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Minnich produced evidence that the flagellum was designed over a very long period of time
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RonO
Mar 15, 2016, 7:43:39 AM3/15/16
to talk-o...@moderators.isc.org
I think that this post deserves it's own thread. I looked up what
Minnich did with his flagellar results that he reported during the
Kitzmiller IDiot fiasco and found a couple of papers that gave evidence
counter to common ID explanations. A paper that he published just
before the Dover court case demonstrated a possible case of exaptation
of the flagellar master regulatory gene. What did Behe's critics claim
about exaptation?
He also published a paper described in my part of the post below that
was evidence that the flagellar tail genes evolved over a very long
period of time. I do not know the rate of flagellar gene evolution, but
the proteins are so divergent after obviously evolving by gene
duplication that there are at least 10s of millions of years of
evolution between them and probably over a hundred million between
several of them. This just means that the first tail protein evolved
and it took a very long time for the entire family to evolve and for the
flagellum to become what we see today.
This result means nothing to guys like Behe and Denton that already
accept that biological evolution is fact and that life evolved over
billions of years, but what about most IDiots that still claim to be
IDiots in the face of decades of failure? Here is evidence produced by
a fellow IDiot that if your designer made the flagellum that he made it
over a very long period of time. The first flagellum may have had only
one type of tail protein for an extended period (millions of years).
There was a gene duplication and you would have two identical protein
genes at first, but one copy diverged enough to evolve a different
function and started to be added to the tail at a different time in tail
development. That copy then duplicated multiple times and some of the
products of those duplication events evolved new functions that added to
the tail.
What do the IDiots do with this type of information when they just want
to lie to themselves about IC and ignore the fact that Behe is telling
the rubes that evolution happened and that he is just talking about his
designer tweeking his designs into existence? Behe has no issue with
the fact that the flagellum may have evolved a couple billion years ago.
Behe's blood clotting and immune systems evolved over 400 million
years ago. Minnich produced evidence that it was tweeking of the
flagellum over millions of years to generate the flagellum that we have
today.
How does that fit into your IDiot alternative?
REPOST:
On 3/7/2016 6:31 PM, jillery wrote:
> So the other Dover trial IDiot did some experiments which he claims
> disproves some of the conclusions of Lenski's LTEE:
>
> <http://jb.asm.org/content/early/2016/01/28/JB.00831-15>
>
> <http://tinyurl.com/zgqu9mk>
>
> Short version: By deleting specific genes involved in E.coli
> metabolism, the authors got E.coli populations to rapidly generate
> multiple strains able to metabolize citrate in oxic environments. From
> this, they conclude that these mutations aren't especially rare among
> E.coli populations, and so isn't evidence of speciation events, as
> claimed by LTEE scientists.
>
> Also the authors conclude that these mutations don't involve the
> creation of new genetic information.
>
> Not surprisingly, those involved with the LTEE drafted a reply:
>
>
<https://telliamedrevisited.wordpress.com/2016/02/20/on-the-evolution-of-citrate-use/>
>
> <http://tinyurl.com/zma9oqx>
>
> Short version: These mutations do in fact involve new information,
> which is necessary to transport citrate through the cell membrane in
> oxic conditions, and also to use citrate as a sole carbon source.
>
> Equally important, these new genes didn't appear de novo, but instead
> were duplications and modifications of existing genes.
>
> Minnich's population's ability to rapidly generate multiple mutations
> is something LTEE already did and reported in 2008.
>
> These cites, accompanied by some interesting comments, are available
> here:
>
>
<http://sandwalk.blogspot.com/2016/02/an-intelligent-design-creationist.html>
>
> <http://tinyurl.com/jttph2k>
>
> One comment I found particularly ironic is that Minnich's population's
> multiple and rapid mutations is evidence against fellow IDiot Michael
> Behe's hypothesis, that advantageous mutations are too rare to explain
> natural selection and speciation.
> --
> This space is intentionally not blank.
>
I just looked up what Minnich has done with the flagellum. Before he
testified he published a paper that the master regulator for the
flagellum FlhD/FlhC operon didn't just regulate flagellar proteins, but
had other functions in the cell. This is consistent with what is
claimed by real scientists about biological evolution using something
that was doing one thing but then using it for some other process. It
is one of the things that Behe has to deal with when he talks about what
an IC system is. A lot of these genes did other things in the cells. I
do not recall this coming up in the court case, but Minnich had just
published in July 2004.
http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.26814-0#tab2
What seems crazy is that he published a paper on a family of 6 flagellar
tail genes and had the sequence comparisons to tell him something about
how they evolved from Sept. 2000
http://jb.asm.org/content/182/17/5001.long
5 are relatively closely related but a 6th is an outlier. It looks like
there was just one flagellar gene at the beginning and then there was a
gene duplication. The two flagellar genes may have been the only ones
needed for some time and then some significant period of time after the
initial duplication there were multiple subsequent duplications of one
of the original duplicated copies to form all the others.
