Is strict atheism a barrier to knowledge and truth?

[Starboard Tack]

In Iris Fry's book The Emergence of Life on Earth, she makes a statement that demonstrates a common, and possibly defective view of knowledge. The preamble to this statement is a complaint against people she refers to as "Creationists" who, in her opinion, pervert science to further their philosophical arguments. The context to the statement is that instead of billions of years for chemicals to self organize into life on the primordial earth, research has shown that the window has shrunk to around 10 million years, prompting those pesky "Creationists" to note that this isn't enough time for a purely naturalistic explanation for life's beginnings. The statement is this:

Notice the paradox that the findings of scientific research are seen fit, under the circumstances, to serve as evidence against science (by creationists). (page 125).

What is intriguing here is that the research simply argues against a long period of time for life to appear, and says nothing about the value of science. However, by noticing it, apparently the theists are guilty of being anti-science. This is a classic illustration of the topic I'd like to explore.

By adopting the view that a belief in God's existence and his involvement in his creation is a priori off limits, Dr. Fry believes that any suggestion that naturalistic explanation may lack explanatory power and be wrong is by definition anti-science. But is it?

God either does, or does not exist. In what form he/she/it exists is another topic, but is it not a given that there is at least a possibility, even if rejected, that he/she/it does exist?

And if it is a possibility, then by excluding supernatural involvement as a matter of philosophic dogma when trying to understand intractable problems doesn't the scientist who insists on pure naturalism guarantee that he or she may never be able to find the truth? In other words, if the existence of God is even the remotest possibility, isn't the rejection of that possibility without consideration itself anti-scientific? Directed panspermia is taken as a scientific proposition for life's origins, proposed by Nobel prize winners. Is that more scientific than the belief that the causal agent who brought the universe into existence is a personal being?

I can think of examples where scientific advancement has been stultified as a result of an insistence on a purely naturalistic understanding of the world. If so, doesn't it behoove scientists to entertain the possibility of supernatural intervention, even if only to be able to rule it out when a naturalistic explanation is found?[/i]

[nygreenguy]

A model that presumes supernatural intervention in origins would make a few predictions about DNA.First would be that the chicken and egg problem of DNA being made of proteins and proteins requiring DNA to be made will not be resolved, and no biochemical pathway that could work on early earth will be discovered that will explain it. Intelligent agents solve chicken and egg problems all the time. Happenstance, never.

This is making the assumption that early genetic mechanisms operated in the same way they do today. Currently, it seems like RNA could duplicate itself AND it could create the mechanisms for protein synthesis.
Anderson et al.J Mol Evol (2007) 64:472"483 Toward Ribosomal RNA Catalytic Activity in the Absence of Protein

So the prediction seems to fail. Sure, we havent got there yet, but the more evidence that come in supports this notion as opposed to falsifying it.

Second, genetic research will continue to identify Homo sapiens sapiens as not possessing any clear immediate ancestor from which we could have evolved. This prediction was made prior to the completion of the sequencing of the Neanderthal genome, and in that case the research confirms it. I don't know if we will recover DNA from Homo sapiens idaltu or not, but if we do, the prediction would be that it will also be shown not to be ancestrally related to us, just as Neanderthal is not considered ancestral.

Immediate? How doesnt neanderthal count?

Third, as research continues, we will find increasing functionality in non-coding regions of human DNA. A corollary to this prediction is that the evolutionary expectation that useless leftover proteins from prior evolutionary ancestors will fit the data less and less, and either be replaced with a new theory or moved into the intractable problem arena.

Functionality wouldnt be direct evidence because you would need to first show thats how the creator would operate.

Actually, God didn't say that what he created was perfect, he said "good," so a creation model would not predict perfection. From the moment of creation, the genome of humans has been subject to the same laws of physics that apply everywhere else, so you will have mutations and a slow degradation of the genome over time. What you won't have is confirming evidence of the evolutionary paradigm that would dictate that large areas of the human genome would be non-functional remnants of prior forms.

Well this is just semantics! Its sort of like if I hand in a paper to the most hard butt teacher there is and if he calls it "good", that means much more than from the push over professor. So if an infinitely good being calls something "good", wouldnt it reason for it to be darn near perfection?

Perhaps that's true, although it wouldn't be unreasonable under a creation paradigm to expect that God, in whose image we are created, would create himself in ways similar to how we do things.

If god can create the universe, to even speculate on his methods is hubris to the extreme. Imagine looking at a 3 month old trying to stack blocks. It look, to be blunt, stupid. It fumbles around and struggles with simple concepts. Now lets take the infinite being again, to compare how he does stuff to how we do stuff takes my examples to an absurd extreme. We would appear less than amoeba to such a being.

We certainly find this in cellular designs, which display molecular machines and sub-optimal functionality in sub systems that in context provides optimal functionality overall.

You frequently use this saying and I am not entirely sure what you mean.

The analogy would be the balance between horsepower and gas mileage in a car. Some would argue for maximum hp, but human designers go for sub-optimal design to achieve a balance between go fast and go cheap.

