the shape of proteins requires an engineer

originally posted by: Kreeate

Back on topic... the idea that natural proteins "needed" some kind of initial spark to exist is laughable.
This topic clearly exhibits the OP's inability to understand fundamental biology and evolution.

Show me the mechanism for life to come from non-life in a natural setting then. You thinking unfounded science is fundamental science shows your level of blind belief.

originally posted by: cooperton

originally posted by: Kreeate

Back on topic... the idea that natural proteins "needed" some kind of initial spark to exist is laughable.
This topic clearly exhibits the OP's inability to understand fundamental biology and evolution.

Show me the mechanism for life to come from non-life in a natural setting then. You thinking unfounded science is fundamental science shows your level of blind belief.

The irony in the term "blind belief" must be lost on you.

All the evidence is out there. I will not entertain your delusion by linking to any of it.
Facts are facts. Your inability to accept those is not for me to change. You are on your own. - Well, at least together with the thousands of other delusional people.

Peace be upon you my friend. May prosperity and good fortune find you wherever you go.

originally posted by: dandandat2
How did God engineer the shape of proteins?

The shape of proteins emerge from the sequence of amino acids in a protein polymer, and the laws of intermolecular and intramolecular forces. To know a sequence that can be over 100,000 DNA monomers long and forecast how these innate molecular forces will bend it, along with the help of chaperone proteins (essentially little assembly bots), you can get a functioning protein. Given the meticulousness of this process, random chance is the last candidate I would assume as the creator

If God is all powerful can God create a universe wherein abiogenesis, (which is the emergence of life from non-life through natural thermodynamic processes) is factual ... or is that beyond God's abilities?

The current laws of thermodynamics say it didn't happen that way. There's known energetic hurdles such as peptide synthesis (protein Polymerization) being thermodynamically unfavorable in water.

This fundamental thermodynamic tenet is most easily understood by the fact that organisms decay when they die, rather than continuing to grow. It has to be this way, otherwise you'd get malignant biomass growing all over the place.

originally posted by: Kreeate

All the evidence is out there. I will not entertain your delusion by linking to any of it.
Facts are facts. Your inability to accept those is not for me to change. You are on your own. - Well, at least together with the thousands of other delusional people.

Lol find it and post it bro, you will get a Nobel prize for uncovering a source that no one even knew about in the science community. Crazy that you found the answer for the resolution of abiogenesis but you just don't want to post it. Its as though you actually have no idea what you're talking about and are now intellectually cornered against a wall for relying on your blind belief

originally posted by: darkbake

originally posted by: SigmaXSquared
a reply to: cooperton

if there is one habitable world, there are a hundred somewhere else...if there is one engineer, there are a hundred somewhere else

whcih brings us to the fermi paradox

on one hand, if there is more life then show us where it is

on the other, perhaps safer for all worlds if that question remains unanswered

The Fermi Paradox is bull# because we DO have evidence of thousands or more encounters with ET and UFOs but they don't "count." The only reason the Fermi Paradox exists is because the government wants to pretend it does.

If anyone "out there" wants to communicate, our government can not stop them, period

So if not Fermi paradox then maybe we are just gross and impractical

Either way, one alien means a hundred aliens and one habitable planet means hundred planets and one engineer means...

originally posted by: SigmaXSquared

If anyone "out there" wants to communicate, our government can not stop them, period

So if not Fermi paradox then maybe we are just gross and impractical

Either way, one alien means a hundred aliens and one habitable planet means hundred planets and one engineer means...

Have you considered the extra-dimensional possibility? Given the frequency of reported alien contact, and the vast distances to any lights in the sky, it would make sense they're extra-dimensional. This would also corroborate with the common description of some sort of telepathic interaction with these entities, they are masters of the universe to a degree where they can communicate in extraordinary ways.

originally posted by: cooperton

The current laws of thermodynamics say it didn't happen that way. There's known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water. This is most easily understood by the fact that organisms decay when they die, rather than continuing to grow if left in water.

Can God create a universe wherein abiogenesis can overcome the known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water? Or is that beyond God's abilities?

originally posted by: dandandat2

originally posted by: cooperton

The current laws of thermodynamics say it didn't happen that way. There's known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water. This is most easily understood by the fact that organisms decay when they die, rather than continuing to grow if left in water.

