Evolution never really struck me as a particularly compelling argument either for or against God. Natural Selection combined with Genetic mutation and process of elimination seemed pretty reasonable with fairly strong explanatory power.
What always bothered me a lot more was studying genetics, and biochemical reactions.
I was reading about Amino-Acyl tRNA synthetase the other day, and really its when I get lost in this world that I think to myself, there is a whole universe of complexity that science has yet to explain.
Amino-Acyl tRNA synthetase is an enzyme which basically brings the proper amino acid, to a particular piece of tRNA.
Once combined with tRNA or "charged", this charged tRNA's will then be used to create proteins.
The process of creating a protein involves a specific portion of the tRNA known as an anti-codon mapping to a portion of the mRNA, the codon.
Succesive tRNAs will attach to the mRNA in a unit known as a ribosome. These successive tRNA's will have their amino acid groups interact with each other to form peptide bonds, which of course are the constituent of proteins.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
Okay, for starters, I don't even see what you're pointing to that's so mysterious. There's no point in protein synthesis where tRNA has to "know what to do"; it's all governed by the rules of chemistry and the geometry of the molecules. But let's assume for the sake of argument that there is such a mystery, and let's further assume that we have no freaking clue how tRNA accomplishes it. Your implicit argument of "We don't know, therefore God" remains invalid, just as it has been throughout history when humanity has been faced with phenomena it could not explain. The only thing we can say is "We don't know, therefore we don't know; let's find out!"
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Vive, vale. Siquid novisti rectius istis,
candidus inperti; si nil, his utere mecum.
Evolution never really struck me as a particularly compelling argument either for or against God.
Evolutionary theory is not an attempt to prove or disprove God or gods. The problem is that the time scale needed for evolution is incompatible with a literal reading of the Bible.
... there is a whole universe of complexity that science has yet to explain.
I will echo Blinking Spirit's comment. The "God of the gaps" is incredibly weak position from which to base your argument.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
This assumes that it takes intelligence to form atomic and molecular bonds. Atoms and molecules bond when and where ever they can. Through random bonding it's not implausible to believe that amino acids may form.
Now, I'm just a nurse and I just have a basic understanding of what they taught us in organic chem. I'm not claiming to be an expert here.
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"I used to think it was awful that life was so unfair. Then I thought, 'Wouldn't it be much worse if life were fair, and all the terrible things that happen to us come because we actually deserve them?' So now I take great comfort in the general hostility and unfairness of the universe." - Marcus Cole, Babylon 5
Honestly I'm more worried by the concept (or illusion) of free will than by chemicals binding.
Izuki, you're a botanist right?
This should be your cup of tea--at least background wise. You've read the myriad of chemical reactions, the ridiculously complex biochemical machinery.
There's a difference between telling someone "it's complex" and for someone who has been in the field to know oh yeah..."it's complex"
Sure science may be lacking some answers, but as far as we know, these are molecules that interact with basic forces---electronegativity and completion of valence shells, london dispersion forces, dipole interactions---nothing more than a bunch of orbitals and charges pushing and pulling each other.
And it's hard to conceive how this could have come together because we're at the level of fundamentality where there really isn't much more there. It's a molecule for God's sake, not a complex system.
It's not like you can explain away complex molecular behavior by virtue of its structure---maybe at the Sn1 nucleophilic substitution level you can....but at the transcription/translation level? Unwinding the DNA from chromosomes bundled with the histones? Undoing the condensed DNA and replicating both sides with two different mechanisms?? (okazaki fragments and straight up base pairing?)
We're talking about the orchestrated interaction of complexes of over a hundred biochemical molecules in some catalytic enzymes. Biochemical reactions that "know" when the DNA is wrong, and will reverse the whole process before starting over again.
Dumb molecules that "know" when the DNA has been supercoiled due to increases in tension from replication, and know where to cut the DNA to relieve the supercoiled tension.
Introns and Exons that know where to "cut" the RNA to know which protein to make, based on what? Concentrations.
Based on [This]
or this
[THIS][THAT]
------------------- = K
[THIS]
But as a scientist, have you ever asked yourself "how did this all come to be?"
You're looking at it backwards. The stuff that doesn't replicate successfuly doesn't persist in the population.
