Is Homology A Result Of Inheritance?

[davidl...@gmail.com]

Evolution surely predicts that homologous structures are the result of inheritance with modification, and are thus should derive from homologous genes. This is completely crucial to the argument of evolution based on the evidence of homology.

I find it disappointing that this claim is not therefore much robustly defended.

What is the up to date evidence?

http://www.talkorigins.org/indexcc/CB/CB811.html

Claim CB811:

Evolutionist Gavin de Beer (1971) has shown that homologous structures arise from different, nonhomologous genes, which means that they cannot be derived from common ancestors.

[broger...@gmail.com]

The short answer is that nowadays people are more careful about the use of the word homologous and do not call structures or sequences homologous unless there is evidence that they are derived from common ancestors.

[broger...@gmail.com]

On Tuesday, August 5, 2014 7:31:11 AM UTC-4, davidl...@gmail.com wrote:

You might try:

http://joelvelasco.net/teaching/systematics/hall%2003%20-%20descent%20with%20modification.pdf

or

http://ib.berkeley.edu/labs/wake/372_homoplasy_ScienceMag.pdf

[Athel Cornish-Bowden]

Not nearly as careful as they should be, however, at least in
protein-sequence work, where it is still common to find expressions
like "70% homology". Many biochemists continue to regard "homologous"
as a synonym of "similar".




--
athel

[Darwin123]

On Tuesday, August 5, 2014 7:31:11 AM UTC-4, davidl...@gmail.com wrote:

That sort of phenomenon was known even before scientists could sequence genes. This type of phenomenon was called either convergent or parallel evolution.

[alias Ernest Major]

On 05/08/2014 12:31, davidl...@gmail.com wrote:
> Evolution surely predicts that homologous structures are the result of inheritance with modification, and are thus should derive from homologous genes. This is completely crucial to the argument of evolution based on the evidence of homology.

You overstate the case. It is conceivable that a gene performing a
function can be replaced by another gene performing the same function
via an intermediate state where both proteins were used. That seems to
be the case for some aminoactly tRNA synthetases

In the vertebrate eye different clades use different repertoires of
crystallins. The alpha and beta/gamma crystallins or more of less
universal (the expression of gamma crystallins is much reduced in
birds), while there are a variety of taxon specific crystallins
(including at least delta, epsilon, eta, zeta, mu, rho, tau).
Cephalopods have the own crystallins, but the omega crystallin of
octopuses has the same origin as the zeta crystallin of vertebrates).

>
> I find it disappointing that this claim is not therefore much robustly defended.
>
> What is the up to date evidence?
>
> http://www.talkorigins.org/indexcc/CB/CB811.html
>
> Claim CB811:
>
> Evolutionist Gavin de Beer (1971) has shown that homologous structures arise from different, nonhomologous genes, which means that they cannot be derived from common ancestors.
>

--
alias Ernest Major

[Roger Shrubber]

Everyone who says percent homology should get their ears boxed,
every time. Alternatively, roll up a hard copy printout of
this or a similar paper

http://bioinformatics.oxfordjournals.org/content/26/19/2498.full

and smack then on the nose with it. And please, at least be
critical when reviewing manuscripts or working with students.
By the way, some of the worst is when software kicks out
things labeled as percent homology, because as we know, people
treat computer output as authoritative holy writ.

[Athel Cornish-Bowden]

Of course, but it won't happen. Reeck et al. (with some distinguished
names among the al.) were saying the same as Marabotti and Facchiano as
long ago as 1987.

> Alternatively, roll up a hard copy printout of
> this or a similar paper

> 1987

> http://bioinformatics.oxfordjournals.org/content/26/19/2498.full
>
> and smack then on the nose with it. And please, at least be
> critical when reviewing manuscripts

I am

> or working with students.

I am.

> By the way, some of the worst is when software kicks out
> things labeled as percent homology, because as we know, people
> treat computer output as authoritative holy writ.

--
athel

[Roger Shrubber]

http://14.139.227.92/mkumar/Teaching/alignment1.pdf
Cell. 1987 Aug 28;50(5):667.
"Homology" in proteins and nucleic acids: a terminology muddle and a way
out of it.
Gerald R. Reeck, Christoph de Ha�n, David C. Teller, Russell F.
Doolittle, Walter M. Fitch, Richard E. Dickerson, Pierre Chambon, Andrew
D. McLachlan, Emanuel Margoliash, Thomas H. Jukes, Emile Zuckerkandl

At the time, I knew 3 of those guys personally. And I like that
reference more.

[davidl...@gmail.com]

Thanks, broger.

Both these papers are not so much a defence of homology but an admission of homoplasy. The notion of "realignment" of homology sounds exactly like PR and so does the tone of much of this first paper. The following is from the conclusion:

> (4) Homoplastic characters turn out to be present to an unexpectedly high degree in phylogenetic analyses of particular lineages.

The second papers seems to express the idea that when we observe homoplasy, what is inherited is the ability to evolve an arm or a wing. I am not positively impressed.

If different kinds of animals are not separately created but evolve through descent via modification, the genetic data should clearly back this up in phylogenetic trees. Instead I am being told:

> Although phylogenetic hypotheses are necessary, they are not always sufficient to resolve major questions involving parallelism and reversibility. Mesoevolution (36) connotes the problem of parallelism, a transitional condition between true homology (recent common ancestry) and true convergence (independent evolution of similarity), convergence (independent evolution of similarity), evolution.

Here the idea of true homology is related to the notion of a recent ancestor, suggesting support for micro-evolution but not macro-evolution. Isn't this evidence of common ancestry within a kind but not across kinds. I will start a new thread on the topic of kinds.

[Athel Cornish-Bowden]

Thabks for giving the full list. I should have given the whole
reference myself, but I thought that as it's given by Marabotti and
Facchiano that was enough. However, it wasn't: the list is even more
distinguished than I remembered -- at least eight household names. I
remembered Fitch, but not the others.


--
athel

[Walter Bushell]

In article <Dc2dnayyBPnQnnzO...@giganews.com>,

Roger Shrubber <rog.sh...@gmail.com> wrote:

> and smack then on the nose with it. And please, at least be
> critical when reviewing manuscripts or working with students.
> By the way, some of the worst is when software kicks out
> things labeled as percent homology, because as we know, people
> treat computer output as authoritative holy writ.

Still? What are they drinking? I want some -- on the gripping hand NO!

--
Never attribute to stupidity that which can be explained by greed. Me.

[John Harshman]

On 8/5/14, 10:16 AM, davidl...@gmail.com wrote:
> On Tuesday, August 5, 2014 2:06:42 PM UTC+1, broger...@gmail.com wrote:
>> On Tuesday, August 5, 2014 7:31:11 AM UTC-4, davidl...@gmail.com wrote:
>>
>>> Evolution surely predicts that homologous structures are the result of inheritance with modification, and are thus should derive from homologous genes. This is completely crucial to the argument of evolution based on the evidence of homology.
>>
>>>
>>
>>>
>>
>>>
>>
>>> I find it disappointing that this claim is not therefore much robustly defended.
>>
>>>
>>
>>>
>>
>>>
>>
>>> What is the up to date evidence?
>>
>>>
>>
>>>
>>
>>>
>>
>>> http://www.talkorigins.org/indexcc/CB/CB811.html
>>
>>>
>>
>>>
>>
>>>
>>
>>> Claim CB811:
>>
>>>
>>
>>>
>>
>>>
>>
>>> Evolutionist Gavin de Beer (1971) has shown that homologous structures arise from different, nonhomologous genes, which means that they cannot be derived from common ancestors.

Incidentally, de Beer showed no such thing. He speculated that this
might be the case, but in the main it turns out not to be. Homologous
structures almost always arise from homologous developmental pathways
with homologous genes. Even some of the basic features of insects and
vertebrates have their origins in homologous genes. I recommend any of
several books by the evo-devo biologist Sean Carroll, e.g. Endless Forms
Most Beautiful.

>> You might try:
>>
>>
>>
>> http://joelvelasco.net/teaching/systematics/hall%2003%20-%20descent%20with%20modification.pdf
>>
>>
>>
>> or
>>
>>
>>
>> http://ib.berkeley.edu/labs/wake/372_homoplasy_ScienceMag.pdf
>
> Thanks, broger.
>
> Both these papers are not so much a defence of homology but an admission of homoplasy. The notion of "realignment" of homology sounds exactly like PR and so does the tone of much of this first paper. The following is from the conclusion:
>
>> (4) Homoplastic characters turn out to be present to an unexpectedly high degree in phylogenetic analyses of particular lineages.
>
> The second papers seems to express the idea that when we observe homoplasy, what is inherited is the ability to evolve an arm or a wing. I am not positively impressed.
>
> If different kinds of animals are not separately created but evolve through descent via modification, the genetic data should clearly back this up in phylogenetic trees. Instead I am being told:
>
>> Although phylogenetic hypotheses are necessary, they are not always sufficient to resolve major questions involving parallelism and reversibility. Mesoevolution (36) connotes the problem of parallelism, a transitional condition between true homology (recent common ancestry) and true convergence (independent evolution of similarity), convergence (independent evolution of similarity), evolution.
>
> Here the idea of true homology is related to the notion of a recent ancestor, suggesting support for micro-evolution but not macro-evolution. Isn't this evidence of common ancestry within a kind but not across kinds. I will start a new thread on the topic of kinds.

I'm afraid you are just picking a few words and phrases out of the
papers you're reading. No, true homology isn't related to the notion of
a recent ancestor, just an ancestor. Consider things at the level of DNA
sequences. We can't be completely sure that any matching bases at
particular sites are homologous; after all, there are only four
possibilities at any one spot. The A you see in two species today could
have originated in two different mutations. We can only decide that
bases are homologous in a statistical sense, i.e. that out of a long
sequence of identical bases, the great majority must be homologous,
because though homoplasy is easy (1/4 chance of identity by chance at
any single site), the similarity of long sequences by chance becomes
increasingly unlikely as length increases. And so the genetic data can
provide us with very, very good evidence of common descent. Humans and
other mammals belong to a single kind, and dozens of genetic studies
show this. Here's one of the first: Hayasaka K, Gojobori T, Horai S.
1988. Molecular phylogeny and evolution of primate mitochondrial DNA.
Mol. Biol. Evol., 5:626-644. I could cite many, many more, based on
many, many genes. They all agree. And since the bible is clear that
humans are a separate kind from all other animals, that settles Genesis
pretty well all by itself.

[davidl...@gmail.com]

On Wednesday, August 6, 2014 1:42:01 PM UTC+1, John Harshman wrote:
> On 8/5/14, 10:16 AM, davidl...@gmail.com wrote:
>
> > On Tuesday, August 5, 2014 2:06:42 PM UTC+1, broger...@gmail.com wrote:
>
> >> On Tuesday, August 5, 2014 7:31:11 AM UTC-4, davidl...@gmail.com wrote:
>
> >>
>
> >>> Evolution surely predicts that homologous structures are the result of inheritance with modification, and are thus should derive from homologous genes. This is completely crucial to the argument of evolution based on the evidence of homology.
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>> I find it disappointing that this claim is not therefore much robustly defended.
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>> What is the up to date evidence?
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>> http://www.talkorigins.org/indexcc/CB/CB811.html
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>> Claim CB811:
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>>
>
> >>
>
> >>> Evolutionist Gavin de Beer (1971) has shown that homologous structures arise from different, nonhomologous genes, which means that they cannot be derived from common ancestors.
>
>
>
> Incidentally, de Beer showed no such thing. He speculated that this
>
> might be the case, but in the main it turns out not to be. Homologous
>
> structures almost always arise from homologous developmental pathways
>
> with homologous genes. Even some of the basic features of insects and
>
> vertebrates have their origins in homologous genes. I recommend any of
>
> several books by the evo-devo biologist Sean Carroll, e.g. Endless Forms
>
> Most Beautiful.