Can God create a universe wherein abiogenesis can overcome the known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water? Or is that beyond God's abilities?

I'll weigh in here...

No "God" cannot.

Evolution has been and is continuously being proven. Denialists will of course refute these facts. Stupid is as stupid does.

In addition...

Regarding the OP that states : "the shape of proteins requires an engineer"...

It absolutely does not. Simple known science and established evolutionary evidence will not only refute this ludicrous claim, but will AND DOES totally obliterate it.

a reply to: cooperton

Aren't you setting up a straw man with your 1000 amino acid strand of protein? Couldn't protein strands start at shorter lengths and then several could attach together to make bigger ones? And might there not be catalyst organic polymers that would preferentially create one chirality? Let's, for example, first entertain the notion of a 100 amino acid strand. The math won't be so ginormous, so the possibility will be considerably greater.

But even before that, let's look at your math. 1 x 2^1000 isn't nearly as large as you claim. Because, for example, 2^10 is not equal to 20,000,000,000, but rather 1,024; and 2^100 = 1.2676506E30 (that's only 30 zeros after the left-hand digit) and 2^500 = 3.273390608E150, and 2^1000 = (2^500)^2, which is then (3.273390608E150)^2 = 10.7150860725E300 or 1.0715E301, which is 10715... (294 0's later )...,000 as per your notation. This number is approximately 2e700 smaller than your claimed number, which would be represented by about four and quarter of the rows of zeroes your erroneous number has, i.e. much, much smaller.

Now, sure, that is still a big number, but a lot more reasonable. And imagine a world full of organic molecules with nothing but time on its hands. Relatively soon, geologically speaking, you'll have some of these L-chirality protein strands, and that gets the wagon rolling. Can't comment on your "amino acid polymerization is thermodynamically unfavorable in water" but to say that again there are likely catalyst polymers that help to create these protein chains.

No nothing about such matters myself I refer you to this video on protein folding, and several of the comments below it.

I'm a chemical biologist. There is an entire class of proteins called chaperone proteins which includes heat shock proteins (e.g. HSP60). These proteins assist unfolded proteins to fold the right way to ensure proper tertiary structure. These evolved as proteins got bigger and more complex. I work on an amyloidogenic disease which has dysfunctional chaperone activity as a component. Obviously the first spontaneously formed proteins/enzymes didn't have the luxury of chaperone proteins, but they were likely much smaller and their function much simpler.

it’s chaperones that enable assembly of complex proteins and not just random chance of a complex sequence folding into the correct shapes on its own. It makes sense that there was an evolution of chaperones in parallel with proteins that explains how it came to be that these complex sequences fold to their perfect shapes.

The solution to this paradox is that during the folding process, proteins pass through a series of INTERMEDIATE states that reduce the number of POSSIBLE conformations. These intermediates are like ANCHOR points that help direct the protein to its "CORRECT" structure. In addition, hydrophobic interactions also play an important role in the folding process.

Now the video and comments concern protein folding, but I am assuming that there is an analogous reason for the creation of a single chirality protein. Could be wrong, but seems likely that this is the case.

As I said already, I know nothing about biochemistry, but if you don't know your math, how do you expect anyone to take you seriously regarding the biochemistry?

Did a little further research and found this:

lthough most amino acids can exist in both left and right handed forms, Life on Earth is made of left handed amino acids, almost exlusively. No one knows why this is the case. However, Drs. John Cronin and Sandra Pizzarello have shown that some of the amino acids that fall to earth from space are more left than right. Thus, the fact that we are made of L amino acids may be because of amino acids from space.

Why do amino acids in space favor L? No one really knows, but it is known that radiation can also exist in left and right handed forms. So, there is a theory called the Bonner hypothesis, that proposes that left handed radiation in space (from a rotating neutron star for example) could lead to left handed amino acids in space, which would explain the left handed amino acids in meteorites. This is still speculative but our paper makes it much more plausible. In fact, this observations was one of the main reasons why we persued this research. Although there were theories about how the amino acids could form in space in the ice, no one had shown that it was viable to make amino acids this way, until now.

