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Apes and humans have different designs

AV1611VET

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Quit changing the subject.
Ontological reductionism.

If you don't know what that is, please don't be so naieve as to think I'm going to accept a false accusation.
 
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Loudmouth

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From what I can tell, here are some of the problems with the study. I surely have something wrong, so I am hoping that sfs can point out my mistakes.

First, large indels are going to be counted differently in the two comparisons. Tomkins uses a very simple blastn search. What this will do is include indels in a straight comparison. What he does is use the top search result from a blastn search and use that for his statistics. A blastn search will not return aligned sequence, it will simply return the best match. Therefore, if an indel contains novel sequence then it may match, by chance, with a random sequence elsewhere in the the other genome. This is reported as a match when it shouldn't be since you are not comparing aligned or orthologous sequences.

Also, Tomkins makes the assumption that DNA kept out of the alignment does not have homology to the other species. This is false. What keeps these chunks of DNA out of the assembly is that they simply don't know where in the genome it goes because there is not enough overlap with other contigs. To use an analogy, it is like finding the same shaped jigsaw piece in two different jigsaw puzzles, but you don't have any other pieces in the current puzzle to attach it to so you aren't sure if they belong at the same place in the overall picture.
 
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Loudmouth

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I also noticed that Tomkins used an ungapped alignment:

"BLASTN algorithm parameters for the main study were as follows: -word_size 11, -evalue 10, -max_target_seqs 1, -dust no, -soft_masking false, -ungapped."
Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% - Answers in Genesis

If I am reading things correctly, this would not match sequences that differ by even a single base indel. Am I wrong about this? I am unable to find the option to do ungapped searches in the browser based blastn, so wondering if anyone has experienced using ungapped blastn searches.

Added by edit: To clarify why this is a possible problem for comparing the two methods, here is an example of what a gapped and ungapped alignment will look like, and the percent similarities that will result. There is just a single base indel in this comparison:

Gapped alignment: 100% similarity, 1 indel
seq A: GCTTATATTGCGGGCAAA
seq B: GCTTAT-TTGCGGGCAAA

Ungapped alignment: 12/18 or 66.7%
seq A: GCTTATATTGCGGGCAAA
seq B: GCTTATTTGCGGGCAAA
 
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FrenchyBearpaw

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Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% - Answers in Genesis

Apparently the DNA overlap is only about 70%. Clearly our own config produces very different results in terms of intelligence etc also. So arguments about a common ancestor rather a common designer seem to be less well founded. We are not comparing like for like cause not only do humans and chimps have a different number of chromosones each are individually differently configured. Talk of the evolutionary fusion of chromosones to explain why humans have a pair less than chimps (and used as a proof of evolution) are also mute because what we are really looking at is a different design in both cases and the differences extend to all chromosones. Thus the evolutionary explanation of these differences is also mute because the differences exist from the socalled source chromosones to the finished result also.

Check this out.


Lactose Intolerance and the Evolution of Human Digestion - YouTube

Oh, and I think you mean "moot," not "mute." :p

Welcome to CF.
 
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And-U-Say

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ProgettoCosmo - An automatic Comparison of the Human and Chimpanzee Genomes

I do not think you understand the significance of the difference between 100% and 99.67%. That might only be a couple of letters to you but it can mean the code for this particular part of the DNA results in a significantly different result. As with computer programming (and really DNA is the most advanced code in the universe yet discovered) the differences make all the difference. (Complex specified information to use the jargon).
DNA is NOT a code. it never has been. it doesn't even qualify as blueprint. It is NOTHING like a computer code. If you understood some Chemistry and how DNA works (in a rough sense) you would know this.
 
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ThouShaltNotPoe

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Ontological reductionism.

If you don't know what that is, please don't be so naieve as to think I'm going to accept a false accusation.

I made the accusation because YOU don't know what it is!

If you THINK you understand the term, then explain how it addresses Nested Hierarchies, your original claim.

[We know that you can't.]
 
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mindlight

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Are you sure you do? If we were to compare your genome to mine, we would see that we are about 99.8% the same. Does this mean we belong to different species?