Thanks. I am actually in the middle of reading that.

Commonality is just as much proof of a common designer as common descent.

But common descent would show up in phylogenetic trees made out the parts that are common, and would be largely consistent with each other and cladistic trees.

[Roger Shrubber]

davidl...@gmail.com wrote:

> Commonality is just as much proof of a common designer as common
> descent.

> But common descent would show up in phylogenetic trees made out the
> parts that are common, and would be largely consistent with each
> other and cladistic trees.

With common design, you would not get a tree, you would get a
complex web. You would get chimeras, for example the designer
could easily put feathers on bats. A designer that was
recycling designs could easily borrow across orders or classes
of animals or plants.

You would not get Australia with marsupials becoming the
thylacine, you'd get a proper carnivore like in the rest of
the world. You would not get Madagascar. You would not get
the rift valley cichlids radiating to fill niches that are
filled by completely different types of fish elsewhere.
Those patterns don't make sense with a biblical creation
model. And neither does restricting "designs" to a branching
hierarchy that shows extremely minimal horizontal transfer.

[RonO]

Common design doesn't make the nested similarity unless there is an
evolution of the design over time. It is obvious that there was an ape
genomic template before there was a human genomic template. There was a
simian genomic template before there was an ape genomic template. There
was a prosimian genomic template before there was a simian genomic
template. Before that there was a mammalian genomic template, a
reptilian, an amphibian, a fish etc. Just as biological evolution
indicates. We do not just have the DNA. We have the vast geologic time
and fossil record. Why is it consistent?

Why could a research team decide to look for the transition between fish
and terrestrial tetrapods think that they should look at exposed rock of
a specific age. They didn't determine the age of these rocks a previous
geological team determined the age of the rocks. Why did they search
the globe and decide to dig in the arctic? Why not just dig in some
nice warm relaxing spot?

The fact that you have to learn to live with is that the science is
consistent with a reality that your interpretation of the Bible is not
consistent with. Reality is so consistent that paleontologists can
predict where to dig in order to find what they are searching for. If
we did not know what rocks were between 300 and 400 million years old
there would be no reason to dig in any one place. Look at the region
that they are searching in Africa for our ancestral fossils. They are
looking at exposed rock between 3 and 10 million years old. Why limit
the search? Why are they successful? When Johanson found Lucy he went
to that region because the rock layers exposed by erosion were of the
age he wanted to search for early relatives of us. He did not use the
Bible to tell him where to look.

The simlarlity that we observe in the DNA tells us that life evolved on
this planet over a long period of time. The intelligent design that it
is consistent with is the one proposed by IDiots like Behe who think
that the designer could have put his finger in the pie every once in a
while and stirred. Over half a billion years ago the designer would
have had to take a cordate genomic template and tweeked it into a
vertebrate genomic template. He would have let that diversify for
several million years, and take one lineage and make it into the lobefin
fish lineage. That would diversify over time and one of the lobefin
fish lineages would have been selected to be tweeked into something like
Tiktaalik. Those would have diversified and one of the lineages would
have been tweeked into becoming amphibians, then reptiles, then mammals,
and one of the mammalian lineages would have eventually been tweeked
into becoming us. As our lineage was evolving all other extant lineages
were evolving at the same time. Supposedly being tweeked along their
evolutionary path.

That is the design that the DNA and fossil record tell us happened.
That is very far from your interpretation of the Bible. It is so far
from your interpretation that your inference of your type of design is
obviously wrong.

Scientists are not making this up just to make your religion look bad.
One of the best ways to make a name for yourself in science is to come
up with a new answer for something. You have to live with that reality.

Have any new answers come out of the guys that ran the intelligent
design creationist scam? It is a certainty that no new answers ever
came out of the scientific Biblical young earth creationists, or there
would have been no reason for the intelligent design scam to take the
place of scientific creationism.

Ron Okimoto

[Burkhard]

Roger Shrubber wrote:
> davidl...@gmail.com wrote:
>
>> Commonality is just as much proof of a common designer as common
>> descent.
>
>> But common descent would show up in phylogenetic trees made out the
>> parts that are common, and would be largely consistent with each
>> other and cladistic trees.
>
> With common design, you would not get a tree, you would get a
> complex web. You would get chimeras, for example the designer
> could easily put feathers on bats. A designer that was
> recycling designs could easily borrow across orders or classes
> of animals or plants.

Unless.... the designer(s) are constraint by intellectual property law.
several designers, all allowed to improve only on the design held by
their group, unless there is cross-licensing.

[John Harshman]

This is a common creationist mantra. But it isn't true. You have already
agreed that god wouldn't fake common descent. A nested hierarchy is a
sign of common descent. We see a nested hierarchy. By your own admission
you can't call that evidence for a common designer.

> But common descent would show up in phylogenetic trees made out the
> parts that are common, and would be largely consistent with each other
> and cladistic trees.

Not sure what you mean by "cladistic trees", as that's pretty much a
synonym for "phylogenetic trees". But in fact trees made from different
data tend to agree with each other. That's what I just said. Are you
denying that, or what?

[Mark Isaak]

On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>
> Commonality is just as much proof of a common designer as common descent.

Then the differences must be disproof of a common designer. Right?

--
Mark Isaak eciton (at) curioustaxonomy (dot) net
"Keep the company of those who seek the truth; run from those who have
found it." - Vaclav Havel

[Glenn]

"Mark Isaak" <eci...@curioustax.onomy.net> wrote in message news:ls5geg$qbl$1...@dont-email.me...

> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>> Commonality is just as much proof of a common designer as common descent.
>
> Then the differences must be disproof of a common designer. Right?
>

You are more fundamentalist than he.

[deadrat]

Commonality is evidence for, not proof of, common descent.
Commonality is evidence for a common designer of human-manufactured items.
Everything and anything is evidence of God.

Lotta ignorance packed into thirteen words.

[deadrat]

On 8/9/14 10:58 AM, Mark Isaak wrote:
> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>> Commonality is just as much proof of a common designer as common descent.
>
> Then the differences must be disproof of a common designer. Right?
>

No, the differences are also proof of a common designer. C'mon, get
with the program.

[Vincent Maycock]

Nested hierarchies, or groups within groups, are known to be produced
by the process of descent with modification (almost by definition, of
course, since if a member of a group becomes modified, its descendants
will form a group within the original group, possessing the traits of
the group from which it was descended, plus the modification it added
in that defines the little subgroup it formed).

The difference between the nested hierarchies found in the biological
world, and the ubiquitous nested hierarchies found elsewhere in the
world, is the lack of functional constraint on the biological
hierarchies. Anytime any thing has any use, or even has much of a
logical structure, nested hierarchies will arise to keep track of what
goes where and for what purpose ("I put all these together because
they have this common property because they all have this effect, and
inside that group there are some others that I like to keep together
because they all do this for me in addition to doing what the entire
group does, or have these logical properties, and then inside *that*
group, I've made a file that has all of the previous properties but
with one more useful property that I've added in that I don't want
spread throughout the entire file system -- I want it right here and
only here, for ease of access").

But in the biological world, there is no functional demand for the
gigantic, intricate nested hierarchy found in genetic and
morphological data. There's no logical connection between the huge
percentage of identical DNA bases found when chimps are compared with
humans (as compared to cats, for example), and no functional
requirement for all birds to have feathers, but not bats or
yellowjackets.

The branching, more or less random nature of the biological nested
hierarchy (as compared to the more exact, precise, and orderly nested
hierarchies found in mathematical set theory -- which *do* have a
logical structure, of course, unlike the biological nested
hierarchies) is also more consistent with the results of a more or
less random process like genetic mutation generation, than the product
of some kind of order-producing super-logical Mind of some sort.
Furthermore, we can tell that it *was* mutation and not some other
factor that caused these genetic differences because mutation rates
can be measured, and those rates produce approximately the amount of
change in living things that we would expect if those mutations were
acting over the amounts of time that geologists tell us that they were
acting over.

[Athel Cornish-Bowden]

On 2014-08-09 08:01:38 +0000, davidl...@gmail.com said:

> [ … ]

>
> Commonality is just as much proof of a common designer as common descent.
>
> But common descent would show up in phylogenetic trees made out the
> parts that are common, and would be largely consistent with each other
> and cladistic trees.

Maybe you might like to read David Penny, L. R. Foulds and M. D. Hendy
(1982) "Testing the theory of evolution by comparing phylogenetic trees
constructed from five different protein sequences" Nature 297, 197-200.

Michael Hendy lists a later paper in his list of publications, which I
thought I had read (I certainly remember the title), but probably I'm
mistaken because I've never seen the book:

M.D.Hendy and D.Penny, "How evolution could be falsified, but isn't",
in Fascination of statistics (ed. R.Brook et al.), Marcel Dekker New
York (1986) 173-182.
--
athel

[Steady Eddie]

On Saturday, 9 August 2014 05:29:10 UTC-6, Roger Shrubber wrote:
> davidl...@gmail.com wrote:
>
>
>
> > Commonality is just as much proof of a common designer as common
>
> > descent.
>
>
>
> > But common descent would show up in phylogenetic trees made out the
>
> > parts that are common, and would be largely consistent with each
>
> > other and cladistic trees.
>
>
>
> With common design, you would not get a tree, you would get a
>
> complex web. You would get chimeras,

CHIMERAS?
You think an ancient Greek mythological monster would be the result of intelligent design?
On what grounds?

> for example the designer
>
> could easily put feathers on bats. A designer that was
>
> recycling designs could easily borrow across orders or classes
>
> of animals or plants.

Ok I'm glad you recognized that because that is our whole point.

>
>
> You would not get Australia with marsupials becoming the
>
> thylacine, you'd get a proper carnivore like in the rest of
>
> the world. You would not get Madagascar. You would not get
>
> the rift valley cichlids radiating to fill niches that are
>
> filled by completely different types of fish elsewhere.
>
> Those patterns don't make sense with a biblical creation
>
> model. And neither does restricting "designs" to a branching
>
> hierarchy that shows extremely minimal horizontal transfer.

Ok, you initiated the challenge; go ahead and substantiate your claim that

[Steady Eddie]

On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>
> >
>
> > Commonality is just as much proof of a common designer as common descent.
>
>
>
> Then the differences must be disproof of a common designer. Right?

What an idiot.
The DIFFERENCES are best explained by a DESIGNER.

[Steady Eddie]

I call your bluff.
Show me the math.

[Öö Tiib]

On Monday, 11 August 2014 01:19:07 UTC+3, Steady Eddie wrote:
> On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
> > On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
> > >
> > > Commonality is just as much proof of a common designer as common descent.
> >
> > Then the differences must be disproof of a common designer. Right?
>
> What an idiot.
> The DIFFERENCES are best explained by a DESIGNER.