He has a phylogeny for these proteins to show how closely related they
are to each other. He knows what three of them do and guess what?
The data is consistent with FljL and FljJ being the first two of the
group to exist. This just means that they were the first duplication.
The tree is unrooted, but from the sequence it looks like FljL is more
closely related to the 4 others than is FljJ. This is consistent with a
fairly long period of time going by and then FljL duplicated and there
were subsequent duplications of the FljL family.
What should be a significant blow to IC is what they know of what these
genes do. Their function is consistent with them evolving sequentially.
I am not making this junk up. Minnich knew this back in 2000.
FljJ is the 29 kDa protein that builds the portion of the tail closest
to body of the bacteria.
FljL is the 27 kDa protein that builds the portion of the tail right
after FljJ.
FljK is the 25 kDa protein that builds the portion of the tail after FljL.
You have to understand that the flagellar tail is built from the tip
out. So it is extended from the distal tip and not extruded from the
bacteria.
The data is consistent with FljL being derived from the protein that
initially made the tail. FljJ still is the first tail protein to be
layed down. When the genes duplicated they would have been identical,
but then the FljL copy diverged and took on a new function and was added
to the tail after FljJ.
The FljL then duplicated at some later time and the FljK gene diverged
and took on a new function and was put down in the tail after FljL.
You can't make this junk up. Minnich had the data indicating that his
flagellar genes evolved in a sensible manner over an extended period of
time and he just forgets about reality to support IDiocy.
This is consistent with the evolution of the flagellum where FljJ made
the initial tail. Then FljL evolved from duplication of FljJ and
eventually evolved to add something new to the tail. Then FljK evolved
from FljL to again evolve a new function that added to the tail.
Minnich is not the type of scientists that you want to get your science
from. He worked up some of the genes that he discovered and found them
to support the biological evolution of the flagellum over an extended
period of time and just ignored reality to support his religious beliefs.
END REPOST:
Ron Okimoto
Minnich did with his flagellar results that he reported during the
Kitzmiller IDiot fiasco and found a couple of papers that gave evidence
counter to common ID explanations. A paper that he published just
before the Dover court case demonstrated a possible case of exaptation
of the flagellar master regulatory gene. What did Behe's critics claim
about exaptation?
He also published a paper described in my part of the post below that
was evidence that the flagellar tail genes evolved over a very long
period of time. I do not know the rate of flagellar gene evolution, but
the proteins are so divergent after obviously evolving by gene
duplication that there are at least 10s of millions of years of
evolution between them and probably over a hundred million between
several of them. This just means that the first tail protein evolved
and it took a very long time for the entire family to evolve and for the
flagellum to become what we see today.
This result means nothing to guys like Behe and Denton that already
accept that biological evolution is fact and that life evolved over
billions of years, but what about most IDiots that still claim to be
IDiots in the face of decades of failure? Here is evidence produced by
a fellow IDiot that if your designer made the flagellum that he made it
over a very long period of time. The first flagellum may have had only
one type of tail protein for an extended period (millions of years).
There was a gene duplication and you would have two identical protein
genes at first, but one copy diverged enough to evolve a different
function and started to be added to the tail at a different time in tail
development. That copy then duplicated multiple times and some of the
products of those duplication events evolved new functions that added to
the tail.
What do the IDiots do with this type of information when they just want
to lie to themselves about IC and ignore the fact that Behe is telling
the rubes that evolution happened and that he is just talking about his
designer tweeking his designs into existence? Behe has no issue with
the fact that the flagellum may have evolved a couple billion years ago.
Behe's blood clotting and immune systems evolved over 400 million
years ago. Minnich produced evidence that it was tweeking of the
flagellum over millions of years to generate the flagellum that we have
today.
How does that fit into your IDiot alternative?
