What do you know that the rest of the world doesn't?
Richard Forrest
This is a curious assertion.
Every university, in every country in which the biological sciences are
taught teaches evolutionary theory as an integral part of the science
of biology. Evidently they think that it is science, as do the
administrative bodies which organise universities, the public and
private bodies which fund universities, the coroporations who employ
the graduates of those universities.
I'm not arguing from authority here, but merely asking the question:
You evidently think that all those people in the science departments of
universities, in university administration, in funding organisations
and business have got it wrong. This seems rather remarkable claim.
What do you know that all those people don't?
RF
sharon
Excerpt from "A Question For the President"
Mr. President, I would ask, how do you reconcile your statement that
Intelligent Design should be taught alongside evolution with the fact
that your administration, like both Republican and Democratic
administrations before it, has supported research in evolution by our
country's leading scientists, while failing to support a single study
that is explicitly based on Intelligent Design? The National Institutes
of Health, the National Science Foundation, and even the Department of
Energy have all decided that evolution is a cornerstone to advances in
our understanding of diseases, the environment, and even biotechnology.
They have found no such value in Intelligent Design. Are they wrong?
Can you tell us why?
- Carl Zimmer
http://www.corante.com/loom/archives/2005/08/02/a_question_for_the_president.php
Rodjk #613
Interesting to read the comments and see Charlie Wagner's name there...
Rodjk #613
shipmodeler1
of
universities, in university administration, in funding organisations
and business have got it wrong. This seems rather remarkable claim."
No more remarkable than claiming the world is only about 10,000 years
old and was created by magic in a single week.
Gordon Hill
There are two silent conflicts within creationism/ID: (1) YEC vs. OEC.
(2) Support ID, but oppose/support evolution.
Why are these issues not debated amongst them? Why are they soft
peddled as misunderstandings of small consequence, not debated openly
and vigorously?
They sould take a cue from science where differences are discussed
calmly, sometimes vigorously and, on occassion, with an ad him barrage.
Come on creationist/IDers. If you want to play like the big boys and
girls, drop the gauntlet! Let the debate within begin.
Until then your are seen as caring more about personal opinion than the
resolution of differences, which is where science excells.
coaster
Would you deliberately kick out the supports of a "Big Tent" while
you're standing inside? No, I think not.
Mark VandeWettering
Ah yes, Charlie. The man who thinks that he's smarter than Richard Feynman.
He asserts that intelligent design must have happened, but he can't tell
you how, where, when or by whom.
Mark
> Rodjk #613
>
Seanpit
Mark VandeWettering wrote:
> He asserts that intelligent design must have happened, but he can't tell
> you how, where, when or by whom.
>
> Mark
But ID can tell you that it was almost certainly not the result of any
non-deliberate process. When SETI scientists find the radio signal
from outer space that they are looking for, which they would widely
hail as evidence of alien intelligence equivalent or even greater than
our own, they probably won't be able to say exactly who, why or even
how such a signal was made. Yet, they will still strongly assert that
it was made intelligently and deliberately.
Beyond this, Richard is quite mistaken in the claim that most
creationists argue that evolution isn't a science. Many if not most of
the creationists trained in various disciplines of science that I know
believe that the theory of evolution is based on many valid scientific
hypotheses and theories. It is just that the weight of current
evidence strongly counters if not outright falsifies many of the most
fundamental supports behind the theory of evolution.
Sean Pitman
www.DetectingDesign.com
moxm...@gmail.com
What current evidence would that be? Assumptions based on the human
tendency to anthromorphize everything? The already-debunked IC proposed
by Behe? Misunderstood (purposely?) interpretations of science?
Richard Forrest
Seanpit wrote:
> Mark VandeWettering wrote:
>
> > He asserts that intelligent design must have happened, but he can't tell
> > you how, where, when or by whom.
> >
> > Mark
>
> But ID can tell you that it was almost certainly not the result of any
> non-deliberate process.
ID is not a scientific theory, so it can't tell you anything about the
scientific theory of evolution.
If you think that ID is a theory, perhaps you can produce a testable
hypothesis. The ID assertion is that an "intelligent designer", using
unspecified but possibly supernatural powers interferes with normal
evolutionary processes using unspecified but possibly supernatural
methods.
I can think of no potential observation or measurement which would
falsify such an assertion, but perhaps you can. If so, you are ahead of
the DI, who are lobbying to have the definition of science changed to
accomodate the supernatural - a clear concession that ID as it stands
is not science.
Of course, if you are prepared to conceede as the DI has that ID is not
science I have no basis to argue with you.
> When SETI scientists find the radio signal
> from outer space that they are looking for, which they would widely
> hail as evidence of alien intelligence equivalent or even greater than
> our own, they probably won't be able to say exactly who, why or even
> how such a signal was made. Yet, they will still strongly assert that
> it was made intelligently and deliberately.
And it's worth noting that the criteria they use for looking for such
signals is the opposite of what the ID proponents do.
>
> Beyond this, Richard is quite mistaken in the claim that most
> creationists argue that evolution isn't a science.
I said that creationists claim that evolution is not science. I didn't
say most, or some, or all creationists.
As I have just been addressing the claims of a creationist on another
thread that evolution is not science, and such a claim is made
regularly not only on this forum but on some creationist web sites, I
don't think I am mistaken.
> Many if not most of
> the creationists trained in various disciplines of science that I know
> believe that the theory of evolution is based on many valid scientific
> hypotheses and theories. It is just that the weight of current
> evidence strongly counters if not outright falsifies many of the most
> fundamental supports behind the theory of evolution.
As has been pointed out on numerous occasions, creating a strawman
model of evolutionary processes and pretending that if you can falsify
it you somehow falsify evolution is offering neither evidence nor
argument against evolution.
Evolution happens. It is the best explanation we have in science for
the diversity of living organisms and the distribution if fossils in
the geological record. You offer a model of evolution which does not
work. This shows that your model is wrong, not that evolution, as
evidenced by numerous other strands of evidence is wrong.
RF
>
> Sean Pitman
> www.DetectingDesign.com
rupert....@gmail.com
Seanpit wrote:
> Mark VandeWettering wrote:
>
> > He asserts that intelligent design must have happened, but he can't tell
> > you how, where, when or by whom.
> >
> > Mark
>
> But ID can tell you that it was almost certainly not the result of any
> non-deliberate process. When SETI scientists find the radio signal
> from outer space that they are looking for, which they would widely
> hail as evidence of alien intelligence equivalent or even greater than
> our own, they probably won't be able to say exactly who, why or even
> how such a signal was made. Yet, they will still strongly assert that
> it was made intelligently and deliberately.
But they will tell us where and when. Can ID answer those questions?
Who and how will be answered sometime later, either by exchanging
messages or by going there. When does ID propose to answer those
questions?
Why the aliens are sending us messages is a much tougher question, and
will require significant knowledge of alien psychology and politics.
However, it seems reasonable that we will eventually find out. When
will ID tell us why we are designed the way we are?
jrs...@sbcglobal.net
<moxm...@gmail.com> wrote in message
news:1164056194.0...@h48g2000cwc.googlegroups.com...
>
> Seanpit wrote:
>> Mark VandeWettering wrote:
>>
>> > He asserts that intelligent design must have happened, but he can't
>> > tell
>> > you how, where, when or by whom.
>> >
>> > Mark
>>
>> But ID can tell you that it was almost certainly not the result of any
>> non-deliberate process. When SETI scientists find the radio signal
>> from outer space that they are looking for, which they would widely
>> hail as evidence of alien intelligence equivalent or even greater than
>> our own, they probably won't be able to say exactly who, why or even
>> how such a signal was made. Yet, they will still strongly assert that
>> it was made intelligently and deliberately.
I completely disagree. If a radio signal were to be found, it would only be
*suspected* of being intelligently made and would, therefore, remain
conjecture until if and when further supporting evidence was discovered.
Scientists would first look to eliminate any natural causes before such a
signal would be concluded to be intelligently and deliberately made. Sans
any supporting evidence, such a signal would be deemed interesting, yet any
conclusions would remain merely speculative.
Which is why, of course, any scientific conclusions of design in biological
systems will always be mere speculation, until (if and when) some semblance
of supporting and testable evidence is proffered. Even then, a supernatural
explanation would not be considered, scientifically, for obvious reasons.
>>
>> Beyond this, Richard is quite mistaken in the claim that most
>> creationists argue that evolution isn't a science. Many if not most of
>> the creationists trained in various disciplines of science that I know
>> believe that the theory of evolution is based on many valid scientific
>> hypotheses and theories. It is just that the weight of current
>> evidence strongly counters if not outright falsifies many of the most
>> fundamental supports behind the theory of evolution.
Such as? Which other natural explanations do you think should replace the
current evolutionary hypotheses?
JR
jrs...@sbcglobal.net
directed at Sean and not you.
JR
jrs...@sbcglobal.net
"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message
news:1164055303....@e3g2000cwe.googlegroups.com...
>
> Mark VandeWettering wrote:
>
>> He asserts that intelligent design must have happened, but he can't tell
>> you how, where, when or by whom.
>>
>> Mark
>
> But ID can tell you that it was almost certainly not the result of any
> non-deliberate process. When SETI scientists find the radio signal
> from outer space that they are looking for, which they would widely
> hail as evidence of alien intelligence equivalent or even greater than
> our own, they probably won't be able to say exactly who, why or even
> how such a signal was made. Yet, they will still strongly assert that
> it was made intelligently and deliberately.
>
*suspected* of being intelligently made and would, therefore, remain
conjecture until if and when further supporting evidence was discovered.
Scientists would first look to eliminate any natural causes before such a
signal would be concluded to be intelligently and deliberately made. Sans
any supporting evidence, such a signal would be deemed interesting, yet any
conclusions would remain merely speculative.
Which is why, of course, any scientific conclusions of design in biological
systems will always be mere speculation, until (if and when) some semblance
of supporting and testable evidence is proffered. Even then, a supernatural
explanation would not be considered, scientifically, for obvious reasons.
> Beyond this, Richard is quite mistaken in the claim that most
> creationists argue that evolution isn't a science. Many if not most of
> the creationists trained in various disciplines of science that I know
> believe that the theory of evolution is based on many valid scientific
> hypotheses and theories. It is just that the weight of current
> evidence strongly counters if not outright falsifies many of the most
> fundamental supports behind the theory of evolution.
Such as? Which other natural explanations do you think should replace the
CreateThis
<seanpi...@naturalselection.0catch.com> wrote:
>
>Mark VandeWettering wrote:
>
>> He asserts that intelligent design must have happened, but he can't tell
>> you how, where, when or by whom.
>>
>> Mark
>
>But ID can tell you that it was almost certainly not the result of any
>non-deliberate process.
ID can tell us that ID is not non-deliberate? Now there's a useful
"science".
CT
Mark VandeWettering
>
> Mark VandeWettering wrote:
>
>> He asserts that intelligent design must have happened, but he can't tell
>> you how, where, when or by whom.
>>
>> Mark
>
> But ID can tell you that it was almost certainly not the result of any
> non-deliberate process.
No, it can't. It can't even tell you what "it" is. Charlie doesn't know
of any single incident of where design actually occurred, and neither can
you.
> When SETI scientists find the radio signal from outer space that they
> are looking for, which they would widely hail as evidence of alien
> intelligence equivalent or even greater than our own, they probably
> won't be able to say exactly who, why or even how such a signal was
> made.
Can you point to any methodology that SETI uses to determine whether
a particular signal represents an intelligence greater than our own?
> Yet, they will still strongly assert that
> it was made intelligently and deliberately.
They didn't do it in 1967 when they detected the first pulsar emissions,
perhaps you should let them speak for themselves when the time comes.
SETI is looking for narrow band emitters with characteristic Doppler
shifts. They aren't looking for "design". It's not really surprising,
after all, nobody knows how to look for design.
> Beyond this, Richard is quite mistaken in the claim that most
> creationists argue that evolution isn't a science.
Unless you can present an actually poll of creationists to support this
idea, it seems pointless to argue. It is not an uncommon claim among
creationists that evolution isn't a science, as even the most cursory
glance will tell you.
> Many if not most of the creationists trained in various disciplines of
> science that I know believe that the theory of evolution is based on
> many valid scientific hypotheses and theories. It is just that the
> weight of current evidence strongly counters if not outright falsifies
> many of the most fundamental supports behind the theory of evolution.
Yes, well...
> Sean Pitman
> www.DetectingDesign.com
Seanpit
jrs...@sbcglobal.net wrote:
> > But ID can tell you that it was almost certainly not the result of any
> > non-deliberate process. When SETI scientists find the radio signal
> > from outer space that they are looking for, which they would widely
> > hail as evidence of alien intelligence equivalent or even greater than
> > our own, they probably won't be able to say exactly who, why or even
> > how such a signal was made. Yet, they will still strongly assert that
> > it was made intelligently and deliberately.
> >
> I completely disagree. If a radio signal were to be found, it would only be
> *suspected* of being intelligently made and would, therefore, remain
> conjecture until if and when further supporting evidence was discovered.
> Scientists would first look to eliminate any natural causes before such a
> signal would be concluded to be intelligently and deliberately made. Sans
> any supporting evidence, such a signal would be deemed interesting, yet any
> conclusions would remain merely speculative.
The evidence for intelligent design can be entirely contained within
the radio signal itself.
Like human-language transmission, certain key repeating patterns at
intervals consistent with coded messages would be excellent evidence of
deliberate design. Its would be much like going to an alien planet and
finding unknown characters carved in a rock - characters that may
appear random by themselves, but which show the same character repeated
over and over again in clustered sequences with other repeated
characters. Like finding the Rosetta Stone, one might not be able to
understand what the character sequences mean, when they were made, who
made them, or exactly how they were made. However, one would very
easily be able to tell that they were indeed deliberately designed and
that they most likely represent some sort of information. This
conclusion would be obvious in such a situation - even to a child.
Science isn't about 100% certainty. There is always the potential for
error with any scientific hypothesis or even theory. Absolute
certainty would remove the need for science. Even a "conjecture" may
have useful and therefore "scientific" predictive value.
You argue that, "Scientists would first look to eliminate any natural
causes before such a signal would be concluded to be intelligently and
deliberately made." Indeed, the attempt to rule out potential
non-deliberate natural causes is a big part of any intelligent design
theory. The problem is that the possibility of non-deliberate causes
can never be excluded with absolute certainty. But, the good thing is,
science does not require absolute certainty before a hypothesis or
theory can be useful - before a good deal of predictive power can be
realized. Additional evidence that does not counter the original
hypothesis may be added to the "supporting evidence" side of the
equation - thereby increasing the predictive power of the hypothesis.
However, there is always the possibility that additional evidence may
undermine the original hypothesis. That's just how science works.
> Which is why, of course, any scientific conclusions of design in biological
> systems will always be mere speculation, until (if and when) some semblance
> of supporting and testable evidence is proffered. Even then, a supernatural
> explanation would not be considered, scientifically, for obvious reasons.
If the supernatural agent acts within the natural world in a way that
can be detected by us humans, that activity can indeed be appreciated
and classified as being almost certainly beyond the capabilities of any
non-deliberate process and well beyond any creative abilities of known
deliberate agents as well. If the evidence presented is limited, the
best scientific "speculation" may have relatively weak predictive
value. However, this predictive value may gain ground with additional
"revelations" provided by the "supernatural" agent.
> > Beyond this, Richard is quite mistaken in the claim that most
> > creationists argue that evolution isn't a science. Many if not most of
> > the creationists trained in various disciplines of science that I know
> > believe that the theory of evolution is based on many valid scientific
> > hypotheses and theories. It is just that the weight of current
> > evidence strongly counters if not outright falsifies many of the most
> > fundamental supports behind the theory of evolution.
>
> Such as? Which other natural explanations do you think should replace the
> current evolutionary hypotheses?
When it comes to functional biosystems that require a minimum of more
than a few thousand specifically arranged amino acid residues, random
mutation and function-based selection don't even come close. The only
known natural process that does produce anything at such levels of
functional complexity and beyond is intelligence. Intelligent
creativity has its own levels. Those possessing a lower level of
intelligence or informational complexity may rightly define those with
higher levels of intelligence or technological information as
"supernatural" - relatively speaking.
In short, the term "supernatural" is only a relative term. Those
powers that might be described as "supernatural" from our perspective
would no doubt be perfectly "natural" from the perspective of those who
possess such powers.
> JR
Sean Pitman
www.DetectingDesign.com
Marc
...snp
> When it comes to functional biosystems that require a minimum of more
> than a few thousand specifically arranged amino acid residues, random
> mutation and function-based selection don't even come close.
Does exon shuffling count as a mutation in regard to this statement?
What about duplication events? (Of a gene or part of a gene, of
a genomic subregion with a number of genes, or of the entire
genome as happened twice in the early vertebrate ancestor.)
Do genome duplications count as "mutations", and how do they
*not* provide large steps towards novel functions, especially when
combined with exon shuffling?
You should be able to look this one up, Sean. Just where did the
class II MHC gene system first arise? Where did the individual
exons of MHC class II come together from? Was it "designed"
or was there expn-shuffling involved?
(signed) marc
> The only
> known natural process that does produce anything at such levels of
> functional complexity and beyond is intelligence. Intelligent
> creativity has its own levels. Those possessing a lower level of
> intelligence or informational complexity may rightly define those with
> higher levels of intelligence or technological information as
> "supernatural" - relatively speaking.
...snp
****************************
It's been a few weeks since you have posted, Sean. (I hope you
are OK and all is well...) Perhaps it is time again to review the
recent literature on gene duplication in evolution. I'll first list the
papers that are available in free full text form (with links), and
the other papers will be listed by title, citation and PMID number.
NOTE - I have deleted many of the "Epub ahead of print" tags, so
many of these papers may be found in "upcoming papers" or such
depending on the journal. PubMed will have this indicated.
Lurkers - to look up the abstracts, authors etc. just go to the
NCBI - MedLine/PubMed site ("PubMed.gov" will work or
use http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed )
and just enter the PubMed ID number (PMID) to get each one.
Oh... this was a search for "gene duplication" and as of today
there were 4891 hits with the more recent 100 going back as
far as August, so I will pick from within this set of 100 citations.
Sean, feel free to double check the papers I don't cite to be
sure I'm not skipping ones that possibly support your case.
Recent papers on gene duplication available in free, full text form:
This paper is the one listed today at #100 and so it will soon
be on page 2 when 100 results are displayed per page, but
from reading the abstract I wanted to be sure to include it.
"Insights into the coupling of duplication events and macroevolution
from an age profile of animal transmembrane gene families."
PLoS Comput Biol. 2006 Aug 11;2(8):e102. Epub 2006 Jun 26.
PMID: 16895434
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0020102
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16895434
"Adaptive evolution of Hox-gene homeodomains after cluster
duplications." BMC Evol Biol. 2006 Nov 1;6(1):86. PMID: 17078881
http://www.biomedcentral.com/1471-2148/6/86
"A highly divergent gene cluster in honey bees encodes a novel silk
family." Genome Res. 2006 Nov;16(11):1414-21. Epub 2006 Oct 25.
PMID: 17065612 http://www.genome.org/cgi/content/full/16/11/1414
"Comparative genomics of vertebrate Fox cluster loci."
BMC Genomics. 2006 Oct 24;7:271. PMID: 17062144
http://www.biomedcentral.com/1471-2164/7/271
"Insights into the evolution of the ErbB receptor family and their
ligands from sequence analysis." BMC Evol Biol. 2006 Oct 6;6:79.
PMID: 17026767 http://www.biomedcentral.com/1471-2148/6/79
"The shape of human gene family phylogenies."
