DNA preserves the integrity of its program

pshun2404 said:

Can you tell the difference between fish and birds? How about the difference between reptiles and mammals? It is that obvious from the observable facts....

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I can also tell the difference between Swedes and Pakistanis. I don't know what point you think you're making here.

pshun2404 said:

Well it seems reasonable to me that the program inherent in the embryo of fish (for example) assures the end result of the early manifest genome (that in the end it will become a fish with appropriate scales, gills, fins, and so on). The genes that assure these very specific end results can be effected (mostly detrimentally) but in the end the result is some form of that fish that the DNA's unfolding stored information is there to produce. The same is true for birds, mammals, and so on.

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Again, the same is also true of Swedes and Pakistanis. Yet I assume you think they're related.

pshun2404 said:

The same is true for the genome of amphibians, reptiles, mammals, and so on...the function of preservation of the genomes integrity (the error correction mechanisms and processes) specific to the pre-coded end result (an adult fish or amphibian or reptile) with all its specific systems, organs, and form would not allow so many changes (even over vast lengths of time) to form an amphibian from fish and so on.

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Yeah, we get that you believe that. What you haven't done is offer any reason to think that you're correct in your belief.

pshun2404 said:

Well it seems reasonable to me that the program inherent in the embryo of fish (for example) assures the end result of the early manifest genome (that in the end it will become a fish with appropriate scales, gills, fins, and so on). The genes that assure these very specific end results can be effected (mostly detrimentally) but in the end the result is some form of that fish that the DNA's unfolding stored information is there to produce. The same is true for birds, mammals, and so on.

The same is true for the genome of amphibians, reptiles, mammals, and so on...the function of preservation of the genomes integrity (the error correction mechanisms and processes) specific to the pre-coded end result (an adult fish or amphibian or reptile) with all its specific systems, organs, and form would not allow so many changes (even over vast lengths of time) to form an amphibian from fish and so on.

The systems and processes that assure every embryonic fish will become an adult FISH remains constant. When errors arise which remain, some of these may cause variance (or deformity) and the variety causing factors (genetic and environmental) may influence form but essentially it will always result in ONLY a variety of fish.

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So do you believe that the differences between reptiles and mammals are such that they cannot be brought about by a process of continuous change? Or that evolution isn't the process that could do it?

pshun2404 said:

So I will say (for the sake of discussion) that NO I do not believe reptiles became mammals by a process of slow continuous change.

If they did then show me...

Could they have? Might they have? Well sure anything is possible, but did they?

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So what do you think happened instead?

pshun2404 said:

If it happened, many of the factors of the evolution hypothesis could be involved, but nothing shows this did actually happen.

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It never stopped happening, like the growth of many mountain ranges, it continues and is measurable.

pshun2404 said:

The notion is precluded. It is a presupposition already believed which then effects and sometimes determines how evidence is interpreted. That is not true objectivity.

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Thanks to religious biases, the opposite is true. A lot of evidence for evolution was historically ignored thanks to people being unwilling to deviate from their creationist ideals. The bias is not in favor of evolution, it is just that the heavy bias against it has started to fade away as the evidence keeps piling up.

pshun2404 said:

Conclusion: Might have...could have...not DID! Now once one realizes this they can then look at what we actually can observe for data through fresh objective eyes.

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-_- scientific findings don't use absolutes about positive claims, because by the nature of science, all scientific findings have the potential to be disproven, regardless as to the amount and strength of the supporting evidence or the absence of conflicting evidence.

However, evolution experiments with bacteria demonstrate that evolutionary processes can result in enough genetic change for genus transitions. "But Sarah, they are still bacteria". No duh, bacteria is a kingdom level of classification. A transition of that scope would take far too long for human experimentation to cover it. However, species to species transitions are easy to observe, and we do get insight into genus transitions from time to time. There's no limit on mutation potential to be found.

pshun2404 said:

What is already accepted as true (though still not proven after 150 years), that was accepted as true long before any evidence that could be interpreted in that way (that is, "believed"), has shaped the interpretive conclusions.

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-_- Darwin shaped his theory AROUND EVIDENCE. If no evidence existed or observations could be made that suggested that populations change over time, Darwin would have never came up with his theory in the first place.

pshun2404 said:

This is the same logic problem YECs demonstrate? They interpret the data through what they already have concluded to be true. So I will say (for the sake of discussion) that NO I do not believe reptiles became mammals by a process of slow continuous change.

If they did then show me...