Yes I know that. Basic evolution 101.
What about the biochemical machinery?
I mean, if we're going to say the stuff that doesn't replicate doesn't persist in the population, that's like saying:
How did we get here?
We got here because if we did not get here, we wouldn't be here to contemplate aforementioned question. Therefore our current existence is tautological.
Evolution never really struck me as a particularly compelling argument either for or against God.
Good, it's not meant to be one.
Evolution should have nothing to do with an argument for or against God. Unless your God is the one that made everything in a literal 6 days exactly 10,000 years ago.
The argument for Evolution is for Evolution, thus is shouldn't strike you as a compelling argument for or against God. It's not meant to be.
I was reading about Amino-Acyl tRNA synthetase the other day, and really its when I get lost in this world that I think to myself, there is a whole universe of complexity that science has yet to explain.
Right. The whole point of science is that we don't have all of the answers, nor would we claim we did. "There are many aspects of the universe that still cannot be explained satisfactorily by science; but ignorance only implies ignorance that may someday be conquered. To surrender to ignorance and call it God has always been premature, and it remains premature today."
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
No more than it bothers me that fire "knows" how to burn. That the oxygen molecule "knows" how to combine with the carbon to form carbon dioxide. The same way, every time.
The environment inside of living organism allow those kinds of combinations you describe to occur regularly, even though they might seem unlikely elsewhere. Do you know what those chances are? Do you know the statistical probability of the events you describe? If not, someone else does. Go find the answer.
If I might say, TomCat26, it seems to me you are looking awful hard for reasons not to believe in science. All I can say is that's a GOOD thing, assuming you don't stop. Keep digging deeper, keep trying to find that flaw, don't be satisfied until you're SURE you have it.
I'd say the process that led to a biological cell is a much more mysterious and thought-provoking thing than mere protein synthesis.
None of the individual processes of cell life and replication are particularly mysterious or hard to explain; even cell replication from DNA is just a series of relatively simple chemical reactions. What's more bewildering is the particular combination of factors that led to RNA, DNA, ATP, cell walls, ion pumps, and the particular set of amino acids we use.
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Sing lustily and with good courage.
Be aware of singing as if you were half dead,
or half asleep:
but lift your voice with strength.
Be no more afraid of your voice now,
nor more ashamed of its being heard,
than when you sang the songs of Satan.
If a replicator (cell, molecule, body) proliferates in an environment, it will change that environment through its own success.
New/mutant replicators build on that, and change environment.
First replicator is a matter for abiogenesis/chemistry, but was probably a very simple carbon & misc.
Evolution can be strawmanned into a tautology but that misses major points.
Re: plants
Plant cells are obvious hack-jobs from multiple sources, the idea that we're looking at highly derived structures with significant lost history shouldn't be so shocking.
Re: learning
Your arguments mostly seem be personal incredulity.
If you're serious about learning biology, the MTGS forums isn't the best place to ask.
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“Tell me who you walk with, and I'll tell you who you are.” Esmeralda Santiago Art is life itself.
Amino-Acyl tRNA synthetase is an enzyme needed for the SYNTHESIS of proteins
enzymes are complex proteins
Then how was Amino-Acyl tRNA synthetase originally made?
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Do to others whatever you would like them to do to you. This is the essence of all that is taught in the law and the prophets. (Matthew 7:12)
Make the white queen run so fast, she hasn't got time to make you wise.
Pilot of the storm who leaves no trace, like thoughts inside a dream.
Doctor, my eyes, tell me what you see. I hear their cries... just say if it's too late for me.
Doctor, my eyes...cannot see the sky. Is this the prize for having learned how not to cry?
If a replicator (cell, molecule, body) proliferates in an environment, it will change that environment through its own success.
New/mutant replicators build on that, and change environment.
First replicator is a matter for abiogenesis/chemistry, but was probably a very simple carbon & misc.
Evolution can be strawmanned into a tautology but that misses major points.
Re: plants
Plant cells are obvious hack-jobs from multiple sources, the idea that we're looking at highly derived structures with significant lost history shouldn't be so shocking.
Re: learning
Your arguments mostly seem be personal incredulity.
