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Author Topic:   The Origin of Novelty
Taq
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Message 609 of 871 (692238)
03-01-2013 11:12 AM
Reply to: Message 597 by mindspawn
03-01-2013 1:18 AM


Re: Evidence again
That's what I said, thanks for confirming my point
So you agree that ID does not predict a nested hierarchy? That seems to be what you are saying.
Your insistence that a designer would not have any consistency is illogical and does not conform to what intelligent designers actually are observed to do.
We observe that intelligent designs do NOT fall into nested hierarchies. Cars do not fall into nested hierarchies. Computers do not fall into nested hierarchies. Airplanes do not fall into nested hierarchies.
There would be groupings and some design duplication between designs that have similar function, anything less is stupid design, not intelligent design.
That is not what we see with life, however. We do not see designs shared across similar functions. We observe that bats share more features with whales than they do with birds even though bats and birds fill a very similar function. Bats have a tidal lung system with a diaphragm just like whales, but completely unlike birds. Bats are placental and produce milk just like whales, and completely unlike birds. Bats have three middle ear bones just like whales, but unlike birds. Even the structure of the wings between bats and birds are not shared.
Nested hierarchies are stupid from an ID perspective because they prevent you from using design elements where they would make the most sense. They prevent you from mixing and matching design elements where they would be the most useful for no other reason than to make it look like life evolved.
So in essence your whole argument that design and nested features are not compatible is a strawman argument.
We are not crediting you with these arguments, so it is not a strawman argument.

This message is a reply to:
 Message 597 by mindspawn, posted 03-01-2013 1:18 AM mindspawn has replied

Replies to this message:
 Message 615 by Tempe 12ft Chicken, posted 03-01-2013 11:53 AM Taq has replied
 Message 630 by mindspawn, posted 03-05-2013 2:28 AM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 611 of 871 (692240)
03-01-2013 11:16 AM
Reply to: Message 599 by mindspawn
03-01-2013 2:25 AM


They are not identical due to a slight fitness advantage.
Evidence please. The yeast chugged along just fine with an exact copy of human cytochrome c.
The differences between cytochrome c fit into nests/grouping due to similarity of organisms.
This is also unsupported. You need evidence to back this claim.
Similar DNA - similar organism.
That doesn't explain why we see a nested hierarchy. Cars have similarities, but they don't fall into a nested hierarchy.
Taq: What evidence, if observed, would not favor creationism/ID?
mindspawn: Nothing.
Then your arguments are pretty meaningless.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 612 of 871 (692242)
03-01-2013 11:23 AM
Reply to: Message 598 by mindspawn
03-01-2013 1:35 AM


Do you honestly think that I am saying that mammals/birds/fish share no features? I never said anything dumb like that, they all have eyes too, so your shared features argument is completely a strawman argument, and not a very well thought out strawman argument.
You still have not explained why shared features should fall into a nested hierarchy if ID is true given that shared features in known human designs do not fall into a nested hierarchy, nor is there any design reason why they should.
Yes I have, an intelligent designer would group features and DNA according to similar functions.
But that is not what we see. Features are not grouped by similar functions. That is the whole point. Squid and fish exist in the very same environments and niches. Squid and fish both have a camera type of eye. However, the actual designs of those eyes are completely different. They are not shared. Instead, they fall into groups based on evolutionary history, NOT SIMILAR FUNCTION.
There are general groupings according to a "package" that works best.
Another empty argument. You have yet to show that feathers and three middle ear bones would not work.
I said birds are grouped for flight
Mammals are grouped for adaptability.
So why do penguins and ostriches share more features with a hummingbird than they do with terrestrial mammals?

