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RE: Documented evolution of new functions and behaviors in bacteria

 
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RE: Documented evolution of new functions and behaviors... - 5/7/2008 12:50:51 PM   
gluadys

 

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quote:

ORIGINAL: Jhud

quote:

Actually, you continually and persistently overlook the impact on the population and that IS the evolutionary perspective.

You tend to use the word "organism" as if it were a synonym for "species", but whenever convenient, you treat it as an individual. I expect that what you are really doing is adopting an essentialist notion of "organism". Well, evolution does not operate in essentialist concepts. It operates in populations and gene pools through changes that occur originally in individual genomes and affect the lives of individuals. Evolution is the study of how differences which first appear in individual genomes come to impact populations.

Until you can deal with a population/gene pool perspective, you will continue to misrepresent what evolution is and what evidence is pertinent to evolution.


Oh, I am quite familiar with the concept - but just to be clear, you agree the trait for sickle cell arose as a mutation in a single human ancestor, correct?


Depends on precisely what you mean.

1. Since mutations affect genetic information encoded in DNA, they necessarily occur in a single cell which either is a single unicellular organism or part of a single complex organism. If that is your meaning, the answer is "yes". But consider the following points as well.

2. While each instance of a mutation necessarily occurs in a single organism, this doesn't mean that the same mutation cannot occur in more than one organism. So it is possible that the trait for sickle cell has arisen in the human population more than once and in fact continues to do so.

3. Since a mutation, by definition, modifies genetic information, the modification is potentially inheritable, and reappears in the human population, subsequent to the first instance(s), following the principles of inheritance and selection.

4. In any specific case whether the occurrence of sickle cell trait was due to a genetic factor inherited from a parent or the consequence of a new mutation could be determined by a genetic analysis of the parents.

IOW, there is no reason to attribute all current occurrences of sickle cell trait to a single mutation in a single ancestor. Yet, each occurrence of sickle cell trait does go back to a specific single mutation in a specific single ancestor--unless it is new in the victim.
Post #: 226
RE: Documented evolution of new functions and behaviors... - 5/7/2008 1:12:04 PM   
Jhud


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quote:

IOW, there is no reason to attribute all current occurrences of sickle cell trait to a single mutation in a single ancestor. Yet, each occurrence of sickle cell trait does go back to a specific single mutation in a specific single ancestor--unless it is new in the victim.


Well, I am just trying to cget some clarity here. So it seems we agree then that each occurence for sickle cell trait arose as a mutation in a single human ancestor.

Okay, now do you agree that the reason sickle cell conveys resistance to malaria is because of a change to the structure of hemoglobin proteins?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 227
RE: Documented evolution of new functions and behaviors... - 5/7/2008 1:41:54 PM   
Method

 

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quote:

ORIGINAL: Jhud
Well, and please be exceedingly honest here – you have no idea how complex the presumed ‘the last common ancestor of all life’ was, do you?


A pretty good idea, yes. The LCA would need to incorporate everything that all species share. This would include metabolic pathways, three base codons, transcription and translation pathways, DNA replication, etc.

quote:

I didn’t say they equated, so the faulty logic is yours, as is the presumption.


Right, you have never claimed that if something is complex that it is designed.

quote:

Again, asking for exceeding honesty here; you have no idea when the Hox genes arose, do you?


Yes. They arose some time prior to the Cambrian explosion and the appearance of complex multicellular life. Given the fact that hox gene paralogs are found in cnideria that the hox genes originated prior to the cnideria/bilaterian split.

quote:

Certainly it is – unless you are going to purport that nothing that exists can be explained as the result of an intelligent cause.


"The Designer Did It" is a placeholder for a real explanation. ID is even worse than an explanation. It results in giving us less information than we had before ID is applied.

Take, for instance, ERV's. Using the theory of evolution we can trace the evolution of retroviruses in past environment and species. When we apply ID suddenly we can't even know if these sequences are viral. We lose information by applying ID. That is the hallmark of a non-expalantion.

quote:

First I would have to know that you agree that intelligent causation is a legitimate consideration when contemplating the origin of any structure – do you?


