> Sorry, about not getting back sooner. We lost our seven year old
> granddaughter. We are still in shock. This is a real tragedy, she had
> personality plus, a brilliant mind and a lot of promise. So, I'm not up
> to more discussions just now.

>> Sorry, about not getting back sooner. We lost our seven year old
>> granddaughter. We are still in shock. This is a real tragedy, she had
>> personality plus, a brilliant mind and a lot of promise. So, I'm not up
>> to more discussions just now.
>I understand.  My deepest condolences.

> >> Sorry, about not getting back sooner. We lost our seven year old
> >> granddaughter. We are still in shock. This is a real tragedy, she had
> >> personality plus, a brilliant mind and a lot of promise. So, I'm not up
> >> to more discussions just now.

> >I understand.  My deepest condolences.

> Mine too.

> Sorry, about not getting back sooner. We lost our seven year old
> granddaughter. We are still in shock. This is a real tragedy, she had
> personality plus, a brilliant mind and a lot of promise. So, I'm not up
> to more discussions just now.

>> On 11/9/2012 12:03 PM, Mark Isaak wrote [a reply to]:

>> Sorry, about not getting back sooner. We lost our seven year old
>> granddaughter. We are still in shock. This is a real tragedy, she had
>> personality plus, a brilliant mind and a lot of promise. So, I'm not up
>> to more discussions just now.

> Oh Mark, I'm so sorry. My deepest condolences.

> >> On 11/9/2012 12:03 PM, Mark Isaak wrote [a reply to]:

> >> Sorry, about not getting back sooner. We lost our seven year old
> >> granddaughter. We are still in shock. This is a real tragedy, she had
> >> personality plus, a brilliant mind and a lot of promise. So, I'm not up
> >> to more discussions just now.

> > Oh Mark, I'm so sorry. My deepest condolences.

> Not Mark.  R. Dean.

> > On 11/9/2012 12:03 PM, Mark Isaak wrote:

> > Sorry, about not getting back sooner. We lost our seven year old
> > granddaughter. We are still in shock. This is a real tragedy, she had
> > personality plus, a brilliant mind and a lot of promise. So, I'm not up
> > to more discussions just now.

> Oh Mark, I'm so sorry. My deepest condolences.

>>>>> Except it doesn't.  There are several small variants of the genetic
>>>>> code.  "Almost no exceptions" means "definitely some exceptions",
>>>>> which
>>>>> blows down your claim for stability.  Besides, you do not know what
>>>>> the
>>>>> genetic code was from the beginning; you only know it since the 1960s.

>>>> I remember reading about a bacteria incorporating arsenic into its
>>>> genetic code and cells.

>>> As Ernest has noted, those reports were in error.

>>>> What do you mean you only know it since the 1960?

>>> It was in the 1960s that the genetic code was first being worked out. To
>>> the best of my knowledge, no investigation of the genetic code -- i.e.,
>>> which codons map to which amino acids -- has been done on any organism
>>> which was alive before 1960, and certainly not much before then.
>>> Ages-old genetic *sequences* have been worked out, but that is not the
>>> same thing.

>> OK, it's not difficult to infer that if living organisms contain a code
>> which is universal, then certainly all their ancestors must have had
>> same ubiquitous genetic code.

> Likewise, it's not difficult to infer that if living organisms within my
> family are universally named "Isaak", then certainly all our ancestors
> must have had the same ubiquitous name.

>> If I saw a large oak tree in my yard, I
>> would conclude it had to have  been there for years, only my neglect or
>> inattention could explain that which I just noticed. I would not conclude
>> it just popped up, fully grown, set out during the night by the designer.

> I have seen large trees pop up overnight (well, over a midday) due to
> the actions of a designer.  Does your statement above mean that you are
> now rejecting intelligent design?

>>> As Ernest has also noted, we can make inferences about the genetic code
>>> in earlier life, but those inferences are based on common descent and
>>> evolution, which would go out the window if your design idea were
>>> correct.

>> Evidently, you are misreading me. I do not have a fundamentalist view of
>> life or design. Please see above.

> Okay, you have me at a loss, then.  Does "design" mean anything to you
> at all?

>> Can you give examples of variant codes? Does the variations argue
>> against the universality of the code?

> http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chap...

> If that link gets mangled, it appears also in the references at
> http://en.wikipedia.org/wiki/List_of_genetic_codes

> That's not true.  It is part of the Second Law of Thermodynamics, not a
> reversal of it, that entropy can drop locally if coupled to a greater
> increase of entropy elsewhere.

>>> Except it doesn't.  There are several small variants of the genetic
>>> code.  "Almost no exceptions" means "definitely some exceptions", which
>>> blows down your claim for stability.  Besides, you do not know what the
>>> genetic code was from the beginning; you only know it since the 1960s.

>> I remember reading about a bacteria incorporating arsenic into its
>> genetic code and cells.

> As Ernest has noted, those reports were in error.

