(April 9, 2016 at 1:43 pm)AAA Wrote: Maybe I'm misunderstanding you, but I think you must be lying if you say that the very complex proteins begin to appear any time we have close to the right conditions. If you're talking about naturally occurring amino acids, then that isn't the same a proteins. That's like saying we see lightning in nature, therefore computers may form if the electricity strikes the right thing in the right sequence. 

And it is reasonable to say we see a feature that is created all the time by intelligence. If we are trying to explain that same feature (irregular sequential information), then there is no reason that intelligence should not be considered as a possible cause. 

I like the cathedral example. It would be completely illogical to assume that the bricks were ordered that way on their own. They needed a designer. I realize that this wasn't the point of the example though. We can invoke unobserved scaffolding as well, but if it is not empirical to invoke unobserved processes/enzymes in order to explain how it arose. It is just as speculative as saying it all came into existence at once because we see parts that depend on each other. 

There are videos where Behe counters the mousetrap response. But I'm not overly concerned with that. Obviously there is a lot more combined brain power trying to debunk ID than to support it. But I recommend that you read Signature in the Cell. It is an excellent book about the scientific credibility of ID. 


And I've already completed genetics, and I understand how allele frequencies change in a population, but that is hardly an explanation of intricate mechanisms arising. For example I have a test monday in Biochemistry, and one of the topics is how glycogen breakdown and synthesis are inversely regulated. Simple version: Glucagon leads to cAMP which causes protein kinase A to phosphorylate both phosphoryl kinase (now active) and glycogen synthase (now inactiv). Phosphoryl kinase then phosphorylates glycogen phosphorylase (now active), which then becomes active and binds protein phosphatase 1 and degrades glycogen. When there is plenty of glucose, then glycogen phosphorylase switches to its inactive conformation which causes protein phosphatase 1(PP1) to unbind. PP1 then dephosphorylates both glycogen phosphorylase (now inactive ) and glycogen synthase (now active). This elegant mechanism ensures that glycogen breakdown and glycogen synthesis are not occurring at the same time. Failure of these mechanisms lead to pathologies, some of which are lethal. How did they reproduce before they had these mechanisms and how could it evolve without them surviving to reproduce? 

As you can see, evolving this is not the same as evolving a larger beak size (which can probably be explained just be a mutation in the consensus sequence to increase the expression of the protein that leads to beak formation). I'm not too concerned with the ID people, I was doubting all out evolution long before I discovered their arguments.

The "intricate mechanisms", such as the biosynthetic pathways you're describing, do evolve by the scaffolding example I gave, where parts function differently in their original form, but add different bits from related systems over time, often due to a duplicate gene, as I previously explained. It's neither a linear process, nor is it one that preserves the full process once bits that formed the scaffolding fall away with successive generations of that population. You're looking at a completed bridge and saying it could not be built except intact, because it only supports its own weight that way. We HAVE found the scaffolding traces, in several of Behe's early ID/IC "mousetrap" arguments, which is what I was talking about in the Kitzmiller v. Dover case... Behe tried to present the argument you're making, and they presented the papers that showed the very scaffolding you guys claim cannot/doesn't exist.

Your way of tearing down my metaphor, in order to try to imply that only intelligence can cause these chemical reactions to happen, ignores that chemical reactions do happen naturally (even though we can duplicate those reactions artificially by duplicating the conditions under which they happen-- something you've done a hundred times in your chemistry labs, by now), while brick-stacking does not. The same applies to Paley's watchmaker analogy (which ID seems to be a modern variant of), since there is no known natural pathway by which metal would even possibly form into such shapes, but we know that humans do it all the time. On the contrary, we know that naturally-occurring reactions cause organic molecules, including ones that are component materials of our cells/DNA, and have managed to duplicate the conditions under which some of those reactions occur. It's a false equivalency, and I'm a little embarrassed for people who make that argument without seeing it for what it is.

And yes, it is the same thing as evolving a larger beak size. It's still just genes, which make amino acids/proteins and direct the function of other DNA, being mutated and selected/deselected.

I mean, really, are you seriously arguing that the biosynthetic pathways you're highlighting were always as they are, today, and that there's no other possible pre-functional form? I get sick of that same argument when people try to point to the complexity of the eye, since we know the process by which eyes developed and then evolved into their modern versions. But it you take one piece out of the modern version, a result of many many many generations of changes and scaffolding, it does look like the mousetrap problem. Except it's only an illusion. Irony!