"The Deisgner Did It" has never been a legitimate explanation. It explains nothing. It's like telling kids that rainbows are caused by magic.
Post #: 228
RE: Documented evolution of new functions and behaviors... - 5/7/2008 1:44:57 PM   
Method

 

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quote:

ORIGINAL: Jhud
Well, I am just trying to cget some clarity here. So it seems we agree then that each occurence for sickle cell trait arose as a mutation in a single human ancestor.


That is a rather poor assumption. Given the size of the human population, both past and present, there is a strong chance that HemS has arisen independently quite a few times. Hemophilia is a dominant autosomal disease that arises spontaneously. In fact, the occurence of this spontaneous mutation is used to directly estimate the human mutation rate. I wouldn't be surprised if there are examples of people with the sickle cell allele where their parents are negative for the mutation.
Post #: 229
RE: Documented evolution of new functions and behaviors... - 5/7/2008 1:50:00 PM   
Jhud


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quote:

A pretty good idea, yes. The LCA would need to incorporate everything that all species share. This would include metabolic pathways, three base codons, transcription and translation pathways, DNA replication, etc.


Well, aside from the obvious complexity of that set-up, it could have been more complex than the 'simplest' species, and later species simply lost certain aspects, couldn't it have?

quote:

Yes. They arose some time prior to the Cambrian explosion and the appearance of complex multicellular life. Given the fact that hox gene paralogs are found in cnideria that the hox genes originated prior to the cnideria/bilaterian split.


Well, that would 'prior than', not when. I mean, obviously hox genes arose prior to the point at which they existed, but you do not know when, do you?

quote:

"The Designer Did It" is a placeholder for a real explanation.


So then, are you saying nothing that exists can be explained as the result of an intelligent cause?

quote:

"The Deisgner Did It" has never been a legitimate explanation. It explains nothing. It's like telling kids that rainbows are caused by magic.


So if I found a lengthy symbolic inscription on a stone wall on another planet where humans had never been, I could not legitimately claim it was the product of the work of an intelligence?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 230
RE: Documented evolution of new functions and behaviors... - 5/7/2008 1:56:23 PM   
Method

 

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quote:

ORIGINAL: Jhud
Well, aside from the obvious complexity of that set-up, it could have been more complex than the 'simplest' species, and later species simply lost certain aspects, couldn't it have?


Sure. We see this in parasitic organisms, for example. But there had to be a minimum level of complexity that would include all of the features that all life shares.

quote:

Well, that would 'prior than', not when. I mean, obviously hox genes arose prior to the point at which they existed, but you do not know when, do you?


Are you looking for a time of day? I already told you. Prior the Cambrian, at the root of the cnidirian/bilaterian tree.

quote:

So then, are you saying nothing that exists can be explained as the result of an intelligent cause?


We never explain anything as "intelligent causation". We explain them as the actual physical process that produces things.

quote:

So if I found a lengthy symbolic inscription on a stone wall on another planet where humans had never been, I could not legitimately claim it was the product of the work of an intelligence?


You would first ask "How was it made" and "What does it mean". Intelligent causation does not answer any of these questions.
Post #: 231
RE: Documented evolution of new functions and behaviors... - 5/7/2008 2:02:39 PM   
Jhud


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quote:

Sure. We see this in parasitic organisms, for example. But there had to be a minimum level of complexity that would include all of the features that all life shares.


Of course there had to be a minimum, but there is no way to know what was actually there, right?

quote:

Are you looking for a time of day? I already told you. Prior the Cambrian, at the root of the cnidirian/bilaterian tree.


Well then, point taken – you don’t when.

quote:

We never explain anything as "intelligent causation". We explain them as the actual physical process that produces things.


Not as a cause. For example, what is causing these words to appear on the screen?

quote:

You would first ask "How was it made" and "What does it mean". Intelligent causation does not answer any of these questions.


