Chimps and humans: How similar are we really?

[mark kennedy]

I'm not trying to pass anything off as proof of anything. I'm simply asking if you accept phylogenetic trees as valid. It's a basic yes or no question.

No, it depends on the tree.

You seem to be doing everything you can to avoid giving a straight answer.

No, I'm not accepting that because I accept one I accept all.

Maybe we should start with a more basic one: do you know what phylogenetic trees represent? Do you know what the data they can contain?

I jumped into a conversation about comparative genomics, if you are interested in something concerning phylogenetic trees I suggest you start a thread on the subject.

 

[pshun2404]

But again, that's not really what biologists refer to when they use the term "Darwinism". It's usually just meant to refer to Darwin's idea of evolution via natural selection.

Do you accept modern phylogenetics as a science? Do you accept that phylogenetic trees represent common ancestry of species? And do you accept that those phylogenetic trees are valid?

There is a lot here so let me start slow....

Any study of Phylogenetics (and in our training to understand it) we see two aspects of it, one being theoretical and the other being empirical. And the opinions for or against are extant dependent on the definition of terms. This means that even though most may agree, it is largely opinion not established fact. In time, it may turn out that much of that accepted by those that accept the idea in a end-all blanket fashion are incorrect. It may turn out they are correct. But as for NOW we actually do not KNOW but think we do depending on this ambiguity of terminology.

For example, we hear the term “relationship” being repeated over and over but when we see what we see (similarities in genetic materials, arrangement, and purpose) the question is “What does this mean?” It can mean related as in somehow similar (size, place, function, etc.) OR does it actually show we are related in the sense of demonstrating lineage (that one comes from the other)? well therein lays the dilemma that breeds discussion and debate.

What it ACTUALLY shows is some semblance of similarity, and this not nearly as exact as the rhetoric would like you to be convinced of.

If you really look at the data (void the narrative attached that explains the data according to the already accepted pre-conceived notion) we suddenly realize that the shoe does not fit the foot....

Look at this alleged “same gene” across species...an ALLEGED shared gene...

Human Gene HDLBP (uc002wba.1) a 110-kD protein that specifically binds HDL molecules, which functions in the removal of cellular cholesteral...it is a section 87,092 base pairs long

Rat Gene Hdlbp (NM_172039) which is only 68, 238 base pairs long performs a similar function but apparently not identically.

The allegedly the “SAME GENE” in Yeast, S. cerevisiae Gene SCP160 (YJL080C) functions differently and is primary to cell division, and only has 3,669 base pairs.

Finally, the alleged “SAME GENE” in D. Melongaster, Gene Dp1 (CG5170-RB). Having 9119 base pairs (3 times that of Yeast) seems to do nothing!

Now as fit as the hypothesis based explanation appears, the actual data shows us they actually are nothing alike...they are different in size AND FUNCTION...yet billed as “commonly shared” in the rhetoric.

Well since what I am telling you is true, how did they convince so many? This process of convincing the masses of the speculative for a definite motive (to prove their theory) requires consistent:

a) Interpretation of all data (even that which could be considered contrary to that theory) though the accepted model as opposed to allowing the raw data shape and remake the model (which is good science and true critical thought)


b) Repetition over and over...early Psychologist William James discovered this characteristic of people...that if they hear, or have had modelled before them, something not really true, over and over and over, they come to believe it as if it is true. Goebbels, capitalized on this insight in the 1930’s in Germany and applying it to politics h says “If you tell a lie big enough and keep repeating it, people will eventually come to believe it. The lie can be maintained only for such time as the State can shield the people from the political, economic and/or military consequences of the lie. It thus becomes vitally important for the State to use all of its powers to repress dissent, for the truth is the mortal enemy of the lie, and thus by extension, the truth is the greatest enemy of the State.” The same is true in this matter. Those aspects which are merely opinion about the data are repeated over and over as if they are fact and the masses swallow it whole with no actual discernment taking place.


c) Appeal to Authority...the above is reinforced by this. In addition to the repetition of the COULD BE/MIGHT BE over and over (which brainwashes) when you get a bunch of alleged authorities saying “Yes It is true”....simply because of their sheepskin people say “Well it must be true after all they know”. Really? NOT!


d) And then finally through c) consensus follows (the argumentum ad populum)....which basically is that “if everyone is saying it is true then it must be true” but if history (even the history of science) has taught us one thing it is that just because a bunch believe it does not make it so.


