Why Does Biological, Organic Life Exist in a Universe that is Inorganic ?

originally posted by: whereislogic
a reply to: cooperton

From the article about protein folding you shared:

In addition, about 80% of the cell’s proteins fall outside these three classes and fold spontaneously without chaperones.

What do you think about that number, since no reference was listed for it and they don't seem to go into it anymore (although I skimmed the paper, could have missed it)? And do you think the sentence above means that in a living cell, 80% of proteintypes that are produced, do not traverse through the folding machine for their final confirmation form, they fold on their own (into their final 100% functional form)?

Or do you think it means that 80% of proteintypes can fold on their own and still retain at least some of their functionality, but they won''t be as efficient as the same proteins produced in a living cell that do use the folding machine for their final confirmation form and 100% functionality?

In contrast, notice how this source talks about it:

How Chaperone-Assisted Protein Folding Works (gbiosciences; 2020)

While it was previously believed that the amino acid sequence of the mRNA polypeptide chain provided all the information the protein needs to assume the correct three-dimensional configuration, more recent studies have proved otherwise. The intervention of other proteins is necessary to ensure the proper folding of the proteins within the cells – and this is where molecular chaperones come in.

No mention of any proteins in the cell that will fold into their 100% biologically functional configuration (in a living cell) without the assistance of chaperones (as it's normal pathway under normal conditions). Quite a contrast with the 80% statement earlier that may give the impression that 80% of proteintypes in living cells will do that without chaperone assistance (depending on how a person reads the sentence I highlighted, notice it isn't spelled out like that, but can easily be misunderstood like that, it wasn't clear to me what they meant with that).

originally posted by: whereislogic

No mention of any proteins in the cell that will fold into their 100% biologically functional configuration (in a living cell) without the assistance of chaperones (as it's normal pathway under normal conditions).

Yes this seems to be the pervading idea among biologists. The only exception is small globular proteins that are small enough to not need assistance with proper folding. The rest require some sort of assistance from other factors in the cell:

"The Anfinsen postulate (that the final tertiary structure of a protein depends only on its primary structure) may still hold for small globular proteins, but folding in vivo is almost certainly always assisted"

That is a layman's representation for this paper, which essentially says that many aspects of the cell beyond just chaperone proteins are integral to protein folding. Such as "lipid bilayers, or cotranslationally folded domains in multidomain proteins".

The other aspect that mention is the danger of freshly produced proteins having the tendency to aggregate together with other proteins of the same kind and thus creating aggregations that are harmful protein build-ups in the cell. These are mediated by various macromolecules that prevent this sort of harmful aggregation. The "proteosome" is the generic term used for the necessary steps that must be taken to properly handle a protein and its homeostatic expression.

originally posted by: Phantom423
a reply to: cooperton

You don't understand the energetics of protein folding. It's a natural process that happens all day long in living organisms.
Here's an online source where you can learn the thermodynamics of protein folding. Pay attention to the science (for a change).

I can't tell if you're dodging the point purposefully or if you're just a bot. Many proteins require chaperone proteins to be folded properly. Of course polypeptide chains will fold spontaneously due to attractions of the various sequences of the peptide strand, but without chaperones many of these will be folded into useless blobs. Chaperones are often close to the translation site (the area where peptide polymerization occurs). This ensures that the polypeptide (protein) doesn't have a chance to spontaneously fold into a useless blob, but instead gets meticulously chaperoned into folding correctly.

The same applies to polymerization. It's basic organic chemistry 101 (which you have never done. Nor have you ever been in a lab).

I don't know how many times I have to go down this road with you. Peptide polymerization requires energetic input and does not occur spontaneously:

"Peptide bond formation is endergonic and has a high activation energy, meaning there is both a thermodynamic and kinetic barrier to the formation of peptide bonds."
link

The words you want to look for when researching this is primary vs. tertiary proteins.



A primary protein is the sequence of proteins in a polypeptide chain, this is the step that absolutely requires enzymatic help and energy to form properly. The tertiary structure is the part of the protein that gets folded into a functional shape. This can and will occur spontaneously, but without proper help from other proteins such as chaperones proteins, they will not get folded properly and will become useless blobs that are actually harmful to the cell.

The primary structure is therefore the main thermodynamic difficulty for abiogenesis, because amino acid polymerization does not occur spontaneously in water, it requires enzyme catalysis. This catalysis occurs at the ribosome. this is basic biology 101, and a known necessity for proper protein polymerization and biological life in general.

a reply to: cooperton


You're wrong, as usual. You don't understand thermodynamics as it applies to biochemical systems. Come back when you have an education.

originally posted by: Phantom423
a reply to: cooperton


You're wrong, as usual. You don't understand thermodynamics as it applies to biochemical systems. Come back when you have an education.