BMC Evol Biol. 2006 Aug 29;6:66. PMID: 16939643
http://www.biomedcentral.com/1471-2148/6/66
Note.... Sean often (wrongly) accuses me of not reading papers
but just pointing them out. I freely admit that - at this point in
time - I will have only read the abstracts of these papers, but
he can rest assured that many of the papers I cite here will find
their way, in complete PDF form, into my reference collection
on my computer at work and backed up here at home. When
Don visited here I gave him a duplicate of a recent backup CD
so Sean should ask Don how many 2005 and 2006 papers I
had on the one CD. While not all papers get read completely,
I do really enjoy this sort of reading and paperbacks rarely get
a look in anymore (although my mom has sent me Dawkins' The
Ancestors Tale, which I certainly will be reading soon).
******************************************
Not available in free full text, but worth reading the abstracts:
"Fructosyltransferase and invertase genes evolved by gene duplication
and rearrangements: rice, perennial ryegrass, and wheat gene families."
Genome. 2006 Sep;49(9):1081-1091. PMID: 17110988
"Understanding the Biases of Generalised Recombination: Part I."
Evol Comput. 2006 Winter;14(4):411-432. PMID: 17109605
(Sean... this has some interesting aspects mentioned in the abstract)
"Multiple Gene Duplication and Rapid Evolution in the groEL Gene:
Functional Implications." J Mol Evol. 2006 Nov 10; PMID: 17103057
"Emergence of primate genes by retrotransposon- mediated
sequence transduction." Proc Natl Acad Sci U S A. 2006 Nov 13;
PMID: 17101974
Sean, this abstract starts with the comment "Gene duplication is
one of the most important mechanisms for creating new genes and
generating genomic novelty.", and also goes into exon shuffling.
"The Conversion of 3' UTRs into Coding Regions."
Mol Biol Evol. 2006 Nov 10; PMID: 170990571
(removal of stop codons to generate novel sequence, plus
a role for duplications)
"Molecular diversification in spider venoms: A web of combinatorial
peptide libraries." Mol Divers. 2006 Nov 10; PMID: 17096075
"Functional divergence after gene duplication and sequence-structure
relationship: a case study of G-protein alpha subunits."
J Exp Zoolog B Mol Dev Evol. 2006 Nov 8; PMID: 17094082
"Disorder and Sequence Repeats in Hub Proteins and Their
Implications for Network Evolution." J Proteome Res. 2006
Nov 3;5(11):2985-2995. PMID: 17081050
>From the abstract, this looks like a *must* for anybody who has
followed SeanPit's complexity and size arguments. Let me know
if anyone - including you, Sean - needs help getting a copy.
"Time Squared: Repeated Measures on Phylogenies."
Mol Biol Evol. 2006 Nov 1; PMID: 17079699
(This abstract is a bit outside of my focus, but others may do
better at grasping the meaning... it doesn't seem to help Sean.)
"Evaluation Of Whether Accelerated Protein Evolution In Chordates
Has Occurred Before, After Or Simultaneously With Gene Duplication."
Mol Biol Evol. 2006 Oct 25; PMID: 17065596
(This abstract is clearer to me, but raises the question of Sean's oft
repeated comment that duplications don't do anything. Just how
quickly they "don't do it" and why is being answered to some degree.)
"Evolutionary history of the ABCB2 genomic region in teleosts."
Dev Comp Immunol. 2006 Sep 20; PMID: 17055577
(Sean... clues to MHC class II origin *may* lie in this paper.)
"Does lack of recombination enhance asymmetric evolution among
duplicate genes? Insights from the Drosophila melanogaster genome."
Gene. 2006 Aug 17; PMID: 17049187
"Birth, life and death of developmental control genes: new
challenges for the homology concept." Theory Biosci. 2005
Nov;124(2):199-212. Epub 2005 Oct 6. PMID: 17046356
(This one is for John Wilkins attention.....)
"Selection for more of the same product as a force to enhance
concerted evolution of duplicated genes."
Trends Genet. 2006 Oct 10; PMID: 17045359
(Another recent paper - I haven't spotted it yet in this search but
it should be nearby - suggests that sets of genes after genomic
duplications are kept or lost logether due to gene dosage effects.)
"Tandem repetitive d domains of the sperm ligand zonadhesin evolve
faster in the paralogue than in the orthologue comparison."
J Mol Evol. 2006 Nov;63(5):602-11. Epub 2006 Oct 6. PMID: 17031461
"Relating tissue specialization to the differentiation of expression
of singleton and duplicate mouse proteins." Genome Biol. 2006
Oct 9;7(10):R89 [Epub ahead of print] PMID: 17029626
(Sean - those comments about duplicates and function? Read this.)
"Evolution of sensory complexity recorded in a myxobacterial genome."
Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15200-5.
Epub 2006 Oct 2. PMID: 17015832
(Anybody want to say "evolution is blind"? - read this first!)
"Molecular genetic analyses of human endogenous retroviral elements
belonging to the HERV-P family in primates, human tissues, and
cancer cells." Genomics. 2006 Sep 26; PMID: 17010565
"Analysis of tandem repeats found in 44 prokaryotic genomes."
In Silico Biol. 2006;6(1-2):147-59. PMID: 17009421
"Evolution of Growth Hormone in Primates: The GH Gene Clusters
of the New World Monkeys Marmoset (Callithrix jacchus) and
White-Fronted Capuchin (Cebus albifrons)." J Mol Evol. 2006
Nov;63(5):591-601. Epub 2006 Sep 26. PMID: 17009125
"Gene regulatory networks in the evolution and development of
the heart." Science. 2006 Sep 29;313(5795):1922-7. Review.
PMID: 17008524
"Duplication, divergence and formation of novel protein topologies."
Bioessays. 2006 Oct;28(10):973-8. Review. PMID: 16998824
"Divergence of the dof gene families in poplar, Arabidopsis, and
rice suggests multiple modes of gene evolution after duplication."
Plant Physiol. 2006 Nov;142(3):820-30. Epub 2006 Sep 15.
PMID: 16980566
"A roadmap of tandemly arrayed genes in the genomes of human,
mouse, and rat." Mol Biol Evol. 2006 Nov;23(11):2134-41.
PMID: 16901985
"Genomic view of the evolution of the complement system."
Immunogenetics. 2006 Sep;58(9):701-13. PMID: 16896831
Note - these last couple were from the latter part of the
first 100 hits, most of the others were in the first 50. Having
just read well over 50 abstracts I'll stop at this point but just
to note - gene duplication is important in all areas of evolution.
Over to you, Sean....
John Wilkins
> "Birth, life and death of developmental control genes: new
> challenges for the homology concept." Theory Biosci. 2005
> Nov;124(2):199-212. Epub 2005 Oct 6. PMID: 17046356
> (This one is for John Wilkins attention.....)
have you got a PDF? I am not at work, so I can't access it now.
--
John S. Wilkins, Postdoctoral Research Fellow, Biohumanities Project
University of Queensland - Blog: scienceblogs.com/evolvingthoughts
"He used... sarcasm. He knew all the tricks, dramatic irony, metaphor,
bathos, puns, parody, litotes and... satire. He was vicious."
Gordon Hill
Good question. Does their insistence that science be absolute while
allowing this inconsistency within creationism/ID voids their premise
of objectivism.
gregwrld
Gee...I don't see any of Sean's papers listed here.
Wonder why...
gregwrld
eyelessgame
Let me channel them for a moment and try to answer.
I think they'd say that what they have, which those people don't, is
knowledge of Jesus Christ.
Yes, we'd answer, but plenty of people are religious, including
Christian, but still accept evolution, and some even become prominent
scientists and still accept evolution.
They'd respond with a No True Scotsman fallacy, which is unfortunate,
because they're right and they don't need to descend into the NTS.
The problem is terminology.
There are two wholly different religions called Christianity. By
"religion" I don't mean a sect or group of sects, as this divide cuts
across the different sects and even cuts right through individual
churches, though seldom evenly. I mean there are two wholly different
lines of dogma, two different sets of beliefs.
One of them in fact *does*, dogmatically, as an article of faith and a
condition of membership, require the rejection evolution.
I've been promising a post on this. I should go write it now. I'll
post later today.
eyelessgame
Marc
I'm still waiting for Sean to answer the questions, above...
> > Over to you, Sean....
>
> Gee...I don't see any of Sean's papers listed here.
> Wonder why...
>
> gregwrld
I'm wondering how he can say that *all* of them are flawed.
Oh... that's right. He'll call them "just so stories". Maybe
Sean should try thinking of them as "what if" stories instead.
(signed) marc
.
Seanpit
Marc wrote:
>
> I'm wondering how he can say that *all* of them are flawed.
Cause they all say exactly the same thing based on exactly the same
assumption - that sequence similarities necessitate common decent via
random mutation and function-based selection. I'd agree that sequence
similarities do suggest a common origin, but not necessarily a common
evolutionary origin. They could just as easily be the result of common
deliberate design. The fact that none of these scenarios has ever
been demonstrated in real life beyond the 1000 specified residue level,
combined with the fact that there is a clear exponential decline in
evolvability as the 1000aa level is approached, should give you a very
clear notion that evolutionary mechanisms simply cannot do the job at
this level or beyond this side of a practical eternity of time.
Yet, you continue to list off dozens of these papers, all of which are
based on exactly the same notion. Not one of them actually presents
any real experiment that demonstrates evolution in action beyond the
1000aa level - not one. You said you'd present something on
flagellar evolution, but you have yet to do so. You seem stuck in rut
here, unable to come up with anything beyond your fairy tale "what if"
stories.
> Oh... that's right. He'll call them "just so stories". Maybe
> Sean should try thinking of them as "what if" stories instead.
LOL - you think calling them "what if" stories makes them sound more
scientific? Please! Give me a break! They are all based on the same
erroneous assumption. They are not based on any statistical evaluation
of the actual time it would take to cross the gaps that exist at levels
of functional complexity beyond the 1000aa level nor do they present
any real time experiment that demonstrates evolution beyond this level.
Suggestion, stop reference mining dozens of references that you haven't
even read yourself and start actually thinking for yourself. Present
an actual relevant argument. Use references if you want, but present
your own argument that you have actually thought about just a little
bit. Listing dozens of bald unread references is worse than quote
mining.
> (signed) marc
Sean Pitman
www.DetectingDesign.com
Robert Maas, see http://tinyurl.com/uh3t
> > He asserts that intelligent design must have happened, but he can't tell
> > you how, where, when or by whom.
> of any non-deliberate process. When SETI scientists find the
> radio signal from outer space that they are looking for, which
> they would widely hail as evidence of alien intelligence
> equivalent or even greater than our own, they probably won't be
> able to say exactly who, why or even how such a signal was made.
There's a difference. With SETI, the scientists will have a
specific signal of interest, and they'll study the signal carefully
to fully understand it, to try to be really sure whether it's from
ETI or just something natural. For example, when spinning neutron
stars were first heard as radio bleeps at regular intervals, it was
taken as a possible ETI signal, but it was studied more carefully,
compared with theoretical models, and the conclusion was it was a
spinning neutron star rather than a signal from ETI. Several of the
pulsar signals were located at the same spot as neutron stars in
the centers of supernova remnants, clinching the case. But IDiots
pick some random feature of life which they personally don't
understand, and insist it *must* have been intelligently designed,
do no investigation as to how it might have appeared by any other
means, and write books citing it as a clear example of ID. Then
when legitimate scientists figure out how it could have arisen by
natural evolution, the IDiots don't retract their claim, they just
ignore the evolutionary models that explain it.
SETI scientists want to discover something real, and properly
present it to the scientific community, and not be laughed at by
the scientific community. IDiots don't care about what the
scientific community thinks about their claims, because their
target audience are suckers willing to part with their money on the
flimsiest of claims.
> ... the weight of current evidence strongly counters if not
> outright falsifies many of the most fundamental supports behind
> the theory of evolution.
That claim is totally false.
Bobby Bryant
"Seanpit" <seanpi...@naturalselection.0catch.com> writes:
>
> Marc wrote:
>
>> I'm wondering how he can say that *all* of them are flawed.
>
> Cause they all say exactly the same thing based on exactly the same
> assumption - that sequence similarities necessitate common decent
> via random mutation and function-based selection.
Not "necessitate". It's about economy of explanation.
(And before you suggest it, adding an unobserved middle man doesn't make
for a more economical explanation.)
> I'd agree that sequence similarities do suggest a common origin, but
> not necessarily a common evolutionary origin. They could just as
> easily be the result of common deliberate design.
Of course, when the Designer designs wings for a bird, he uses a common
low-level implementation. But when he designs wings for a bug, he uses
an entirely different low-level implementation.
"Because he wanted to."
You can handwave that 'explanation' over *any* observation.
Common descent doesn't have to appeal to the arbitrary will of an
unknown agent: the sequence similarities fall out of the theory
naturally.
--
Bobby Bryant
Reno, Nevada
Remove your hat to reply by e-mail.
noctiluca
Seanpit wrote:
> Marc wrote:
>
> >
> > I'm wondering how he can say that *all* of them are flawed.
>
> Cause they all say exactly the same thing based on exactly the same
> assumption - that sequence similarities necessitate common decent via
> random mutation and function-based selection. I'd agree that sequence
> similarities do suggest a common origin, but not necessarily a common
> evolutionary origin.
Oh good god, I'd come to expect a higher grade of nonsense from you,
this is just regular ol' garden variety creationist silliness.
> They could just as easily be the result of common deliberate design.
No, they most definitely could not. The fact is that there exists vast
amounts of scholarship (fossil record, phylogenetic analysis, molecular
analysis etc.) demonstrating the validity of an inference to
evolutionary processes and common descent.
There is no - zip, zero, nada - evidence that independently suggests we
can infer a deliberate desiger.
It is true that we cannot logically exclude the possibility of
deliberate design of the natural intelligent variety (aliens etc.), and
that is a hypothesis that is putatively amenable to scientific
methodology. (However, only if you wish to acknowledge that your
"common design" specifically repudiates any inference to the
non-natural could this suggestion even be considered.)
Even so, the huge disparity in evidence makes it clear that in no way
could "this...just as easily be the result of common deliberate
design." It would be no more nonsensical (in fact less, as I've
actually seen evidence that he exists) to say it could just as easily
be the result of an intelligent, though incredibly annoying, purple
dinosaur.
In truth, your inference to common design makes sense only if we remove
all meaning from the word "explanation" and it's synonyms, allowing
idle speculation and wishful thinking to be considered legitimate
counterexamples to evidentially supported theories.
No, not by any stretch of logic could "common deliberate design" "just
as easily" serve as an explication of common origin. Not without
abandoning reason, something you try hard to appear as if you employ.
You'll have to do much better.
> The fact that none of these scenarios has ever
> been demonstrated in real life beyond the 1000 specified residue level,
> combined with the fact that there is a clear exponential decline in
> evolvability as the 1000aa level is approached, should give you a very
> clear notion that evolutionary mechanisms simply cannot do the job at
> this level or beyond this side of a practical eternity of time.
Well, this is certainly no improvement. Standard issue creationist
"gap" argument here.
> Yet, you continue to list off dozens of these papers, all of which are
> based on exactly the same notion. Not one of them actually presents
> any real experiment that demonstrates evolution in action beyond the
> 1000aa level - not one. You said you'd present something on
> flagellar evolution, but you have yet to do so. You seem stuck in rut
> here, unable to come up with anything beyond your fairy tale "what if"
> stories.
There's a reason all of them are based upon similar assumptions. There
are bedrock concepts in any discipline, achieving that status through
hundreds of years and countless man-hours of corroborative research.
> > Oh... that's right. He'll call them "just so stories". Maybe
> > Sean should try thinking of them as "what if" stories instead.
>
> LOL - you think calling them "what if" stories makes them sound more
> scientific? Please! Give me a break! They are all based on the same
> erroneous assumption. They are not based on any statistical evaluation
> of the actual time it would take to cross the gaps that exist at levels
> of functional complexity beyond the 1000aa level nor do they present
> any real time experiment that demonstrates evolution beyond this level.
Ah, yes, "real time." A dead giveaway for the standard issue
creationist "were you there" argument.
> Suggestion, stop reference mining dozens of references that you haven't
> even read yourself and start actually thinking for yourself.
You mean "thinking for yourself" as in trying to step outside a line of
inquiry circumscribed by unquestioned dogma leading to extreme
confirmation bias? Well, you've certainly got the whole projection
thing down.
Now, here's a suggestion for you; why not stop for a moment and
consider which kind of "dogma" it would make sense to allow to
circumscribe your thinking - one based upon the accumulated replicated
work of thousands of highly trained scientists, or one based upon a
book of legends and parables.
I would think no less of you for merely chosing the latter, but when
you extend that to accusing others who are involved in expanding our
knowledge of the universe of wearing blinders then I feel compelled to
note that you are a self-deluded prat.
> Present
> an actual relevant argument. Use references if you want, but present
> your own argument that you have actually thought about just a little
> bit. Listing dozens of bald unread references is worse than quote
> mining.
Let's see, presenting legitimate research is worse than the
disingenuous act of changing the context of someone's words?
I'd have to say that the extreme silliness of this assertion leads me
to wonder if perhaps you simply don't wish to address the evidence?
Hey, it's just a thought.
RLC
Robert Maas, see http://tinyurl.com/uh3t
> The ID assertion is that an "intelligent designer", using
> unspecified but possibly supernatural powers interferes with
> normal evolutionary processes using unspecified but possibly
> supernatural methods.
I heard the ID assertion differently, basically that there's no
such thing as evolution, every new species was specially created
from a design in the mind of some unknown designer (and possibly
using supernatural methods as you say). Maybe we should use
different terms for the two versions: The Strong and Weak ID
assertion, strong = special design in each case, weak = just
interfering with evolution but not doing all the work by itself.
> Evolution happens. It is the best explanation we have in science
> for the diversity of living organisms and the distribution if [sic]
> fossils in the geological record.
Even moreso, evolution explains why there's so much in common
between diverse organisms, including sequences of DNA that
apparently have no useful role except possibly just as bulk filler
but where the sequence is most similar precisely in organisms where
for other reasons we believe they are closely related. The way
sequences all over the genome are more similar within apparent
clades than between those clades and other clades, with the same
consistent clade hierarchy across nearly all segments of DNA, with
only occasional exceptions where horizonal gene flow apparently
happened. Furthermore, for any resonably long piece of DNA, so it
wouldn't recur by chance, we always get a concensus tree structure,
never a closed loop. Evolution with branching tree of life from
common ancestor is the only model that fits this data. This model
predicts that newly sequenced DNA will fit into old cladograms,
clearing up some local ambiguities but never grossly contradicting
the old cladograms, and indeed time and time again that's the
result. That's prediction after prediction of evolution confirmed.
Robert Maas, see http://tinyurl.com/uh3t
> The evidence for intelligent design can be entirely contained
> within the radio signal itself.
That's a theoretical possibility. For example, if we received a
signal containing an obvious binary code, and upon examination we
discovered that via a simple representation it was conveying the
sequence of prime numbers for a considerable distance (let's say at
least a hundred consecutive prime numbers without not a single
mistake), a sequence very very unlikely to occur at random, we
would suspect the signal was deliberately constructed by somebody
intelligent.
> Like finding the Rosetta Stone, one might not be able to
> understand what the character sequences mean, when they were
> made, who made them, or exactly how they were made. However, one
> would very easily be able to tell that they were indeed
> deliberately designed and that they most likely represent some
> sort of information.
As I understand it, the Rosetta Stone had the same passage in three
different languages, one of which we already knew, so the one
language we knew made it obvious the stone deliberately conveyed
some language, and so obviously the other two languages were also
deliberately conveyed. But if we found a fossil containing
impressions of lots of regular patterns, for all we knew those were
just impressions of several species of tree-leaves.
> the attempt to rule out potential non-deliberate natural causes
> is a big part of any intelligent design theory.
Too bad none of the advocates of ID have bothered to do that yet.