Except now we have the tesla roadster which is amazingly fast and get amazing "mpg"

[Starboard Tack]

A model that presumes supernatural intervention in origins would make a few predictions about DNA.First would be that the chicken and egg problem of DNA being made of proteins and proteins requiring DNA to be made will not be resolved, and no biochemical pathway that could work on early earth will be discovered that will explain it. Intelligent agents solve chicken and egg problems all the time. Happenstance, never.

This is making the assumption that early genetic mechanisms operated in the same way they do today. Currently, it seems like RNA could duplicate itself AND it could create the mechanisms for protein synthesis.
Anderson et al.J Mol Evol (2007) 64:472"483 Toward Ribosomal RNA Catalytic Activity in the Absence of Protein

I think that if you look into the topic (I'm auditing a graduate course on OoL research now), you will see that the number of problems in the RNA world scenario are monumental. I fully expect that in the lab, exemplified by this study, we will be able to synthesize life at some point. However, the conditions in the lab are irrelevant to OoL on the early earth since there was a noticeable shortage of sterile apparatus, brilliant scientists and super computers on primordial earth.

Second, genetic research will continue to identify Homo sapiens sapiens as not possessing any clear immediate ancestor from which we could have evolved. This prediction was made prior to the completion of the sequencing of the Neanderthal genome, and in that case the research confirms it. I don't know if we will recover DNA from Homo sapiens idaltu or not, but if we do, the prediction would be that it will also be shown not to be ancestrally related to us, just as Neanderthal is not considered ancestral.

Immediate? How doesnt neanderthal count?

The Neanderthal genome has been almost entirely sequenced, and we now know they are not directly related to us, but from an evolutionary perspective, a side branch. That is why there is interest in idaltu. We don't have any genetic information on that hominid yet, however.

Third, as research continues, we will find increasing functionality in non-coding regions of human DNA. A corollary to this prediction is that the evolutionary expectation that useless leftover proteins from prior evolutionary ancestors will fit the data less and less, and either be replaced with a new theory or moved into the intractable problem arena.

Functionality wouldnt be direct evidence because you would need to first show thats how the creator would operate.

That is a higher standard of proof than you would apply to any other scientific theory because you are requiring that the theory be completely proved before allowing evidence to be admitted that supports the theory.

Actually, God didn't say that what he created was perfect, he said "good," so a creation model would not predict perfection. From the moment of creation, the genome of humans has been subject to the same laws of physics that apply everywhere else, so you will have mutations and a slow degradation of the genome over time. What you won't have is confirming evidence of the evolutionary paradigm that would dictate that large areas of the human genome would be non-functional remnants of prior forms.

Well this is just semantics! Its sort of like if I hand in a paper to the most hard butt teacher there is and if he calls it "good", that means much more than from the push over professor. So if an infinitely good being calls something "good", wouldnt it reason for it to be darn near perfection?

Words mean something. I'm not sure how good an argument it is to insist that they mean something other than what they say. Ancient Hebrew had a word for perfection, and it wasn't used to describe creation.

Perhaps that's true, although it wouldn't be unreasonable under a creation paradigm to expect that God, in whose image we are created, would create himself in ways similar to how we do things.

If god can create the universe, to even speculate on his methods is hubris to the extreme. Imagine looking at a 3 month old trying to stack blocks. It look, to be blunt, stupid. It fumbles around and struggles with simple concepts. Now lets take the infinite being again, to compare how he does stuff to how we do stuff takes my examples to an absurd extreme. We would appear less than amoeba to such a being.

However, this isn't just any infinite being. This is a being that cares enough for mankind to become one of us for the purposes of providing for our salvation. We know we can't understand his thoughts, but since he created us in his image and shows so much interest in us, it should not be a stretch to assume that part of being created in that image is an inclination to build things just like he would. Support for this is the existence of molecular machines that appear to be built along the precise same principals of mechanical design men use. Check out bacterial flagella, or brownian motors.

We certainly find this in cellular designs, which display molecular machines and sub-optimal functionality in sub systems that in context provides optimal functionality overall.

You frequently use this saying and I am not entirely sure what you mean.

Many cellular metabolic functions could occur faster, but if they did, it would compromise other function that is critical. For example the enzyme RuBisCo that is involved in CO2 metabolism operates very slowly, but if it sped up, its ability to differentiate between CO2 and not CO2 has been shown to be compromised, with detrimental effects. This is an example of sub-optimal design where a component could be optimized for one function at a cost to the overall functionality. A classic example of this is in sailboat racing. Masts are taller but very lightweight. They are dismasted routinely, but the trade off is lighter weight for more speed, requiring more care in keeping the darn thing erect. They could be made even lighter, with an increase in dismastings, or made heavier with a decrease in dismastings but at a cost of speed. The mast is sub-optimally designed, but overall is in balance when both speed and strength are considered. This kind of balance is characteristic of designed systems, and we see the same thing in cellular systems.

Except now we have the tesla roadster which is amazingly fast and get amazing "mpg"

And if you look at it, it will probably be light weight, meaning good gas mileage but don't run it into walls.

