Chimps and Humans

[Administrator2]

[Administrator: this thread is spinning off of the Haldane's Dilemma thread and in our opinion deserves its own thread.]

JOHN PAUL

1. Walter ReMine has claimed that human evolution can’t be explained from a primitive ancestor accruing 1667 beneficial mutations (and for the record, 25,000 neutral expressed mutations).
2. I, as well as others have pressed Mr. ReMine for validation of this claim.
3. John Paul responded to my post, but instead of answering the questions I brought up, he tried to change the subject and asked me to provide support for claims I never made!
4. I continued to press John Paul for some answers, and he repeatedly passed.

John Paul:
1. Evolutionists have claimed that humans have evolved from some primitive ancestor, which is also the ancestor of chimps. As a matter of fact they claim that all of life's diversity evolved from some genetically unknowable population(s) of single-celled organisms. By the very nature of these claims most cannot be substantiated.

2. I, as well as others have pressed evolutionists for validation of their claims.

3 and 4. The purpose of my response was to show evolutionists ask things of their opponents that they themselves are unwilling or unable to do. Don’t want the lurkers to get the feeling this alleged scenario is unique to the Creationist camp.

As evident by a previous statement Also I am trying to get clarification on what you (evolutionists) want Walter to substantiate, as it is unclear to me- what you want and what ancestor Walter is saying 1667 beneficial (plus x neutral) is too few. I am also looking for clarification. (personally I would be willing to wager no amount of mutations would do the trick) But even without it we may still be able to go with Helen’s suggestion. Might as well start somewhere.

: John Paul:
You misrepresent what Walter stated. From your first post in this thread:
”Those must explain the origin of upright posture, speech, language, the appreciation of music, and all the other human adaptations over that period.” – Walter ReMine, January 13, 2002.

Just because our alleged ancestors are alleged to have walked upright does NOT explain its origin.

Robert:
There is no misrepresentation, you just misunderstood the point.

John Paul:
I think you misrepresented what was being said. Sure chimps can walk upright, so can bears, dogs and other animals. Of course these animals can NOT do so habitually. Therein lies the difference.

The following can be read in its entirety at: http://www.uia.ac.be/crc/foot_morphology.html

Background of the study

The development of habitual bipedal locomotion is a key factor in the hominisation process. Bipedalism, together with quadrupedalism, climbing (see also "climbing in bonobos")and brachiation, makes part of the locomotory behaviour of many primates. But, during human evolution, bipedalism has formed an increasing percentage of the locomotory repertoire and ultimately becomes the only type of locomotion in modern humans.
This gradual development of habitual bipedalism is coupled with the transition of an arboreal way of life, where the foot with an opposable hallux has mainly a grasping function, to a terrestrial way of life, where the foot functions as a rigid lever. These changes in locomotion and biotope are reflected in the structure of the foot, the shortening of the phalanges, the occurrence of a longitudinal foot arch and the gradual loss of the opposability of the hallux.

Why study gibbons & bonobos?
The question can be asked why only hominids became habitual bipeds. Indeed, all recent genera of the Hominoidea (apes) show some bipedalism in their locomotor repertoire. It may thus seem surprising that the closest relatives of man, namely the common chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus), make only limited use of bipedal locomotion, despite the large morphological and morphometrical similarity with humans and the hominid ancestors. Gibbons (Family Hylobatidae), the furthest relatives of man within the Hominoidea, are, in contrast, the most bipedal of all non-human primates and this despite their specific adaptations to an other type of locomotion, namely brachiation.

All you have to do is go to http://www.google.com/ plug in bipedal locomotion or evolution of language. The language links I gave earlier (in a post above) are good examples of what we know about its evolution and support Walter’s premise. And to put it another way, no one has brought forth any evidence that would show his assumption to be in error.

For example the following is a pro-evolutionary look at the issue (locomotion):

http://www.pbs.org/wgbh/evolution/library/07/1/l_071_02.html

Although they make it seem like an easy enough process (because they have no doubt it happened), do we even know if it is genetically plausible? IOW, are the adaptive differences even achievable by mutations culled by natural selection? Chimps and humans upright posture and bipedal locomotion are only similar in the fact they are both upright and both bipedal. Seeing we are discussing what is the alleged common ancestor of the two (regarding its posture & locomotion), either the chimps lost the ability or the ancestor didn’t have it, and humans & the chimps gained it, albeit to differing extents.

A little Internet research shows us that, using the knowledge we do have, Walter’s assumptions are good. Our means of locomotion, posture and language (including speech) are unique to us. The only reason to assume that those adaptations can evolve is to infer that they did.

John Paul:
I understand design, design standards (which allow different companies’ products to work together) and what is required to allow separate components to form a symbiotic relationship. Therefore I find this argument to be very strong.

Robert: So, you understand design, and you extrapolate that into thinking you know what God might have done? Are you saying that God is somehow limited to the methods of mankind? After all, I don’t envision him a lab cooking up DNA sequences and saying “Aha, this one works. Let’s stick with the plan.” This seems to be your implication.

John Paul:
No, that is your inference (btw I didn’t mention God). Sometimes design is mind correlative. For example if you are walking across a meadow and come upon 10000 trees in 100 x 100 evenly spaced rows, would you think nature dispersed seeds in that neat arrangement or would you think it was planted that way intentionally? It is not necessary to know the mind of the designer or the designer in order to detect design.
Do I think the designer was limited? Yes, in the sense that in the physical plane designs are limited by physical law. As far as we know there is only one DNA coding sequence that gives us humans. The ends justify the means so God could have used any method to get the human OS up, running and with the proper hardware.

Do I know why the designer used similar DNA sequences for different organisms? Not exactly but by using science we can hazard an educated guess (IOW we can infer). (see the AiG article I linked to above and my earlier post)

As far as the AiG article it was on topic pertaining to homology and DNA similarity being evidence for a Common Creator. Also it is very relevant to what I had posted. Did you even read it? Has the complete chimp genome been sequenced? No. Have entire genome sequences of chimps and humans been compared? No. In fact much less than 1% of each organisms’ genome has been compared (70 genes).

When AiG proclaims “The DNA similarity data don’t quite mean what the evolutionary popularizers claim!” They are of course referring to the evolutionary claim of similar DNA equals close evolutionary relationships via common descent. Why you think that proclamation undermines the Common Creator scenario is beyond me. To me it shows ingenuity- that is making many different things out of common parts. It also calls into to question the power of DNA. http://www.mindfully.org/GE/GE4/DNA-Myth-CommonerFeb02.htm

It could be that we find out that changes in DNA won’t give us the great transformations required by the ToE.

Homology, including DNA similarity, has been used as evidence for a Common Creator for years. As far as inferring design is concerned once the double helix was discovered any doubts of the validity of design should have been removed. Knowledge is the ally of Creationists and IDists.

On to some numbers:

To further Helen’s point until we have finished the Human Genome Project and the Chimp Genome Project (some 70 genes (well less than 1%) have been compared with less than 1% difference found- 99.01% similar)

[ http://www.uchicago.edu/aff/mwc-amacad/biocomplexity/conference_papers/goodman.pdf *],

we won’t have the proper numbers to work with.
If we use 1% that would be a difference of 32 million base pairs (assuming both genomes are of 3.2 Gbp (Giga (= billion) base pairs)). However until we learn the loci of the differences and what those positions do to an organism all we have are numbers. IOW, in order to get the full effect we may have to wait until Human (chimp) Proteome Project (identifying all proteins) and then the Human (chimp) Physiome Project (how the proteins interact) are complete, or at least underway. But sometimes you work with what you have.

As you will read in the above article “However, there are also differences in the structure of the proteins encoded by genes, which undoubtedly account for some of the observed differences in phenotypes.” David Plaisted offers some insight as to the problems with changing the structure of a protein:

http://www.cs.unc.edu/~plaisted/ce/mutation.html and http://www.cs.unc.edu/~plaisted/ce/blocked.html

The basics of which is just how much change can a protein’s structure take and still be a functional part of the chain or function properly in its particular job? How many malfunctioning proteins can an organism handle?

[*from the article: “In order to analyze which amino acid replacements have occurred during the evolution of humans and apes, the evolutionary relationships among the species being studied must be inferred.” Which makes me wonder what happens when a Common Creator is inferred?]

Just for reference:

From: http://imbs.massey.ac.nz/evo2.pdf

genetic differences, chimp/human:
- one chromosome fusion
- one enzyme lost (sialic acid)
- a couple of differences in copy number
- many small inversions
- transposable elements activated
- Many indels (insertions/deletions)
- many point mutations
- Some introns expanded/contracted

Using just the numbers saying we have a 32 million base pair difference we would have to figure out the mutation accumulation rate of each branch. If we use Helen’s starting assumption of a 50/50 split that would be 16 million base pairs for each divergent branch. 16 million base pair differences/ 5 million years = 3 base pairs per year. We know that can’t be so we break it down into generations. A ten-year generation period would be 30 base pairs becoming fixed in a population every ten years. A twenty-year generation period would be 60, and so on. That is not to have 60 different base pairs in the population, but 60 bp that must become fixed (on average) per organism throughout the population. And if those organisms don’t take over, or get isolated from the population you add the risk of losing that 60 bp in the ensuing generations. One step forward, 2 steps back.