Using math, they've ruled out two strawmen, tornado in a junkyard,
and build-up by pieces with never a modification to an already
extant piece, but they haven't ruled out anything that evolutionary
theory actually claims could have happened, such as modifications
that change function, specialization after duplication, or a
"scaffold" whereby removing a piece obtains the current system.
> If the supernatural agent acts within the natural world in a way
> that can be detected by us humans, that activity can indeed be
> appreciated and classified as being almost certainly beyond the
> capabilities of any non-deliberate process and well beyond any
> creative abilities of known deliberate agents as well.
I'm not sure what you mean by "detected". For example, we can
detect collapses of the wave function in quantum mechanics, and it
seems random to us, but what if its actually done by a supernatural
agent. How would we know?? Why do you say it'd be appreciated and
classified in the way you do?? How can anybody tell the difference
between something truly random and something deliberately done by a
supernatural agent?
> this predictive value may gain ground with additional
> "revelations" provided by the "supernatural" agent.
Suppose an actual revelation happened. How would we know it was
really a revelation from a supernatural agent, not a communication
from space aliens with superior technology, or just a burp of
random noise, or a halucination? How could we test such an alleged
revelation to determine whether it really was a revelation or not?
> When it comes to functional biosystems that require a minimum of
> more than a few thousand specifically arranged amino acid residues,
No such biosystem has ever been observed. Are you talking
hypothetically about if and when any such would be discovered?
Perplexed in Peoria
"Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1164212267.2...@h54g2000cwb.googlegroups.com...
>
> Marc wrote:
>
> > [Regarding cited papers]
> > I'm wondering how he can say that *all* of them are flawed.
>
> Cause they all say exactly the same thing based on exactly the same
> assumption - that sequence similarities necessitate common decent via
> random mutation and function-based selection. I'd agree that sequence
> similarities do suggest a common origin, but not necessarily a common
> evolutionary origin. They could just as easily be the result of common
> deliberate design.
How does that work exactly? The polymorphism (SNPs) withing a species
is the result of mutation from the nominal true sequence specified
by the Creator? But the differences between species are the result
of design decisions of the Designer?
Well, I suppose that I should be grateful that you are not claiming
that the alignments are bogus. You recognize that these are the
'same genes in different species' in some sense.
> The fact that none of these scenarios has ever
> been demonstrated in real life beyond the 1000 specified residue level, ...
There must be some confusion here. What does sequence evolution have
to do with *specified* complexity? In the simplest sequence evolution
model, some sites evolve and are informative regarding phylogeny. Other
sites do not evolve, and are therefore useful only for producing an
alignment. It seems to me that you should be claiming that those
unchanging sites are the 'specified' ones and that the ones that are
subject to mutation without apparent ill-effect are ones that the
Designer didn't specify at design-time (though, perforce, He had to
make an arbitrary choice and put something there at creation-time).
In more sophisticated models of sequence evolution, the binary distinction
between specified and unspecified sites is blurred into a spectrum.
Some sites are more specified (evolutionists prefer the term 'conserved')
than others. But you probably don't like to think about such models
because they complicate your probability calculations and call into
question your entire ideology of "If it ain't what was specified, then
it doesn't work at all".
> combined with the fact that there is a clear exponential decline in
> evolvability as the 1000aa level is approached, should give you a very
> clear notion that evolutionary mechanisms simply cannot do the job at
> this level or beyond this side of a practical eternity of time.
The clarity of this exponential decline you keep talking about is
just not clear to me. Is this exponential decline curve a conclusion
reported in laboratory experiments? Is it an inference which you
draw from consideration of your own models of the sequence-to-function
landscape? Or is it something that can be inferred from the sequence
data? No, that last can't be correct, because you don't believe that
sequence data is informative about evolution - that is why you don't
believe the cited articles.
So, I'm guessing that your 'exponential decline' arises from your
estimates of what the landscape looks like. I would criticize those
estimates, but to do so, I would have to use sequence data on evolution.
But you don't believe such data is informative regarding evolution.
I believe this is what they call an 'impass'.
Don Cates
<seanpi...@naturalselection.0catch.com> posted:
>
>Marc wrote:
>
>>
>> I'm wondering how he can say that *all* of them are flawed.
>
>Cause they all say exactly the same thing based on exactly the same
>assumption
Not an assumption, rather a conclusion based on an enormous amount of
evidence from many branches of science. Denial of common descent
requires ignorance or willful, biased rejection of that evidence.
- that sequence similarities necessitate common decent via
>random mutation and function-based selection.
No, they all start with common descent as a given (and rightly so). The
sequence similarities are evidence for the particular line of descent
and the proposed functional intermediates a possible selective pathway.
The existence of mutation based variation is also a given.
I'd agree that sequence
>similarities do suggest a common origin, but not necessarily a common
>evolutionary origin. They could just as easily be the result of common
>deliberate design.
The idea of common descent is not based on similarities, it is based on
the pattern of similarities and differences in heritable
charactaristics in existing life and the fossil record. I would sure
like to see a non-'special pleading' "common deliberate design"
explanation for the majority of the sequence difference/similarity
pattern which is neutral, either in non-functional sequences or
functionally neutral differences in coding sequences.
The fact that none of these scenarios has ever
>been demonstrated in real life beyond the 1000 specified residue level,
>combined with the fact that there is a clear exponential decline in
>evolvability as the 1000aa level is approached, should give you a very
>clear notion that evolutionary mechanisms simply cannot do the job at
>this level or beyond this side of a practical eternity of time.
And you have never shown that such sequences exist (your definition of
"specified residue" varies all over the place) or that evolvability
declines (your "fact" is based on bogus calculations that assume that
functional sequences are evenly distributed over all of sequence space,
sequence space is two dimensional, and that all existing sequences are
expected to have the potential to reach any other existing sequence
easily).
Seanpit
Don Cates wrote:
< snip >
> >I'd agree that sequence
> >similarities do suggest a common origin, but not necessarily a common
> >evolutionary origin. They could just as easily be the result of common
> >deliberate design.
>
> The idea of common descent is not based on similarities, it is based on
> the pattern of similarities and differences in heritable
> charactaristics in existing life and the fossil record. I would sure
> like to see a non-'special pleading' "common deliberate design"
> explanation for the majority of the sequence difference/similarity
> pattern which is neutral, either in non-functional sequences or
> functionally neutral differences in coding sequences.
The sequence similarities/differences are not functionally neutral.
This is the pseudogene argument - that genetic non-functional baggage
is left over from previous ancestors. The problem is, such sequences
similarities are maintained over time because they are functional - not
neutral.
"Pseudogenes have been defined as nonfunctional sequences of
genomic DNA originally derived from functional genes. It is therefore
assumed that all pseudogene mutations are selectively neutral and have
equal probability to become fixed in the population. Rather,
pseudogenes that have been suitably investigated often exhibit
functional roles, such as gene expression, gene regulation, generation
of genetic (antibody, antigenic, and other) diversity. Pseudogenes are
involved in gene conversion or recombination with functional genes.
Pseudogenes exhibit evolutionary conservation of gene sequence, reduced
nucleotide variability, excess synonymous over nonsynonymous nucleotide
polymorphism, and other features that are expected in genes or DNA
sequences that have functional roles. . .
An extensive and fast-increasing literature does not justify a
sharp division between genes and pseudogenes that would place
pseudogenes in the class of genomic "junk" DNA that lacks function and
is not subject to natural selection. Pseudogenes are often extremely
conserved and transcriptionally active. . .
There seems to be the case that some functionality has been
discovered in all cases, or nearly, whenever this possibility has been
pursued with suitable investigations. One may well conclude that most
pseudogenes retain or acquire some functionality and, thus, that it may
not be appropriate to define pseudogenes as nonfunctional sequences of
genomic DNA originally derived from functional genes, or as "genes that
are no longer expressed but bear sequence similarity to active genes".
Rather, pseudogenes might be defined as DNA sequences derived by
duplication or retroposition from functional genes that are often
subject to natural selection and therefore retain much of the original
sequence and structure because they have acquired new regulatory or
other functions, or may serve as reservoirs of genetic variability."
Hirotsun, Shinji et. al., An expressed pseudogene regulates the
messenger-RNA stability of its homologous coding gene, Nature
423:91-96. 2003
> >The fact that none of these scenarios has ever
> >been demonstrated in real life beyond the 1000 specified residue level,
> >combined with the fact that there is a clear exponential decline in
> >evolvability as the 1000aa level is approached, should give you a very
> >clear notion that evolutionary mechanisms simply cannot do the job at
> >this level or beyond this side of a practical eternity of time.
>
> And you have never shown that such sequences exist (your definition of
> "specified residue" varies all over the place) or that evolvability
> declines (your "fact" is based on bogus calculations that assume that
> functional sequences are evenly distributed over all of sequence space,
> sequence space is two dimensional, and that all existing sequences are
> expected to have the potential to reach any other existing sequence
> easily).
Lots of functions exist that require far more than 1000 fairly
specified amino acid residues. Take the popular flagellar motility
system, for example, which requires well over 10,000 codons coding for
a minimum of over 10,000 specifically arranged residues.
It is also a strawman mischaracterization to say that my position
requires even distribution of potentially beneficial sequences
throughout sequence space. That's just not true. My position holds as
long as potentially beneficial sequences do not remain equally
clustered within one tiny corner of sequence space at higher and higher
levels of functional complexity.
Also, I never said that sequence space was two-dimensional. It isn't.
It has a great many dimensions. This does not remove the fact that
potentially beneficial sequences are surrounded on all sides by vast
oceans of non-beneficial sequences at higher levels of functional
complexity and that this ocean expands exponentially faster than the
number of potentially beneficial island clusters expands with each step
up the ladder of functional complexity.
Why all these strawmen? Don't you have a real argument that can hold
water?
Sean Pitman
www.DetectingDesign.com
Don Cates
<seanpi...@naturalselection.0catch.com> posted:
>
>Don Cates wrote:
>
>< snip >
>
>> >I'd agree that sequence
>> >similarities do suggest a common origin, but not necessarily a common
>> >evolutionary origin. They could just as easily be the result of common
>> >deliberate design.
>>
>> The idea of common descent is not based on similarities, it is based on
>> the pattern of similarities and differences in heritable
>> charactaristics in existing life and the fossil record. I would sure
>> like to see a non-'special pleading' "common deliberate design"
>> explanation for the majority of the sequence difference/similarity
>> pattern which is neutral, either in non-functional sequences or
>> functionally neutral differences in coding sequences.
>
>The sequence similarities/differences are not functionally neutral.
Depending on the species, there is anywhere from very little to almost
all of the DNA sequencr that is non-functional. If it is not conserved
it is almost certainly not functional and the wide range of genome size
unrelated to mophological conplexity indicates that in some cases much
of it must be non-functional and non-functional sequences can change
neutrally.
>This is the pseudogene argument - that genetic non-functional baggage
>is left over from previous ancestors. The problem is, such sequences
>similarities are maintained over time because they are functional - not
>neutral.
There is a lot more non-functional sequence than pseudogenes. Those
that are conserved are almost certainly functional in some way, those
that aren't, aren't.
And then even within functiional sequences there are many neutral
changes possible and your response doesn't address these
similarity/differences at all.
>
[snip abstract showing function for a pseudogene and claiming many
other preudogenes also have functions. I agree and it doesn't affect my
argument]
>
>Hirotsun, Shinji et. al., An expressed pseudogene regulates the
>messenger-RNA stability of its homologous coding gene, Nature
>423:91-96. 2003
>
>> >The fact that none of these scenarios has ever
>> >been demonstrated in real life beyond the 1000 specified residue level,
>> >combined with the fact that there is a clear exponential decline in
>> >evolvability as the 1000aa level is approached, should give you a very
>> >clear notion that evolutionary mechanisms simply cannot do the job at
>> >this level or beyond this side of a practical eternity of time.
>>
>> And you have never shown that such sequences exist (your definition of
>> "specified residue" varies all over the place) or that evolvability
>> declines (your "fact" is based on bogus calculations that assume that
>> functional sequences are evenly distributed over all of sequence space,
>> sequence space is two dimensional, and that all existing sequences are
>> expected to have the potential to reach any other existing sequence
>> easily).
>
>Lots of functions exist that require far more than 1000 fairly
>specified amino acid residues. Take the popular flagellar motility
>system, for example, which requires well over 10,000 codons coding for
>a minimum of over 10,000 specifically arranged residues.
>
so how many of them are "fairly specified" (how do you determine this)
and how many could be changed to a similar residue and still function?
How do you know any of this?
>It is also a strawman mischaracterization to say that my position
>requires even distribution of potentially beneficial sequences
>throughout sequence space. That's just not true. My position holds as
>long as potentially beneficial sequences do not remain equally
>clustered within one tiny corner of sequence space at higher and higher
>levels of functional complexity.
>
This is what you claim but when you do your calculations the resultss
depend on that even distribution. Otherwise your 'average distance' is
meaningless.
>Also, I never said that sequence space was two-dimensional. It isn't.
>It has a great many dimensions. This does not remove the fact that
>potentially beneficial sequences are surrounded on all sides by vast
>oceans of non-beneficial sequences at higher levels of functional
>complexity and that this ocean expands exponentially faster than the
>number of potentially beneficial island clusters expands with each step
>up the ladder of functional complexity.
>
Gee, "oceans" and "islands"; sure sounds two dimensional. Your claim is
that as sequences get longer the functional neighbours get sparser, but
if you consider higher dimensional space, as the sequences get longer
the number of neighbours gets larger so the odds of having a
functioinal neighbour do not decrease as per your calculation.
>Why all these strawmen? Don't you have a real argument that can hold
>water?
>
'It's all pseudogenes' is the only strawman up there, and it's not mine.
B Richardson
>
> Don Cates wrote:
>
>< snip >
>
>> >I'd agree that sequence
>> >similarities do suggest a common origin, but not necessarily a common
>> >evolutionary origin. They could just as easily be the result of common
>> >deliberate design.
>>
>> The idea of common descent is not based on similarities, it is based on
>> the pattern of similarities and differences in heritable
>> charactaristics in existing life and the fossil record. I would sure
>> like to see a non-'special pleading' "common deliberate design"
>> explanation for the majority of the sequence difference/similarity
>> pattern which is neutral, either in non-functional sequences or
>> functionally neutral differences in coding sequences.
>
> The sequence similarities/differences are not functionally neutral.
But even in a functional gene some sites are neutral. Do you
know of an example where many or most of the sites that contribute
to phylogenetic signal are not silent?
> This is the pseudogene argument - that genetic non-functional baggage
> is left over from previous ancestors. The problem is, such sequences
> similarities are maintained over time because they are functional - not
> neutral.
>
You can't make a sweeping generalization like that, some sequences
are highly conserved, some not at all. There's 88 known variants
of the gene that produces the ABO blood types in humans.
So he defines pseudogenes as "DNA sequences derived by duplication
or retroposition from functional genes that are often subject
to natural selection". So you are arguing that this is what
a pseudogene is, and also that shared pseudogenes are not
evidence of common descent?
>
> Hirotsun, Shinji et. al., An expressed pseudogene regulates the
> messenger-RNA stability of its homologous coding gene, Nature
> 423:91-96. 2003
>
[snip]
Marc
Seanpit wrote:
> Marc wrote:
>
> >
> > I'm wondering how he can say that *all* of them are flawed.
>
> Cause they all say exactly the same thing based on exactly the same
> assumption -
They say many *different* things, about many different genes in
many different species - but they all disagree with your unsupported
contention that duplication events are not able to contribute to the
development of novel genes. Every paper I cited - all published in
the few months since I cited the last bunch for you - shows the
importance of duplication and divergence. Every one of these.
> that sequence similarities necessitate common decent via
> random mutation and function-based selection. I'd agree that sequence
> similarities do suggest a common origin, but not necessarily a common
> evolutionary origin. They could just as easily be the result of common
> deliberate design.
They could have all been created last Thursday. Or the data it correct.
> The fact that none of these scenarios has ever
> been demonstrated in real life beyond the 1000 specified residue level,
> combined with the fact that there is a clear exponential decline in
> evolvability as the 1000aa level is approached, should give you a very
> clear notion that evolutionary mechanisms simply cannot do the job at
> this level or beyond this side of a practical eternity of time.
All the proteins larger than 1000 aa show that 1000aa is just your
hand waving - go look at the papers and tell me which ones are
smaller that 1000aa (lots will be, some won't). It's your bogus number.
And you keep changing it. Sometimes it's basepairs, sometimes
it's two thousand. Sometimes it's trillions (your number for "bigger
that two thousand").
> Yet, you continue to list off dozens of these papers, all of which are
> based on exactly the same notion.
There are actually some with quite novel notions. Read a few of them.
That they have similar conclusions is the point of interest.
>Not one of them actually presents
> any real experiment that demonstrates evolution in action beyond the
> 1000aa level - not one. You said you'd present something on
> flagellar evolution, but you have yet to do so.
Oh yes, I did. But I haven't felt up to it. I've been dealing with
a bad chest cold for several weeks and while I did read those
50 abstracts the other day I haven't felt at all like going into
aq bunch of reading on a topic that has nothing to do with
my work. I've told you that I wasn't very interested in reading
the papers I had found - plus the ones that there would be
since that or that I would need for background. And with your
attitude about sequence data, what would be the point. The
data from the flagella is based on such data and much of it
is way older than the data for vertebrate immune evolution that
I am interested in learning more about. If you reject the more
recent, fairly clear-cut data as "stories", how can my reading
papers on flagellar evolution be worth the time?
But to give you something to chew on - here is a science blog
article that makes a lot of sense to me. Maybe you can tell
me just why you think it is incorrect (as you no doubt will think).
http://scienceblogs.com/loom/2006/11/13/getting_the_mooney_treatment.php
Now - don't fuss about my readin up on bacteria. I might and
I might not - but explain instead why duplication does not lead
to novel function as is not as important as *EVERY* paper I
just cited says it is.
> You seem stuck in rut
> here, unable to come up with anything beyond your fairy tale "what if"
> stories.
D'Oh, man.... it's those *scientists*. They are the ones publishing.
Every month I go back to PubMed and - darn it - there are just two
or three dozen more papers that use duplication to understand the
biological evolution of some family or another. Gosh darn it, I do
wish they would just stop publishing that stuff. More stories for you
to ignore, and you just got used to ignoring the last lot. Heck.
> > Oh... that's right. He'll call them "just so stories". Maybe
> > Sean should try thinking of them as "what if" stories instead.
>
> LOL - you think calling them "what if" stories makes them sound more
> scientific? Please! Give me a break! They are all based on the same
> erroneous assumption. They are not based on any statistical evaluation
> of the actual time it would take to cross the gaps that exist at levels
> of functional complexity beyond the 1000aa level nor do they present
> any real time experiment that demonstrates evolution beyond this level.
Yeah? They do explain 300 aa quite well, and sometimes 500 aa.
And exon shuffling of a 300aa and a 500 aa domain gets you 800aa.
(You have even agreed with this.) Your magic "1000aa" is just
a figment of your limited thinking, Sean. It's arbitrary (and wrong).
> Suggestion, stop reference mining dozens of references that you haven't
> even read yourself and start actually thinking for yourself.
Hey - that's how literature searches are done. Do a search, read
the abstracts then choose which papers to collect. I'm doing that.
(Ask John Wilkins - we've just shared a few I found in addition to
the one I had flagged for him he asked me to forward.) Let me ask
*you* if you have looked at even one of the full papers I cited. One?
Have you bothered to get even one paper, even a free, full text one,
and look at it carefully or did you reject all those papers after
just reading the titles of the papers? (You are not likely to have
bothered with the abstracts since you haven't even bothered with
any of the free papers.) At least I get the PDFs, Sean - and I do
read them for the most part, sooner or later. But not to please you.
