How We Detect Design

[Loudmouth]

Such as?

The time and resources necessary to change the sequence of entire genomes for the sole purpose of producing a nested hierarchy. For example, humans have genetically modified fish so that they carry a jellyfish gene that produces a fluorescent protein. It causes the fish to glow under UV light. First, let's look at the phylogenetic tree that includes fish and jellyfish:

http://tolweb.org/Animals/2374

If fish and cnidarian share a gene, this puts the node really close to the root of the animal tree. Only sponges would be excluded. With that in mind . . .

According to you, there is no reason why human designers would not . . .

1. Extensively mutate the jellyfish gene so that it has the proper divergence for a gene shared by all animals except for sponges.

2. Insert the same gene into every single non-sponge animal, making sure to again mutate the gene in such a way that it produces a nested hierarchy when comparing the homologous gene between all of these animal species.

Does that make sense, just to get one species of fish that glows in UV light?

First of all a nested hierarchy is a man made organizing tool originated to group organisms that had common design.

Unlike the subjective opinions of the appearance of design, the nested hierarchy can be detected through objective methodologies, has a unit of measure, and is backed by statistical tests that could detect a false positive.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy
​

That's how OBJECTIVE EVIDENCE works.

Secondly, we do see similar nested hierarchy in man made designs that show for instance transportation. We see the first man made transportation systems being grouped in ever evolving designs up to today.

No, we don't. We can find the same radio in trucks from two different manufacturers while two trucks of the same model and from the same manufacturer can have two different radios. That is just one example. We can find two cars of different models with the same engine while two cars of the same model have two different engines. We can find the same tires and rims on a Ford and Chevy, yet find different rims and tires on two Chevy Silverado's from the same model year.

We are the ones that are making interpretations based on past history, what do you think would be deceptive in the nested hierarchy?

The nested hierarchy is an objective fact, and we have the science to back it.

Like the faith based belief that evolution can account for the design biologists see in structures and systems in organisms?

Once again, a theist uses the word "faith" to cast doubt on a proposition.

 

[Loudmouth]

Ok, you are now passing from bizarre into realms unknown.

Just in case you missed bhsmte's post:

From post #273 and I quote:

"Not to mention that if he were to claim that evolution could not produce such features his position would be at risk. He is walking a tight rope."

This would appear to be a positive claim that Collins concludes what he does, because if he didn't, his position would be at risk.

Did I miss it, was there any evidence provided to support this claim?

Does this appear to be a claim Collins is lying, to go along with the consensus?

 

[Oncedeceived]

Just in case you missed bhsmte's post:

From post #273 and I quote:

"Not to mention that if he were to claim that evolution could not produce such features his position would be at risk. He is walking a tight rope."

This would appear to be a positive claim that Collins concludes what he does, because if he didn't, his position would be at risk.

Let me clarify my position here. Collins concludes what he does because that is what he believes, however, he does believe that God had input into what makes us human that evolution did not. He does not make many comments about that belief because it causes some issues for him. When he was nominated for director of NIH, there were scientists that were outspoken about his faith and their concerns with him as the director. He understands the secular concerns and thus walks a tight rope making sure his faith does not become something that can't be overcome in his career.

Did I miss it, was there any evidence provided to support this claim?

Does this appear to be a claim Collins is lying, to go along with the consensus?[/QUOTE]

 

[Loudmouth]

Let me clarify my position here. Collins concludes what he does because that is what he believes, however, he does believe that God had input into what makes us human that evolution did not.

Quotes? References?

He does not make many comments about that belief because it causes some issues for him.

Evidence?

When he was nominated for director of NIH, there were scientists that were outspoken about his faith and their concerns with him as the director. He understands the secular concerns and thus walks a tight rope making sure his faith does not become something that can't be overcome in his career.

And yet he is still the head of the NIH, is still a well respected scientist, and is still outspoken about his beliefs. You are seeing a conspiracy where there is none. Your claims that he really does see evidence for design but doesn't dare speak about it is completely untrue.

 

[bhsmte]

He doesn't make public comments about his beliefs, are you serious???????????????????

In fact of all the Christian scientists, Collins has been one of the most aggressive, in stating his belief in a God.

Is that he wrote a book; "The language of God" and created a website to discuss the same????????

Collins appears quite willing to speak about his faith beliefs and also appears quite willing, state his scientific beliefs.

