Bonus material on The Evolution of Antievolution Policies After Kitzmiller v. Dover

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Nick Matzke

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Dec 19, 2015, 9:07:35 AM12/19/15
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Hi TO! Is it just me or is talk.origins ticking up in activity lately?

Anyhoo -- I just put this up, there is intro stuff and advanced stuff...

Bonus material on The Evolution of Antievolution Policies After Kitzmiller v. Dover
http://pandasthumb.org/archives/2015/12/bonus-material.html

Specifically:
http://phylo.wikidot.com/matzke-2015-science-paper-on-the-evolution-of-antievolution

Cheers!
Nick




Steady Eddie

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Dec 19, 2015, 10:02:35 AM12/19/15
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So what?

BTW, has anyone gotten around to conducting any REAL "scientific research programs" into the development of the flagellum, like you
suggested in your paper some TEN YEARS AGO?

https://www.ocf.berkeley.edu/~matzke/matzke_cv/_pubs/Pallen_Matzke_2006_NRM_origin_flagella.pdf

How's that working out for ya?

RonO

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Dec 19, 2015, 10:17:33 AM12/19/15
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This seems to be creationist legislation. What about efforts like the
Texas and Louisiana textbook supplements in 2013. Nothing seems to have
been tried since by IDiots. Louisiana attempted to use their switch
scam legislation to alter textbooks several years before that. Both
attempts were stopped by the Discovery Institute's bait and switch
policy. Sell the rubes ID, then only give them something that doesn't
even mention that ID ever existed, and tell them not to try to teach ID.

You might be able to track the extinction of various IDiot
organizations, their special creations in time and when they went
extinct. The association between the Discovery Institute and ARN and
the branching of the various ID Networks and their separate extinctions.
The evolution of places like ARN, UD and the IDEA where they have
degenerated over the years and lost functional (disfunctional?) parts.

The ISCID creation and demise and the evolution and demise of the
various ID networks and the resurrection as COPE. With ID in the name
of your creationist scam organization it is difficult to sell a switch
scam that doesn't even mention that ID ever existed, so why not change
the name and start over?

You could have branch terminations for the ID perps that have bailed out
of the ID scam over the years. Philip Johnson may be the first of the
big names, then Beckwith and now Dembski. Mike Gene seems to have
bailed and has apparently been claiming that ID isn't science since
around 2007. No one seems to have mentioned that change of heart on TO,
and I only found out when they started barking about Salvador Cordova
getting banned from UD for his apparent view changes this month.

In your tree of legislation can you break down the branches where the ID
perps have run the bait and switch on the clueless? This would be the
Teach ID creationist legislation that the ID perps at the Discovery
Institute come out against every time they pop up.

The last case that I recall was Florida around 2010 when 9 county school
boards and several legislators were claiming that they were going to
teach intelligent design in the Florida public schools. The Discovery
Institute had to run the bait and switch on one clueless Florida
legislator the next year when he tried to introduce IDiocy after having
the bait and switch run on him the previous year.

Does that type of legislation show the same tree like structure or is it
just random clueless individuals of the type that wouldn't know that the
bait and switch has been going down since 2002 in Ohio.

The start of your phylogeny around 2004 was after the ID perps went to
the switch scam in 2002 instead of the teach ID scam, and they had put
out their sample switch scam legislation that doesn't mention that ID
ever existed. It stand to reason that any creationists that would be
clueless and or dishonest enough to bend over for such a bait and switch
scam would run with the junk that they got from the ID perps, so the
relationship should be obvious in creationist switch scam legislation.
The creationist teach ID legislation might be some weird hybrid form
related to the scientific creationist legislation. There would just be
a fossil gap between between the Supreme Court decision against
scientific creationism in 1987 and the start of the Teach ID creationist
scam around 1995 but the phylogenetic relationships may still be apparent.

Ron Okimoto

Ernest Major

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Dec 19, 2015, 11:47:34 AM12/19/15
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Should you have any interest in the answer, you could start with the
various works citing that article.


https://scholar.google.com/scholar?cites=11002494352465895462&as_sdt=2005&sciodt=0,5&hl=en

and the works citing the relevant members of that set of works, and so on.

If instead you wish to support the Intelligent Design movement you could
provide us with the scientific research into the origin of the flagellum
performed by the Intelligent Design movement.

--
alias Ernest Major

Steady Eddie

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Dec 19, 2015, 1:42:31 PM12/19/15
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various works citing that article, and find me ONE CASE of Matzke's prophesied "research programs"
being conducted in the past decade,where REAL empirical research has demonstrated ONE evolutionary
path of the flagellum from the most recent functional "precursor".

Until you produce such studies, as promised by Matzke, you're just quote bluffing again.