I say that *you* haven't read any of them, and that makes you a fraud.
> Present
> an actual relevant argument. Use references if you want, but present
> your own argument that you have actually thought about just a little
> bit. Listing dozens of bald unread references is worse than quote
> mining.
No, it's science. You don't have an argument with *me* here, boy-o.
Your argument is with the literature and every time more of it is
published, your head goes farther down into the sand. You never
did read that protein domain review in the Annual Reviews series,
did you? (It was in last year's Biochemistry one IIRC.) You most
likely have never read one paper I have cited to you at all. You just
reject papers on principle (after reading the titles). A mental giant.
I've made my argument and supported it with dozens of papers,
and done it again with more recent papers and even yet again.
You haven't done a thing except dismiss all published scientific
literature as "a bunch of stories". And *then* you want me to go
back to another really stupid topic you misunderstand and do
some additional reading which you won't do yourself. Go figure.
(signed) marc
Seanpit
Don Cates wrote:
> On 22 Nov 2006 13:34:08 -0800, "Seanpit"
> <seanpi...@naturalselection.0catch.com> posted:
>
> >
> >Don Cates wrote:
> >
> >< snip >
> >
> >> >I'd agree that sequence
> >> >similarities do suggest a common origin, but not necessarily a common
> >> >evolutionary origin. They could just as easily be the result of common
> >> >deliberate design.
> >>
> >> The idea of common descent is not based on similarities, it is based on
> >> the pattern of similarities and differences in heritable
> >> charactaristics in existing life and the fossil record. I would sure
> >> like to see a non-'special pleading' "common deliberate design"
> >> explanation for the majority of the sequence difference/similarity
> >> pattern which is neutral, either in non-functional sequences or
> >> functionally neutral differences in coding sequences.
> >
> >The sequence similarities/differences are not functionally neutral.
>
> Depending on the species, there is anywhere from very little to almost
> all of the DNA sequencr that is non-functional. If it is not conserved
> it is almost certainly not functional and the wide range of genome size
> unrelated to mophological conplexity indicates that in some cases much
> of it must be non-functional and non-functional sequences can change
> neutrally.
Certainly there are sequences that have a significant neutrality with
respect to many different types of substitutions. This is the basis of
Moto Kimura's neutral theory of evolution. However, significant
stretches of neutral genetic material are becoming more and more rare
the more and more we learn. Your statement that the genomes of some
species are almost entirely neutral just isn't thought to be true
anymore - even by mainstream scientists. Even very repetitive elements,
long thought to have no function, are showing signs of function after
all.
In yet another recent Science article by Wojciech Makalowski, the
following comments are made that seem to echo what design theorists
have been saying for a very long time:
"Although catchy, the term "junk DNA" for many years repelled
mainstream researchers from studying noncoding DNA. Who, except a
small number of genomic clochards, would like to dig through genomic
garbage? However, in science as in normal life, there are some
clochards who, at the risk of being ridiculed, explore unpopular
territories. Because of them, the view of junk DNA, especially
repetitive elements, began to change in the early 1990s. Now, more and
more biologists regard repetitive elements as genomic treasure."
Makalowski, Wojciech. 2003. Not Junk After All, Science 300:1246-1247
> >Lots of functions exist that require far more than 1000 fairly
> >specified amino acid residues. Take the popular flagellar motility
> >system, for example, which requires well over 10,000 codons coding for
> >a minimum of over 10,000 specifically arranged residues.
> >
> so how many of them are "fairly specified" (how do you determine this)
> and how many could be changed to a similar residue and still function?
> How do you know any of this?
The ratio is about 1e-30 per 100aa based on studies like Sauer, Olsen,
and Yockey. That allows for a fair degree of flexibility, but not
nearly enough to save the proposed mechanism behind the ToE.
> >It is also a strawman mischaracterization to say that my position
> >requires even distribution of potentially beneficial sequences
> >throughout sequence space. That's just not true. My position holds as
> >long as potentially beneficial sequences do not remain equally
> >clustered within one tiny corner of sequence space at higher and higher
> >levels of functional complexity.
> >
> This is what you claim but when you do your calculations the resultss
> depend on that even distribution. Otherwise your 'average distance' is
> meaningless.
The average linear distance most certainly does increase in a linear
manner as long as the ratio in all portions of sequence space between
potentially beneficial and non-beneficial decreases exponentially - and
it does. No portion of sequence space maintains the same ratio at
higher and higher levels of minimum size and specificity requirements.
> >Also, I never said that sequence space was two-dimensional. It isn't.
> >It has a great many dimensions. This does not remove the fact that
> >potentially beneficial sequences are surrounded on all sides by vast
> >oceans of non-beneficial sequences at higher levels of functional
> >complexity and that this ocean expands exponentially faster than the
> >number of potentially beneficial island clusters expands with each step
> >up the ladder of functional complexity.
> >
> Gee, "oceans" and "islands"; sure sounds two dimensional. Your claim is
> that as sequences get longer the functional neighbours get sparser, but
> if you consider higher dimensional space, as the sequences get longer
> the number of neighbours gets larger so the odds of having a
> functioinal neighbour do not decrease as per your calculation.
You're wrong. Increasing the dimensions does not make it easier to
find one's neighbors given the same decrease in ratio. Mathematically,
it makes no differences.
Using terms like "oceans" and "islands" is just an easy way to help one
visualize what is going on mathematically. It is not meant to indicate
literal 2 or even 3 dimensional space. There are many more dimensions
and the dimensions increase with each increase in the level of
functional complexity.
> >Why all these strawmen? Don't you have a real argument that can hold
> >water?
> >
> 'It's all pseudogenes' is the only strawman up there, and it's not mine.
Your argument just doesn't hold water anymore. Beyond that, your
proposed mechanism is demonstrably incapable of doing much of anything
beyond very very low levels of functional complexity.
Sean Pitman
www.DetectingDesign.com
Don Cates
<seanpi...@naturalselection.0catch.com> posted:
Maybe a bit less pervasive but certainly not "rare".
Your statement that the genomes of some
>species are almost entirely neutral just isn't thought to be true
>anymore - even by mainstream scientists.
Yes it is, by many mainstream scientists.
Even very repetitive elements,
>long thought to have no function, are showing signs of function after
>all.
>
>In yet another recent Science article by Wojciech Makalowski, the
>following comments are made that seem to echo what design theorists
>have been saying for a very long time:
>
A 'Perspectives' piece, which tend to be a little more 'folksy' than
the peer reviewed pieces, but a nice, well supported article.
> "Although catchy, the term "junk DNA" for many years repelled
>mainstream researchers from studying noncoding DNA. Who, except a
>small number of genomic clochards, would like to dig through genomic
>garbage? However, in science as in normal life, there are some
>clochards who, at the risk of being ridiculed, explore unpopular
>territories. Because of them, the view of junk DNA, especially
>repetitive elements, began to change in the early 1990s. Now, more and
>more biologists regard repetitive elements as genomic treasure."
>
>Makalowski, Wojciech. 2003. Not Junk After All, Science 300:1246-1247
>
Addresses almost exclusively repetative Alu elements (~10% of the human
genome) which are known for their habit of inserting copies,
appearently randomly, into the genome. There is an estimate that 1 in
200 births has a new Alu repeat sequence. Depending on where it inserts
it can cause disease, novel proteins, changed expression, or nothing.
*Some* of it certainly has some function and that is conserved and
falls outside the sequence space I am referring to.
I note that the similarity/difference of the *position* within the
genome of these Alu repeats is strong evidence for common descent.
>> >Lots of functions exist that require far more than 1000 fairly
>> >specified amino acid residues. Take the popular flagellar motility
>> >system, for example, which requires well over 10,000 codons coding for
>> >a minimum of over 10,000 specifically arranged residues.
>> >
Here's the bit you snipped without marking and didn't address from my
previous post.
-------------restored---------
There is a lot more non-functional sequence than pseudogenes. Those
that are conserved are almost certainly functional in some way, those
that aren't, aren't.
And then even within functiional sequences there are many neutral
changes possible and your response doesn't address these
similarity/differences at all.
------------end restored---------
>> so how many of them are "fairly specified" (how do you determine this)
>> and how many could be changed to a similar residue and still function?
>> How do you know any of this?
>
>The ratio is about 1e-30 per 100aa based on studies like Sauer, Olsen,
>and Yockey. That allows for a fair degree of flexibility, but not
>nearly enough to save the proposed mechanism behind the ToE.
>
Ratio of what? Did they take a functional sequence, determine (somehow;
How?) the "fairly specified" part, add/delete/change residues and test
for 'function' (what definition for function)?
>> >It is also a strawman mischaracterization to say that my position
>> >requires even distribution of potentially beneficial sequences
>> >throughout sequence space. That's just not true. My position holds as
>> >long as potentially beneficial sequences do not remain equally
>> >clustered within one tiny corner of sequence space at higher and higher
>> >levels of functional complexity.
>> >
>> This is what you claim but when you do your calculations the resultss
>> depend on that even distribution. Otherwise your 'average distance' is
>> meaningless.
>
>The average linear distance most certainly does increase in a linear
>manner as long as the ratio in all portions of sequence space between
>potentially beneficial and non-beneficial decreases exponentially - and
>it does.
Oh really? And how do you know this? Just what is the distribution of
functional sequences in sequence space? How did you determine it? How
does it correspond to the existing sequences?
Your interpretation of your calculation depends on the assumption that
all portions of sequence space are homogeneous with respect to
beneficial/non-beneficial density. Even if you are correct that
beneficial sequences are confined to well sepatated 'islands', you
would have to show that the sequence space of existing DNA is not
confined to one of these islands.
No portion of sequence space maintains the same ratio at
>higher and higher levels of minimum size and specificity requirements.
>
The ratio doesn't matter. All that matters is that there be *some*
nearby beneficial sequence.
Let's say we have functional sequences X and Y with 1000aas each.
Evolution does not require that there be a 1000aa path from X to Y,
only that there be a path from 200aa B to 1000aa X and from 200aa B to
1000aa Y. There is no requirement that any organism can aquire any
function. That is why your lactase example is so bogus. All it shows is
that for that organism if you remove all the close sequences there are
no close sequences.
>
>> >Also, I never said that sequence space was two-dimensional. It isn't.
>> >It has a great many dimensions. This does not remove the fact that
>> >potentially beneficial sequences are surrounded on all sides by vast
>> >oceans of non-beneficial sequences at higher levels of functional
>> >complexity and that this ocean expands exponentially faster than the
>> >number of potentially beneficial island clusters expands with each step
>> >up the ladder of functional complexity.
>> >
>> Gee, "oceans" and "islands"; sure sounds two dimensional. Your claim is
>> that as sequences get longer the functional neighbours get sparser, but
>> if you consider higher dimensional space, as the sequences get longer
>> the number of neighbours gets larger so the odds of having a
>> functioinal neighbour do not decrease as per your calculation.
>
>You're wrong. Increasing the dimensions does not make it easier to
>find one's neighbors given the same decrease in ratio. Mathematically,
>it makes no differences.
>
Yes, I was wrong about that. The problem is not the calculation but
rather the interpretation of the result. IIRC your argument is that an
increasing neutral space must be traversed as sequences get longer.
That we are starting with a functional sequence pretty much guarantees
that the immediate neighbourhood will be enriched with functional
sequences compared to all of sequence space. The types of mutations
available also means that the sequence is directly connected to many
lower (and higher) dimensional spaces, again, due to the starting point
being functional, enriched with functional sequences.
>Using terms like "oceans" and "islands" is just an easy way to help one
>visualize what is going on mathematically. It is not meant to indicate
>literal 2 or even 3 dimensional space. There are many more dimensions
>and the dimensions increase with each increase in the level of
>functional complexity.
>
>> >Why all these strawmen? Don't you have a real argument that can hold
>> >water?
>> >
>> 'It's all pseudogenes' is the only strawman up there, and it's not mine.
>
>Your argument just doesn't hold water anymore. Beyond that, your
>proposed mechanism is demonstrably incapable of doing much of anything
>beyond very very low levels of functional complexity.
>
Again, just your unevidenced claim.
Seanpit
Don Cates wrote:
< snip >
> >> Gee, "oceans" and "islands"; sure sounds two dimensional. Your claim is
> >> that as sequences get longer the functional neighbours get sparser, but
> >> if you consider higher dimensional space, as the sequences get longer
> >> the number of neighbours gets larger so the odds of having a
> >> functioinal neighbour do not decrease as per your calculation.
> >
> >You're wrong. Increasing the dimensions does not make it easier to
> >find one's neighbors given the same decrease in ratio. Mathematically,
> >it makes no difference.
> >
> Yes, I was wrong about that. The problem is not the calculation but
> rather the interpretation of the result. IIRC your argument is that an
> increasing neutral space must be traversed as sequences get longer.
> That we are starting with a functional sequence pretty much guarantees
> that the immediate neighbourhood will be enriched with functional
> sequences compared to all of sequence space.
Not true. The immediate neighborhood will no doubt have many different
closely spaced sequences with the ability to perform the same function
to the same or slightly different degrees. But, it is most unlikely
that any sequence within the immediate neighborhood will have the
ability to perform a *novel* function that requires the same minimum
size and specificity requirements.
So, yes, there most certainly are islands of sequences within sequence
space made up of many slightly different sequences that can indeed
perform the same type of function. However, trying to get to a
different island with a different type of function gets to be more and
more challenging at higher and higher levels of functional complexity.
The clustered islands start to increase their linear distance from each
other in a linear manner. Increasing the number of dimensions within
sequence space only results in an exponential increase in the average
random walk/selection distance that needs to be traversed before
success.
> The types of mutations
> available also means that the sequence is directly connected to many
> lower (and higher) dimensional spaces, again, due to the starting point
> being functional, enriched with functional sequences.
Not true. Just because the starting point is located on an island of
beneficial sequences does not mean that this island is going to be in
close contact with any other islands with novel functions in sequence
space. In fact, because of the exponential decrease in the ratio of
potentially beneficial vs. non-beneficial sequences within all of
sequence space, very quickly those potentially beneficial islands that
do exist within sequence space become completely surrounded, on all
sides and in all dimensions, with non-beneficial sequences.
Consider that if your scenario were actually true, there would be no
exponential decrease in the evolvability of any type of function,
regardless of its minimum size and specificity requirements. However,
in reality, evolutionary mechanisms simply do not evolve functions that
require anything more than a few hundred fairly specified amino acid
residues working together at the same time. It just doesn't happen.
There isn't a single example in all of literature. Even at lower
levels, like the evolution of single protein enzymes, evolution is
often very limited in its potential. For example, most bacterial
genomes, made up of over 4 million base pairs, cannot evolve a
relatively simple lactase function even in 100,000 generations in a
lactose rich environment.
What does this mean? It obviously means that your notions just aren't
correct. Relatively simple functions, that can be achieved with small
single protein sequences, seem to be more than a single residue change
away from any of millions of beneficial starting points that already
exist in hundreds of billions of individuals within the gene pool. If
the distance were really just one character change away from anything
within the gene pool, as you suggest, evolution of such a function
would happen in at least one individual within a single generation.
This just doesn't happen in the majority of cases - even at this
relatively low level of functional complexity. It never happens at
even slightly higher levels.
As far as your neutral sequence argument goes, those sequences that are
shared between creatures like humans and chimps or humans and other
mammals like rabbits or between humans and very different creatures
like turtles, are not neutral. They have been maintained, in their
different states, because they are indeed functional.
The whole molecular clock theory is seriously flawed. Initially, it was
based on the notion that genetic differences were indeed neutral. The
mutation rate itself wasn't based on direct experimentation, but on
evolutionary assumptions of assumed periods of elapsed time since the
most recent common ancestors of various types of creatures (derived
from interpretations of the fossil record and radiometric dating).
Eventually, scientists, who study historical families and their genetic
histories, started questioning the mutation rates that were based on
evolutionary phylogenetic assumptions. These scientists were surprised
to find that the mutation rate was in fact much higher than previously
thought. In fact it was about 20 times higher at around one mutation
every 25 to 40 generations (about 500 to 800 years for humans). It
seems that in this section of the control region [mitochondrial], which
has about 610 base pairs, humans typically differ from one another by
about 18 mutations. By simple mathematics, it follows that modern
humans share a common ancestor some 300 generations back in time. If
one assumes a typical generation time of about 20 years, this places
the date of the common ancestor at around 6,000 years before present.
"The observed substitution rate reported here is very high
compared to rates inferred from evolutionary studies. A wide range of
CR substitution rates have been derived from phylogenetic studies,
spanning roughly 0.025-0.26/site/Myr, including confidence intervals. A
study yielding one of the faster estimates gave the substitution rate
of the CR hypervariable regions as 0.118 +- 0.031/site/Myr. Assuming a
generation time of 20 years, this corresponds to ~1/600 generations and
an age for the mtDNA MRCA of 133,000 y.a. Thus, our observation of the
substitution rate, 2.5/site/Myr, is roughly 20-fold higher than would
be predicted from phylogenetic analyses. Using our empirical rate to
calibrate the mtDNA molecular clock would result in an age of the mtDNA
MRCA of only ~6,500 y.a., clearly incompatible with the known age of
modern humans. Even acknowledging that the MRCA of mtDNA may be younger
than the MRCA of modern humans, it remains implausible to explain the
known geographic distribution of mtDNA sequence variation by human
migration that occurred only in the last ~6,500 years."
Parsons, Thomas J. A high observed substitution rate in the human
mitochondrial DNA control region, Nature Genetics vol. 15, April 1997,
pp. 363-367
"Mutation rates of mtDNA in humans are usually estimated by
comparing sequences of DNA from people and other animals. 'This is kind
of analysis that was used to determine that the African origin of
modern humans was about 200,000 years ago,' says Thomas. 'The problem
with this approach is that you are looking at both the mutation rate
and the effects of natural selection,' he says. The technique would
also miss multiple mutations in the same stretch of mtDNA, says Paul
Sharp of the Institute of Genetics at Nottingham University, UK.
More recent studies have looked at the mtDNA of people who are
distantly related but share a female ancestor. This approach has
revealed higher mtDNA mutation rates. But the results have not been
accepted by many scientists."
Denver DR, Morris K, Lynch M, Vassilieva LL, Thomas WK. High direct
estimate of the mutation rate in the mitochondrial genome of
Caenorhabditis elegans. Science. 2000 Sep 29;289(5488):2342-4. (
http://www.sciencemag.org/cgi/content/full/289/5488/2342?ck=nck )
Now, either such mutations are not entirely neutral, there is a problem
with interpretations based on the fossil record, or humans really
haven't been around that long, or some mix of all of the above. Note
that Denver el. al. suggest that mutations are indeed affected by
natural selection - and that this affects the apparent mutation rate.
This little problem seems to counter your notion that the majority of
genetic differences are entirely neutral. They just aren't.
< snip >
Sean Pitman
www.DetectingDesign.com
Don Cates
<seanpi...@naturalselection.0catch.com> posted:
>
>Don Cates wrote:
>
>< snip >
>
If all you are going to do is snip away most of my substantial rebutals
to your previous post, then cherry pick the bits where you think you
have a rebutal while dishonestly snip away unmarked other parts of my
post that already partly answer your comments, reply with non sequiturs
(Nothing in my post had to do with the molecular clock), and just
repost your previous unevidenced claims, there is not much point in
continuing this discussion.
Bye
[snip what I'm talking about above]
Seanpit
Don Cates wrote:
> On 24 Nov 2006 08:17:21 -0800, "Seanpit"
> <seanpi...@naturalselection.0catch.com> posted:
>
> >
> >Don Cates wrote:
> >
> >< snip >
> >
> If all you are going to do is snip away most of my substantial rebutals
> to your previous post, then cherry pick the bits where you think you
> have a rebutal while dishonestly snip away unmarked other parts of my
> post that already partly answer your comments, reply with non sequiturs
> (Nothing in my post had to do with the molecular clock),
Actually, your post had a lot to do with the molecular clock
hypothesis. You think that most of the differences between species are
neutral. Real time studies of mutation rates showed that this just
isn't true. The differences are not neutral, but functional and
restricted by natural selection.