However the article on the chimp genome project estimates chimps & humans differ in 445,000 coding positions. 445,000/ 2 = 222,500, which amounts to just under 1 (.89) becoming fixed (per generation) in a population with a generation of 20 years. (Plus a number of non-coding mutations. this is considering a split of 5 million years ago).

The article then goes on to say ” Of these differences, the key ones at the nonsynonymous (nucleotide substitutions that change amino acids) sites are predicted to be found on between 2850 and 4000 genes.” So, still assuming a 50/50 split that would be between 1425 & 2000. If it takes much more than (an average of) 1 difference per gene to be one of the key ones, that would mean 1667 would be too few.

Are the assumptions used above good or not? Let the discussion begin.

Here is another article by David Plaisted that is relevant to this part of the discussion although he discusses from the ape-human split which was allegedly before the chimp-human split:

http://www.bearfabrique.org/Evolution/plaisted/

[ July 25, 2002, 09:35 AM: Message edited by: Administrator ]

 

[Administrator2]

ROBERT RAPIER

First of all, let me comment on John Paul’s analysis of the problem. I thought he did a thorough and commendable job, and I largely agree with his treatment of Haldane’s Dilemma. I actually like his analysis better than the one I worked up. Both of them demonstrate that Mr. ReMine’s fundamental premise is unjustified. We approached the problem slightly differently, but our numbers are in close agreement. Since John Paul has posted his analysis, I have also asked that mine be posted. It may be found in the Haldane’s Dilemma thread, since my response to John Paul in this thread strays somewhat off of the topic of Haldane’s Dilemma. The other response is very specific to Haldane’s Dilemma.

But first things first:

By the very nature of these claims most cannot be substantiated.

In the same way that O.J. Simpson’s claim not to have murdered his wife can’t be substantiated. After all, we don’t have a video of him doing it. But certain logical inferences can be made based on circumstantial evidence. Regardless, a certain segment of the population still thinks him innocent. Sometimes it seems like no amount of evidence is good enough when one doesn’t have a photo of the crime being committed.

John Paul: I think you misrepresented what was being said. Sure chimps can walk upright, so can bears, dogs and other animals. Of course these animals can NOT do so habitually. Therein lies the difference.

At least now you only think there was misrepresentation. Read carefully what Mr. ReMine is saying. He is stating that all of these traits had to originate on the path from unidentified human/chimp ancestor to modern man. The fact that the ancestor is unidentified alone invalidates his claim. Add to that the varying degrees of bipedalism for hominid relatives, extinct and living, and Mr. ReMine’s hypothesis is further weakened. While it may be true that the ancestor could not walk fully upright, Mr. ReMine’s has provided no support for this assumption. Furthermore, the links you have provided have not helped support his claim. Think about it this way. If the common ancestor did exist, it would be expected to have some blend of human and chimpanzee traits. Since humans do walk upright, chimpanzees can, australopithecines are believed to have, Neanderthals did, etc., then it is reasonable to assume that the common ancestor could have walked upright. Claims to the contrary are hyperbole.

Although they make it seem like an easy enough process (because they have no doubt it happened), do we even know if it is genetically plausible? IOW, are the adaptive differences even achievable by mutations culled by natural selection?

As you correctly pointed out, many of the differences between humans and chimps are made up of insertions/deletions, intron changes, point substitutions, etc. These are well known mechanisms for mutating DNA from generation to generation. Therefore, it is certainly within the realm of possibility that the changes could have taken place over the course of many generations. Of course you may wish to offer evidence for a mechanism that might halt these changes at some point. This is admittedly not my area of expertise, but I am unaware of any such mechanism. Your implication seems to be that there is a barrier in place.

It is not necessary to know the mind of the designer or the designer in order to detect design.

This is easily shown to be false. While it is normally true with respect to items that we know are designed (such as a watch), DNA does not fall into that category. Here is an example. Let’s say that the DNA of a certain organism mutates from one generation to the next. Let’s say that a gene duplicates. Now, take that duplicate gene, and tell me how you will distinguish this portion, which is clearly present due to an error in the DNA copying mechanism, from the original DNA which you assert is designed. In other words, we all agree that DNA changes. Which part of it is designed?

In addition, using the same logic that you just used to “detect” design, the designer would also require a designer. After all, the designer would meet anyone’s definition of a complex entity. We would clearly recognize design in this entity. If you disagree, please explain why the designer would not fit the category of something requiring a designer.

As far as the AiG article it was on topic pertaining to homology and DNA similarity being evidence for a Common Creator. Also it is very relevant to what I had posted. Did you even read it?

Yes I did. If you read it, you see that they are ridiculing the possibility that humans and chimps would be 99% similar in their DNA. Why? If this is strong evidence for a common designer, why was this not predicted? Why were Creationists everywhere playing down the possibility of 99% similarity? AIG also makes the argument that DNA and homology are not as closely linked as many people claim. So, why 99% similarity between humans and chimps? Why not 99% similarity between humans and birds? They seem to be trying to stake out a position that no matter how the DNA sequencing turned out, they could claim victory. I would like to see Creationists make some bold predictions, as John Morris did in 1989 when he predicted that molecular biology would falsify evolution within 5 years.

Why you think that proclamation undermines the Common Creator scenario is beyond me.

See above. When the Common Creator is used to justify any possible scenario, this explanation is not very useful.

The article then goes on to say ” Of these differences, the key ones at the nonsynonymous (nucleotide substitutions that change amino acids) sites are predicted to be found on between 2850 and 4000 genes.” So, still assuming a 50/50 split that would be between 1425 & 2000. If it takes much more than (an average of) 1 difference per gene to be one of the key ones, that would mean 1667 would be too few.

Are the assumptions used above good or not? Let the discussion begin.

It is actually a really good start. I don’t want this to get too long or technical, but I want to point out the logical error in your last sentence. You mentioned earlier a mutation involving sialic acid. This particular mutation is caused by a 92 base pair deletion in a gene. As far as Haldane’s Dilemma goes, this would count as a single mutation (if it had been beneficial). So to be clear, 1667 beneficial mutation is not 1667 base pair changes. A beneficial mutation could theoretically arise from a single base pair change, but other mechanisms can result in more significant changes. Also, the key word is beneficial as far as Haldane’s Dilemma is concerned. The sialic acid mutation would fall into the deleterious category, as it made humans more susceptible to certain diseases. Source: http://www.pnas.org/cgi/content/full/95/20/11751

I would like to call attention to the link you posted above, as it was an excellent source of information. That link was: http://www.uchicago.edu/aff/mwc-amacad/biocomplexity/conference_papers/goodman.pdf From this link, we find that they discovered that 5 out of 70, and possibly as many as 7 out of 70 genes examined were undergoing positive selection. After you crunch the numbers, you state that extrapolating back to the common ancestor would give us between 1425 and 2000. I agree, with the following caveats. The article didn’t have a date on it, but they are assuming 1.5% gene coding positions. The Science article announcing the decoding of the genome puts this figure at 1.1%. Source: http://www.sciencemag.org/cgi/content/full/291/5507/1304

If the 1.1% number is correct, that reduces the range to 1045 to 1467. Also, the assumption was made that the genome has 40,000 genes. From what I have read this is probably about correct, but if the final number comes in lower then it lowers the range even more. As a point of reference, the Human Genome Project website estimates the number of genes as 30,000 to 35,000.

Finally, the article points out that the diversity among chimpanzees is much greater than among humans. This implies that more genetic changes have taken place in the chimp line of descent. In other words, more of the 2850-4000 total probably accumulated in the chimp line. But, I am willing to give you the benefit of the doubt in each case and see what we come up with.

Next, you state “If it takes much more than (an average of) 1 difference per gene to be one of the key ones…”. Let’s take a statistical approach. At most, they found that 10% of the genes under consideration were undergoing positive selection. If only 10% of the total is under positive selection, what is the probability that 1 gene among the 10% actually received 2 beneficial mutations? Simply put, it is once again 10%. So in the best case, we can say that in the range from 1425 to 2000, with an average of 1713, we might expect that 171 had received 2 beneficial mutations (17.1 had received 3 and 1.7 had received 4). Total it all up, and we get 1903 beneficial mutations, and that’s giving you all the benefit of the doubt. So let me ask you, Is Mr. ReMine justified in unequivocally stating that 1667 beneficial mutations can’t account for human evolution? At the very least, this exercise should have demonstrated that 1667 is not as unreasonable a number as Mr. ReMine has made it out to be. Remember, we are not really haggling over whether 1667 is enough when the actually number might be 2000. Mr. ReMine is suggesting that the actual number is orders of magnitude higher than this.