A designer with rather shaky hands it appears?
http://en.wikipedia.org/wiki/List_of_genetic_disorders

[John Harshman]

On 8/10/14, 3:12 PM, Steady Eddie wrote:

> Ok, you initiated the challenge; go ahead and substantiate your claim that
> Those patterns don't make sense with a biblical creation
> model.

I'm so glad that you are ready to present a biblical creation model. Go
ahead.

[deadrat]

On 8/10/14 5:12 PM, Steady Eddie wrote:
> On Saturday, 9 August 2014 05:29:10 UTC-6, Roger Shrubber wrote:
>> davidl...@gmail.com wrote:
>>
>>
>>
>>> Commonality is just as much proof of a common designer as common
>>
>>> descent.
>>
>>
>>
>>> But common descent would show up in phylogenetic trees made out the
>>
>>> parts that are common, and would be largely consistent with each
>>
>>> other and cladistic trees.
>>
>>
>>
>> With common design, you would not get a tree, you would get a
>>
>> complex web. You would get chimeras,
> CHIMERAS?
> You think an ancient Greek mythological monster would be the result of intelligent design?
> On what grounds?

You're such a fan of the dictionary, look it up. It's definition 2 from
genetics, not definition 1 from mythology.

>
>> for example the designer
>>
>> could easily put feathers on bats. A designer that was
>> recycling designs could easily borrow across orders or classes
>> of animals or plants.
>
> Ok I'm glad you recognized that because that is our whole point.

That bats have feathers? 'Cause they don't.

>
>> You would not get Australia with marsupials becoming the
>> thylacine, you'd get a proper carnivore like in the rest of
>> the world. You would not get Madagascar. You would not get
>> the rift valley cichlids radiating to fill niches that are
>> filled by completely different types of fish elsewhere.
>> Those patterns don't make sense with a biblical creation
>> model. And neither does restricting "designs" to a branching
>> hierarchy that shows extremely minimal horizontal transfer.
>
> Ok, you initiated the challenge; go ahead and substantiate your claim that
> Those patterns don't make sense with a biblical creation
> model.

So how did the kangaroos get to Australia? Are ya going with the
hopping-across-the-Timor-Sea theory?

[deadrat]

On 8/10/14 5:19 PM, Steady Eddie wrote:
> On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
>> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>>>
>>
>>> Commonality is just as much proof of a common designer as common descent.
>>
>>
>>
>> Then the differences must be disproof of a common designer. Right?
>
> What an idiot.
> The DIFFERENCES are best explained by a DESIGNER.

Er, Steadfastly? When everything, differences and commonalities, can be
explained by a designer, then you don't have an explanation. Just Goddidit.

[Mark Isaak]

On 8/10/14 3:19 PM, Steady Eddie wrote:
> On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
>> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>>>
>>
>>> Commonality is just as much proof of a common designer as common descent.
>>
>>
>>
>> Then the differences must be disproof of a common designer. Right?
>
> What an idiot.
> The DIFFERENCES are best explained by a DESIGNER.

So you admit that design, as you use the term, is meaningless. You
could have saved people a lot of time if you said that when you were
first asked what you meant by design.

[Vincent Maycock]

No, there's nothing to bluff about, since anyone familiar with
molecular systematics is aware of how common it is for researchers in
that field to try to calculate divergence times of groups based on
rough estimates of mutation rates, and the fact that these estimates
don't give ridiculous numbers like a minimum of 300 trillion years for
the time of divergence of mammals and reptiles with the maximum
conceivable rate of mutation (and these rates are indeed
well-constrained by empirical data) implies that mutations do have
something do with the genetic differences between living things.

In cases where we don't have direct biochemical measurements of
mutation rates, this "molecular clock" is calibrated by geological
data. Superficially this is circular reasoning, but that would only be
true if you used the rate of mutation derived from the divergence time
of those two groups to show that mutations were responsible for the
genetic divergence of exactly those two groups; if you apply that
calibration method to *other* groups, one would wonder what process is
forcing the other groups to match up with their time of appearance in
the fossil record, as predicted by the mutation rate calculated using
the calibration of the molecular clock using the first two groups.

And that's just the beginning of the involvement of mutations with the
genetic differences between major groups of living things. Genes
which code for functionally less constrained proteins can be expected
on theoretical grounds to evolve more quickly, and when we compare two
groups, they tend to be more dissimilar in the parts of DNA that code
for exactly those types of proteins, indicating again that it's the
mutation process that's leading to the DNA differences between the
major groups. More generally, it's common for molecular systematists
to talk about how "such and such a protein is known to evolve at a
high rate, or mitochondrial DNA evolves at a higher rate than nuclear
DNA, and that's why we find this large divergence between groups when
we use those high-rate evolvers as a measure of genetic divergence."

So that's pretty much the big picture on the reasons why we think
mutations are responsible for the major genetic differences between
living things (if we ever had to wonder, really; I mean seriously,
since mutations happen in the genome, and nothing much else, and there
are differences in the genome, you would really have to suspect that
it was the mutations in there causing the differences and not Super
Yahweh of the Bible or whatever fantasy Fundamentalists want to think
up as an alternative was responsible).

And the fact that mutations are responsible for genetic divergences
among living things is just a subset of the more general evidence that
the genome in general has been modified by physical processes, and not
The Divine Command of Yahweh; other examples of this set of processes
include evidence that many genomes have undergone the physical
processes of gene duplication, genome duplication, and DNA viral
insertion.

Now, you wanted some math, as in you were in your mode where you're
pretending to want to learn rather than your usual blustering attempts
to bolster your religious prejudices with attempts at criticizing the
scientific data. The following Web site outlines the basics of
calculating the chimp-human divergence time from known measured
mutation rates among humans:

http://sandwalk.blogspot.com/2013/03/estimating-human-mutation-rate.html

You can use that, or you can use Wikipedia's numbers to do the
calculations yourself. I'll take the latter route, and you can follow
either Larry Moran's reasoning there or mine here.

The human genome is about 3200 mega-bases long (or 3.2*10^9 bases;
we'll be using scientific notation to simply and clarify the
calculation). The human mutation rate is about a couple of hundred
millionths of a mutation per base pair per generation, according to
Wikipedia, i.e., 10^-9 yr-1, if you want to use fancy hertz notation
for the mutation rate, but written out in long-hand this would be
10^-9 mutations per base pair per year, where I've converted from
generations to years by assuming a generation time of 20 years). This
idea of mutations per base pair per year seems too complex to allow us
to use our familiar formula of

distance = rate * time

but it's not really. The quantity "mutations per base pair per year,"
with all those per's in it is just a regular rate of change if we
refer to mutations per base pair as the quantity whose rate of change
we calculate by dividing by years. So let's plug it into the distance
formula

rate = 10^-9 yr -1 (i.e., that many something or others per year,
where the something or other is the concatenation of words: mutations
per base pair). Okay.

time = ?

Well, we can estimate this from our knowledge of hominid evolution.
The first australopithecines showed up around 4 million years ago.
These primitive ape-human intermediates are similar enough to
chimpanzees that a round number of 5 million years for the time of
divergence between chimps and humans is not unreasonable.

so time = 5 million years = 5*10^6

Plug in the numbers to get:

(10^-9) *( 5*10^6)

Now, because we're using scientific notation, you don't even have to
use your calculator to do this multiplication (remember that with
scientific notation, you just add or subtract the exponents and leave
the other numbers alone). We get

5*10^-3 (since we added the -9 exponent to the 6 exponent
to get -3, and put the 5 right next to it)


Because our changing quantity was (mutations per base pair) per
(year), when we multiplied by years, we got mutations per base pair.
Now let's use the known size of the human genome, 3.2*10^9 bp, to
calculate how many mutations in one genome that would be (since
(mutations/base pair)*(base pair/genome) should equal mutations per
genome (using the type of dimensional analysis they taught us in high
school chemistry, or the laws of fraction cancellation we learned in
high school algebra). That's

(3.2*10^9) * (5*10^-3)

or 16*10^6

(with scientific notation, you actually have to multiply the
non-exponent numbers if there's more than one of them; you can't just
put the five there to get the answer like we did in the first
calculation; but your calculator will do this for you, so nothing to
worry about there). 16*10^6 is of course 16 million, since 10^6 is
a million.

That means in 5 million years, 16 million mutations would have
occurred in a mutating human or chimp genome. So if the human and
chimp genomes physically separated from each other 5 million years ago
and began to become different from each other due to the mutation
process, 16 million mutations would have occurred in the human genome
and 16 million mutations would have occurred in the human genome. The
human and chimp genomes are approximately the same size, so that we
can consider this to be one big genome of 3.2 giga bases (i.e., 3200
mega bases) that has accumulated 32 million mutations in it, 16
million from the human part of it that was mutating for 5 million
years, and 16 million from the chimp part of it that was mutating for
16 million years. What percentage of this genome has mutations in it?
To get that, we'll just divide the number of mutations by the size of
the genome.

The rules of scientific notation become a bit too unwieldy for this
last step in the calculation, so we'll just use regular numbers:

32 million/3.2 billion = 0.01

That means 1% of this big human-and-chimpanzee genome entity should
have mutations in it, which is pretty much the same thing as saying
that there should be a 1% difference between chimps and humans in
their genomes. Wikipedia lists the chimp-human difference as less
than 2%, so it looks like we got the right answer using the idea that
mutations (and not the Power of Jesus at Creation) are the source of
the genetic differences between chimps and humans.

Now, that being said, I have one more thing to say. You seized on the
last statement in my post about the origin of nested hierarchies, as
if that nested-hierarchy evidence for evolution was somehow weaker
than the math-based one you claimed you were interested in. But I'm
not going to buy the idea that you evaluate the evidence in such an
idiotic proof-text based manner.

You don't need a mathematical disproof of your views; the smoking-gun
association of the biological nested hierarchy with common descent
(due to its lack of functional or logical structure) should in itself
have been enough to show you that you evolution is the correct
explanation of the origin of life's diversity -- unless you want to be
an irrational person, in which case there's no hope for you.

[TomS]

"On Mon, 11 Aug 2014 05:07:58 -0400, in article
<g3ugu9pf08mi6bs3j...@4ax.com>, Vincent Maycock stated..."
[...snip...]

>You don't need a mathematical disproof of your views; the smoking-gun
>association of the biological nested hierarchy with common descent
>(due to its lack of functional or logical structure) should in itself
>have been enough to show you that you evolution is the correct
>explanation of the origin of life's diversity -- unless you want to be
>an irrational person, in which case there's no hope for you.

This nested hierarchy has been found to be explained by common descent
with non-directed modifications in two other completely different fields
of study: the history of languages and the history of manuscript
traditions. The fit is so good that the computer software developed for
biology has been used for languages and manuscripts.

(I'd also note that the use of this model in biology is substantially
stronger for a few reasons. Languages and manuscripts borrow from
one another more often than the similar case in biology. The quantity
of information for biology is much greater than for languages and
manuscripts. The predictive power in the case of biology is much more,
and it ties together different features of living things: It began from
studies of anatomy and embryology, and continued with the discovery of
DNA.)