> and just
> repost your previous unevidenced claims, there is not much point in
> continuing this discussion.
Sorry, I just don't have time to respond to everything everybody
considers important. But, I did answer many of what I consider to be
your main points as presented in your original post. You are mistaken
with your whole neutrality argument - regardless of the type of genetic
sequence you think to consider. You are also mistaken in every one of
your strawman mischaracterizations of my position.
> Bye
No one is twisting your arm here. L8r . . .
Sean Pitman
www.DetectingDesign.com
Seanpit
> Don Cates wrote:
In order to answer your all important arguments that I snipped last
time . . .
> >Certainly there are sequences that have a significant neutrality with
> >respect to many different types of substitutions. This is the basis of
> >Moto Kimura's neutral theory of evolution. However, significant
> >stretches of neutral genetic material are becoming more and more rare
> >the more and more we learn.
>
> Maybe a bit less pervasive but certainly not "rare".
Sequence neutrality is much much less common than previously thought -
as demonstrated by fairly recent real time studies of mutation rates.
> >Your statement that the genomes of some
> >species are almost entirely neutral just isn't thought to be true
> >anymore - even by mainstream scientists.
>
> Yes it is, by many mainstream scientists.
You're wrong. Recent studies are showing that the majority of what
were once thought to be "junk" sequences are actually functional. It
only makes sense. It takes a lot of energy to maintain sequences
within a genome that are truly non-functional junk. Over time, natural
selection would select to eliminate such an energy sink from the gene
pool.
Actually, this is strong evidence for conservation via natural
selection and therefore of functionality - not necessarily common
descent.
> >> >Lots of functions exist that require far more than 1000 fairly
> >> >specified amino acid residues. Take the popular flagellar motility
> >> >system, for example, which requires well over 10,000 codons coding for
> >> >a minimum of over 10,000 specifically arranged residues.
> >> >
>
> Here's the bit you snipped without marking and didn't address from my
> previous post.
>
> -------------restored---------
>
> There is a lot more non-functional sequence than pseudogenes. Those
> that are conserved are almost certainly functional in some way, those
> that aren't, aren't.
Those that aren't conserved don't survive very long to use for sequence
comparisons. They disappear from the genome because nature selects to
remove true junk from the gene pool over time.
> And then even within functiional sequences there are many neutral
> changes possible and your response doesn't address these
> similarity/differences at all.
Actually, it does. It is hard to say, really, weather a change within
a functional sequence is truly neutral with respect to function. Even
a slight functional effect will add up over time to be selectable by
nature. The real time mutation rate studies suggest that relatively
few of these sites are actually neutral.
> ------------end restored---------
>
> >> so how many of them are "fairly specified" (how do you determine this)
> >> and how many could be changed to a similar residue and still function?
> >> How do you know any of this?
> >
> >The ratio is about 1e-30 per 100aa based on studies like Sauer, Olsen,
> >and Yockey. That allows for a fair degree of flexibility, but not
> >nearly enough to save the proposed mechanism behind the ToE.
> >
> Ratio of what?
Beneficially functional vs. not.
> Did they take a functional sequence, determine (somehow;
> How?) the "fairly specified" part, add/delete/change residues and test
> for 'function' (what definition for function)?
Yep, that's exactly what they did. Read the papers for a detailed
explanation.
> >> >It is also a strawman mischaracterization to say that my position
> >> >requires even distribution of potentially beneficial sequences
> >> >throughout sequence space. That's just not true. My position holds as
> >> >long as potentially beneficial sequences do not remain equally
> >> >clustered within one tiny corner of sequence space at higher and higher
> >> >levels of functional complexity.
> >> >
> >> This is what you claim but when you do your calculations the resultss
> >> depend on that even distribution. Otherwise your 'average distance' is
> >> meaningless.
> >
> >The average linear distance most certainly does increase in a linear
> >manner as long as the ratio in all portions of sequence space between
> >potentially beneficial and non-beneficial decreases exponentially - and
> >it does.
>
> Oh really? And how do you know this? Just what is the distribution of
> functional sequences in sequence space? How did you determine it? How
> does it correspond to the existing sequences?
> Your interpretation of your calculation depends on the assumption that
> all portions of sequence space are homogeneous with respect to
> beneficial/non-beneficial density. Even if you are correct that
> beneficial sequences are confined to well sepatated 'islands', you
> would have to show that the sequence space of existing DNA is not
> confined to one of these islands.
You don't really seem to understand the definition of sequence space.
Existing DNA does not comprise "sequence space". Existing DNA exists
within the larger limits of sequence space. And, the various existing
genes are most certainly part of islands that exist within the
potential of sequence space. However, getting from one occupied island
to another that is not yet occupied is the challenge here.
With each step up the ladder of functional complexity the size of
sequence space increases exponentially - and that's an undeniable fact.
At the same time, the number of potentially beneficial sequences also
increases. The problem is that the number of potentially
non-beneficial sequences increases as well - exponentially faster than
does the number of potentially beneficial sequences.
This little problem happens in all corners of sequence space. Such a
disparity in ratio results in a drifting of potentially beneficial
islands away from each other, in a linear manner, with each step up the
ladder of functional complexity. Each linear increase in distance
translates into an exponential increase in the average time required to
traverse the gap via random walk or selection.
> > No portion of sequence space maintains the same ratio at
> >higher and higher levels of minimum size and specificity requirements.
> >
> The ratio doesn't matter. All that matters is that there be *some*
> nearby beneficial sequence.
Yes, and the odds that there will be a "nearby" beneficial sequence
depends upon the ratio. The odds that a potentially beneficial
sequence will be just mutational step away drop exponentially as the
ratio drops exponentially.
> Let's say we have functional sequences X and Y with 1000aas each.
> Evolution does not require that there be a 1000aa path from X to Y,
> only that there be a path from 200aa B to 1000aa X and from 200aa B to
> 1000aa Y. There is no requirement that any organism can aquire any
> function. That is why your lactase example is so bogus. All it shows is
> that for that organism if you remove all the close sequences there are
> no close sequences.
It shows that the ratio of lactases within sequence space is relatively
low and that the odds of there being a "close" lactase within all of
sequence space to anything within even a very large gene pool of
millions of islands is quite remote. These odds get more and more
remote with each additional size and/or specificity requirement.
Sure, there is no requirement that a gene pool evolve anything new.
Evolution is not required. However, if you argue that evolution
happened, you have to consider the odds of this notion actually being
true. The odds that your notion is true start to drop off
precipitously when you start talking about higher and higher levels of
functional complexity. A neutral gap of only a few dozen residues
would take a population of several trillion an average of trillions of
years to cross.
That's a problem.
> >> >Also, I never said that sequence space was two-dimensional. It isn't.
> >> >It has a great many dimensions. This does not remove the fact that
> >> >potentially beneficial sequences are surrounded on all sides by vast
> >> >oceans of non-beneficial sequences at higher levels of functional
> >> >complexity and that this ocean expands exponentially faster than the
> >> >number of potentially beneficial island clusters expands with each step
> >> >up the ladder of functional complexity.
> >> >
> >> Gee, "oceans" and "islands"; sure sounds two dimensional. Your claim is
> >> that as sequences get longer the functional neighbours get sparser, but
> >> if you consider higher dimensional space, as the sequences get longer
> >> the number of neighbours gets larger so the odds of having a
> >> functioinal neighbour do not decrease as per your calculation.
> >
> >You're wrong. Increasing the dimensions does not make it easier to
> >find one's neighbors given the same decrease in ratio. Mathematically,
> >it makes no differences.
> >
> Yes, I was wrong about that.
I'm glad you recognize that.
> The problem is not the calculation but
> rather the interpretation of the result. IIRC your argument is that an
> increasing neutral space must be traversed as sequences get longer.
> That we are starting with a functional sequence pretty much guarantees
> that the immediate neighbourhood will be enriched with functional
> sequences compared to all of sequence space.
As previously noted, this assumption just isn't true when it comes to
sequences with a novel function. The odds that a neighboring sequence
will have a truly novel beneficial function get exponentially lower
with each additional minimum size and specificity requirement.
> The types of mutations
> available also means that the sequence is directly connected to many
> lower (and higher) dimensional spaces, again, due to the starting point
> being functional, enriched with functional sequences.
Also as previously noted, the odds that multicharacter mutations
(duplications, insertions, deletions, etc) will land on a potentially
beneficial island with a novel function essentially the same as the
odds that a single point mutation will be successful. There really is
no advantage. Sure, it is theoretically possible to achieve success
with a single multicharacter mutation. However, it is much much more
likely that such a random mutation will land in the middle of the ocean
of non-beneficial sequences.
> >Using terms like "oceans" and "islands" is just an easy way to help one
> >visualize what is going on mathematically. It is not meant to indicate
> >literal 2 or even 3 dimensional space. There are many more dimensions
> >and the dimensions increase with each increase in the level of
> >functional complexity.
> >
> >> >Why all these strawmen? Don't you have a real argument that can hold
> >> >water?
> >> >
> >> 'It's all pseudogenes' is the only strawman up there, and it's not mine.
> >
> >Your argument just doesn't hold water anymore. Beyond that, your
> >proposed mechanism is demonstrably incapable of doing much of anything
> >beyond very very low levels of functional complexity.
> >
> Again, just your unevidenced claim.
You're the one spouting off many bald assertions that are either
mischaracterizations or are simply not true any more. You're just
behind the times I'm afraid. The available evidence speaks strongly for
the existence of non-beneficial gap and their linear expansion with
each step of the ladder of functional complexity.
Sean Pitman
www.DetectingDesign.com
Seanpit
Bobby Bryant wrote:
> In article <1164212267.2...@h54g2000cwb.googlegroups.com>,
> "Seanpit" <seanpi...@naturalselection.0catch.com> writes:
> >
> > Marc wrote:
> >
> >> I'm wondering how he can say that *all* of them are flawed.
> >
> > Cause they all say exactly the same thing based on exactly the same
> > assumption - that sequence similarities necessitate common decent
> > via random mutation and function-based selection.
>
> Not "necessitate". It's about economy of explanation.
>
> (And before you suggest it, adding an unobserved middle man doesn't make
> for a more economical explanation.)
The problem is that the other alternative is not even considered nor is
the current assumption subjected to statistical analysis and testing.
It is just assumed that if the mechanism works at all, regardless of
the level of functional complexity, that it can easily do the job given
millions of years. No one actually sits down and analyses the
capability of the proposed mechanism to see if even millions of years
are likely to be enough time. The belief that millions of years are
enough time is simply a faith-based assumption. It is not based on any
real analysis of the likely capabilities of the mechanism itself.
> > I'd agree that sequence similarities do suggest a common origin, but
> > not necessarily a common evolutionary origin. They could just as
> > easily be the result of common deliberate design.
>
> Of course, when the Designer designs wings for a bird, he uses a common
> low-level implementation. But when he designs wings for a bug, he uses
> an entirely different low-level implementation.
>
> "Because he wanted to."
>
> You can handwave that 'explanation' over *any* observation.
You can also handwave the "explanation" that random mutation and
natural selection did it "somehow" over any observation.
The fact is, if there are limits to your mechanism, the only viable
alternative is deliberate design. This is the same argument upon when
SETI is based.
> Common descent doesn't have to appeal to the arbitrary will of an
> unknown agent: the sequence similarities fall out of the theory
> naturally.
The detection of arbitrary will can indeed be done - via science.
Sequence similarities just aren't enough. You have to analyze your
proposed mechanism to see if it is really up to the task.
> Bobby Bryant
> Reno, Nevada
Sean Pitman
www.DetectingDesign.com
Seanpit
noctiluca wrote:
> Seanpit wrote:
> > Marc wrote:
> >
> > >
> > > I'm wondering how he can say that *all* of them are flawed.
> >
> > Cause they all say exactly the same thing based on exactly the same
> > assumption - that sequence similarities necessitate common decent via
> > random mutation and function-based selection. I'd agree that sequence
> > similarities do suggest a common origin, but not necessarily a common
> > evolutionary origin.
>
> Oh good god, I'd come to expect a higher grade of nonsense from you,
> this is just regular ol' garden variety creationist silliness.
Yes it is ; )
> > They could just as easily be the result of common deliberate design.
>
> No, they most definitely could not. The fact is that there exists vast
> amounts of scholarship (fossil record, phylogenetic analysis, molecular
> analysis etc.) demonstrating the validity of an inference to
> evolutionary processes and common descent.
The problem is that your proposed mechanism just isn't up to the task .
. . and this problem is overwhelming demonstrable in real time
demonstration and statistical evaluation.
> There is no - zip, zero, nada - evidence that independently suggests we
> can infer a deliberate desiger.
LOL - The fool has said in his heart . . .
The evidence is everywhere. Tell me, where is there any demonstration
or statistical analysis of the abilities of random mutation and
function-based selection beyond extremely low levels of functional
complexity? There simply aren't such published analysis because
everything published simply assumes it happened based on the notion
that sequence similarities much have been the result of common descent
via random mutation and natural selection.
No one sits down and says, "Wait a minute! Let's do a few calculations
and see if random mutations and function-based selection are remotely
likely to produce higher-level functions given billions much less
millions of years of time. That just isn't done. It is just assumed
by blind faith to be true.
> It is true that we cannot logically exclude the possibility of
> deliberate design of the natural intelligent variety (aliens etc.), and
> that is a hypothesis that is putatively amenable to scientific
> methodology. (However, only if you wish to acknowledge that your
> "common design" specifically repudiates any inference to the
> non-natural could this suggestion even be considered.)
ID theory only suggests that science can detect deliberate manipulation
of or within the natural world.
> Even so, the huge disparity in evidence makes it clear that in no way
> could "this...just as easily be the result of common deliberate
> design." It would be no more nonsensical (in fact less, as I've
> actually seen evidence that he exists) to say it could just as easily
> be the result of an intelligent, though incredibly annoying, purple
> dinosaur.
ID theory doesn't say who, why, or even how. ID only argues that
deliberate manipulation was required. It could have been via some
intelligent purple dinosaur or an alien from Zorg. But, whoever did it
and however he/she/it did it, it was intelligent and deliberate.
> In truth, your inference to common design makes sense only if we remove
> all meaning from the word "explanation" and it's synonyms, allowing
> idle speculation and wishful thinking to be considered legitimate
> counterexamples to evidentially supported theories.
LOL - uh huh. Tell that to SETI scientists.
You know, you guys can argue that "nature" did it whenever you see a
new phenomenon. You might not know how, but you automatically know
that it was a mindless natural process that did it. That's your
default explanation for absolutely everything. At least IDists are a
bit more discriminating. IDists do not automatically argue for design
when they see a new phenomenon. They argue for detailed investigation
first in an attempt to rule out, as much as is reasonably possible, any
potential non-deliberate cause. Only after such extensive
investigation has been carried out is it reasonable to promote the
hypothesis of ID.
> No, not by any stretch of logic could "common deliberate design" "just
> as easily" serve as an explication of common origin. Not without
> abandoning reason, something you try hard to appear as if you employ.
>
> You'll have to do much better.
Ditto
> > The fact that none of these scenarios has ever
> > been demonstrated in real life beyond the 1000 specified residue level,
> > combined with the fact that there is a clear exponential decline in
> > evolvability as the 1000aa level is approached, should give you a very
> > clear notion that evolutionary mechanisms simply cannot do the job at
> > this level or beyond this side of a practical eternity of time.
>
> Well, this is certainly no improvement. Standard issue creationist
> "gap" argument here.
All scientific theories are based on a gap in knowledge. It is because
we have subperfect knowledge that science is so useful. Some new bit of
information could always come along and falsify any hypothesis or
theory. That is the nature of science. For you to argue that no true
scientific theory can be based on a gap between what is and what might
be shows that you don't really understand how science works.
> > Yet, you continue to list off dozens of these papers, all of which are
> > based on exactly the same notion. Not one of them actually presents
> > any real experiment that demonstrates evolution in action beyond the
> > 1000aa level - not one. You said you'd present something on
> > flagellar evolution, but you have yet to do so. You seem stuck in rut
> > here, unable to come up with anything beyond your fairy tale "what if"
> > stories.
>
> There's a reason all of them are based upon similar assumptions. There
> are bedrock concepts in any discipline, achieving that status through
> hundreds of years and countless man-hours of corroborative research.
None of which have been employed in analyzing the actual proposed
mechanism.
> > > Oh... that's right. He'll call them "just so stories". Maybe
> > > Sean should try thinking of them as "what if" stories instead.
> >
> > LOL - you think calling them "what if" stories makes them sound more
> > scientific? Please! Give me a break! They are all based on the same
> > erroneous assumption. They are not based on any statistical evaluation
> > of the actual time it would take to cross the gaps that exist at levels
> > of functional complexity beyond the 1000aa level nor do they present
> > any real time experiment that demonstrates evolution beyond this level.
>
> Ah, yes, "real time." A dead giveaway for the standard issue
> creationist "were you there" argument.
We aren't talking about turning a dog into a cat or anything like that.
We are talking about very small subsystem biofunctions that can indeed
be observed in real time. Why is it that functions like single protein
enzymes, which require no more than a few hundred fairly specified
residues, can be observed to evolve in real time while functions that
require just a few more residues at minimum, just 1000 or so, are never
evolved? - not one example ever? Just think about that for a minute .
. .
> > Suggestion, stop reference mining dozens of references that you haven't
> > even read yourself and start actually thinking for yourself.
>
> You mean "thinking for yourself" as in trying to step outside a line of
> inquiry circumscribed by unquestioned dogma leading to extreme
> confirmation bias? Well, you've certainly got the whole projection
> thing down.
>
> Now, here's a suggestion for you; why not stop for a moment and
> consider which kind of "dogma" it would make sense to allow to
> circumscribe your thinking - one based upon the accumulated replicated
> work of thousands of highly trained scientists, or one based upon a
> book of legends and parables.
>
> I would think no less of you for merely chosing the latter, but when
> you extend that to accusing others who are involved in expanding our
> knowledge of the universe of wearing blinders then I feel compelled to
> note that you are a self-deluded prat.
Show me any scientific publication that seriously deals with the odds
of the actual proposed mechanism of evolution working at higher and
higher levels of functional complexity. Show me some mathematical
calculations, statistical analysis, or real time demonstrations that go
beyond the 1000aa level. I'm waiting . . .
> > Present
> > an actual relevant argument. Use references if you want, but present
> > your own argument that you have actually thought about just a little
> > bit. Listing dozens of bald unread references is worse than quote
> > mining.
>
> Let's see, presenting legitimate research is worse than the
> disingenuous act of changing the context of someone's words?
>
> I'd have to say that the extreme silliness of this assertion leads me
> to wonder if perhaps you simply don't wish to address the evidence?
> Hey, it's just a thought.
There is no actual experimental or even statistical evidence in
published literature when it comes to the proposed mechanism. That's
the whole point. All that is published on this topic is based on
assumption that the mechanism is indeed capable and responsible for
doing the job. This assumption is made without statistical analysis or
demonstration of any kind beyond very very low levels of functional
complexity. No mention is made of the fact that this mechanism shows a
demonstrable stalling out effect well before the 1000aa level is
reached.
> RLC
Sean Pitman
www.DetectingDesign.com
Seanpit
Perplexed in Peoria wrote:
> "Seanpit" <seanpi...@naturalselection.0catch.com> wrote in message news:1164212267.2...@h54g2000cwb.googlegroups.com...
> >
> > Marc wrote:
> >
> > > [Regarding cited papers]
> > > I'm wondering how he can say that *all* of them are flawed.
