Apes and humans have different designs

[sfs]

What I would like to see is for Tomkins to apply the same analysis to the chimp and orangutan genomes.

I'd like to see him apply it to two human genomes.

 

[mindlight]

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?

As a conservative Evangelical (a definition that probably places me beyond the pale round here) I believe that human beings once lived much longer than they do today (Methuselah) and that indeed we are designed to live forever. We were created to live in a world of abundance which included the tree of life and no doubt innumerable orange trees also. That we have fallen away from that perfect environment, that faults may have developed in our coding etc (although I do not know if this inability to synthesise Vitamin C is an original design feature of people made to garden creation and to harvest its fruits or a fault)-

So from my perspective your question is the wrong one. We were created perfect in a perfect world which has fallen and the comparison with abilities in other creatures is what is erroneous here as that is quite simply not the way we were made. But we shall be restored one day to whatever our original state of perfection was.

 

[FrenchyBearpaw]

As a conservative Evangelical (a definition that probably places me beyond the pale round here) I believe that human beings once lived much longer than they do today (Methuselah) and that indeed we are designed to live forever. We were created to live in a world of abundance which included the tree of life and no doubt innumerable orange trees also. That we have fallen away from that perfect environment, that faults may have developed in our coding etc (although I do not know if this inability to synthesise Vitamin C is an original design feature of people made to garden creation and to harvest its fruits or a fault)-

So from my perspective your question is the wrong one. We were created perfect in a perfect world which has fallen and the comparison with abilities in other creatures is what is erroneous here as that is quite simply not the way we were made. But we shall be restored one day to whatever our original state of perfection was.

This is where we part ways then, when deciding what I hold to be true, compared to you.

I let the evidence lead me to the obvious, most parsimonious, conclusions. You, on the other hand, begin with a belief (what I consider a myth) and then look for selective evidence to support your beliefs.

 

[Loudmouth]

As a conservative Evangelical (a definition that probably places me beyond the pale round here) I believe that human beings once lived much longer than they do today (Methuselah) and that indeed we are designed to live forever. We were created to live in a world of abundance which included the tree of life and no doubt innumerable orange trees also. That we have fallen away from that perfect environment, that faults may have developed in our coding etc (although I do not know if this inability to synthesise Vitamin C is an original design feature of people made to garden creation and to harvest its fruits or a fault)-

So from my perspective your question is the wrong one. We were created perfect in a perfect world which has fallen and the comparison with abilities in other creatures is what is erroneous here as that is quite simply not the way we were made. But we shall be restored one day to whatever our original state of perfection was.

This is where humility comes in. You are claiming that your beliefs trump the evidence that is found in science, and that your beliefs somehow show hundreds of thousands of biologists to be wrong. That is not humility.

What we would like to see is evidence for your claims. Show us evidence that we were once able to live forever. Show us this perfect genome. Show us why the shared genetic markers between humans and chimps is not evidence of common ancestry. Show us why intelligent design would produce a nested hierarchy, and only a nested hierarchy.

 

[sfs]

I also noticed that Tomkins used an ungapped alignment:

Yes, I was going to comment on that. It seems a very odd choice if you're really looking for the degree of similarity between two related species. An indel in the middle will give you two possible matches, each much worse than the original. I'm not a BLAST guru, though, so I'm not sure whether it will align the two pieces (albeit with a lower score) as separate alignments or not. I suppose I should download BLAST and do some experimenting.

It's not a trivial concern: with 5 million known insertion/deletion differences between humans and chimpanzees, there's one every ~500 base pairs, which matters a lot when you're looking at queries of a few hundred bp.

I don't think the large indels themselves (which you mention in another post) will matter very much: to the extent that they are novel sequence (rather than duplication of existing sequence), they won't align, but they only amount to 1.5% of chimpanzee sequence.

 

[sfs]

No but it clearly shows the 0.2% difference makes a difference as we are different in many ways.