Amino Acid Chirality

In other words, chirality of amino acids is not random.

originally posted by: dandandat2

Can God create a universe wherein abiogenesis can overcome the known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water? Or is that beyond God's abilities?

Peptide polymerization is possible with lab-grade experiments, or a ribosome. If God coded the genetic code then a ribosome was part of it since it is coded for by DNA.

Amino acid polymerization is thermodynamically unfavorable in water... similar to how lighting a match is thermodynamically unfavorable in water. They have appealed to this by saying it must have been in an acidic environment near hydrothermal vents, since the low pH would allow amino acids to polymerize... but this would denature any resulting protein strand rendering it permanently useless even if it triumphed against all odds.

originally posted by: Kreeate
In addition...

Regarding the OP that states : "the shape of proteins requires an engineer"...

It absolutely does not. Simple known science and established evolutionary evidence will not only refute this ludicrous claim, but will AND DOES totally obliterate it.

How about instead of arm waving, you elucidate the matter a bit for us.

originally posted by: MrInquisitive

originally posted by: Kreeate
In addition...

Regarding the OP that states : "the shape of proteins requires an engineer"...

It absolutely does not. Simple known science and established evolutionary evidence will not only refute this ludicrous claim, but will AND DOES totally obliterate it.

How about instead of arm waving, you www.engineeringtoolbox.com... the matter a bit for us.

No elucidation required. The science and actual facts speak for itself.
If you are biased about these facts, that's on you. No concern of mine.

Just stop trying to push pseudo-science nonsense. It's counter productive to society.
We have real world issues to deal with. This flat-earth/creationist nonsense is really not helping.

originally posted by: cooperton

originally posted by: dandandat2

Can God create a universe wherein abiogenesis can overcome the known energetic hurdles such as peptide synthesis (protein. Polymerization) being thermodynamically unfavorable in water? Or is that beyond God's abilities?

Peptide polymerization is possible with lab-grade experiments, or a ribosome. If God coded the genetic code then a ribosome was part of it since it is coded for by DNA.

Amino acid polymerization is thermodynamically unfavorable in water... similar to how lighting a match is thermodynamically unfavorable in water. They have appealed to this by saying it must have been in an acidic environment near hydrothermal vents, since the low pH would allow amino acids to polymerize... but this would denature any resulting protein strand rendering it permanently useless even if it triumphed against all odds.

You seem to be avoiding the question and reciting the same argument over and over again.

But I'll ask the question again in another way:

Can God light a match underwater? Or is that beyond God's abilities?

originally posted by: MrInquisitive
a reply to: cooperton

Aren't you setting up a straw man with your 1000 amino acid strand of protein? Couldn't protein strands start at shorter lengths and then several could attach together to make bigger ones? And might there not be catalyst organic polymers that would preferentially create one chirality? Let's, for example, first entertain the notion of a 100 amino acid strand. The math won't be so ginormous, so the possibility will be considerably greater.

Thank you for a well thought out response. I try not to go into excessive detail with these write-ups, but it would be most accurate to say 7459 amino acids rather than 1000, because even E. Coli, a rudimentary prokaryotic organism, has a ribosome comprised of 7459 amino acids.

source

But even before that, let's look at your math. 1 x 2^1000 isn't nearly as large as you claim. Because, for example, 2^10 is not equal to 20,000,000,000, but rather 1,024; and 2^100 = 1.2676506E30 (that's only 30 zeros after the left-hand digit) and 2^500 = 3.273390608E150, and 2^1000 = (2^500)^2, which is then (3.273390608E150)^2 = 10.7150860725E300 or 1.0715E301, which is 10715... (294 0's later )...,000 as per your notation. This number is approximately 2e700 smaller than your claimed number, which would be represented by about four and quarter of the rows of zeroes your erroneous number has, i.e. much, much smaller.

Yes good catch you're right. But luckily for me my low-ball estimate for the number of coin flips needed brings it back to being even less probable than my original estimate. To flip heads 7459 times in a row to get a fully L-oriented ribosome would be 2^7459, making the odds approximately 1 in 2.4^2245. This is really high up on the asymptote to impossibility.

Can't comment on your "amino acid polymerization is thermodynamically unfavorable in water" but to say that again there are likely catalyst polymers that help to create these protein chains.

