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Author Topic:   DNA sequence comparisons, a similar designer or heredity?
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 1 of 26 (289352)
02-21-2006 7:48 PM


Time and again when presented with a certain piece of evidence Creationists seem to reply with the same unsatisfying retort.
There is a particular line of reasoning I want to discuss here. In various threads recently we've seen it. Let me show you an example:
If a diety created life, how would you expect it to look. The fact that your interpretation of the design of things leads you to believe that evolution is fact has no bearing on what God's design would look like. I would, for instance, expect homology within many organisms if they all had a common creator.
The most compelling (to me) piece of evidence for common descent (macroevolution) is found in DNA sequence comparisons. It is possible to compare the DNA sequences of organisms. The basic idea being that if common descent is true, we should find that these comparisons produce a nested hierarchy similar to the ones produced by cladistics.
Until I learned of this line of evidence, I could understand in some way the creationist position, but having learned of it - I couldn't understand how anyone could say 'There is no evidence for macroevolution'. There is a wonderful debate out there that sums all this up.
The first part can be found here
Evolution demands similarities in the genes and proteins of species thought to have recently evolved from a common ancestor. Since biologists think that humans and chimps both descended from an ancestor who lived just five to eight million years ago, the molecules of inheritance (DNA) and the DNA's expressed proteins should be quite similar between these two species. Conversely, one would expect many more differences between creatures related more distantly, such as humans and turtles.
In fact, there is no difference between the cytochrome c's of human and chimp. Human cytochrome c differs from a rhesus monkey's by just one amino acid, and from an erythrocebus patas monkey's by a different one (Dayhoff 1979). But, humans differ from whales at ten different cytochrome c sites, at 15 for turtles, and so on (Figure 1). There is a "Message" in these proteins: species thought to be closely related turn out to have proteins that are also closely related. If human cytochrome sequences were completely different from those of the apes, or even all other creatures, evolution would have collapsed overnight. Instead, the molecules were in perfect accord with evolutionary expectations - independent and compelling confirmation
The response from creationists? Generally it is 'similar designer', but that doesn't explain why Chimpanzees DNA is more similar to humans than Turtle DNA is. In the interests of fairness you can read ReMine's response here. The whole debate can be viewed here. If someone can make heads or tails out of ReMine's response and its relevance, that would great.
Do any of our creationists/IDers have any response to this nested hierarchy from DNA sequence comparison?
Do they have any response as to why this common designer decided to put this hierarchy in line with cladistics?

Bio evo seems the best place don't you think?

Replies to this message:
 Message 3 by Faith, posted 02-21-2006 11:07 PM Modulous has replied
 Message 4 by Faith, posted 02-21-2006 11:14 PM Modulous has replied
 Message 22 by Brad McFall, posted 02-23-2006 7:47 AM Modulous has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 7 of 26 (289458)
02-22-2006 5:36 AM
Reply to: Message 3 by Faith
02-21-2006 11:07 PM


nesting
I think the way you are going to have to approach this to make it understandable to nonscientists is by first explaining how the DNA of known close relatives looks, so we can see the relevance of the sequencing.
Known relatives (ie related by a few generations) would show up as 100% for the tests noted...since most of them examine highly conserved parts of the genome. Paternal tests do it differently.
Also please explain "nested hierarchy."
All of life falls into a nested hierarchy. I think I'll leave it up to an expert to explain:
http://evolution.berkeley.edu/evosite/lines/IVDhierarchies.shtml writes:
Evolution predicts that living things will be related to one another in what scientists refer to as nested hierarchies”rather like nested boxes. Groups of related organisms share suites of similar characteristics and the number of shared traits increases with relatedness. This is indeed what we observe in the living world and in the fossil record and these relationships can be illustrated as shown below.
Its the classic 'tree' which has a branch of verterbrates, which has sub-branches of reptiles, mammals etc which have sub branches which have sub branches. It forms a hierarchy with sub hierarchies...hence 'nested' hierarchy.
abe: I just remembered this explanation (which I recommend you read)
29+ Evidences for macroevolution writes:
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.
I know we're generally encouraged to use our own wordings, but I feel that a well worded page like this one should be referred to first, if you need further clarification, gimme a shout.
Yes it does, because design-wise, as far as basic physical structure goes, chimpanzees ARE more similar to humans than turtles.
Indeed. However, this also works for those areas of the DNA which are known to have no effect on the morphology (the way an organism looks/physical structure). The classic example is cytochrome c. Its a protein that (as far as I am aware) all life has because it essential for cells to function properly. There are countless ways (ok, not countless, but its an astronomical number) to make functional cytochrome c.
The thing is, we know that the cytochrome c that humans have is perfectly functional in yeast. Cytochrome c can be used alone to detect relatedness, though it won't give totally accurate results it will give a good general trend.
This message has been edited by Modulous, Wed, 22-February-2006 05:52 PM