And then, no one has even suggested another explanation for this
complex web of information which makes predictions. (Much more complex,
and more predictive than something like the structure of the eye or
the flagellum; and thus more in need of explanation.) "Prudence, indeed,
will dictate that [science] long established should not be changed for
light and transient causes ..." (Geocentrism was not overthrown by just
pointing out difficulties with it, but was replaced by a well-worked
out heliocentric model.)

And, of course, the tree of life is only one of the kinds of evidence
for an evolutionary history of life as we know it.


--
La trahison des images, Ren� Magritte ("Ceci n'est pas un pipe")
"the map is not the territory", Alfred Korzbyski
Design is not production.
---Tom S.

[Steady Eddie]

You deleted your argument and added words to my statement. That makes you an idiot and a coward.

[Steady Eddie]

Waiting...

[Steady Eddie]

On Sunday, 10 August 2014 17:21:21 UTC-6, John Harshman wrote:

Sorry, you're not a coward; I thought you added words to my comment but you didn't. I retract
that insult.

[Steady Eddie]

When everything can be explained by a designer, it's called a COMPREHENSIVE explanation, idiot.

[Steady Eddie]

HA ha ha. What a twisted thought.
Now you're saying that because design explains both similarities and differences, it is invalid!
I would call that an inference to the best explanation.
By the way, do you claim that EVOLUTION explains both the similarities and differences in life?
If so, your theory is just as invalid as mine.
If not, your theory is inadequate.

[Burkhard]

Steady Eddie wrote:
> On Sunday, 10 August 2014 18:21:52 UTC-6, Mark Isaak wrote:
>> On 8/10/14 3:19 PM, Steady Eddie wrote:
>>
>>> On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
>>
>>>> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>>>>
>>
>>>>>
>>
>>>>
>>
>>>>> Commonality is just as much proof of a common designer as common descent.
>>
>>>>
>>
>>>>
>>
>>>>
>>
>>>> Then the differences must be disproof of a common designer. Right?
>>
>>>
>>
>>> What an idiot.
>>
>>> The DIFFERENCES are best explained by a DESIGNER.
>>
>>
>>
>> So you admit that design, as you use the term, is meaningless. You
>>
>> could have saved people a lot of time if you said that when you were
>>
>> first asked what you meant by design.
>>
>>
>>
>> --
>>
>> Mark Isaak eciton (at) curioustaxonomy (dot) net
>>
>> "Keep the company of those who seek the truth; run from those who have
>>
>> found it." - Vaclav Havel
>
> HA ha ha. What a twisted thought.
> Now you're saying that because design explains both similarities and differences, it is invalid!
> I would call that an inference to the best explanation.

Then you'd be wrong. A theory that without constraints explains
everything doesn't explain anything at all.

> By the way, do you claim that EVOLUTION explains both the similarities and differences in life?
> If so, your theory is just as invalid as mine.
> If not, your theory is inadequate.
>

It's doing rather more than that, it explains precisely why we see the
specific patterns of similarity and dissimilarity. And that is a crucial
difference, with that, we get testable claims - not every difference or
similarity that we could in theory observe is permitted by the theory.

[John Harshman]

I didn't delete my argument either; I deleted someone else's argument.
Care to retract the other insult too?

But I really would like to see the biblical creation model. What is it?
Go into as much detail as you can, and try to make it testable.

[John Harshman]

Nobody can answer until you tell us what a biblical creation model
entails. How many kinds are there? How do you tell whether two organisms
belong to the same or different kinds? How much change (evolution?) has
there been since creation? Did it all happen in a week? Etc.

[TomS]

"On Mon, 11 Aug 2014 07:38:48 -0700, in article
<v9adneqRUsrkSHXO...@giganews.com>, John Harshman stated..."
[...snip...]

>Nobody can answer until you tell us what a biblical creation model
>entails. How many kinds are there? How do you tell whether two organisms
>belong to the same or different kinds? How much change (evolution?) has
>there been since creation? Did it all happen in a week? Etc.
>

Here's a simple request and a suggestion as to what a biblical
model ought to be able to tell us.

What was it like on day six when the cattle-kind were created?

Was it just a couple of individuals of the cattle-kind that made
their sudden appearance, or was it a whole herd? What was their
apparent age? When they first appeared, was there already the
remains of food in their digestive tract (were they chewing their
cud, for example)? Did they have the kind of knowledge which
mammals typically learn only by experience? Did they recognize
one another (mother and calf, for example)? What kind of activity
were they engaged in?

The biological family (taking that as a first approximation to
"kind") contains a diverse number of species, including in addition
to cows, also sheep and goats - well, you look that up in Wikipedia.
What did this individual of the cattle-kind look like?

ISTM that these are obvious, simple questions which the large
number of scientists and clever people who have taken the biblical
model seriously as an alternative should have suggested answers
for.

[Mark Isaak]

On 8/11/14 5:11 AM, Steady Eddie wrote:
> On Sunday, 10 August 2014 18:21:52 UTC-6, Mark Isaak wrote:
>> On 8/10/14 3:19 PM, Steady Eddie wrote:
>>> On Saturday, 9 August 2014 09:58:09 UTC-6, Mark Isaak wrote:
>>>> On 8/9/14 1:01 AM, davidl...@gmail.com wrote:
>>
>>>>> Commonality is just as much proof of a common designer as common descent.
>>
>>>> Then the differences must be disproof of a common designer. Right?
>>
>>> What an idiot.
>>> The DIFFERENCES are best explained by a DESIGNER.
>>
>> So you admit that design, as you use the term, is meaningless. You
>> could have saved people a lot of time if you said that when you were
>> first asked what you meant by design.
>

> HA ha ha. What a twisted thought.
> Now you're saying that because design explains both similarities
> and differences, it is invalid!

Of course. An "explanation" that explains everything explains nothing.
An explanation needs to say why something is one way and not another,
or it is pointless, meaningless, because it works just as well at
"explaining" why things should be entirely different than they are. By
your own admission, the design inference disallows the "not another"
part. If the similarities were differences and the differences were
similarities, design theory would give you the same answer. If anything
were arranged any which way, design theory would give you the same answer.

If I told you that "foo" was the correct answer to every mathematical
equation ever written, would you think it was a good answer? Design
theory is the equivalent of that sort of universal answer.

> I would call that an inference to the best explanation.

What is your measure of "best"? Containing the most pablum?

> By the way, do you claim that EVOLUTION explains both the
> similarities and differences in life?

Evolution explains the *pattern* of similarities and differences. If
the pattern were different, evolution could not be the explanation.

[TomS]

"On Mon, 11 Aug 2014 07:38:48 -0700, in article
<v9adneqRUsrkSHXO...@giganews.com>, John Harshman stated..."
[...snip...]

>Nobody can answer until you tell us what a biblical creation model
>entails. How many kinds are there? How do you tell whether two organisms
>belong to the same or different kinds? How much change (evolution?) has
>there been since creation? Did it all happen in a week? Etc.
>

[jillery]

You're using different meanings of "everything". In order for
something to be a comprehensive (or COMPREHENSIVE) explanation, it
needs to be explain the evidence of what is known to be correct and
incorrect, and to make distinctions between possible outcomes. In
that sense, Big Bang, Evolution, Relativity, and the Standard Model
are comprehensive explanations.

The problem with the Common Design hypothesis that assumes an
omnipotent or unknown designer, is that such a designer could do
anything. That hypothesis can't distinguish between a biosphere
created yesterday fully formed, and one that evolved over billions of
years into it's present form. The Common Design hypothesis is
consistent with all possibilities, and so it explains none of them.

[eridanus]

El s�bado, 9 de agosto de 2014 12:29:10 UTC+1, Roger Shrubber escribi�:

> davidl...@gmail.com wrote:
>
>
>
> > Commonality is just as much proof of a common designer as common
>
> > descent.
>
>
>

> > But common descent would show up in phylogenetic trees made out the
>
> > parts that are common, and would be largely consistent with each
>
> > other and cladistic trees.
>
>
>
> With common design, you would not get a tree, you would get a
>

> complex web. You would get chimeras, for example the designer

>
> could easily put feathers on bats. A designer that was
>
> recycling designs could easily borrow across orders or classes
>
> of animals or plants.
>
>
>

> You would not get Australia with marsupials becoming the
>
> thylacine, you'd get a proper carnivore like in the rest of
>
> the world. You would not get Madagascar. You would not get
>
> the rift valley cichlids radiating to fill niches that are
>
> filled by completely different types of fish elsewhere.
>
> Those patterns don't make sense with a biblical creation
>
> model. And neither does restricting "designs" to a branching
>
> hierarchy that shows extremely minimal horizontal transfer.

it seems a persuasive arguments except when someone would tell you
you cannot put barriers to the whims of a god. Then, you must go
to consult the bible, to see why it does not tell about kangaroos,
or chimps, etc. It seems the holy writer was simple talking about
what he knew that existed. Not that god was dictating what to
write. For if god was telling the writer what he had done and
the correct order or the sequence of creations... the writer would
that written a different story. It would had not written the story
of the Flood, by example.
Eri

[deadrat]

Yes, of course. You've just given the thing a different label, but the
problem isn't with the label; it's with the thing labeled. If you have
an explanation that can explain any evidence, then it's not falsifiable,
so it's not scientific. It has too much explanatory power.

There's nothing you can throw at Goddidit that Goddidit can't explain.
That's because God is omnipotent: he can do anything. There's really
no point in examining the biosphere because a priori we know that God
could arrange anything we find.

[deadrat]

No, for evolution there are some types of similarities and difference
that it couldn't explain.

[Öö Tiib]

You can explain differences with mutations and you can explain
commonality with common decent. It is done in great detail, down
to nucleotide. That is comprehensive.

You can also explain both with "Goddidit, idiot, LOL". That is
avoiding saying anything comprehensive.

[Nick Roberts]

In message <g3ugu9pf08mi6bs3j...@4ax.com>

Vincent Maycock <vam...@aol.com> wrote:

> On Sun, 10 Aug 2014 15:26:58 -0700 (PDT), Steady Eddie
> <1914o...@gmail.com> wrote:
>
> >On Sunday, 10 August 2014 02:39:54 UTC-6, Vincent Maycock wrote:

[SNIP]

I think you've signally failed to understand Steadly's post. When he
says "show me the math", he doesn't want you to show him the
mathematical derivation, just as when he posts "Cite?" he isn't
actually asking for a cite.

He doesn't want an answer (because he won't understand it) - he's just
playing for time, and trying to sound all sciency.

--
Nick Roberts tigger @ orpheusinternet.co.uk

Hanlon's Razor: Never attribute to malice that which
can be adequately explained by stupidity.

[jillery]

You're almost certainly right. Which is a real shame, because Vincent
Maycock's mathematical explanation is most impressive.

[Vincent Maycock]

On Mon, 11 Aug 2014 23:27:08 +0100, Nick Roberts
<tig...@orpheusinternet.co.uk> wrote:

That's what I told him before I did it, but I couldn't assume that he
would agree with me, in which case refusing to do the calculation on
the grounds that he wasn't interested in it (which he probably wasn't)
would look from his perspective like an inability to do it.