Some of that 0.2% makes us different; much of it does not (to the best of anyone's ability to tell).

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.

No, the code mostly functions exactly the same.

 

[Loudmouth]

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.

I have pointed this out on multiple occasions as well. It is interesting to press creationists to answer the question as to why reusing designs makes sense. The only reason it makes sense is to save time and resources, two things that the supposed Creator had an infinite supply of. Why would an all knowing and all powerful Creator with an endless supply of both time and resources need to reuse a single design? Creationists can't seem to answer this one.

Even more, the God of Creationism is even less capable than humans. When we design a new car or truck we are not limited to a nested hierarchy. We can borrow designs from disparate car and truck lineages to hobble together a chimera that works really well. We are free to mix and match as we see fit without ever worrying about a nested hierarchy. Even when we design organisms we regularly borrow and steal from disparate taxa and easily violate a nested hierarchy. So why would an all powerful, all knowing God be limited to a pattern of similarity and divergence that only evolution produces? Humans aren't limited in this way, so why God?

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.

Even more, it can't borrow from other lineages like designers can.

 

[Loudmouth]

I'd like to see him apply it to two human genomes.

You might find this webpage interesting:

Finally, the average number of pattern matches per chromosome, shown at the bottom of the table, was very different in the two cases: 9616 for human vs. human comparisons, but only 6173 for chimp vs. human comparisons. The average number of patterns without a match for human vs. human comparisons was (10000 – 9616) = 384, or in percentage terms, 384/10000 = 3.84%.
A statistical comparison of two human genomes | Uncommon Descent

​

Using the creationist 30 bp "all or nothing" comparison humans are only 96% similar to each other.

 

[Standing_Ultraviolet]

I was just thinking, using the typical methods of determining genetic similarity rather than the ones that were apparently used in this study (ie., comparing a sequence of 30 base pairs and counting one difference as a zero percent similarity for that sequence), wouldn't a thirty percent difference be absolutely enormous? Other than non-coding DNA, which is fairly similar between most species, there's not a lot you can tinker with before you start getting colossally different results. A thirty percent difference sounds a lot more like the distinction between a human being and an antelope than the difference between a human being and any primate.

 

[mindlight]

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.

Common designer works with a Theistic evolutionary perspective also true but in a different way. But if there are subtle differences in each of the chromosones then a better view is that each was specifically created for what the creator had conceived for that type of creature. A single letter can entirely change the direction of one process or another. Our Creator did not have any limit on the resources He could employ. The way He has created bears His signature and also shows the immense complexity and diversity of ways in which he has implemented it.

 

[mindlight]

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.



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.



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

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



You seem to be missing the evolutionary signal in these genomes.

In computing there are multiple levels of implementation. There is the hardware level, the OS that interfaces beween the other layers and this hardware, the application logic layer and the presentation layer. It is not an exact analogy to DNA and the information contained in it but I think it is a helpful one. With DNA the hardware is the biological and this distinguishes in from most computer hardware in existence. However see here. If we can work out how to store information in molecules then in a sense we have a possible OS sorted out. But we have still to understand the higher levels of information organisation and logic- the mind if you like of the programmer. The depth and sophistication of this coding in DNA is beyond brilliant in my view and could not have occurred by accident. It is evidence of a master creator /designer.

 

[Eight Foot Manchild]

The depth and sophistication of this coding in DNA is beyond brilliant in my view and could not have occurred by accident.

No one is claiming it happened by accident.

It is evidence of a master creator /designer.

No it isn't. You are anthropomorphizing.

 

[And-U-Say]

Common designer works with a Theistic evolutionary perspective also true but in a different way. But if there are subtle differences in each of the chromosones then a better view is that each was specifically created for what the creator had conceived for that type of creature. A single letter can entirely change the direction of one process or another. Our Creator did not have any limit on the resources He could employ. The way He has created bears His signature and also shows the immense complexity and diversity of ways in which he has implemented it.