>> What do you mean you only know it since the 1960?

> It was in the 1960s that the genetic code was first being worked out. To
> the best of my knowledge, no investigation of the genetic code -- i.e.,
> which codons map to which amino acids -- has been done on any organism
> which was alive before 1960, and certainly not much before then.
> Ages-old genetic *sequences* have been worked out, but that is not the
> same thing.

> As Ernest has also noted, we can make inferences about the genetic code
> in earlier life, but those inferences are based on common descent and
> evolution, which would go out the window if your design idea were
> correct.  So when you say "unchanged and stable from the beginning", you
> are simply guessing, with no basis at all for your guess.

> And, as it turns out, you are almost certainly guessing wrong.  There
> *are* variations to the genetic code, which strongly implies that it --
> or rather they -- have not always been the same.

>>>>>> Except it doesn't.  There are several small variants of the genetic
>>>>>> code.  "Almost no exceptions" means "definitely some exceptions",
>>>>>> which
>>>>>> blows down your claim for stability.  Besides, you do not know what
>>>>>> the
>>>>>> genetic code was from the beginning; you only know it since the
>>>>>> 1960s.

>>>>> I remember reading about a bacteria incorporating arsenic into its
>>>>> genetic code and cells.

>>>> As Ernest has noted, those reports were in error.

>>>>> What do you mean you only know it since the 1960?

>>>> It was in the 1960s that the genetic code was first being worked
>>>> out. To
>>>> the best of my knowledge, no investigation of the genetic code -- i.e.,
>>>> which codons map to which amino acids -- has been done on any organism
>>>> which was alive before 1960, and certainly not much before then.
>>>> Ages-old genetic *sequences* have been worked out, but that is not the
>>>> same thing.

>>> OK, it's not difficult to infer that if living organisms contain a code
>>> which is universal, then certainly all their ancestors must have had
>>> same ubiquitous genetic code.

>> Likewise, it's not difficult to infer that if living organisms within my
>> family are universally named "Isaak", then certainly all our ancestors
>> must have had the same ubiquitous name.

>>> If I saw a large oak tree in my yard, I
>>> would conclude it had to have  been there for years, only my neglect or
>>> inattention could explain that which I just noticed. I would not
>>> conclude
>>> it just popped up, fully grown, set out during the night by the
>>> designer.

>> I have seen large trees pop up overnight (well, over a midday) due to
>> the actions of a designer.  Does your statement above mean that you are
>> now rejecting intelligent design?

> I would have to see this for myself.

>>> Evidently, you are misreading me. I do not have a fundamentalist view of
>>> life or design. Please see above.

>> Okay, you have me at a loss, then.  Does "design" mean anything to you
>> at all?

> Yes, it took place eons ago and nothing is happening at the present.

>> http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chap...

>> If that link gets mangled, it appears also in the references at
>> http://en.wikipedia.org/wiki/List_of_genetic_codes

> Things are back to some kind of normal, but it's a new kind of normal
> with our grandchild gone. Things have changed - I've changed; things
> that were important don't seem so now.

>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>> life
>>>>> began.

>>>>>> The very fact that
>>>>>> all life functions with the exact same genetic code implies that the
>>>>>> code must have come about over three billion years ago, and has
>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>> beginning.

>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>> (The
>>>>> near universality of the genetic code and the nature and phylogenetic
>>>>> distribution of the variants is one of the lines of evidence for
>>>>> common
>>>>> descent, but as far I can see it is silent on the question of
>>>>> spontaneous versus supernatural abiogenesis.)

>>>> It could just as well be seen as empirical evidence of a common
>>>> designer. The fact that the universality of the code considering
>>>> the same genetic code function in the bacteria and blue-green algae
>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>> jelly fish and other still extant ancient forms is the same code: that
>>>> the genetic code is ubiquitous throughout the plant and animal
>>>> kingdoms.

>>> The hypothesis of common descent makes predictions about the genetic
>>> code. The hypothesis of common design does not. (The putative designer
>>> could have give every species a different genetic code, to inhibit
>>> hybridisation, and to inhibit viruses jumping species.)

>> But why, from an engineers prospective, it makes no sense. If a wheel
>> serves other functions and purposes why _not_ use it? hybrids usually
>> do not produce offspring, I know about virus jumping specie, carrying
>> new genetic data, but how often is this detrimental even fatal?

>> Therefore the
>>> putative universality of the genetic code is empirical evidence against
>>> a common designer. (Note that by invoking separate abiogenesis you are
>>> moving your expressed position closer to conventional creationism.)

>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>> 2) a universal flood: 3) that creation was by the specific God of the
>> Bible: I don't know what else they believe. However, Intelligent design
>> does not advocate this.

> That is an unhelpfully narrow definition of Creationism.

>> I'm sorry, I disagree.