(April 8, 2016 at 11:08 pm)AAA Wrote:

(April 8, 2016 at 11:00 pm)LadyForCamus Wrote: LOL.  Except in the case for abiogenesis, right?   Because in THAT case you won't be satisfied until a protocell forms before your very eyes.  Wow.  Thank you for exposing your hypocritical approach to determining whether or not things are true.  I didn't even have to do any of the work this time.

Do you see the difference though? I have required rigorous evidence to demonstrate whether or not a designer exists. After I have concluded yes, then I don't require the rigorous evidence for the identity (although maybe you're right and I should). 

An analogy with abiogenesis would then be if we somehow used rigorous evidence to conclude that it did happen (analogous to me concluding designer above), then we would not require extreme evidence for how it happened (analogous to determining the identity). This seems to actually be what most scientists have done. Do you see the analogy I was trying to make?

I see the analogy you are trying to make, but it fails as an analogy, and it fails because it misses the point I am making to you.

In order to be intellectually honest, the methodology a person uses to determine whether or not a claim is most likely to be true should be consistent, no matter WHAT the nature of the claim. If I tell you that I flew to Paris last week, you might believe me, or you might require a bit of evidence to accept that belief. Perhaps you'll need me to show you a few photographs, or a picture of my tickets. This should suffice, as my claim is not an overly extraordinary one, and (religious stuff aside), you seem like a fairly reasonable person.

On the other hand, the claim that a God exists and designed universe is a far more extraordinary claim (which you've acknowledged) and so your requirements for evidence (or your idea of evidence) are far stricter. Therefore, in order to stay consistent and intellectually honest in regards to how you determine the likelihood of ANY claim being true, you should certainly require at LEAST the same (if not stricter) standards of evidence for the specific details about the nature of your God.


It's a moot point though, because your "scientific evidence" for a designer is not actually evidence, and so your analogy fails. "How," is what builds the case for a claim. We can tentatively throw our hats into the ring for abiogenesis as a reasonable (if speculative) hypothesis for the origin of life based on what we already know, but when scientists DO parse out the details, that mechanism of action will BE the case beyond reasonable doubt for abiogenesis as a scientific fact.

In other words, We can be reasonably certain that it happened once we can demonstrate HOW it happened. Unfortunately for your designer claim, no one yet has been able to present a single shred of detailed, positive evidence for god's mechanism of action; for HOW God designed and created the universe; for HOW he exists in the state that Christians believe he does. And we haven't even gotten to the cesspool of supernatural claims found in the scripture. Your only answer for these questions so far is, "well, he's God; he can do anything he wants," which is not an explained mechanism at all. And your "scientific evidence" for his existence in the first place is nothing more than an argument from personal incredulity; an attempt (and failure) to poke holes in scientific theory, which is not evidence for God. But this has been explained to you ad nauseam...hasn't it?

Not to mention, LFC, that if you go with the "God magically shaped molecules into DNA and proteins that make up life" hypothesis (I shudder to even call it that), you have to accept that this meddler-in-the-mud then deliberately created:

The Marburg/Ebola viruses:


Hantavirus:

(It mostly causes internal bleeding, so no pictures of the patients on this one.)

HIV/AIDS:


Need I go on? I could get into the parasitic creatures and fungal infections and bacteria/archaea, if we need to.

They think they're doing God a favor when they posit that he shaped all life's DNA by magic, but the problem is that if God used magic to deliberately shape life on earth, then he is a sick bastard. It's much kinder to God to say that evolution is the Creation process, as random and amoral as it is, and that God is not intervening in the natural world other than to save our souls after death...because if this is on purpose, then we need to catch and execute this deity for crimes against humanity. (And also the rest of the plant/animal kingdoms, all of which are similarly infected by parasitic creatures, including viruses.)

(April 9, 2016 at 2:35 pm)TheRocketSurgeon Wrote:

(April 9, 2016 at 1:43 pm)AAA Wrote: Maybe I'm misunderstanding you, but I think you must be lying if you say that the very complex proteins begin to appear any time we have close to the right conditions. If you're talking about naturally occurring amino acids, then that isn't the same a proteins. That's like saying we see lightning in nature, therefore computers may form if the electricity strikes the right thing in the right sequence. 

And it is reasonable to say we see a feature that is created all the time by intelligence. If we are trying to explain that same feature (irregular sequential information), then there is no reason that intelligence should not be considered as a possible cause. 

I like the cathedral example. It would be completely illogical to assume that the bricks were ordered that way on their own. They needed a designer. I realize that this wasn't the point of the example though. We can invoke unobserved scaffolding as well, but if it is not empirical to invoke unobserved processes/enzymes in order to explain how it arose. It is just as speculative as saying it all came into existence at once because we see parts that depend on each other. 

