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Author Topic:   DNA sequence comparisons, a similar designer or heredity?
Modulous
Member (Idle past 185 days)
Posts: 7789
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 responded
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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 26 (289386)
02-21-2006 10:01 PM


Thread moved here from the Proposed New Topics forum.
  
Faith
Inactive Member


Message 3 of 26 (289395)
02-21-2006 11:07 PM
Reply to: Message 1 by Modulous
02-21-2006 7:48 PM


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.

Also please explain "nested hierarchy."

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.

Yes it does, because design-wise, as far as basic physical structure goes, chimpanzees ARE more similar to humans than turtles.


This message is a reply to:
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Faith
Inactive Member


Message 4 of 26 (289397)
02-21-2006 11:14 PM
Reply to: Message 1 by Modulous
02-21-2006 7:48 PM


Do they have any response as to why this common designer decided to put this hierarchy in line with cladistics?

I always have this uncomfortable feeling about cladistics that it's really some kind of trick or hoax. That is, correct me if I'm wrong, but I understand it to be a scheme that maps traits and finds that they follow the pattern of the taxonomic tree. But the taxonomic chart was based on observed similarities, so what exactly is it that we find out by observing that cladistics discovers the same kinds of similarities, the same patterns? Shouldn't we expect this?

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.

And then I guess we could map these similarities in a systematic way, getting more refined about it, and it would follow the same sequence as the pebbles, and that would be the equivalent of cladistic's relation to taxonomy, if I grasp it that is.

It seems to me that you are comparing apples and apples and they SHOULD exhibit similar patterns because the whole thing is based on the observation that it is possible to arrange creatures in this fashion. It's like those figure-arranging tasks on IQ tests. None of it proves descent, all it shows is that it is possible for the human mind to recognize similarities of form and group forms in a SEEMING arrangement of progressive design features.

This message has been edited by Faith, 02-21-2006 11:23 PM

This message has been edited by Faith, 02-21-2006 11:57 PM


This message is a reply to:
 Message 1 by Modulous, posted 02-21-2006 7:48 PM Modulous has responded

Replies to this message:
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crashfrog
Inactive Member


Message 5 of 26 (289406)
02-21-2006 11:58 PM
Reply to: Message 4 by Faith
02-21-2006 11:14 PM


And yet there would be no progression in any sense except a sense of similarity that exists in our own minds.

If we didn't have a record of the relative ages of fossil organisms, that would be a legitimate concern.

The proof is not that we can arrange a cladistic diagram. The proof is that when we do, it's entirely consistent with the relative ages and time periods of these different organisms. And the further proof is that when we compare these two diagrams to the diagram derived by genetics, it agrees, too.

When you measure something three different ways and you get the same result each time, the proper conclusion is that you're actually measuring what you claim to be measuring, not that you're experiencing a coincidence or a hoax.


This message is a reply to:
 Message 4 by Faith, posted 02-21-2006 11:14 PM Faith has responded

Replies to this message:
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Faith
Inactive Member


Message 6 of 26 (289407)
02-22-2006 12:28 AM
Reply to: Message 5 by crashfrog
02-21-2006 11:58 PM


The proof is not that we can arrange a cladistic diagram. The proof is that when we do, it's entirely consistent with the relative ages and time periods of these different organisms. And the further proof is that when we compare these two diagrams to the diagram derived by genetics, it agrees, too.

Well, but a creationist of course denies the "relative ages and time periods" part of the picture here. And why wouldn't the genetic diagram agree if we're talking even only about mere design similarity? I see nothing more than that proved by this.

When you measure something three different ways and you get the same result each time, the proper conclusion is that you're actually measuring what you claim to be measuring, not that you're experiencing a coincidence or a hoax.

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.

This message has been edited by Faith, 02-22-2006 12:31 AM


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Modulous
Member (Idle past 185 days)
Posts: 7789
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


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Modulous
Member (Idle past 185 days)
Posts: 7789
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.


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Wounded King
Member (Idle past 2176 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 9 of 26 (289473)
02-22-2006 7:41 AM
Reply to: Message 4 by Faith
02-21-2006 11:14 PM


I always have this uncomfortable feeling about cladistics that it's really some kind of trick or hoax. That is, correct me if I'm wrong, but I understand it to be a scheme that maps traits and finds that they follow the pattern of the taxonomic tree.

You are wrong.

Early taxonomic systems and the original linnean system are rather crude precursor forms of cladistics. Living things were categorised based on apparent similarities.