John Harshman

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Dec 19, 2015, 2:27:32 PM12/19/15
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All you had to do was follow the link. Here's one:

http://www.pnas.org/content/104/17/7116.short

Steady Eddie

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Dec 19, 2015, 2:47:33 PM12/19/15
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What about it?
Does the TITLE convince you that the paper provides any empirical research into how ONE of the
subunits of ONE particular flagellum was EXAPTED from its immediate precursor function?

Steady Eddie

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Dec 19, 2015, 2:57:32 PM12/19/15
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...Or do you just enjoy quote-bluffing?

RonO

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Dec 19, 2015, 3:32:32 PM12/19/15
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What an IDiot. One protein is so much more than Behe or any IDiot has
that you have to be joking to make the stupid claim above. Where is the
design protein example and how did they verify that it was designed by
your intelligent designer? The laughable thing is that it isn't all
that has been done. That paper was from 2007. You can use PubMed to
get more such references. Minnich was involved in identifying some of
the functional proteins. Do you think that science is just sitting on
its hands like the IDiots. Real scientists actually do something other
than lie to a bunch of clueless rubes. Minnich could be looking into
the origin of the genes that he identified, but what has he done for ID
in the last decade? I haven't heard anything out of him since his
failed performance in Kitzmiller.

Two ways to get more information using PubMed:
http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed_citedin&from_uid=17438286

http://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed&from_uid=17438286

Ron Okimoto

The Masked Lapavenger

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Dec 19, 2015, 4:12:32 PM12/19/15
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You can read the full text and SI for free (red link above the word "ABSTRACT").

Ray Martinez

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Dec 19, 2015, 4:22:33 PM12/19/15
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Over at Pandas where Nick debuted his "brilliant" work he, as one could expect, evaded criticism that completely undermines his work:

http://pandasthumb.org/archives/2015/12/the-evolution-o-9.html#comment-347670

"Creationism, whatever variety, became unconstitutional after the rise of evolution in science, higher education, and law. Only in the 20th century did judges "suddenly see" the Constitution as reflecting their bias."

Ray

John Harshman

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Dec 19, 2015, 4:57:33 PM12/19/15
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Title? Read the abstract, at least, if you can't be bothered with the
whole think. I give you exactly what you ask for but you won't even look.

Steady Eddie

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Dec 19, 2015, 5:22:35 PM12/19/15
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Go ahead and quote the passage that provides any empirical research into how ONE of the
subunits of ONE particular flagellum was EXAPTED from its immediate precursor function.
Or scurry back under your bridge.

John Harshman

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Dec 19, 2015, 5:27:33 PM12/19/15
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Once again you refuse to even look at the things you ask for. I produced
a study. Now it's up to you to read it.

Burkhard

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Dec 19, 2015, 6:57:32 PM12/19/15
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Strange Ray, when you claimed this last time, you were asked to cite the
pre-Darwin SCOTUS decisions that ruled the teaching of religion in
public science classes is constitutional, but I can't for the life of
me remember what decisions(s) you eventually posted




Steady Eddie

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Dec 19, 2015, 9:47:31 PM12/19/15
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What makes you think I didn't read it?

Now it's up to you to demonstrate that it says what you say it says.

I don't waste my time with quote-bluffs.

John Harshman

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Dec 19, 2015, 10:52:32 PM12/19/15
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Be serious. You've never read any scientific papers. Did you read this
one, as you imply without actually saying??


Nick Matzke

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Dec 19, 2015, 11:22:40 PM12/19/15
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Heh. Well.

Since you asked nicely:


http://www.the-scientist.com/?articles.view/articleNo/42284/title/Evolutionary-Rewiring/
===================
Evolutionary Rewiring
Strong selective pressure can lead to rapid and reproducible evolution in bacteria.

By Ruth Williams | February 26, 2015

Bacteria that lack a vital protein for growing flagella--tail-like structures that enable the microbes to swim--can attain flagella in as little as four days given enough pressure to evolve, according to a paper published in Science today (February 26). Furthermore, this fast fix evolves in nearly the same way in each independent strain: through the repurposing of a distantly related protein.