[nygreenguy]

I think that if you look into the topic (I'm auditing a graduate course on OoL research now), you will see that the number of problems in the RNA world scenario are monumental. I fully expect that in the lab, exemplified by this study, we will be able to synthesize life at some point. However, the conditions in the lab are irrelevant to OoL on the early earth since there was a noticeable shortage of sterile apparatus, brilliant scientists and super computers on primordial earth.

If you have covered any interesting papers in that course, I would love to see some!

Also, the fact that people are recreating it has nothing to do with early earth. We are recreating the possible circumstances, based upon the evidence we have.

The Neanderthal genome has been almost entirely sequenced, and we now know they are not directly related to us, but from an evolutionary perspective, a side branch. That is why there is interest in idaltu. We don't have any genetic information on that hominid yet, however.

The problem with that is I believe you are asking for something which, from a genetics standpoint, doesnt make sense. If we could step back and watch evolution from beginning to end, we could (almost) never pick out immediate direct ancestors. To us, it would simply appear as a gradual change. It is like examining a rainbow up close. Yes, its easy to point out yellow, red, blue BUT if you get really close when does red become "not" red? Where does orange stop and yellow begin? We can only classify things as species when they become sufficiently different, our most immediate ancestor would be nearly indistinguishable from a primitive human.

Third, as research continues, we will find increasing functionality in non-coding regions of human DNA. A corollary to this prediction is that the evolutionary expectation that useless leftover proteins from prior evolutionary ancestors will fit the data less and less, and either be replaced with a new theory or moved into the intractable problem arena.

Functionality wouldnt be direct evidence because you would need to first show thats how the creator would operate.

That is a higher standard of proof than you would apply to any other scientific theory because you are requiring that the theory be completely proved before allowing evidence to be admitted that supports the theory.

Absolutely not. With natural selection, Darwin observed animals with different characteristics and noted those characteristics led to differential breeding success. From there, he proposed that this could lead to a shift in traits in the population. He started with an observation, from what was known, and built from there. His theory was open to more observation and testing.

With yours, you are speculating on an unknown agent being the driving cause. You are also speculating on the properties of that agent. Additionally, we have the false dichotomy fallacy, where if this part of science is wrong, then God. Also, it would appear that your evidence here is unfalsifiable. Even if we never find ANY more function for these pseudogenes, you can still say "we just havent found it" or you can say "thats what the creator decided"

Words mean something. I'm not sure how good an argument it is to insist that they mean something other than what they say. Ancient Hebrew had a word for perfection, and it wasn't used to describe creation.

I never claimed it meant perfection. I used my comparison to show relative meaning of "good"

However, this isn't just any infinite being. This is a being that cares enough for mankind to become one of us for the purposes of providing for our salvation.

More speculation.

We know we can't understand his thoughts, but since he created us in his image and shows so much interest in us, it should not be a stretch to assume that part of being created in that image is an inclination to build things just like he would.

You so quickly dismiss OoL research and abiogenesis, yet have no problem accepting these propositions?

Support for this is the existence of molecular machines that appear to be built along the precise same principals of mechanical design men use. Check out bacterial flagella, or brownian motors.

The flagella operate nothing like machines we use.

Many cellular metabolic functions could occur faster, but if they did, it would compromise other function that is critical. For example the enzyme RuBisCo that is involved in CO2 metabolism operates very slowly, but if it sped up, its ability to differentiate between CO2 and not CO2 has been shown to be compromised, with detrimental effects. This is an example of sub-optimal design where a component could be optimized for one function at a cost to the overall functionality.

Yet we still have C4 plants which use pep carboxylase which is FAR more efficient. So we have 2 (3 if we count CAM) different systems, with varying levels of efficiency, all made by the same creator?

And if you look at it, it will probably be light weight, meaning good gas mileage but don't run it into walls.

It is electric which is why it is so fast, has minimal emissions, is as safe as any comparable car. See, humans can get rid of inefficiencies. We can overcome them with knowledge and technology. It appears we are becoming better designers than god.

[Starboard Tack]

I think that if you look into the topic (I'm auditing a graduate course on OoL research now), you will see that the number of problems in the RNA world scenario are monumental. I fully expect that in the lab, exemplified by this study, we will be able to synthesize life at some point. However, the conditions in the lab are irrelevant to OoL on the early earth since there was a noticeable shortage of sterile apparatus, brilliant scientists and super computers on primordial earth.

If you have covered any interesting papers in that course, I would love to see some!

The reading list is pretty interesting. Paul Davies "The Fifth Miracle", Iris Fry's "The Emergence of Life on Earth", William Schopf "Life's Origins" are all by agnostics and atheists. Fazale Rana's "Creating Life in the Lab" and "Origins of Life" present the science from a bio-chemical and theistic perspective. There are lectures, interviews with notable bio-chemists like Robert Shapiro who is an agnostic and a major pain in the rear for RNA world fans.

Also, the fact that people are recreating it has nothing to do with early earth. We are recreating the possible circumstances, based upon the evidence we have.

Yes, and that is essential. First you have to understand how it might have happened, but for it to have relevance to the OoL question is has to be able to happen on the early earth. That is where the research is really running aground. You can synthesize organics molecules, but you can't do so unless you provide significant oversight of the process under conditions no one thinks could be replicated in the wild.