So Phylogenetics, which says different groups and in some sense ALL living organisms share genes, this is correct (but not nearly as many as they claim...see my above “shared gene” example)...but what this means is where we enter the twilight zone of opinion and interpretation. So let me ask...

If you were NOT ALREADY CONVINCED of the theory, and you were to just view the “shared gene” data above for the first time...(please be honest here) objectively, as a scientist, would you really come to some conclusion of lineage? They do not progress and they are not in any way the same (not actually)!

 

[pshun2404]

Next because they INTERPRET these similarities presence (the empirical) as demonstrative of shared HISTORY (the theoretical) as objective scientists, if we eliminate pre-convinced notion can we still come to the same conclusion? Now yes, there are some similar genes between all living things but these are NOT neatly progressive, nor are they in the same places, nor do they perform the same function in many cases.

In many cases the same gene (biochemically) performs and is used for (by the genetic program) very very different things AND in many cases it is very different genes that perform the same function/result in different species.

Therefore as valuable as Phylogenetics can be, it does not demonstrate transmutational lineage.

Some of the genes are simply what are required to be a living thing as opposed to a bunch of organic molecules. Some genes are common to what we call kingdoms, families, etc. Some genes are common to all members of particular phylum. Each species carries others totally unique to them. That is what IS. Nothing in that says one species came from or developed out of any other.

 

[Speedwell]

If you were NOT ALREADY CONVINCED of the theory, and you were to just view the “shared gene” data above for the first time...(please be honest here) objectively, as a scientist, would you really come to some conclusion of lineage? They do not progress and they are not in any way the same (not actually)!

If you are going to assert that phylogenic data does not do what science claims for it--i.e. be consistent with common ancestry--you are going to have to show examples where it is inconsistent.

 

[pshun2404]

If you are going to assert that phylogenic data does not do what science claims for it--i.e. be consistent with common ancestry--you are going to have to show examples where it is inconsistent.

Sorry, not meaning to insult you but I am not sure your statement relates to what I presented. Perhaps there are associations I am not privy to in your thinking, or there were ones in mine that I was not clear about! I showed this instance of how one example of accepted "shared genes" are not necessarily "shared" at all. And even in the case of "the exact same gene" present in all again does not necessitate genealogy only that living things require this gene.

My position is not to belittle or do away with or deny the value we get from areas of study like Phylogenetics. It is to get the people in all the various camps to clearly separate between the actual data and the story told (these are not the same). When Ernst Mayr (What Makes Biology Unique?, p. 198, Cambridge University Press, 2004) revealed “The earliest fossils of Homo… are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative" I see this as a much more far reaching admission. One that even as an avid supporter of the phylogenetic tree concept adnits and brings attention to this dichotomy.

As for showing examples where the concept/narrative is inconsistent the burden is on them to prove their position and as for now all they offer is plausible possibilities. Simply put, just because one thing precedes another, does NOT equal the former NECESSARILY being causative of the latter.

It could play a causative role in development but it may not at all (as we see in the bat example I gave).

 

[Speedwell]

As for showing examples where the concept/narrative is inconsistent the burden is on them to prove their position and as for now all they offer is plausible possibilities.

Where plausible possibilities are offered which you wish to deny the plausibility of then the burden of proof is on you. No one who offers plausible possibilities as such is required to "prove" them.
Do you or do you not have any examples of phylogeny which disprove common descent?

 

[mark kennedy]

When Ernst Mayr (What Makes Biology Unique?, p. 198, Cambridge University Press, 2004) revealed “The earliest fossils of Homo… are separated from Australopithecus by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative" I see this as a much more far reaching admission.

A children book entitled Days Before History. I was an adventure story about the Stone Age Men of Britain and featured the exploits of a young boy named Tig. There were pen sketches of primitive men bearded, muscular and dressed in animal skins, living in caves making stone tools and hunting mammoths ...'He lived in that book,' said his sister Julia, 'it became the Bible really. (Ancestral Passions, Virginia Morell)
​

That's about Louis Leaky the famous paleontologist who found so many hominid fossils in Oldovia Gorge. In the area of Africa where he was raised after a rain obsidian stones that resembled cutting tools, "Kikuyu friends knew about these glassy chips and called them 'spirit razors' because many of them appeared after rainfall." (Morell)