No but it clearly shows the 0.2% difference makes a difference as we are different in many ways. This study is saying that 100% matches could not be found in 30% of the DNA examined when comparing chimps and people. In other words the code is for a completely different config that nonetheless functions and produces a workable human in the one case and animal in the other. There is no proof of linkage and indeed the complexity of the code argues against that. Change one of these code sequences and the chimp or man starts to die or does not develop properly. There is a certain irreducible complexity to the design of creatures that evolution cannot work with. The better explanation is a supreme designer who knwos how to code better than any programmer I have ever met. Add in the supernatural dimension of a humans existence over which science has no purview and the genetic and the spiritual distinction of a human from a chimp is well nigh enormous
 
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mindlight

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Define the selection criteria by which we can differentiate between design and non design.

A design produces a working model whereas nondesign does not. Malfunctions and impairments degrade design, evolution generally loads it with things it cannot support or takes away from its core functionality and concept. But looking at DNA we are faced with a complexity we did not conceive , may never master and which we understand only superficially. That goes as much for the experts in this area as the beginners. I think this is the main difference between someone who believes in a common ancestor and someone who believes in a common creator. The one trusts the master workman and other pretends to be him and imposes his theories on a complexity that is always more than they describe and suggests he knows how it works. It is humility versus pride, reality versus deception.
 
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ThouShaltNotPoe

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There is no proof of linkage and indeed the complexity of the code argues against that.


Do you assume that the EVIDENCE goes away just by saying so?

Complexity is irrelevant to the question. Why would the "complexity" prevent God from creating evolutionary processes to diversify life on earth?
 
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mindlight

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DNA is NOT a code. it never has been. it doesn't even qualify as blueprint. It is NOTHING like a computer code. If you understood some Chemistry and how DNA works (in a rough sense) you would know this.

Fine DNA is the molecule that biologically encodes the genetic information that distinguishes one form of life from another. It is the information, the way that it is organised and the complexity of that organisation that leads me to compare it to advanced computer programming. As with such programming every line matters and each piece of information is important to the end result. Indeed to achieve a certain result there needs to be a certain irreducible complexity to the information structures, processes and functions and specific complex information makes all the difference to the ability to develop normally, reproduce, freedom from disease etc.

So I would say you were very wrong here and indeed cripplingly so. If you see just the biology you miss the creators hand and the real depth and purpose of what is stored in DNA.
 
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mindlight

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From what I can tell, here are some of the problems with the study. I surely have something wrong, so I am hoping that sfs can point out my mistakes.

First, large indels are going to be counted differently in the two comparisons. Tomkins uses a very simple blastn search. What this will do is include indels in a straight comparison. What he does is use the top search result from a blastn search and use that for his statistics. A blastn search will not return aligned sequence, it will simply return the best match. Therefore, if an indel contains novel sequence then it may match, by chance, with a random sequence elsewhere in the the other genome. This is reported as a match when it shouldn't be since you are not comparing aligned or orthologous sequences.

Also, Tomkins makes the assumption that DNA kept out of the alignment does not have homology to the other species. This is false. What keeps these chunks of DNA out of the assembly is that they simply don't know where in the genome it goes because there is not enough overlap with other contigs. To use an analogy, it is like finding the same shaped jigsaw piece in two different jigsaw puzzles, but you don't have any other pieces in the current puzzle to attach it to so you aren't sure if they belong at the same place in the overall picture.

To some extent I agree with this- that we do not know enough about where the pieces are meant to go in order to make meaningful analyses and come up with meaningful statistics. This should result in a degree of humility in approaching studies of this kind. I see more of that humility in the creationist camp than I have encountered here where people often seem blinded by a wierd kind of deceived academic pride.
 
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FrenchyBearpaw

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A design produces a working model whereas nondesign does not. Malfunctions and impairments degrade design, evolution generally loads it with things it cannot support or takes away from its core functionality and concept. But looking at DNA we are faced with a complexity we did not conceive , may never master and which we understand only superficially. That goes as much for the experts in this area as the beginners. I think this is the main difference between someone who believes in a common ancestor and someone who believes in a common creator. The one trusts the master workman and other pretends to be him and imposes his theories on a complexity that is always more than they describe and suggests he knows how it works. It is humility versus pride, reality versus deception.