If you're serious about learning biology, the MTGS forums isn't the best place to ask.
How does DNA Gyrase & Topoisomerase know how to relieve the supercoiling tension of the DNA molecule?
How can a molecule sense when another molecule's (in this case DNA's), torsional tension is too high?
For those of you who don't understand the science here, let me explain it to you:
DNA replicates. As you know it is a double stranded helix. In order to replicate this DNA, the helix must be unwound, and the DNA begins replication at a site known as a replication fork. As this DNA is further unwound, the rest of the DNA's coil, the helix is compressed increasing the tension in the DNA molecule.
Like trying to unzip a braided rope, the rope's helical structure will become compressed as the DNA attempts to replicate. Something is required to relieve this tension. Enter DNA gyrase, which knows how to cut the DNA in a manner to relieve the super coiling tension.
So let's get back to why biomolecular evolution is insufficient:
You're saying look: molecules replicate, the ones that don't replicate wouldn't be here.
My response is: that's great, and I understand that. But what about this biomechanical mechanism in particular? Are we just sticking to the tautological evolutionary answer?
The ability of these non-sentient molecules to act with orchestrated purpose in concert with easily 100 different actors is nothing short of miraculous. I didn't list the other molecules at play in this process. But I could. DNA gyrase is but one actor in the role of my example here---DNA replication.
Like a conductor playing a symphony, each molecule works with the biomechanical machinery in the right place, at the right time, with the right amount of chemical activity.
Amino-Acyl tRNA synthetase is an enzyme needed for the SYNTHESIS of proteins
enzymes are complex proteins
Then how was Amino-Acyl tRNA synthetase originally made?
It was probably a ribozyme doing it at first, with it slowly being replaced by an enzyme because they're generally more efficient.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
To say these molecules are 'dumb' is the same as saying my table is not fit for presidency: a thoroughly useless statement. Molecules do what they do because of their physical properties.
The ability of these non-sentient molecules to act with orchestrated purpose in concert with easily 100 different actors is nothing short of miraculous. I didn't list the other molecules at play in this process. But I could. DNA gyrase is but one actor in the role of my example here---DNA replication.
Like a conductor playing a symphony, each molecule works with the biomechanical machinery in the right place, at the right time, with the right amount of chemical activity.
Let's say we start out with a plank. On that plank, we can carry more food than we would've been able to by hand. We take a piece of string to pull the plank forward. We find that putting logs under the plank allows us to pull with significantly less difficulty than before. We keep adding stuff to this, reusing parts in new ways and refining it. In the end, we have a car. Now, do we say about a car that it's miraculous that a bunch of non-sentient molecules which allow us to move fast from one location to the others ?
Which you're posting on a machine that has literally tens of thousands of moving parts.
Life is a series of chemical processes - when the chemistry changes, the complex molecules that are proteins interact differently. Why these processes go from step to step isn't mysterious, it's chemistry. They don't 'know' anything - they react to their environment. And when they've 1 billion years of random changes to get here with slight deviations in each generation with failures being excluded from continuing in the process, it stands to reason that the ensuing molecules and accompanying processes might be really complex.
Amino-Acyl tRNA synthetase is an enzyme needed for the SYNTHESIS of proteins
enzymes are complex proteins
Then how was Amino-Acyl tRNA synthetase originally made?
It was probably a ribozyme doing it at first, with it slowly being replaced by an enzyme because they're generally more efficient.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
To say these molecules are 'dumb' is the same as saying my table is not fit for presidency: a thoroughly useless statement. Molecules do what they do because of their physical properties.
Ok good. Work with me here. Let's go through molecular properties.
--disproportionate polarities due to varying electronegativities.
--valence shell completions.
--differences in atomic size
--different bond types (ionic, covalent, metallic)
--hybridized electron cloud orbitals.
--dipole moments
--resonance of internal bonds therein.
Now let's go from that.
To the biochemical symphony that is DNA replication.
How does DNA Gyrase know how to relieve the supercoiling tension of the DNA molecule?
Note that this question is both leading and doesn't make any sense. Molecules are not intelligent beings -- they don't "know how" to do things. They operate in a "mundane" fashion in accordance with the rules of physics and chemistry, so if you want to know why a molecule does something, don't look to a will or an intelligence which cannot be present within the molecule.