Well, those are answers to how an intelligence might have worked or what an intelligence might have intended, but this does not tell us what caused the symbols to be put on the wall, does it?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 232
RE: Documented evolution of new functions and behaviors... - 5/7/2008 3:32:44 PM   
gluadys

 

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quote:

ORIGINAL: Jhud

quote:

IOW, there is no reason to attribute all current occurrences of sickle cell trait to a single mutation in a single ancestor. Yet, each occurrence of sickle cell trait does go back to a specific single mutation in a specific single ancestor--unless it is new in the victim.


Well, I am just trying to cget some clarity here. So it seems we agree then that each occurence for sickle cell trait arose as a mutation in a single human ancestor.


I think your wording muddies more than clarifies. It is not that each occurrence of sickle cell trait arose as a mutation in a single human ancestor. Rather each mutation leading to sickle cell trait occurs in a single individual. That individual is not his/her own ancestor. S/he may have many descendants who inherit the mutation though, and they would also exhibit sickle cell trait. Also identical mutations can also occur in other individuals as well, and they can also have descendants who inherit it.

So, to sum up: each mutation occurs in a single individual.

quote:

Okay, now do you agree that the reason sickle cell conveys resistance to malaria is because of a change to the structure of hemoglobin proteins?


That is my understanding, yes.
Post #: 233
RE: Documented evolution of new functions and behaviors... - 5/7/2008 3:39:56 PM   
gluadys

 

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quote:

ORIGINAL: Jhud

Not as a cause. For example, what is causing these words to appear on the screen?

quote:

You would first ask "How was it made" and "What does it mean". Intelligent causation does not answer any of these questions.


Well, those are answers to how an intelligence might have worked or what an intelligence might have intended, but this does not tell us what caused the symbols to be put on the wall, does it?


You do realize you are equivocating with different meanings of "cause", right?
Post #: 234
RE: Documented evolution of new functions and behaviors... - 5/7/2008 3:56:37 PM   
drmark

 

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quote:

You do realize you are equivocating with different meanings of "cause", right?
No, it is you who are "equivocating, gluadys. "To cause" means to bring about or result in. No mention of how, why, or any other philosophical qualifiers.

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Post #: 235
RE: Documented evolution of new functions and behaviors... - 5/7/2008 3:57:18 PM   
Method

 

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quote:

ORIGINAL: Jhud
Of course there had to be a minimum, but there is no way to know what was actually there, right?


All of it? Of course not, and no one is claiming to know this. What we can know, if we use the theory of evolution, is what traits were definitely there.

quote:

Well then, point taken – you don’t when.


Last I checked, between the pre-cambrian and cambrian is a "when".

quote:

Not as a cause. For example, what is causing these words to appear on the screen?


Electric excitation of chemicals in the screen, electric charges in the computer, electric oscillations in the Cat 5 line, firing of your neurons, etc.

quote:

Well, those are answers to how an intelligence might have worked or what an intelligence might have intended, but this does not tell us what caused the symbols to be put on the wall, does it?


Yes, it does. The way in which things are manufactured tells a lot about the manufacturer and the purpose of the item. Those are important things that "intelligent causation" can not explain. "Intelligent causation" tells us bupkus.
Post #: 236
RE: Documented evolution of new functions and behaviors... - 5/7/2008 4:16:24 PM   
Jhud


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quote:

All of it? Of course not, and no one is claiming to know this. What we can know, if we use the theory of evolution, is what traits were definitely there.


So you can't know what was there, but we can know what had to be there. Good enough.

I don't think we need evolution for this.

quote:

Last I checked, between the pre-cambrian and cambrian is a "when".


Given that you conceded you don't know what the last common ancestor of all life had in terms of genetic capabiities, you really don't know if the last common ancestor didn't also have a genetic toolkit, do you?

quote:

Electric excitation of chemicals in the screen, electric charges in the computer, electric oscillations in the Cat 5 line, firing of your neurons, etc.