"This is a fascinating set of evolution experiments," wrote evolutionary biologist Richard Lenski of Michigan State University in an e-mail to The Scientist. "Their experiments show how a biological function--in this case, flagellar motility in Pseudomonas fluorescens--can re-evolve after the deletion of a seemingly critical gene. The bacteria regained motility not by reacquiring the lost gene . . . but instead by mutations in other genes that put their products to new uses."
===================


T.B. Taylor et al., "Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system," Science, 347:1014-17, 2015.
http://www.sciencemag.org/content/347/6225/1014.short
=================
A central process in evolution is the recruitment of genes to regulatory networks. We engineered immotile strains of the bacterium Pseudomonas fluorescens that lack flagella due to deletion of the regulatory gene fleQ. Under strong selection for motility, these bacteria consistently regained flagella within 96 hours via a two-step evolutionary pathway. Step 1 mutations increase intracellular levels of phosphorylated NtrC, a distant homolog of FleQ, which begins to commandeer control of the fleQ regulon at the cost of disrupting nitrogen uptake and assimilation. Step 2 is a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator. Our results demonstrate that natural selection can rapidly rewire regulatory networks in very few, repeatable mutational steps.
=================

Please admit you were wrong before switching to other emergency backup claims.

Cheers, Nick



Nick Matzke

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Dec 19, 2015, 11:27:32 PM12/19/15
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Unfortunately, that particular PNAS paper is highly problematic:
http://www.pandasthumb.org/archives/2007/06/correction_to_l.html

The main empirical claims were due to failure to correct BLAST for multiple searches and database size:
http://www.pandasthumb.org/archives/2007/04/flagellum_evolu_3.html

Somehow, it's still got 100 citations, ugh.

John Harshman

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Dec 20, 2015, 12:17:32 AM12/20/15
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Oh my. How did that get into PNAS? Science, I could see. Nature, I could
see. So, I retract my claim about that one.

RonO

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Dec 20, 2015, 12:17:31 PM12/20/15
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On 12/19/2015 8:05 AM, Nick Matzke wrote:

Nick:

Are you still associated with the NCSE?

In searching for other junk related to the IDiotic past and ARN I found
a copy of the final draft of the Ohio model lesson plan on some Texas
site today.

The NCSE link to the Ohio lesson plan is broken and so is everyone
elses. The Discovery Institute only had up the initial draft that had
the Wellsian lie about no moths on tree trunks and the creationist web
links, but that is now deleted from their site.

The final draft dropped all mention of the ID scam artists and
organizations from the text.

http://www.texscience.org/files/critical-analysis-evolution.pdf

This is the Texas Science site that has the final draft.

As far as I know it is about the only copy of the switch scam left that
can be downloaded.

Ron Okimoto


Steady Eddie

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Dec 20, 2015, 12:42:30 PM12/20/15
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Where's your evidence of QUOTE MINING?
Put up or shut up.

Steady Eddie

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Dec 20, 2015, 1:02:29 PM12/20/15
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Good idea.

Steady Eddie

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Dec 20, 2015, 1:02:29 PM12/20/15
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Yes, QUOTE BLUFFS are always "PROBLEMATIC" for you jokers.

Steady Eddie

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Dec 20, 2015, 1:07:30 PM12/20/15
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Easily - the PEER REVIEWERS have on the same rose-colored glasses (and blinders) that the researchers
had on.
"As long as it supports Darwinism, it's GOOD SCIENCE. No need to look too closely."

LOL!

Steady Eddie

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Dec 20, 2015, 1:07:30 PM12/20/15
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So, John, what's your next QUOTE BLUFF going to be?
AGAIN:
Please show ANY research in the last TEN YEARS since the Pallin Matzke paper that has successfully
demonstrated that ONE protein component of ONE specific flagellum has be EXAPTED from ONE particular
protein that was doing a different job.

Good luck.

Steady Eddie

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Dec 20, 2015, 1:12:29 PM12/20/15
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So, the resiliency and a degree of redundancy in the gene regulatory networks are purportedly demonstrated
(at least until further investigation renders this study "PROBLEMATIC" also).

That's excellent evidence of the intelligence and capabilities of the designer of the system.

An example of self-repair is NOT evidence of one pre-existing protein being EXAPTED from a previous
task to make up the structure of a flagellum.

Nice try, though.

John Harshman

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Dec 20, 2015, 2:17:30 PM12/20/15
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That should be obvious even from the quotes. It's stated as disagreeing
with Matzke, but the quote, even read in isoaltion, doesn't disagree
with Matzke.

John Harshman

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Dec 20, 2015, 2:17:30 PM12/20/15
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Not a bluff. The paper says what I claimed it said. It just happened to
have methodological flaws that are only apparent if you try to reproduce
the study.

> AGAIN:
> Please show ANY research in the last TEN YEARS since the Pallin Matzke paper that has successfully
> demonstrated that ONE protein component of ONE specific flagellum has be EXAPTED from ONE particular
> protein that was doing a different job.

Nick has cited some. You won't accept any evidence of that.

Nick Matzke

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Dec 20, 2015, 4:42:29 PM12/20/15
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Yeah, that's too bad! IMHO everything should get archived on some permanent web archive. Is wikileaks for that?