In his book, Mr. ReMine is clearly incorrect when he writes:

Take an ape-like creature from 10 million years ago, substitute a maximum of 500,000 selectively significant nucleotides and would you have a poet philosopher? How much information can be packed into 500,000 nucleotides? It is roughly one-hundredth of one percent of the nucleotide sites in each human ovum. Is this enough to account for the significantly improved skull, jaws, teeth, feet, upright posture, abstract thought, and appreciation of music, to name just a few? If you find it doubtful, then you are beginning to understand why this is important. It sets a limit on the number of traits that can be substituted by differential survival in the available time.

Your analysis was very good and the final results are not that different from mine. At the very least, it should demonstrate to Creationists that Mr. ReMine’s fundamental premise in this matter is on shaky ground. I think we can agree that he should have put forth some kind of logical justification for dismissing 1667 beneficial mutations outright. It should now be crystal clear why so many evolutionists have been pressing Mr. ReMine for such a long time to do just that.

[ July 27, 2002, 03:56 PM: Message edited by: Administrator ]

 

[Administrator2]

[bJHAPPEL[/b]

This is easily shown to be false. While it is normally true with respect to items that we know are designed (such as a watch), DNA does not fall into that category. Here is an example. Let's say that the DNA of a certain organism mutates from one generation to the next. Let's say that a gene
duplicates. Now, take that duplicate gene, and tell me how you will distinguish this portion, which is clearly present due to an error in the
DNA copying mechanism, from the original DNA which you assert is designed.
In other words, we all agree that DNA changes. Which part of it is designed?

A software program might copy some data and save it in a different memory location and an interrupt might corrupt the data that it stores but that does nothing to refute the fact that the software was designed. The DNA has all the characteristics of a software program including syntax, semantics, pragmatics, and apobetics. It also has a very complex error checking mechanism. Just because an error may happen once every 10,000 base pair copies, which is about a typist making one error every 5 pages, doesn't
negate the evidence for design. DNA must be specified with a meaningful sequence of nucleoides. Chance is simply beyond possibility.

In addition, using the same logic that you just used to "detect" design, the designer would also require a designer. After all, the designer would meet anyone's definition of a complex entity. We would clearly recognize design in this entity. If you disagree, please explain why the designer would not fit the category of something requiring a designer.

To evaluate the evidence for design you do not have to know who designed the designer. If you saw a bulldozer or a flying disk on Europa you would quickly identify design even though there may be no evidence for intelligent life elsewhere on the moon. Besides an alien lifeform that is perhaps made up of a different chemistry that is more easily assembled by natural process could be speculated as the designer if an eternal being isn't acceptable to many in science.

 

[Administrator2]

ROBERT RAPIER

A software program might copy some data and save it in a different memory location and an interrupt might corrupt the data that it stores but that does nothing to refute the fact that the software was designed. The DNA has all the characteristics of a software program including syntax, semantics, pragmatics, and apobetics. It also has a very complex error checking mechanism. Just because an error may happen once every 10,000 base pair copies, which is about a typist making one error every 5 pages, doesn't negate the evidence for design. DNA must be specified with a meaningful sequence of nucleoides. Chance is simply beyond possibility.

I never really understood the software analogy, although I have seen it several times. It seems to be popular among computer programmers, electrical engineers, and other areas far removed from biology. But I am really not interested in generalities and analogies. I prefer specifics. How, specifically do you determine that DNA was designed? Please don’t send me to a link, explain it to me. Quantify it for me.

In your software example above, could you detect the portion that was a result of the error? Could you say that this portion was clearly different from the main body of the program? Could this software program and its offspring continue to function over many generations, occasionally improving upon the previous generation? If the answer to this question is “No”, then you have set up a false analogy.

To evaluate the evidence for design you do not have to know who designed the designer.

No, but if the test used to detect design results in illogical conclusions, namely designers who require designers ad infinitum, then there is a problem with the test.

If you saw a bulldozer or a flying disk on Europa you would quickly identify design even though there may be no evidence for intelligent life elsewhere on the moon.

Just a couple of questions. Are you aware of any cases of bulldozers or flying disks giving birth to offspring slightly different than the parents? If not, you have offered up another false analogy. As I mentioned, sure we can detect design in objects that we know to be designed. But these are not self-replicating organisms.

Also, in another thread John Paul stated the following:

John Paul: I do know (first hand knowledge) that in engineering (applied science) extrapolating knowns to unknowns most often will get you in trouble.

This is in direct contrast to your assertion that you can apply the knowns of detecting design in man made objects to the unknowns of detecting it in objects which are not man made.

I am not really interested in going off on a long tangent with respect to detecting design. I just don’t have the time to carry on too many of these debates at once, and this one is straying well off of the human/chimp theme. I am well aware of Creationist writings purporting to detect design. Suffice to say, if any of their proposals were compelling, mainstream science would have taken notice and the debate would be over.

John Paul linked to a paper above from a conference on biocomplexity: http://www.uchicago.edu/aff/mwc-amacad/biocomplexity/conference_papers/goodman.pdf (FYI, I have had some intermittent problems with the link; occasionally it inserts a period at the end of the line and indicates a dead link).

[ July 30, 2002, 01:17 PM: Message edited by: Administrator ]

 

[Administrator2]

ROBERT RAPIER

I have been thinking about John Paul’s argument regarding evidence for a common designer. Earlier, he wrote:

John Paul: Homology, including DNA similarity, has been used as evidence for a Common Creator for years.

He also linked to an AIG article that said essentially the same thing. However, if this is to be taken seriously as science, a falsification test is needed. I would like to hear from a Creationist regarding any hypothetical finding that might falsify this argument. I will propose one of my own.

Here is a thought experiment. Let’s say that we have sequenced the DNA of all living species. We begin to compare those species, keeping in mind the DNA similarity/homology/common designer argument. Let’s look at the following generic species: bird, bat, and turtle. Using John Paul’s argument, I would predict that the DNA of the bird and the bat should be most similar and the turtle would be the outlier. Correct? If the bird and turtle ended up having the closest DNA similarity then the argument is potentially falsified, and we should seek an alternative explanation. Agreed? If not, please explain why not.

Alternatively, we can compare a shark to two separate species of mammal – whales and rabbits. The DNA of the shark should most resemble that of the whale under John Paul’s argument. It should in fact show a closer similarity to the DNA of whales and dolphins than to any land mammal. This must be true if John Paul’s argument is valid. Agreed? I can think of a few other examples, but they are all along the same theme. Can anyone offer a reason that these two falsification tests should not be valid?

Here is a 2nd thought experiment along a slightly different line. Let’s say lots of experiments with DNA have been performed, and it is discovered that a large portion truly is junk. Let’s say that 2-3 billion base pairs can be completely eliminated from the genome with absolutely no effect on humans. Under the evolutionary scenario, this accumulation has occurred over billions of years for a variety of reasons. What would the Creationist explanation be for this useless DNA? Also, what if it is determined that large portions of the useless DNA are shared by chimps, and they also have no use for this DNA. Remember, this is just a thought experiment so there is no need to point out that we don’t know whether or not there are large sections of junk. For this hypothetical, we will assume that this has been established. What are your thoughts?

 

[Administrator2]

JOHN PAUL

1. Evolutionists have claimed that humans have evolved from some primitive ancestor, which is also the ancestor of chimps. As a matter of fact they claim that all of life's diversity evolved from some genetically unknowable population(s) of single-celled organisms. By the very nature of these claims most cannot be substantiated.

Robert:
In the same way that O.J. Simpson’s claim not to have murdered his wife can’t be substantiated.

John Paul:
No, not even close.
I have posted the following link several times in this forum:

Approaching Biology From a Different Angle:

http://www.arn.org/docs2/news/approachingbiology041701.htm/

Understanding what life is is different than understanding what life does and how life functions. Before you can understand a design you first have to accept that it is designed. Once you do that you need people who understand design to work shoulder-to-shoulder with those who are trying understand what life does and how it functions.

But I can understand why evolutionists would want people to think that computer programming and engineering are far removed from biology, they have enough problems trying to substantiate their dogma in the field their theory is the alleged foundation. Take away 1% * of the known fossils and there wouldn’t be any reason to infer the ToE is indicative of reality without first assuming it was.

* http://www.evolutionfairytale.com/articles_debates/fossil_illusion.htm/

I would leave the study of organisms to their respective branches of science and the understanding of codes, how to decipher them to understand the meaning to those who do that best. Then I would hope the two sides could work together for the common good of all.

It is not necessary to know the mind of the designer or the designer in order to detect design.

Robert:
This is easily shown to be false. While it is normally true with respect to items that we know are designed (such as a watch)…

John Paul:
That would be a contradiction.

Robert:
… DNA does not fall into that category.