It would appear then you are not claiming Collin's scientific conclusions are not motivated by his desire to "keep his position", but are based on science and that science just so happens to be in line with the vast majority of other scientists with similar credentials as him.

What a coincidence.

 

[bhsmte]

Quotes? References?



Evidence?



And yet he is still the head of the NIH, is still a well respected scientist, and is still outspoken about his beliefs. You are seeing a conspiracy where there is none. Your claims that he really does see evidence for design but doesn't dare speak about it is completely untrue.

This just keeps getting better.

Collin's goes out of his way to state; "no God of the gaps allowed" and the evidence to support evolution is overwhelming and now someone is claiming he may feel differently, but isn't willing to state that? Where is the evidence to support this?

 

[SkyWriting]

We can never prove that it is impossible.

I haven't said it was impossible.

I claim there is no supporting data
in the field of science that hints
at the idea of life forming life
from non-life
or complexity from the simple,
or intelligent or useful design
by way of natural processes.

There are no non-living "arrows"
pointing in the direction of life.

And the roadblocks are infinite in number.

 

[Loudmouth]

I haven't said it was impossible.

I claim there is no supporting data
in the field of science that hints
at the idea of life forming life
from non-life
or complexity from the simple,
or intelligent or useful design
by way of natural processes.

400 years ago, there was no evidence that matter was made up of atoms. Are you sure you want to base your beliefs on a gap in our knowledge?

There are no non-living "arrows"
pointing in the direction of life.

Where are the arrows for a supernatural cause for life?

 

[Oncedeceived]

The time and resources necessary to change the sequence of entire genomes for the sole purpose of producing a nested hierarchy. For example, humans have genetically modified fish so that they carry a jellyfish gene that produces a fluorescent protein. It causes the fish to glow under UV light. First, let's look at the phylogenetic tree that includes fish and jellyfish:

http://tolweb.org/Animals/2374

If fish and cnidarian share a gene, this puts the node really close to the root of the animal tree. Only sponges would be excluded. With that in mind . . .

According to you, there is no reason why human designers would not . . .

1. Extensively mutate the jellyfish gene so that it has the proper divergence for a gene shared by all animals except for sponges.

2. Insert the same gene into every single non-sponge animal, making sure to again mutate the gene in such a way that it produces a nested hierarchy when comparing the homologous gene between all of these animal species.

Does that make sense, just to get one species of fish that glows in UV light?

You still are under the false assumption that if evolution no God and if God no evolution.

Unlike the subjective opinions of the appearance of design, the nested hierarchy can be detected through objective methodologies, has a unit of measure, and is backed by statistical tests that could detect a false positive.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).
http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchy​

I find it interesting that you use very old sources for your information. Could it be that since we are now able to determine from multilocus and genomic data which is showing discordance in the tree and those close relationships of the nested organisms. Using those new technologies and testing we are not finding these neat orderly nests but very different ones than expected.
The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.

Copyright © 2009 Elsevier Ltd. All rights reserved.

And:

In conclusion, phylogenies of recently evolved species, which may still exchange genes, are inevitably difficult to resolve. The markers studied here provide well-supported gene genealogies, but the general lack of concordant reciprocal monophyly between closely related species and the disagreements between loci highlight the importance of multiple locus comparisons in resolving sister species relationships. Fast-evolving nuclear genes such as those described here are likely to become an important tool for phylogenetic analysis. Furthermore, it is clear that biologically and ecologically relevant species may sometimes not be recognizable under phylogenetic (Cracraft 1989<$REFLINK> ) or genealogical species concepts (Baum and Shaw 1995<$REFLINK> ). Speciation does not necessarily isolate all regions of the genome and therefore cannot be expected to produce instantaneous reciprocal monophyly.
http://mbe.oxfordjournals.org/content/19/12/2176.full

​

That's how OBJECTIVE EVIDENCE works.

Yes, and as you see not always what you expect.

No, we don't. We can find the same radio in trucks from two different manufacturers while two trucks of the same model and from the same manufacturer can have two different radios. That is just one example. We can find two cars of different models with the same engine while two cars of the same model have two different engines. We can find the same tires and rims on a Ford and Chevy, yet find different rims and tires on two Chevy Silverado's from the same model year.