Anyhow, often sites are archived by archive.org, or other websites -- I cite some at the end of the Supplemental Material of the Science paper, to show people old DI and Ouachita policies...

Cheers!
Nick

Steady Eddie

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Dec 20, 2015, 6:12:29 PM12/20/15
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I see that we are getting ourselves tangled up in discussion of different papers by different authors.
The QUOTE MINING accusation was on a different thread (Berlinski vs Matzke), in regards to a different
paper (Ohno), and I apologize for confusing this thread by bringing that topic up here.

So let's please stop talking about the Ohno paper here, and I will concentrate on the papers you have
so far cited on this thread.

So, back to the first SPECIFIC study you cited:

Stepwise formation of the bacterial flagellar system
http://www.pnas.org/content/104/17/7116.short

Good thing your buddy was Johnny-on-the-spot and told you:
"Unfortunately, that particular PNAS paper is highly problematic"

Okay, so you're 0 for 1 so far.

NEXT citation, please.

Remember what you said is so plentifully available in the literature, and what you are now tasked with
producing:
The studies that have been prophesied in the Pallin/Matzke paper of 2006:

https://www.ocf.berkeley.edu/~matzke/matzke_cv/_pubs/Pallen_Matzke_2006_NRM_origin_flagella.pdf

The prophesy I'm specifically referring to is:

"Similar studies could RECREATE PLAUSIBLE ANCESTORS for various FLAGELLAR COMPONENTS (for example, the common ancestor of flagel- lins and HAP3 proteins). These proteins could then be REPRODUCED IN THE LABORATORY in order to EXAMINE THEIR PROPERTIES (for example, how well they self-assemble into filaments and what those filaments look like)."

And don't forget your "plausible" precursors to the MAIN FUNCTIONAL PARTS of the flagellum, not just the TRIVIAL flagellin comprising the simple whip -

-Where are the precursors to the ROTOR AND STATOR?

-How about the BUSHINGS that allow torque to pass through the cell membrane?

-And where did all of the GENETIC ASSEMBLY INSTRUCTIONS come from - where are their precursors?

-How did the ELECTROCHEMICAL POWER SUPPLY happen to get involved in the assembly in just such a way as to power an apparatus that cannot work without power?

These are just a few examples of the types of questions Matzke envisioned being answered in the
"fantastic years to come".

How's that research going for you folks?

Let's have the citations, by all means!

Steady Eddie

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Dec 20, 2015, 6:12:29 PM12/20/15
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LOL!
How do you like back-peddling with your foot in your mouth, Professor?

> > AGAIN:
> > Please show ANY research in the last TEN YEARS since the Pallin Matzke paper that has successfully
> > demonstrated that ONE protein component of ONE specific flagellum has be EXAPTED from ONE particular
> > protein that was doing a different job.
>
> Nick has cited some. You won't accept any evidence of that.

I haven't SEEN any evidence of such research being successful.
And I'm not asking Nick - YOU are the one that claims the research shows what Matzke prophesied.

Don't forget - cite AND QUOTE, just to prove that you aren't quote-bluffing.

Steady Eddie

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Dec 20, 2015, 6:17:29 PM12/20/15
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On Saturday, 19 December 2015 21:27:32 UTC-7, Nick Matzke wrote:
So, Nick, John tells me that you have cited some articles that demonstrate your prophesied research
program in full swing.
Any luck yet in identifying ONE component of ONE species of flagellum having ONE functional precursor
that demonstrates the evolutionary pathway to its present form and use?

Steady Eddie

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Dec 20, 2015, 6:27:31 PM12/20/15
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"Unfortunately the correction leaves out the well-known fact that removing the default filters (the "-F F" option on bl2seq) means that many homology hits with moderate e-values (like the paper's original e=10-4 cutoff, and the even weaker revised cutoff of basically 10-3) will be spurious hits and not truly indicative of homology. HOW ONE CAN THEN SAY THAT THIS DOESN'T EFFECT THE CONCLUSIONS, when the main conclusion was that all of the core flagellar proteins are homologous (which was what the paper said, going beyond the long-known and well-established fact that many of the axial proteins are homologous), IS BEYOND ME."
http://www.pandasthumb.org/archives/2007/06/correction_to_l.html

I think I'll be generous and just forget you brought that study up.

NEXT STUDY! Come on, keep them coming - according to you there are plenty!

RonO

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Dec 20, 2015, 9:02:31 PM12/20/15
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The ISCID did not get archived because they set up their web site so
that Wayback could not back it up. Did anyone save the ISCID "science"
journal. Just the article on flood science would have been worth having
it archived somewhere.

Ron Okimoto

Steady Eddie

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Dec 20, 2015, 10:42:29 PM12/20/15