So, humans have the necessary genes to synthesize vitamin C (ascorbate), but a mutation prevents us from doing so. Would you consider this to be good, or bad design?
 
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Loudmouth

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This study is saying that 100% matches could not be found in 30% of the DNA examined when comparing chimps and people.

Why is this a problem for evolution?

In other words the code is for a completely different config that nonetheless functions and produces a workable human in the one case and animal in the other.

How does this study show that the genomes have a completely different config?

What if a comparison of the chimp and orangutan genomes had more differences than the chimp and human genomes? What then?

There is no proof of linkage and indeed the complexity of the code argues against that.

How so? How does a 70% similarity using the conditions Tomkins describes rule out common ancestry?

Change one of these code sequences and the chimp or man starts to die or does not develop properly.

Based on what evidence?

The better explanation is a supreme designer who knwos how to code better than any programmer I have ever met.

Why is it a better explanation? When have we ever seen this supposed programmer changing any DNA?
 
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Loudmouth

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To some extent I agree with this- that we do not know enough about where the pieces are meant to go in order to make meaningful analyses and come up with meaningful statistics. This should result in a degree of humility in approaching studies of this kind. I see more of that humility in the creationist camp than I have encountered here where people often seem blinded by a wierd kind of deceived academic pride.

How do the creationists have more humility? You seem to make a lot of claims that are backed by zero evidence.

What I would like to see is for Tomkins to apply the same analysis to the chimp and orangutan genomes. I would strongly suspect that there are more differences between those two apes than there are between chimps and humans. Even more, I would also bet that the% difference between the chimp and orangutan genomes is close the the % difference between the human and orangutan genomes.

You can treat the sequences however you want and come up with whatever qualifications for homology that you want. Those are just numbers. What matters is the relative differences between species using the same method. Evolution makes very specific predictions where this is concerned while ID does not. That is what separates the science of evolution from the pseudoscience of Intelligent Design.
 
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mindlight

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Check this out.

Lactose intolerance and the evolution of the human digestion

I just swam a mile and then had a pint of milk despite being an adult and it tasted very good. While it interesting to know that a specific gene contains or permits this ability in me and also to know how humans contrast or compare with chimps in this respect I am not sure what points come from this that in any way bear on the main points of this discussion. There is a flexibility in our design that allows for these individual variations and overlaps and there may also be reasons for some people being in a sense impaired and lacking certain capacities like the pleasure of a pint of milk after exercise.

Oh, and I think you mean "moot," not "mute." :p

Welcome to CF.

Thanks for correcting my spelling was that worthy of a Razz?
 
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Loudmouth

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It is the information, the way that it is organised and the complexity of that organisation that leads me to compare it to advanced computer programming.

Perhaps you could explain this more. I see a lot of dissimilarity between DNA and computer code, so I am intrigued why your view is so different than mine.

For example, computer code does not chemically react with itself to form three dimensional structures that stop machine code. DNA does. DNA forms stem-loop structures that stops the physical advancement of RNA transcriptases.

Stem-loop - Wikipedia, the free encyclopedia

In my view, DNA is much more like the cogs in a clock than computer code. It is the chemical and physical interactions between DNA and it's environment that matter, and this is completely unlike computer code.

As with such programming every line matters and each piece of information is important to the end result.

From studies done thus far, only 20% of the sequence in the human genome matters. The rest can can apparently be mutated without affecting function.

Indeed to achieve a certain result there needs to be a certain irreducible complexity to the information structures, processes and functions and specific complex information makes all the difference to the ability to develop normally, reproduce, freedom from disease etc.

Irreducible complexity is an expected outcome of evolutionary pathways. Always has been.

The Mullerian Two-Step, or Why Behe's "Irreducible Complexity" is silly

If you see just the biology you miss the creators hand and the real depth and purpose of what is stored in DNA.

You seem to be missing the evolutionary signal in these genomes.
 
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And-U-Say

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So arguments about a common ancestor rather a common designer seem to be less well founded.