This is the guy that crafted the stone age ape man myth. Arthur Keith, Leaky's mentor had built his career based on the Piltdown Hoax, as that was exposed this narrative was developed to replace it. Some fossilized ape schools, fossilized foot prints and supposed tools and Homo habilis (handy man), the tool making apes became the key transitional from ape to man. Concurrent with the prominence of the Piltdown fossil Raymond Dart had reported on the skull of an ape that had filled with lime creating an endocast or a model of what the brain would have looked like. Everyone considered it a chimpanzee child since it’s cranial capacity was just over 400cc but with the demise of Piltdown, a new icon was needed in the Darwinian theater of the mind. Raymond Dart suggests to Louis Leakey that a small brained human ancestor might have been responsible for some of the supposed tools the Leaky family was finding in Africa.

Calico Hills in California's Mojave Desert was an archaeological site Leaky argued was a place where he could find evidence of Upper Pleistocene man. To this day it's believed that people only arrived in North America only 12,000 years ago. "Many archeologists would come to regard Calico as Louis's downfall." His arguments were received with silence, at a conference where Louis pressured his colleagues for their opinions. His attempt to fabricate tools from unusually shaped rocks had convinced no one. That only worked in Oldovia and only because of the treasure trove of fossils that are so unique to central Africa since that's the only place your going to find ancient prehistoric apes.

Some call it narrative, I call it mythography.

 

[pshun2404]

Where plausible possibilities are offered which you wish to deny the plausibility of then the burden of proof is on you. No one who offers plausible possibilities as such is required to "prove" them.
Do you or do you not have any examples of phylogeny which disprove common descent?

But I do not deny the plausibility at all, so NO you are incorrect! The idea of Phylogenesis is the evolutionary development and diversification of A species or A group of organisms, or of a particular feature of an organism. I in no way have one bit of doubt as to that.

What I challenge is the idea that one organism (with its own genome, that can vary via natural selection and genetic drift) becoming and entirely different organism (which has NEVER yet been shown to be true, yet is accepted by them and taught by them, as OBVIOUSLY true when in fact it is not "obvious" based on the evidence).

Organisms accumulate mutation and other factors that lead to speciation (VARIETY), but all examples from nature, and even those tests accomplished in labs, ALL only produce variation of the SAME ORGANISM. The examples are so many for what I am saying it is ludicrous (even Darwin's finches).

Why must I accept their "explanation", their attached "narrative", they have repeatedly imposed to explain their position when the actual evidence all and only demonstrates my point?

 

[pshun2404]

A children book entitled Days Before History. I was an adventure story about the Stone Age Men of Britain and featured the exploits of a young boy named Tig. There were pen sketches of primitive men bearded, muscular and dressed in animal skins, living in caves making stone tools and hunting mammoths ...'He lived in that book,' said his sister Julia, 'it became the Bible really. (Ancestral Passions, Virginia Morell)
​

That's about Louis Leaky the famous paleontologist who found so many hominid fossils in Oldovia Gorge. In the area of Africa where he was raised after a rain obsidian stones that resembled cutting tools, "Kikuyu friends knew about these glassy chips and called them 'spirit razors' because many of them appeared after rainfall." (Morell)

This is the guy that crafted the stone age ape man myth. Arthur Keith, Leaky's mentor had built his career based on the Piltdown Hoax, as that was exposed this narrative was developed to replace it. Some fossilized ape schools, fossilized foot prints and supposed tools and Homo habilis (handy man), the tool making apes became the key transitional from ape to man. Concurrent with the prominence of the Piltdown fossil Raymond Dart had reported on the skull of an ape that had filled with lime creating an endocast or a model of what the brain would have looked like. Everyone considered it a chimpanzee child since it’s cranial capacity was just over 400cc but with the demise of Piltdown, a new icon was needed in the Darwinian theater of the mind. Raymond Dart suggests to Louis Leakey that a small brained human ancestor might have been responsible for some of the supposed tools the Leaky family was finding in Africa.

Calico Hills in California's Mojave Desert was an archaeological site Leaky argued was a place where he could find evidence of Upper Pleistocene man. To this day it's believed that people only arrived in North America only 12,000 years ago. "Many archeologists would come to regard Calico as Louis's downfall." His arguments were received with silence, at a conference where Louis pressured his colleagues for their opinions. His attempt to fabricate tools from unusually shaped rocks had convinced no one. That only worked in Oldovia and only because of the treasure trove of fossils that are so unique to central Africa since that's the only place your going to find ancient prehistoric apes.