> >
> > Cause they all say exactly the same thing based on exactly the same
> > assumption - that sequence similarities necessitate common decent via
> > random mutation and function-based selection. I'd agree that sequence
> > similarities do suggest a common origin, but not necessarily a common
> > evolutionary origin. They could just as easily be the result of common
> > deliberate design.
>
> How does that work exactly? The polymorphism (SNPs) withing a species
> is the result of mutation from the nominal true sequence specified
> by the Creator? But the differences between species are the result
> of design decisions of the Designer?
The term "species" is a bit fuzzy, but that's the basic idea.
> Well, I suppose that I should be grateful that you are not claiming
> that the alignments are bogus. You recognize that these are the
> 'same genes in different species' in some sense.
True . . .
> > The fact that none of these scenarios has ever
> > been demonstrated in real life beyond the 1000 specified residue level, ...
>
> There must be some confusion here. What does sequence evolution have
> to do with *specified* complexity? In the simplest sequence evolution
> model, some sites evolve and are informative regarding phylogeny. Other
> sites do not evolve, and are therefore useful only for producing an
> alignment. It seems to me that you should be claiming that those
> unchanging sites are the 'specified' ones and that the ones that are
> subject to mutation without apparent ill-effect are ones that the
> Designer didn't specify at design-time (though, perforce, He had to
> make an arbitrary choice and put something there at creation-time).
Once a function is established, it can easily be modified, over time,
in different environments/situations, via random mutation and function
based selection. However, getting a fairly complex function to begin
with (i.e., requiring a minimum of more than a few thousand specified
residues) is a different story.
> In more sophisticated models of sequence evolution, the binary distinction
> between specified and unspecified sites is blurred into a spectrum.
> Some sites are more specified (evolutionists prefer the term 'conserved')
> than others. But you probably don't like to think about such models
> because they complicate your probability calculations and call into
> question your entire ideology of "If it ain't what was specified, then
> it doesn't work at all".
>
> > combined with the fact that there is a clear exponential decline in
> > evolvability as the 1000aa level is approached, should give you a very
> > clear notion that evolutionary mechanisms simply cannot do the job at
> > this level or beyond this side of a practical eternity of time.
>
> The clarity of this exponential decline you keep talking about is
> just not clear to me. Is this exponential decline curve a conclusion
> reported in laboratory experiments? Is it an inference which you
> draw from consideration of your own models of the sequence-to-function
> landscape? Or is it something that can be inferred from the sequence
> data? No, that last can't be correct, because you don't believe that
> sequence data is informative about evolution - that is why you don't
> believe the cited articles.
>
> So, I'm guessing that your 'exponential decline' arises from your
> estimates of what the landscape looks like. I would criticize those
> estimates, but to do so, I would have to use sequence data on evolution.
> But you don't believe such data is informative regarding evolution.
> I believe this is what they call an 'impass'.
The stalling out effect is based on real time observations of evolution
in action. Random mutation and function-based selection are indeed
capable of producing novel beneficial functions. However, all of the
ones produced so far via this mechanism require a minimum structure of
no more than a few hundred fairly specified residues working together
at the same time. Those functions that have a lower minimum structural
threshold requirement evolve much more easily or more commonly than do
those functions that have a greater minimum threshold requirement.
Interestingly, no evolution has ever been demonstrated beyond the
1000aa threshold. Evolutionary mechanisms simply stall out well before
this threshold level is reached. Why?
Obviously, the reason for this stalling out effect is found in the
problem of expanding non-beneficial gaps with each step up the
threshold ladder. Each additional minimum size or specificity
limitation reduces the ratio of potentially beneficial vs.
non-beneficial sequences within sequence space in an exponential
manner. This effect is realized in all portions of sequence space.
Eventually, it results in potentially beneficial islands drifting
apart, in a linear manner, with each step up the threshold ladder.
Each linear increase in distance results in an exponential increase in
the random walk/selection time needed to find the next closest
potentially beneficial island cluster. And, evolution stalls out - in
an exponential manner.
Sean Pitman
www.DetectingDesign.com
John Harshman
> Marc wrote:
>
>
>>I'm wondering how he can say that *all* of them are flawed.
>
>
> Cause they all say exactly the same thing based on exactly the same
> assumption - that sequence similarities necessitate common decent via
> random mutation and function-based selection. I'd agree that sequence
> similarities do suggest a common origin, but not necessarily a common
> evolutionary origin. They could just as easily be the result of common
> deliberate design.
Let's try this again. How would a common deliberate design produce a
nested hierarchy? A designed, nested hierarchy in functional characters
requires that functions form a nested hierarchy themselves. What
evidence do you have for a nested hierarchy of function? And a designed,
nested hierarchy in non-functional characters is just perverse, unless
you have some reason why one should exist. And you need some reason why
there should be the same nested hierarchy in functionally unrelated
parts of the genome -- apparently all functions and non-functions form
exactly parallel nested hierarchies. Waving your hands and saying
"common design" doesn't begin to explain this.
Note, by the way, that you are once again conflating common descent with
common descent by a particular mechanism, random mutation and natural
selection.
[snip neutral gaps, which is irrelevant to common descent]
John Harshman
> Don Cates wrote:
>
>>On 24 Nov 2006 08:17:21 -0800, "Seanpit"
>><seanpi...@naturalselection.0catch.com> posted:
>>
>>
>>>Don Cates wrote:
>>>
>>>< snip >
>>>
>>If all you are going to do is snip away most of my substantial rebutals
>>to your previous post, then cherry pick the bits where you think you
>>have a rebutal while dishonestly snip away unmarked other parts of my
>>post that already partly answer your comments, reply with non sequiturs
>>(Nothing in my post had to do with the molecular clock),
>
>
> Actually, your post had a lot to do with the molecular clock
> hypothesis. You think that most of the differences between species are
> neutral. Real time studies of mutation rates showed that this just
> isn't true. The differences are not neutral, but functional and
> restricted by natural selection.
Even if that's true, it has nothing to do with the molecular clock
hypothesis. Neutral evolution doesn't require a molecular clock,
becausse mutation rates can vary among species. And a molecular clock
doesn't require neutral evolution; there are many models of molecular
clocks under selection too.
I suspect you're going to trot out your little paper on mutation rates
in the hypervariable region of mitochondrial D loop. Yes?
>>and just
>>repost your previous unevidenced claims, there is not much point in
>>continuing this discussion.
>
> Sorry, I just don't have time to respond to everything everybody
> considers important. But, I did answer many of what I consider to be
> your main points as presented in your original post. You are mistaken
> with your whole neutrality argument - regardless of the type of genetic
> sequence you think to consider. You are also mistaken in every one of
> your strawman mischaracterizations of my position.
Then you should be able to respond to every one of his
mischaracterizations without snipping them.
Here, by the way, is the central point of my position: common descent is
the only sensible explanation for a nested hierarchy. Would you care to
present an alternative?
John Harshman
>>Don Cates wrote:
>
>
> In order to answer your all important arguments that I snipped last
> time . . .
>
>
>>>Certainly there are sequences that have a significant neutrality with
>>>respect to many different types of substitutions. This is the basis of
>>>Moto Kimura's neutral theory of evolution. However, significant
>>>stretches of neutral genetic material are becoming more and more rare
>>>the more and more we learn.
>>
>>Maybe a bit less pervasive but certainly not "rare".
>
>
> Sequence neutrality is much much less common than previously thought -
> as demonstrated by fairly recent real time studies of mutation rates.
>
>
>>>Your statement that the genomes of some
>>>species are almost entirely neutral just isn't thought to be true
>>>anymore - even by mainstream scientists.
>>
>>Yes it is, by many mainstream scientists.
>
>
> You're wrong. Recent studies are showing that the majority of what
> were once thought to be "junk" sequences are actually functional.
Can you back up that "majority" claim?
> It
> only makes sense. It takes a lot of energy to maintain sequences
> within a genome that are truly non-functional junk. Over time, natural
> selection would select to eliminate such an energy sink from the gene
> pool.
If it were a significant cost. What if it weren't? How do you explain
close relatives with radically different genome sizes? What is the
functional significant of the huge genomes (much bigger than yours) of
most ferns and frogs?
[snip]
>>There is a lot more non-functional sequence than pseudogenes. Those
>>that are conserved are almost certainly functional in some way, those
>>that aren't, aren't.
>
> Those that aren't conserved don't survive very long to use for sequence
> comparisons. They disappear from the genome because nature selects to
> remove true junk from the gene pool over time.
Do you have any evidence for these claims?
[snip]
noctiluca
Seanpit wrote:
> noctiluca wrote:
> > Seanpit wrote:
> > > Marc wrote:
> > >
> > > >
> > > > I'm wondering how he can say that *all* of them are flawed.
> > >
> > > Cause they all say exactly the same thing based on exactly the same
> > > assumption - that sequence similarities necessitate common decent via
> > > random mutation and function-based selection. I'd agree that sequence
> > > similarities do suggest a common origin, but not necessarily a common
> > > evolutionary origin.
> >
> > Oh good god, I'd come to expect a higher grade of nonsense from you,
> > this is just regular ol' garden variety creationist silliness.
>
> Yes it is ; )
>
> > > They could just as easily be the result of common deliberate design.
> >
> > No, they most definitely could not. The fact is that there exists vast
> > amounts of scholarship (fossil record, phylogenetic analysis, molecular
> > analysis etc.) demonstrating the validity of an inference to
> > evolutionary processes and common descent.
>
> The problem is that your proposed mechanism just isn't up to the task .
> . . and this problem is overwhelming demonstrable in real time
> demonstration and statistical evaluation.
You're arguing about nickels while I'm talking about milllions. Whether
you realize this I don't know but my point remains untouched by your
response. The big picture, the one that collates countless bits of
information from varied disciplines - many of which don't rely on any
particular mechanism - demonstrates that evolution by common descent is
an inference so strong as to be reasonably considered fact.
There is no such similar independent body of evidence for common
design.
Puny protests over silly "real time" gap arguments do nothing to
diminish this obvious imbalance.
> > There is no - zip, zero, nada - evidence that independently suggests we
> > can infer a deliberate desiger.
>
> LOL - The fool has said in his heart . . .
>
> The evidence is everywhere.
Are you really going to be so foolish as to argue based upon intuition?
>Tell me, where is there any demonstration
> or statistical analysis of the abilities of random mutation and
> function-based selection beyond extremely low levels of functional
> complexity? There simply aren't such published analysis because
> everything published simply assumes it happened based on the notion
> that sequence similarities much have been the result of common descent
> via random mutation and natural selection.
This is evasion. This has nothing to do with my point. You are simply
regurgitating your neutral gap nonsense either because you are unable
to follow the plot of discussion or you are afraid of discussing larger
scale issues.
My reply to you dealt very specifically with whether "common design"
was just as reasonable an inference as common descent. Your god of the
gaps business is an irrelevant digression.
> No one sits down and says, "Wait a minute! Let's do a few calculations
> and see if random mutations and function-based selection are remotely
> likely to produce higher-level functions given billions much less
> millions of years of time. That just isn't done. It is just assumed
> by blind faith to be true.
It is, of course, a bald lie (an accusation I try very hard not to
make) to say that it is assumed by blind faith. I would ask you to try
to muster the integrity to acknowledge the accumulated scientific
understanding that underlies such an inference and retract that bit of
nonsense.
> > It is true that we cannot logically exclude the possibility of
> > deliberate design of the natural intelligent variety (aliens etc.), and
> > that is a hypothesis that is putatively amenable to scientific
> > methodology. (However, only if you wish to acknowledge that your
> > "common design" specifically repudiates any inference to the
> > non-natural could this suggestion even be considered.)
>
> ID theory only suggests that science can detect deliberate manipulation
> of or within the natural world.
And as such wishes to assume its conclusions by not bothering to test
its hypothesis. Yes, we all know.
This dog doesn't hunt anymore. An ID proponent's choices are clear,
either repudiate non-natural design inferences or acknowledge that ID
is non-scientific.
> > Even so, the huge disparity in evidence makes it clear that in no way
> > could "this...just as easily be the result of common deliberate
> > design." It would be no more nonsensical (in fact less, as I've
> > actually seen evidence that he exists) to say it could just as easily
> > be the result of an intelligent, though incredibly annoying, purple
> > dinosaur.
>
> ID theory doesn't say who, why, or even how. ID only argues that
> deliberate manipulation was required. It could have been via some
> intelligent purple dinosaur or an alien from Zorg. But, whoever did it
> and however he/she/it did it, it was intelligent and deliberate.
See above.
> > In truth, your inference to common design makes sense only if we remove
> > all meaning from the word "explanation" and it's synonyms, allowing
> > idle speculation and wishful thinking to be considered legitimate
> > counterexamples to evidentially supported theories.
>
> LOL - uh huh. Tell that to SETI scientists.
Try to think these things through. If and when a SETI scientist feels
compelled to make a design inference it will be supported by empirical
evidence. As such, this inference will comport with the underlying
assumptions of scientific methodology - that a subject of investigation
is amenable to observation, measurement and replicative testing, i.e.
that it exists in the natural universe.
There is nothing in the methodology or putative conclusions of SETI
science that puts it in the category of wishful thinking or idle
speculation. The same cannot be said of ID, or whatever flavor of
creationism it is that you prefer.
> You know, you guys can argue that "nature" did it whenever you see a
> new phenomenon. You might not know how, but you automatically know
> that it was a mindless natural process that did it. That's your
> default explanation for absolutely everything.
Don't be naive. That may or may not be some individual's default
explanation but that's beside the point. Science is a tool, not a
materialist cudgel (regardless of how some people use it), and as such
it doesn't default to nature so much as recognize that non-nature is a
non-starter. The methodology cannot accommodate the non-natural.
You know this. All the ID guys know this (which is why they constantly
whine that methodological naturalism should be amended). Yet all of you
want us to relive the Enlightenment and hope that things turn out
differently.
You may wish to return to ignorance but I don't. I want my planes to
fly and my medicines to work and my universe to be explicable. There's
a reason science developed over the centuries into what we see today:
because it works.
> At least IDists are a bit more discriminating.
You either know little of ID or misconstrue the meaning of
"discriminating."
> IDists do not automatically argue for design
> when they see a new phenomenon. They argue for detailed investigation
> first in an attempt to rule out, as much as is reasonably possible, any
> potential non-deliberate cause. Only after such extensive
> investigation has been carried out is it reasonable to promote the
> hypothesis of ID.
At which point the hypothesis needs to be tested in order to have
followed through on scientific methodology. ID deliberately avoids this
step. It allows its unsubstantiated inference to stand wholly
unexamined. And this, to you, is discriminating?
> > No, not by any stretch of logic could "common deliberate design" "just
> > as easily" serve as an explication of common origin. Not without
> > abandoning reason, something you try hard to appear as if you employ.
> >
> > You'll have to do much better.
>
> Ditto
I'll just note here that my entire argument went unaddressed.
> > > The fact that none of these scenarios has ever
> > > been demonstrated in real life beyond the 1000 specified residue level,
> > > combined with the fact that there is a clear exponential decline in
> > > evolvability as the 1000aa level is approached, should give you a very
> > > clear notion that evolutionary mechanisms simply cannot do the job at
> > > this level or beyond this side of a practical eternity of time.
> >
> > Well, this is certainly no improvement. Standard issue creationist
> > "gap" argument here.
>
> All scientific theories are based on a gap in knowledge. It is because
> we have subperfect knowledge that science is so useful. Some new bit of
> information could always come along and falsify any hypothesis or
> theory. That is the nature of science. For you to argue that no true
> scientific theory can be based on a gap between what is and what might
> be shows that you don't really understand how science works.
Nice try, but either intentionally disingenuous or foolishly naive,
again.
Of course all science is born of gaps in knowledge. The key to whether
you're doing science or not is how you address the gaps, and what you
do with the information you've gained. I've already noted how ID does
not address the gaps with appropriate scientific methodology. How they
treat the results of their inquiries is even worse. No scientist (at
least not while doing science) is left with an unanswered question and
then feels justified in inferring unevidenced cause. But this is
exactly what ID produces.
Science accepts incomplete knowledge. Science recognizes "We don't
know" (a gap) as a position that leads to future understanding. This is
as opposed to cutting off such increased knowledge by declaring a gap
filled by an unevidenced designer. The same goes for silly
pronouncements as to what nature cannot do, whether that's building an
eye or building amino acid chains beyond low levels of complexity.
These kinds of unwarranted inferences take gaps in our knowledge and
force them to serve ideology. Science takes gaps and increases our
understanding of the universe.
So, of course I don't argue that science cannot be based on a gap.
Quite the reverse, actually. But you knew that didn't you?
> > > Yet, you continue to list off dozens of these papers, all of which are
> > > based on exactly the same notion. Not one of them actually presents
> > > any real experiment that demonstrates evolution in action beyond the
> > > 1000aa level - not one. You said you'd present something on
> > > flagellar evolution, but you have yet to do so. You seem stuck in rut
> > > here, unable to come up with anything beyond your fairy tale "what if"
> > > stories.
> >
> > There's a reason all of them are based upon similar assumptions. There
> > are bedrock concepts in any discipline, achieving that status through
> > hundreds of years and countless man-hours of corroborative research.
>
> None of which have been employed in analyzing the actual proposed
> mechanism.
But of course they have. There's that integrity thing again.
> > > > Oh... that's right. He'll call them "just so stories". Maybe
> > > > Sean should try thinking of them as "what if" stories instead.
> > >
> > > LOL - you think calling them "what if" stories makes them sound more
> > > scientific? Please! Give me a break! They are all based on the same
> > > erroneous assumption. They are not based on any statistical evaluation
> > > of the actual time it would take to cross the gaps that exist at levels
> > > of functional complexity beyond the 1000aa level nor do they present
> > > any real time experiment that demonstrates evolution beyond this level.
> >
> > Ah, yes, "real time." A dead giveaway for the standard issue
> > creationist "were you there" argument.
>
> We aren't talking about turning a dog into a cat or anything like that.
> We are talking about very small subsystem biofunctions that can indeed
> be observed in real time. Why is it that functions like single protein
> enzymes, which require no more than a few hundred fairly specified
> residues, can be observed to evolve in real time while functions that
> require just a few more residues at minimum, just 1000 or so, are never
> evolved? - not one example ever? Just think about that for a minute .
I've thought about it for much more than a minute. I've thought about
it ever since you first began talking about it. And it's clear that it
is nothing more than a dressed up god of the gaps assertion. I'm sure
it feels to you like a compelling argument, but in essence it has no
more intellectual validity than complaining that we don't see dogs give
birth to cats. Why? Because it presents a false picture of how
evolution works and what we should be able to observe given certain
time-spans, and most importantly because it presents incomplete
knowledge as a positive argument for non-natural inference.
> > > Suggestion, stop reference mining dozens of references that you haven't
> > > even read yourself and start actually thinking for yourself.
> >
> > You mean "thinking for yourself" as in trying to step outside a line of
> > inquiry circumscribed by unquestioned dogma leading to extreme
> > confirmation bias? Well, you've certainly got the whole projection
> > thing down.
> >
> > Now, here's a suggestion for you; why not stop for a moment and
> > consider which kind of "dogma" it would make sense to allow to
> > circumscribe your thinking - one based upon the accumulated replicated
> > work of thousands of highly trained scientists, or one based upon a
> > book of legends and parables.
> >
> > I would think no less of you for merely chosing the latter, but when
> > you extend that to accusing others who are involved in expanding our
> > knowledge of the universe of wearing blinders then I feel compelled to
> > note that you are a self-deluded prat.
>
> Show me any scientific publication that seriously deals with the odds
> of the actual proposed mechanism of evolution working at higher and
> higher levels of functional complexity. Show me some mathematical
> calculations, statistical analysis, or real time demonstrations that go
> beyond the 1000aa level. I'm waiting . . .