John Paul:
Even if you don’t understand JHappel’s analogy, DNA exemplifies that category. The DNA of a living organism has all the qualities one would expect to see in a designed molecule. It is complex, specified, has a function and contains information. Besides we see biochemical systems (sequences of DNA) being designed today. How long before entire sequences are synthesized? The only other place we see DNA is in a cell of a living organism. And you can’t have a cell of a living organism without DNA. Add alternative gene splicing to the mix and the only reason I see not to infer design would be personal incredulity.
That said, it wouldn’t matter to me scientifically if the God of Abraham, a harmonic/ version thereof, E.T. or the force set up the initial conditions. What I can do is make observations, use science to try to make sense of those observations to better understand the design so that we can maintain it in its present state. We could also use science to determine what those initial conditions were and how things got the way they are under that framework.

Robert:
Here is an example. Let’s say that the DNA of a certain organism mutates from one generation to the next. Let’s say that a gene duplicates. Now, take that duplicate gene, and tell me how you will distinguish this portion, which is clearly present due to an error in the DNA copying mechanism, from the original DNA which you assert is designed. In other words, we all agree that DNA changes. Which part of it is designed?

John Paul:
First how would you determine that this gene duplication was clearly present due to an error in the DNA copying mechanism? How do we know that gene duplication isn’t part of that population of organisms’ genetic program? To me that would be the sign of Intelligent Design. Write a genetic algorithm that allows organisms to react, population wide, to fluctuating environments. Natural selection weeds out the GA(s) that either can’t respond quickly enough or an organism (population) that can’t move to a more suitable environment. Gene duplication followed by a mutation (recombination/ insertion/ deletion/ transposition) to the duplicated gene that in turn gave the population a needed adaptive change for survival could hardly be viewed as a random mutation culled by natural selection, especially if it occurs throughout a population.

In an earlier thread I ran DNA through the design explanatory filter. The following shows my preliminary results:

http://www.baptistboard.com/cgi-bin/ultimatebb.cgi?ubb=get_topic&f=36&t=000151&p=

BTW, what were you trying to show as being false? I said:

It is not necessary to know the mind of the designer or the designer in order to detect design.

You countered with:

This is easily shown to be false.

Yet you didn’t falsify that premise nor did you give any positive evidence that would lead us to infer DNA originated via purely natural processes.

Robert:
In addition, using the same logic that you just used to “detect” design, the designer would also require a designer. After all, the designer would meet anyone’s definition of a complex entity. We would clearly recognize design in this entity. If you disagree, please explain why the designer would not fit the category of something requiring a designer.

John Paul:
If you say so Robert, but I would be skeptical *. Right now I am focused on the issue of the obvious design exhibited in living organisms and why anyone would oppose such a premise given our current level of knowledge. I know some people have an issue with religions but that should not interfere with objectivity in science which is ultimately the search for the truth via our never-ending quest for knowledge (what Adam doomed us to

).

*AiG answered this question and I see no need to elaborate as it is irrelevant to the detection of design and this debate. It is a good Philosophy 101 topic though.

http://www.answersingenesis.org/docs/3791.asp/

SETI- Searching for designers by looking for design without knowing who designed the designers or even if they exist.

jhappel:
To evaluate the evidence for design you do not have to know who designed the designer.

Robert:
No, but if the test used to detect design results in illogical conclusions, namely designers who require designers ad infinitum, then there is a problem with the test.

John Paul:
That is not an illogical conclusion. It is unnecessary baggage you keep trying to throw on. Archaeology is used to detect design without necessarily knowing the designer(s). And what about SETI? Or anthropology in its search for artifacts? By studying the artifacts anthropologists make determinations about the designer(s) of those artifacts. Scientists can be totally wrong about the designers but that doesn’t mean the have to stop looking at an obviously designed object as if it were not designed. They can still study the object & design with the hope of coming to understand it. Then by understanding the design may help us to understand the designer. And unless the designer was going to tell you all about the design, even the knowledge of the designer’s existence will most likely not help you. Although that knowledge would be reason to discard materialistic naturalism.

How do we know that humans designed everything humans ever made? Did I mention SETI? Do we have to know who/ what designed ET before we can determine if the message ET transmitted (we received) was in fact designed? No, we don’t even have to know what type of an organism ET is to make that determination.

John Paul: I do know (first hand knowledge) that in engineering (applied science) extrapolating knowns to unknowns most often will get you in trouble.

Robert:
This is in direct contrast to your assertion that you can apply the knowns of detecting design in man made objects to the unknowns of detecting it in objects which are not man made.

John Paul:
The reality is we can apply knowns in detecting design in something that is not man-made. Have I mentioned SETI yet? Care to guess what the ET stands for? The designer could be a spider- If you never seen a spider or a spider’s web what would run through your mind when observing a web 3’ in diameter? Would you think it was man-made or grew there? Would you believe someone when they told you a spider did it?

Robert:
I am well aware of Creationist writings purporting to detect design.

John Paul:
How about IDist or evolutionist writings purporting to detect design? Being aware of is very different from reading & understanding. ID type processes are already being used in science and other fields of investigation. I don’t understand the resistance to trying them on biological organisms.

Robert:
Suffice to say, if any of their proposals were compelling, mainstream science would have taken notice and the debate would be over.

John Paul:
The fact that ID has to be misrepresented before being rebutted tells me it is pretty close to being over. For example there is no such thing as Intelligent Design Creationism, yet that is what ID is often (if not always) referred as. Evolutionists can’t stand the fact that religion has been taken out of an alternative so they make-up little catch phrases to mislead the public.


Tell you what. If you really want to falsify ID all you have to do is answer the riddle of IC and show that purely natural processes are enough to bring life from non-life. At least give people some positive evidence that would lead us to infer it could. Even with life being a given the IC hurdle has yet to be crossed.

Common Creator stuff:

As far as the AiG article it was on topic pertaining to homology and DNA similarity being evidence for a Common Creator. Also it is very relevant to what I had posted. Did you even read it?

Robert:
Yes I did. If you read it, you see that they are ridiculing the possibility that humans and chimps would be 99% similar in their DNA. Why?

John Paul:
I have read it several times and I see nothing that would be ridiculing the possibility that humans and chimps would be 99% similar in their DNA. The article questions the methods used and the extrapolation of the data.

Two things you have to remember:
1. The article was published in the December 1996- February 1997 issue of Creation Ex Nihilo.
2. The method cited was published in 1987.

If questionable methods were never questioned peer-review would be an oxymoron.

Robert:
If this is strong evidence for a common designer, why was this not predicted? Why were Creationists everywhere playing down the possibility of 99% similarity?

John Paul:
It probably wasn’t predicted because of the obvious differences between the two organisms. If “Creationists everywhere [were] playing down the possibility of 99% similarity” it would most likely have been caused by the methods used for the determination and our (humans) ignorance of genomes. The work is ongoing but as I mentioned (in the Chimps & Humans thread), in order to get the full effect we may have to wait until Human (chimp) Proteome Project (identifying all proteins) and then the Human (chimp) Physiome Project (how the proteins interact) are complete, or at least underway.
Sure we have similarities, but 99%? I don’t think anyone could have predicted that. It could turn out that DNA is just another part in the irreducible complexity of life. Perhaps it controls traits & phenotypic plasticity but isn’t entirely responsible for the type of organism. An eyeless fish is still a fish, those famous finches are still finches and after billions of generations of bacteria not one bacterium has jumped kingdoms.

Robert:
AIG also makes the argument that DNA and homology are not as closely linked as many people claim. So, why 99% similarity between humans and chimps?

John Paul:
From the article you said you read:

We know that DNA in cells contains much of the information necessary for the development of an organism. In other words, if two organisms look similar, we would expect there to be some similarity also in their DNA. The DNA of a cow and a whale, two mammals, should be more alike than the DNA of a cow and a bacterium. If it were not so, then the whole idea of DNA being the information carrier in living things would have to be questioned. Likewise, humans and apes have a lot of morphological similarities, so we would expect there would be similarities in their DNA. Of all the animals, chimps are most like humans[1], so we would expect that their DNA would be most like human DNA.

1 However, Jeffrey Swartz, an evolutionary anthropologist at the University of Pittsburg, maintains that man is closer to orangutans in gross morphology. Acts and Facts, 16(5):5, 1987.

But I am sure with all the obvious differences no one suspected 99%. (the exact % is still to be determined)

Robert:
Why not 99% similarity between humans and birds?

John Paul:
Because we are not similar to birds.

Robert:
They seem to be trying to stake out a position that no matter how the DNA sequencing turned out, they could claim victory.

John Paul:
From the comments you are making I am not sure we are talking about the same article.

Robert:
I would like to see Creationists make some bold predictions, as John Morris did in 1989 when he predicted that molecular biology would falsify evolution within 5 years.

John Paul:
The ToE should have been rewritten (it will never be falsified, just changed- the evolution of evolution) in 1953 with the identification of the double-helix. With the widening acceptance of endo-symbiosis as the mechanism responsible for eucaryotes, the modern synthesis is already undergoing a little evolution. The fact it has survived just tells me how vehement the opposition to any alternative is. Personally I don’t see the attraction of materialistic naturalism, scientifically or philosophically.