If you train yourself not to think this way, you will at least ask better questions, if not get better answers.
How can a molecule sense when another molecule's (in this case DNA's), torsional tension is too high?
This is a better question. Not being a molecular biologist myself, I don't know the first thing about how gyrase works, but I had a look at the wikipedia page that you linked. If it is to believed, the mechanism of action is not known with anything approaching certainty. There is an as yet unproven hypothesis on the table that the mechanism is mechanochemical. (i.e. the torsion of the DNA mechanically causes the bound gyrase molecule's bonds to shift in such a way as to change its chemical properties in the expected fashion)
Do you have evidence weighing against this hypothesis? Do you have another hypothesis to offer?
Amino-Acyl tRNA synthetase is an enzyme needed for the SYNTHESIS of proteins
enzymes are complex proteins
Then how was Amino-Acyl tRNA synthetase originally made?
It was probably a ribozyme doing it at first, with it slowly being replaced by an enzyme because they're generally more efficient.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
To say these molecules are 'dumb' is the same as saying my table is not fit for presidency: a thoroughly useless statement. Molecules do what they do because of their physical properties.
Ok good. Work with me here. Let's go through molecular properties.
--disproportionate polarities due to varying electronegativities.
--valence shell completions.
--differences in atomic size
--different bond types (ionic, covalent, metallic)
--hybridized electron cloud orbitals.
--dipole moments
--resonance of internal bonds therein.
Now let's go from that.
To the biochemical symphony that is DNA replication.
So, basically: irreducible complexity + argument from ignorance?
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We have laboured long to build a heaven, only to find it populated with horrors.
To be honest, I probably put this in the wrong section. It belongs in a science section if we have one.
But what I was trying to say was evolution tends to fill a void of explanation for many in religion, when really perhaps the greater complexity that needed the void filled was biochemical processes.
I'd like to point out that every single one of you has pretty much avoided addressing any of the point's im making. It's so much easier to try to attack what you think is my purpose, my rationale for why i posted, my motives, etc.
I'd like to point out that every single one of you has pretty much avoided addressing any of the point's im making.
Your initial post doesn't bring up any points. It says "I read a bunch of stuff and there's a ton of things that are still unexplained." Then you finish with:
How does DNA Gyrase know how to relieve the supercoiling tension of the DNA molecule?
Note that this question is both leading and doesn't make any sense. Molecules are not intelligent beings -- they don't "know how" to do things. They operate in a "mundane" fashion in accordance with the rules of physics and chemistry, so if you want to know why a molecule does something, don't look to a will or an intelligence which cannot be present within the molecule.
If you train yourself not to think this way, you will at least ask better questions, if not get better answers.
How can a molecule sense when another molecule's (in this case DNA's), torsional tension is too high?
This is a better question. Not being a molecular biologist myself, I don't know the first thing about how gyrase works, but I had a look at the wikipedia page that you linked. If it is to believed, the mechanism of action is not known with anything approaching certainty. There is an as yet unproven hypothesis on the table that the mechanism is mechanochemical. (i.e. the torsion of the DNA mechanically causes the bound gyrase molecule's bonds to shift in such a way as to change its chemical properties in the expected fashion)
Do you have evidence weighing against this hypothesis? Do you have another hypothesis to offer?
The hypothesis offered is the one that must be proven before it is accepted.
So the onus is not on me to offer a counter-hypothesis.
The argument of course makes sense and is necessary. In other words, if topoisomerase and DNA gyrase work to relieve torsional tension, then there must be some means of detection said tension.
But this is really controversial and new. Our currently understanding of molecular bonding typically doesn't account for this. Mechanical tension at the quantum level? We're talking about bonds here.
We do have some knowledge about secondary and tertiary structures of enzymes whose bonding properties may change. After all Allostery is well known.
it's also true that we do keep in mind the torsional potential energy of some covalent bonds, but this again is the torsion of a DNA helix, not a single bond.
At the end of the day, conformational changes in the DNA molecule will probably be the method by which these topoisomerases work. That's a guess of course, but I wouldnt be surprised if it turned out to be that way.