The Neanderthal genome has been almost entirely sequenced, and we now know they are not directly related to us, but from an evolutionary perspective, a side branch. That is why there is interest in idaltu. We don't have any genetic information on that hominid yet, however.

The problem with that is I believe you are asking for something which, from a genetics standpoint, doesnt make sense. If we could step back and watch evolution from beginning to end, we could (almost) never pick out immediate direct ancestors. To us, it would simply appear as a gradual change. It is like examining a rainbow up close. Yes, its easy to point out yellow, red, blue BUT if you get really close when does red become "not" red? Where does orange stop and yellow begin? We can only classify things as species when they become sufficiently different, our most immediate ancestor would be nearly indistinguishable from a primitive human.

That would not be the view of the geneticists. There was just a bio-chemical discovery that indicates that the current understanding of the relationship between archea, bacteria and eukaryotic life is probably wrong, and that the last common ancestor, contrary to predictions of evolutionary science was far more complex than previously imagined. http://www.sciencedaily.com/releases/20 ... 112145.htm

The same people can look at the neanderthal genome and conclude that we are not directly related to them, meaning from an evolutionary standpoint there has to have been a very recent precedent ancestor to use kicking around 50,000 - 100,000 years that could be our ancestor. They haven't found that critter, but we can say that neanderthal isn't a direct ancestor to us.

With yours, you are speculating on an unknown agent being the driving cause. You are also speculating on the properties of that agent. Additionally, we have the false dichotomy fallacy, where if this part of science is wrong, then God. Also, it would appear that your evidence here is unfalsifiable. Even if we never find ANY more function for these pseudogenes, you can still say "we just havent found it" or you can say "thats what the creator decided"

No, I would never use the "science in the gaps" defense.... If we don't find function in the pseudogenes, that would support evolutionary biology, since that is what is predicted. If we do, it doesn't support that theory but would be consistent with my predictions. Let the research continue and see what happens.

Words mean something. I'm not sure how good an argument it is to insist that they mean something other than what they say. Ancient Hebrew had a word for perfection, and it wasn't used to describe creation.

I never claimed it meant perfection. I used my comparison to show relative meaning of "good"

However, this isn't just any infinite being. This is a being that cares enough for mankind to become one of us for the purposes of providing for our salvation.

More speculation.

There is no reasonable speculation regarding whether Jesus Christ existed, and no reasonable speculation that he claimed to be God. Whether he was or not is dependent on other factors.

We know we can't understand his thoughts, but since he created us in his image and shows so much interest in us, it should not be a stretch to assume that part of being created in that image is an inclination to build things just like he would.

You so quickly dismiss OoL research and abiogenesis, yet have no problem accepting these propositions?

I haven't dismissed OoL research, I am merely pointing out what the researchers are saying. You have 10 million years or so for life to appear and no explanation on how it could have happened on the early earth even though we have been studying the problem with years with smart people and big budgets. I take my understanding of what Scripture means when it talks about the Imago dei from the orthodox interpretation of that concept developed over 3,500 years. It could be wrong, but it certainly has a basis.

Support for this is the existence of molecular machines that appear to be built along the precise same principals of mechanical design men use. Check out bacterial flagella, or brownian motors.

The flagella operate nothing like machines we use.

Quite wrong. They are a rotary motor complete with ball bearings. "Each of the outer 9 doublet microtubules extends a pair of dynein arms (an "inner" and an "outer" arm) to the adjacent microtubule; these dynein arms are responsible for flagellar beating, as the force produced by the arms causes the microtubule doublets to slide against each other and the flagellum as a whole to bend. These dynein arms produce force through ATP hydrolysis. The flagellar axoneme also contains radial spokes, polypeptide complexes extending from each of the outer 9 microtubule doublets towards the central pair, with the "head" of the spoke facing inwards. The radial spoke is thought to be involved in the regulation of flagellar motion, although its exact function and method of action are not yet understood."

Many cellular metabolic functions could occur faster, but if they did, it would compromise other function that is critical. For example the enzyme RuBisCo that is involved in CO2 metabolism operates very slowly, but if it sped up, its ability to differentiate between CO2 and not CO2 has been shown to be compromised, with detrimental effects. This is an example of sub-optimal design where a component could be optimized for one function at a cost to the overall functionality.

Yet we still have C4 plants which use pep carboxylase which is FAR more efficient. So we have 2 (3 if we count CAM) different systems, with varying levels of efficiency, all made by the same creator?

Yes, and all apparently optimized for the particular application. Man produces not one type of lubricant, but many depending on what will work best in a given system. These are not interchangeable without loss of function, and that is the same for biologic alternatives.

And if you look at it, it will probably be light weight, meaning good gas mileage but don't run it into walls.

It is electric which is why it is so fast, has minimal emissions, is as safe as any comparable car. See, humans can get rid of inefficiencies. We can overcome them with knowledge and technology. It appears we are becoming better designers than god.

Yes, but can it pull my camper? Why not? Can I fit my 12 kids in it (don't actually have 12....)? Can I use it as a school bus? How about as a belly dump truck? If not, why not?