> You concede below that you have not read any of the literature on the
> subject,

>>>> It is incredible that it could have arisen so early in the history of
>>>> life and retain its universality.
>>>> It's really unbelievable that random, chance operations could have
>>>> hit upon a code that functions so well throughout the earliest period
>>>> of time since it's last common ancestor.

>>> Have you read any of the literature on this subject. For example, have
>>> you red Robin Douglas Knight's Ph.D thesis?

>> No, I unaware of this thesis.

>>>> To me an intelligent designer
>>>> seems a far more rational explanation for the consistence of the code
>>>> over such a vast span of time and over such a broad distribution of
>>>> existing organisms.

>>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>>> life
>>>>>> began.

>>>>>>> The very fact that
>>>>>>> all life functions with the exact same genetic code implies that the
>>>>>>> code must have come about over three billion years ago, and has
>>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>>> beginning.

>>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>>> (The
>>>>>> near universality of the genetic code and the nature and phylogenetic
>>>>>> distribution of the variants is one of the lines of evidence for
>>>>>> common
>>>>>> descent, but as far I can see it is silent on the question of
>>>>>> spontaneous versus supernatural abiogenesis.)

>>>>> It could just as well be seen as empirical evidence of a common
>>>>> designer. The fact that the universality of the code considering
>>>>> the same genetic code function in the bacteria and blue-green algae
>>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>>> jelly fish and other still extant ancient forms is the same code: that
>>>>> the genetic code is ubiquitous throughout the plant and animal
>>>>> kingdoms.

>>>> The hypothesis of common descent makes predictions about the genetic
>>>> code. The hypothesis of common design does not. (The putative designer
>>>> could have give every species a different genetic code, to inhibit
>>>> hybridisation, and to inhibit viruses jumping species.)

>>> But why, from an engineers prospective, it makes no sense. If a wheel
>>> serves other functions and purposes why _not_ use it? hybrids usually
>>> do not produce offspring, I know about virus jumping specie, carrying
>>> new genetic data, but how often is this detrimental even fatal?

>>> Therefore the
>>>> putative universality of the genetic code is empirical evidence against
>>>> a common designer. (Note that by invoking separate abiogenesis you are
>>>> moving your expressed position closer to conventional creationism.)

>>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>>> 2) a universal flood: 3) that creation was by the specific God of the
>>> Bible: I don't know what else they believe. However, Intelligent design
>>> does not advocate this.

>> That is an unhelpfully narrow definition of Creationism.

>It's about all I know, except it based on a few paragraphs in Genesis.
>But this is not what I am defending. Personally, I see I.D. and the
>Genesis creation as two different version of origins.

>The definition
>> I prefer is the religiously motivated rejection of substantial portions
>> of the scientific consensus, especially as related to biology and geology.

>Perhaps this is true of the Genesis account and those who defend it.
>>> The
>>>> nature and phylogenetic distribution of the variants in the genetic code
>>>> is stronger empirical evidence for common descent.

>>> I'm sorry, I disagree.

>> You concede below that you have not read any of the literature on the
>> subject,

>No, I was asked about one man's doctoral thesis. Which I had not heard
>about.

>implying that you are unaware of the nature and phylogenetic
>> distribution of the variants in the genetic code - a conclusion which is
>> confirmed by you bringing up the red herring of As-DNA. This would mean
>> that you have no rational grounds to disagree.

>So, in effect, you are saying that the genetic code is different - not
>universal in different life forms from kingdom, phylum, class etc up
>through species. Is this what you are saying?

>>>>> It is incredible that it could have arisen so early in the history of
>>>>> life and retain its universality.
>>>>> It's really unbelievable that random, chance operations could have
>>>>> hit upon a code that functions so well throughout the earliest period
>>>>> of time since it's last common ancestor.

>>>> Have you read any of the literature on this subject. For example, have
>>>> you red Robin Douglas Knight's Ph.D thesis?

>>> No, I unaware of this thesis.

>>>>> To me an intelligent designer
>>>>> seems a far more rational explanation for the consistence of the code
>>>>> over such a vast span of time and over such a broad distribution of
>>>>> existing organisms.

>>>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>>>> life
>>>>>>> began.

>>>>>>>> The very fact that
>>>>>>>> all life functions with the exact same genetic code implies that
>>>>>>>> the
>>>>>>>> code must have come about over three billion years ago, and has
>>>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>>>> beginning.

>>>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>>>> (The
>>>>>>> near universality of the genetic code and the nature and
>>>>>>> phylogenetic
>>>>>>> distribution of the variants is one of the lines of evidence for
>>>>>>> common
>>>>>>> descent, but as far I can see it is silent on the question of
>>>>>>> spontaneous versus supernatural abiogenesis.)

>>>>>> It could just as well be seen as empirical evidence of a common
>>>>>> designer. The fact that the universality of the code considering
>>>>>> the same genetic code function in the bacteria and blue-green algae
>>>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>>>> jelly fish and other still extant ancient forms is the same code:
>>>>>> that
>>>>>> the genetic code is ubiquitous throughout the plant and animal
>>>>>> kingdoms.