Nevertheless, at the end of the day, we're left again with a patchwork explanation never seeming to address to broader question of the systemic interactivity of each molecular actor in concert.
I've been seeking a better answer, but it appears that the best anyone can give is simply "life evolved that way" due to macroscopic survival pressures.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
If that's not begging the question, I don't know what is.[/QUOTE]
I think you probably don't know what begging the question is then.
Begging the question is circularity of logic in which the point sought to be made is assumed. I wasn't seeking to make any logical point with that statement.
I was seeking to ask a question. It cannot possibly be begging the question, because the statement is not even a part of any kind of argument.
I think you probably don't know what begging the question is then.
Begging the question is circularity of logic in which the point sought to be made is assumed. I wasn't seeking to make any logical point with that statement.
You're right, I used the wrong phrase. I'm not sure what phrase I need to use. I'll try to spell out how I'm feeling.
I think you probably don't know what begging the question is then.
Begging the question is circularity of logic in which the point sought to be made is assumed. I wasn't seeking to make any logical point with that statement.
You're right, I used the wrong phrase. I'm not sure what phrase I need to use. I'll try to spell out how I'm feeling.
I know you didn't outright ask such a question. It would be pretty stupid to do it like that. That doesn't change what it looks like, and how people react to it. It's worded in a way that might as well have been "Sure looks like God did it, right?" so people are going to treat you as if you did.
This thread would probably have been better served in science thread, but to my knowledge we dont have one.
I think the problem is there's hardly any discussion to be had. I mean, this is the full extent of the conversation we can have on the subject:
"This stuff sure is complicated."
"Yeah, most of it is stuff science can't even answer yet."
"Well, there's this one guy who has a hypothesis."
"Ok. I guess we'll wait until he tests it."
Done.
That's all we've got. Anything else will be speculation, not science. That's why this is so easy to come across as a "I don't know, therefore God" kind of discussion.
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"[Screw] you and the green you ramped in on." - My EDH battle cry. If I had one. Which I don't.
I think you probably don't know what begging the question is then.
Begging the question is circularity of logic in which the point sought to be made is assumed. I wasn't seeking to make any logical point with that statement.
You're right, I used the wrong phrase. I'm not sure what phrase I need to use. I'll try to spell out how I'm feeling.
Yes, you were seeking to ask a question that you didn't actually type. The question you typed was meant only to imply another question.
"Sure looks like God did it, right?"
That's what I see in your initial post.
Then that was my fault. Everyone assumed that I asked
"Sure looks like God did it, right?"
In fact I asked no such question. This thread would probably have been better served in science thread, but to my knowledge we dont have one.
I did want to point out the explanatory gap with evolution however being less troublesome than any that may arise from biochemical processes.
I'd say that it's less of a catch-all and more of a working hypothesis. We know that evolution works, so why not assume that this machinery was conceived the same way until evidence is found otherwise? If you want, I could detail some stuff about research into RNA-world to DNA world and do some highly suspicious theorycrafting as to the workings of some of the other components.
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We have laboured long to build a heaven, only to find it populated with horrors.
What always bothered me a lot more was studying genetics, and biochemical reactions.
I was reading about Amino-Acyl tRNA synthetase the other day, and really its when I get lost in this world that I think to myself, there is a whole universe of complexity that science has yet to explain.
Amino-Acyl tRNA synthetase is an enzyme which basically brings the proper amino acid, to a particular piece of tRNA.
Once combined with tRNA or "charged", this charged tRNA's will then be used to create proteins.
The process of creating a protein involves a specific portion of the tRNA known as an anti-codon mapping to a portion of the mRNA, the codon.
Succesive tRNAs will attach to the mRNA in a unit known as a ribosome. These successive tRNA's will have their amino acid groups interact with each other to form peptide bonds, which of course are the constituent of proteins.
For anyone who has studied science, does it bother anyone that "dumb" molecules always seem to know what to do?
candidus inperti; si nil, his utere mecum.
Evolutionary theory is not an attempt to prove or disprove God or gods. The problem is that the time scale needed for evolution is incompatible with a literal reading of the Bible.
I will echo Blinking Spirit's comment. The "God of the gaps" is incredibly weak position from which to base your argument.