Ummmm. No. You are trying to say "well, they are the same, but not exactly the same". Every animal is filled with "re-used" design. Again, all of this is sub-optimal and thus does not reflect a creator at all.

 

[Loudmouth]

The depth and sophistication of this coding in DNA is beyond brilliant in my view and could not have occurred by accident.

I must have missed where you demonstrated that DNA could not come about by evolution. Care to point to that evidence?

It is evidence of a master creator /designer.

How is a nested hierarchy evidence of a master creator/designer? That is a question that creationists never seem to answer.

 

[Loudmouth]

But if there are subtle differences in each of the chromosones then a better view is that each was specifically created for what the creator had conceived for that type of creature.

Why?

Our Creator did not have any limit on the resources He could employ.

Then why create species so that they fall into a nested hierarchy? Why did the Creator limit himself to a very restrictive pattern of divergence and homology that only evolution produces?

 

[sfs]

I checked: the low percentage of matches does in fact result from only looking for ungapped alignments. I downloaded the human and chimpanzee genomes and the BLAST executable. As a test set, I pulled 500 randomly sampled, non-overlapping slices from chimpanzee chromosome 12, each 300 base pairs long. After dropping any slices that contained unknown sequence (i.e. 'N's), I had 471 test sequences. I fed these into BLASTN against human chromosome 12, using the parameters specified by Tomkins, with and without allowing gaps in the alignment. With no gaps, 68% of my queries yielded matches, in good agreement with Tomkins's finding. With gaps allowed, 100% of queries matched; of these, one or two were of poor quality and likely represent random matches. So the actual matching rate, when doing a proper alignment, was 99.6%.

I could add some sarcastic comments about the quality of creationist research, but it doesn't seem worth the trouble.

 

[StormanNorman]

I checked: the low percentage of matches does in fact result from only looking for ungapped alignments. I downloaded the human and chimpanzee genomes and the BLAST executable. As a test set, I pulled 500 randomly sampled, non-overlapping slices from chimpanzee chromosome 12, each 300 base pairs long. After dropping any slices that contained unknown sequence (i.e. 'N's), I had 471 test sequences. I fed these into BLASTN against human chromosome 12, using the parameters specified by Tomkins, with and without allowing gaps in the alignment. With no gaps, 68% of my queries yielded matches, in good agreement with Tomkins's finding. With gaps allowed, 100% of queries matched; of these, one or two were of poor quality and likely represent random matches. So the actual matching rate, when doing a proper alignment, was 99.6%.

I could add some sarcastic comments about the quality of creationist research, but it doesn't seem worth the trouble.

Pretty cool.

 

[Loudmouth]

With no gaps, 68% of my queries yielded matches, in good agreement with Tomkins's finding. With gaps allowed, 100% of queries matched; of these, one or two were of poor quality and likely represent random matches. So the actual matching rate, when doing a proper alignment, was 99.6%.

What was the average identity for the gapped matches by your estimation?

 

[sfs]

What was the average identity for the gapped matches by your estimation?

Single-base mismatches: median 3, mean 4.0 per 300 bp slice. Based on a mean substitution divergence of 1.3%, you'd expect a mean of 3.9.

Looking more closely at the results, I see another three matches with good scores but large numbers (> 40) of mismatches. These are probably bogus matches as well -- probably matching to the wrong repetitive sequence. The fact that the analysis is done with unmasked sequence (i.e. no filtering to remove repetitive elements) means that everything should be taken with a large grain of salt. But if you really want to do the job right, you don't use BLAST at all, but instead use alignment code tuned for the purpose, and you do a lot of work to make sure you're making sensible comparisons -- which is of course what was done in the chimpanzee genome paper. Reading the AiG paper reminds me of judging high school science fair projects. They really have no clue what they're doing.

 

[sfs]

Also, there were a mean of 0.44 indels per 300 bp slice. Based on the chimp genome paper I'd expect something like 0.56.