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 613 of 871 (692243)
03-01-2013 11:25 AM
Reply to: Message 603 by mindspawn
03-01-2013 4:10 AM


What you see is EXACTLY what a designer is observed to do.
Since when? Show me a set of human designs that falls into a nested hierarchy.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 617 of 871 (692251)
03-01-2013 12:11 PM
Reply to: Message 615 by Tempe 12ft Chicken
03-01-2013 11:53 AM


Re: Evidence again
Mindspawn, you keep claiming that cars fall into a nested heirarchy, but this is definitely not the case. You speak of specific "types" of cars, such as the SUVs, the Trucks, the Sedans, the Off-road vehicles.
If those are our first tier of groupings then it is even easier to show how vehicles do not fall into a nested hierarchy.
For example, we can find trucks and sedans that have the same engine while different cars do not share this same engine. This is a violation of the nested hierarchy. We can find a truck and a car that share the same color of paint, but two cars from the same model that have different paint. This is another violation of the nested hierarchy. We can find a sedan and a truck that have the same radio, but two different sedans that have different radios. Another violation of the truck and sedan nestings. We can do the same with trucks, showing that an SUV and a truck share the same engine while two different trucks have two different engines.
There are clear violations of a nested hierarchy when comparing vehicles. Why? Because designers have no need nor any reason to follow a nested hierarchy. If an engine will work in both a truck and an SUV then they put it in both, not worrying about the need to keep adaptations in the two groups separate. We can find GPS systems that start in one make of car, and all of the sudden show up in a completely different make an style of vehicle as if it was stripped from one branch and just randomly showed up on another branch. Again, clear and obvious violations of a nested hierarchy.
Yes, there are similarities between vehicles. Yes, these design units are put together where they make sense as far as design. However, the PATTERN of similarity between vehicles does NOT fall into a nested hierarchy. No human designs do this. Even when humans design organisms they regularly violate the nested hierarchy.
Also, the reason that all of this is being stressed is that phylogenies (i.e. nested hierarchies) are used to determine when specific mutations arose, and this relates directly to the origin of novel features. Also, novel adaptations stay within evolutionary lineages unlike novel human designs that move into all sorts of different groups in human designs without any considerations of a design's history.

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Replies to this message:
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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 622 of 871 (692285)
03-01-2013 4:15 PM
Reply to: Message 620 by JonF
03-01-2013 3:10 PM


Re: Evidence again
I've not read all of this thread, but I think it's worth pointing out while vehicles do not fall into a nested hierarchy, there are many ways of arranging them in a nested hierarchy, with no objective reason to prefer one over another. OTOH, life falls into one nested hierarchy, as measured by at least two objective measures, and there is no other objectively equivalent nested hierarchy of life.
That is a very, very good point. This is also stressed in the very well written talkorigins page on nested hierarchy. I apologize for the large chunk of copy pasta, but I think it is very important for others to read this:
quote:
Although it is trivial to classify anything subjectively in a hierarchical manner, only certain things can be classified objectively in a consistent, unique nested hierarchy. The difference drawn here between "subjective" and "objective" is crucial and requires some elaboration, and it is best illustrated by example. Different models of cars certainly could be classified hierarchicallyperhaps one could classify cars first by color, then within each color by number of wheels, then within each wheel number by manufacturer, etc. However, another individual may classify the same cars first by manufacturer, then by size, then by year, then by color, etc. The particular classification scheme chosen for the cars is subjective. In contrast, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies (Pei 1949; Ringe 1999). Nobody would reasonably argue that Spanish should be categorized with German instead of with Portugese.
The difference between classifying cars and classifying languages lies in the fact that, with cars, certain characters (for example, color or manufacturer) must be considered more important than other characters in order for the classification to work. Which types of car characters are more important depends upon the personal preference of the individual who is performing the classification. In other words, certain types of characters must be weighted subjectively in order to classify cars in nested hierarchies; cars do not fall into natural, unique, objective nested hierarchies.
Because of these facts, a cladistic analysis of cars will not produce a unique, consistent, well-supported tree that displays nested hierarchies. A cladistic analysis of cars (or, alternatively, a cladistic analysis of imaginary organisms with randomly assigned characters) will of course result in a phylogeny, but there will be a very large number of other phylogenies, many of them with very different topologies, that are as well-supported by the same data. In contrast, a cladistic analysis of organisms or languages will generally result in a well-supported nested hierarchy, without arbitrarily weighting certain characters (Ringe 1999). Cladistic analysis of a true genealogical process produces one or relatively few phylogenetic trees that are much more well-supported by the data than the other possible trees.
Interestingly, Linnaeus, who originally discovered the objective hierarchical classification of living organisms, also tried to classify rocks and minerals hierarchically. However, his classification for non-living objects eventually failed, as it was found to be very subjective. Hierarchical classifications for inanimate objects don't work for the very reason that unlike organisms, rocks and minerals do not evolve by descent with modification from common ancestors.
29+ Evidences for Macroevolution: Part 1

