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What is "design" and how to detect it

SkyWriting

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Chimpanzees are our closest relatives and, as your article points out, the worm and fly are distant relatives.

I guess you're ignoring the title of the article.
Human, Fly and Worm Genome More Similar Than You Think
(Much LESS distant than our science preachers claimed.)

A Worm is More Like a Human Than Previously Thought
A Tiny Worm Challenges Evolution
Humans May Have Fewer Genes Than Worms
Scientists looking across human, fly and worm genomes find shared biology

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.”
 
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SkyWriting

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Why wouldn't those changes produce decay and disease in different species?Why are species different to begin with?

Because they are not related is one answer.
Good design is another.
Independently created is another.
 
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Loudmouth

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Because they are not related is one answer.
Good design is another.
Independently created is another.

Why couldn't separately created species look identical to one another?

Why do you think that separately created species look different from one another? What is the explanation?
 
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SkyWriting

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Why couldn't separately created species look identical to one another? Why do you think that separately created species look different from one another? What is the explanation?

If I take clay and make three bowls, they may or may not look identical.
There are thousands of reasons they may or may not look the same.
The technique
The material used
The coloring used
The time spent on each
etc.

8705903-three-handmade-clay-pots.jpg
 
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Loudmouth

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If I take clay and make three bowls, they may or may not look identical.
There are thousands of reasons they may or may not look the same.
The technique
The material used
The coloring used
The time spent on each
etc.

Obviously, all the life we see now is the product of biological reproduction. So why do species look different from each other while individual organisms look like their ancestors? What causes this? What is the basis for the inheritance of these traits?
 
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ChetSinger

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Then you would have to specify the version. From what I have seen, all of the versions have fatal flaws.
I don't feel like doing that kind of legwork. If you do, look for work Dr. Humphreys has done since he consulted with Dr. Hartnett. I think that's within the last 5 or 10 years, and includes Humphrey's development of a new metric.

I don't see why that justifies the rejection of scientific evidence in the defense of a dogmatic belief.
YMMV. What I'm saying is that my beliefs have developed because of my experiences with God. And they include supernatural experiences. God isn't bound by natural laws because he's above them: medical science says a man can't come back to life after being dead, yet Jesus did exactly that, for both himself and for others.
 
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sfs

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I guess you're ignoring the title of the article.
Human, Fly and Worm Genome More Similar Than You Think
I guess you're ignoring the contents of the article: "Their commonalities reflect their shared ancestry".

(Much LESS distant than our science preachers claimed.)
Funny -- that's not in the article.

A Worm is More Like a Human Than Previously Thought
A Tiny Worm Challenges Evolution
Humans May Have Fewer Genes Than Worms
Are you quoting something here? It's certainly not from the Nat Geo article or the press release.

Scientists looking across human, fly and worm genomes find shared biology
Well, duh. That's exactly what they were looking for.

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content,” found that Y chromosomes in humans and chimps “differ radically in sequence structure and gene content,” showing “extraordinary divergence” where “wholesale renovation is the paramount theme.”
So are human Y chromosomes more similar to fly or worm Y chromosomes than to chimpanzee Y chromosomes?
 
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Black Dog

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They based it on specified complexity. William Dembski, for intelligent design theory, said this in 1998: "On an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function."

These were the predictions of evolutionists:
Predictions of non-functionality of “junk DNA” were made by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980, Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions.

By contrast, predictions of functionality of “junk DNA” were made based on teleological bases by Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004).
http://www.uncommondescent.com/comment-policy/put-a-sock-in-it/

This is the rabbit hole I referred to:
"Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA. ."
http://www.sciencemag.org/content/300/5623/1246.short

You didn't answer my question. I asked if Dembski was just guessing, or if his hypothesis was falsifiable. If it wasn't falsifiable, it means nothing.

The Rabbit Hole you negatively referred to ended up going in a direction that led scientists to a more complete understanding of DNA. Typical science. Why do you see this as a negative?
 
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Paul of Eugene OR

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I don't feel like doing that kind of legwork. If you do, look for work Dr. Humphreys has done since he consulted with Dr. Hartnett. I think that's within the last 5 or 10 years, and includes Humphrey's development of a new metric.

So you are defending Humphrey's model of cosmology even though you can't tell us what it is. Well, some of us don't take that as a very serious challenge to standard cosmology.
 
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ChetSinger

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So you are defending Humphrey's model of cosmology even though you can't tell us what it is. Well, some of us don't take that as a very serious challenge to standard cosmology.
I can't defend it because I don't have the PhD in physics required to understand cosmological maths. I told Loudmouth I was intrigued by it.