Regarding us becoming better designers than God, I'm reminded of Icarus....

[nygreenguy]

The reading list is pretty interesting. Paul Davies "The Fifth Miracle", Iris Fry's "The Emergence of Life on Earth", William Schopf "Life's Origins" are all by agnostics and atheists. Fazale Rana's "Creating Life in the Lab" and "Origins of Life" present the science from a bio-chemical and theistic perspective. There are lectures, interviews with notable bio-chemists like Robert Shapiro who is an agnostic and a major pain in the rear for RNA world fans.

Sorry, I meant papers, not books. Sorry. Small examples of in depth science. My "leisure reading" time is unfortunately limited.

Yes, and that is essential. First you have to understand how it might have happened, but for it to have relevance to the OoL question is has to be able to happen on the early earth. That is where the research is really running aground. You can synthesize organics molecules, but you can't do so unless you provide significant oversight of the process under conditions no one thinks could be replicated in the wild.

in vitro can never equal in vivo. What we do is try to eliminate unnecessary variables. For example, you criticized the lab for using sterile situations, but the primordial earth would be, by definition, sterile. In fact, if it WASNT sterile, your argument would already be lost!

That would not be the view of the geneticists.

Ive done a fair amount of genetics myself, including population genetics, and I dont see how my statement is wrong

There was just a bio-chemical discovery that indicates that the current understanding of the relationship between archea, bacteria and eukaryotic life is probably wrong, and that the last common ancestor, contrary to predictions of evolutionary science was far more complex than previously imagined. http://www.sciencedaily.com/releases/20 ... 112145.htm

Not really sure how this relates to my statement.

The same people can look at the neanderthal genome and conclude that we are not directly related to them, meaning from an evolutionary standpoint there has to have been a very recent precedent ancestor to use kicking around 50,000 - 100,000 years that could be our ancestor. They haven't found that critter, but we can say that neanderthal isn't a direct ancestor to us.

I never said neanderthal WAS a direct ancestor. I was trying to demonstrate how what you are asking for isnt logical or realistic. From a population genetics standpoint is a bit easier to determine ancestry, but when we expand the timeframes, it makes it harder.

Its like my rainbow example. If you stap back, you can see a distinct red region, a blue region, etc.. Genetics help to solve this for things which posses viable genetic information. With fossils, we have to rely on morphological changes. This is how/when we get the nested hierarchy that provides such incredible evidence for evolution.

This is similar to how we do paternity testing and other type of blood evidence. I dont need your parents, your grandparents, your siblings to prove that you and your cousin are related. So from that I can show you and your cousin share a common ancestor even if I cant prove, or show who that is.

No, I would never use the "science in the gaps" defense.... If we don't find function in the pseudogenes, that would support evolutionary biology, since that is what is predicted. If we do, it doesn't support that theory but would be consistent with my predictions. Let the research continue and see what happens.

I mentioned this before, but I shall mention it again. The genome is made up of MUCH more than genes and pseudogenes. The concept of "junk dna" includes much, much, much, more.

As I stated before, much of population genetics relies on these non-functional regions. If something has a function that is beneficial, that its removal will cost the organism. Therefore, we can see how conserved areas are to help indicate function. If we see them varying at a rapid rate, we can see they have limited to no functionality. So we can follow these changes and trace lineages. The opposite can happen for conserved regions. Earlier you posted the article about the functional "pseudogene". We could tell by the differences in humans and other primates when the genes became non-functional.

And these are not just "hypotheses" these are well supported by volumes of literature. So there is no doubt that there are non-functional regions of the genome.

Now, you claim it supports your predictions but your predictions are based on a false premises. As with any logical argument, you can have a valid argument that is not sound. If you wish to make the argument about god not having wasted dna, you must first prove the premises of how god operates.

For evolution, we say:
Mutations, inactivated genes, etc... result in non-functional portions of the genome.
Natural selection would not select these portions out meaning junk dna would persist
We observe many non-functional parts of the genome
Therefore, natural selection exists.

(yes it is a bit simplified, but I think it shows my point)

Your argument is:
A creator would not place non-functional dna in the genome
We find a lot of functional dna in the genome
Therefore a creator exists.

Now, I wont argue with the argument as a whole, but your initial premises is not shown to be true. The evolution example above relies on observation and experimental evidence to support the truth of the initial premises. So far, it would appear the only support for your argument is premises two, which is functional dna. So, how do you support the initial premises?

There is no reasonable speculation regarding whether Jesus Christ existed,

Really? I would beg to differ.

and no reasonable speculation that he claimed to be God. Whether he was or not is dependent on other factors.

Im unsure about how this relates to the topic at hand.

I haven't dismissed OoL research, I am merely pointing out what the researchers are saying. You have 10 million years or so for life to appear

Im quite sure those numbers are still up in the air.

and no explanation on how it could have happened on the early earth even though we have been studying the problem with years with smart people and big budgets.

There are lots of explanations. If the explanations were so utterly wrong, they wouldnt persist in todays science.