>>>>> The hypothesis of common descent makes predictions about the genetic
>>>>> code. The hypothesis of common design does not. (The putative designer
>>>>> could have give every species a different genetic code, to inhibit
>>>>> hybridisation, and to inhibit viruses jumping species.)

>>>> But why, from an engineers prospective, it makes no sense. If a wheel
>>>> serves other functions and purposes why _not_ use it? hybrids usually
>>>> do not produce offspring, I know about virus jumping specie, carrying
>>>> new genetic data, but how often is this detrimental even fatal?

>>>> Therefore the
>>>>> putative universality of the genetic code is empirical evidence
>>>>> against
>>>>> a common designer. (Note that by invoking separate abiogenesis you are
>>>>> moving your expressed position closer to conventional creationism.)

>>>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>>>> 2) a universal flood: 3) that creation was by the specific God of the
>>>> Bible: I don't know what else they believe. However, Intelligent design
>>>> does not advocate this.

>>> That is an unhelpfully narrow definition of Creationism.

>> It's about all I know, except it based on a few paragraphs in Genesis.
>> But this is not what I am defending. Personally, I see I.D. and the
>> Genesis creation as two different version of origins.

>> The definition
>>> I prefer is the religiously motivated rejection of substantial portions
>>> of the scientific consensus, especially as related to biology and
>>> geology.

>> Perhaps this is true of the Genesis account and those who defend it.
>>>> The
>>>>> nature and phylogenetic distribution of the variants in the genetic
>>>>> code
>>>>> is stronger empirical evidence for common descent.

>>>> I'm sorry, I disagree.

>>> You concede below that you have not read any of the literature on the
>>> subject,

>> No, I was asked about one man's doctoral thesis. Which I had not heard
>> about.

> You were asked if you had read any of the literature on the subject -
> "Have you read any of the literature on this subject. For example, have
> you red Robin Douglas Knight's Ph.D thesis?"

>> implying that you are unaware of the nature and phylogenetic
>>> distribution of the variants in the genetic code - a conclusion which is
>>> confirmed by you bringing up the red herring of As-DNA. This would mean
>>> that you have no rational grounds to disagree.

>> So, in effect, you are saying that the genetic code is different - not
>> universal in different life forms from kingdom, phylum, class etc up
>> through species. Is this what you are saying?

> Yes. The genetic code is not universal. It differs in a number of
> clades. The standard code is used in most prokaryotes and nuclear
> genomes in the great majority of eukaryotes. However some bacteria and
> some eukaryotes use variant codes, and there are several different
> variant mitochondrial codes.

> Variant codes are predominantly associated with small genomes, where
> conservative selection is weaker.

> To reiterate, you are unaware of the nature and phylogenetic
> distribution of the variants in the genetic code - that means you have
> no rational grounds to disagree with the statement that the nature and
> phylogenetic distribution of the variants in the genetic code is
> empirical evidence for common descent.

>>>>>> It is incredible that it could have arisen so early in the history of
>>>>>> life and retain its universality.
>>>>>> It's really unbelievable that random, chance operations could have
>>>>>> hit upon a code that functions so well throughout the earliest period
>>>>>> of time since it's last common ancestor.

>>>>> Have you read any of the literature on this subject. For example, have
>>>>> you red Robin Douglas Knight's Ph.D thesis?

>>>> No, I unaware of this thesis.

>>>>>> To me an intelligent designer
>>>>>> seems a far more rational explanation for the consistence of the code
>>>>>> over such a vast span of time and over such a broad distribution of
>>>>>> existing organisms.

>>>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>>>> life
>>>>>>> began.

>>>>>>>> The very fact that
>>>>>>>> all life functions with the exact same genetic code implies that the
>>>>>>>> code must have come about over three billion years ago, and has
>>>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>>>> beginning.

>>>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>>>> (The
>>>>>>> near universality of the genetic code and the nature and phylogenetic
>>>>>>> distribution of the variants is one of the lines of evidence for
>>>>>>> common
>>>>>>> descent, but as far I can see it is silent on the question of
>>>>>>> spontaneous versus supernatural abiogenesis.)

>>>>>> It could just as well be seen as empirical evidence of a common
>>>>>> designer. The fact that the universality of the code considering
>>>>>> the same genetic code function in the bacteria and blue-green algae
>>>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>>>> jelly fish and other still extant ancient forms is the same code: that
>>>>>> the genetic code is ubiquitous throughout the plant and animal
>>>>>> kingdoms.

>>>>> The hypothesis of common descent makes predictions about the genetic
>>>>> code. The hypothesis of common design does not. (The putative designer
>>>>> could have give every species a different genetic code, to inhibit
>>>>> hybridisation, and to inhibit viruses jumping species.)

