Saturday, March 19, 2011

UD - "Congrats Nick Matzke for Publishing ID Sympathetic Paper in Nature!"

This may be the early beginnings of a new partnership...

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**they won’t stay that way.

Also…

jonnyb, I looked over your site and I can already say for sure that we have a TON that we could
 work on! I’ve been looking for an IDer with a programming background for something… Well, I’ll
 just email you when I get the chance about it.

I’m currently set to publish three books on ID with an “emergent” publisher that is just
beginning to orient itself (it’s sole proprietor is already giving me the means to remain
pseudonymous).

There is one book I have in mind (outside the three for Janus) in particular that I may want to
 look into submitting a manuscript of for your consideration. Since it would help if someone had
 a programming background to understand it, and I’m especially glad to see you know a thing or
 two about Linux!

I’ll drop you an email soon with the details once I get the chance…
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UD - "Congrats Nick Matzke for Publishing ID Sympathetic Paper in Nature!"

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John Sanford’s book, “Genetic Entropy” was one of the books shipped to me once the IDEA
Club I founded was approved. It took a few reads for it to sink in, but it definitely convinced me
 that front-loading had it’s fair share of limits.

More importantly it changed the way I think about neutral mutations; though they may not have
 any initial effects at the level of phenotype, the accumulating effects that follow generations
later guarantee won’t stay that way.
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UD - "We Will if You Will"

 I think this might be the first time outside of Crypto-IDEA that I've used the term cybermormon.

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Matteo,

You pretty much summed up everything that I think is wrong with the first generation of
cybermormons that have started to take any chance they can to spam on about non-belief.

I’d explain the origins of that conjunction, but it would require linking to a video that might
not fit the tastes of UD.

To the mods on UD: Is it okay if I link to a video featuring a consistently swearing agnostic
ranting against atheists (aka “…the Jehovah’s Witnesses of Youtube”)?

@ NielBJ-“His reasoning may be flawed, and it is certainly legitimate to point out where he
has gone wrong.”

Then by all means, please do so.



I do have a question though about what exactly distinguishes an IDer from a non-IDer. Here’s
 the definition that I typically refer to:

http://www.discovery.org/v/2

Now let’s say I do feel that taking a design-theoretic approach leads to a far greater
understanding of physical features than non-telic alternatives, but don’t actually hold that a
designer actually exists. Under this view I would hold that agency is sort of like the typical
textbook atom diagram which while not correct, does allow people to understand what
someone is actually working with.

Am I no longer in the ID camp if I take this sort of view?
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Friday, March 18, 2011

The Universe Is Haunted: Reflections on the "Nature of Nature" - First comment

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Just ordered it! I've been anticipating this for a while ever since Dembski
 mentioned it on Uncommon Descent. Glad to see such a diverse set of contributions whether
it be on the pro-ID side or non-ID (e.g. Michael Shermer).
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Thursday, March 17, 2011

Second Comment on UD - "The Conway Morris Disclaimer"

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Dembski,

If I were devoting this comment strictly to explaining how much your work has changed my
worldview, I'm not sure I would find the words to explain it (Assuming that I would be able to
finish it of course).

Along with the other folks with the CSC, you really shifted my focus in life permanently, and I
mean that in a good way. We've met briefly over a year ago (signing a copy of the Design of
Life), and I really didn't say much because frankly I didn't know where to start.

In the coming years I hope to really boost the number of people who value your work for what it
 is. While we definitely have some disagreements in some areas, they are trivial compared to
the big picture that is ID.

Very glad to be a part of this now, and for everyone else, thanks for the welcomes/dialogue in
the last post about front-loading. I can tell I will be a regular visitor here for some time to come.
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More on "Michael Behe Hasn't Been Refuted on the Flagellum"

In cases where I make multiple comments in short succession and don't have access to my key or VPN, I'll just sign multiple comments at once.

As I have promised...

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Stuart Rayner said: "So no one remembers how in the dover trial Behe admitted under
oath that intelligent design wasn't science..."