What cladistics does is to produce a much more formalised and rationalised taxonomic tree based on specific shared traits known as synapomorphies which is a phylogenetic tree rather than merely taxonomic.

Synapomorphies are traits which are common to one or more taxa (taxa is the plural of taxon, a taxon being a specific grouping of organisms) and which are thought, or known, to be inherited from a common ancestor.

A taxonomic tree simply categorises into nested hierarchies, a phylogenetic tree contains inferences about the common ancestry of organisms based on synapomorphic characteristics.

The strength of the evidence that Modulous has been discussing is that independent Genetic traits, such as those involved in basic cellular metabolism, which do not affect the synapomorphic morphological characteristics which have been used to produce traditional cladistic analyses, produce remarkably consistent results when used as the basis for cladistic analysis.

So both the morphological cladistic analysis and the cladistic analysis of genetic sequences produce similar phylogenetic trees despite being as independent a measure as possible.

An argument can of course be made that this is all down to 'common design' but this is an ad hoc argument with purely explanatory and no predictive power.

Someone who believes in common descent would have good cause to predict that genes with no effect on morphology would produce the same patterns through cladistic analysis as would analysis of morphological characteristics or the genes controlling them since they have all been inherited through the same ancestors. What would compell a believer in common design to make such a prediction?

TTFN,

WK

This message has been edited by Wounded King, 22-Feb-2006 12:42 PM


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nator
Member (Idle past 251 days)
Posts: 12961
From: Ann Arbor
Joined: 12-09-2001


Message 10 of 26 (289491)
02-22-2006 9:04 AM
Reply to: Message 6 by Faith
02-22-2006 12:28 AM


When you measure something three different ways and you get the same result each time, the proper conclusion is that you're actually measuring what you claim to be measuring, not that you're experiencing a coincidence or a hoax.

quote:
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.

You are misunderstanding.

When crash talks about measuring something three different ways, it isn't like having the same three recipes, or even just similar recipes.

It's like checking a fact in a criminal investigation; corroborating evidence from several independent sources tends to increase one's confidence that the fact is correct.


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FliesOnly
Member (Idle past 2226 days)
Posts: 797
From: Michigan
Joined: 12-01-2003


Message 11 of 26 (289495)
02-22-2006 9:23 AM
Reply to: Message 6 by Faith
02-22-2006 12:28 AM


Independent Measurements.
Faith writes:

Well, but a creationist of course denies the "relative ages and time periods" part of the picture here.

Which is exactly what I mentioned in another thread. When confronted with overwhelming evidence...simply deny it.

Cladistics is a wonderful tool that predicts an outcome. Let me make an attempt to explain the basics behind this concept. We set up rules on how organisms can be listed. Namely, we look at shared, derived characteristics. That is...things that are NEW. Species that then share this novel characteristic are grouped past a given branch point. Groups closer on the cladogram share a more recent common ancestor than those further apart. It’s a very objective way to list organisms…and importantly, it can be falsified. A cladogram would be useless if many species were found that combined characteristics of different nested groups. But yet we don’t see this. If it were impossible to place species into nested groups, evolution would be, for the most part, shown to be false. But yet again, we don’t see this.

Now, before you hand wave this all away by saying, “Well God simply designed them that way”, you should look at other evidences and take them as a whole. You say creationists don’t accept evolutionary time lines. But yet, organisms listed on these cladograms match up with a time line as we would predict using the ToE. Keep in mind that a cladogram does not use any sort of dating method. It simply lists organisms based on novel traits. Yet they match.

Faith writes:

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.

I'm not sure what you're trying to get at here. Are you suggesting that three different cupcakes from three different locations are all basically the same? So what. How does this compare in any way to crashfrogs example of measuring something using three different, completely independent, methods all giving the same answer? All you've done is determine that they are cupcakes using their "DNA" (ingredients), so to speak. Big deal.

Let me see if I can use your cupcake example to teach you about time, cladistics, and genetics. We find a cupcake…or better yet…what we think “might” be a cupcake. We want to know if it is a cupcake and how it is related to other baked goods that we have found (which consists of a brownie, a cake, a cookie, a pie, a loaf of bread, and a butter tart). Let’s make a cladogram to list these baked goods. I’ll spare you all the details (because I cannot cook), but I would predict that on a cladogram, the cupcake would be nested with the cake, based on novel characteristics. And it does.

Next we would use genetics to group the baked goods. Again, not knowing the ingredients of all of these things, I would predict that the cupcake would again be nested with the cake. And it is.