>>>> But why, from an engineers prospective, it makes no sense. If a wheel
>>>> serves other functions and purposes why _not_ use it? hybrids usually
>>>> do not produce offspring, I know about virus jumping specie, carrying
>>>> new genetic data, but how often is this detrimental even fatal?

>>>> Therefore the
>>>>> putative universality of the genetic code is empirical evidence against
>>>>> a common designer. (Note that by invoking separate abiogenesis you are
>>>>> moving your expressed position closer to conventional creationism.)

>>>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>>>> 2) a universal flood: 3) that creation was by the specific God of the
>>>> Bible: I don't know what else they believe. However, Intelligent design
>>>> does not advocate this.

>>> That is an unhelpfully narrow definition of Creationism.

>>It's about all I know, except it based on a few paragraphs in Genesis.
>>But this is not what I am defending. Personally, I see I.D. and the
>>Genesis creation as two different version of origins.

>>The definition
>>> I prefer is the religiously motivated rejection of substantial portions
>>> of the scientific consensus, especially as related to biology and geology.

>>Perhaps this is true of the Genesis account and those who defend it.
>>>> The
>>>>> nature and phylogenetic distribution of the variants in the genetic code
>>>>> is stronger empirical evidence for common descent.

>>>> I'm sorry, I disagree.

>>> You concede below that you have not read any of the literature on the
>>> subject,

>>No, I was asked about one man's doctoral thesis. Which I had not heard
>>about.

>You were asked if you had read any of the literature on the subject -
>"Have you read any of the literature on this subject. For example, have
>you red Robin Douglas Knight's Ph.D thesis?"

>>implying that you are unaware of the nature and phylogenetic
>>> distribution of the variants in the genetic code - a conclusion which is
>>> confirmed by you bringing up the red herring of As-DNA. This would mean
>>> that you have no rational grounds to disagree.

>>So, in effect, you are saying that the genetic code is different - not
>>universal in different life forms from kingdom, phylum, class etc up
>>through species. Is this what you are saying?

>Yes. The genetic code is not universal. It differs in a number of
>clades. The standard code is used in most prokaryotes and nuclear
>genomes in the great majority of eukaryotes. However some bacteria and
>some eukaryotes use variant codes, and there are several different
>variant mitochondrial codes.

>Variant codes are predominantly associated with small genomes, where
>conservative selection is weaker.

>To reiterate, you are unaware of the nature and phylogenetic
>distribution of the variants in the genetic code - that means you have
>no rational grounds to disagree with the statement that the nature and
>phylogenetic distribution of the variants in the genetic code is
>empirical evidence for common descent.

>>>>> Have you read any of the literature on this subject. For example, have
>>>>> you red Robin Douglas Knight's Ph.D thesis?

>>>> No, I unaware of this thesis.

>>>>>> To me an intelligent designer
>>>>>> seems a far more rational explanation for the consistence of the code
>>>>>> over such a vast span of time and over such a broad distribution of
>>>>>> existing organisms.

>>In message <EgPqs.422345$Bz2.125...@fx11.am4>, R. Dean <"R.
>>Dean"@gmail.com> writes
>>>On 11/8/2012 12:01 PM, Ernest Major wrote:
>>>> In message <xkRms.235860$9W6.121...@fx08.am4>, R. Dean <"R.
>>>> Dean"@gmail.com> writes
>>>>> On 11/8/2012 6:37 AM, Ernest Major wrote:
>>>>>> In message <YzIms.126544$W63.121...@fx05.am4>, R. Dean <"R.
>>>>>> Dean"@gmail.com> writes
>>>>>>> On 11/6/2012 3:17 PM, Ernest Major wrote:
>>>>>>>> In message <L5ems.182064$Sr2.106...@fx01.am4>, R. Dean <"R.
>>>>>>>> Dean"@gmail.com> writes
>>>>>>>>> I have no problem with saying we simply don't know how life began,
>>>>>>>>> this, in my view is the far more straight-forward and up-front than
>>>>>>>>> claiming it happens through natural processes.

>>>>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>>>>> life
>>>>>>>> began.

>>>>>>>>> The very fact that
>>>>>>>>> all life functions with the exact same genetic code implies that the
>>>>>>>>> code must have come about over three billion years ago, and has
>>>>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>>>>> beginning.

>>>>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>>>>> (The
>>>>>>>> near universality of the genetic code and the nature and phylogenetic
>>>>>>>> distribution of the variants is one of the lines of evidence for
>>>>>>>> common
>>>>>>>> descent, but as far I can see it is silent on the question of
>>>>>>>> spontaneous versus supernatural abiogenesis.)

>>>>>>> It could just as well be seen as empirical evidence of a common
>>>>>>> designer. The fact that the universality of the code considering
>>>>>>> the same genetic code function in the bacteria and blue-green algae
>>>>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>>>>> jelly fish and other still extant ancient forms is the same code: that
>>>>>>> the genetic code is ubiquitous throughout the plant and animal
>>>>>>> kingdoms.

