Chimps and humans: How similar are we really?

[pshun2404]

Take a look at this as an example:

Human: AGTACGATGGC T A CA

Chimp: AGTACTATGGC T A CG

Here we have an actual segmented sequence of the human genome and its chimpanzee equivalent. This is noted, and then G,T and A,G differences are called “substitutions” but why? In other words one has been substituted for the other.

They say one or the other is a mutation, only if that is true then which one? When asked if they qould please show when it was not mutated so we can SEE which one is the actual mutation, they cannot show us one example! Instead they then say it happened in a Common Ancestor.

So being told that and we also ask, “Okay fine, can you please show me a sample of their genome so I can compare the sequence”? So I can really see which one is the mutation and which one is not?” Again they cannot.

In fact, they cannot show us the Common Ancestor at all let, alone it’s genome, and here’s the thing, when pressured it turns out they have never seen it either! WHAT!!! So why do they believe it true as if it is true, and why teach this assumption to us as if it is an established fact, without actual demonstrable evidence that such a “substitution” actually occurred?

We’re just supposed to believe it because they told us it is true? No...show us!

To be confirmed to actually be substituted one would have to show they once were one thing, and now are another, and I have not seen this demonstrated in either the human or chimp genome (just that one differs from the other in these places) or in a common ancestor.

Now the burden is not on someone to show they are NOT substitutions (that is asking someone to prove a negative which is illogical) because they very well may be. But the claim is made that they ARE this and so the burden is theirs to demonstrate it (not just assume it based on a presupposed hypothesis or belief).




Here is another:

Human: AGTCGTACCAGTCGTACC

Chimp: AGTCATACCAGTCTACC

So via computer programs they separate the chimp genome after AGTC and then call the human G an insertion, or the lack thereof in the Chimp a deletion, but what if the difference is the whole idea? What if the two respective genomes are exactly what they are supposed to be and nothing was inserted or deleted?

Human: AGTCGTACCAGTCGTACC

Chimp: AGTCGTACCAGTC TACC

That gap does not really exist! If they were always a normal part of each respective genome, just as they are, one in one order with their sequence, and the other in their order with a different sequence. Thus always what it is in each (making each creature what they are uniquely), then there is no need to automatically assume one is inserted and/or the other is deleted.

One has to ASSUME that at one time the genomes were the same (in a Common Ancestor). Now to confirm it one must produce an example of the original model for comparison or else the whole assumption remains in the realm of the theoretical and hypothetical. You CAN see that makes sense can't you?

I mean in all cases of contract law any claims of insertions or deletions must be demonstrated to assure confirmation. The person or persons making the claim of an insertion or deletion into an existing contract or agreement, to demonstrate credibility of the claim, must produce an example of the earlier copy for comparison. If it can be seen that something previously not there now is, or that something previously there now is missing, then it is considered an insertion (to have been inserted) or a deletion (to have been deleted).

How can one prove a deletion in a data set? If we have access to the complete database by comparing earlier versions with the latest version we can easily detect a deletion with assurance. One can never assume a deletion without comparison to the earlier version. Hearsay, and opinion, regardless of alleged expertise, is not confirmation of the claim.

In accounting systems the same rule applies. If one claims an insertion or deletion into the record has taken place, confirmation can only be demonstrated when the auditor or examiner is allowed to see or discovers the earlier version which does or does not contain the insertion or deletion, and compare.

MacDonalds was once questioned on their claim that all their food was natural. After investigation it could be shown against the genome of a true actual russet potato that an insertion had occurred. They had inserted a segment of butterfly gene into their potato crop to fight a particular pestilence. But the insertion had been confirmed and so now they are quite honest about it.

In choosing a cloning vector, they must be small molecules because they are easier to manipulate. The sequence being inserted must be capable of prolific replication inside the recipient cell in order to enable the amplification of the inserted donor fragment.

Identifying such an insertion is easily confirmed. It is conformed because we can see how it was not there, and now is there! The same is true when we splice out a segment from an extant genome. We can confirm this actually happened by comparing the genome which previously contained the segment, with the same genome from which it is now deleted. Otherwise such a claim may be interpreted to suggest it happened, and dozens could even claim it happened, but that does not confirm it.

So...the ONLY way we can actually confirm that this is an insertion or deletion in the genomes is by showing something not there once, now is, or that something that was there, now is not. Can you see the sense of this? This is not unreasonable at all, In fact, it is totally logical!

We actually should be insulted to have them insist we accept it as true when they cannot show such an event took place in either the human or the chimp genome, and even less likely in some common ancestor. Yet they do and when people like me insist they SHOW ME? I am called all sorts of names...

 

[Jimmy D]

Take a look at this as an example:

Human: AGTACGATGGC T A CA

Chimp: AGTACTATGGC T A CG

Here we have an actual segmented sequence of the human genome and its chimpanzee equivalent. This is noted, and then G,T and A,G differences are called “substitutions” but why? In other words one has been substituted for the other.

They say one or the other is a mutation, only if that is true then which one? When asked if they qould please show when it was not mutated so we can SEE which one is the actual mutation, they cannot show us one example! Instead they then say it happened in a Common Ancestor.

So being told that and we also ask, “Okay fine, can you please show me a sample of their genome so I can compare the sequence”? So I can really see which one is the mutation and which one is not?” Again they cannot.