So those thing alone can cause words representing cohesive thoughts to appear on the screen?

quote:

Yes, it does. The way in which things are manufactured tells a lot about the manufacturer and the purpose of the item. Those are important things that "intelligent causation" can not explain. "Intelligent causation" tells us bupkus.


Why would we need to consider purpose and the existence of a manufacturer upon discovering the symbols on a wall on another planet?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 237
RE: Documented evolution of new functions and behaviors... - 5/7/2008 4:27:22 PM   
Jhud


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quote:

So, to sum up: each mutation occurs in a single individual.


Good enough.

quote:

That is my understanding, yes.


Very good then. So while evolution might provide us with some insights as to how this trait spread throughout a population, It is wholly unnecessary in terms of understanding how the trait occurred, or how it confers resistance, is it not?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 238
RE: Documented evolution of new functions and behaviors... - 5/7/2008 4:38:46 PM   
Method

 

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quote:

ORIGINAL: Jhud
So you can't know what was there, but we can know what had to be there. Good enough.


Just to make sure there are no misunderstandings, we can know what was there, just not all of it.

quote:

I don't think we need evolution for this.


You would need evolution if you were doing the actual science.

quote:

Given that you conceded you don't know what the last common ancestor of all life had in terms of genetic capabiities, you really don't know if the last common ancestor didn't also have a genetic toolkit, do you?


I would expect to see some bacteria or archaebacteria with hox genes if it was present in the LCA.

quote:

So those thing alone can cause words representing cohesive thoughts to appear on the screen?


It appears so. We could shut off the firing of your brain neurons and see if the words still appear.;)

quote:

Why would we need to consider purpose and the existence of a manufacturer upon discovering the symbols on a wall on another planet?


It tells us a lot about their technology, environment, etc. For example, the materials used to make cave paintings tell us a lot about the technology of those people. The way in which a piece of pottery is constructed allows us to trace cultural changes, migrations, etc. If I simply state that a piece of pottery was produced through "intelligent causation" what does that tell us about the culture, technology, history, etc. of the pot maker? Zip. Nada. Zero. Intelligent Causation is nothing more than a phrase to appease people's religious convictions. It has never been meant as a helpful explanation, because it is obviously not helpful.
Post #: 239
RE: Documented evolution of new functions and behaviors... - 5/7/2008 4:47:29 PM   
Jhud


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quote:

Just to make sure there are no misunderstandings, we can know what was there, just not all of it.


No difference.

quote:

You would need evolution if you were doing the actual science.


No, you wouldn’t need evolution because as a theory it is unnecessary to make such a statement; it is self-evident that the minimum genetic information present in the first life form was required genetic information. Evolution adds nothing to this.

quote:

I would expect to see some bacteria or archaebacteria with hox genes if it was present in the LCA.


Not if they lost them.

quote:

It appears so. We could shut off the firing of your brain neurons and see if the words still appear.


We could shut off the computer or the network as well as well to the same effect; are they equivalent?

Also, a baby, and an insect also have brain neurons that fire – could they produce the words we currently have on the screen? Why or why not?

quote:

It tells us a lot about their technology, environment, etc. For example, the materials used to make cave paintings tell us a lot about the technology of those people. The way in which a piece of pottery is constructed allows us to trace cultural changes, migrations, etc. If I simply state that a piece of pottery was produced through "intelligent causation" what does that tell us about the culture, technology, history, etc. of the pot maker? Zip. Nada. Zero. Intelligent Causation is nothing more than a phrase to appease people's religious convictions. It has never been meant as a helpful explanation, because it is obviously not helpful.


You didn’t answer the question. If the marks on the walls were merely pits produced by wind blowing sand grains, would we have to consider the purpose or existence of a manufacturer? What is it about written symbols that would cause us to consider these things?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 240
RE: Documented evolution of new functions and behaviors... - 5/7/2008 5:19:56 PM   
Method

 

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quote:

ORIGINAL: Jhud
No, you wouldn’t need evolution because as a theory it is unnecessary to make such a statement; it is self-evident that the minimum genetic information present in the first life form was required genetic information. Evolution adds nothing to this.