Could they have? Might they have? Well sure anything is possible, but did they?

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Mammals that lay eggs have the same sort of eggs that reptiles do. The genetics match up with the idea that mammals and reptiles share ancestry. At least 1 modern reptile, the leatherback turtle, can regulate its body temperature at an intermediate level between that of mammals and other reptiles, and a few mammals have a lot of problems maintaining body temperature without the environmental temperature interfering with it. Synapsids had mammary glands, and they are derived from skin associated glands similar to apocrine glands (glands in your armpits and groin, and the major reason the armpits get smelly).

Also, slow, continuous change as a model in evolution has been out of favor for quite some time. More recent findings suggest that evolutionary change can come in fits and bursts, as well as go periods of minimal change, depending on the environment and the organism in question. That is, how quickly evolutionary change occurs depends on how much the environment is changing, whether or not many species have recently gone extinct and left many niches open, and how adaptable to change a population already is. And when I say "more recent findings", I mean evidence from back before I was born.

pshun2404 said:

According to the Evolutionary Biologists and Geneticists of the Third Way Evolution movement, "The DNA record does not support the assertion that small random mutations are the main source of new and useful variations" (which is the idea of this thread) and believe there is "a need for a more open “third way” of discussing evolutionary change based on empirical observations."

Actually the genetics do not support the notion of even a million random mutations producing anything new (like amphibians becoming reptiles, or eventually mammals)...it is how the data is being interpreted (based on the already held belief that they do transform over time).

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Where is the evidence to back these claims?

We must separate the actual data from the story we are told that this means. We are all living creatures so we have genetic material in common, but this does not automatically imply lineage. Animal life shares more in common than with plant life but that is because they are even less likely related in a lineal sense.

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No one is saying that homology implies lineage. What we are saying is that a phylogenetic signal implies lineage. It is the nested hierarchy which evidences evolution and common ancestry.

pshun2404 said:

For evidence of their claims you can examine their works...go to the website and begin there.

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Haven't you examined their work? Can't you present some of it?

Also it is incorrect to conclude Nested Hierarchies do any such thing (which are based on homology which you admit does NOT prove lineage).

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Nested hierarchies are based on similarities and differences. Why is it incorrect to cite a nested hierarchy as evidence for shared ancestry? After all, we can observe modern life creating nested hierarchies right in front of us through the mechanisms of evolution.

So what is called “phylogenetic signal” is based on one’s statistical analysis where in one must attribute these patterns to the evolutionary process.

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If there was no evolutionary process, then there would be no phylogenetic signal when you use these analyses. That's the point. For example, when you analyze things like cars for a phylogenetic signal, there is no statistically significant signal.

The conclusions are due to one’s perception and in this application even among people who believe it is relevant to lineage they differ drastically among themselves (if it is a valuable as an actual indicator does the high cause the low or the low cause the high?).

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What they are saying is that high rates of evolution can produce homoplasies which can mask a phylogenetic signal.

pshun2404 said:

It is a wonderful curiosity how the program of DNA has within it the means to preserve its own integrity. ...
What are your thoughts?

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How do error correction mechanisms jive with the claims of many prominent creationists that God cursed us to have mutations?

The crack science experts at the Institute for Creation Science tell us that:

"The curse God placed on all of creation because of Adam’s disobedience led to disease and death."

Cancer Research Confirms the Curse


And how is this all-loving God's 'curse' manifested (let us ignore, for now, the repugnant immorality of 'cursing' all humanity for the 'sin' of one human...), according to ICR?

"Cancer occurs when pockets of cells proliferate out of control, a growth that DNA copying errors sometimes trigger. Living cells copy their DNA just before they divide. Human DNA strands have millions of specific chemicals, like letters in an encyclopedia, that record information for core life processes. Precision protein machines copy DNA “letters” at jet-engine speeds, yet perform so efficiently that only about one wrong letter arises among a billion. But even these few mutations can garble DNA’s information enough to lead to cancer, especially in tissues that undergo many cell divisions within a human lifetime."


So, did God 'curse' us with mutations, or 'save' us with mutation-correction enzymes?

Please explain this internally contradictory creationist conundrum.

pshun2404 said:

For evidence of their claims you can examine their works...go to the website and begin there. No one said anyone had said "homology" indicated lineage...I said shared genetic segments do not indicate lineage. Also it is incorrect to conclude Nested Hierarchies do any such thing (which are based on homology which you admit does NOT prove lineage).