Dehydration synthesis of peptide monomers is endergonic, meaning non-spontaneous. This reaction is difficult in water because one of the products is water, which dramatically ruins the rate of a reaction. Again think of lighting a match underwater, lighting a match produces CO2 and water from combustion so it is difficult to light it in water. The opposite reaction is actually favorable: hydrolysis. Hydrolysis degrades peptide and DNA bonds spontaneously... meaning over time bonds will break rather than form.

I'm a chemical biologist. There is an entire class of proteins called chaperone proteins which includes heat shock proteins (e.g. HSP60). These proteins assist unfolded proteins to fold the right way to ensure proper tertiary structure. These evolved as proteins got bigger and more complex. I work on an amyloidogenic disease which has dysfunctional chaperone activity as a component. Obviously the first spontaneously formed proteins/enzymes didn't have the luxury of chaperone proteins, but they were likely much smaller and their function much simpler.

This is the pervading theory, but it quickly gets dismantled by the fact that all the integral proteins, necessary in even the most rudimentary self-replicating organism, are too big to be folded without chaperones. ATP synthase for example, the micromolecular motor in all living organisms that generates energy for the cell, requires proper folding for it to take shape. Without ATP synthase, a cell cannot have an equilibrated supply of ATP (energy).

"The chaperones Atp11 and Atp12 promote formation of the F1 domain (of ATP synthase)." source

Just look at the complexity involved in making this one aspect of energy creation in even the most basic organism. ATP synthase is literally a micromolecular organic motor that is coded for in DNA.

it’s chaperones that enable assembly of complex proteins and not just random chance of a complex sequence folding into the correct shapes on its own. It makes sense that there was an evolution of chaperones in parallel with proteins that explains how it came to be that these complex sequences fold to their perfect shapes.

The problem is there can be no evolution without these basic necessary proteins to already be in fully functioning existence. There's no half-working ATP synthase that only kind of works. Just like a motor that is missing half of its components would not work. Chaperones can't evolve without ribosomes existing because chaperones can't be made without ribosomes existing.

The solution to this paradox is that during the folding process, proteins pass through a series of INTERMEDIATE states that reduce the number of POSSIBLE conformations. These intermediates are like ANCHOR points that help direct the protein to its "CORRECT" structure. In addition, hydrophobic interactions also play an important role in the folding process.

If proteins aren't fully folded they will not perform the same function. This is a major flaw that if Darwin knew about I don't think he would support his own theory any more because he realized the fatal flaw would be if successive piece-by-piece mutations could not culminate biological life. Surely enough, it's all or nothing with most of these proteins. Even if an ATP synthase were to appear out of nowhere, you'd need the rest of the electron transport chain for it to even be relevant!

Now the video and comments concern protein folding, but I am assuming that there is an analogous reason for the creation of a single chirality protein. Could be wrong, but seems likely that this is the case.

If someone were to find a natural mechanism for this it would be HUGE. But even if they did, it would be one small step of many that need to be resolved. At this point the data is majorly favoring the necessity of logic in the contrivance of biological organisms

Why do amino acids in space favor L? No one really knows, but it is known that radiation can also exist in left and right handed forms. So, there is a theory called the Bonner hypothesis, that proposes that left handed radiation in space (from a rotating neutron star for example) could lead to left handed amino acids in space, which would explain the left handed amino acids in meteorites. This is still speculative but our paper makes it much more plausible. In fact, this observations was one of the main reasons why we persued this research. Although there were theories about how the amino acids could form in space in the ice, no one had shown that it was viable to make amino acids this way, until now.

This comes up a lot regarding meteors containing amino acids. My initial instinct tells me it is due to impact with life on earth and it gets contaminated with molecules from living organisms, or even just in the atmosphere. I don't know enough to make further comment, but the ratio would need to be 100%. If it is 100% on the meteor then its probably because it impacted life on earth which consists of L-amino acids.

originally posted by: dandandat2

Can God light a match underwater? Or is that beyond God's abilities?

Of course. If God created law, then thermodynamic law can certainly be temporarily changed by this extra-dimensional Being. If God has the power to create and manipulate matter at a whim, then God creating all existent biological forms through random mutations would be quite a comedy. They certainly wouldn't rely on random chance for their creation, although it would of course be possible among the infinitude of other 'ways' in which God could have created existence.