Why you think that proclamation undermines the Common Creator scenario is beyond me.

Robert:
See above. When the Common Creator is used to justify any possible scenario, this explanation is not very useful.

John Paul:
Also from the AiG article that you said you read:

If humans were entirely different from all other living things, or indeed if every living thing was entirely different, would this reveal the Creator to us? No! We would logically think that there must be many creators rather than one. The unity of the creation is testimony to the One True God who made it all (Romans 1:18–23).

and

If humans were entirely different from all other living things, how would we then live? If we are to eat food to provide nutrients and energy to live, what would we eat if every other organism on earth were fundamentally different biochemically? How could we digest them and how could we use the amino acids, sugars, etc., if they were different from the ones we have in our bodies? Biochemical similarity is necessary for us to have food!

As everyone can now see the Common Creator cannot justify any scenario.

For all I care when scientifically detecting design it could have been a team of creators with a common plan or a team of creators with a random plan that worked to the degree we observe.

But as for be useful- what use is it to think all of life owes it common ancestry to some genetically unknowable population(s) of single-celled organisms? Acknowledging the Creator will free us to start deciphering the code. How can we find the message when we don’t know to look? I have a feeling only that will tell us why our (chimps/ humans) DNA is so similar yet we are so different.

Robert:
I have been thinking about John Paul’s argument regarding evidence for a common designer. Earlier, he wrote:

John Paul: Homology, including DNA similarity, has been used as evidence for a Common Creator for years.

Robert:
He also linked to an AIG article that said essentially the same thing. However, if this is to be taken seriously as science, a falsification test is needed.

John Paul:
Just so we are all clear on this: The Common Creator is a framework from which science is conducted. ID is another framework and materialistic naturalism is yet another.

Robert:
I would like to hear from a Creationist regarding any hypothetical finding that might falsify this argument. I will propose one of my own.

John Paul:
The AiG article I linked to provided one. Maybe you should read it again:

http://www.answersingenesis.org/docs/2453.asp

2. If humans were entirely different from all other living things, or indeed if every living thing was entirely different, would this reveal the Creator to us? No! We would logically think that there must be many creators rather than one. The unity of the creation is testimony to the One True God who made it all (Romans 1:18–23).

3. If humans were entirely different from all other living things, how would we then live? If we are to eat food to provide nutrients and energy to live, what would we eat if every other organism on earth were fundamentally different biochemically? How could we digest them and how could we use the amino acids, sugars, etc., if they were different from the ones we have in our bodies? Biochemical similarity is necessary for us to have food!

Robert:
Here is a thought experiment. Let’s say that we have sequenced the DNA of all living species. We begin to compare those species, keeping in mind the DNA similarity/homology/common designer argument. Let’s look at the following generic species: bird, bat, and turtle. Using John Paul’s argument, I would predict that the DNA of the bird and the bat should be most similar and the turtle would be the outlier. Correct? If the bird and turtle ended up having the closest DNA similarity then the argument is potentially falsified, and we should seek an alternative explanation. Agreed? If not, please explain why not.

John Paul:
Why? Because birds & bats both have wings? I could see where one might make that initial assumption if the only exposure to each organism was when one of each flew by. But I would expect that assumption to be overturned upon closer inspection of the evidence (non-DNA). We would start by noting the total number (& scope) of similarities as well as the total number of differences (& scope) in each possible pair.

Robert:
Alternatively, we can compare a shark to two separate species of mammal – whales and rabbits. The DNA of the shark should most resemble that of the whale under John Paul’s argument. It should in fact show a closer similarity to the DNA of whales and dolphins than to any land mammal. This must be true if John Paul’s argument is valid. Agreed? I can think of a few other examples, but they are all along the same theme. Can anyone offer a reason that these two falsification tests should not be valid?

John Paul:
That is not correct. You would only get that result if you didn’t know how to apply my argument. I see more differences between sharks and whales than I do between whales and land mammals. However I could see where one might make that initial assumption, from a long distance with only a glimpse of the organisms in question. But I would expect that assumption to be overturned upon closer inspection of the evidence (non-DNA).

Rule number one when applying my argument:

Never judge a book by its cover.

DNA isn’t just responsible for the outward appearance. There’s a whole new world of wonders lying under the skin that must also be considered. Whales’ DNA has the coding for bones whereas sharks’ DNA does not. Lungs vs. gills. Horizontal Fluke vs. [vertical] caudal fin, the eyes are different, skin is different, pectoral fins vs. flippers, etc.- similarities- both live in water and have at least one dorsal fin.

In both cases knowledge wins out. What is first assumed to be morphological similarity is soon shown to be not so similar at all. That is exactly the case with marsupials and their placental counterparts (discussed in the AiG article below).

The Common Creator is seen in the symbiotic relationships that are observed; the most obvious being between the plant & animal kingdoms. And yes that premise could be wrong, it could have been a team of Creators acting randomly, but as of today I see no reason to infer that scenario.

Here are a couple relevant links:

http://www.trueorigin.org/homology.asp/

http://www.answersingenesis.org/docs/1133.asp

 

[Administrator2]

ROBERT RAPIER

First of all, I should apologize to John Paul for not making myself clear. It looks like he spent a good deal of effort on something that is clearly irrelevant to the logical point that I made. Here is my point again:

John Paul stated that he rejects the conclusions he arrived at regarding Haldane’s Dilemma because he rejects the possibility of common descent. No common descent, no argument. What appears to be common descent is to him illusory.

Playing devil’s advocate, I say:

I reject any conclusions with respect to apparent design in organisms, because I reject the possibility of a designer. No designer, no design. What appears to be design is to me illusory. Therefore I reject everything that he has written to try and establish that design (or a designer) exists, in the same fashion that he rejects evidence presented to him to establish that common descent is a fact.

Let me add that I am rather busy, and I don’t have time to chase down 7 links. I would request in the future that you try and summarize in your own words whatever point you wish to make, and just use the links as references. I am not debating ARN or AIG, I am debating you. It is not very stimulating to find that when I ask a question, I am asked to follow a link. Not everyone has that kind of time. I would also ask that you focus your arguments, as they ranged across many subjects in this post.

I will address a few points.

Take away 1% * of the known fossils and there wouldn’t be any reason to infer the ToE is indicative of reality without first assuming it was.

I am aware of Fred’s article, and I am also aware that he does not make it clear that this 1% still amounts to millions of fossils. That is why so many museums are chock full of fossils. The article gives the impression that there are very few vertebrate fossils. This is not true.

I am skipping over the sections on design, because in my devil’s advocate role I reject it all because I reject the possibility of a designer. (In reality, I don’t. My actual position is that it is something that can never be known one way or another).

John Paul:I have read it several times and I see nothing that would be ridiculing the possibility that humans and chimps would be 99% similar in their DNA.

Quotes from the article to substantiate my position:

1. The idea that human beings and chimps have close to 100% similarity in their DNA seems to be common knowledge. The figures quoted vary: 97%, 98%, or even 99%, depending on just who is telling the story.
2. What of the 97% (or 98% or 99%!) similarity claimed between humans and chimps?
3. Upon inspecting the data, I discovered that, even if everything else was above criticism, the 97% figure came from making a very basic statistical error — averaging two figures without taking into account differences in the number of observations contributing to each figure. When a proper mean is calculated it is 96.2%, not 97%.
4. If humans were ‘only’ 4% different this still amounts to 120 million base pairs, equivalent to approximately 12 million words, or 40 large books of information. This is surely an impossible barrier for mutations (random changes) to cross.

Note the continued theme of downplaying the 99% possibility. It is also interesting to note the last statement. As pointed out in the “Wolves and Dogs” thread, wolves and coyotes differ by an estimated 180 million base pairs. Chimps and humans differ by around 40 million.

John Paul:The ToE should have been rewritten (it will never be falsified, just changed- the evolution of evolution) in 1953 with the identification of the double-helix.

That’s the way it goes with science – new discoveries sometimes cause theories to be modified. Darwin had never heard of DNA, yet he made predictions that were fulfilled by the discoveries of Watson and Crick. He wrote that there had to be a mechanism for driving evolution, but he had no way of knowing what it was. Errors in the DNA copying mechanism provided him with the answer.

Robert: When the Common Creator is used to justify any possible scenario, this explanation is not very useful.

John Paul: Also from the AiG article that you said you read:
quote:
If humans were entirely different from all other living things, or indeed if every living thing was entirely different, would this reveal the Creator to us? No! We would logically think that there must be many creators rather than one. The unity of the creation is testimony to the One True God who made it all (Romans 1:18–23).

Strawman. I never said that we should expect different forms of life to be non-DNA based. But a common creator would have had no trouble making a human and a chimpanzee with 25% similarity. True? That’s my point; there is no reason to expect a priori that 99% similarity is the way the Designer would have done it. The AIG argument only holds water under the assumption that different forms of life are based on completely different chemistries. That is not at all what I am suggesting.