Since you're a Christian, I would've expected your approval, or at least your tolerance, of Christian physicists using GR maths to try and interpret God's account of his creation.
 
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Vaccine

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Because it has obvious signs of manufacture. You can, for example, show marks where the various parts were stamped, cut, or machined. And of course, we have all sorts of evidence that people make watches.

Thanks for making the case for intelligent design. Life has obvious signs of manufacture. We can show how the genetic code is digital encoded information with semantic and syntactic properties. We have all sorts of evidence intelligent causes make encoded information with semantic and syntactic properties, for example the binary programming language.


Barbarian observes:
Failing to show that geneticists saw non-coding DNA as being functionless, you repeated your assertion. When will we see your supporting data?

We're going in circles. You say show us, I do. Then you deny Darwinists had anything to do with junk DNA because one anecdotal example. We're back to the "show us" the presuppositions so here it is:

Susumu Ohno (1972)- So much junk DNA in our genome.
http://www.ncbi.nlm.nih.gov/pubmed/5065367

Richard Dawkins (1976) - The selfish gene.
"The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."


Crick and Orgel (1980)- Selfish DNA: the ultimate parasite.
http://www.ncbi.nlm.nih.gov/pubmed/...nel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum

Pagel and Johnstone (1992)- Variation across species in the size of the nuclear genome supports the junk-DNA explanation for the c-value paradox.
http://www.ncbi.nlm.nih.gov/pubmed/1360673

Ken Miller (1994)-
In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival.
http://www.millerandlevine.com/km/evol/lgd/

It was those views, based on Darwinist presuppositions, that "..for many years REPELLED mainstream researchers from studying noncoding DNA." It's a good thing some were willing to challenge those Darwinist presuppositions, "However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories."
http://www.sciencemag.org/content/300/5623/1246.short



Barbarian explaining why transitional forms to the "gear" exist:
The basic idea is repetitive "teeth" in which two parts of the exoskeleton interdigitate and move against each other. So, this is a pretty good example of exaption, a feature evolved for one purpose, that's recruited for another.

There's simpler examples of this for locomotion as well; the furca of springtails has teeth that interdigitate and then release to allow jumping. So the argument boils down to "I just don't think it could evolve, even though there are simpler examples."

That's the problem, it's "Barbarian explaining...". Get some peer-reviewed sources saying teeth are simpler forms of functional gears, otherwise this is just pseudo-science assertions.


It shows that evolution of developmental gene regulation is a fact, contrary to your denials. The genes persist, but contrary to your assumptions, they evolve over time, so they aren't the same.

I've never denied things evolve, I was quoting a passage about dGRN's:
"In other words, while cis-regulatory sequence variation may have continuing adaptive significance at the dGRN periphery, at upper levels of the dGRN hierarchy it does not have the same significance because the system level output IS VERY IMPERVIOUS TO CHANGE, except for catastrophic loss of the body part or loss of viability altogether" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

Quoting a paper, that couldn't stress it enough, that the developmental gene regulatory network remaining unaltered for half a billion years doesn't help your case at all. It actually affirms the part in bold.
 
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Vaccine

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So is every molecule.

You explained how generic information exists in all particles, which was never in doubt. But what makes you think coded digital information is in every molecule? And cite your source.


It is a part of H2O also.

If you think water has syntactic and semantic properties I doubt you understand what these words mean.
The definition of syntactic is relating to the rules of language and semantic is relating to meaning in language or logic.
Water doesn't have these properties DNA does.
"Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information"
http://link.springer.com/article/10.1007/s00018-013-1394-1


We translate water into H2O in the same way. Also, substrates such as metals serve as translation machinery to create H2O from H2 and O2 in the very same way that ribosomes act as catalysts for translation of proteins.

Of course if we redefine "condensation" to mean "translation" and redefine "reaction" to mean "catalyst", then that makes sense. Resorting to redefining words to make your case only shows how incredibly weak and hopeless it is.


You find the words "complex" and "specificity" in different parts of an abstract and think that somehow relates to the term "specified complexity" used by ID/creationists? Seriously?

Well of course it does. That was the collaborative effort of over a hundred scientists over several years. They anticipated the stir the paradigm shift would create, which is why they presented a unified front instead of leaving one or two people to defend their work. "Furthermore" is conjunctive adverb. It connects two independent clauses, any 4th grader knows that.