You keep hammering on your 1000aa nonsense instead of addressing my
comments. You made a foolish and unsupported accusation, one that is
countered by all of the available evidence. Do you really think
slipping back into your gap argument makes that go away?
Perhaps you avoid discussion of the larger issues involved because you
realize that without keeping everyone running around shooting down your
molecular misapprehensions you are without any compelling argument?
<snip>
RLC
> Sean Pitman
> www.DetectingDesign.com
Seanpit
noctiluca wrote:
> > > No, they most definitely could not. The fact is that there exists vast
> > > amounts of scholarship (fossil record, phylogenetic analysis, molecular
> > > analysis etc.) demonstrating the validity of an inference to
> > > evolutionary processes and common descent.
> >
> > The problem is that your proposed mechanism just isn't up to the task .
> > . . and this problem is overwhelming demonstrable in real time
> > demonstration and statistical evaluation.
>
> You're arguing about nickels while I'm talking about milllions. Whether
> you realize this I don't know but my point remains untouched by your
> response. The big picture, the one that collates countless bits of
> information from varied disciplines - many of which don't rely on any
> particular mechanism - demonstrates that evolution by common descent is
> an inference so strong as to be reasonably considered fact.
>
> There is no such similar independent body of evidence for common
> design.
>
> Puny protests over silly "real time" gap arguments do nothing to
> diminish this obvious imbalance.
Without a viable mechanism, your inference is meaningless. You can
assume that sequence similarities and the fossil record point toward an
evolutionary process all you want. However, with evidence speaking
strongly against the potential of your stated mechanism, random
mutation and function-based selection, your whole little theory is
completely undermined. It just doesn't work. Evolutionary processes
do indeed stall out, in a demonstrable manner, at very low levels of
functional complexity. No one has published anything in literature
dealing with these obvious limitations and no one attempts to explain
how the actual mechanism could really have done what it is supposed to
have done. There is no statistical analysis concerning the mechanism
at all. There is simply one assumption after another without any
further thought that perhaps, just perhaps, the abilities of the
proposed mechanism should be scrutinized before such a mechanism is
promoted as such an amazingly powerful process.
> > > There is no - zip, zero, nada - evidence that independently suggests we
> > > can infer a deliberate desiger.
> >
> > LOL - The fool has said in his heart . . .
> >
> > The evidence is everywhere.
>
> Are you really going to be so foolish as to argue based upon intuition?
Who's arguing for intuition here? - It seems to me that you
evolutionists would just love it if everyone just accepted your
assumptions of mechanism based solely on your intuition without any
need for actual demonstration or statistical analysis.
> >Tell me, where is there any demonstration
> > or statistical analysis of the abilities of random mutation and
> > function-based selection beyond extremely low levels of functional
> > complexity? There simply aren't such published analysis because
> > everything published simply assumes it happened based on the notion
> > that sequence similarities much have been the result of common descent
> > via random mutation and natural selection.
>
> This is evasion. This has nothing to do with my point. You are simply
> regurgitating your neutral gap nonsense either because you are unable
> to follow the plot of discussion or you are afraid of discussing larger
> scale issues.
>
> My reply to you dealt very specifically with whether "common design"
> was just as reasonable an inference as common descent. Your god of the
> gaps business is an irrelevant digression.
Not true. It strikes directly at your proposed process creation. Your
mechanism just isn't viable.
> > No one sits down and says, "Wait a minute! Let's do a few calculations
> > and see if random mutations and function-based selection are remotely
> > likely to produce higher-level functions given billions much less
> > millions of years of time. That just isn't done. It is just assumed
> > by blind faith to be true.
>
> It is, of course, a bald lie (an accusation I try very hard not to
> make) to say that it is assumed by blind faith. I would ask you to try
> to muster the integrity to acknowledge the accumulated scientific
> understanding that underlies such an inference and retract that bit of
> nonsense.
Provide just one reference that shows calculations dealing with the
actual proposed mechanism and its potential to find novel beneficial
functions at higher and higher levels of functional complexity (i.e.,
like beyond the 1000 specified residue level).
> > > It is true that we cannot logically exclude the possibility of
> > > deliberate design of the natural intelligent variety (aliens etc.), and
> > > that is a hypothesis that is putatively amenable to scientific
> > > methodology. (However, only if you wish to acknowledge that your
> > > "common design" specifically repudiates any inference to the
> > > non-natural could this suggestion even be considered.)
> >
> > ID theory only suggests that science can detect deliberate manipulation
> > of or within the natural world.
>
> And as such wishes to assume its conclusions by not bothering to test
> its hypothesis. Yes, we all know.
>
> This dog doesn't hunt anymore. An ID proponent's choices are clear,
> either repudiate non-natural design inferences or acknowledge that ID
> is non-scientific.
ID doesn't say if the source of the design was natural or non-natural.
It only says that the source acted on natural physical things in an
intelligent deliberate manner. Certainly you aren't arguing that
high-level intelligences cannot exist in this physical universe? - or
that their actions cannot be detected as deliberate and intelligent?
> > > Even so, the huge disparity in evidence makes it clear that in no way
> > > could "this...just as easily be the result of common deliberate
> > > design." It would be no more nonsensical (in fact less, as I've
> > > actually seen evidence that he exists) to say it could just as easily
> > > be the result of an intelligent, though incredibly annoying, purple
> > > dinosaur.
> >
> > ID theory doesn't say who, why, or even how. ID only argues that
> > deliberate manipulation was required. It could have been via some
> > intelligent purple dinosaur or an alien from Zorg. But, whoever did it
> > and however he/she/it did it, it was intelligent and deliberate.
>
> See above.
Your argument makes no sense.
> > > In truth, your inference to common design makes sense only if we remove
> > > all meaning from the word "explanation" and it's synonyms, allowing
> > > idle speculation and wishful thinking to be considered legitimate
> > > counterexamples to evidentially supported theories.
> >
> > LOL - uh huh. Tell that to SETI scientists.
>
> Try to think these things through. If and when a SETI scientist feels
> compelled to make a design inference it will be supported by empirical
> evidence. As such, this inference will comport with the underlying
> assumptions of scientific methodology - that a subject of investigation
> is amenable to observation, measurement and replicative testing, i.e.
> that it exists in the natural universe.
Almost. SETI scientists will be able to observe and measure,
repeatable, a given phenomenon, but they may not be able to reproduce
it themselves - and still be able to propose an intelligent origin. ID
proposed to be able to do the same thing. Both disciplines are based
on the notion that potential non-intelligent non-deliberate sources of
creativity can be ruled out to a sufficient degree to obtain useful
predictive value for the design hypothesis.
> There is nothing in the methodology or putative conclusions of SETI
> science that puts it in the category of wishful thinking or idle
> speculation. The same cannot be said of ID, or whatever flavor of
> creationism it is that you prefer.
You're wrong. Both processes can use the very same methodology.
> > You know, you guys can argue that "nature" did it whenever you see a
> > new phenomenon. You might not know how, but you automatically know
> > that it was a mindless natural process that did it. That's your
> > default explanation for absolutely everything.
>
> Don't be naive. That may or may not be some individual's default
> explanation but that's beside the point. Science is a tool, not a
> materialist cudgel (regardless of how some people use it), and as such
> it doesn't default to nature so much as recognize that non-nature is a
> non-starter. The methodology cannot accommodate the non-natural.
Again you are wrong. If an entity above nature where to act within
nature, science most certainly could identify if the activity within
nature was different than normal. As such scientists most certainly
could reasonable infer that the usual non-deliberate forces at play had
been interrupted. If the interruption was particularly creative and
clearly beyond the likely limits of what non-deliberate natural forces
are capable of achieving, scientists should be clearly able to
hypothesize at least that some sort of high informational complexity
and probably deliberate intelligent design was at work.
> You know this. All the ID guys know this (which is why they constantly
> whine that methodological naturalism should be amended). Yet all of you
> want us to relive the Enlightenment and hope that things turn out
> differently.
>
> You may wish to return to ignorance but I don't. I want my planes to
> fly and my medicines to work and my universe to be explicable. There's
> a reason science developed over the centuries into what we see today:
> because it works.
Sure, science works very well. It just isn't nearly as limited in its
potential as you seem to think. Science can indeed detect the
deliberate workings of high-level intelligences acting upon the
physical universe - even if the source of this intelligence goes beyond
the limits of what some might call "natural". Personally, I believe
that nothing is unnatural. It is all a matter of perspective. If
someone is more intelligent or has access to higher-level information
or technology, their activities might appear "supernatural" from my
perspective. However, they would be perfectly "natural" from their own
perspective. It's all relative.
> > At least IDists are a bit more discriminating.
>
> You either know little of ID or misconstrue the meaning of
> "discriminating."
>
> > IDists do not automatically argue for design
> > when they see a new phenomenon. They argue for detailed investigation
> > first in an attempt to rule out, as much as is reasonably possible, any
> > potential non-deliberate cause. Only after such extensive
> > investigation has been carried out is it reasonable to promote the
> > hypothesis of ID.
>
> At which point the hypothesis needs to be tested in order to have
> followed through on scientific methodology. ID deliberately avoids this
> step. It allows its unsubstantiated inference to stand wholly
> unexamined. And this, to you, is discriminating?
Not true. It is the ID position that is testable and potentially
falsifiable, not the naturalist position. All that has to be done to
falsify the notion that a given phenomenon could only have been
designed with high-level information is to demonstrate some
non-intelligent non-deliberate process actually giving rise to the
phenomenon in question. As soon as this happens, the ID-only
hypothesis is falsified.
For comparison, the notion that a given phenomenon must have been
produced by a non-deliberate mindless process is not falsifiable - only
verifiable. Therefore, it really doesn't meet the criteria of the
scientific method. ID is the real scientific position here since only
ID can be falsified with additional testing over time.
> > > No, not by any stretch of logic could "common deliberate design" "just
> > > as easily" serve as an explication of common origin. Not without
> > > abandoning reason, something you try hard to appear as if you employ.
> > >
> > > You'll have to do much better.
> >
> > Ditto
>
> I'll just note here that my entire argument went unaddressed.
See above . . . The ID position is really the only valid scientific
position to take here.
> > > > The fact that none of these scenarios has ever
> > > > been demonstrated in real life beyond the 1000 specified residue level,
> > > > combined with the fact that there is a clear exponential decline in
> > > > evolvability as the 1000aa level is approached, should give you a very
> > > > clear notion that evolutionary mechanisms simply cannot do the job at
> > > > this level or beyond this side of a practical eternity of time.
> > >
> > > Well, this is certainly no improvement. Standard issue creationist
> > > "gap" argument here.
> >
> > All scientific theories are based on a gap in knowledge. It is because
> > we have subperfect knowledge that science is so useful. Some new bit of
> > information could always come along and falsify any hypothesis or
> > theory. That is the nature of science. For you to argue that no true
> > scientific theory can be based on a gap between what is and what might
> > be shows that you don't really understand how science works.
>
> Nice try, but either intentionally disingenuous or foolishly naive,
> again.
>
> Of course all science is born of gaps in knowledge. The key to whether
> you're doing science or not is how you address the gaps, and what you
> do with the information you've gained. I've already noted how ID does
> not address the gaps with appropriate scientific methodology. How they
> treat the results of their inquiries is even worse. No scientist (at
> least not while doing science) is left with an unanswered question and
> then feels justified in inferring unevidenced cause. But this is
> exactly what ID produces.
That's BS. For example, how many times would Arnold Schwarzenegger
have to win the California lottery, in a row, before someone would
rightly be able to hypothesize some sort of deliberate design going on?
Let's say he won 10 times in a row. Would you need any more evidence
to reasonably cross the gap to deliberate cheating? I mean, it is
possible that he did indeed win by natural non-deliberate process, but
what are the odds? What is the predictive value of that hypothesis
being the true bridge across the gap compared to the cheating
hypothesis?
> Science accepts incomplete knowledge. Science recognizes "We don't
> know" (a gap) as a position that leads to future understanding.
Science is all about predicting the likely bridge across a gap in
knowledge - about predicting a reality that cannot be fully known this
side of eternity. It isn't that scientists say "we don't know". It is
that scientists accept that they can never fully know, but present
their best prediction as to what seems to be most likely true - what
has the best predictive power.
> This is
> as opposed to cutting off such increased knowledge by declaring a gap
> filled by an unevidenced designer.
The goal of science it to try and fill the gap with something. If the
hypothesis with the best predictive value of crossing the gap is
deliberate design, then that's the hypothesis that should be used until
something better comes along (see Schwarzenegger illustration above).
> The same goes for silly
> pronouncements as to what nature cannot do, whether that's building an
> eye or building amino acid chains beyond low levels of complexity.
> These kinds of unwarranted inferences take gaps in our knowledge and
> force them to serve ideology. Science takes gaps and increases our
> understanding of the universe.
Can mindless natural process end up with Schwarzenegger winning the CA
lottery 10 times in a row? Certainly! But, what are the odds? What
hypothesis carries with it the best predictive power?
> So, of course I don't argue that science cannot be based on a gap.
> Quite the reverse, actually. But you knew that didn't you?
Clearly, but you are indeed arguing that science cannot be based on a
gap when it comes to determining origins of living things.
> > > > Yet, you continue to list off dozens of these papers, all of which are
> > > > based on exactly the same notion. Not one of them actually presents
> > > > any real experiment that demonstrates evolution in action beyond the
> > > > 1000aa level - not one. You said you'd present something on
> > > > flagellar evolution, but you have yet to do so. You seem stuck in rut
> > > > here, unable to come up with anything beyond your fairy tale "what if"
> > > > stories.
> > >
> > > There's a reason all of them are based upon similar assumptions. There
> > > are bedrock concepts in any discipline, achieving that status through
> > > hundreds of years and countless man-hours of corroborative research.
> >
> > None of which have been employed in analyzing the actual proposed
> > mechanism.
>
> But of course they have. There's that integrity thing again.
Oh really? - show me the paper.
> > > > > Oh... that's right. He'll call them "just so stories". Maybe
> > > > > Sean should try thinking of them as "what if" stories instead.
> > > >
> > > > LOL - you think calling them "what if" stories makes them sound more
> > > > scientific? Please! Give me a break! They are all based on the same
> > > > erroneous assumption. They are not based on any statistical evaluation
> > > > of the actual time it would take to cross the gaps that exist at levels
> > > > of functional complexity beyond the 1000aa level nor do they present
> > > > any real time experiment that demonstrates evolution beyond this level.
> > >
> > > Ah, yes, "real time." A dead giveaway for the standard issue
> > > creationist "were you there" argument.
> >
> > We aren't talking about turning a dog into a cat or anything like that.
> > We are talking about very small subsystem biofunctions that can indeed
> > be observed in real time. Why is it that functions like single protein
> > enzymes, which require no more than a few hundred fairly specified
> > residues, can be observed to evolve in real time while functions that
> > require just a few more residues at minimum, just 1000 or so, are never
> > evolved? - not one example ever? Just think about that for a minute .
>
> I've thought about it for much more than a minute. I've thought about
> it ever since you first began talking about it. And it's clear that it
> is nothing more than a dressed up god of the gaps assertion.
That's exactly what it is. It's a god of the gaps argument - just like
all good scientific hypotheses and theories. All rely on a gaps
argument - an argument that is potentially falsifiable with additional
evidence that shows that your proposed bridge really doesn't cross the
gap like you thought it did.
> I'm sure
> it feels to you like a compelling argument, but in essence it has no
> more intellectual validity than complaining that we don't see dogs give
> birth to cats. Why? Because it presents a false picture of how
> evolution works and what we should be able to observe given certain
> time-spans, and most importantly because it presents incomplete
> knowledge as a positive argument for non-natural inference.
Oh please. How does evolution work and what is it that makes the
observation of 100 and 200 and 300 and 400 residue functions possible
to observe, but never functions that require at least 1000 specified
residues? We aren't talking about dogs and cats poofing into existence
here. We are talking about relatively simple subsystem biosystems.
> > > > Suggestion, stop reference mining dozens of references that you haven't
> > > > even read yourself and start actually thinking for yourself.
> > >
> > > You mean "thinking for yourself" as in trying to step outside a line of
> > > inquiry circumscribed by unquestioned dogma leading to extreme
> > > confirmation bias? Well, you've certainly got the whole projection
> > > thing down.
> > >
> > > Now, here's a suggestion for you; why not stop for a moment and
> > > consider which kind of "dogma" it would make sense to allow to
> > > circumscribe your thinking - one based upon the accumulated replicated
> > > work of thousands of highly trained scientists, or one based upon a
> > > book of legends and parables.
> > >
> > > I would think no less of you for merely chosing the latter, but when
> > > you extend that to accusing others who are involved in expanding our
> > > knowledge of the universe of wearing blinders then I feel compelled to
> > > note that you are a self-deluded prat.
> >
> > Show me any scientific publication that seriously deals with the odds
> > of the actual proposed mechanism of evolution working at higher and
> > higher levels of functional complexity. Show me some mathematical
> > calculations, statistical analysis, or real time demonstrations that go
> > beyond the 1000aa level. I'm waiting . . .
>
> You keep hammering on your 1000aa nonsense instead of addressing my
> comments. You made a foolish and unsupported accusation, one that is
> countered by all of the available evidence. Do you really think
> slipping back into your gap argument makes that go away?
Prove my accusation wrong by actually presenting just one paper that
deals with the statistical odds of the proposed evolutionary mechanism
actually doing the job beyond the 1000aa level of functional
complexity.
> Perhaps you avoid discussion of the larger issues involved because you
> realize that without keeping everyone running around shooting down your
> molecular misapprehensions you are without any compelling argument?
The are a lot of problems with your notions of the fossil record,
geologic column, radiometric dating, etc. However, the most serious of
the problems with the ToE have to do with the fact that the proposed
mechanism, random mutation and function-based selection, is far too
limited to do much of anything beyond very low levels of functional
complexity. That problem is so obvious and so key that it is going to
end up being the death knell for the ToE.
> RLC
Sean Pitman
www.DetectingDesign.com
noctiluca
> noctiluca wrote:
(Apologies if this is a duplicate)
> > > > No, they most definitely could not. The fact is that there exists vast
> > > > amounts of scholarship (fossil record, phylogenetic analysis, molecular
> > > > analysis etc.) demonstrating the validity of an inference to
> > > > evolutionary processes and common descent.
> > >
> > > The problem is that your proposed mechanism just isn't up to the task .
> > > . . and this problem is overwhelming demonstrable in real time
> > > demonstration and statistical evaluation.
> >
> > You're arguing about nickels while I'm talking about milllions. Whether
> > you realize this I don't know but my point remains untouched by your
> > response. The big picture, the one that collates countless bits of
> > information from varied disciplines - many of which don't rely on any
> > particular mechanism - demonstrates that evolution by common descent is
> > an inference so strong as to be reasonably considered fact.
> >
> > There is no such similar independent body of evidence for common
> > design.
> >
> > Puny protests over silly "real time" gap arguments do nothing to
> > diminish this obvious imbalance.
>
> Without a viable mechanism, your inference is meaningless.
I need no viable mechanism to look at the nested hierarchy of life on
this planet and see common descent. What's more it is obvious that
*you* require no mechanism for this kind of inference either, otherwise
your attribution to common design would be worthless (where is your
mechanism for this?).
Do you wish to retract the common design silliness, or the meaningless
inference silliness?
Of course they are both wrong, but for different reasons than your
inability to be logically consistent.
In the case of inference to common design, you are wrong for the
obvious reason that one need not know the mechanism of evolution to
notice that it has happened in a heirarchichal,
descent-with-modification, fashion, and thus infer common descent.
These conclusions are independent of mechanism. This is the difference
between observation and theory. It's fundamental, and it's obvious.