Robert: I would like to hear from a Creationist regarding any hypothetical finding that might falsify this argument. I will propose one of my own.

John Paul: The AiG article I linked to provided one. Maybe you should read it again:

See above. I got it the first time I read it, but it misses the point. Their version of falsification is that “entirely different” should imply different chemistries. What I have in mind is DNA based life, but life that shares little in common. In other words, life that doesn’t look like evolution occurred when doing genetic analyses. I am actually proposing a realistic test – one that can be performed in the lab.

John Paul: Why? Because birds & bats both have wings? I could see where one might make that initial assumption if the only exposure to each organism was when one of each flew by. But I would expect that assumption to be overturned upon closer inspection of the evidence (non-DNA). We would start by noting the total number (& scope) of similarities as well as the total number of differences (& scope) in each possible pair.

You missed the point. Please describe under a Creationist scenario why a bird might have a closer genetic similarity to a turtle than a bat. You may take some time to research this, but please put the arguments into your own words. I can tell you why under the evolutionary scenario a bird might be more closely related to a turtle (or snake). The truth is that I don’t know for sure, but I predict that this is what we will see if we can dig up some information on it. What does Creationism predict we will see?

The common morphology argument as I have typically seen Creationists use it goes something like this: Chimps and humans share 99% DNA similarity due to common morphology. A Creator would have no reason to reinvent the wheel. I am just logically extending this argument to other organisms. Bird and bats are adapted for flying. They should share significant stretches of DNA that govern flying. Turtles have a shell and crawl on the ground. If the common morphology argument can’t address this situation, then exactly what good is it?

John Paul:That is not correct. You would only get that result if you didn’t know how to apply my argument. I see more differences between sharks and whales than I do between whales and land mammals.

Once again you missed the point. If you had carefully read my post, you would see that I am not asking you to compare a whale to another land mammal. I am asking you to compare the genetic difference of a shark to two separate mammals: a rabbit and a whale (or even better, a bat). If the common morphology argument is correct, I would put my money on the shark and the whale as having a closer DNA similarity than a shark and a rabbit. After all, whales and sharks are adapted for life in the ocean. If the common morphology argument can’t explain this, that more or less undermines the use of it. What do think?

DNA isn’t just responsible for the outward appearance. There’s a whole new world of wonders lying under the skin that must also be considered. Whales’ DNA has the coding for bones whereas sharks’ DNA does not. Lungs vs. gills. Horizontal Fluke vs. [vertical] caudal fin, the eyes are different, skin is different, pectoral fins vs. flippers, etc.- similarities- both live in water and have at least one dorsal fin.

Those are all very nice bits of trivia, John Paul, but can you explain the relevance to my argument? I asked whether a shark would be more closely related to a whale or a rabbit. Please apply your common morphology argument and let me know. My prediction is that the genetic distance of a shark will be random when compared to various mammals, including whales.

 

[Administrator2]

JOHN PAUL

Robert:
John Paul stated that he rejects the conclusions he arrived at regarding Haldane’s Dilemma because he rejects the possibility of common descent.

John Paul:
I don’t recall stating that. Could you please point it out for me? I remember reaching the conclusion that 1667 mutations wouldn’t be enough. So why would I reject that? We don’t get to choose the mutations Robert so even if the numbers game we played was relevant to Haldane’s Dilemma you still have many assumptions that require support. Also even if we assume a primitive ancestor does not also mean we have to assume we shared a common ancestor with chimps. Why not assume convergent evolution instead of divergent?

All that has been shown by the numbers game is that if all* the assumptions & estimates are right, with some specified sequence of mutations it may be possible for some number of mutations to accumulate in a time period given that may allow for the evolution of some alleged primitive ancestor to modern humans. All the while remembering there is no way to predict what will be selected for at any point in time- meaning beneficial is a relative word as it pertains to evolution & natural selection. Your criterion for selection is based on a long-range goal. That is not how natural selection works. Those are why I reject the numbers game as a meaningful argument.

*some assumptions:
humans had a primitive ancestor
that ancestor was also an ancestor to chimpanzees
changes in DNA can lead to such a transformation
estimates on the number of genes are correct (the HGP’s primary concern was the sequencing, not gene counting) http://www.the-scientist.com/yr2001/oct/hollon_p1_011015.html

estimates on the number of key genes are correct
1.5 mutations per key gene can account for the key differences
the sequence of mutations was just as specified
junk DNA
the assumption that a functioning gene can take a big mutation and not adversely effect the organism
the assumption those bigger mutations are caused by copying errors

For the record: I too am very busy. This is a debate about information, regardless of who gives it. I usually don’t have time to write essays or reports. When I do I have the time I do make the effort. If the information is already posited somewhere else that is what you will get if I don’t have the time. If the article is very lengthy I try to snip the relevant parts and post those, as sometimes summaries are insufficient. I do that for convenience & time saving only. I don’t understand the difference between reading my words or the words of the people who did the research. Who better to substantiate the claims of Creationists than a Creationist organization? What better way to learn about what it is you are debating against than to read from its authors? I am not debating you I am debating whether or not the theory of evolution is indicative of reality and trying to find out why people believe it to be. It just so happens at this time I am debating with you.

On Fred’s article pertaining to the fossil record:

If 1% = millions of fossils what would 99% equal? I would still stick with the 99% especially knowing that fossil evidence can’t differentiate between phenotypic plasticity or genotypic (?) changes (mutations). It also can’t differentiate between adaptive mutations and random mutations culled by natural selection.

On Homology & the Common Creator:

Questioning methods or downplaying the possibility are not synonymous with ridiculing.

Robert:
If you had carefully read my post, you would see that I am not asking you to compare a whale to another land mammal. I am asking you to compare the genetic difference of a shark to two separate mammals: a rabbit and a whale (or even better, a bat).

John Paul:
In order to be scientifically thorough so that a good determination can be made, each organism would have to be compared with each of the others. If I am to conduct an experiment the first thing I would do is do away with unnecessary restrictions that would hinder an objective conclusion. If I compared a whale to a shark and a rabbit to a shark, without comparing a whale to a rabbit, I would only see that the whale may have more similarities with a shark than a rabbit does. However when doing a thorough comparison, including of whales & rabbits, I would see that those two have the most in common of the three possible pairings. After having all the knowledge available I would conclude that none of the organisms were related (unless being descended from organisms that were created makes them related- ie related by Common Creator) but because of the number of similarities I would predict a rabbit’s DNA would be more similar to a whale’s than a whale’s to a shark’s. Bird, bat, turtle- same thing.

The only reason I infer a Common Creator is by looking at the evidence as a whole (including the mathematical comprehensibility of the world), not just bits-n-pieces (chimps, humans, whales, sharks, rabbits, birds, bats & turtles). Then I would speculate as to why specific scenarios arose (and are arising) using scientific investigation based on that premise. It doesn’t have to be a Common Creator. My inference could be wrong, it could have been a team of creators- harmonics of the One- that put the plan(s) into action, but I can live with that. What I can’t & won’t live with is the rejection, for no logical reason, of an alternative at least as scientific as the reigning paradigm. ID is concerned with the design, not the designer. The Creation model of biological evolution states all we observe owes its ancestry to the created kinds. Leave origins out of it- just like abiogenesis is separated from the ToE- or even mention the Creator just like Darwin did at the end of his book On the Origins of Species…, and the rest is pure nature acting on a designed genetic algorithm. I don’t see anything un-scientific about that. Leave the religious aspects out of it, that can be handled (or not) at home and/ or Church. Teach the evidence and stop pigeonholing conclusions.

Robert:
The common morphology argument as I have typically seen Creationists use it goes something like this: Chimps and humans share 99% DNA similarity due to common morphology.

John Paul:
A whale’s structure is not the same a shark’s and a bird’s wing is structurally different than a bat’s. Morphology also goes down to the molecular level. DNA is allegedly responsible for the whole organism, not just its shape. So when comparing organisms we have to keep that in mind.

From Britannica.com:

Morphology in biology, the study of the size, shape, and structure of animals, plants, and microorganisms and of the relationships of the parts comprising them. The term refers to the general aspects of biological form and arrangement of the parts of a plant or an animal.

We would expect chimps & humans to have similar DNA because of all the similarities between the two. Like I said before because of all the differences no one expected the respective genomes to only be some 1% different. That tells me we have much to learn about DNA and developmental biology.
If chimps & humans had only 25% genetic similarity? That would depend on how all the other organisms’ genomes compared. We would have to then look at the DNA that does make a difference to see how it compares. For one it could add credence to the ‘junk’ DNA premise because if such a small portion is really all that matters what difference would the larger irrelevant portion make? But that would also contradict some experiments and hypotheses that the ‘junk’ DNA really isn’t ‘junk’.

Why would it (the alleged junk) be copied so neatly in the evolutionary scheme of things? Why copied at all?

 

[Administrator2]

HELEN

I'm not sure if this should be in the chimps or Haldane's thread, but here goes:

A couple of points which I think have to do with the material being presented here.