This message is a reply to:
 Message 3 by Faith, posted 02-21-2006 11:07 PM Faith has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 8 of 26 (289459)
02-22-2006 5:39 AM
Reply to: Message 4 by Faith
02-21-2006 11:14 PM


Also, couldn't we take a collection of anything whatever, say pebbles, and arrange them in a sequence that appears to show a progression from one to another? And yet there would be no progression in any sense except a sense of similarity that exists in our own minds.
Try it, you'll find two things:
1) It'll be difficult to arrange them in any objective way to form a nested hierarchy
2) You'll definitely not be able to find an entirely unrelated way to make the same hierarchy
The methods for making these trees has been tested on organisms that are known to be related, and it generates a nested hierarchy that matches the relatedness that we know exists.

This message is a reply to:
 Message 4 by Faith, posted 02-21-2006 11:14 PM Faith has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 21 of 26 (289589)
02-22-2006 2:50 PM
Reply to: Message 6 by Faith
02-22-2006 12:28 AM


NESTED hierarchies are the key.
Unless what you are measuring is, say, cupcakes, and you find that they are all composed of similar but different proportions of sugar and flour and eggs and baking powder, amazing coincidence, and then you also check the recipes by which they were made, and oh double amazing coincidence, there is the flour, the sugar, the eggs and the baking powder, and in VERY SPECIFIC QUANTITIES TOO, oh happy day.
As has been pointed out to you, you have just used independent lines of enquiry to arrive at a conclusion.
However, the difference between your cupcakes and the sequence comparisons is that we can independently generate the same nested hierarchy with different methods. You can't make a nested hierarchy with cupcakes. Once again referencing the 29+ Evidences:
quote:
. 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
Any phylogeny generated surrounding your cupcakes would be subjective rather than objective (at least that is my prediction). I don't know the maths, but on the subject of common descent:
quote:
Seventy-five independent studies from different researchers, on different organisms and genes, with high values of CI (P < 0.01) is an incredible confirmation with an astronomical degree of combined statistical significance (P << 10-300, Bailey and Gribskov 1998; Fisher 1990). If the reverse were true”if studies such as this gave statistically significant values of CI (i.e. cladistic hierarchical structure) which were lower than that expected from random data”common descent would have been firmly falsified.
Its confusing so let me explain. CI stands for consistency index. It depends on the number of different categories the objects are being nested into. Clever maths can be used to determine what would be a statistically significant result, and what could just be chance.
This is where the big difference lies. Not only can we develop objective nested hierarchies, but we can develop them using different data, and they will all arrive at the same hierarchical structure. This is so highly improbable it surely can't be a coincidence. So:
1) A designer deliberately designed it that way
2) A designer accidentally desigend it that way (coincidence again, we can strike this)
3) Common descent through heredity.
Option 1: As far as I can see leads us back to the Loki scenario
Option 3: Macroevolution
If you want to consider coincidence you have to also start considering the possibility that a random pool of amino acids spontaneously got together and became alive.

This message is a reply to:
 Message 6 by Faith, posted 02-22-2006 12:28 AM Faith has not replied

  
Modulous
Member
Posts: 7801
From: Manchester, UK
Joined: 05-01-2005


Message 26 of 26 (293686)
03-09-2006 1:52 PM


bump due to indirect request
Ooook! writes:
As WK has already pointed out, I don't think this is a fair asessment of the molecular evidence but that is definitely a topic's worth on its own.
I shamelessly bumping this as a response to some of the issues in the Dissecting the Evolutionist Approach thread, I think this is a good place to explore in depth some of the ideas that are being scratched upon there.

  
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