>just as when he posts "Cite?" he isn't
>actually asking for a cite.
>
>He doesn't want an answer (because he won't understand it)

That's probably true. He recently admitted that he doesn't
understand macroevolution, and if high school biology is a problem for
him, the even more confusing subject of mathematical biology is going
to cause him even more problems. So when deciding whether or not to
do the SE calculation, there were two excuses not to: he doesn't give
a damn about the answer, and he wouldn't understand the answer if he
did want to know the answer. Both reasons were insufficient to avoid
the calculation, though, on the grounds that these reasons might be
difficult to prove unless the calculation was done.

[Nick Roberts]

In message <chjju9p3ufd6qm3v4...@4ax.com>

Although I doubt if Steadly was in the slightest bit interested (and
could understand it), as per jillery I do appreciate the effort.

> >just as when he posts "Cite?" he isn't
> >actually asking for a cite.
> >
> >He doesn't want an answer (because he won't understand it)
>
> That's probably true. He recently admitted that he doesn't
> understand macroevolution, and if high school biology is a problem
> for him, the even more confusing subject of mathematical biology is
> going to cause him even more problems. So when deciding whether or
> not to do the SE calculation, there were two excuses not to: he
> doesn't give a damn about the answer, and he wouldn't understand the
> answer if he did want to know the answer. Both reasons were
> insufficient to avoid the calculation, though, on the grounds that
> these reasons might be difficult to prove unless the calculation was
> done.

It's just such a shame that the invincible ignorance of Steadly and his
ilk (or "kind"?) make them incapable of ever coming close to
understanding the grandeur of reality, and have to make do with a few
thousand pages of mistranslated Hebrew.

I can sort-of appreciate those who have managed to successfully
integrate their faith and science, and see their science as a way of
revealing the glory of their God; while what comes out most strongly
from YEC and OEC adherents is a small-minded determination that their
God will do as he is told.

> > - he's just
> >playing for time, and trying to sound all sciency.
>

[Roger Shrubber]

I don't read your posts except where they are quoted by
others. This is because you steadily avoid question while
being obnoxious in demanding answers from others. That's
just too obviously an immature scam for my tastes. However,
I will answer.

> Nobody can answer until you tell us what a biblical creation model
> entails. How many kinds are there? How do you tell whether two
> organisms belong to the same or different kinds? How much change
> (evolution?) has there been since creation? Did it all happen in a
> week? Etc.

My comment about a nested tree being consistent with a
common descent model but not a 'common design' model does
assume some things, largely from filling in the blanks
of apologists invoking design arguments.

They keep claiming that the reason for similarities between
species is that "designs" are being recycled. However, if
that were the case, there's no legitimate reason why the
next weasil species has to borrow from other weasil-like
species exclusively. It could borrow from canines or feline
and we know that, at a biochemical level, the various
enzymes or structural proteins would work just as well.

So 'common design' does not explain the pattern. Instead,
you need many additional arbitrary and functionally irrational
constraints regarding which other 'designs' to recycle.

Short version: the observed details are consistent with
common descent but not by a creator who could freely pick
and choose across all of life. No, you need to invent
some extensive additional constraints to achieve the observed
pattern.

And of course, as John notes, no design advocates ever
rise that that challenge.

[Steady Eddie]

What an idiot.

[Nick Roberts]

In message <d6ff3981-242c-4f8d...@googlegroups.com>

So you are simply going to join the long list of desighn advocates who
never rise to the challenge without any attempt to refute the claim?

No response at all? That's all you've got? Zilch? Nada? Nil? Zero?

[Bob Casanova]

On Sat, 16 Aug 2014 12:51:25 +0100, the following appeared
in talk.origins, posted by Nick Roberts
<tig...@orpheusinternet.co.uk>:

You left out "and post cut/pastes from references you
understand poorly, if at all".
--

Bob C.

"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"

- Isaac Asimov

[Steady Eddie]

On Sunday, 10 August 2014 02:39:54 UTC-6, Vincent Maycock wrote:

> On Sat, 09 Aug 2014 06:06:32 -0700, John Harshman
>
> <jhar...@pacbell.net> wrote:
>
>
>
> >On 8/9/14, 1:01 AM, davidl...@gmail.com wrote:
>
> >> On Wednesday, August 6, 2014 1:42:01 PM UTC+1, John Harshman wrote:
>
> >>> On 8/5/14, 10:16 AM, davidl...@gmail.com wrote:
>
> >>>
>
> >>>> On Tuesday, August 5, 2014 2:06:42 PM UTC+1, broger...@gmail.com wrote:
>
> >>>
>
> >>>>> On Tuesday, August 5, 2014 7:31:11 AM UTC-4, davidl...@gmail.com wrote:
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> Evolution surely predicts that homologous structures are the result of inheritance with modification, and are thus should derive from homologous genes. This is completely crucial to the argument of evolution based on the evidence of homology.
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> I find it disappointing that this claim is not therefore much robustly defended.
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> What is the up to date evidence?
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> http://www.talkorigins.org/indexcc/CB/CB811.html
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> Claim CB811:
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>> Evolutionist Gavin de Beer (1971) has shown that homologous structures arise from different, nonhomologous genes, which means that they cannot be derived from common ancestors.
>
> >>>
>
> >>>
>
> >>>
>
> >>> Incidentally, de Beer showed no such thing. He speculated that this
>
> >>>
>
> >>> might be the case, but in the main it turns out not to be. Homologous
>
> >>>
>
> >>> structures almost always arise from homologous developmental pathways
>
> >>>
>
> >>> with homologous genes. Even some of the basic features of insects and
>
> >>>
>
> >>> vertebrates have their origins in homologous genes. I recommend any of
>
> >>>
>
> >>> several books by the evo-devo biologist Sean Carroll, e.g. Endless Forms
>
> >>>
>
> >>> Most Beautiful.
>
> >>
>
> >> Thanks. I am actually in the middle of reading that.
>
> >>
>
> >>>>> You might try:
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>> http://joelvelasco.net/teaching/systematics/hall%2003%20-%20descent%20with%20modification.pdf
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>> or
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>>
>
> >>>
>
> >>>>> http://ib.berkeley.edu/labs/wake/372_homoplasy_ScienceMag.pdf
>
> >>>
>
> >>>>
>
> >>>
>
> >>>> Thanks, broger.
>
> >>>
>
> >>>>
>
> >>>
>
> >>>> Both these papers are not so much a defence of homology but an admission of homoplasy. The notion of "realignment" of homology sounds exactly like PR and so does the tone of much of this first paper. The following is from the conclusion:
>
> >>>
>
> >>>>
>
> >>>
>
> >>>>> (4) Homoplastic characters turn out to be present to an unexpectedly high degree in phylogenetic analyses of particular lineages.
>
> >>>
>
> >>>>
>
> >>>
>
> >>>> The second papers seems to express the idea that when we observe homoplasy, what is inherited is the ability to evolve an arm or a wing. I am not positively impressed.
>
> >>>
>
> >>>>
>
> >>>
>
> >>>> If different kinds of animals are not separately created but evolve through descent via modification, the genetic data should clearly back this up in phylogenetic trees. Instead I am being told:
>
> >>>
>
> >>>>
>
> >>>
>
> >>>>> Although phylogenetic hypotheses are necessary, they are not always sufficient to resolve major questions involving parallelism and reversibility. Mesoevolution (36) connotes the problem of parallelism, a transitional condition between true homology (recent common ancestry) and true convergence (independent evolution of similarity), convergence (independent evolution of similarity), evolution.
>
> >>>
>
> >>>>
>
> >>>
>
> >>>> Here the idea of true homology is related to the notion of a recent ancestor, suggesting support for micro-evolution but not macro-evolution. Isn't this evidence of common ancestry within a kind but not across kinds. I will start a new thread on the topic of kinds.
>
> >>>
>
> >>>
>
> >>>
>
> >>> I'm afraid you are just picking a few words and phrases out of the
>
> >>>
>
> >>> papers you're reading. No, true homology isn't related to the notion of
>
> >>>
>
> >>> a recent ancestor, just an ancestor. Consider things at the level of DNA
>
> >>>
>
> >>> sequences. We can't be completely sure that any matching bases at
>
> >>>
>
> >>> particular sites are homologous; after all, there are only four
>
> >>>
>
> >>> possibilities at any one spot. The A you see in two species today could
>
> >>>
>
> >>> have originated in two different mutations. We can only decide that
>
> >>>
>
> >>> bases are homologous in a statistical sense, i.e. that out of a long
>
> >>>
>
> >>> sequence of identical bases, the great majority must be homologous,
>
> >>>
>
> >>> because though homoplasy is easy (1/4 chance of identity by chance at
>
> >>>
>
> >>> any single site), the similarity of long sequences by chance becomes
>
> >>>
>
> >>> increasingly unlikely as length increases. And so the genetic data can
>
> >>>
>
> >>> provide us with very, very good evidence of common descent. Humans and
>
> >>>
>
> >>> other mammals belong to a single kind, and dozens of genetic studies
>
> >>>
>
> >>> show this. Here's one of the first: Hayasaka K, Gojobori T, Horai S.
>
> >>>
>
> >>> 1988. Molecular phylogeny and evolution of primate mitochondrial DNA.
>
> >>>
>
> >>> Mol. Biol. Evol., 5:626-644. I could cite many, many more, based on
>
> >>>
>
> >>> many, many genes. They all agree. And since the bible is clear that
>
> >>>
>
> >>> humans are a separate kind from all other animals, that settles Genesis
>
> >>>
>
> >>> pretty well all by itself.

>
> >>
>
> >> Commonality is just as much proof of a common designer as common descent.
>
> >
>

> >This is a common creationist mantra. But it isn't true. You have already
>
> >agreed that god wouldn't fake common descent. A nested hierarchy is a
>
> >sign of common descent.
>
>
>
> Nested hierarchies, or groups within groups, are known to be produced
>
> by the process of descent with modification (almost by definition, of
>
> course, since if a member of a group becomes modified, its descendants
>
> will form a group within the original group, possessing the traits of
>
> the group from which it was descended, plus the modification it added
>
> in that defines the little subgroup it formed).
>
>
>
> The difference between the nested hierarchies found in the biological
>
> world, and the ubiquitous nested hierarchies found elsewhere in the
>
> world, is the lack of functional constraint on the biological
>
> hierarchies. Anytime any thing has any use, or even has much of a
>
> logical structure, nested hierarchies will arise to keep track of what
>
> goes where and for what purpose ("I put all these together because
>
> they have this common property because they all have this effect, and
>
> inside that group there are some others that I like to keep together
>
> because they all do this for me in addition to doing what the entire
>
> group does, or have these logical properties, and then inside *that*
>
> group, I've made a file that has all of the previous properties but
>
> with one more useful property that I've added in that I don't want
>
> spread throughout the entire file system -- I want it right here and
>
> only here, for ease of access").
>
>
>
> But in the biological world, there is no functional demand for the
>
> gigantic, intricate nested hierarchy found in genetic and
>
> morphological data. There's no logical connection between the huge
>
> percentage of identical DNA bases found when chimps are compared with
>
> humans (as compared to cats, for example), and no functional
>
> requirement for all birds to have feathers, but not bats or
>
> yellowjackets.