REPOST:
On 3/7/2016 6:31 PM, jillery wrote:
> So the other Dover trial IDiot did some experiments which he claims
> disproves some of the conclusions of Lenski's LTEE:
>
> <http://jb.asm.org/content/early/2016/01/28/JB.00831-15>
>
> <http://tinyurl.com/zgqu9mk>
>
> Short version: By deleting specific genes involved in E.coli
> metabolism, the authors got E.coli populations to rapidly generate
> multiple strains able to metabolize citrate in oxic environments. From
> this, they conclude that these mutations aren't especially rare among
> E.coli populations, and so isn't evidence of speciation events, as
> claimed by LTEE scientists.
>
> Also the authors conclude that these mutations don't involve the
> creation of new genetic information.
>
> Not surprisingly, those involved with the LTEE drafted a reply:
>
>
<https://telliamedrevisited.wordpress.com/2016/02/20/on-the-evolution-of-citrate-use/>
>
> <http://tinyurl.com/zma9oqx>
>
> Short version: These mutations do in fact involve new information,
> which is necessary to transport citrate through the cell membrane in
> oxic conditions, and also to use citrate as a sole carbon source.
>
> Equally important, these new genes didn't appear de novo, but instead
> were duplications and modifications of existing genes.
>
> Minnich's population's ability to rapidly generate multiple mutations
> is something LTEE already did and reported in 2008.
>
> These cites, accompanied by some interesting comments, are available
> here:
>
>
<http://sandwalk.blogspot.com/2016/02/an-intelligent-design-creationist.html>
>
> <http://tinyurl.com/jttph2k>
>
> One comment I found particularly ironic is that Minnich's population's
> multiple and rapid mutations is evidence against fellow IDiot Michael
> Behe's hypothesis, that advantageous mutations are too rare to explain
> natural selection and speciation.
> --
> This space is intentionally not blank.
>
I just looked up what Minnich has done with the flagellum. Before he
testified he published a paper that the master regulator for the
flagellum FlhD/FlhC operon didn't just regulate flagellar proteins, but
had other functions in the cell. This is consistent with what is
claimed by real scientists about biological evolution using something
that was doing one thing but then using it for some other process. It
is one of the things that Behe has to deal with when he talks about what
an IC system is. A lot of these genes did other things in the cells. I
do not recall this coming up in the court case, but Minnich had just
published in July 2004.
http://mic.microbiologyresearch.org/content/journal/micro/10.1099/mic.0.26814-0#tab2
What seems crazy is that he published a paper on a family of 6 flagellar
tail genes and had the sequence comparisons to tell him something about
how they evolved from Sept. 2000
http://jb.asm.org/content/182/17/5001.long
5 are relatively closely related but a 6th is an outlier. It looks like
there was just one flagellar gene at the beginning and then there was a
gene duplication. The two flagellar genes may have been the only ones
needed for some time and then some significant period of time after the
initial duplication there were multiple subsequent duplications of one
of the original duplicated copies to form all the others.
He has a phylogeny for these proteins to show how closely related they
are to each other. He knows what three of them do and guess what?
The data is consistent with FljL and FljJ being the first two of the
group to exist. This just means that they were the first duplication.
The tree is unrooted, but from the sequence it looks like FljL is more
closely related to the 4 others than is FljJ. This is consistent with a
fairly long period of time going by and then FljL duplicated and there
were subsequent duplications of the FljL family.
What should be a significant blow to IC is what they know of what these
genes do. Their function is consistent with them evolving sequentially.
I am not making this junk up. Minnich knew this back in 2000.
FljJ is the 29 kDa protein that builds the portion of the tail closest
to body of the bacteria.
FljL is the 27 kDa protein that builds the portion of the tail right
after FljJ.
FljK is the 25 kDa protein that builds the portion of the tail after FljL.
You have to understand that the flagellar tail is built from the tip
out. So it is extended from the distal tip and not extruded from the
bacteria.
The data is consistent with FljL being derived from the protein that
initially made the tail. FljJ still is the first tail protein to be
layed down. When the genes duplicated they would have been identical,
but then the FljL copy diverged and took on a new function and was added
to the tail after FljJ.
The FljL then duplicated at some later time and the FljK gene diverged
and took on a new function and was put down in the tail after FljL.
You can't make this junk up. Minnich had the data indicating that his
flagellar genes evolved in a sensible manner over an extended period of
time and he just forgets about reality to support IDiocy.
This is consistent with the evolution of the flagellum where FljJ made
the initial tail. Then FljL evolved from duplication of FljJ and
eventually evolved to add something new to the tail. Then FljK evolved
from FljL to again evolve a new function that added to the tail.