>>>>>> The hypothesis of common descent makes predictions about the genetic
>>>>>> code. The hypothesis of common design does not. (The putative designer
>>>>>> could have give every species a different genetic code, to inhibit
>>>>>> hybridisation, and to inhibit viruses jumping species.)

>>>>> But why, from an engineers prospective, it makes no sense. If a wheel
>>>>> serves other functions and purposes why _not_ use it? hybrids usually
>>>>> do not produce offspring, I know about virus jumping specie, carrying
>>>>> new genetic data, but how often is this detrimental even fatal?

>>>>> Therefore the
>>>>>> putative universality of the genetic code is empirical evidence against
>>>>>> a common designer. (Note that by invoking separate abiogenesis you are
>>>>>> moving your expressed position closer to conventional creationism.)

>>>>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>>>>> 2) a universal flood: 3) that creation was by the specific God of the
>>>>> Bible: I don't know what else they believe. However, Intelligent design
>>>>> does not advocate this.

>>>> That is an unhelpfully narrow definition of Creationism.

>>>It's about all I know, except it based on a few paragraphs in Genesis.
>>>But this is not what I am defending. Personally, I see I.D. and the
>>>Genesis creation as two different version of origins.

>>>The definition
>>>> I prefer is the religiously motivated rejection of substantial portions
>>>> of the scientific consensus, especially as related to biology and geology.

>>>Perhaps this is true of the Genesis account and those who defend it.
>>>>> The
>>>>>> nature and phylogenetic distribution of the variants in the genetic code
>>>>>> is stronger empirical evidence for common descent.

>>>>> I'm sorry, I disagree.

>>>> You concede below that you have not read any of the literature on the
>>>> subject,

>>>No, I was asked about one man's doctoral thesis. Which I had not heard
>>>about.

>>You were asked if you had read any of the literature on the subject -
>>"Have you read any of the literature on this subject. For example, have
>>you red Robin Douglas Knight's Ph.D thesis?"

>>>implying that you are unaware of the nature and phylogenetic
>>>> distribution of the variants in the genetic code - a conclusion which is
>>>> confirmed by you bringing up the red herring of As-DNA. This would mean
>>>> that you have no rational grounds to disagree.

>>>So, in effect, you are saying that the genetic code is different - not
>>>universal in different life forms from kingdom, phylum, class etc up
>>>through species. Is this what you are saying?

>>Yes. The genetic code is not universal. It differs in a number of
>>clades. The standard code is used in most prokaryotes and nuclear
>>genomes in the great majority of eukaryotes. However some bacteria and
>>some eukaryotes use variant codes, and there are several different
>>variant mitochondrial codes.

>>Variant codes are predominantly associated with small genomes, where
>>conservative selection is weaker.

>>To reiterate, you are unaware of the nature and phylogenetic
>>distribution of the variants in the genetic code - that means you have
>>no rational grounds to disagree with the statement that the nature and
>>phylogenetic distribution of the variants in the genetic code is
>>empirical evidence for common descent.

>You are likely correct about R.Dean's familiarity with what is known
>about these subjects, but from the cite I provided earlier, ISTM the
>variations in the DNA code represent a small part of the total:

><http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapte
>r=tgencodes#SG2>

>AIUI most of the differences do not necessarily result in a
>fundamentally different protein structure on translation.  My
>impression is these changes occurred gradually over time.
>Is it your opinion that these different DNA codes were different from
>the beginning of each lineage and remained unchanged since then?  If
>so, how do you square that with Common Descent?

>>>>>>> It is incredible that it could have arisen so early in the history of
>>>>>>> life and retain its universality.
>>>>>>> It's really unbelievable that random, chance operations could have
>>>>>>> hit upon a code that functions so well throughout the earliest period
>>>>>>> of time since it's last common ancestor.

>>>>>> Have you read any of the literature on this subject. For example, have
>>>>>> you red Robin Douglas Knight's Ph.D thesis?

>>>>> No, I unaware of this thesis.

>>>>>>> To me an intelligent designer
>>>>>>> seems a far more rational explanation for the consistence of the code
>>>>>>> over such a vast span of time and over such a broad distribution of
>>>>>>> existing organisms.

>>>In message <EgPqs.422345$Bz2.125...@fx11.am4>, R. Dean <"R.
>>>Dean"@gmail.com> writes
>>>>On 11/8/2012 12:01 PM, Ernest Major wrote:
>>>>> In message <xkRms.235860$9W6.121...@fx08.am4>, R. Dean <"R.
>>>>> Dean"@gmail.com> writes
>>>>>> On 11/8/2012 6:37 AM, Ernest Major wrote:
>>>>>>> In message <YzIms.126544$W63.121...@fx05.am4>, R. Dean <"R.
>>>>>>> Dean"@gmail.com> writes
>>>>>>>> On 11/6/2012 3:17 PM, Ernest Major wrote:
>>>>>>>>> In message <L5ems.182064$Sr2.106...@fx01.am4>, R. Dean <"R.
>>>>>>>>> Dean"@gmail.com> writes
>>>>>>>>>> I have no problem with saying we simply don't know how life began,
>>>>>>>>>> this, in my view is the far more straight-forward and up-front than
>>>>>>>>>> claiming it happens through natural processes.