All of my references to thermodynamics were correct, and you can't prove otherwise. You just hate real empirical science because it spoils your fragile belief system

a reply to: cooperton

Sort of puts the claims made by those marketing programs that predict protein folds based solely on amino acid sequence into perspective doesn't it (similar to Foldit, the one Phantom brought up)? Especially since the folds they predict are not representative of the tertiary structures of proteins in living cells which are not solely based on amino acid sequence.

It also makes all this talk about energy landscapes and kinetic "traps" (see Arthur Horwich's video I linked about chaperones, 6:00 and 4:21) rather dubious. There doesn't seem to be any useful information that could help you predict tertiary structure in living cells there (in the amino acid sequence and the kinetics of it all, you still don't get the final fully functional biological form from that information alone). So the energy landscape isn't as important as they make it out to be, because it's not the deciding factor as to what the tertiary structure will be in a living cell (in vivo).

The Arthur Horwich video I linked earlier (under some text, so it may not be obvious):

originally posted by: cooperton

originally posted by: Phantom423
a reply to: cooperton


You're wrong, as usual. You don't understand thermodynamics as it applies to biochemical systems. Come back when you have an education.

All of my references to thermodynamics were correct, and you can't prove otherwise. You just hate real empirical science because it spoils your fragile belief system

Your "references" are cut-and-paste frenzies. But there's one thing you never seem to include and that's your guy in the sky with the magic wand. None of the references you post show the necessity of a magic wand. If nothing is spontaneous, where is this magic wand? Probably looks something like this???

Part 1



Part 2

originally posted by: whereislogic
a reply to: cooperton

Sort of puts the claims made by those marketing programs that predict protein folds based solely on amino acid sequence into perspective doesn't it (similar to Foldit, the one Phantom brought up)?

edit: just for clarity, I wasn't talking about "marketing programs" (programs for marketing) but 'those people that are marketing programs that predict protein folds...' (I was using the word "marketing" as a verb).

originally posted by: Phantom423

Your "references" are cut-and-paste frenzies.

Lol no it was a simple reference that tells you straight-forward that peptide bonds (amino acid polymerization) is an endergonic process that requires energy input and catalysis. You will learn this in any basic biology course when being taught enzymes or protein production/translation. You consistently prove you're incapable of biological discussion.

originally posted by: cooperton

originally posted by: Phantom423

Your "references" are cut-and-paste frenzies.

Lol no it was a simple reference that tells you straight-forward that peptide bonds (amino acid polymerization) is an endergonic process that requires energy input and catalysis. You will learn this in any basic biology course when being taught enzymes or protein production/translation. You consistently prove you're incapable of biological discussion.

And YOU have never posted that magic wand. Where is it???

originally posted by: whereislogic
a reply to: cooperton

Sort of puts the claims made by those marketing programs that predict protein folds based solely on amino acid sequence into perspective doesn't it (similar to Foldit, the one Phantom brought up)? Especially since the folds they predict are not representative of the tertiary structures of proteins in living cells which are not solely based on amino acid sequence.

Yeah it's quite astounding that even having all the chaperones available would not be enough to have proper handling of a protein after it is created. This also doesn't take into consideration the necessity to destroy these proteins when they become too abundant. Without these sorts of checks and balances the cell would quickly get overrun with excess proteins to the point of toxic overload. These are the things that abiogenesis could not have pulled off due to the vast amounts of interdependent facets for even the most basic functioning cell.

Notice phantom avoids actually having a discussion because they know they don't stand a chance. Their faith relies on ignoring the counter-argument, while stubbornly refusing to disbelieve their pre-conditioned notions. The thing is, any self-aware biologist trained in the field would be able to see the conundrum that the necessity of protein post-production modification (proteostasis) presents:

"An interesting puzzle is how any arbitrary new protein that could be produced by evolution can be handled properly by a proteostasis network that has never seen that protein before."
source

originally posted by: Phantom423

And YOU have never posted that magic wand. Where is it???

It is not a magic wand. It is a host of mathematically predictable laws (Logos) that uphold the created universe. These intelligible laws were obviously implemented by something intelligent, because the laws are certainly not dumb. Although I'm sure as you normally do you will faithfully appeal to unintelligence, and loathe intelligence.

But back to the topic at hand, do you concede that the immense necessity of co-factors for protein production, among many other interdependent facets of biology, disproves the possibility of abiogenesis?

a reply to: cooperton

......disproves the possibility of abiogenesis?

Your position has always been that there's some supernatural being initiating everything. Where is it? Where is the magic wand? If there is none, then admit it.

originally posted by: Phantom423

Your position has always been that there's some supernatural being initiating everything. Where is it? Where is the magic wand? If there is none, then admit it.