Minnich is not the type of scientists that you want to get your science
from. He worked up some of the genes that he discovered and found them
to support the biological evolution of the flagellum over an extended
period of time and just ignored reality to support his religious beliefs.
END REPOST:
Ron Okimoto
jillery
Mar 15, 2016, 2:43:37 PM3/15/16
to talk-o...@moderators.isc.org
example, Behe can't make up his mind about IC parts. First he says
parts have to evolve for the function they will perform in the IC
system. Then he admits parts have additional functions. First he
says it's the parts themselves that count. Then he claims it's the
functions that are the key, not the parts. First he defines IC
without defining "well-matched". Then he argues only precisely
matched parts count, totally ignoring their function.
David Deutsch warned of such ad hoc argumentation. He gave the
analogy of the myth of Persephone, that she has to live part of the
year with Hades, and so cause her mother Demeter to grieve, which
causes winter. This hypothesis is testable but not rigorous, ie the
details have no explanatory power. And when it's pointed out that the
southern hemisphere has winter opposite the northern hemisphere,
mythologists could make an ad hoc claim that Demeter merely pushes the
fixed amount of heat from one side of the Earth to the other.
IDiots' arguments for IC, and by extension ID, are very much ad hoc
myths.
RonO
Mar 16, 2016, 7:38:36 AM3/16/16
to talk-o...@moderators.isc.org
creationist rubes with. There may be alternative explanations of what
IDiots call IC, but IC is literally just something to pretend that life
did not evolve on this planet. It is so bankrupt that even Behe admits
that life evolved on this planet and all he thinks that IC might be
evidence for is that some designer messes with some things at some time
in the distant past. He seems to be stuck out past around 400 million
years ago, so Behe admits that his designer may no longer exist.
IC is not the IDiot alternative. Behe uses it to support his tweeking
and IDiots like Nyikos use it to support other stupidity like space
alien designers. Denton just thinks that the designer designed the
basic laws of nature so that life would evolve somewhere in the universe
those laws of nature created.
>
> David Deutsch warned of such ad hoc argumentation. He gave the
> analogy of the myth of Persephone, that she has to live part of the
> year with Hades, and so cause her mother Demeter to grieve, which
> causes winter. This hypothesis is testable but not rigorous, ie the
> details have no explanatory power. And when it's pointed out that the
> southern hemisphere has winter opposite the northern hemisphere,
> mythologists could make an ad hoc claim that Demeter merely pushes the
> fixed amount of heat from one side of the Earth to the other.
>
> IDiots' arguments for IC, and by extension ID, are very much ad hoc
> myths.
That is one of the reasons no IDiots want to put up their alternative
because their failure or success does not depend on whether or not the
IDiot type of IC actually exists in nature. They do not care that Behe
never has demonstrated that his type of IC actually exists because they
do not want to know what IC would tell them about their designer.
Really, what if Behe was actually able to test and verify his notion of
IC and he found out that the intelligent designer tweeked the flagellum
2 billion years ago, and that the designer had used parts whose
ancestors had existed for hundreds of millions of years before the
tweeking happened. How many IDiots would want to know that? Look what
Minnich's work on the flagellar genes told him about where the parts of
the flagellum came from. IDiots do not want to know these things
because then they would know that their alternative is bogus.
Behe even tells guys like Grasso that their creationist alternative is
bogus, but IDiots like Grasso sill lap up the stupidity about IC with no
regard to reality.
Ron Okimoto
Steady Eddie
Mar 16, 2016, 10:48:36 PM3/16/16
to talk-o...@moderators.isc.org
jillery
Mar 17, 2016, 2:28:32 AM3/17/16
to talk-o...@moderators.isc.org
appearance of novel features, that would be strong evidence against
biological evolution, as described by Behe in DBB. Since the evidence
is not of de novo and abrupt appearance, but of modification of
existing parts over long periods of time, that is evidence not of IC
but of biological evolution, as described by Darwin in OoS.
HTH but I doubt it.
RonO
Mar 17, 2016, 7:33:32 AM3/17/16
to talk-o...@moderators.isc.org
flagellum evolved with 10s of millions of years separating their
existence. Just like it matters for how long the light of super nova
explosions take to reach earth from galaxies millions of light years
away. When the JWs believed that each day was only 7,000 years long it
would have made a big difference. Now all you have to worry about is
whether the sun and moon existed before or after the flagellum evolved.