Quite wrong. They are a rotary motor complete with ball bearings. "Each of the outer 9 doublet microtubules extends a pair of dynein arms (an "inner" and an "outer" arm) to the adjacent microtubule; these dynein arms are responsible for flagellar beating, as the force produced by the arms causes the microtubule doublets to slide against each other and the flagellum as a whole to bend. These dynein arms produce force through ATP hydrolysis. The flagellar axoneme also contains radial spokes, polypeptide complexes extending from each of the outer 9 microtubule doublets towards the central pair, with the "head" of the spoke facing inwards. The radial spoke is thought to be involved in the regulation of flagellar motion, although its exact function and method of action are not yet understood."

You must be very, very, liberal with your meaning of similar. Something made through DNA replication, out of organic molecules, powered by ATP vs. something made of metals or plastics, powered by gasoline or electricity. The similarities are only broadly superficial.

Yes, and all apparently optimized for the particular application.

Optimized for the particular application? So god made things with certain applications? Well, why do we see these applications changing? Why do we see organisms evolving to their surroundings if they were created for one?

then there is the problem of competition. Is the lion optimized to catch prey or are the zebras optimized to escape? If one becomes more optimized, the other dies. There is a constant battle, and this is expressed in the genetics.

Then we have invasive species. If native plants are optimized, how is it invasives can come in and take over?

This is the problem with the creation account because it has to be modified to the point it is indistinguishable from evolution.

Man produces not one type of lubricant, but many depending on what will work best in a given system. These are not interchangeable without loss of function, and that is the same for biologic alternatives.

Not at all. We have taken genes from one organism and put them in another and increased their efficiency with no loss.

Same goes for cars. We have created technology which is just better. The benefits keep increasing while the faults keep decreasing.

Yes, but can it pull my camper? Why not?

With ~300hp and ~300 ft/lbs of torque, no proble.

Can I fit my 12 kids in it (don't actually have 12....)?

nope, most cars cant!

Can I use it as a school bus? How about as a belly dump truck? If not, why not?

Nope. However, you are looking at specialty applications. Despite these, the technology CAN be adapted to those application. The gain is still more than the loss or tradeoff.

Regarding us becoming better designers than God, I'm reminded of Icarus....

Pshaw...that was a long time ago! as Arthur Clarke said "Any sufficiently advanced technology is indistinguishable from magic"

[Starboard Tack]

The reading list is pretty interesting. Paul Davies "The Fifth Miracle", Iris Fry's "The Emergence of Life on Earth", William Schopf "Life's Origins" are all by agnostics and atheists. Fazale Rana's "Creating Life in the Lab" and "Origins of Life" present the science from a bio-chemical and theistic perspective. There are lectures, interviews with notable bio-chemists like Robert Shapiro who is an agnostic and a major pain in the rear for RNA world fans.

Sorry, I meant papers, not books. Sorry. Small examples of in depth science. My "leisure reading" time is unfortunately limited.

Understood.

Yes, and that is essential. First you have to understand how it might have happened, but for it to have relevance to the OoL question is has to be able to happen on the early earth. That is where the research is really running aground. You can synthesize organics molecules, but you can't do so unless you provide significant oversight of the process under conditions no one thinks could be replicated in the wild.

in vitro can never equal in vivo. What we do is try to eliminate unnecessary variables. For example, you criticized the lab for using sterile situations, but the primordial earth would be, by definition, sterile. In fact, if it WASNT sterile, your argument would already be lost!

Perhaps I chose my words inexactly. You are using sterile in the sense of biologic contaminants, which is perfectly reasonable. The contaminants that I am talking about are chemical contaminants that would create interfering reactions to those done in labs under intelligent control. For example, the only clays that will produce the kind of results OoL researchers are looking for in RNA synthesis come from Wyoming, and must be processed to create a pure enough substrate that interfering reactions don't occur. How much processed clay do you reckon existed on early earth? Additionally, polymers less than 50 long have no utility for biologic systems. Once over 50 chains long, the polymers become hopelessly bonded to the purified clay. Researcher intervention is required to lift them off of the substrate, so have zero relevance to early earth conditions, what with the paucity of researchers and all.

There was just a bio-chemical discovery that indicates that the current understanding of the relationship between archea, bacteria and eukaryotic life is probably wrong, and that the last common ancestor, contrary to predictions of evolutionary science was far more complex than previously imagined. http://www.sciencedaily.com/releases/20 ... 112145.htm

Not really sure how this relates to my statement.

I don't mean to challenge your credentials, which I accept as superior to my own. My point was that the idea that tracking relationships between genomes is not something that "from a genetic standpoint makes no sense". My impression is that this is certainly one of the benefits of genetic research, we can determine who is related to who based on inheritable characteristics. If we can determine the evolutionary tree from 3.9 billion years ago, certainly we can determine from the genomes of Neanderthals and us whether we are related. At least I believe geneticists believe they can.

The same people can look at the neanderthal genome and conclude that we are not directly related to them, meaning from an evolutionary standpoint there has to have been a very recent precedent ancestor to use kicking around 50,000 - 100,000 years that could be our ancestor. They haven't found that critter, but we can say that neanderthal isn't a direct ancestor to us.