This assumes that it takes intelligence to form atomic and molecular bonds. Atoms and molecules bond when and where ever they can. Through random bonding it's not implausible to believe that amino acids may form.
Now, I'm just a nurse and I just have a basic understanding of what they taught us in organic chem. I'm not claiming to be an expert here.
Art is life itself.
Izuki, you're a botanist right?
This should be your cup of tea--at least background wise. You've read the myriad of chemical reactions, the ridiculously complex biochemical machinery.
There's a difference between telling someone "it's complex" and for someone who has been in the field to know oh yeah..."it's complex"
Sure science may be lacking some answers, but as far as we know, these are molecules that interact with basic forces---electronegativity and completion of valence shells, london dispersion forces, dipole interactions---nothing more than a bunch of orbitals and charges pushing and pulling each other.
And it's hard to conceive how this could have come together because we're at the level of fundamentality where there really isn't much more there. It's a molecule for God's sake, not a complex system.
It's not like you can explain away complex molecular behavior by virtue of its structure---maybe at the Sn1 nucleophilic substitution level you can....but at the transcription/translation level? Unwinding the DNA from chromosomes bundled with the histones? Undoing the condensed DNA and replicating both sides with two different mechanisms?? (okazaki fragments and straight up base pairing?)
We're talking about the orchestrated interaction of complexes of over a hundred biochemical molecules in some catalytic enzymes. Biochemical reactions that "know" when the DNA is wrong, and will reverse the whole process before starting over again.
Dumb molecules that "know" when the DNA has been supercoiled due to increases in tension from replication, and know where to cut the DNA to relieve the supercoiled tension.
Introns and Exons that know where to "cut" the RNA to know which protein to make, based on what? Concentrations.
Based on [This]
or this
[THIS][THAT]
------------------- = K
[THIS]
But as a scientist, have you ever asked yourself "how did this all come to be?"
Art is life itself.
Yes I know that. Basic evolution 101.
What about the biochemical machinery?
I mean, if we're going to say the stuff that doesn't replicate doesn't persist in the population, that's like saying:
How did we get here?
We got here because if we did not get here, we wouldn't be here to contemplate aforementioned question. Therefore our current existence is tautological.
True. But it doesn't address the problem.
Evolution should have nothing to do with an argument for or against God. Unless your God is the one that made everything in a literal 6 days exactly 10,000 years ago.
The argument for Evolution is for Evolution, thus is shouldn't strike you as a compelling argument for or against God. It's not meant to be.
Right. The whole point of science is that we don't have all of the answers, nor would we claim we did.
"There are many aspects of the universe that still cannot be explained satisfactorily by science; but ignorance only implies ignorance that may someday be conquered. To surrender to ignorance and call it God has always been premature, and it remains premature today."
No more than it bothers me that fire "knows" how to burn. That the oxygen molecule "knows" how to combine with the carbon to form carbon dioxide. The same way, every time.
The environment inside of living organism allow those kinds of combinations you describe to occur regularly, even though they might seem unlikely elsewhere. Do you know what those chances are? Do you know the statistical probability of the events you describe? If not, someone else does. Go find the answer.
If I might say, TomCat26, it seems to me you are looking awful hard for reasons not to believe in science. All I can say is that's a GOOD thing, assuming you don't stop. Keep digging deeper, keep trying to find that flaw, don't be satisfied until you're SURE you have it.
I know that's how I started.
None of the individual processes of cell life and replication are particularly mysterious or hard to explain; even cell replication from DNA is just a series of relatively simple chemical reactions. What's more bewildering is the particular combination of factors that led to RNA, DNA, ATP, cell walls, ion pumps, and the particular set of amino acids we use.
Be aware of singing as if you were half dead,
or half asleep:
but lift your voice with strength.
Be no more afraid of your voice now,
nor more ashamed of its being heard,
than when you sang the songs of Satan.
If a replicator (cell, molecule, body) proliferates in an environment, it will change that environment through its own success.
New/mutant replicators build on that, and change environment.
First replicator is a matter for abiogenesis/chemistry, but was probably a very simple carbon & misc.
Evolution can be strawmanned into a tautology but that misses major points.