>
>
>
> The branching, more or less random nature of the biological nested
>
> hierarchy (as compared to the more exact, precise, and orderly nested
>
> hierarchies found in mathematical set theory -- which *do* have a
>
> logical structure, of course, unlike the biological nested
>
> hierarchies) is also more consistent with the results of a more or
>
> less random process like genetic mutation generation, than the product
>
> of some kind of order-producing super-logical Mind of some sort.
>
> Furthermore, we can tell that it *was* mutation and not some other
>
> factor that caused these genetic differences because mutation rates
>
> can be measured, and those rates produce approximately the amount of
>
> change in living things that we would expect if those mutations were
>
> acting over the amounts of time that geologists tell us that they were
>
> acting over.

-so goes the theory.

[Nick Roberts]

In message <0c24d5a5-2501-4ab4...@googlegroups.com>

So still no counter-argument? That's it? Nothing about the evidence,
the interpretation, the logic?

You're just going to wave it away with a nothing?

You demonstrate all that is best about ID theory - its lack or rigour,
refusal to engage in real science, and above all its vacuity. You
should be proud.

[Steady Eddie]

On Thursday, 21 August 2014 10:55:25 UTC-6, Nick Roberts wrote:
> In message <0c24d5a5-2501-4ab4...@googlegroups.com>
>

Nested hierarchy is just as much an indication of design as any explanation you have espoused.
I just laugh at the wide-eyed childishness of claiming "nested hierarchies - therefore neoDarwinism!"

[RonO]

You would be the first to demonstrate that if you want to try. Go for
it. Don't you want to be the first at something? Why hasn't any ID
perp demonstrated your assertion? Why can't you find such a
demonstration and all you get is bluster and unsubstantiated claims. So
just do it. Demonstrate that design would generate the nested hierarchy
that we observe in nature. Remember that all extant life shows this
nesting so it has to be that universal.

All real science needs to generate the nesting is cell theory (look it
up because you likely don't even know what it is, but it is a basic
concept in biology) and descent with modification. How would you create
the nesting using design? Go for it. You would be the first and could
become world famous if your try ever amounted to anything.

http://en.wikipedia.org/wiki/Cell_theory
http://evolution.berkeley.edu/evosite/evo101/IIIADescent.shtml

Ron Okimoto

[solar penguin]

On Sun, 31 Aug 2014 05:43:57 -0700, Steady Eddie wrote:

>
> Nested hierarchy is just as much an indication of design as any
> explanation you have espoused.

Is it? If so, then all objects designed by humans should fit uniquely
into one single nested hierarchy. Do they? What is this hierarchy? Who
discovered it? And where exactly do flint arrowheads, chocolate sponge
cakes, New York, and the Mona Lisa all fit into it?

> I just laugh at the wide-eyed
> childishness of claiming "nested hierarchies - therefore neoDarwinism!"

Yes, that would be a silly thing to claim. Good job that what people are
actually claiming is “one single unique nested hierarchy - therefore
descent with modification from one single common ancestor, for which the
best explanation is neoDarwinism."

This has been explained to you before, but you don't seem to have taken
it in...

[Mark Isaak]

On 8/31/14 5:43 AM, Steady Eddie wrote:
> [...]

> Nested hierarchy is just as much an indication of
> design as any explanation you have espoused.

Wrong. Nested hierarchy is very different from what intelligent design
produces. Don't you know anything about design?

[Nick Roberts]

In message <ltvd7f$8im$1...@dont-email.me>

Mark Isaak <eci...@curioustax.onomy.net> wrote:

> On 8/31/14 5:43 AM, Steady Eddie wrote:
> > [...]
> > Nested hierarchy is just as much an indication of
> > design as any explanation you have espoused.
>
> Wrong. Nested hierarchy is very different from what intelligent
> design produces. Don't you know anything about design?

Be fair - an Intelligent Designer _could_ produce a nested hierarchy.
Of course, it's a very inefficient method of design, and is indicative
of a designer who is deliberately trying to make his designs look like
they evolved as there is no reason other than deception why they
should, but that's another matter.

If SE is willing to accept a deliberately deceptive designer (who is
also remarkably shy about revealing his presence) then fine.

[jillery]

On Sun, 31 Aug 2014 05:43:57 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>Nested hierarchy is just as much an indication of design as any explanation you have espoused.
>I just laugh at the wide-eyed childishness of claiming "nested hierarchies - therefore neoDarwinism!"

Intelligent design as practiced by humans applies features to
functions, regardless of historical origin. As a trivial example, the
feature of an electric start motor was designed independently into
many lines of automobiles more or less at the same time. Because of
that, the existence of electric start motors isn't evidence for the
relationships among automobiles.

OTOH biological evolution is historically contingent. As a trivial
example, the feature of lungs is very good for breathing in an
atmosphere, but not at all for breathing in an ocean. Without
exception, all organisms which use only lungs quickly die when they
breathe water. Despite this, there are many species which live in the
sea and also have lungs. How can this apparent paradox be explained?

One way is with a hypothesis that sea creatures with lungs evolved
from land animals. That hypothesis predicts the existence of
additional shared features. For example, sea mammals have hair,
placentas, and mammary glands, none of which exist on species with
gills.

An intelligent designer almost certainly would have provided sea
mammals with gills, or at least some other mechanism better suited to
an aquatic environment. Some ID proponents argue that an Intelligent
Designer (note upper case) might have some quixotic reason for
Designing sea creatures with lungs, and we humans are too stupid to
figure out what it is. Such an argument always remains an
unfalsifiable possibility, but it's the very opposite of a design
inference. When ID proponents fall back on the whims of an unseen and
undefined designer, they actually argue against intelligent design,
and for Creationism.

[Steady Eddie]

On Sunday, 31 August 2014 10:49:21 UTC-6, jillery wrote:
> On Sun, 31 Aug 2014 05:43:57 -0700 (PDT), Steady Eddie
>
>
>
>

Creationism isn't 'against' intelligent design. And, just as you claim 'historical contingencies' explain
some things for nD, we have no way of knowing the Creator's (or 'designer', it doesn't matter) reasons
for all of his design choices.
So what if it's unfalsifiable. What matters is, is it true?

Besides, your concept of 'nested hierarchies' is based essentially on question begging; I presume
cladistics is involved in coming up with these 'nested hierarchies'.

Relationships do not prove inheritance when the whole subject of inheritance is being challenged.
That's called begging the question, or a circular argument.

BTW, so what if fish with lungs were designed? Is that breaking some fundamental law, or something?

[RSNorman]

On Sun, 31 Aug 2014 12:49:21 -0400, jillery <69jp...@gmail.com>
wrote:

It is very difficult to design a warm-blooded sea creature with gills,
not to mention designing a gilled sea creature that can reuse many
aspects of mammalian organ systems and physiology. It is especially
difficult to design a gilled creature that could live in the interface
of air and water, sometimes in one and sometimes in the other. My
impression is that any argument as to what an "intelligent" designer
could or would do can be countered with a different argument, equally
valid (or, to be more precise, equally invalid) which is rather the
opposite.

I do not at all have any problem with your strong criticism of
intelligent design. I just think some of your examples, like the one
I mentioned or that of an electric start motor for autos, cuts rather
both ways.

[Steady Eddie]

Sorry I'm replying piecemeal; I have a short attention span.

On Sunday, 31 August 2014 10:49:21 UTC-6, jillery wrote:

> On Sun, 31 Aug 2014 05:43:57 -0700 (PDT), Steady Eddie
>
>
>
>

> >Nested hierarchy is just as much an indication of design as any explanation you have espoused.
>
> >I just laugh at the wide-eyed childishness of claiming "nested hierarchies - therefore neoDarwinism!"
>
>
>
>
>
> Intelligent design as practiced by humans applies features to
>
> functions, regardless of historical origin. As a trivial example, the
>
> feature of an electric start motor was designed independently into
>
> many lines of automobiles more or less at the same time. Because of
>
> that, the existence of electric start motors isn't evidence for the
>
> relationships among automobiles.
>
>
>
> OTOH biological evolution is historically contingent. As a trivial
>
> example, the feature of lungs is very good for breathing in an
>
> atmosphere, but not at all for breathing in an ocean. Without
>
> exception, all organisms which use only lungs quickly die when they
>
> breathe water. Despite this, there are many species which live in the
>
> sea and also have lungs. How can this apparent paradox be explained?
>
>
>
> One way is with a hypothesis that sea creatures with lungs evolved
>
> from land animals. That hypothesis predicts the existence of
>
> additional shared features. For example, sea mammals have hair,
>
> placentas, and mammary glands, none of which exist on species with
>
> gills.
>
>
>
> An intelligent designer almost certainly would have provided sea
>
> mammals with gills, or at least some other mechanism better suited to
>
> an aquatic environment.

They seem in my humble opinion to be competing just fine in the oceans.
Your implication that they aren't is just part of your confirmed ignorance of that topic.
No offense, it's just frustrating when people assume sub-optimal design when they really
don't know the first thing about building them, and, for that matter, building the entire ecosystem to support them.

>Some ID proponents argue that an Intelligent
>
> Designer (note upper case) might have some quixotic reason for
>
> Designing sea creatures with lungs, and we humans are too stupid to
>
> figure out what it is.

I of course agree about the part that we're too stupid to know what the Creator's reasons were.
Which leads to your expression "quixotic". Perhaps it only looks quixotic to people stupid enough
to think that they're smart enough to decide what is a "quixotic" piece of creation.

[Glenn]

"RSNorman" <r_s_n...@comcast.net> wrote in message news:u7l60a1g6ivq711k3...@4ax.com...

Know of a research project where one has been designed? Or is your claim that "it is difficult to design" is just more bs?

[broger...@gmail.com]

On Sunday, August 31, 2014 1:18:05 PM UTC-4, Steady Eddie wrote:
> Sorry I'm replying piecemeal; I have a short attention span.

That has not escaped our attention.

[RSNorman]

On Sun, 31 Aug 2014 10:29:00 -0700, "Glenn" <g...@invalid.invalid>
wrote:

To answer your questions directly:
(1) I do not know of a research project where one has been designed.
(2) My claim is not just more bs.

You would do better to make some assertions demonstrating my claims to
be invalid rather than by just creating inane questions thinking that
they somehow point out something.

[jillery]

Of course it isn't, since humans practice intelligent design (note
lower case) all the time. What is against Intelligent Design (note
upper case) is the argument that an unseen and undefined Designer
would violate the principles of intelligent design, as I described
above.

>And, just as you claim 'historical contingencies' explain
>some things for nD, we have no way of knowing the Creator's (or 'designer', it doesn't matter) reasons
>for all of his design choices.

The two are not equivalent, but opposites. As I show above,
historical contingency makes falsifiable predictions. The whims of an
unseen and undefined Designer are unpredictable by definition, and so
unfalsifiable.

>So what if it's unfalsifiable. What matters is, is it true?

What matters is, can it be disproved? Since it can't, then you can't
even begin to answer if it's true.

>Besides, your concept of 'nested hierarchies' is based essentially on question begging; I presume
>cladistics is involved in coming up with these 'nested hierarchies'.

Wrong again. The conclusion of a nested hierarchy derives from
accumulated evidence. Question begging is what you do; it's designed
because it looks designed because it's designed.

>Relationships do not prove inheritance when the whole subject of inheritance is being challenged.
>That's called begging the question, or a circular argument.