> You can
> assume that sequence similarities and the fossil record point toward an
> evolutionary process all you want. However, with evidence speaking
> strongly against the potential of your stated mechanism, random
> mutation and function-based selection, your whole little theory is
> completely undermined.
Well, of course. But your little "low levels of functional complexity"
(LLFC) argument is not evidence. It is an observation that there is
something for which we have no explanation. It is no more evidence
against NS+RM than is the fact that there are genetic sequences for
which we, at present, have no phylogeny. And it is no more evidence
against NS+RM than are all of the accumulated, and profoundly silly,
probability arguments made by Dembski and others.
What is clear is that things which you and Dembski and those of your
ilk claim could not have happened, have actually happened. There are
only two ways to procede from this reality with any intellectual
integrity: One - seek legitimate empirical understanding, reserving
provisionally open questions for future investigation, and, Two -
decide that open questions evidence a preferred personal philosophy,
and accept that this is not a scientific position.
Your difficulty is that your science is too inept to follow the first
path, and your faith is too insecure to follow the second.
I'll say once more - I don't know if you are incapable of seeing beyond
these red herrings, or you're aware of your misapprehensions but are
submerging them in favor of what you see as the greater good. But the
fact is that there are implications of your arguments, as there are
with all gap arguments, that you apparently refuse to see, and
certainly refuse to discuss. I can understand this, as they reveal them
to be losing positions.
<snip more evasion and LLFC nonsense>
> > > > It is true that we cannot logically exclude the possibility of
> > > > deliberate design of the natural intelligent variety (aliens etc.), and
> > > > that is a hypothesis that is putatively amenable to scientific
> > > > methodology. (However, only if you wish to acknowledge that your
> > > > "common design" specifically repudiates any inference to the
> > > > non-natural could this suggestion even be considered.)
> > >
> > > ID theory only suggests that science can detect deliberate manipulation
> > > of or within the natural world.
> >
> > And as such wishes to assume its conclusions by not bothering to test
> > its hypothesis. Yes, we all know.
> >
> > This dog doesn't hunt anymore. An ID proponent's choices are clear,
> > either repudiate non-natural design inferences or acknowledge that ID
> > is non-scientific.
>
> ID doesn't say if the source of the design was natural or non-natural.
Of course not, this inference is intentionally left open, and as such
disqualifies ID as science.
> It only says that the source acted on natural physical things in an
> intelligent deliberate manner.
But unless you are speaking of some designer for which we have evidence
(i.e. humans) then these attributions of "intelligent" and "deliberate"
are meaningless, they have no legitimate referent in the universe of
our experience, much less our accumulated empirical data. Only if that
which you are trying to prove (the existence of your designer God) is
assumed can those adjectives have meaning beyond our natural world (and
even then only for you). You cannot argue for the existence of a
designer by using arguments which depend upon the designer's existence
for support.
In order to convince non-believers (or anyone who thinks this through)
that ID is a legitimate enterprise, you need to be able to craft your
propositions in a cognitive environment where God is not a given. It is
a problem you share with Dembksi, Behe, and all the creationisms, and
it invariably undermines your efforts to put together a logical
argument.
> Certainly you aren't arguing that
> high-level intelligences cannot exist in this physical universe? - or
> that their actions cannot be detected as deliberate and intelligent?
Of course not, I'm arguing that the detection of deliberation and
intelligence has to coincide with, well... actual existence.
Being able to reproduce it themselves is not what is meant by
replication. They need merely to confirm the initial observation enough
to support their conclusions. Stop being intentionally thick.
> ID proposed to be able to do the same thing. Both disciplines are based
> on the notion that potential non-intelligent non-deliberate sources of
> creativity can be ruled out to a sufficient degree to obtain useful
> predictive value for the design hypothesis.
However only one discipline accepts that putative intelligent phenomena
are natural and empirically quantifiable. Only one disciplne assumes
that putative intelligent phenomena are understandable by way of known
intelligent referents (the logic underlying this being that the
putative intelligence occupies the same universe and is subject to the
same natural laws as are we). And only one discipline recognizes that
putative intelligent phenomena can be classified as "designed"
providing something of the designer's methods and motivations is
understood.
That would be SETI, and the above would be a good starting place for
recognizing the difference between real scientific investigation of
intelligence (SETI) and apologetics.
> > There is nothing in the methodology or putative conclusions of SETI
> > science that puts it in the category of wishful thinking or idle
> > speculation. The same cannot be said of ID, or whatever flavor of
> > creationism it is that you prefer.
>
> You're wrong. Both processes can use the very same methodology.
Can, but don't. If ID did use the same methodology, it would be
superfluous as we already have sciences that investigate natural
intelligence. In addition it would be superfluous as a tool for
apologetics because it would be theologically toothless.
'Tis a thing to be wished for, I'll admit.
> > > You know, you guys can argue that "nature" did it whenever you see a
> > > new phenomenon. You might not know how, but you automatically know
> > > that it was a mindless natural process that did it. That's your
> > > default explanation for absolutely everything.
> >
> > Don't be naive. That may or may not be some individual's default
> > explanation but that's beside the point. Science is a tool, not a
> > materialist cudgel (regardless of how some people use it), and as such
> > it doesn't default to nature so much as recognize that non-nature is a
> > non-starter. The methodology cannot accommodate the non-natural.
>
> Again you are wrong. If an entity above nature where to act within
> nature, science most certainly could identify if the activity within
> nature was different than normal. As such scientists most certainly
> could reasonable infer that the usual non-deliberate forces at play had
> been interrupted. If the interruption was particularly creative and
> clearly beyond the likely limits of what non-deliberate natural forces
> are capable of achieving, scientists should be clearly able to
> hypothesize at least that some sort of high informational complexity
> and probably deliberate intelligent design was at work.
There are a lot of words here but little substance. You've spun quite a
fantasy but established no support for your point.
There are many questions to be asked before we can even get past your
first couple of sentences, including: Does any activity which is
different than normal constitute non-natural intervention? If not, then
how would you distinguish this activity from natural activity such that
you can conclusively attribute the activity to non-natural
intervention.? And even in the case that you could do so (and you
cannot) how would you connect the "non-natural act" within nature with
the entity above nature? How do we recognize an "interruption" in
non-deliberate activity? How do we recognize a particularly creative
"interruption?"
I may well be wrong, as you say. But you don't appear to be up to the
task of demonstrating that.
> > You know this. All the ID guys know this (which is why they constantly
> > whine that methodological naturalism should be amended). Yet all of you
> > want us to relive the Enlightenment and hope that things turn out
> > differently.
> >
> > You may wish to return to ignorance but I don't. I want my planes to
> > fly and my medicines to work and my universe to be explicable. There's
> > a reason science developed over the centuries into what we see today:
> > because it works.
>
> Sure, science works very well. It just isn't nearly as limited in its
> potential as you seem to think. Science can indeed detect the
> deliberate workings of high-level intelligences acting upon the
> physical universe - even if the source of this intelligence goes beyond
> the limits of what some might call "natural". Personally, I believe
> that nothing is unnatural.
What a coincidence, so do I. Of course commensurate with this position
is an acceptance that a legitimate inference to a particular natural
phenomenon depends upon positive evidence for the proposed phenomenon,
not the lack thereof.
If on this point we part company, it becomes obvious that you are a
non-naturalist in naturalist's clothing.
> It is all a matter of perspective. If
> someone is more intelligent or has access to higher-level information
> or technology, their activities might appear "supernatural" from my
> perspective. However, they would be perfectly "natural" from their own
> perspective. It's all relative.
No one disputes this aphoristic truism (truistic aphorism?). It's a
semantic game. It does not absolve you of your obligations vis a vis
the argument over whether science can evidentially establish the
supernatural. It cannot.
> > > At least IDists are a bit more discriminating.
> >
> > You either know little of ID or misconstrue the meaning of
> > "discriminating."
> >
> > > IDists do not automatically argue for design
> > > when they see a new phenomenon. They argue for detailed investigation
> > > first in an attempt to rule out, as much as is reasonably possible, any
> > > potential non-deliberate cause. Only after such extensive
> > > investigation has been carried out is it reasonable to promote the
> > > hypothesis of ID.
> >
> > At which point the hypothesis needs to be tested in order to have
> > followed through on scientific methodology. ID deliberately avoids this
> > step. It allows its unsubstantiated inference to stand wholly
> > unexamined. And this, to you, is discriminating?
>
> Not true. It is the ID position that is testable and potentially
> falsifiable, not the naturalist position. All that has to be done to
> falsify the notion that a given phenomenon could only have been
> designed with high-level information is to demonstrate some
> non-intelligent non-deliberate process actually giving rise to the
> phenomenon in question. As soon as this happens, the ID-only
> hypothesis is falsified.
Come on Sean. The above is grade-school evasion.
I accepted your observation that ID proposes a hypothesis. I then
suggested that the fact that ID does not test the hypothesis, that it
is allowed to stand unexamined, establishes that ID is not science.
You say "not true," then respond not with a demonstraton of how ID does
indeed test its hypothesis, but with a challenge that opponents of ID
should go falsify something or other.
At least make a pretense that you're going to offer something that
speaks to my comments.
> For comparison, the notion that a given phenomenon must have been
> produced by a non-deliberate mindless process is not falsifiable - only
> verifiable.
Well, you could always just show us God. Ask him to post here, I know
I've got a lot of questions.
> Therefore, it really doesn't meet the criteria of the
> scientific method. ID is the real scientific position here since only
> ID can be falsified with additional testing over time.
I'll ignore the silly fundamentalist sophistry about science not being
science and just address the second part. So, at what point would you
say we would be justified in declaring there is no God?
> > > > No, not by any stretch of logic could "common deliberate design" "just
> > > > as easily" serve as an explication of common origin. Not without
> > > > abandoning reason, something you try hard to appear as if you employ.
> > > >
> > > > You'll have to do much better.
> > >
> > > Ditto
> >
> > I'll just note here that my entire argument went unaddressed.
>
> See above . . . The ID position is really the only valid scientific
> position to take here.
Yeah, I know, and Kent Hovind is a real doctor. Try to be serious.
Why, just a few, of course. But noting that this is highly improbable
is not doing science. Demonstrating that there is another explanation
would be.
> Let's say he won 10 times in a row. Would you need any more evidence
> to reasonably cross the gap to deliberate cheating?
No. Call me when this happens, or when "the moon could be made of green
cheese" arguments become acceptable astrophysics.
> I mean, it is
> possible that he did indeed win by natural non-deliberate process, but
> what are the odds? What is the predictive value of that hypothesis
> being the true bridge across the gap compared to the cheating
> hypothesis?
For our intents and purposes? None? So what?
However, if you wish to assert that he won ten times in a row because
God willed it, and you try to support that argument with probability
calculations, you'll be suitably regarded as a nutcase, just as when
you argue that God had to bridge a biological gap in functional
complexity.
The obvious value in your little story, for anyone who thinks it
through, lies in the observation that there is a natural explanation,
even for improbable events.
> > Science accepts incomplete knowledge. Science recognizes "We don't
> > know" (a gap) as a position that leads to future understanding.
>
> Science is all about predicting the likely bridge across a gap in
> knowledge - about predicting a reality that cannot be fully known this
> side of eternity. It isn't that scientists say "we don't know". It is
> that scientists accept that they can never fully know, but present
> their best prediction as to what seems to be most likely true - what
> has the best predictive power.
And predictive power will most often be based upon the quality and
volume of empirical evidence informing the predictions. Filling in
blanks with theological constructs is not a foundation for, nor is it a
result of, scientific prediction. It is an expression of insecure
ideology hoping to find empirical validation.
> > This is
> > as opposed to cutting off such increased knowledge by declaring a gap
> > filled by an unevidenced designer.
>
> The goal of science it to try and fill the gap with something. If the
> hypothesis with the best predictive value of crossing the gap is
> deliberate design, then that's the hypothesis that should be used until
> something better comes along (see Schwarzenegger illustration above).
Works for me. I'll take from this that you believe until a better
natural explanation for the evolution of life on earth comes along we
should stick with the current one (or did you draw a shallow and
specious lesson from the Schwarzenegger illustration?).
> > The same goes for silly
> > pronouncements as to what nature cannot do, whether that's building an
> > eye or building amino acid chains beyond low levels of complexity.
> > These kinds of unwarranted inferences take gaps in our knowledge and
> > force them to serve ideology. Science takes gaps and increases our
> > understanding of the universe.
>
> Can mindless natural process end up with Schwarzenegger winning the CA
> lottery 10 times in a row? Certainly! But, what are the odds? What
> hypothesis carries with it the best predictive power?
That some other natural explanation applies. Problems with the lottery
software. Problems with communication between lottery administration
and public information outlets. Even intelligent intervention could be
the cause, but of course this would be intelligence for which we have
some sort of corroborating evidence.
I can't believe you're still having trouble with this analogy.
> > So, of course I don't argue that science cannot be based on a gap.
> > Quite the reverse, actually. But you knew that didn't you?
>
> Clearly, but you are indeed arguing that science cannot be based on a
> gap when it comes to determining origins of living things.
Disingenuous once again. I am, of course, arguing that a causal
inference to non-natural intelligence cannot be based on a gap. That
you cannot see the difference is further evidence of your inability to
conceive of your argument in such a way that it does not assume its
conclusions.
<snip still more LLFC evasion>
> > Perhaps you avoid discussion of the larger issues involved because you
> > realize that without keeping everyone running around shooting down your
> > molecular misapprehensions you are without any compelling argument?
>
> The are a lot of problems with your notions of the fossil record,
> geologic column, radiometric dating, etc. However, the most serious of
> the problems with the ToE have to do with the fact that the proposed
> mechanism, random mutation and function-based selection, is far too
> limited to do much of anything beyond very low levels of functional
> complexity. That problem is so obvious and so key that it is going to
> end up being the death knell for the ToE.
Could you give us a date for that? I mean, this is the first I've heard
of it, and I try to keep up with these things.
Robert
david ford
> Mark VandeWettering wrote:
>
> > He asserts that intelligent design must have happened, but he can't tell
> > you how, where, when or by whom.
How does a seeingwatchmakingist account for the origin of
the recorded-in-DNA/ genetic information within:
a human? a bacterium? the first biological lifeform?
http://groups.google.com/groups?selm=dford3-348nj6F47evohU1%40individual.net
> But ID can tell you that it was almost certainly not the result of any
> non-deliberate process. When SETI scientists find the radio signal
> from outer space that they are looking for, which they would widely
> hail as evidence of alien intelligence equivalent or even greater than
> our own, they probably won't be able to say exactly who, why or even
> how such a signal was made. Yet, they will still strongly assert that
> it was made intelligently and deliberately.
Well said.
> Beyond this, Richard is quite mistaken in the claim that most
> creationists argue that evolution isn't a science.
Meaning of "evolution"?
http://groups.google.com/groups?selm=dford3-386md9F5lsv5cU1%40individual.net
> Many if not most of
> the creationists trained in various disciplines of science that I know
> believe that the theory of evolution is based on many valid scientific
> hypotheses and theories. It is just that the weight of current
> evidence strongly counters if not outright falsifies many of the most
> fundamental supports behind the theory of evolution.
shipmodeler1
ID has no rules or expectations -- it just makes excuses for
already-observed phenomena.
Ask yourself: If ID is a theory, why weren't preachers in the 19th
Century predicting the existence of DNA, and the genetic linkages we
see between species?
ID isn't a theory. It isn't even a hypothesis. It's just an appeal to
incredulity.
david ford
> At least the SETI people have groundrules for what they're looking for.
What are those "groundrules"?
> ID has no rules or expectations -- it just makes excuses for
> already-observed phenomena.
There's a listing of 13 items in "RTB's Human Origins Creation Model
Predictions" in
Rana, Fazale with Hugh Ross. 2005. _Who was Adam?: A Creation Model
Approach to the Origin of Man_, 51-52.
About the book:
http://www.reasons.org/shop/customer/product.php?productid=690&cat=0&page=1
What are some predictions of:
the theory of natural selection?
the hypothesis that [1949 Simpson]"man is the result of a purposeless
materialistic process that did not have him in mind"?
////////////////////////////////////////////////////
Simpson cite in
Timeline of Materialism, Spontaneous Generation, and Blindwatchmaking
Views
http://groups.google.com/groups?selm=dford3-348jecF47mfcjU1%40individual.net
1952 Goldschmidt on the theory of NS's "crazy-quilt" prediction
http://groups.google.com/groups?selm=b1c67abe.0401271936.9a5dfd2%40posting.google.com
Essay on Problems with Darwin's Theory of Natural Selection
http://groups.google.com/groups?selm=Pine.LNX.4.10A.B3.10005310900310.17702-100000%40jabba.gl.umbc.edu
Rana on Design Hypothesis Evidence
http://groups.google.com/groups?selm=b1c67abe.0405071913.10142d50%40posting.google.com
> Ask yourself: If ID is a theory, why weren't preachers in the 19th
> Century predicting the existence of DNA, and the genetic linkages we
> see between species?
"the genetic linkages we see between species"
As far as you know, do ORFans fit into a nested hierarchy?
http://groups.google.com/groups?selm=dford3-1165334818.498006.131640%40f1g2000cwa.googlegroups.com
> ID isn't a theory. It isn't even a hypothesis. It's just an appeal to
> incredulity.
In my view, ID can provide for a metaphysical research program.
http://groups.google.com/groups?selm=dford3-1129317540.779352.231140%40f14g2000cwb.googlegroups.com
Ghod
news:dford3-11653449...@l12g2000cwl.googlegroups.com...
> shipmodeler1 wrote:
> > At least the SETI people have groundrules for what they're looking
for.
>
> What are those "groundrules"?
Here stupid, do some reading:
http://www.seti.org/site/pp.asp?c=ktJ2J9MMIsE&b=178025
[snipped the fordling's spew]
Earle Jones
"eyelessgame" <aa...@surewest.net> wrote:
> Richard Forrest wrote:
> > Creationists frequently assert that evolution is not science.
> >
> > This is a curious assertion.
> >
> > Every university, in every country in which the biological sciences are
> > taught teaches evolutionary theory as an integral part of the science
> > of biology. Evidently they think that it is science, as do the
> > administrative bodies which organise universities, the public and
> > private bodies which fund universities, the coroporations who employ
> > the graduates of those universities.
> >
> > I'm not arguing from authority here, but merely asking the question:
> >
> > You evidently think that all those people in the science departments of
> > universities, in university administration, in funding organisations
> > and business have got it wrong. This seems rather remarkable claim.
> >
> > What do you know that all those people don't?
>
> Let me channel them for a moment and try to answer.
>
> I think they'd say that what they have, which those people don't, is
> knowledge of Jesus Christ....
*
Some of them have the knowledge of Allah, some of Buddha, and some
of Babalu-aye (the Cuban/Bantu god who has only one leg and goes
around in poor tramp's clothes with his dog and cures disease,
including HIV). Some (like me) have no knowledge of any God and
have never seen any evidence that any God exists.
What does your Jesus Christ have that these other "Gods" lack?
About 17% of the world's population (2 billion out of 6 billion)
would agree that Jesus Christ is the divine son of God. About 83%
would not agree.
You have a burden of proof.
Hint: A 2,000 year-old book written by bronze-age goatherders is
not very good evidence. Especially a book that is full of parables,
some good morals and poetry, bad advice, and downright lies. The
worshipers of Allah, Buddha, and Babalu-aye also have books.
earle
*
"The Judaical and Christian theology show us a partial god who
chooses or rejects, who loves or hates, according to his caprice; in
short, a tyrant who plays with his creatures; who punishes in this
world the whole human species for the crimes of a single man; who
predestines the greater number of mortals to be his enemies, to the
end that he may punish them to all eternity, for having received
from him the liberty of declaring against him."
--Denis Diderot, Footnote to d'Holbach's "The System of Nature"