Some call it narrative, I call it mythography.

Mythography? Nice I will remember that. To me it would be like if some alien a million years from now came here after we are long gone and discovered my power drill and about a football field away found the partial remains of a dog, and so assumed the dog or the dog's family could made this tool and that because of the footprints we had left in the back yard they must have also had human looking feet. Amazing assumption based conclusionism yet hailed as final proof....this is what happens when the hypothesis interprets the data instead of the other way around. Evolutionist David Pilbeam, (Pro-Evolution, Vol. 14, p.127), once said “...in my own subject of Paleo-anthropology the “theory” heavily influenced by implicit ideas, almost always dominates data...ideas that are totally unrelated to the actual fossils have dominated theory building, which in turn strongly influences the way fossils are interpreted ”.

 

[mark kennedy]

Mythography? Nice I will remember that. To me it would be like if some alien a million years from now came here after we are long gone and discovered my power drill and about a football field away found the partial remains of a dog, and so assumed the dog or the dog's family could made this tool and that because of the footprints we had left in the back yard they must have also had human looking feet. Amazing assumption based conclusionism yet hailed as final proof....this is what happens when the hypothesis interprets the data instead of the other way around. Evolutionist David Pilbeam, (Pro-Evolution, Vol. 14, p.127), once said “...in my own subject of Paleo-anthropology the “theory” heavily influenced by implicit ideas, almost always dominates data...ideas that are totally unrelated to the actual fossils have dominated theory building, which in turn strongly influences the way fossils are interpreted ”.

I would describe the prevailing a priori assumption to be exclusively naturalistic causes. This drives and directs all modern academic and scientific thought on natural history. I honestly have no problem with natural science making naturalistic assumptions since they are not offered a miraculous cause. Just don't pass that off as a conclusion because there is more then enough room for skepticism with regards to Darwinian natural history narratives.

 

[mark kennedy]

Organisms accumulate mutation and other factors that lead to speciation (VARIETY), but all examples from nature, and even those tests accomplished in labs, ALL only produce variation of the SAME ORGANISM. The examples are so many for what I am saying it is ludicrous (even Darwin's finches).

About the role of mutations in adaptive evolution, there isn't a lot of empirical support for that and most of what they have is anecdotal:

Among the mutations that affect a typical gene, different kinds produce different impacts. A very few are at least momentarily adaptive on an evolutionary scale. Many are deleterious. (Rates of Spontaneous Mutation, Genetics 1998)​

Mutations are little more then copy errors:

In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA repair. (Kimbal, Mutations)
​

Even Richard Dawkins, the leading Darwinian of our times, realized the the changes of Finches are cyclical. Readily explainable in Mendelian Laws of Inheritance and dominant and recessive traits occurring at roughly a 3:1 ratio. It seems to me there is ample evidence that genomic molecular mechanisms protect the fidelity of the DNA sequences on a broad scale while molecular mechanisms changing the DNA sequence are far less common:

DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides. (DNA Repair)​

Major genetic change most often results in deleterious (harmful) effects when it has any effect at all. Mutations seldom have any adaptive effect on an evolutionary scale so it makes sense there must be another explanation. The concept of mutation plus selection equals evolution boarders on absurdity given the enormous amount of change required across broad taxa. Functional restraint is a major obstacle of change on an evolutionary scale, see my signature.

 

[pshun2404]

About the role of mutations in adaptive evolution, there isn't a lot of empirical support for that and most of what they have is anecdotal:

Among the mutations that affect a typical gene, different kinds produce different impacts. A very few are at least momentarily adaptive on an evolutionary scale. Many are deleterious. (Rates of Spontaneous Mutation, Genetics 1998)​

Mutations are little more then copy errors:

In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA repair. (Kimbal, Mutations)
​

Even Richard Dawkins, the leading Darwinian of our times, realized the the changes of Finches are cyclical. Readily explainable in Mendelian Laws of Inheritance and dominant and recessive traits occurring at roughly a 3:1 ratio. It seems to me there is ample evidence that genomic molecular mechanisms protect the fidelity of the DNA sequences on a broad scale while molecular mechanisms changing the DNA sequence are far less common:

DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides. (DNA Repair)​

Major genetic change most often results in deleterious (harmful) effects when it has any effect at all. Mutations seldom have any adaptive effect on an evolutionary scale so it makes sense there must be another explanation. The concept of mutation plus selection equals evolution boarders on absurdity given the enormous amount of change required across broad taxa. Functional restraint is a major obstacle of change on an evolutionary scale, see my signature.