This was to show how the Nested Hierarchy works with cars.
Dr. Tim M. Berra is Professor Emeritus of Evolution
“If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.” — T. Berra, Evolution and the Myth of Creationism, 1990, pg 117-119

The nested hierarchy is an objective fact, and we have the science to back it.

It is an organization of life forms that actually exist and have adapted and modified. How is this not applicable to ID?

Once again, a theist uses the word "faith" to cast doubt on a proposition.

No I use faith because that is all you have.

 

[Oncedeceived]

Quotes? References?

Evidence?

And yet he is still the head of the NIH, is still a well respected scientist, and is still outspoken about his beliefs. You are seeing a conspiracy where there is none. Your claims that he really does see evidence for design but doesn't dare speak about it is completely untrue.

I am not claiming a conspiracy, I am saying that there is a line one must not cross if you want to remain a well respected scientist.

What follows are a series of slides, presented in order, from a lecture on science and belief that Dr. Collins gave at the University of California, Berkeley, in 2008:

Slide 1: “Almighty God, who is not limited in space or time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.”

Slide 2: “God’s plan included the mechanism of evolution to create the marvelous diversity of living things on our planet. Most especially, that creative plan included human beings.”

Slide 3: “After evolution had prepared a sufficiently advanced ‘house’ (the human brain), God gifted humanity with the knowledge of good and evil (the moral law), with free will, and with an immortal soul.”

Slide 4: “We humans used our free will to break the moral law, leading to our estrangement from God. For Christians, Jesus is the solution to that estrangement.”

Slide 5: “If the moral law is just a side effect of evolution, then there is no such thing as good or evil. It’s all an illusion. We’ve been hoodwinked. Are any of us, especially the strong atheists, really prepared to live our lives within that worldview?”

So do you have an apology for me? I didn't lie about Collins.

 

[Loudmouth]

You still are under the false assumption that if evolution no God and if God no evolution.

Red herring. Stop trying to change the subject. You asked why a designer would not produce a nested hierarchy, and I just showed you why. Are you going to address it or not?

Also, you have already stated that ID can be falsified if we find an evolutionary pathway for IC systems, did you not?

I find it interesting that you use very old sources for your information. Could it be that since we are now able to determine from multilocus and genomic data which is showing discordance in the tree and those close relationships of the nested organisms. Using those new technologies and testing we are not finding these neat orderly nests but very different ones than expected.
The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.

So how are those problems solved? By looking at more than a few genes.

In conclusion, phylogenies of recently evolved species, which may still exchange genes, are inevitably difficult to resolve.

Do humans and other ape species still exchange DNA? Nope.

Yes, and as you see not always what you expect.

Yes, we do. The phylogenetic signal is there, as expected.

This was to show how the Nested Hierarchy works with cars.
Dr. Tim M. Berra is Professor Emeritus of Evolution
“If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.” — T. Berra, Evolution and the Myth of Creationism, 1990, pg 117-119

It shows no such thing. It doesn't even discuss apomorphies, synapomorphies, nodes, or anything related to determining a nested hierarchy.

It is an organization of life forms that actually exist and have adapted and modified. How is this not applicable to ID?

Because there is no reason that a designer would design life so that it falls into a nested hierarchy. When humans design life, they don't put mountains of effort into making sure that any changes they make fall into a nested hierarchy. I have already shown you this, AND YOU STILL IGNORE IT.

No I use faith because that is all you have.

I already showed you the objective evidence for a nested hierarchy which evidences evolution. That isn't faith.

 

[Loudmouth]

I am not claiming a conspiracy, I am saying that there is a line one must not cross if you want to remain a well respected scientist.

Same thing.

What follows are a series of slides, presented in order, from a lecture on science and belief that Dr. Collins gave at the University of California, Berkeley, in 2008:

Slide 1: “Almighty God, who is not limited in space or time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.”

Slide 2: “God’s plan included the mechanism of evolution to create the marvelous diversity of living things on our planet. Most especially, that creative plan included human beings.”

Slide 3: “After evolution had prepared a sufficiently advanced ‘house’ (the human brain), God gifted humanity with the knowledge of good and evil (the moral law), with free will, and with an immortal soul.”

Slide 4: “We humans used our free will to break the moral law, leading to our estrangement from God. For Christians, Jesus is the solution to that estrangement.”

