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

[Nick Matzke]

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]

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]

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]

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]

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]

All you had to do was follow the link. Here's one:

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

[Steady Eddie]

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]

...Or do you just enjoy quote-bluffing?

[RonO]

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]

You can read the full text and SI for free (red link above the word "ABSTRACT").

[Ray Martinez]

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]

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]

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]

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]

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]

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]

Be serious. You've never read any scientific papers. Did you read this
one, as you imply without actually saying??

[Nick Matzke]

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]

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]

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]

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]

Where's your evidence of QUOTE MINING?
Put up or shut up.

[Steady Eddie]

Good idea.

[Steady Eddie]

Yes, QUOTE BLUFFS are always "PROBLEMATIC" for you jokers.

[Steady Eddie]

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]

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]

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]

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]

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]

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]

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]

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]

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]

"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]

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]

On Saturday, 19 December 2015 21:22:40 UTC-7, Nick Matzke wrote:

Do you think those were just random mutations, or some kind of pre-programmed
distress protocol?

> 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

Let's start with step 1, shall we?

"Step 1. mutations increase intracellular levels of phosphorylated NtrC"
What mutations are you talking about here?

"Step 2 .a switch-of-function mutation that redirects NtrC away from nitrogen uptake and toward its novel function as a flagellar regulator"
Okay, I can see that there's no way you are talking about RANDOM mutations getting such consistent
results.
So, what you call "mutations", I call "adaptations".

[Nick Matzke]

There are many mutations. Only the few that help improve bacterial movement cause the bacteria to end up in new parts of the agar plate where food is abundant. Having lots of food, these lucky mutants replicate more and soon the vast majority of the bacterial population have the beneficial mutation.

The student who discovered this literally didn't know it was going on. He accidentally left some agar plates too long, and then found the bacterial colonies had grown much further than should have been possible for non-motile bacteria. They did the sequencing and discovered the mutations responsible.

So yes, it's an adaptation, but adaptations is just random mutation + natural selection. Here, it modified a protein being used in a totally different system to fix a flagellar system that was non-functional due to researchers having knocked out the native protein. In other words, "ONE of the subunits of ONE particular flagellum was EXAPTED from its immediate precursor function" -- exactly what you requested.

Please admit that your challenge on this point has been met, and that the natural process of random mutation + natural selection can at least produce adaptations/exaptations of this sort, at least sometimes. If you don't, you're not a serious person and I won't discuss anything else with you.

Cheers,
Nick

[Steady Eddie]

Perhaps, sometimes, on fabulously rare occasions. And mutation may well be the cause in this case, but:

Please admit that adaptation in REAL populations in the REAL world is due to random ALLELE FREQUENCY
VARIATION + natural selection, based on PRE-EXISTING alleles, and generally has nothing to do with
MUTATIONS.

Further, please admit that this arrangement of a built-in redundancy for such a vital function could be a
demonstration of THE FORETHOUGHT AND THOROUGHNESS OF THE CREATOR'S DESIGN, making the
entire system even more complex and robust than previously thought.

[Steady Eddie]

On Saturday, 19 December 2015 07:07:35 UTC-7, Nick Matzke wrote:
> 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

Hey, Nick, while you're handy, did you take my taxpayer's money, intended for SERIOUS RESEARCH, to
conduct your pointless political "study"?

"If Matzke used TAXPAYER FUNDS intended to underwrite SERIOUS SCIENTIFIC RESEARCH to produce
this silly piece about the politics of the evolution debate, then the National Science Foundation should
consider asking for some of its GRANT MONEY BACK."
-John West
Did Nick Matzke Misuse National Science Foundation Money Intended to Fund Science Research?

http://www.evolutionnews.org/2015/12/did_nick_matzke101761.html

"A more serious issue is WHETHER MATZKE MISAPPROPRIATED TAXPAYER FUNDS in order to write his
article. Matzke discloses in the article's acknowledgements that his research was FUNDED BY TWO
NATIONAL SCIENCE FOUNDATION GRANTS. But if you look up those grants, they appear to have
NOTHING TO DO WITH THE ARTICLE HE PUBLISHED.

Indeed, NSF Grant 0919124 is a $422,000 grant intended to "develop BIVALVE MOLLUSCS as a
preeminent model for evolutionary studies...." And NSF Grant DBI-1300426 is a $12 million+ grant for the
National Institute for Mathematical and Biological Synthesis, which told the NSF it would "provide scientific
insights into problems such as the control of INVASIVE SPECIES, limiting impacts of INFECTIOUS
DISEASES, and suggesting new methods for DRUG DESIGN."

[jillery]

The existence of mutations in populations is well documented, both in
the lab and in the field. To deny the existence of mutations is
analogous to denying the existence of atoms. To argue that all
alleles were prepackaged from the beginning is analogous to arguing
that the Biblical Ark held two of every kind.

>Further, please admit that this arrangement of a built-in redundancy for such a vital function could be a
>demonstration of THE FORETHOUGHT AND THOROUGHNESS OF THE CREATOR'S DESIGN, making the
>entire system even more complex and robust than previously thought.

If you so argued, then you would have to explain why your Creator
didn't apply such FORETHOUGHT AND THOROUGHNESS to all functions. Is
that really what you want to say?
--
This space is intentionally not blank.

[Nick Matzke]

Already dealt with:
http://pandasthumb.org/archives/2015/12/discovery-insti-11.html

Your reply on the flagellum was sufficiently out there that I don't see how further engagement would be productive. (Reality is: mutations are common, not rare -- common enough that similar adaptations happened repeatedly in the study; bacterial colonies can be founded by single individuals so we know later mutations are new and not preexisting; and we know allelic variation is produced by the build-up of mutations, this is what the entire field of population genetics is about, basically.)

[Steady Eddie]

I agree, you wouldn't see much "productive" engagement out of me.
Unfortunately, I'm the type to ask questions of those who have been given much responsibility.

So, run back under your bridge if you want, or you can stick around and answer some direct questions.

Such as, what do you mean by this:

"...bacterial colonies can be founded by single individuals so we know later mutations are new and not preexisting..."

...and do you think there may be a problem with the logic behind this statement?

[Dana Tweedy]

Why do you assume that mutations are rare?

> And mutation may well be the cause in this case, but:
>
> Please admit that adaptation in REAL populations in the REAL world is due to random ALLELE FREQUENCY
> VARIATION + natural selection, based on PRE-EXISTING alleles, and generally has nothing to do with
> MUTATIONS.

No, because that would be false. Mutations are how the variations got
there to begin with.

>
> Further, please admit that this arrangement of a built-in redundancy for such a vital function could be a
> demonstration of THE FORETHOUGHT AND THOROUGHNESS OF THE CREATOR'S DESIGN, making the
> entire system even more complex and robust than previously thought.

Considering that most mutations are neutral, it hardly demonstrates
forethought, or thoroughness in the "creators design". Also, the fact
of extinction means that the same creator must have lacked forethought
in those cases.


DJT

[Steady Eddie]

On Saturday, 19 December 2015 07:07:35 UTC-7, Nick Matzke wrote:
> 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

My considered opinion after some reading:

What a Jackass. Not worth spending time on.

[August Rode]

Because...?

[Steady Eddie]

Matzke is obviously some political activist disguised in a lab coat.

[RAM]

No that is a false accusation and his publications belie your distorted snideness.

Yours, however, is an obviously transparent and arrogantly compulsive religious activism that is an undisguised willful ignorance of any science that demonstrates evolution.

Your religious beliefs are clearly the problem not evolution.

[Robert Camp]