There are videos where Behe counters the mousetrap response. But I'm not overly concerned with that. Obviously there is a lot more combined brain power trying to debunk ID than to support it. But I recommend that you read Signature in the Cell. It is an excellent book about the scientific credibility of ID. 


And I've already completed genetics, and I understand how allele frequencies change in a population, but that is hardly an explanation of intricate mechanisms arising. For example I have a test monday in Biochemistry, and one of the topics is how glycogen breakdown and synthesis are inversely regulated. Simple version: Glucagon leads to cAMP which causes protein kinase A to phosphorylate both phosphoryl kinase (now active) and glycogen synthase (now inactiv). Phosphoryl kinase then phosphorylates glycogen phosphorylase (now active), which then becomes active and binds protein phosphatase 1 and degrades glycogen. When there is plenty of glucose, then glycogen phosphorylase switches to its inactive conformation which causes protein phosphatase 1(PP1) to unbind. PP1 then dephosphorylates both glycogen phosphorylase (now inactive ) and glycogen synthase (now active). This elegant mechanism ensures that glycogen breakdown and glycogen synthesis are not occurring at the same time. Failure of these mechanisms lead to pathologies, some of which are lethal. How did they reproduce before they had these mechanisms and how could it evolve without them surviving to reproduce? 

As you can see, evolving this is not the same as evolving a larger beak size (which can probably be explained just be a mutation in the consensus sequence to increase the expression of the protein that leads to beak formation). I'm not too concerned with the ID people, I was doubting all out evolution long before I discovered their arguments.

The "intricate mechanisms", such as the biosynthetic pathways you're describing, do evolve by the scaffolding example I gave, where parts function differently in their original form, but add different bits from related systems over time, often due to a duplicate gene, as I previously explained. It's neither a linear process, nor is it one that preserves the full process once bits that formed the scaffolding fall away with successive generations of that population. You're looking at a completed bridge and saying it could not be built except intact, because it only supports its own weight that way. We HAVE found the scaffolding traces, in several of Behe's early ID/IC "mousetrap" arguments, which is what I was talking about in the Kitzmiller v. Dover case... Behe tried to present the argument you're making, and they presented the papers that showed the very scaffolding you guys claim cannot/doesn't exist.

Your way of tearing down my metaphor, in order to try to imply that only intelligence can cause these chemical reactions to happen, ignores that chemical reactions do happen naturally (even though we can duplicate those reactions artificially by duplicating the conditions under which they happen-- something you've done a hundred times in your chemistry labs, by now), while brick-stacking does not. The same applies to Paley's watchmaker analogy (which ID seems to be a modern variant of), since there is no known natural pathway by which metal would even possibly form into such shapes, but we know that humans do it all the time. On the contrary, we know that naturally-occurring reactions cause organic molecules, including ones that are component materials of our cells/DNA, and have managed to duplicate the conditions under which some of those reactions occur. It's a false equivalency, and I'm a little embarrassed for people who make that argument without seeing it for what it is.

And yes, it is the same thing as evolving a larger beak size. It's still just genes, which make amino acids/proteins and direct the function of other DNA, being mutated and selected/deselected.

I mean, really, are you seriously arguing that the biosynthetic pathways you're highlighting were always as they are, today, and that there's no other possible pre-functional form? I get sick of that same argument when people try to point to the complexity of the eye, since we know the process by which eyes developed and then evolved into their modern versions. But it you take one piece out of the modern version, a result of many many many generations of changes and scaffolding, it does look like the mousetrap problem. Except it's only an illusion. Irony!

I know how they theorized it happens, but just assuming the scaffolding that you're talking about ever existed is highly speculative. How did the enzymes get there? 'well other enzymes that were less developed morphed into them over time'. How did it survive before it had a mechanism to accomplish the regulation? 'well these other enzymes could regulate it too, but they were simpler and less intricate'. I read an article a few weeks ago about how catalytic promiscuity may aid enzymes in their evolution. One of the many speculations that they made were that enzymes with < 10% amino acid similarity were closely related because they shared the sequence for an active site. 


And I genuinely have no idea what you are talking about with the chemical reactions done hundreds of times to show polypeptide formation. Forming nucleotides or amino acids is NOT the same or equivalent to forming a functional sequence of them. And nobody is saying that you couldn't simplify the biochemical pathway a little, but you would really have to do some mental gymnastics to try to get it reasonably simple for the mechanisms of evolution to be sufficient.

