enough to see the error in their interpretations.

originally posted by: Kreeate


Knowledgeable people find it hard to discuss science with people who make up their own and then insist it's real because they are not informed enough to see the error in their interpretations.

originally posted by: Phantom423
a reply to: cooperton

You don't understand laboratory chemistry -

Show specifically where I was inaccurate and we can go from there.

originally posted by: cooperton

originally posted by: Kreeate


Knowledgeable people find it hard to discuss science with people who make up their own and then insist it's real because they are not informed enough to see the error in their interpretations.

originally posted by: Phantom423
a reply to: cooperton

You don't understand laboratory chemistry -

Show specifically where I was inaccurate and we can go from there.

It's been pointed out to you multiple times. I'm not going to entertain your ignorance. The problem is not that you can't see it, it's that you won't, due to your agenda and bias.

Good day to you Sir.

originally posted by: Kreeate

It's been pointed out to you multiple times. I'm not going to entertain your ignorance. The problem is not that you can't see it, it's that you won't, due to your agenda and bias.

Good day to you Sir.

Brilliant evasion. It's almost as if you can't actually point out where I was incorrect regarding biochemical processes

a reply to: cooperton

Way to move those goalposts first you say it can't happen, Then well it cant happen outside a lab. Your argument is funny because you have no clue the early oceans were acidic. CO2 and water produce carbonic acid, so it stands to reason that the early oceans would have been more acidic. But higher early CO2 levels would also have resulted in acidic rainwater meaning it also could have started in tidal pools as well.

See we will never know how life was created unless we invent a time machine all we can do is show possible paths it could have taken. There are some very smart researchers tackling this problem mostly because we don't want to be alone in the universe. Did you realize the building blocks of life are created in nebulas? So the universe itself could e predisposed to create life.

www.universetoday.com...

originally posted by: dragonridr
a reply to: cooperton

Way to move those goalposts first you say it can't happen, Then well it cant happen outside a lab.

Lol no I stand by what I said earlier and in the prior post: amino acid monomers do not polymerize in water. In the experiment they polymerized the monomers in a highly concentrated acid, not water.

Your argument is funny because you have no clue the early oceans were acidic.

As acidic as battery acid? Such acidity is favorable for polymerization, but the second, tertiary and quaternary structure of a protein will denatured in such high acidity:

"Acid-induced denaturation (of proteins) often occurs between pH 2 and 5"

This yields yet another impossibility for random chance generation. If low pH is required to polymerize amino acids, yet it is unfavorable to protein folding, that shows acidic oceans also wouldn't be favorable for making functional proteins.

This is why enzymatic catalysis is so necessary, and this is also why these protein structures could not have formed by random chance

a reply to: cooperton

This is a mic drop moment:

As acidic as battery acid? Such acidity is favorable for polymerization, but the second, tertiary and quaternary structure of a protein will denatured in such high acidity:

"Acid-induced denaturation (of proteins) often occurs between pH 2 and 5"

This yields yet another impossibility for random chance generation. If low pH is required to polymerize amino acids, yet it is unfavorable to protein folding, that shows acidic oceans also wouldn't be favorable for making functional proteins.

This is why enzymatic catalysis is so necessary, and this is also why these protein structures could not have formed by random chance.

I don't know how your points can be any clearer. A natural interpretation of evolution is a fantasy that should have been discarded after we discovered a supercomputer in the cell.

a reply to: cooperton

Find a single paper in the peer-reviewed scientific literature that says: "amino acid monomers do not polymerize in water".

The truth is there are no humans no chimpanzees etc. just life. Discriminatory "thinking" or more accurately "remembering" is Occam's "razor" but in reality it is just names not the life witnessed of experienced. it is said that death carries those names... and that whatever it is has names all their own in and their own families.

Seeing life as life is equanimity... that discriminatory razor has gone so far as to cut on each other in oh so many ways.

"Junk" "DNA" trimming the fat... wasn't fat when it was used as an insulation against the cold winter winds was it,wasn't fat when it was used as excess water storage in the case of drought was it? Wasn't seen as waste when it was used as oil for lamps was it?

Making excuses for the razor is easy... going back to equanimity as life is life is easier. Seeing and hearing the discriminatory that people have labeled "hell" in oh so many names as well? Is even easier, allowing one to learn the skill to avoid it.

Pure from the beginning means seeing nothing as heaped on anyone or anything as a label. Emptiness of all that? Is fullness of being allowing true sentience of life.

DNA was "junk" when a precedent found it inadmissible by trial. I suppose "science" hasn't gotten the memo that DNA is an inadmissible "evidence." Since there was a supreme court case determining such a thing? Why try to go against it? What value is placed on DNA? By the very title of this OP? "Junk" dealing in and with "Junk" goes on every day. Obviously many find value in "Junk" like; Look at this corpse just laying there... Junk? No that is a "fly" maternity ward... a backbone of a very large species that feeds others daily in various ways.

Other an "life" there are elements or what is termed "matter" awake and aware matter... would wonder what in the world is wrong with life? Now that's quite a big question now isn't it? Those two have come into "contact" so many times over an incalculable amount of time... that it is wise not to differentiate one from the other. To do so would be a hangman making his own noose every night before he goes to bed not knowing he's the one actually hanging there. What's worse is there's no way to tell him that... he has to learn it by direct experience and wisdom of it as rote won't work, it just makes followers... and some people just can't be followed. They go through heavens they go through hell's and there is no difference. In the followers however? Hang man or noose who knows which is guilty? Maybe they love each other and just don't know it.

All "saviors" needed freedom from their "followers" and still do; it's one of the only things worth remembering... equal to and surpassing them is what they actually applaud as the sound of one hand clapping.

n/m

n/m

a reply to: cooperton

One more paper and I'm done with you and the Great Bloviator:

Single amino acid based self-assembled structure†
Shama Perween, Balasaheb Chandanshive, Hema Chandra Kotamarthi
and Deepa Khushalani*

pubs.rsc.org...

Single amino acids (phenylalanine, tyrosine and glycine) have been evaluated for fibrillar structure under
neutral, aqueous conditions using scanning electron microscopy, transmission electron microscopy, circular
dichroism, FTIR, and Congo red and thioflavin T histological dye assays. All these techniques prove that
aromatic amino acids, such as phenylalanine and tyrosine, do in fact form distinct fibrillar structures
albeit without any secondary structural characteristics such as an a-helix or a b-sheet. The nature of the
interactions between neighbouring amino acids in the fibrillar structures are purported to simply be
non-covalent p–p interactions.

Experimental section
Phenylalanine, tyrosine, and glycine were purchased from
Sigma and used without further purication. The purity of the
amino acids procured was 99.9%. Deionized water was used for
preparing all the solutions (Millipore). Scanning electron
microscopy (SEM) images were taken using a Zeiss Ultra FEG 55
microscope (the accelerating voltage ranged from 5 to 20 kV).
SEM samples were prepared on either silicon, glass, gold-coated
glass, mica or aluminium substrates by directly depositing 20
mL of the solution.

Amino acids are ZWITTERIONS - they have both hydrophobic and hydrophilic end groups. That's why a BUFFER is used and the pH of water is adjusted based on what the goal of the experiment is. The isoelectric point of amino acids is 7. Polymerization of amino acids is a DEHYDRATION reaction - that means 2 molecules of water are released for every polymerization bond. AND IT TAKES PLACE IN WATER.