>>>>>>>>> Perhaps then you will stop claiming on spurious grounds to know how
>>>>>>>>> life
>>>>>>>>> began.

>>>>>>>>>> The very fact that
>>>>>>>>>> all life functions with the exact same genetic code implies that the
>>>>>>>>>> code must have come about over three billion years ago, and has
>>>>>>>>>> remained, with almost no exceptions, unchanged and stable from the
>>>>>>>>>> beginning.

>>>>>>>>> Why on earth do you think that it as argument against abiogenesis.
>>>>>>>>> (The
>>>>>>>>> near universality of the genetic code and the nature and phylogenetic
>>>>>>>>> distribution of the variants is one of the lines of evidence for
>>>>>>>>> common
>>>>>>>>> descent, but as far I can see it is silent on the question of
>>>>>>>>> spontaneous versus supernatural abiogenesis.)

>>>>>>>> It could just as well be seen as empirical evidence of a common
>>>>>>>> designer. The fact that the universality of the code considering
>>>>>>>> the same genetic code function in the bacteria and blue-green algae
>>>>>>>> that expressed for the forms of the stromatolites, horseshoe Crabs,
>>>>>>>> jelly fish and other still extant ancient forms is the same code: that
>>>>>>>> the genetic code is ubiquitous throughout the plant and animal
>>>>>>>> kingdoms.

>>>>>>> The hypothesis of common descent makes predictions about the genetic
>>>>>>> code. The hypothesis of common design does not. (The putative designer
>>>>>>> could have give every species a different genetic code, to inhibit
>>>>>>> hybridisation, and to inhibit viruses jumping species.)

>>>>>> But why, from an engineers prospective, it makes no sense. If a wheel
>>>>>> serves other functions and purposes why _not_ use it? hybrids usually
>>>>>> do not produce offspring, I know about virus jumping specie, carrying
>>>>>> new genetic data, but how often is this detrimental even fatal?

>>>>>> Therefore the
>>>>>>> putative universality of the genetic code is empirical evidence against
>>>>>>> a common designer. (Note that by invoking separate abiogenesis you are
>>>>>>> moving your expressed position closer to conventional creationism.)

>>>>>> Creationism advocates: 1) a 6 day creation period 6-10,000 years ago;
>>>>>> 2) a universal flood: 3) that creation was by the specific God of the
>>>>>> Bible: I don't know what else they believe. However, Intelligent design
>>>>>> does not advocate this.

>>>>> That is an unhelpfully narrow definition of Creationism.

>>>>It's about all I know, except it based on a few paragraphs in Genesis.
>>>>But this is not what I am defending. Personally, I see I.D. and the
>>>>Genesis creation as two different version of origins.

>>>>The definition
>>>>> I prefer is the religiously motivated rejection of substantial portions
>>>>> of the scientific consensus, especially as related to biology and geology.

>>>>Perhaps this is true of the Genesis account and those who defend it.
>>>>>> The
>>>>>>> nature and phylogenetic distribution of the variants in the genetic code
>>>>>>> is stronger empirical evidence for common descent.

>>>>>> I'm sorry, I disagree.

>>>>> You concede below that you have not read any of the literature on the
>>>>> subject,

>>>>No, I was asked about one man's doctoral thesis. Which I had not heard
>>>>about.

>>>You were asked if you had read any of the literature on the subject -
>>>"Have you read any of the literature on this subject. For example, have
>>>you red Robin Douglas Knight's Ph.D thesis?"

>>>>implying that you are unaware of the nature and phylogenetic
>>>>> distribution of the variants in the genetic code - a conclusion which is
>>>>> confirmed by you bringing up the red herring of As-DNA. This would mean
>>>>> that you have no rational grounds to disagree.

>>>>So, in effect, you are saying that the genetic code is different - not
>>>>universal in different life forms from kingdom, phylum, class etc up
>>>>through species. Is this what you are saying?

>>>Yes. The genetic code is not universal. It differs in a number of
>>>clades. The standard code is used in most prokaryotes and nuclear
>>>genomes in the great majority of eukaryotes. However some bacteria and
>>>some eukaryotes use variant codes, and there are several different
>>>variant mitochondrial codes.

>>>Variant codes are predominantly associated with small genomes, where
>>>conservative selection is weaker.

>>>To reiterate, you are unaware of the nature and phylogenetic
>>>distribution of the variants in the genetic code - that means you have
>>>no rational grounds to disagree with the statement that the nature and
>>>phylogenetic distribution of the variants in the genetic code is
>>>empirical evidence for common descent.