<snipped to preserve sanity>

OK, I have about had it with this "common designer" argument. It is an absolutely appalling argument and we need to nip this thing in the bud. So now I will teach you why this claim is utter idiocy and works in exactly the opposite direction of what you, AiG, and all other creationists intend.

The common designer claim centers on the use of a given item or set of items and designs for a second unit as compared to a first unit. It is the use of the same 357 engine in two different Chevy cars. To understand why common design is such a bad proposition, you need to understand why Chevy (or any other industrial manufacturing firm) uses items or designs in multiple units.

Imagine two units being made by Chevy. One is a car, the other a pick-up truck. Each unit has a slightly different size and shape as well as slightly different performance requirements. Yet each is designed with the same engine (and many other parts/systems). Why? Why doesn't Chevy design two different engines so that each of these units will have the perfect engine for its size and requirements?

Chevy reuses the same engine in each of these units (and others as well) because Chevy is limited in design and production resources. Chevy does not have the money and resources to design and manufacture a unique set of parts and systems for each model it produces. If it did have these resources, it would make a complete set of unique parts for each model and there would be no commonalities.

And History bears this out. In the golden age of auto manufacturing in the 1950s and 1960s, American auto manufacturers had vastly less commonality than they do today. At that time, imports were low and profits were high so this could be done. But as competition increased and profits shrank, commonality became, well, more common.

So the reason common parts and designs are used in human manufacturing is because there is a limit on the resources both in design time and manufacturing capability. Common parts and designs are accepted not because they are the best, but because they are good enough. By definition, a commonality in parts or design is sub-optimal. There would be no such thing as common parts or designs if resources were unlimited. That bears repeating; commonality in parts and designs is sub-optimal.

So when creationists use the common designer excuse to explain why common designs are seen in nature, they are (probably unknowingly) stating that their god has limited resources. That he didn't have the time to design the perfect thing so he went with what he used on the previous animal. He used something sub-optimal. And this pretty much flies in the face of this whole universe in six days thing.

The common designer explanation actually supports evolution. Evolution cannot come up with something new and unique for every design, so it has to re-use/re-purpose what it has to start with.

The common designer explanation perfectly supports evolution and perfectly refutes creationism. So why do creationists use it? Because they don't know any better. Because they have not thought it through. And mostly because the evidence of "common design" in nature is so ubiquitous and so perfectly supports evolution that it screams for some sort of rebuttal if creationism is to survive at all. So the common design explanation is a desperate attempt to explain why nature is perfectly at odds with their claims. And the slightest bit of thought reveals the bankruptcy of their efforts.

So please, creationists, don't use this one any more. It obviously does not support your position. In fact, it derails it. Time to come up with something different.

And its "moot", not "mute". I hate it when people do that.
 
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FrenchyBearpaw

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I just swam a mile and then had a pint of milk despite being an adult and it tasted very good. While it interesting to know that a specific gene contains or permits this ability in me and also to know how humans contrast or compare with chimps in this respect I am not sure what points come from this that in any way bear on the main points of this discussion. There is a flexibility in our design that allows for these individual variations and overlaps and there may also be reasons for some people being in a sense impaired and lacking certain capacities like the pleasure of a pint of milk after exercise.



Thanks for correcting my spelling was that worthy of a Razz?


No disrespect intended, but I posted this before I saw your join date. Just based on your post about ID/IR, etc., I just assumed you were a newbie drive-by poster that we get 'round these parts. My apologies. :blush:
 
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sfs

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Perhaps you could explain this more. I see a lot of dissimilarity between DNA and computer code, so I am intrigued why your view is so different than mine.

For example, computer code does not chemically react with itself to form three dimensional structures that stop machine code. DNA does. DNA forms stem-loop structures that stops the physical advancement of RNA transcriptases.
Computer code also does not rely on the computer sometimes failing to execute instructions properly, as DNA does in some cases ("stop codon readthrough").

From studies done thus far, only 20% of the sequence in the human genome matters. The rest can can apparently be mutated without affecting function.
I think the fraction is somewhere in the range of 9% to 20% functional.
 
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