No one remembers because that's not what he said. You must be referring to the claim that
for ID to be science astrology would be included as well so therefore ID isn't science. Actually,
 there's more to the picture. His definition of science really doesn't differ much from the NAS.
 Casey Luskin did a post several years ago (and you thought Dover would be the nail in the
coffin of ID - boy did that turn out to be wrong) pointing out that the NAS definition leads to
the same conclusions as the one Behe presented:


http://www.evolutionnews.org/2005/10/500_years_ago_geocentrism_aamp_astrology001085.html


The problem with astrology isn't that it's not science, it's just plain wrong. Period. It's been
tested and found wanting.


<i>"...and that he had read none of the material that showed his hypothesis to be, at the
very least, flawed?"</i>


Once again you fail to recall an accurate account of what actually happen in that local district
 case. You must be referring to the claim that Behe was presented with literature that
(supposedly) gave detailed evolutionary origins of the immune system. This has been
covered on ENV before:


http://www.evolutionnews.org/2009/07/ken_millers_only_a_theory_atta_1023151.html


http://www.evolutionnews.org/2010/02/ken_miller_and_the_evolution_o031531.html


http://www.evolutionnews.org/2010/12/five_years_later_evolutionary_042001.html


Behe didn't read the material because (like many counter arguments made against him) it
 wasn't addressed at the anything he said.


<i>"When building a house, you don't make it rely on hundreds of parts that need to be
exactly right, so why would it be any different for a simple propulsion system?"</i>


Correct me if I'm wrong but I believe a house <i>does</i> require certain constraints to be
met in it's construction. The same goes for the flagellum. Below in a comment Luskin
highlighted the fact that showing the origin of parts alone doesn't mean we know for sure an
evolutionary origin to the bacterial flagellum is confirmed. Questions go from availability,
synchronization, localization, interfering proteins, interfacing, assembly order, to general
configuration.



SECOND COMMENT


"I have also read that certain long term tests with bacteria have shown that anything
requiring more than two mutations is hard to come by."



Not just any mutations per se, but in cases where there is nothing that is selectable enough
 to replace the wildtype unless two complementary changes occur. Here you have the
problem of evolution being limited by the fact that selection is pretty much incapable of
improving upon anything.



Ralph Seelke has done some pretty cool stuff in this area as well as Doug Axe (ID the Future
 recently did some interviews with him regarding his latest paper on this subject). Not to
mention Behe's latest paper on this very subject.



http://www.evolutionnews.org/2010/12/michael_behes_first_rule_of_ad041461.html



But nonetheless you're pretty much right, you would be very hard pressed to find anything
 requiring multiple amino acid changes before selective benefit is present to easily be within
 the reach of evolutionary processes.

All in all the limit to evolutionary processes stem not so much from selection by itself being
 ineffective but rather because it frequently has nothing significant to "select" in the first place.

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Wednesday, March 16, 2011

Second Comment on Design Matrix - "Convergence Website"

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I've had an interest in Simon's views on evolution ever since I heard of his book, "Life's Solution."
While I haven't had the chance to read it yet, I've heard elsewhere that he does hold a somewhat
telic view of evolution, so I look forward to what he presents on this site.

At any rate, he definitely is a go-to researcher on the Cambrian era.
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More Comments on Homologous Legs

UPDATE: The dialogue on this blog has given me an idea that I probably won't be able to cash in on until several years from now. Hopefully it will encourage people to raise the level of discourse on any subject really.

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"If i was going to say that, I would have. I did not..."


You did claim that Behe has done nothing beyond proofs by assertion, so I would think that

would apply to what he's written so far.


"I'm claiming Micheal Behe repeatedly restates that irreducible complexity is true when each

of his arguments he uses to support that claim has been contradicted, repeatedly."


Now we're beginning to scratch the surface here. Can you elaborate on what these repeated

contradictions are? Miller? Matzke? Anything along those lines?


+


"If I asserted "the sky is blue", and then wondered off into the distance, would you shout after

me "that was a Bare Assertion Fallacy you fool!"."


No, I consider that to be almost axiomatic, but if I someone argued that ID was either just as

self-evident or just as verifiably wrong, I would ask for a little more than just a bare assertion.


"I may make a 'Bare Assertion', but that does not mean it is unsupported, only that I have

not provided said 'support'."


Then why not provide the said support?