If all life did not evolve from the proposed LCA then how can you claim this?

quote:

Not if they lost them.


All lineages of bacteria lost them? Extremely, extremely unlikely.

quote:

We could shut off the computer or the network as well as well to the same effect; are they equivalent?


Equivalent as to the appearance of letters on my screen.

quote:

Also, a baby, and an insect also have brain neurons that fire – could they produce the words we currently have on the screen?


Not anymore than you sprouting insect wings. The ability to write sentences is a function of our genetics and development as much as an insect's ability to grow wings and fly.

quote:

You didn’t answer the question. If the marks on the walls were merely pits produced by wind blowing sand grains, would we have to consider the purpose or existence of a manufacturer? What is it about written symbols that would cause us to consider these things?


Humans use symbols to communicate, so we would assume that the purpose of unknown symbols is communication. "Intelligent causation" is incapable of giving us purpose. I could splatter a wall with mud and it would be "intelligent causation".
Post #: 241
RE: Documented evolution of new functions and behaviors... - 5/7/2008 5:34:04 PM   
Agahnim

 

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Jhud, I know you’re debating with a few people at once here, but I would like you to at least attempt to address the point I’m making about how your own point with me relies on the evolution of bats’ wings being impossible, and why in order to support this argument you’ll need to show that natural selection definitely wouldn’t have favored any of the mutations responsible for their structure. Do you understand what I’ve said in post #185 and #215 about why when your argument relies one something being impossible, the burden of proof is on you to show that it is?

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Post #: 242
RE: Documented evolution of new functions and behaviors... - 5/7/2008 5:41:48 PM   
Jhud


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quote:

Jhud, I know you’re debating with a few people at once here, but I would like you to at least attempt to address the point I’m making about how your own point with me relies on the evolution of bats’ wings being impossible, and why in order to support this argument you’ll need to show that natural selection definitely wouldn’t have favored any of the mutations responsible for their structure. Do you understand what I’ve said in post #185 and #215 about why when your argument relies one something being impossible, the burden of proof is on you to show that it is?


Did I say it was impossible? I mean I may have somewhere, but I don't think I did.

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 243
RE: Documented evolution of new functions and behaviors... - 5/7/2008 5:53:27 PM   
Jhud


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quote:

If all life did not evolve from the proposed LCA then how can you claim this?


If a minimum genetic contingent was required for life to exist, then that would be true however life came about or developed.

quote:

All lineages of bacteria lost them? Extremely, extremely unlikely.


Why, if they were unnecessary?

quote:

Equivalent as to the appearance of letters on my screen.


Exactly; so this doesn't demonstrate the cause of such letters appearing on the screen.

quote:

Not anymore than you sprouting insect wings. The ability to write sentences is a function of our genetics and development as much as an insect's ability to grow wings and fly.


You said it was a function neurons firing; are you changing this now? And a baby obviously doesn't differ significantly genetically.

quote:

Humans use symbols to communicate, so we would assume that the purpose of unknown symbols is communication.


One thing I appreciate about you Method is that you dance so fiercely around something that it becomes obvious to everyone how absurd your positions are.

Nonetheless, I will keep demonstrating it.

So while we might assume that symbols indicate communication, this doesn't tell us about the cause; but it might help us there - what would be the cause of written symbolic communication?

quote:

"Intelligent causation" is incapable of giving us purpose. I could splatter a wall with mud and it would be "intelligent causation".


Well, no, because intelligence is not a neccesary requirement of splattering mud - it is though a necessary requirement of symbolic communication, is it not?

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 244
RE: Documented evolution of new functions and behaviors... - 5/7/2008 6:10:39 PM   
Agahnim

 

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quote:

Did I say it was impossible? I mean I may have somewhere, but I don't think I did.