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 634 of 871 (692579)
03-05-2013 10:44 AM
Reply to: Message 630 by mindspawn
03-05-2013 2:28 AM


Re: Evidence again
Cars do fall into nested groupings.
No, they don't. We can find a Subaru with a Porsche engine, as one example. We can find a Ford Focus and a Ford Taurus with the same color body paint while two Ford Focus have different paint. That is a violation of the nested groupings. There are many, many, many more examples of this. I can point to violation after violation of nested groupings amongst cars.
Not so with life. Life does fall into a nested hierarchy. We do not find characteristics shared by bats and birds that are not also shared by other mammals, as one example.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 635 of 871 (692580)
03-05-2013 10:49 AM
Reply to: Message 631 by mindspawn
03-05-2013 3:07 AM


1) Some of you feel that the designer should make varieties that are highly individualistic, not in groupings of features, and that these organisms arranged in nests of features point to evolution.
We OBSERVE that designers do not force their designs to fall into nested hierarchies. We OBSERVE that there is not reason for them to do so. Therefore, nested hierarchies are not predicted by ID.
I am saying that a designer actually does groupings and exceptions, and both are perfectly logical, cars are such an example of intelligent design, or alternatively look at the wider category of forms of transport. (a balloon, a jetski, a car).
Let's do look at a wider category. We can find vehicles with a mixture of characteristics from:
1. Cars and boats.
2. Planes and boats.
3. Cars and planes.
This is quite different from what we see with life. We do NOT see species with a mixture of derived avian and mammalian features. We do NOT see species with a mixture of derived cephalopod and fish features. We only see the mixtures of characteristics that fall into a nested hierarchy. Not so with vehicles.
By creating both groupings, and the variety of exceptions to the groupings, this shows creative design.
Nested hierarchies show a lack of creativity.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(2)
Message 636 of 871 (692581)
03-05-2013 10:52 AM
Reply to: Message 632 by mindspawn
03-05-2013 5:28 AM


Re: Evidence again
wikipedia indicates the cephalopod eye is specialized for marine purposes:
Then what was stopping the designer from including the cephalopod style eye in fish with backbones?
We have two eyes that largely negates the blind spot propblem.
That is only true for species that have a large overlap between the eyes for stereo scopic vision which is not all species.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 647 of 871 (692647)
03-06-2013 9:20 AM
Reply to: Message 643 by mindspawn
03-06-2013 6:19 AM


Re: Evidence again
I'm not a biologist. Who knows, maybe the eye NEEDS to be continuously fed by the retinal artery in non-marine conditions.
That doesn't explain why vertebrate fish and and vertebrate terrestrial species share the same eye while vertebrate fish and cephalopods, who share the very same environment and niches, have different eyes.
Maybe your land based cephaloid eye would make you color-blind AND shortly thereafter completely blind as your vitreous body dries up without being continuously nourished by the retinal artery.
Complete and utter speculation that just doesn't add up. Color vision is a result of having multiple types of photoreceptors that react to a narrow spectrum of light. Humans have three such receptors for blue, green, and red. There is absolutely no reason why a forward facing retina could not support color vision, or be able to support adequate perfusion of blood.

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Replies to this message:
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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 648 of 871 (692648)
03-06-2013 9:22 AM
Reply to: Message 644 by mindspawn
03-06-2013 6:42 AM


Re: Evidence again
These are REDUCED complexity mutations, ie disabled regions. The insertion mutation of these mice caused the promotor to disable.
The promoter still functions just fine. It is a gain in function mutation as the paper discusses:
"In the laboratory mouse, loss-of-function mutations at Mc1r are recessive and result in light color, whereas gain-of-function alleles are dominant and result in dark color (16). "
Just a moment...
These mice are dark in color, so it is a mutation that confers a gain in function.

This message is a reply to:
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Replies to this message:
 Message 650 by Bolder-dash, posted 03-06-2013 9:26 AM Taq has replied
 Message 671 by mindspawn, posted 03-06-2013 4:04 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 649 of 871 (692649)
03-06-2013 9:24 AM
Reply to: Message 645 by Bolder-dash
03-06-2013 7:39 AM


Re: Evidence again
Since you are already making about stories about zero explanations about the pocket mouse, . . .
We have the mutations. We observe a gain in function. What more is there to demonstrate?