And we find no disagreement here on the bible.


"So, having addressed your implied claim that my assertion was 'unsupported',"


You admitted that you didn't provide said support so how did you address it?


"Arguing on the internet ROCKS! Love you!"


I wouldn't even consider this anywhere near an argument, I think you've been pretty civil so

 far.


+


"These posts are not written with the intention of being anywhere near argumentatively

airtight or particularly persuasive to those who are ID proponents."


This makes more sense in that case then. I thus won't hold you to a standard that nobody

 should intend to strive for since every disagreement is not settled by making the the other

 side change their mind.


+


"Assertion is fine if everyone already can see your point and follow your logic implicitly."


I guess that's a good description of your approach then.
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Second (sort of) Comment on Homologous Legs

Lesson for all: Don't use bare assertions to accuse someone of making them.

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"No matter how much evidence and arguments are given in contradiction to irreducible
complexity, he still claims it is?"

Making a claim without substantiating it so...

"Logical Fallacy Fail!"

QED
http://en.wikipedia.org/wiki/Proof_by_assertion
http://en.wikipedia.org/wiki/Bare_assertion_falla...

If you're going to claim Behe simply wrote two books based around bare assertion alone, then
at least give specific examples. Then the irony of your comment won't be as apparent.
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Comment on the Definition and Nature of Irreducible Complexity

 This is continued from my last comments in the previous post. Because I'm dealing with a lot of stuff related to how Irreducible Complexity is defined (as well as misdefined), these comments require a separate post altogether.

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drs said: "Perhaps my understanding of "Irreducibly Complex" is incorrect..."

While it's not a total misunderstanding, I think it misses the point.

"...but I thought the concept meant that certain systems are too complex to have evolved."

Here's a good starting point on this subject:

Primer: Irreducible Complexity in a Nutshell

And in case you have some beef with the mousetrap example because an intelligent agent
can modify the parts to get a one-piece system (in which the analogy would no longer apply to
 features in question), see the following:

A Mousetrap Defended: Response to Critics
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Tuesday, March 15, 2011

My First (Really???) Comment on Uncommon Descent

I have followed this blog every once and a while but until a friend took the initiative for me, I was never sure about whether or not I should take part in any of the discussions on UD.

Can't believe this is my first comment there...

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For several years now, I have considered joining a site like this. A friend finally registered me
saying I could use the fresh air, so I guess that settles it.

I would say more but to keep under the radar there’s a limit to what I can say for now. I’ll just
state right now that I’m honored to be a part of a community like this - period.

In terms of physics, I think front-loading should almost universally be the default view for
anyone in the ID camp. So far as we can tell, such constraints have remained the same since
 the singularity.

What I do in my reasoning is I try and take a minimalist view on apparent intervention;
meaning that I start with the assumption that everything is front-loaded. From there I look for
 examples that place a limitation on how far this can go (abiogenesis for instance).

For this reason I totally agree with that last paragraph of yours, life and physics (along with
 chemistry) are in an entirely different class when it comes to the efficacy of front-loading
explanations. Unlike laws, the constituents of life depend on more than just pure existence
to achieve their purpose.

This reminds me of the “Humpty Dumpty” dilemma that Jonathan Wells has highlighted in
the past. Break a cell membrane so the contents leak, and you no longer have a living cell
despite the presence of organic materials.

I think this gives us a clue as to where we can draw the line on front-loading. Simply ask
yourself, “Does the presence of a given law, element, or some set of circumstances allow for
 living systems to thrive or does there appear to be something else added to the picture for
 this to happen?”

As an example, Meyer has repeated countless times the fact that DNA and it’s chemical
 properties by itself cannot arrange into anything functional, hence front-loading loses it’s
 potential in the origins of life.
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First Comments on Homologous Legs

A few years ago I figured it would be a matter of time before this blog would end up on Scienceblogs. While that hasn't happened, it seems like the teen turned young undergrad has scored the next best thing

MENTAL NOTE: Always take a moment to read the blog in question before giving it any kind of feedback...

Aside from the first two comments, this is the main one where I highlight my biggest criticism of the post in question, as well as Homologous Legs in general...