What you said, in reference to the mutations that would have been responsible for flight in bats, is “every independent change poses a number of potential problems for the survivability of the organism to which they are occurring”. If this is really true, then for all practical purposes the origin of flight in bats via evolution alone is impossible, and you’re right that we’d have to come up with another explanation for their origin, even if that involves some sort of unknown and unobserved process. In order to support this assertion, though, you will need to show that every independent change really does pose a problem to the organism that has it. The burden of proof is definitely on you for this.

I pointed this out twice before in this thread. The first time you didn’t appear to understand my point, and responded that even though your argument relies on knowing for certain that these mutations couldn’t have provided any advantage, the burden of proof was on me to show that they did. When I explained why the burden of proof definitely is not on me for this, you didn’t respond at all. This is the point I made in post #215, and I’d appreciate you not ignoring it.

_____________________________

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Post #: 245
RE: Documented evolution of new functions and behaviors... - 5/7/2008 6:14:57 PM   
Jhud


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quote:

What you said, in reference to the mutations that would have been responsible for flight in bats, is “every independent change poses a number of potential problems for the survivability of the organism to which they are occurring”. If this is really true, then for all practical purposes the origin of flight in bats via evolution alone is impossible, and you’re right that we’d have to come up with another explanation for their origin, even if that involves some sort of unknown and unobserved process. In order to support this assertion, though, you will need to show that every independent change really does pose a problem to the organism that has it. The burden of proof is definitely on you for this.

I pointed this out twice before in this thread. The first time you didn’t appear to understand my point, and responded that even though your argument relies on knowing for certain that these mutations couldn’t have provided any advantage, the burden of proof was on me to show that they did. When I explained why the burden of proof definitely is not on me for this, you didn’t respond at all. This is the point I made in post #215, and I’d appreciate you not ignoring it.


Well, for the record, I don't consider it impossible; simple so improbable as to be not worth taking seriously.

_____________________________

Jack

“I mean to live my life an obedient man, but obedient to God, subservient to the wisdom of my ancestors; never to the authority of political truths arrived at yesterday at the voting booth”

William F. Buckley Jr. 1925-200
Post #: 246
RE: Documented evolution of new functions and behaviors... - 5/7/2008 6:17:19 PM   
Method

 

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quote:

ORIGINAL: Jhud
If a minimum genetic contingent was required for life to exist, then that would be true however life came about or developed.


If life were designed the minimum genetic contingent could be different for every design.

quote:

quote:

All lineages of bacteria lost them? Extremely, extremely unlikely.


Why, if they were unnecessary?


If they were unnecessary they wouldn't have been in the LCA, nor would they have survived genetic drift in order to be inherited by multicellular life.

quote:

Exactly; so this doesn't demonstrate the cause of such letters appearing on the screen.


It does demonstrate the appearance of letters on my screen. Shutting off the computer or the network makes them disappear. Therefore, the computer and network are part of the mechanism.

quote:

You said it was a function neurons firing; are you changing this now? And a baby obviously doesn't differ significantly genetically.


I guess you are unaware that our brains are a product of our DNA and development?

quote:

One thing I appreciate about you Method is that you dance so fiercely around something that it becomes obvious to everyone how absurd your positions are.

Nonetheless, I will keep demonstrating it.

So while we might assume that symbols indicate communication, this doesn't tell us about the cause; but it might help us there - what would be the cause of written symbolic communication?


Bob: Wow, look at these symbols. I wonder how they got there?

Frank: Intelligent causation, obviously.

Bob: I know that Frank, I mean how did they write those symbols and what does it mean?

Frank: Intelligent causation, Bob. Weren't you listening?

Bob: Ok, let me simplify this for you. Why is that squiggly line next to the buffalo?

Frank: Intelligent causation, Bob. I don't know what else to say.

Joe: Hey Bob, how you doin'?

Bob: Well, I hav