I hear you and I did read your signature, but of course we already know Mendel was spot on.

 

[pitabread]

No, it depends on the tree.

Would you accept a tree like this?

I jumped into a conversation about comparative genomics, if you are interested in something concerning phylogenetic trees I suggest you start a thread on the subject.

The reason I'm talking about phylogenetics is because it is related to comparative genomics.

What I believe is that you would largely reject phylogenetics, yet you continually laud comparative genomics. Which I find odd given certain comparative genomics methodologies are based on phylogenetics with respect to multi-species comparative analyses.

 

[pitabread]

It seems to me there is ample evidence that genomic molecular mechanisms protect the fidelity of the DNA sequences on a broad scale while molecular mechanisms changing the DNA sequence are far less common

Look up HLA genes. There are HLA genes for which there are thousands of identified alleles.

 

[mark kennedy]

Look up HLA genes. There are HLA genes for which there are thousands of identified alleles.

MHC class II genes provide instructions for making proteins that are present almost exclusively on the surface of certain immune system cells. (Human leukocyte antigens)

Clustered, regularly interspaced, short palindromic repeats (CRISPR) loci are found in the genomes of many bacteria and most archaea, and underlie an adaptive immune system that protects the host cell against invasive nucleic acids such as viral genomes. (The Bacterial Origins of the CRISPR Genome-Editing Revolution. NCBI 2015)
​

These are involved in immune systems, not the same thing as protein coding genes and certainly not highly conserved brain related functions.

 

[Speedwell]

What I challenge is the idea that one organism (with its own genome, that can vary via natural selection and genetic drift) becoming and entirely different organism (which has NEVER yet been shown to be true, yet is accepted by them and taught by them, as OBVIOUSLY true when in fact it is not "obvious" based on the evidence).

What do you mean by "an entirely different organism?" Speciation has been observed.

 

[pitabread]

These are involved in immune systems, not the same thing as protein coding genes

These *are* protein coding genes.

Humans have three main MHC class I genes, known as HLA-A, HLA-B, and HLA-C. The proteins produced from these genes are present on the surface of almost all cells. On the cell surface, these proteins are bound to protein fragments (peptides) that have been exported from within the cell. MHC class I proteins display these peptides to the immune system. If the immune system recognizes the peptides as foreign (such as viral or bacterial peptides), it responds by triggering the infected cell to self-destruct.

Human leukocyte antigens

 

[mark kennedy]

These *are* protein coding genes.



Human leukocyte antigens

These are involved in immune systems, everything works from proteins or regulatory genes. That's the point.

 

[pshun2404]

What do you mean by "an entirely different organism?" Speciation has been observed.

Yes speciation has definitely been observed, and demonstrated. It produces variety in the same organism only. For example, speciation in Darwin's finches helped produce varieties of finches each more successful in their environment. No indication they ever were some other creature or ever will become one. The E-Coli experiments after 50,000 plus generations still remain E-Coli, Homo sapien Neanderthalis/Homo sapien Altai/and Homo sapien Sapiens are another great example (very fitting to Kimuru's Neutral Theory), some staphylococcus aureus became antibiotic resistant but guess what? Yup! Still staphylococcus aureus, and on and on....see? Varieties of the same organism via things like mutation, genetic drift, allele reinforcement, and so on...nothing to confirm they might become something new, say like fish becoming amphibians becoming reptiles, etc.

 

[mark kennedy]

I wonder what the replies were the last 3 times you posted this exact same thing on this forum? Or when you posted this on 'worthychristiansforums'? Or on carm.org? Maybe we should look rather than waste time coming up with new and unique replies...


Nah... Why bother?

I haven't been on carm in years and I put it on worthchristianforums so it didn't get lost in the stacks. Indeed it's a lot the same thing but it builds, the latest was the paranthropous fossils. Those genes I keep bring up, trollers tell me about them. So I just bait them with facts and wait for them to actually try using real evidence. None of the veterans would dare but sometimes newbies don't know any better.