1. DNA is not all there is to heritability. This is brought out clearly in Harold's The Way of the Cell. He has an entire chapter entitled "It Takes a Cell to Make a Cell" which I can provide quotes from if you like, as I have the book here. So arguing only about DNA is not going to settle the argument on the chimp/human thing.

2. I am on a listserve where something akin to this is being discussed right now and I asked permission to quote one of the emails and received that permission. I am not including the name, but the person is a professional in the field and I think the information in the email can stand on its own without a name attached:

Of relevance here is an article in Nature, Vol. 418, pp. 122-124. It talks
about the non-coding parts of the genome and the possibility that they may
have a very large role in regulation. Specific mention is made of microRNA's
(miRNA's), short sequences of transcribed RNA that bind to mRNA to block
their translation into proteins. One of the geneticists, John Mattick
states, "complexity is hidden in the non-coding output of the genome."

After reading this article, it strikes me that the reason the protein coding
regions may be so similar but the non-coding regions aren't is that both
organisms use many of the same proteins, but how they are regulated is quite
a bit different. This would result in the non-coding, but transcribed,
regulatory regions to be quite divergent.

I suspect that complex folded proteins, as impossible as they are for
natural processes to produce, will be orders of magnitude simpler to explain
in comparison to the internally interacting regulatory 'operating system'
that controls the genomic output for each different organism.

I think if the differences between any two kinds of organisms are going to be discussed, both of these points might be important to the discussion.

 

[Administrator2]

ROBERT RAPIER

This will be my last post in this thread. I will briefly address a few comments that John Paul made, then make a brief comment on Helen’s post.

John Paul: I don’t recall stating that. Could you please point it out for me? I remember reaching the conclusion that 1667 mutations wouldn’t be enough.

I am repeating myself, but that was not your conclusion. Your conclusion was:

John Paul: So, still assuming a 50/50 split that would be between 1425 & 2000. If it takes much more than (an average of) 1 difference per gene to be one of the key ones, that would mean 1667 would be too few.

You proposed a range of 1425-2000. 1667 is within the range of the estimate you provided. Simple as that. But I did the math to show the probability of multiple substitutions per gene. I also pointed out the logical error you made with respect to assuming that each change had to consist of a single nucleotide substitution. But most importantly, your number was based on 1.5% coding portion of the genome as opposed to 1.1%. This adjustment reduces the range to 1045 to 1467. Regardless, these ranges are just estimates, but they are clearly “in the ballpark” (even if you consider some contribution from outside the coding region). I address this in detail in my latest post in the Haldane’s Dilemma thread.

John Paul: estimates on the number of key genes are correct
1.5 mutations per key gene can account for the key differences

You confuse mutations with single nucleotide substitutions. While they can be equivalent, there are many other mutation mechanisms that can give thousands of nucleotide substitutions with a single mutation. Some examples are gene duplications, inversions, insertions, and deletions.

John Paul: If the information is already posited somewhere else that is what you will get if I don’t have the time. If the article is very lengthy I try to snip the relevant parts and post those, as sometimes summaries are insufficient. I do that for convenience & time saving only. I don’t understand the difference between reading my words or the words of the people who did the research.

The difference is very simple. If this were the approach that everyone took in these debates, it would suddenly degrade into a debate of dueling links and dueling quotes. Also, copying and pasting material does not demonstrate that one understands the material. If there are questions, then the person who cut and pasted may be unable to answer and once again has to refer the person to AIG or ARN. I have seen this happen countless times.

John Paul: I would predict a rabbit’s DNA would be more similar to a whale’s than a whale’s to a shark’s. Bird, bat, turtle- same thing.

And yet for the 2nd time I have to point out that I am not asking whether a rabbit is more closely related to a whale. Do you just not understand the test I am proposing? I am simply saying that a shark shares more characteristics with a whale than it does a rabbit. Please make a list of characteristics common to rabbits and sharks but not whales and sharks if you wish to refute this. I am not saying that a shark is completely like a whale, just more so than it is like a rabbit. Therefore, a test of the common morphology argument would be to test whether a shark is closer genetically to a whale or rabbit. If I happened to be a Creationist, and I believed in the common morphology argument, I would think that such a test should prove the point.

John Paul: A whale’s structure is not the same a shark’s and a bird’s wing is structurally different than a bat’s. Morphology also goes down to the molecular level. DNA is allegedly responsible for the whole organism, not just its shape. So when comparing organisms we have to keep that in mind.

You are merely stating the obvious. In order to address my argument, the 2nd example of which is to establish the genetic distance of a bird and a bat compared to the genetic distance of a bird and a turtle, all you have to do is list all the ways in which a bird is closer morphologically to a turtle than it is to a bat. If a bird is closer morphologically to a turtle than a bat, then my argument is moot. Are you suggesting that this is the case? But look no further than the Bible for classification of bats. The Bible lists bats among the birds, not among the turtles.

Helen: I think if the differences between any two kinds of organisms are going to be discussed, both of these points might be important to the discussion.

See my latest post in the Haldane’s Dilemma thread. Even if we consider all of the differences, it still doesn’t help the ReMine/Williams argument. I also highlight this point in my summary, which will be posted as soon as Fred has posted his next reply.

 

[Administrator2]

HELEN

Helen: I think if the differences between any two kinds of organisms are going to be discussed, both of these points might be important to the discussion.


See my latest post in the Haldane’s Dilemma thread. Even if we consider all of the differences, it still doesn’t help the ReMine/Williams argument.

This thread is not about Haldane's Dilemma; it's about chimps and men. And I am very curious as to your response to the fact that there are other PARTS of the cell that are involved in heredity and that it appears that perhaps it is the regulation of the proteins and not their construction which would be expected to be the area where the differences should be looked for.

 

[Administrator2]

JOHN PAUL

John Paul: I don't recall stating that. Could you please point it out for me? I remember reaching the conclusion that 1667 mutations wouldn't be enough.

Robert:
I am repeating myself, but that was not your conclusion. Your conclusion was:

John Paul: So, still assuming a 50/50 split that would be between 1425 & 2000. If it takes much more than (an average of) 1 difference per gene to be one of the key ones, that would mean 1667 would be too few.

John Paul:
Excuse me but when I say 1667 would be too few that would mean that 1667 wouldn't be enough. However, if we use the chimp/ human split of 5 million years ago that would mean 833 would be the most that could accrue. At 7 million you get a little more- 1167. The 1667 was deduced using 10 million years/ 300 generations/ 20 years per generation. 1 million years = 167 mutations.

Robert:
You proposed a range of 1425-2000. 1667 is within the range of the estimate you provided. Simple as that.

John Paul:
The reality is it is not as simple as that. Neither of us gets to pick the mutations or the sequence. Also the 1425-2000 was the estimated number of key genes, not the number of mutations. There is a difference. What is meant by key genes? What are they? How are you determining how many mutations it took to make the observed differences?

The paper I cited (assuming a 50/50 split) shows there would be a difference in 222,500 coding positions (445,000 between humans & chimps). The point being how many other beneficial mutations were there?

Robert:
But I did the math to show the probability of multiple substitutions per gene. I also pointed out the logical error you made with respect to assuming that each change had to consist of a single nucleotide substitution.

John Paul:
If I made any error it was assuming that these mutations would be random mutations culled by natural selection. If you are calling all mutations random then that is another claim that you need to substantiate. If you are saying that evolution includes directed mutations then the present day ToE needs a re-write.

Robert:
But most importantly, your number was based on 1.5% coding portion of the genome as opposed to 1.1%. This adjustment reduces the range to 1045 to 1467. Regardless, these ranges are just estimates, but they are clearly "in the ballpark" (even if you consider some contribution from outside the coding region). I address this in detail in my latest post in the Haldane's Dilemma thread.

John Paul:
They are only "in the ballpark" on paper where there are quite a few assumptions being made. For one it is just a number. That number being how many (estimated) key genes that exist between us & chimps. That number doesn't tell us how many mutations it took to get the key differences or how many non-key genes were involved (if any). Also we must take into account the adjusted primary number- from 1667 to 833-1167. That would mean using your lowest number in order to be in the ballpark no more than 1.12 mutations (on average) are allowed per key gene. Where is the data that supports less than 2 mutations per gene can make a beneficial difference? We know that 1 mutation per gene can cause harmful effects but I would think harmful mutations accumulating wouldn't give us the result you require.

John Paul: estimates on the number of key genes are correct
1.5 mutations per key gene can account for the key differences

Robert:
You confuse mutations with single nucleotide substitutions. While they can be equivalent, there are many other mutation mechanisms that can give thousands of nucleotide substitutions with a single mutation. Some examples are gene duplications, inversions, insertions, and deletions.

John Paul:
No, I didn't confuse anything. I am well aware that evolutionists are now trying to say every type of mutation is random, but even that doesn't help you. If you mess with something that functions as it is you are messing with that function. You just can't go inserting, deleting, recombining and duplicating at your leisure.