I never said neanderthal WAS a direct ancestor. I was trying to demonstrate how what you are asking for isnt logical or realistic. From a population genetics standpoint is a bit easier to determine ancestry, but when we expand the timeframes, it makes it harder.

My point is this. There is such a quantifiable difference between modern man and whatever hominid you look at, where is our direct ancestor? It's not like this was a long time ago, relatively speaking. Homo sapiens sapiens is at most 100,000 years old. We have fossils we think are definitive to allow us to track the evolution of whales or horses from critters that existed 50 million years ago. Why can't we determine what our ancestors were since they only lived 100,000 years ago? Does that make sense to you?

No, I would never use the "science in the gaps" defense.... If we don't find function in the pseudogenes, that would support evolutionary biology, since that is what is predicted. If we do, it doesn't support that theory but would be consistent with my predictions. Let the research continue and see what happens.

I mentioned this before, but I shall mention it again. The genome is made up of MUCH more than genes and pseudogenes. The concept of "junk dna" includes much, much, much, more.

Yes, I understand. However, from a theistic point of view, it is more likely that we will find function in all those regions rather than what is predicted by evolutionary theory, which is that we would not find such function as the norm.

Now, I wont argue with the argument as a whole, but your initial premises is not shown to be true. The evolution example above relies on observation and experimental evidence to support the truth of the initial premises. So far, it would appear the only support for your argument is premises two, which is functional dna. So, how do you support the initial premises?

That is a fair challenge - why assume that God would not create pointless junk? I dunno, but if you were God, would you create useless junk? Do human engineers? The argument that the vastness of the universe is largely junk is incorrect, as I have shown and as is demonstrated by the fine tuning of the mass energy density for life to exist. So I think the burden is on you to prove the logic of creating junk at a cellular level when we don't see it elsewhere in God's creation.

There is no reasonable speculation regarding whether Jesus Christ existed,

Really? I would beg to differ.

As you wish, but you will need to refute Tacitus and Josephus to do so, as well as the Talmud. Quite honestly, and in all respect, that is not an argument that can be made without it being made solely on the basis that you wish it were so.

and no reasonable speculation that he claimed to be God. Whether he was or not is dependent on other factors.

Im unsure about how this relates to the topic at hand.

It relates because of the law of the excluded middle. If Jesus claimed to be God, he either was, or wasn't. There is no third option. If he was who he claimed to be, then a lot of mystery is solved. I can't think of any issue that could be more pertinent to the discussion of origins.

I haven't dismissed OoL research, I am merely pointing out what the researchers are saying. You have 10 million years or so for life to appear

Im quite sure those numbers are still up in the air.

and no explanation on how it could have happened on the early earth even though we have been studying the problem with years with smart people and big budgets.

There are lots of explanations. If the explanations were so utterly wrong, they wouldnt persist in todays science.

You need to catch up. OoL research is no longer attracting new researchers, because it is viewed as a career dead end. No solutions present themselves. That is why exobiology is such a hot area right now - it's the only game in town because it is clear that given the conditions on early earth, the problem of the origin of life here is intractable.

Quite wrong. They are a rotary motor complete with ball bearings. "Each of the outer 9 doublet microtubules extends a pair of dynein arms (an "inner" and an "outer" arm) to the adjacent microtubule; these dynein arms are responsible for flagellar beating, as the force produced by the arms causes the microtubule doublets to slide against each other and the flagellum as a whole to bend. These dynein arms produce force through ATP hydrolysis. The flagellar axoneme also contains radial spokes, polypeptide complexes extending from each of the outer 9 microtubule doublets towards the central pair, with the "head" of the spoke facing inwards. The radial spoke is thought to be involved in the regulation of flagellar motion, although its exact function and method of action are not yet understood."

You must be very, very, liberal with your meaning of similar. Something made through DNA replication, out of organic molecules, powered by ATP vs. something made of metals or plastics, powered by gasoline or electricity. The similarities are only broadly superficial.

Not at all. the flagellum is a molecular machine. It has bearings, it works just like a machine. The analogy is precise.

Yes, and all apparently optimized for the particular application.

Optimized for the particular application? So god made things with certain applications? Well, why do we see these applications changing? Why do we see organisms evolving to their surroundings if they were created for one?

this goes back to an unanswered question for me. Why did God create the laws of physics he did, and why does he let reality unfold almost solely within the limitations imposed by those laws? Life changes over time because conditions change over time. If Gods plan is to create a world with sufficient bio resources to support advanced human civilization, then all those species are needed. Read psalm 104 for an elegant description of extinction, and recreation.

This is the problem with the creation account because it has to be modified to the point it is indistinguishable from evolution.

Some theists believe in evolution. I don't, not from a theistic point of view, but because the science is largely incoherent. I just don't like theories that can't predict what is observed. In its simplest form, evolution is simply change over time. I agree that has happened. We disagree on the mechanism, so the fact that we can both look at the same data and one thinks it purely unguided processes, while I see the evidence of a mind at work is not remarkable.