(April 9, 2016 at 3:15 pm)LadyForCamus Wrote:

(April 8, 2016 at 11:08 pm)AAA Wrote: Do you see the difference though? I have required rigorous evidence to demonstrate whether or not a designer exists. After I have concluded yes, then I don't require the rigorous evidence for the identity (although maybe you're right and I should). 

An analogy with abiogenesis would then be if we somehow used rigorous evidence to conclude that it did happen (analogous to me concluding designer above), then we would not require extreme evidence for how it happened (analogous to determining the identity). This seems to actually be what most scientists have done. Do you see the analogy I was trying to make?

I see the analogy you are trying to make, but it fails as an analogy, and it fails because it misses the point I am making to you.  

In order to be intellectually honest, the methodology a person uses to determine whether or not a claim is most likely to be true should be consistent, no matter WHAT the nature of the claim.  If I tell you that I flew to Paris last week, you might believe me, or you might require a bit of evidence to accept that belief.  Perhaps you'll need me to show you a few photographs, or a picture of my tickets.  This should suffice, as my claim is not an overly extraordinary one, and (religious stuff aside), you seem like a fairly reasonable person.  

On the other hand, the claim that a God exists and designed universe is a far more extraordinary claim (which you've acknowledged) and so your requirements for evidence (or your idea of evidence) are far stricter.  Therefore, in order to stay consistent and intellectually honest in regards to how you determine the likelihood of ANY claim being true, you should certainly require at LEAST the same (if not stricter) standards of evidence for the specific details about the nature of your God.


It's a moot point though, because your "scientific evidence" for a designer is not actually evidence, and so your analogy fails.  "How," is what builds the case for a claim.  We can tentatively throw our hats into the ring for abiogenesis as a reasonable (if speculative) hypothesis for the origin of life based on what we already know, but when scientists DO parse out the details, that mechanism of action will BE the case beyond reasonable doubt for abiogenesis as a scientific fact.

In other words, We can be reasonably certain that it happened once we can demonstrate HOW it happened.  Unfortunately for your designer claim, no one yet has been able to present a single shred of detailed, positive evidence for god's mechanism of action; for HOW God designed and created the universe; for HOW he exists in the state that Christians believe he does.  And we haven't even gotten to the cesspool of supernatural claims found in the scripture.  Your only answer for these questions so far is, "well, he's God; he can do anything he wants," which is not an explained mechanism at all.  And your "scientific evidence" for his existence in the first place is nothing more than an argument from personal incredulity; an attempt (and failure) to poke holes in scientific theory, which is not evidence for God.  But this has been explained to you ad nauseam...hasn't it?

I don't think you necessarily need stricter evidence for the identity than whether there is a designer or not. I am not overly concerned with who the designer is, but I am more concerned with if there is one in the first place. I don't know why, that's just the question that interests me more. But you're right, I will examine the identity more carefully.

(April 9, 2016 at 4:54 pm)TheRocketSurgeon Wrote: Not to mention, LFC, that if you go with the "God magically shaped molecules into DNA and proteins that make up life" hypothesis (I shudder to even call it that), you have to accept that this meddler-in-the-mud then deliberately created:

The Marburg/Ebola viruses:


Hantavirus:

(It mostly causes internal bleeding, so no pictures of the patients on this one.)

HIV/AIDS:


Need I go on? I could get into the parasitic creatures and fungal infections and bacteria/archaea, if we need to.

They think they're doing God a favor when they posit that he shaped all life's DNA by magic, but the problem is that if God used magic to deliberately shape life on earth, then he is a sick bastard. It's much kinder to God to say that evolution is the Creation process, as random and amoral as it is, and that God is not intervening in the natural world other than to save our souls after death...because if this is on purpose, then we need to catch and execute this deity for crimes against humanity. (And also the rest of the plant/animal kingdoms, all of which are similarly infected by parasitic creatures, including viruses.)

Yeah, no kidding! Some design, eh? So, either God couldn't have done any better than what we've got, or he chose not to for whatever reason. Either way...what a fucktard...

As bad as viruses can be, it turns out that they may be the 'missing link'.

A scientist proposes the hypothesis that viruses have helped to drive evolution by adding to the DNA chain.





Agent Smith may be right.

(April 9, 2016 at 4:54 pm)TheRocketSurgeon Wrote: Need I go on? I could get into the parasitic creatures and fungal infections and bacteria/archaea, if we need to.