This intelligent designer implemented logic into the creation, which is clearly shown by the logically perpetuating laws that uphold all creation. You can't see gravity, but you can see the effect that it has. You can't see the Logical Creator God, but you can see the effect that it has in the existence of logical laws.

Let's put it this way, logical laws certainly don't come from no logic. Such an appeal is the most illogical assertion that could be made regarding the existence of the ordered universe.

This intelligent designer

a reply to: cooperton

Science can say NOTHING about a magic wand or intelligent designer without evidence. And you have none.
No evidence = no science. Your "logic" is simply your own. But science requires evidence. Once again, you have none.

None of the equations, biochemical structures or processes require the input of some unseen creature. They happen naturally.

NO MAGIC WAND REQUIRED.

originally posted by: Phantom423
They happen naturally.

NO MAGIC WAND REQUIRED.

Then show an instance of peptide polymerization occurring spontaneously in water enough times to create a polymer that gets folded into a properly functioning protein. This would be a necessity if life can indeed emerge by natural means without intelligence design.

No evidence = no science.

Exactly! so since you can't show evidence that amino acid polymers can form from their components naturally with enzymatic catalysis, then there is no evidence for the feasibility of the theory. You are left with faith. Sadly, it's faith in nothing.

originally posted by: cooperton

originally posted by: Phantom423
They happen naturally.

NO MAGIC WAND REQUIRED.

Then show an instance of peptide polymerization occurring spontaneously in water enough times to create a polymer that gets folded into a properly functioning protein. This would be a necessity if life can indeed emerge by natural means without intelligence design.

No evidence = no science.

Exactly! so since you can't show evidence that amino acid polymers can form from their components naturally with enzymatic catalysis, then there is no evidence for the feasibility of the theory. You are left with faith. Sadly, it's faith in nothing.

That was shown multiple times with references and examples. Perhaps you can show examples of how it DOES NOT happen. Where are the peer-reviewed research papers that say polymerization requires the input of a supernatural creature. Where is the evidence? There is none. Polymerization happens every day, every hour, every minute of the day.
Where's your experimental evidence?

originally posted by: Phantom423
Polymerization happens every day, every hour, every minute of the day.

Yeah under enzymatic catalysis lol. It doesn't happen spontaneously without it. Here's literally millions of sources that show you this basic tenet of biology:

Let me google this for you

a reply to: cooperton

Chiral Amplification of Oligopeptides in the Polymerization of
-Amino Acid
N-Carboxyanhydrides in Water
by Thomas Hitz and Pier Luigi Luisi*
Institut f¸r Polymere, ETH-Zentrum, Universit‰tstrasse 6, CH-8092 Z¸rich
(fax:
41-1-632 10 73; e-mail: [email protected])
Dedicated to Professor Jack D. Dunitz on the occasion of his 80th birthday


This article is concerned with the chiral amplification of oligopeptides formedin the polymerization of
chiral, nonracemic mixtures of the N-carboxyanhydride (NCA) of Leu and Glu in aqueous solution. Labeling
(deuteration) of one enantiomer and reversed-phase and normal-phase high-performance liquid chromatography mass spectrometry (RP- and NP-HPLC/MS, respectively) were used to determine the product
distribution, both with respect to oligopeptide chain length and stereoisomer distribution. Starting the
polymerization with an enantiomeric excess (ee) of 20% of the
-enantiomer (
-amino acid/-amino acid 6 : 4)
leads to an ee of 73% at the level of the homochiral enantiomeric (Leu)5 , and of 71% at the level of the
homochiral enantiomeric (Glu)7. For the Leu system and in the presence of a solid support (quartz), the ee
reached values of up to 100%. We argue that such amplification processes could be relevant for the chemical
evolution towards single-handednes

There are literally dozens of research papers demonstrating polymerization in water.

I'm ending this conversation because, per usual, you're hell bent on this supernatural creature performing feats of magic where there are none.

originally posted by: Phantom423

There are literally dozens of research papers demonstrating polymerization in water.

Every time you try to post one it's describing something else besides amino acid polymerization, and it further proves you don't know how to properly analyze research papers or biological terms. You're the archetypal example of the blind believer.

I can't believe dishonest illogical threads like this are STILL being made after 20+ years of refuting nonsensical creation arguments.

originally posted by: Toothache
I can't believe dishonest illogical threads like this are STILL being made after 20+ years of refuting nonsensical creation arguments.

Evolutionary theory by its own definition is the most illogical theory ever contrived. It insists there is no logical source for the logical world. You just blindly believe in evolutionary theory and trusts "experts" to think for you. When debated you will inevitably give up and have to rely on faith rather than empirical evidence to support the possibility of evolution