Think of how in our dreams we imagine vast worlds and people, imagine what a more intelligible extra-dimensional Being not confined by time could do with their mind. Reminds me of this Max Planck quote:

a reply to: cooperton

Another epic example of utter verbal diarrhea. This and the post above. Spew forth the none-science and the simple minded will swallow it. Hook, line and sinker. Just more of the same generic propaganda aimed at the gullible in order to gain more "souls" so as to enrich the already ludicrously rich. Yay for the church!

originally posted by: Kreeate
a reply to: cooperton

Another epic example of utter verbal diarrhea. This and the post above. Spew forth the none-science and the simple minded will swallow it. Hook, line and sinker. Just more of the same generic propaganda aimed at the gullible in order to gain more "souls" so as to enrich the already ludicrously rich. Yay for the church!

lolol mods can someone takeout this trash? This guy is like a sore thumb in so many threads, never offering any content.

Anyway, if you're capable, which I am assuming you are not, please show where I am wrong in my assessment with detail and we can go from there. Blanket statements that merely defend your blind belief do not count. The fact that you think empirical science is verbal diarrhea shows how ass-backwards you are.

originally posted by: Kreeate

originally posted by: MrInquisitive

originally posted by: Kreeate
In addition...

Regarding the OP that states : "the shape of proteins requires an engineer"...

It absolutely does not. Simple known science and established evolutionary evidence will not only refute this ludicrous claim, but will AND DOES totally obliterate it.

How about instead of arm waving, you www.engineeringtoolbox.com... the matter a bit for us.

No elucidation required. The science and actual facts speak for itself.
If you are biased about these facts, that's on you. No concern of mine.

Just stop trying to push pseudo-science nonsense. It's counter productive to society.
We have real world issues to deal with. This flat-earth/creationist nonsense is really not helping.

Hello? Did you read my prior post? I was refuting the OP. I'm a believer in science and that fancy-schmancy evolution theory, but I know not a whit about evolutionary biochemistry. I would honestly like a short explanation of why what you claim is true -- both for myself and for those less inclined to believe in science and evolution. I'm not biased, I just want some solid information on the matter. But I am no going to accept your arm waving either, as that would be even worse than accepting the OP, which at least provided an explanation, albeit a severely flawed one.

originally posted by: MrInquisitive

Hello? Did you read my prior post? I was refuting the OP. I'm a believer in science and that fancy-schmancy evolution theory, but I know not a whit about evolutionary biochemistry. I would honestly like a short explanation of why what you claim is true -- both for myself and for those less inclined to believe in science and evolution. I'm not biased, I just want some solid information on the matter. But I am no going to accept your arm waving either, as that would be even worse than accepting the OP, which at least provided an explanation, albeit a severely flawed one.

You're wasting your time he's just a troll. He doesn't even know who's on his own side for an argument lol.

originally posted by: cooperton

originally posted by: Kreeate
a reply to: cooperton

Another epic example of utter verbal diarrhea. This and the post above. Spew forth the none-science and the simple minded will swallow it. Hook, line and sinker. Just more of the same generic propaganda aimed at the gullible in order to gain more "souls" so as to enrich the already ludicrously rich. Yay for the church!

lolol mods can someone takeout this trash? This guy is like a sore thumb in so many threads, never offering any content.

Anyway, if you're capable, which I am assuming you are not, please show where I am wrong in my assessment with detail and we can go from there. Blanket statements that merely defend your blind belief do not count. The fact that you think empirical science is verbal diarrhea shows how ass-backwards you are.

The mods can do as they please.

The fact that I don't agree with you is not an automatic qualifier for "post deletion" mate. I have an opinion. It's different from yours. These are facts. Grow up, lol.

I don't need to "show" where you are wrong in your "assessment". YOU, are making the claim. The onus is on YOU to prove your "assessment", which you cannot do. It has never been done and it never will be. Because it is bogus. It is nonsense. Utter and complete fantasy.

Kindly provide your empirical evidence and proof. THEN we can have a conversation. Until then, you are just another fundamentalist in my opinion.