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"Charged rhetoric, bold sweeping conclusions and cursory analysis? Where have I heard those
things before? Surely not from Casey Luskin, the King of Bloated Rhetoric! My irony meter
melted."

Interesting...

"It’s not “outlandish rhetoric” if it’s true."

"Again, it’s not outlandish if it’s true."

"It’s descriptive and rather accurate, I think."

"I see no outlandish rhetoric here."

"...but, again, it’s hardly outlandish."

"Nothing bad here, just accurate and calm descriptors of Behe’s definitions. Note that the
authors do spend the majority of the paper backing up these specific claims, so they’re
hardly throwaway lines used for argumentative purposes only." (how?)

"It’s emotive and not all that defensible, but again, not outlandish by any stretch of the
imagination."

"Again, that’s rather light stuff. Nothing to get worked up over."
http://en.wikipedia.org/wiki/Proof_by_assertion
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Comments on "Michael Behe Hasn't Been Refuted on the Flagellum"

 Lately there seems to be a lot on ENV regarding Irreducibility and the Flagellum mainly because of a recent Quarterly Review of Biology Paper which Casey Luskin mentions here.

I've been waiting for posts like this for such a long time, particularly because I'm tired of hearing the same dead straw man over and over again which I will cover soon.

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I'm glad to see a post like this. Surprised at how the straw man Ken Miller first formulated is still
alive and well though.


If anything, the only criticism that doesn't receive enough attention from either side of the
debate is Matzke's Evolution in Brownian Space. I think me and Casey would agree on this,
namely that while Miller and many others tend to flatly misrepresent what Behe actually tries to
argue, Matzke at least tries to make responses that keep Behe in original context.


Bookmarking this as one of the better posts on Irreducibility. In a moment though, there's a few
things that need to be said about Miller's argument because it's so prevalent. I'll get to that in a
moment...
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Here's my second comment replying to Nick Matzke:

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There's a lot that needs to be asked and said in this area...

Nick Said: "And that most of the required proteins have known alternative functions in
nonflagellar systems. Oh well."

You mean this?

"Flagellum evolution in Nature Reviews Microbiology"

I would really like to know the rationale behind using Default BLAST search settings to come
to the conclusion that you did. Exactly how similar are these homologies you present and how
 would we know each flagellar protein came about from the homologies and not vice-versa?
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Saturday, March 5, 2011

Fifth/Sixth Comment and more on ENV - Reply to CRW

ieshttp://www.evolutionnews.org/2011/02/lobbyists_resort_to_myth-infor044241.html

I will digitally sign the comments on this post once I turn on my VPN again and paste the signed copies.

Update: Okay, I have done what I have promised.

Here's this comment below, followed by this one thereafter.


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While I wholeheartedly doubt the alleged efficacy of things such as horizontal gene transfer or
duplication (I think they both just shuffle information that's already there while not producing
anything new), I understand that time and space constraints make that a difficult topic to
address here, but nonetheless the following caught my attention:

"ID is religious but not of a particular religion."

So it's not of any particular religion but it's still religious? Could you elaborate on this?

"To assert "intelligence" logically implies a designer/creator. Call it god, Yahweh, Allah, whatever.
ID requires a designer, which means some supernatural force is required."

I am the intelligence behind this very comment, so by your logic I must be a supernatural entity
right?
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Now the next one:

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Now here I find some things worth disputing:

"Unfortunately, there has yet to be a biological trait or attribute that is irreducibly complex. All
of the core examples from ID can be shown to be sliding scales from more to less complex."

This is probably one of the most common misunderstandings of Behe's arguments - he was
not arguing that IC systems are impossible to evolve any more than it's "impossible" to win
the lottery. It might happen, but this is not something we should treat as a real likelihood.

Are you claiming that not a single cellular system is unable evolve piece-by-piece while
retaining the same basic function or are you rehashing Ken Miller's straw man?

I think a good start in clarifying this dispute can be found here:

http://www.discovery.org/a/3408

...the fact the positive mutation is shown regularly in at least microorganisms..."

Can you give me a few key examples? And how do you define "positive" mutation?

I think Ryan has tackled the rest of what I disagree with on your comment but in the
meantime I look forward to your response to what I had said/asked so far.
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