You deny the reality of biological inheritance? Please continue to
dig that hole you're in.

>BTW, so what if fish with lungs were designed? Is that breaking some fundamental law, or something?

You're still evading the questions: What is the evidence that lungs
were designed? What predictions can be made based on that hypothesis?

[Steady Eddie]

WHAT has not escaped your attention?
LOL

[jillery]

On Sun, 31 Aug 2014 13:09:50 -0400, RSNorman <r_s_n...@comcast.net>

There exist species which maintain temperatures above ambient; ex
tuna, billfish. There exist gilled species which occupy the
interfaces of air and water; ex. lungfish, mudskippers. Nor does my
argument above rest on maintaining any of the aspects of mammalian
organ systems and physiology.

My argument above identifies a clear dichotomy. ID can't coherently
argue a design inference illuminated by the properties of human design
*and* the whims of an unseen and undefined Designer.

>My
>impression is that any argument as to what an "intelligent" designer
>could or would do can be countered with a different argument, equally
>valid (or, to be more precise, equally invalid) which is rather the
>opposite.

If you want to actually argue that the exclusive use of lungs in
organism living primarily in water is intelligent design, then go
ahead.

>I do not at all have any problem with your strong criticism of
>intelligent design. I just think some of your examples, like the one
>I mentioned or that of an electric start motor for autos, cuts rather
>both ways.

If you want to actually state your problems with my electric start
motor analogy, then go ahead.

[Steady Eddie]

On Sunday, 31 August 2014 11:39:05 UTC-6, broger...@gmail.com wrote:

Just what IS the evidence for nested hierarchies, anyway?

[jillery]

On Sun, 31 Aug 2014 10:18:05 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>> An intelligent designer almost certainly would have provided sea
>> mammals with gills, or at least some other mechanism better suited to
>> an aquatic environment.
>
>They seem in my humble opinion to be competing just fine in the oceans.
>Your implication that they aren't is just part of your confirmed ignorance of that topic.

I make no such implication, nor does my argument rely on it. Of
course they're competing just fine, else they wouldn't exist. But
they do so in spite of their reliance on lungs, not because of it. How
much better if the sperm whale could stay underwater indefinitely
seeking giant squid, or dolphins didn't drown trapped in fishing nets.

>No offense, it's just frustrating when people assume sub-optimal design when they really
>don't know the first thing about building them, and, for that matter, building the entire ecosystem to support them.

Your implication is that one can't recognize sub-optimal design unless
one knows how to build it. Can you build a computer? Or an
automobile? Or a refrigerator? Or a house? Think of all the things
that you use, that you couldn't build if your life depended on it. Yet
it's almost certain that you have complained about their performance
when they didn't meet your expectations.

[jillery]

QED

[Steady Eddie]

On Sunday, 31 August 2014 11:46:20 UTC-6, jillery wrote:
> On Sun, 31 Aug 2014 10:04:54 -0700 (PDT), Steady Eddie
>
>
>
>

When did you figure out the design principles involved in creating life?
Are you too stupid to know you're not that smart?

>
>
>
>
>
> >And, just as you claim 'historical contingencies' explain
>
> >some things for nD, we have no way of knowing the Creator's (or 'designer', it doesn't matter) reasons
>
> >for all of his design choices.
>
>
>
>
>
> The two are not equivalent, but opposites. As I show above,
>
> historical contingency makes falsifiable predictions. The whims of an
>
> unseen and undefined Designer are unpredictable by definition, and so
>
> unfalsifiable.
>
>
>
>
>
> >So what if it's unfalsifiable. What matters is, is it true?
>
>
>
>
>
> What matters is, can it be disproved? Since it can't, then you can't
>
> even begin to answer if it's true.

Sorry, the truth does not have to be 'disprovable' to be true.

>
>
>
>
>
> >Besides, your concept of 'nested hierarchies' is based essentially on question begging; I presume
>
> >cladistics is involved in coming up with these 'nested hierarchies'.
>
>
>
>
>
> Wrong again. The conclusion of a nested hierarchy derives from
>
> accumulated evidence.

By all means, bring it on. This is the thread for it.

>Question begging is what you do; it's designed
>
> because it looks designed because it's designed.
>
>
>
>
>
> >Relationships do not prove inheritance when the whole subject of inheritance is being challenged.
>
> >That's called begging the question, or a circular argument.
>
>
>
>
>
> You deny the reality of biological inheritance? Please continue to
>
> dig that hole you're in.

Define "biological inheritance".

>
>
>
>
>
> >BTW, so what if fish with lungs were designed? Is that breaking some fundamental law, or something?
>
>
>
>
>
> You're still evading the questions: What is the evidence that lungs
>
> were designed? What predictions can be made based on that hypothesis?

It's very hard to 'predict' the workings

...Whenever you're done changing the subject I'm waiting to see the scientific evidence for the
hypothesis that homology means inheritance.

[RSNorman]

On Sun, 31 Aug 2014 14:11:59 -0400, jillery <69jp...@gmail.com>

There are large fish that do some partial thermal regulation. There
are many smaller aquatic animals that are air breathers. The
midskippers and lungfish in fact do not use their gills to breathe
air.

I admire your argments against intelligent design but I find weakness
in some of the ways you go about it. You want to find coherence
between human design and some unknown intelligent designer when none
is required. One of the great retorts of the ID crowd is that the
unknown intelligent designer possesses a greater intelligence beyond
the limitations of human designer. I don't see any value in
criticizing ID based on what human design is like. There is no
answering "we cannot fathom the purposes or intents of the designer"
just as there is no answer to "it is not for us to judge the reasons
of God." Those arguments are so far beyond science, reason, and
intelligent discourse that I can see no value in trying to refute
them.

-However I did give some reason why an intelligent human designer
would have some aquatic animals breathe air with lungs and there do
exist rather a large number of such including whale and dolphins,
seals and sea lions, and even otters and beavers and a variety of
other fresh-water mammals. Then there are numerous birds. And many
insects and some spiders live aquatic lives air breathing though not
using lungs. So my examples are as good for design as yours of the
mudskipper and lungfish are against my claim. The problem is that you
can pretty much argue anything anyway you want that way.

You used the independent invention of electric starting motors in
automobiles as an argument against design relationships -- reuse of
design features -- in human based design. However the independent
"invention" of things like lactose tolerance in different human groups
is not evidence against the close relationship between them.

Your examples illustrate points but do not rule out the alternatives.
That is my only point.

[deadrat]

In fact, for the type of design we know about, i.e., the kind that human
beings do, nested hierarchy is not a feature. Look at internal
combustion engines. You can classify them in many ways: chamber design
(piston, radial), number of cylinders (There are engines with 1 to 20
cylinders excepting 13, 17, and 19. The largest I could find is 28.),
number of banks of cylinders (1, 2, 4), arrangement of cylinder banks
(straight, H, V, W, X), valve placement (none, side, top), fuel mixing
method (carbureted or fuel injected), number of strokes (1, 2, 4, 6),
ignition source (electric, compression), fuel type (gasoline, diesel,
vegetable oil, natural gas), and many more.

You can pick any characteristic you want and arrange the engines in any
order that suits you, but they won't nest when you consider other
characteristics. Even when you find a general rule, it will have
exceptions. For instance, diesel fuel isn't as volatile as gasoline, so
it's not best suited for carburetors, but International Harvester once
produced a carbureted diesel engine anyway.

This is opposed to what we see in the biosphere where all cats are
mammals which are all carnivora which are all vertebrates which are all
chordates. These classifications are not arbitrary. You'd never
confuse the stomach or dentition of a carnivore with those of a cow.

For living things, You'll find a parallel classification works at the
genetic level. You won't be able to do the same thing with engines.
Use the design drawings for engines as their "genetics." Try to figure
out how the piston engine and the rotary engine are related.

[Mark Isaak]

On 8/31/14 10:04 AM, Steady Eddie wrote:
> [...]

> So what if it's unfalsifiable. What matters is, is it true?

If "is it true?" is what matters, then unfalsifiability is crucial,
because you need some way to *determine* whether it is true.

>
> Besides, your concept of 'nested hierarchies' is based essentially on question begging; I presume
> cladistics is involved in coming up with these 'nested hierarchies'.

Ever heard of Linnaeus? He was coming up with nested hierarchies about
200 years before cladistics.

> [...]

> BTW, so what if fish with lungs were designed? Is that breaking
> some fundamental law, or something?

Yes. Claiming something to be true solely because you want it to be
true breaks several fundamental laws.

[RSNorman]

I'll accept your last point -- that nested hierarchies obtained from
very different features (genome vs. morphology) agree -- as truly
significant evidence of evolution from common ancestry.

I don't accept your diversity of engine story. In the biosphere we
see wings on insects and wings on bats and wings on birds and wings on
pterosaurs when they are all quite different.

We see swimming in all sorts of aquatic creatures that swim using very
different machineries. The same for walking or for crawling.

What you have done is cherry picked an example to disprove common
design in machinery ignoring examples that do show it. You also
picked examples of shared inherited features in animals ignoring other
examples that were not shared by common descent.

[Glenn]

"RSNorman" <r_s_n...@comcast.net> wrote in message news:o4n60a128p0566ueo...@4ax.com...

But you just demonstrated that very point.

[alias Ernest Major]

There are a few warm-blooded fish (for appropriate values of warm-blooded).

http://jeb.biologists.org/content/205/15/2251.full.pdf

> not to mention designing a gilled sea creature that can reuse many
> aspects of mammalian organ systems and physiology. It is especially
> difficult to design a gilled creature that could live in the interface
> of air and water, sometimes in one and sometimes in the other. My
> impression is that any argument as to what an "intelligent" designer
> could or would do can be countered with a different argument, equally
> valid (or, to be more precise, equally invalid) which is rather the
> opposite.
>
> I do not at all have any problem with your strong criticism of
> intelligent design. I just think some of your examples, like the one
> I mentioned or that of an electric start motor for autos, cuts rather
> both ways.
>

--
alias Ernest Major

[alias Ernest Major]

The distribution of morphological, biochemical, and genetic traits among
organisms.

--
alias Ernest Major

[John Harshman]

But there are quite a few warmblooded fish, some of which warm up the
entire body core and swimming muscles, and some that just heat up the
brain and eyes.

So it might be hard, but it's certainly happens. Not that design had
anything to do with it.

[jillery]

Non sequitur. The principles involved in creating life have nothing
to do with recognizing and measuring the functionality of life's
processes.

>Are you too stupid to know you're not that smart?

Apparently you're too stupid to ask relevant questions.

>> >And, just as you claim 'historical contingencies' explain
>> >some things for nD, we have no way of knowing the Creator's (or 'designer', it doesn't matter) reasons
>> >for all of his design choices.
>>
>> The two are not equivalent, but opposites. As I show above,
>> historical contingency makes falsifiable predictions. The whims of an
>> unseen and undefined Designer are unpredictable by definition, and so
>> unfalsifiable.
>>
>> >So what if it's unfalsifiable. What matters is, is it true?
>>
>> What matters is, can it be disproved? Since it can't, then you can't
>> even begin to answer if it's true.
>
>Sorry, the truth does not have to be 'disprovable' to be true.

The truth must be disprovable else it can't be known to be true.
Wishful thinking, self-evident and Revealed Truth don't count as
Truth.