Man produces not one type of lubricant, but many depending on what will work best in a given system. These are not interchangeable without loss of function, and that is the same for biologic alternatives.

Not at all. We have taken genes from one organism and put them in another and increased their efficiency with no loss.

Example?

Can I use it as a school bus? How about as a belly dump truck? If not, why not?

Nope. However, you are looking at specialty applications. Despite these, the technology CAN be adapted to those application. The gain is still more than the loss or tradeoff.

My point is that all designed systems are optimized for a particular function. This is how the car you describe was designed, and this is how cells are designed. That is why I assume that just as a mind was involved in creating the Tesla, so a mind was involved in creating you.

[McCulloch]

The best evidence [that the creative agent is personal], IMHO, presented for a personal causal agent are the design features of the universe. These are dismissed by some as unremarkable under the theory that regardless of the odds against something happening, it becomes unremarkable once it happens. That is called the fallacy of necessity. However, once one looks at the odds against a life supporting universe existing at all, the only out seems to be the multiverse, which I would argue is not the 'simpler' explanation.

You misunderstand Okham. Given the choice between a scenario which requires exactly one of two very different types of entities; God and Universe and another scenario which requires multiple instances of only one type of entity; Universe, the second scenario is preferred. The fact that there is no tangible evidence that there are any gods is just icing on the cake.

An intractable problem is one that on examination becomes increasingly unsolvable the more is learned. Origins of life research would qualify.

And the cause of cancer, apparently. I believe that the research over the past 100 years has brought us closer to knowing the origins of life, so I don't see where you can call this an intractable problem. Yes it is difficult and the evidence is really hard to come by, but that is no reason to give up on reason and use the God cop-out.

[Starboard Tack]

The best evidence [that the creative agent is personal], IMHO, presented for a personal causal agent are the design features of the universe. These are dismissed by some as unremarkable under the theory that regardless of the odds against something happening, it becomes unremarkable once it happens. That is called the fallacy of necessity. However, once one looks at the odds against a life supporting universe existing at all, the only out seems to be the multiverse, which I would argue is not the 'simpler' explanation.

You misunderstand Okham. Given the choice between a scenario which requires exactly one of two very different types of entities; God and Universe and another scenario which requires multiple instances of only one type of entity; Universe, the second scenario is preferred. The fact that there is no tangible evidence that there are any gods is just icing on the cake.

I think you may misunderstand multiverse theories. Level 1, I happen to agree with. Level 2-4 involved increasing levels of speculation, with zero empirical data, just like you would say is the case with God. Occam's razor would favor the simpler solution between two solutions both of which have no empirical evidence to support them (according to you on God, and according to physicists with respect to the multiverse.)

There may be some support for level 2 multiverse based on data from the Planck satellite which isn't in yet, but we'll just have to wait for that data to see.

An intractable problem is one that on examination becomes increasingly unsolvable the more is learned. Origins of life research would qualify.

And the cause of cancer, apparently. I believe that the research over the past 100 years has brought us closer to knowing the origins of life, so I don't see where you can call this an intractable problem. Yes it is difficult and the evidence is really hard to come by, but that is no reason to give up on reason and use the God cop-out.

You don't understand the current state of OoL research. Cancer research has increased our knowledge of a very complicated subject and we are getting closer to a cure. OoL research has produced some marvelous science, all of which points to the impossibility of the chemistry to ever have occurred on the early earth, which is why the father of the most prominent theory - the RNA World hypothesis - said at the ISOOL meeting in 2002 that "it would be a miracle if a single strand of RNA ever appeared on the early earth", and why Robert Shapiro, the father of the only other hypothesis - the Metabolism first hypothesis - recently commented that the work being done by RNA world enthusiasts makes a strong case for Intelligent Design, which he doesn't happen to agree with.

The problem is that the only advances in OoL research are being made in the lab under conditions that can't have existed on early earth, and have to unfold in impossibly short time periods if they did somehow occur. That is why I refer to the problem as intractable, which no one considers cancer research to be.

[McCulloch]

OoL research has produced some marvelous science, all of which points to the impossibility of the chemistry to ever have occurred on the early earth, which is why the father of the most prominent theory - the RNA World hypothesis - said at the ISOOL meeting in 2002 that "it would be a miracle if a single strand of RNA ever appeared on the early earth", and why Robert Shapiro, the father of the only other hypothesis - the Metabolism first hypothesis - recently commented that the work being done by RNA world enthusiasts makes a strong case for Intelligent Design, which he doesn't happen to agree with.

The problem is that the only advances in OoL research are being made in the lab under conditions that can't have existed on early earth, and have to unfold in impossibly short time periods if they did somehow occur. That is why I refer to the problem as intractable, which no one considers cancer research to be.

Were you at that ISOOL meeting? I cannot seem to find that quote.

Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth "would have been a near miracle."

But regardless of the status of the various hypotheses, I believe that your methodology is flawed. Essentially it boils down to this, "We cannot figure out how X occurred, therefore it must have been a miracle. "

[Autodidact]

Imagine a puddle waking up one morning and thinking, "This is an interesting world I find myself in " an interesting hole I find myself in " fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!"
--Douglas Adams