Lastly, we want to know when these items were baked. We could use moisture content and/or a “staleness” level to determine this. (Of course, for this information to be of any value we would first have to have a theory which we would use to predict the outcomes of each of these measurements. Let’s say we have something called the Theory of Baked Goods (ToBG), and that this theory predicts that in the evolution of baking, bread was the first thing to ever be made. Archeological digs have determined that this was followed by butter tarts, then pies, cookies, brownies, cakes and lastly cupcakes (in that order)). Anyway, we date the item and we find that it is the most fresh.

Now we have even more confidence that we have found is a cupcake. Why? Well let’s go back to crashfrog and his example.:

What crashfrog was trying to tell you was that if we use three, independent methods of measurement to determine if what we have found is indeed a cupcake, and if each method leads us to the same conclusion, then the likely hood of it being anything else is diminished with each “positive” outcome. And, as even more measurement “types” are discovered and utilized, and if they support the predictions based on the ToBG, then the likelihood of it being anything other than a cupcake is lessened each time…and, IMPORTANTLY, the theory is supported and strengthened, and we are more and more certain of our claim. Does this help?


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Wounded King
Member (Idle past 2176 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 12 of 26 (289496)
02-22-2006 9:29 AM
Reply to: Message 11 by FliesOnly
02-22-2006 9:23 AM


Re: Independent Measurements.
Too... much.... tortured... analogy...

and now I want a brownie.

TTFN,

WK


This message is a reply to:
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crashfrog
Inactive Member


Message 13 of 26 (289497)
02-22-2006 9:29 AM
Reply to: Message 6 by Faith
02-22-2006 12:28 AM


Well, but a creationist of course denies the "relative ages and time periods" part of the picture here.

Well, they don't, actually. Granted they reject the geologic scale of the timetable, but they certainly don't reject the idea that it is a timetable.

If you're burying things by sedimentation, the stuff on the bottom has to be older than the stuff on the top. How do you sediment something below another layer? It's physically impossible.

The reason that I said "relative age", and not "absolute age", is because creationists and evolutionists alike agree that the geologic column is a timetable of relative ages - this came before that, that came before the other, etc. Never mind the actual time involved.

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.

Absolutely irrelevant example. You proposed that cladistics measures something that doesn't exist. The conclusion, when you try to measure something in three different ways and succeed three times, is that you actually measured what you claim to have measured - not that you were hoodwinked three seperate times.

You didn't propose cupcakes from one cosmic baker; you said that the cupcakes didn't exist. Or didn't have any sugar in them, let's say. If you measure these cupcakes with three different means, and you find the same amount of sugar now matter how you measure it, the proper conclusion is that you've accurately measured the sugar content of these cupcakes, not that the cupcakes are sugar-free.


This message is a reply to:
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Parasomnium
Member (Idle past 777 days)
Posts: 2191
Joined: 07-15-2003


Message 14 of 26 (289499)
02-22-2006 9:31 AM
Reply to: Message 6 by Faith
02-22-2006 12:28 AM


Failing analogy
crashfrog writes:

When you measure something three different ways and you get the same result each time, the proper conclusion is that you're actually measuring what you claim to be measuring, not that you're experiencing a coincidence or a hoax.

Faith writes:

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.

I'm afraid the gospel choir can sit down again, because your analogy does not disprove Crashfrog's point. On the contrary, it is just another example of it.

Crashfrog's statement basically describes, in very general terms, a way of proving a certain claim by doing measurements in different ways, and understanding that if the different results independently confirm the claim, then that is evidence for it.

Your analogy, albeit more specific, is no different: it describes the process of proving the claim that certain cupcakes are made according to certain recipes. You do this by "measuring" cupcakes in two ways, one of which is an analysis of the actual cupcakes, the other an examination of the recipes. The results of both measurements point in the direction that this cupcake is made according to that recipe, & cetera.


"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.

Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
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FliesOnly
Member (Idle past 2226 days)
Posts: 797
From: Michigan
Joined: 12-01-2003


Message 15 of 26 (289505)
02-22-2006 9:53 AM
Reply to: Message 12 by Wounded King
02-22-2006 9:29 AM


Re: Independent Measurements.
Wounded King writes:

Too... much.... tortured... analogy...
and now I want a brownie.

I know, I typed the damned thing...how do you think I feel? And my jaw is still pretty sore from yesterday, which makes the whole thing that much more "painful". :)

Personally though...I want a butter tart!


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