>> >Besides, your concept of 'nested hierarchies' is based essentially on question begging; I presume
>> >cladistics is involved in coming up with these 'nested hierarchies'.
>>
>> Wrong again. The conclusion of a nested hierarchy derives from
>> accumulated evidence.
>
>By all means, bring it on. This is the thread for it.

Not really.

>>Question begging is what you do; it's designed
>> because it looks designed because it's designed.
>>
>> >Relationships do not prove inheritance when the whole subject of inheritance is being challenged.
>> >That's called begging the question, or a circular argument.
>>
>> You deny the reality of biological inheritance? Please continue to
>> dig that hole you're in.
>
>Define "biological inheritance".

Too many syllables for you? What part don't you understand,
"biological" or "inheritance"?

>> >BTW, so what if fish with lungs were designed? Is that breaking some fundamental law, or something?
>> You're still evading the questions: What is the evidence that lungs
>> were designed? What predictions can be made based on that hypothesis?
>
>It's very hard to 'predict' the workings

Workings? Apparently you don't even understand the questions.

>...Whenever you're done changing the subject I'm waiting to see the scientific evidence for the
>hypothesis that homology means inheritance.

<PING> Dang it!

[jillery]

On Sun, 31 Aug 2014 15:25:15 -0400, RSNorman <r_s_n...@comcast.net>

Both lungfish and mudskippers have gills. Both occupy the
interfaces of air and water. Those were your original specifications.
I'm almost certain that you know of other species which meet those
specifications. Why do you now shift your argument to "use their
gills to breathe air"?

>I admire your argments against intelligent design but I find weakness
>in some of the ways you go about it. You want to find coherence
>between human design and some unknown intelligent designer when none
>is required. One of the great retorts of the ID crowd is that the
>unknown intelligent designer possesses a greater intelligence beyond
>the limitations of human designer. I don't see any value in
>criticizing ID based on what human design is like. There is no
>answering "we cannot fathom the purposes or intents of the designer"
>just as there is no answer to "it is not for us to judge the reasons
>of God." Those arguments are so far beyond science, reason, and
>intelligent discourse that I can see no value in trying to refute
>them.

To say that I "want to find coherence between human design and some
unknown intelligent designer" fundamentally misstates my entire line
of reasoning. When someone asserts the design inference, that human
design infers that apparent design infers a designer, then it's valid
to refute that inference. If you actually disagree with that, then go
ahead and make your case.

>-However I did give some reason why an intelligent human designer
>would have some aquatic animals breathe air with lungs and there do
>exist rather a large number of such including whale and dolphins,
>seals and sea lions, and even otters and beavers and a variety of
>other fresh-water mammals.

The only reason I recognized is that of reuse "of many aspects of
mammalian organ systems and physiology." Please restate immediately
below any others I missed.

>Then there are numerous birds. And many
>insects and some spiders live aquatic lives air breathing though not
>using lungs. So my examples are as good for design as yours of the
>mudskipper and lungfish are against my claim. The problem is that you
>can pretty much argue anything anyway you want that way.

My argument against Steadly's assertion doesn't need to identify all
cases, but only those cases which refute an implication that such and
so doesn't exist.

>You used the independent invention of electric starting motors in
>automobiles as an argument against design relationships -- reuse of
>design features -- in human based design. However the independent
>"invention" of things like lactose tolerance in different human groups
>is not evidence against the close relationship between them.

You misstate the point of my analogy. My argument is against
Steadly's expressed assertion, still preserved above, and copied
immediately below for your convenience:

"Nested hierarchy is just as much an indication of design as any
explanation you have espoused."

Multiple origins, as with lactose tolerance, still radiate out over
space and time from point sources, and so remain good evidence of
historical contingency. While there are cases of human inventions
which also give a pattern of multiple origins, I know of no case where
biological "inventions" emulate the pattern in my analogy, where all
populations which could benefit from an "invention" adapt it at the
same time throughout the world.

>Your examples illustrate points but do not rule out the alternatives.
>That is my only point.

I believe I ruled out the relevant alternatives as stated in Steadly's
assertion as expressed.

If you actually believe I did not, then go ahead and make your case.

If you actually believe there are other relevant alternatives
described by neither Steadly nor myself, then go ahead and make your
case for that.

[Steady Eddie]

Thank you, RSNorman.

[deadrat]

You're right. They're basically the same thing.

> And, just as you claim 'historical contingencies' explain
> some things for nD, we have no way of knowing the Creator's (or 'designer', it doesn't matter) reasons
> for all of his design choices.

Before we decide that, we have to decide whether there's a Creator at all.

> So what if it's unfalsifiable. What matters is, is it true?

Because if it's unfalsifiable then it's not science. If it's not
science, then you have no rational basis for deciding whether it's true
or not. You've still got personal revelation and the dictates of
authority to inform you of the truth. If that's good enough for you,
then go and prosper.

> Besides, your concept of 'nested hierarchies' is based essentially on question begging;

It's not true. So you should probably stop saying this. The
hierarchies are based on sets of observable characteristics. All of
which nest. Try doing that with something that we know is designed,
like the internal combustion engine.

> I presume
> cladistics is involved in coming up with these 'nested hierarchies'.

Why do you presume? Why not look up what's "involved."

> Relationships do not prove inheritance when the whole subject of inheritance is being challenged.

Are you denying that living things inherit from their parents?

> That's called begging the question, or a circular argument.

> BTW, so what if fish with lungs were designed? Is that breaking some fundamental law, or something?

If fish with lungs were designed, then fish with lungs were designed.
But that's about all you can say. What you can't demonstrate (because
as you note it's unfalsifiable), is whether fish with lungs were
actually designed.

[jillery]

On Sun, 31 Aug 2014 16:20:26 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

>> What you have done is cherry picked an example to disprove common
>> design in machinery ignoring examples that do show it. You also
>> picked examples of shared inherited features in animals ignoring other
>> examples that were not shared by common descent.
>
>Thank you, RSNorman.

Will you give examples relevant to your point, of features that you
think show common design?

[deadrat]

You don't "accept" it? What does that mean? You think engines can be
arranged in a nested hierarchy?

> In the biosphere we
> see wings on insects and wings on bats and wings on birds and wings on
> pterosaurs when they are all quite different.

> We see swimming in all sorts of aquatic creatures that swim using very
> different machineries. The same for walking or for crawling.

So what? Did you think that I meant that you could take every
observable characteristic and fit it into a nested hierarchy?

> What you have done is cherry picked an example to disprove common
> design in machinery ignoring examples that do show it.

Please provide examples of design in machinery that show major change
over their history and fit into a nested hierarchy. You can't because
that's not how human beings design things, especially when we're
encouraged to innovation by things like patent offices. The internal
combustion engine is an example, but it's not cherries. If machinery
ordinarily falls into nested hierarchies, then something as influential
and widespread in human technology as the internal combustion engine
ought to qualify.

> You also
> picked examples of shared inherited features in animals ignoring other
> examples that were not shared by common descent.

So what? Are you maintaining that we can find meaningful
classifications of animals with "flying things" and "swimming" things?
What do you suppose happens when you try that?

The meaningful arrangement of observable features of living things
follows that other nested hierarchy of genomes. Something else, as I've
noted, that doesn't work for machinery.

Check out Steadfastly's one-sentence reply to you. Congratulations. In
failing to understand my explanation, you've confirmed Steadfastly in
his ignorance.

I leave it as an exercise to figure out which of you that makes dumber.

[RSNorman]

On Sun, 31 Aug 2014 19:09:58 -0400, jillery <69jp...@gmail.com>

I did make my case but apparently we disagree on some issues and
misunderstand each other on others.

Please resume you attack on Steady without my interference.

[RSNorman]

Yes there are a small number of heterothermic fish although no true
homeotherms. But there are are rather larger number of successful
homeothermic mammals living in water breathing air. I said it is very
difficult, not that it is impossible. A truly intelligent designer
would try to avoid what is really difficult and go for what seems more
effective, just as biology has done.

[RSNorman]

On Sun, 31 Aug 2014 16:20:26 -0700 (PDT), Steady Eddie
<1914o...@gmail.com> wrote:

<snip more than 400 mostly empty lines of text>
>
>Thank you, RSNorman.

There is nothing to thank me for. Your argument is totally wrong. It
is just that deadrat gave some invalid arguments against it, just as I
argued jillery did earlier. However both deadrat and jillery also had
many very effective and cogent arguments against your point.

You are profoundly wrong and seemingly ignorant of the facts of
biology in being so. And you have demonstrated a total unwillingness
to answer many questions posed to you and to proesent evidence and
logical argument for your points.

So that is why I write there is nothing to thank me for.

[RSNorman]

I believe you presented a relatively weak argument against Steady. Had
he any intelligence at all he would be able to produce a rejoinder to
some of your points. That he is unable to do so does not make your
argument stronger.

Consider the 8008, 8080, 8006, 80286, 80386, Pentium, ... chip
sequence and throw in the Z80 and several other alternatives. Consider
the 6800, 6801, 6805 followed by the 68000, 68100, 68200, 68300...
chips.
Consider even the progression from semiconductor transistors to small
scale integration to medium scale and then to large scale.
There are a number of families showing clear evolution within design
yet preserving a core of inherited features.

I still believe your argument is flawed. That in no way indicates
Steady is correct.

[Mark Isaak]

Deadrat may not have explained it well, but his point is solid.

Literally any group of separate objects can be arranged in a nested
hierarchy merely by drawing an arbitrary tree of the appropriate size
and labeling the nodes at random. In a natural nested hierarchy,
though, you can consider all the sets defined by individual characters,
and those sets will be either entirely inside or entirely outside other
sets. I can't think of any intelligently designed products that come
close to working like that, except when they originate via a
biology-like system of common descent. If you think the engine example
was cherry-picked, try it with any type of object you see lying around
-- calculators, calendars, books, paper clips, chairs, armored vehicles,
bottled drinks, whatever -- none will show a natural nested hierarchy.

Sure, there is some messiness involved. We are, after all, talking
biology. Some characters would not be useful since they might be
acquired from the environment, or might vary a lot even within the same
population. Some characters (like wings) can evolve separately several
times. But when you consider multiple characters, it is clear that the
pattern with intelligently designed stuff is nothing like the pattern
with biological stuff.

[jillery]

On Sun, 31 Aug 2014 22:33:45 -0400, RSNorman <r_s_n...@comcast.net>
wrote:

>Please resume you attack on Steady without my interference.

I didn't attack anybody. I did reply to comments he made. Just as I
do with you.

[jillery]

On Sun, 31 Aug 2014 22:41:11 -0400, RSNorman <r_s_n...@comcast.net>
wrote:

>On Sun, 31 Aug 2014 16:20:26 -0700 (PDT), Steady Eddie
><1914o...@gmail.com> wrote:
>
><snip more than 400 mostly empty lines of text>
>>
>>Thank you, RSNorman.
>
>There is nothing to thank me for. Your argument is totally wrong. It
>is just that deadrat gave some invalid arguments against it, just as I
>argued jillery did earlier. However both deadrat and jillery also had
>many very effective and cogent arguments against your point.

It would be nice if you would stick at it a bit longer to clarify just
what it is you find invalid.