The process that added mutations to model DNA sequence was not looking for a target. The mutations were random. All the model did was apply selection to the resulting random changes, and what resulted was an increase in binding efficiency. It showed how a DNA promoter region and a DNA binding protein can co-evolve. If that isn't functional information by your definition, then evolution doesn't need to produce functional information as you define it. Having promoter regions and DNA binding proteins change their binding capacity will change protein expression of the gene downstream from the promoter. This can cause phenotypic change, exactly what evolution needs to produce.

An "increase in binding efficiency" seems like a target to me, unless they painted a bullseye on that after the fact? At any rate a computer simulation might help aveneus of research but isn't evidence of evolution. Actual evolution is evidence of evolution.


How does a nested hierarchy fit common design? Why would common design produce a nested hierarchy?

Common design explains all the examples of convergent evolution that fail to fit into a nested hierarchy. Common design also explains all the molecular phylogeny incongruities with a nested hierarchy. With common design genes are viewed as tools in a designer's toolkit. As Meyer points out the pax 6 gene (eyeless) helps regulate development of the eyes in fruit flies, squid, and mice. This contradicts the textbook expectations of Neo-Darwinism and convergent evolution is invoked to explain it. It makes more sense a designer would reuse the same tools in mammals, insects, and cephalopods than the same gene would independently evolve three times.
 
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Vaccine

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About 90% of the human genome is junk DNA. As sfs mentions, only 10% of the human genome shows evidence of selectable function.

Where's your source that says 10%?

Over a hundred scientists collaborated to get these results:
"These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/

The real problem is that you are trying to use a definition of "function" that is rather ridiculous...

And asserting the only way to define function is in accord with Darwinism isn't ridiculous?
 
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sfs

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Where's your source that says 10%?
This paper is a good place to start. This is also a relevant one.

Over a hundred scientists collaborated to get these results:
"These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/
Quite. 80% has biochemical function -- which just means that a protein binds to it, or that it is transcribed at a low level some of the time. That fraction includes all of the introns, which are transcribed and then excised from the mature messenger RNA. (A fraction of intronic sequence does have regulatory function, but it's a small fraction.) Quoting from the PNAS followup paper from some of the ENCODE folks, "In short, although biochemical signatures are valuable for identifying candidate regulatory elements in the biological context of the cell type examined, they cannot be interpreted as definitive proof of function on their own."

And asserting the only way to define function is in accord with Darwinism isn't ridiculous?
I've defined functional as having any effect on any meaningful biological trait. Pretty much the way a human/medical geneticist would: if the sequence composition can affect your health, your strength, your ability to have kids, your looks -- anything you might care about -- then it's functional. The best estimates are that that fraction is around 10% of the genome. Perhaps it's as high as 20%, but there's no way that most of the genome is functional.
 
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The Barbarian

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Barbarian explains:
Because it has obvious signs of manufacture. You can, for example, show marks where the various parts were stamped, cut, or machined. And of course, we have all sorts of evidence that people make watches.

Thanks for making the case for intelligent design.

No problem. As you see, "Intelligent Design" applies to man-made things, but not to nature, which was created, not designed.

Life has obvious signs of manufacture.

I know you want to believe that but so far, nothing like that has been found.

We can show how the genetic code is digital encoded information with semantic and syntactic properties.

Sorry, analogue, not digital. And almost any string of characters can be "decoded" to have "semantic and syntactic properties." But IDers can't detect them, unless they've agreed in advance if they have it or not. Would you like to put that to a test?

Barbarian observes:
Failing to show that geneticists saw non-coding DNA as being functionless, you repeated your assertion. When will we see your supporting data?

We're going in circles. You say show us, I do.

Then you deny Darwinists had anything to do with junk DNA

Scientists refer to it as "non-coding" DNA. There is some that is obviously junk, and the fact that huge amounts of it have been removed from the genome of animals with no detectable effects, pretty much ends the idea that it was "designed."



because one anecdotal example. We're back to the "show us" the presuppositions so here it is:

Susumu Ohno (1972)- So much junk DNA in our genome.
http://www.ncbi.nlm.nih.gov/pubmed/5065367

Richard Dawkins (1976) - The selfish gene.
"The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Ken Miller (1994)-
In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival.

http://www.millerandlevine.com/km/evol/lgd/

This doesn't say what you seem to think it says.

Barbarian explaining why transitional forms to the "gear" exist:
The basic idea is repetitive "teeth" in which two parts of the exoskeleton interdigitate and move against each other. So, this is a pretty good example of exaption, a feature evolved for one purpose, that's recruited for another.