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 651 of 871 (692652)
03-06-2013 9:46 AM
Reply to: Message 646 by mindspawn
03-06-2013 8:27 AM


Re: Novel protein coding gene in an Antarctic fish
If in a laboratory they choose a particular organism that is lacking amplification, when the normal state of the species is known to be amplified, then they are pre-empting expected results by artificially creating amplification where nature already has it. They are just copying nature.
Then all evolution needs to do is copy nature in order to produce the biodiversity we see today and to produce novel function. As we have already seen, mutations produce the copies which then result in novel function.
The e.coli example of novel genetic function is close, involves the promoter and not the gene, and mimics a close relative , the staphylococcus.
A close relative? Hardly. E. coli are Gram negative while Staph is Gram positive. They are not closely related. Secondly, we observe that changes in promoter regions produces novel function, so why is this a problem given the topic of the thread? The differences between us and other apes is probably due, in part, to changes in gene regulation, as are many of the differences between us and more distantly related species.
Please! I'm happy with any proof or even schoolbook illustration of long-term nested hierarchies, I believe in short term hierarchies but everyone just seems to make sweeping statements in overconfident fashion on this site.
We are confident because you can not show us a species with a mixture of derived mammalian and avian features. We observe the nested hierarchies just as evolution predicts while we do not observe this pattern in things that are designed.
This logic is incomplete because it is a well known fact that mutation rates are higher during prolonged sun exposure, and so the higher mutations in African DNA does not necessarily reflect the older population
This definitely needs backing up. The mitochondria that you receive as an offspring comes from your mother's egg, not from your mother's skin.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 652 of 871 (692653)
03-06-2013 9:51 AM
Reply to: Message 650 by Bolder-dash
03-06-2013 9:26 AM


Re: where did the recess come from
How can you have a recessive gene in a population without first having a dominant gene? I am pretty sure that is impossible.
Before the dark allele showed up there was one phenotype. The small differences in the light allele did not cause changes in fur color, so there wasn't a recessive/dominant relationship between the different genotypes because any combination produced the same phenotype. It wasn't until the dark allele showed up that you had differences in phenotype, and only then can you determine the relationship between dominant and recessive genes.
Biologically, it would appear that the mutations in mc1r allow for the continuation of melanin production. Having just one copy of the gene ensures that this increased melanin production continues causing the gain in function to dominate over the light colored genotype.

This message is a reply to:
 Message 650 by Bolder-dash, posted 03-06-2013 9:26 AM Bolder-dash has replied

Replies to this message:
 Message 653 by Bolder-dash, posted 03-06-2013 10:40 AM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 654 of 871 (692659)
03-06-2013 10:58 AM
Reply to: Message 653 by Bolder-dash
03-06-2013 10:40 AM


Re: where did the recess come from
The function of mcr1 is to produce melanin.
Sort of. mc1r is a protein that spans the cell membrane and receives signals from outside of the cell. That then starts a signal cascade that results in the production of melanin. Think of mc1r as the trigger. Changes in that trigger produce novel expression patterns for melanin.
I believe you are a biology major, correct Taq? There are at least 3 or 4 things wrong with your reasoning, that take too long to explain without getting into boring details, but that you really should be aware of.
I have a zoology degree. Plants bored me. As to the details, bring them on.
The case of the pocket mouse is a terrible example of an organism gaining function, when it was the light colored mice that originally had lost function for melanin.
Light colored mice have melanin function as well. They had never lost the ability to produce melanin. That is why their fur is brown instead of white. What has changed is the amount of melanin that is expressed, and the timing of that expression. This is due to a gain of function mutation in mc1r. The mc1r gene in light colored mice is also operational and has function.
I can't believe you are pinning so much hope of this far-fetched example.
What is far fetched about it? We have mutations that produce a gain in function which results in a novel phenotype. That is exactly what the thread is asking for.
But the problem is, you don't have any ones better to use, so I certainly don't mind you trying to make a case for it, but frankly its a pretty easy example to debunk.
I have millions of examples just in the human and chimp genomes alone.

This message is a reply to:
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