Beats me how they decided that the Bible story was wrong. Do you know
how they made the decision to say that the sun and moon were not made on
the fourth day? When is your interpretation going to come to the
realization that angiosperm fruit trees really were not created on the
third day? It must have been a heck of a debate to change the literal
interpretation, since guys like Grasso likely still believe that the sun
and moon were created on the fourth day.
So in your alternative how was the flagellum created? Minnich's
evidence indicates that it evolved over a very long period of time. By
mechanisms that we have documented occur natually. A much longer period
of time than how long ago we separated from the chimp lineage. It looks
like it took 10s of millions of years to evolve the flagellum, so what
is your alternative? What did the designer do and how did he do it?
Ron Okimoto
Steady Eddie
Mar 22, 2016, 2:28:15 PM3/22/16
to talk-o...@moderators.isc.org
Quotation, please...
RonO
Mar 22, 2016, 7:13:16 PM3/22/16
to talk-o...@moderators.isc.org
think it means to refer to the flagellar protein "family," and then put
up the genetic relationship within the family? Read the paper. They
actually acknowledge that the proteins are related as a "family."
There is no reason to put up and calculate a phylogeny unless the
proteins are derived from a common ancestral protein. Just think about
it for a minute.
The paper doesn't have to state the mechanism of how the family of
proteins was derived because it is obviously gene duplication. Not only
that, but you can tell the order of the gene duplication events from the
phylogeny that the paper provides.
Learn something about molecular biology.
What do you think that Behe would make of the results? He already
acknowledges that biological evolution is a fact of nature. There is
absolutely no way that he would deny that gene duplication happened. It
is a known mechanism and you know for a fact that we can document it
happening today. So what is your beef? Do you think that Minnich
doesn't believe that evolution is a fact of nature? Demonstrate that he
disagrees with Behe. They both seem to be tweekers as far as I can tell.
Ron Okimoto
Steady Eddie
Mar 22, 2016, 8:28:15 PM3/22/16
to talk-o...@moderators.isc.org
Is anybody surprised?
The reason Minnich doesn't attribute similarities to Darwinian evolution is that it is already demonstrated
that Darwinian evolution (gene duplication, or anything else) is insufficient to cause the changes required
for one protein to turn into another functional, useful protein.
Read up on it:
The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
Ann K. Gauger, Douglas D. Axe
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
Enzyme Families--Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family
Mariclair A. Reeves, Ann K. Gauger, Douglas D. Axe
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.4
Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention--Selection Itself Is Not Inventive
Douglas D. Axe, Ann K. Gauger
http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2015.2
You may have missed the above papers, but I doubt Minnich did.
RonO
Mar 22, 2016, 9:33:16 PM3/22/16
to talk-o...@moderators.isc.org
QUOTE:
To facilitate comparison of members of the flagellin gene family, the
nucleotide sequences of the flagellin genes were aligned. There were 455
variable sites in the 822-bp sequence. Most of the variable sites were
found in the fljJ gene, which encodes the 29-kDa flagellin. The most
similar pair of genes, fljM andfljN, contained 46 differences (5.6%),
indicating that there has been considerable nucleotide divergence among
all of the genes.
END QUOTE:
What does "indicating that there has been considerable nucleotide
divergence among all of the genes." mean? There was a founder common
ancestral sequence and all these genes have diverged from it, and the
phylogeny that they put up in figure 1 tells you something about the
order of the duplication and divergence events.
>
> The reason Minnich doesn't attribute similarities to Darwinian evolution is that it is already demonstrated
> that Darwinian evolution (gene duplication, or anything else) is insufficient to cause the changes required
> for one protein to turn into another functional, useful protein.
doesn't claim that biological evolution does not happen. So demonstate
what you claim.
>
> Read up on it:
>
> The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway
> Ann K. Gauger, Douglas D. Axe
> http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1
>
> Enzyme Families--Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family
> Mariclair A. Reeves, Ann K. Gauger, Douglas D. Axe
> http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2014.4
>
> Model and Laboratory Demonstrations That Evolutionary Optimization Works Well Only If Preceded by Invention--Selection Itself Is Not Inventive
> Douglas D. Axe, Ann K. Gauger
> http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2015.2
>
> You may have missed the above papers, but I doubt Minnich did.
>
even know what these papers are talking about. Go for it tell me why
these papers negate what is obvious. Where is it in this stupidity
where they demonstrate that Minnich thinks the way you claim. It would
be nice if they demonstrated that they had some designer that could do
their designing. Since they have none what does their naysaying amount
to? Why would this junk negate the flagellar protein story and the
obvious relationship between the genes? Go for it.
Ron Okimoto
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