They think they're doing God a favor when they posit that he shaped all life's DNA by magic, but the problem is that if God used magic to deliberately shape life on earth, then he is a sick bastard. It's much kinder to God to say that evolution is the Creation process, as random and amoral as it is, and that God is not intervening in the natural world other than to save our souls after death...because if this is on purpose, then we need to catch and execute this deity for crimes against humanity. (And also the rest of the plant/animal kingdoms, all of which are similarly infected by parasitic creatures, including viruses.)

Read your recent comments and I really feel like I have a better understanding of the material thanks very much. I do have a question to your above quote (I deleted the images, didn't wana spam the thread).

Do we have evidence of small things, like bacteria and viruses evolving? I mean, don't they see how the flu virus changes in order to make the vaccine each year?

(April 9, 2016 at 8:15 pm)Goosebump Wrote:

(April 9, 2016 at 4:54 pm)TheRocketSurgeon Wrote: Need I go on? I could get into the parasitic creatures and fungal infections and bacteria/archaea, if we need to.

They think they're doing God a favor when they posit that he shaped all life's DNA by magic, but the problem is that if God used magic to deliberately shape life on earth, then he is a sick bastard. It's much kinder to God to say that evolution is the Creation process, as random and amoral as it is, and that God is not intervening in the natural world other than to save our souls after death...because if this is on purpose, then we need to catch and execute this deity for crimes against humanity. (And also the rest of the plant/animal kingdoms, all of which are similarly infected by parasitic creatures, including viruses.)

Read your recent comments and I really feel like I have a better understanding of the material thanks very much. I do have a question to your above quote (I deleted the images, didn't wana spam the thread).

Do we have evidence of small things, like bacteria and viruses evolving? I mean, don't they see how the flu virus changes in order to make the vaccine each year?

Archaea and Bacteria (which constituted all of life on earth for roughly the first 3/4ths of its existence) are observed to evolve all the time. An excellent example is the bacteria which evolved a biosynthetic pathway that allows them to "digest" (use metabolically) nylon, an artificial substance that didn't exist before 1935. https://en.wikipedia.org/wiki/Nylon-eating_bacteria

The evolution of bacteria under the fierce Natural Selection pressures imposed by our antibiotics has become a major issue in hospitals, as resistant strains of Staphylococcus aureus (among others) have become effectively immune to anything we can throw at them. https://en.wikipedia.org/wiki/Methicilli...cus_aureus

As you noted, viruses evolve quite rapidly, due to the relative simplicity of their genomes, but we understand their evolutionary pathways pretty well--that's what the numbers in the H1N1 (etc.) Influenza virus refer to. In fact, because the Flu virus evolves as it moves from its origin in birds to pigs to humans, we look at the genome of the virus that appears each year in order to get ahead of manufacturing a vaccine that will impact the human version when it emerges. Sometimes we get it partially wrong, as occurred a couple of years ago, and the companies must scramble to make enough of the "right" version. It's why you must get a new flu shot every year; the old one usually won't work on next year's version, because it will have evolved.

It's also one of the major reasons people still die of HIV, despite highly-effective antiviral medicines; the virus population "learns" (by the deaths of those that have the wrong genome to resist the medication, leaving only the resistant ones to breed) to resist the cocktail being taken by the patient.

(April 9, 2016 at 10:09 pm)TheRocketSurgeon Wrote: The evolution of bacteria under the fierce Natural Selection pressures imposed by our antibiotics has become a major issue in hospitals, as resistant strains of Staphylococcus aureus (among others) have become effectively immune to anything we can throw at them. https://en.wikipedia.org/wiki/Methicilli...cus_aureus

As you noted, viruses evolve quite rapidly, due to the relative simplicity of their genomes, but we understand their evolutionary pathways pretty well--that's what the numbers in the H1N1 (etc.) Influenza virus refer to. In fact, because the Flu virus evolves as it moves from its origin in birds to pigs to humans, we look at the genome of the virus that appears each year in order to get ahead of manufacturing a vaccine that will impact the human version when it emerges. Sometimes we get it partially wrong, as occurred a couple of years ago, and the companies must scramble to make enough of the "right" version. It's why you must get a new flu shot every year; the old one usually won't work on next year's version, because it will have evolved.

It's also one of the major reasons people still die of HIV, despite highly-effective antiviral medicines; the virus population "learns" (by the deaths of those that have the wrong genome to resist the medication, leaving only the resistant ones to breed) to resist the cocktail being taken by the patient.

So, isn't this good evidence of evolution? Doesn't it take the theory and put it into law? Or is that never possible? Rather, why is evolution still just a theory when we can see it now with super duper microscopes and such?