Re: plants
Plant cells are obvious hack-jobs from multiple sources, the idea that we're looking at highly derived structures with significant lost history shouldn't be so shocking.
Re: learning
Your arguments mostly seem be personal incredulity.
If you're serious about learning biology, the MTGS forums isn't the best place to ask.
Art is life itself.
enzymes are complex proteins
Then how was Amino-Acyl tRNA synthetase originally made?
Make the white queen run so fast, she hasn't got time to make you wise.
Pilot of the storm who leaves no trace, like thoughts inside a dream.
Doctor, my eyes, tell me what you see. I hear their cries... just say if it's too late for me.
Doctor, my eyes...cannot see the sky. Is this the prize for having learned how not to cry?
How does DNA Gyrase & Topoisomerase know how to relieve the supercoiling tension of the DNA molecule?
How can a molecule sense when another molecule's (in this case DNA's), torsional tension is too high?
For those of you who don't understand the science here, let me explain it to you:
DNA replicates. As you know it is a double stranded helix. In order to replicate this DNA, the helix must be unwound, and the DNA begins replication at a site known as a replication fork. As this DNA is further unwound, the rest of the DNA's coil, the helix is compressed increasing the tension in the DNA molecule.
Like trying to unzip a braided rope, the rope's helical structure will become compressed as the DNA attempts to replicate. Something is required to relieve this tension. Enter DNA gyrase, which knows how to cut the DNA in a manner to relieve the super coiling tension.
So let's get back to why biomolecular evolution is insufficient:
You're saying look: molecules replicate, the ones that don't replicate wouldn't be here.
My response is: that's great, and I understand that. But what about this biomechanical mechanism in particular? Are we just sticking to the tautological evolutionary answer?
The ability of these non-sentient molecules to act with orchestrated purpose in concert with easily 100 different actors is nothing short of miraculous. I didn't list the other molecules at play in this process. But I could. DNA gyrase is but one actor in the role of my example here---DNA replication.
Like a conductor playing a symphony, each molecule works with the biomechanical machinery in the right place, at the right time, with the right amount of chemical activity.
It was probably a ribozyme doing it at first, with it slowly being replaced by an enzyme because they're generally more efficient.
To say these molecules are 'dumb' is the same as saying my table is not fit for presidency: a thoroughly useless statement. Molecules do what they do because of their physical properties.
Let's say we start out with a plank. On that plank, we can carry more food than we would've been able to by hand. We take a piece of string to pull the plank forward. We find that putting logs under the plank allows us to pull with significantly less difficulty than before. We keep adding stuff to this, reusing parts in new ways and refining it. In the end, we have a car. Now, do we say about a car that it's miraculous that a bunch of non-sentient molecules which allow us to move fast from one location to the others ?
Life is a series of chemical processes - when the chemistry changes, the complex molecules that are proteins interact differently. Why these processes go from step to step isn't mysterious, it's chemistry. They don't 'know' anything - they react to their environment. And when they've 1 billion years of random changes to get here with slight deviations in each generation with failures being excluded from continuing in the process, it stands to reason that the ensuing molecules and accompanying processes might be really complex.
Ok good. Work with me here. Let's go through molecular properties.
--disproportionate polarities due to varying electronegativities.
--valence shell completions.
--differences in atomic size
--different bond types (ionic, covalent, metallic)
--hybridized electron cloud orbitals.
--dipole moments
--resonance of internal bonds therein.
Now let's go from that.
To the biochemical symphony that is DNA replication.
Note that this question is both leading and doesn't make any sense. Molecules are not intelligent beings -- they don't "know how" to do things. They operate in a "mundane" fashion in accordance with the rules of physics and chemistry, so if you want to know why a molecule does something, don't look to a will or an intelligence which cannot be present within the molecule.
If you train yourself not to think this way, you will at least ask better questions, if not get better answers.
This is a better question. Not being a molecular biologist myself, I don't know the first thing about how gyrase works, but I had a look at the wikipedia page that you linked. If it is to believed, the mechanism of action is not known with anything approaching certainty. There is an as yet unproven hypothesis on the table that the mechanism is mechanochemical. (i.e. the torsion of the DNA mechanically causes the bound gyrase molecule's bonds to shift in such a way as to change its chemical properties in the expected fashion)
Do you have evidence weighing against this hypothesis? Do you have another hypothesis to offer?