There's simpler examples of this for locomotion as well; the furca of springtails has teeth that interdigitate and then release to allow jumping. So the argument boils down to "I just don't think it could evolve, even though there are simpler examples."

That's the problem,

Yep. What you were told was irreducibly complex, turns out to be entirely consistent with incremental change.

Barbarian observes:
It shows that evolution of developmental gene regulation is a fact, contrary to your denials. The genes persist, but contrary to your assumptions, they evolve over time, so they aren't the same.

Quoting a paper, that couldn't stress it enough, that the developmental gene regulatory network remaining unaltered for half a billion years doesn't help your case at all.

As you learned, some of it hasn't changed much. But that's consistent with evolutionary theory. And of course, it still changed, albeit slowly. Which is the difficulty for ID. If it was designed by God, it wouldn't change at all. Of course, if it was designed by what your guys call the "space alien", that might make some sense. Is that your position?
 
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Loudmouth

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I don't feel like doing that kind of legwork. If you do, look for work Dr. Humphreys has done since he consulted with Dr. Hartnett. I think that's within the last 5 or 10 years, and includes Humphrey's development of a new metric.

You don't want to do the legwork, but you expect me to? You expect me to do all of the legwork to back your claim?


YMMV. What I'm saying is that my beliefs have developed because of my experiences with God. And they include supernatural experiences. God isn't bound by natural laws because he's above them: medical science says a man can't come back to life after being dead, yet Jesus did exactly that, for both himself and for others.

The difference is that we don't have evidence that refutes the claim of a miracle. What you have is a story without any evidence for or against it. With biology, that is very different. We do have evidence that life evolved over billions of years. That evidence is inconsistent with intelligent design (e.g. a nested hierarchy).
 
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Loudmouth

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It was those views, based on Darwinist presuppositions, that "..for many years REPELLED mainstream researchers from studying noncoding DNA."

Non-coding DNA is not the same thing as junk DNA. Promoters with known function are still non-coding DNA, but they aren't junk DNA. This is known as a sleight of hand, where you deftly change words without telling the audience that the new word has a different meaning.

I've never denied things evolve, I was quoting a passage about dGRN's:
"In other words, while cis-regulatory sequence variation may have continuing adaptive significance at the dGRN periphery, at upper levels of the dGRN hierarchy it does not have the same significance because the system level output IS VERY IMPERVIOUS TO CHANGE, except for catastrophic loss of the body part or loss of viability altogether" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

And this is a problem how?

Did it take a completely different dGRN to get both chimps and humans from a common ancestor? Nope, sure didn't.

Quoting a paper, that couldn't stress it enough, that the developmental gene regulatory network remaining unaltered for half a billion years doesn't help your case at all. It actually affirms the part in bold.

That's not what it says. It says that the upper levels of the hierarchy are highly impervious to change. The lower levels are not as impervious to change, and nowhere does it say that the upper levels were unaltered.
 
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Loudmouth

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Where's your source that says 10%?

Over a hundred scientists collaborated to get these results:
"These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439153/

The trash in your kitchen trash bin has biochemical function. It has the ability to react with the oxygen in your kitchen and release biomolecules into the air. However, the trash in your kitchen trash bin is still junk. The ENCODE definition of biochemical function includes DNA that has no impact on anything important, just like the trash in your kitchen. It is still disposable DNA.

And asserting the only way to define function is in accord with Darwinism isn't ridiculous?

Defining "function" as "it does something" is much worse. The trash in your house does something. It releases odor molecules into the air. It is still trash and can be thrown out. The same for 80-90% of the human genome.
 
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ChetSinger

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You don't want to do the legwork, but you expect me to?
If you're interested in the subject why not pursue it yourself? That's what I did.

You expect me to do all of the legwork to back your claim?
Did I make a "claim"? I recall saying that I thought their ideas were intriguing.

The difference is that we don't have evidence that refutes the claim of a miracle...
Sure we do: our experiences say that people don't rise from the dead, or shout down storms, or heal diseases with a touch or word, or feed thousands with basketful of food. The New Testament says Jesus did all these things, and more.
 
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Loudmouth

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If you're interested in the subject why not pursue it yourself? That's what I did.

Apparently, you didn't. You are asking me to pursue it and report back to you.

Did I make a "claim"? I recall saying that I thought their ideas were intriguing.

You certainly implied that Humphreys had found a way to explain the data and a young Earth.

Sure we do: our experiences say that people don't rise from the dead, or shout down storms, or heal diseases with a touch or word, or feed thousands with basketful of food. The New Testament says Jesus did all these things, and more.

I already responded to this in the previous post.
 
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