Revell, Harmon, and Collar in Phylogenetic Signal, Evolutionary Process, and Rate ...

So what is called “phylogenetic signal” is based on one’s statistical analysis where in one must attribute these patterns to the evolutionary process. The conclusions are due to one’s perception and in this application even among people who believe it is relevant to lineage they differ drastically among themselves (if it is a valuable as an actual indicator does the high cause the low or the low cause the high?).

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It is so awesome that you are able to do keyword searches and find quotes that always seem to prop up your cause. Until they are looked into a bit more.


In a more hands-on approach, such as what I did when doing phylogenetic analyses, 'phylogenetic signal' was what we called lots of unique mutations - noncoding regions, largely unconstrained by conservation, tends to accumulate more mutations than coding regions and thus, in our practical view, provided more phylogenetic signal.

As seems to be the case with those doing keyword-search science, the trees obscure the forest view.

The use of 'DNA homologies' is, after all, a tested method, shown to recover known and experimentally generated phylogenies. I believe that several examples of this have been posted on this forum, earlier in the summer perhaps?
Semantic arguments and contrary assertions will not erase that.

pshun2404 said:

For evidence of their claims you can examine their works...go to the website and begin there. No one said anyone had said "homology" indicated lineage...I said shared genetic segments do not indicate lineage. Also it is incorrect to conclude Nested Hierarchies do any such thing (which are based on homology which you admit does NOT prove lineage).


Revell, Harmon, and Collar in Phylogenetic Signal, Evolutionary Process, and Rate (https://watermark.silverchair.com/a...f4KLZvUWTFhuac1LSzF29lLc-xmoipfCELE910G3nQni4 )



Reveal that “Phylogenetic signal is a measure of the statistical dependence among species’ trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species).

So what is called “phylogenetic signal” is based on one’s statistical analysis where in one must attribute these patterns to the evolutionary process. The conclusions are due to one’s perception and in this application even among people who believe it is relevant to lineage they differ drastically among themselves (if it is a valuable as an actual indicator does the high cause the low or the low cause the high?).

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That is not accurate.

The abstract ends with "For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal"

They are arguing against making a linkage between evolutionary rates and phylogenetic signal.


When I was working on molecular phylogenies, we literally did not care about rates (within reason). We knew that noncoding DNA accumulated phylogenetic signal because it is under less constraint (for the most part). We knew that function (e.g., of pseudogenes) was IRRELEVANT to their use as strong phylogenetic signal-producers because they too were able to accumulate more mutation.

These are things that one does not pick up doing keyword searches or dredging through YEC websites to find.

pshun2404 said:

Swedes and Pakastanis? Really? Another avoidance game? You know these are both the same animal...both humans...that is no comparison to the example I gave.

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On a cellular scale, mammalian cells are often near indistinguishable. Mouse brain cells and human brain cells are so similar that I can't reliably search for picture comparisons without labels existing on the images themselves.







So, I'll tell you, this last picture is a human nerve cell. Try and find the other picture/s among these that are human based on it.

pshun2404 said:

Bats are an excellent example. There are none at a certain point and then they are there (the actual observable data we have)...now I know the undemonstrated pat story of how they evolved from tiny shrew-like creatures that fell out of or jumped out of trees for 1000s of generations eventually evolving wings but there is no evidence to such that s true.

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Suppose that what you say is true, that the first bats appeared without parents or other ancestors by some unknown process. The fact remains that the first fossil bats date back to the Early Eocene epoch, about 52 million years ago - http://www.batworld.com/bat-evolution and Eocene - Wikipedia . However, there are about 490 million years worth of fossiliferous rock systems extending back to the beginning of the Cambrian period, when the first fossils of animals with readily preserved hard shells appeared. However the first bats came into existence, they did not appear until long after non-avian dinosaurs, ammonites, ichthyosaurs, and trilobites had become extinct.

This means that the sudden appearance of bats doesn't give any support to a creation of the universe in six days, or the creation of animals in one day, nor does it support 'flood geology'. How, then, do you interpret the sudden appearance of bats in the context of the whole fossil record?

pshun2404 said:

Swedes and Pakastanis? Really? Another avoidance game?

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No. Your argument about DNA applied equally well to Swedes and Pakistanis.

pshun2404 said:

You know these are both the same animal...both humans...that is no comparison to the example I gave.

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I also know that humans and fish are both vertebrates. Two humans are animals that differ genetically. A human and a fish are animals that differ genetically. Why does your argument apply to one pair and not the other?