This just in… (grin). It appears that in the evolutionary scenario they have all but admitted our ancestor of 10 million years ago did not have the capability for language & speech:

http://www.sciam.com/article.cfm?articleID=000CCE7E-A2A7-1D5A-90FB809EC5880000

… "strongly suggest that this gene has been the target of selection during recent human evolution."

The investigators speculate that the changes evident in human FOXP2 may account for our ability to exert fine control over movements of the mouth and larynx--a talent that the great apes lack. If so, and if, as the team's estimates suggest, the variant became established in the human population during the last 200,000 years of human history--roughly the time at which anatomically modern humans arose--the gift of gab may have been a driving force in their expansion. -Kate Wong

Another article has this to say pertaining to the gene involved:

http://story.news.yahoo.com/news?tmpl=story&u=/nm/20020814/hl_nm/speech_apes_dc_1

A few key changes in a single gene help explain why people can talk while mice and apes cannot, researchers said on Wednesday.

The gene, called FOXP2, seems to be involved in the face and jaw movements necessary for speech, the researchers in Germany and Britain said.

What is surprising is that the gene is so similar in animals ranging from mice to orangutans to chimpanzees, with a relatively small change having emerged--just as modern humans did--between 120,000 and 200,000 years ago, the researchers report in this week's online issue of the journal Nature.

"It is not the gene that made language possible," geneticist Wolfgang Enard of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, stressed in a telephone interview.

He said it is probably one of many genes involved in speech and language, which are complex abilities.

The cool part is there is only "two amino acids changes on the human lineage", assuming divergent evolution is the rule in the common descent scheme of things (ie mice, humans and apes common ancestor). Can anyone say genetic engineering? Did they take some mice, make the change and get a mouse that could grin? Or snarl? Or do they just know that when a human's FOXP2 is messed with it messes us up?

A slight amino acid change would alter the resulting protein and, as is the case with FOXP2, the consequences can be enormous.

from http://www.nature.com/nature/links/011004/011004-4.html/

For the first time, a gene has been identified as responsible for a specific human language disorder. The gene encodes an unusual member of a family of proteins involved in embryogenesis, the Winged Helix/Forkhead transcription factors. Disruption of the FOXP2 gene appears to affect the brain at an early stage in development, leading to abnormality in neural structures important for speech and language.

from the article titled: (the article that spawned the evolutionarily embellished reports)

A forkhead-domain gene is mutated in a severe speech and language disorder

Our findings suggest that FOXP2 is involved in the developmental process that culminates in speech and language.

Far from showing common descent (because of the similarity in the FOXP2 gene from mice to men) the report shows what does happen when mutations infiltrate the coding region. It does show us how a common part can be used & reused, slightly modified and refitted.

The best is yet to come:

"We have not so many genes and many things that have to be done in the body," Enard said. "Most of the time a single gene will have several functions. FOXP2 is not an exception."

Enard said geneticists will be taking a long, hard look at FOXP2 now.

"The really hard part will be to find out what human FOXP2 does differently from other FOXP2s," he said.

Which brings us to alternative splicing which is the reshuffling of the RNA transcription of a gene's nucleotide sequence that generates multiple proteins.
http://www.mindfully.org/GE/GE4/DNA-Myth-CommonerFeb02.htm And that is why small changes can have far reaching effects. In the case of FOXP2 from what we know those effects are not good. That is also the key point against genetically engineered crops. What are the effects going to be in the future generations? From what I heard that was one of the reasons Monsanto was making genetically engineered crops that wouldn't produce seeds. That way they could keep any freaky evolution in check. The farmers were outraged when they heard this but they didn't realize that even if they had to keep buying seeds every year the crop yield would be so much higher they wouldn't even miss the money required for the new seeds. Knowledge should be free but research costs $$$.

On debate style:

John Paul: If the information is already posited somewhere else that is what you will get if I don't have the time. If the article is very lengthy I try to snip the relevant parts and post those, as sometimes summaries are insufficient. I do that for convenience & time saving only. I don't understand the difference between reading my words or the words of the people who did the research.

Robert:
The difference is very simple. If this were the approach that everyone took in these debates, it would suddenly degrade into a debate of dueling links and dueling quotes. Also, copying and pasting material does not demonstrate that one understands the material. If there are questions, then the person who cut and pasted may be unable to answer and once again has to refer the person to AIG or ARN. I have seen this happen countless times.

John Paul:
Information wins debates, not rhetoric. As anyone can tell by the length between my posts I don't have the time to redo what has already been done. If I can read it I can understand it. The purpose of having an opponent or lurker read it is for education as that solves debates also. IOW when someone says they don't understand why Creationists do this or do that, it is very relevant, informative and efficient to send that person to an article that already exists and then discuss the article if necessary. If all else fails at the very least you can email the person or organization about the article. That is unless you just want to argue.

Again I am not debating a person, I am debating evidence and information.

On homology and DNA similarity:

John Paul: I would predict a rabbit's DNA would be more similar to a whale's than a whale's to a shark's. Bird, bat, turtle- same thing.

Robert:
And yet for the 2nd time I have to point out that I am not asking whether a rabbit is more closely related to a whale. Do you just not understand the test I am proposing? I am simply saying that a shark shares more characteristics with a whale than it does a rabbit. Please make a list of characteristics common to rabbits and sharks but not whales and sharks if you wish to refute this. I am not saying that a shark is completely like a whale, just more so than it is like a rabbit. Therefore, a test of the common morphology argument would be to test whether a shark is closer genetically to a whale or rabbit. If I happened to be a Creationist, and I believed in the common morphology argument, I would think that such a test should prove the point.

John Paul:
I gave a very good explanation already but here it is again:

John Paul:
In order to be scientifically thorough so that a good determination can be made, each organism would have to be compared with each of the others. If I am to conduct an experiment the first thing I would do is do away with unnecessary restrictions that would hinder an objective conclusion. If I compared a whale to a shark and a rabbit to a shark, without comparing a whale to a rabbit, I would only see that the whale may have more similarities with a shark than a rabbit does. However when doing a thorough comparison, including of whales & rabbits, I would see that those two have the most in common of the three possible pairings. After having all the knowledge available I would conclude that none of the organisms were related (unless being descended from organisms that were created makes them related- ie related by Common Creator) but because of the number of similarities I would predict a rabbit's DNA would be more similar to a whale's than a whale's to a shark's. Bird, bat, turtle- same thing.

That said, if a shark shared more similarities (depending on those similarities) with a whale than it does with a rabbit I would predict the genome of a shark to be more similar to a whale's than it is to a rabbit. However noticing the differences I just might be inclined to say any genetic similarities that aren't essential are coincidental. I would expect every free-living organism to have some genetic similarities.

John Paul: A whale's structure is not the same a shark's and a bird's wing is structurally different than a bat's. Morphology also goes down to the molecular level. DNA is allegedly responsible for the whole organism, not just its shape. So when comparing organisms we have to keep that in mind.

Robert:
You are merely stating the obvious.

John Paul:
If it's so obvious I wonder why you are even asking for these comparisons as if they mean something.

Robert:
In order to address my argument, the 2nd example of which is to establish the genetic distance of a bird and a bat compared to the genetic distance of a bird and a turtle, all you have to do is list all the ways in which a bird is closer morphologically to a turtle than it is to a bat. If a bird is closer morphologically to a turtle than a bat, then my argument is moot. Are you suggesting that this is the case? But look no further than the Bible for classification of bats. The Bible lists bats among the birds, not among the turtles.

John Paul:
The Bible isn't a science text. Never was meant to be. Again you seemed to be focused on outward appearance only. As I have pointed out several times now DNA is responsible for more than that.

However this should satisfy your requirement:

http://birding.about.com/gi/dynamic/offsite.htm?site=http%3A%2F%2Fwww.ups.edu%2Fbiology%2Fmuseum%2Fbirddissection.html

A bird without feathers is shaped something like a turtle, with compact trunk, long neck, and short tail (uropygium).

(bold added)

Another similarity is both lay eggs as part of each organism's reproduction process.

For bat/ bird:

http://www.bergen.org/Smithsonian/GreaterSpearNosedBat/MORPH.HTM/

As in birds, bats have some reduced bones; note in the picture below that the radius and fibula are shortened and thin. Bats, like birds, also have fused cranial bones for additional lightness.
Like most birds and pterosaurs, bats have a keel on the sternum, or breastbone, to which the large flight muscles attach. Unlike birds and pterosaurs, in which the wing is supported by the bones of the arm and one finger, a bat's wing membrane, or patagium, is supported by the arm and by four highly elongated fingers (hence the name Chiroptera, or "hand-wing," for the bats).

The similarities between bat & bird do not extend beyond a flight mechanism and even that is limited. Also not all birds can fly and the moa is said not to even have had wings.

Based upon what I have read my prediction would be the bird's DNA would be closer to a turtle's DNA than it would be to a bat's.