Slide 5: “If the moral law is just a side effect of evolution, then there is no such thing as good or evil. It’s all an illusion. We’ve been hoodwinked. Are any of us, especially the strong atheists, really prepared to live our lives within that worldview?”

So do you have an apology for me? I didn't lie about Collins.

All Collins is referring to is the non-material soul that he believes humans have. He says nothing about God changing our genomes or bodies outside of the confines of evolution.

 

[bhsmte]

Same thing.


All Collins is referring to is the non-material soul that he believes humans have. He says nothing about God changing our genomes or bodies outside of the confines of evolution.

Was there any evidence provided to support the CLAIM that there is a line a scientist must not cross, to remain a well respected scientist? I can't recall seeing any.

This would appear to be a claim of knowledge that this exists, so evidence should be forthcoming, to prove the same.

It does sound like a conspiracy though, scientists can't say certain things, to remain a well respected scientist.

 

[Oncedeceived]

Same thing.

No, no it isn't.

All Collins is referring to is the non-material soul that he believes humans have. He says nothing about God changing our genomes or bodies outside of the confines of evolution.

You said he doesn't see design.

“Almighty God, who is not limited in space or time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.” Emphasis mine.

 

[Loudmouth]

Was there any evidence provided to support the CLAIM that there is a line a scientist must not cross, to remain a well respected scientist? I can't recall seeing any.

This would appear to be a claim of knowledge that this exists, so evidence should be forthcoming, to prove the same.

It does sound like a conspiracy though, scientists can't say certain things, to remain a well respected scientist.

It is not dissimilar to the fake stories of persecution that some Christians use. There are also some people who think that science is a form of post-modernism, where all claims have equal truth value. Some Christians confuse being wrong with being a creationist, although there is a lot of overlap in that Venn diagram.

 

[Oncedeceived]

Was there any evidence provided to support the CLAIM that there is a line a scientist must not cross, to remain a well respected scientist? I can't recall seeing any.

This would appear to be a claim of knowledge that this exists, so evidence should be forthcoming, to prove the same.

It does sound like a conspiracy though, scientists can't say certain things, to remain a well respected scientist.

Really, what about Behe?

 

[Loudmouth]

“Almighty God, who is not limited in space or time, created a universe 13.7 billion years ago with its parameters precisely tuned to allow the development of complexity over long periods of time.” Emphasis mine.

Need some help moving those goalposts?

 

[Loudmouth]

Really, what about Behe?

"Well, all a scientist has to do to prove me wrong is to take a bacterium without a flagellum, or knock out the genes for the flagellum in a bacterium, go into his lab and grow that bug for a long time and see if it produces anything resembling a flagellum. If that happened, intelligent design, as I understand it, would be knocked out of the water."--Michael Behe
http://www.uncommondescent.com/intelligent-design/michael-behe-on-falsification/

 

[Oncedeceived]

Red herring. Stop trying to change the subject. You asked why a designer would not produce a nested hierarchy, and I just showed you why. Are you going to address it or not?

You didn't show how ID would not produce a nested hierarchy. You made assertions and put forth opinion but I haven't seen anything to show ID would not produce NH.

Also, you have already stated that ID can be falsified if we find an evolutionary pathway for IC systems, did you not?

No, I said ID as a science would be falsified if an evolutionary pathway for IC systems did not provide step by step increments that were beneficial and functional for an organism.

So how are those problems solved? By looking at more than a few genes.

Show where they have been solved.

Do humans and other ape species still exchange DNA? Nope.

And your point?

Yes, we do. The phylogenetic signal is there, as expected.

You are really reaching.

It shows no such thing. It doesn't even discuss apomorphies, synapomorphies, nodes, or anything related to determining a nested hierarchy.

Rolling my eyes.

Because there is no reason that a designer would design life so that it falls into a nested hierarchy. When humans design life, they don't put mountains of effort into making sure that any changes they make fall into a nested hierarchy. I have already shown you this, AND YOU STILL IGNORE IT.

What!!!!!!!!!!!!!!!!!!!!!!!!! When humans design life!!!!!!!!!!!!!!!! When have humans designed life?

I already showed you the objective evidence for a nested hierarchy which evidences evolution. That isn't faith.

Your mistaken assumption once again...if evolution no God.

 

[Oncedeceived]

Need some help moving those goalposts?

I will ask how you feel I've moved the goalposts but of course you never give anything of substance so I won't hold my breath.