>>You are likely correct about R.Dean's familiarity with what is known
>>about these subjects, but from the cite I provided earlier, ISTM the
>>variations in the DNA code represent a small part of the total:

>><http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapte
>>r=tgencodes#SG2>

>>AIUI most of the differences do not necessarily result in a
>>fundamentally different protein structure on translation.  My
>>impression is these changes occurred gradually over time.
>>Is it your opinion that these different DNA codes were different from
>>the beginning of each lineage and remained unchanged since then?  If
>>so, how do you square that with Common Descent?

>The model for a change to a genetic code is that, due to the redundancy
>in the genetic code (and the existence of codon usage biases) in a small
>genome a particular codon may be used only a few (or even no) times.
>This allows the specificity of a tRNA to drift. (In the case of a stop
>codon this would be one copy of a duplicated tRNA.) The end result of
>this is a different genetic code. If the codon becomes used again
>normalising selection fixes the genetic code.

>Robin Douglas Knight explains this better.

>>>>>>> Have you read any of the literature on this subject. For example, have
>>>>>>> you red Robin Douglas Knight's Ph.D thesis?

>>>>>> No, I unaware of this thesis.

>>>>>>>> To me an intelligent designer
>>>>>>>> seems a far more rational explanation for the consistence of the code
>>>>>>>> over such a vast span of time and over such a broad distribution of
>>>>>>>> existing organisms.

>>>>>>> Except it doesn't.  There are several small variants of the genetic
>>>>>>> code.  "Almost no exceptions" means "definitely some exceptions",
>>>>>>> which
>>>>>>> blows down your claim for stability.  Besides, you do not know what
>>>>>>> the
>>>>>>> genetic code was from the beginning; you only know it since the
>>>>>>> 1960s.

>>>>>> I remember reading about a bacteria incorporating arsenic into its
>>>>>> genetic code and cells.

>>>>> As Ernest has noted, those reports were in error.

>>>>>> What do you mean you only know it since the 1960?

>>>>> It was in the 1960s that the genetic code was first being worked
>>>>> out. To
>>>>> the best of my knowledge, no investigation of the genetic code --
>>>>> i.e.,
>>>>> which codons map to which amino acids -- has been done on any organism
>>>>> which was alive before 1960, and certainly not much before then.
>>>>> Ages-old genetic *sequences* have been worked out, but that is not the
>>>>> same thing.

>>>> OK, it's not difficult to infer that if living organisms contain a code
>>>> which is universal, then certainly all their ancestors must have had
>>>> same ubiquitous genetic code.

>>> Likewise, it's not difficult to infer that if living organisms within my
>>> family are universally named "Isaak", then certainly all our ancestors
>>> must have had the same ubiquitous name.

>>>> If I saw a large oak tree in my yard, I
>>>> would conclude it had to have  been there for years, only my neglect or
>>>> inattention could explain that which I just noticed. I would not
>>>> conclude
>>>> it just popped up, fully grown, set out during the night by the
>>>> designer.

>>> I have seen large trees pop up overnight (well, over a midday) due to
>>> the actions of a designer.  Does your statement above mean that you are
>>> now rejecting intelligent design?

>> I would have to see this for myself.

> In this case, a few palm trees arrived via flatbed truck, and a crane
> helped the landscapers raise them into place.  I believe holes were dug
> in advance.  The trees, of course, would have been grown at a nursery
> over previous years.  There was nothing particularly outstanding about
> the process once you have seen it done.

>>>>> As Ernest has also noted, we can make inferences about the genetic
>>>>> code
>>>>> in earlier life, but those inferences are based on common descent and
>>>>> evolution, which would go out the window if your design idea were
>>>>> correct.

>>>> Evidently, you are misreading me. I do not have a fundamentalist
>>>> view of
>>>> life or design. Please see above.

>>> Okay, you have me at a loss, then.  Does "design" mean anything to you
>>> at all?

>> Yes, it took place eons ago and nothing is happening at the present.

> Could this mean evolution is designed?

>>>> Can you give examples of variant codes? Does the variations argue
>>>> against the universality of the code?

>>> http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chap...

>>> If that link gets mangled, it appears also in the references at
>>> http://en.wikipedia.org/wiki/List_of_genetic_codes

>> Things are back to some kind of normal, but it's a new kind of normal
>> with our grandchild gone. Things have changed - I've changed; things
>> that were important don't seem so now.

> Again, you and your family have my sympathies.

> > That's not true.  It is part of the Second Law of Thermodynamics, not a
> > reversal of it, that entropy can drop locally if coupled to a greater
> > increase of entropy elsewhere.

> Ok, wrong choice of words, but with in input of energy there can be a
> brief decrease of entropy in a given location.

> [...]

> >> God is the magical word.  He is not content with anything less than a
> >> supernatural god.

> >God is a generic term which includes an vast number of fanciful  entities.

> Exactly so, and certaintly not worth presenting as a mechanism for
> creating life.