Which if thou dost not use for clearing away the clouds from thy mind
It will go and thou wilt go, never to return.
So, basically: irreducible complexity + argument from ignorance?
I don't know, therefore God.
It's like you all think I'm an idiot.
To be honest, I probably put this in the wrong section. It belongs in a science section if we have one.
But what I was trying to say was evolution tends to fill a void of explanation for many in religion, when really perhaps the greater complexity that needed the void filled was biochemical processes.
I'd like to point out that every single one of you has pretty much avoided addressing any of the point's im making. It's so much easier to try to attack what you think is my purpose, my rationale for why i posted, my motives, etc.
exception: Crashing00 did.
Because this is exactly what it sounds like. I mean, you started with this:
What are we supposed to think?
Your initial post doesn't bring up any points. It says "I read a bunch of stuff and there's a ton of things that are still unexplained." Then you finish with:
If that's not begging the question, I don't know what is.
Pristaxcontrombmodruu!
The hypothesis offered is the one that must be proven before it is accepted.
So the onus is not on me to offer a counter-hypothesis.
The argument of course makes sense and is necessary. In other words, if topoisomerase and DNA gyrase work to relieve torsional tension, then there must be some means of detection said tension.
But this is really controversial and new. Our currently understanding of molecular bonding typically doesn't account for this. Mechanical tension at the quantum level? We're talking about bonds here.
We do have some knowledge about secondary and tertiary structures of enzymes whose bonding properties may change. After all Allostery is well known.
it's also true that we do keep in mind the torsional potential energy of some covalent bonds, but this again is the torsion of a DNA helix, not a single bond.
At the end of the day, conformational changes in the DNA molecule will probably be the method by which these topoisomerases work. That's a guess of course, but I wouldnt be surprised if it turned out to be that way.
Nevertheless, at the end of the day, we're left again with a patchwork explanation never seeming to address to broader question of the systemic interactivity of each molecular actor in concert.
I've been seeking a better answer, but it appears that the best anyone can give is simply "life evolved that way" due to macroscopic survival pressures.
If that's not begging the question, I don't know what is.[/QUOTE]
I think you probably don't know what begging the question is then.
Begging the question is circularity of logic in which the point sought to be made is assumed. I wasn't seeking to make any logical point with that statement.
I was seeking to ask a question. It cannot possibly be begging the question, because the statement is not even a part of any kind of argument.
It's a pure interrogatory.
You're right, I used the wrong phrase. I'm not sure what phrase I need to use. I'll try to spell out how I'm feeling.
Yes, you were seeking to ask a question that you didn't actually type. The question you typed was meant only to imply another question.
"Sure looks like God did it, right?"
That's what I see in your initial post.
Pristaxcontrombmodruu!
Then that was my fault. Everyone assumed that I asked
"Sure looks like God did it, right?"
In fact I asked no such question. This thread would probably have been better served in science thread, but to my knowledge we dont have one.
I did want to point out the explanatory gap with evolution however being less troublesome than any that may arise from biochemical processes.
I know you didn't outright ask such a question. It would be pretty stupid to do it like that. That doesn't change what it looks like, and how people react to it. It's worded in a way that might as well have been "Sure looks like God did it, right?" so people are going to treat you as if you did.
I think the problem is there's hardly any discussion to be had. I mean, this is the full extent of the conversation we can have on the subject:
"This stuff sure is complicated."
"Yeah, most of it is stuff science can't even answer yet."
"Well, there's this one guy who has a hypothesis."
"Ok. I guess we'll wait until he tests it."
Done.
That's all we've got. Anything else will be speculation, not science. That's why this is so easy to come across as a "I don't know, therefore God" kind of discussion.
Pristaxcontrombmodruu!
I'd say that it's less of a catch-all and more of a working hypothesis. We know that evolution works, so why not assume that this machinery was conceived the same way until evidence is found otherwise? If you want, I could detail some stuff about research into RNA-world to DNA world and do some highly suspicious theorycrafting as to the workings of some of the other components.