In fact, they cannot show us the Common Ancestor at all let, alone it’s genome, and here’s the thing, when pressured it turns out they have never seen it either! WHAT!!! So why do they believe it true as if it is true, and why teach this assumption to us as if it is an established fact, without actual demonstrable evidence that such a “substitution” actually occurred?

We’re just supposed to believe it because they told us it is true? No...show us!

To be confirmed to actually be substituted one would have to show they once were one thing, and now are another, and I have not seen this demonstrated in either the human or chimp genome (just that one differs from the other in these places) or in a common ancestor.

Now the burden is not on someone to show they are NOT substitutions (that is asking someone to prove a negative which is illogical) because they very well may be. But the claim is made that they ARE this and so the burden is theirs to demonstrate it (not just assume it based on a presupposed hypothesis or belief).




Here is another:

Human: AGTCGTACCAGTCGTACC

Chimp: AGTCATACCAGTCTACC

So via computer programs they separate the chimp genome after AGTC and then call the human G an insertion, or the lack thereof in the Chimp a deletion, but what if the difference is the whole idea? What if the two respective genomes are exactly what they are supposed to be and nothing was inserted or deleted?

Human: AGTCGTACCAGTCGTACC

Chimp: AGTCGTACCAGTC TACC

That gap does not really exist! If they were always a normal part of each respective genome, just as they are, one in one order with their sequence, and the other in their order with a different sequence. Thus always what it is in each (making each creature what they are uniquely), then there is no need to automatically assume one is inserted and/or the other is deleted.

One has to ASSUME that at one time the genomes were the same (in a Common Ancestor). Now to confirm it one must produce an example of the original model for comparison or else the whole assumption remains in the realm of the theoretical and hypothetical. You CAN see that makes sense can't you?

I mean in all cases of contract law any claims of insertions or deletions must be demonstrated to assure confirmation. The person or persons making the claim of an insertion or deletion into an existing contract or agreement, to demonstrate credibility of the claim, must produce an example of the earlier copy for comparison. If it can be seen that something previously not there now is, or that something previously there now is missing, then it is considered an insertion (to have been inserted) or a deletion (to have been deleted).

How can one prove a deletion in a data set? If we have access to the complete database by comparing earlier versions with the latest version we can easily detect a deletion with assurance. One can never assume a deletion without comparison to the earlier version. Hearsay, and opinion, regardless of alleged expertise, is not confirmation of the claim.

In accounting systems the same rule applies. If one claims an insertion or deletion into the record has taken place, confirmation can only be demonstrated when the auditor or examiner is allowed to see or discovers the earlier version which does or does not contain the insertion or deletion, and compare.

MacDonalds was once questioned on their claim that all their food was natural. After investigation it could be shown against the genome of a true actual russet potato that an insertion had occurred. They had inserted a segment of butterfly gene into their potato crop to fight a particular pestilence. But the insertion had been confirmed and so now they are quite honest about it.

In choosing a cloning vector, they must be small molecules because they are easier to manipulate. The sequence being inserted must be capable of prolific replication inside the recipient cell in order to enable the amplification of the inserted donor fragment.

Identifying such an insertion is easily confirmed. It is conformed because we can see how it was not there, and now is there! The same is true when we splice out a segment from an extant genome. We can confirm this actually happened by comparing the genome which previously contained the segment, with the same genome from which it is now deleted. Otherwise such a claim may be interpreted to suggest it happened, and dozens could even claim it happened, but that does not confirm it.

So...the ONLY way we can actually confirm that this is an insertion or deletion in the genomes is by showing something not there once, now is, or that something that was there, now is not. Can you see the sense of this? This is not unreasonable at all, In fact, it is totally logical!

We actually should be insulted to have them insist we accept it as true when they cannot show such an event took place in either the human or the chimp genome, and even less likely in some common ancestor. Yet they do and when people like me insist they SHOW ME? I am called all sorts of names...

You examples are overly simplified to the point of being ridiculous.

Don't get me wrong, I don't claim to understand the science behind it, but the papers I've looked at after reading your post bare little resemblance to what you're saying.

For example
Evolution of genetic and genomic features unique to the human lineage
Hotspots of Biased Nucleotide Substitutions in Human Genes
Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

It appears to me that the subjects your post brings up are much better understood than you imply.

 

[pshun2404]

You examples are overly simplified to the point of being ridiculous.

Don't get me wrong, I don't claim to understand the science behind it, but the papers I've looked at after reading your post bare little resemblance to what you're saying.

For example
Evolution of genetic and genomic features unique to the human lineage
Hotspots of Biased Nucleotide Substitutions in Human Genes
Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

It appears to me that the subjects your post brings up are much better understood than you imply.

I just finished (and already had read 1 and 3). You say "the subjects your post brings up are much better understood than you imply." It is not about HOW they understand it or that they do or not from their perspective, but the understanding they demonstrate is a form of confirmation bias (most always subconsciously and not intentional).

So they give convincing explanation for all who already accept the premise, except for the fact that the explanations have never been shown to be true. The hypothesis is dictating the explanation, but zero real example is produced to demonstrate it. They have given zero comparative samples to support their explanation.

 

[pshun2404]

Jim...can YOU show them to be true? Can you show something not there then being there or something being there and then not there in either genome or in a common ancestor? OR can YOU show that the mutation actually occurred causing one of these "substitutions" (you know first the un-mutated then the mutated)?

Yes or no? It is okay if you cannot...but I would like an honest answer. Show me and with an open mind I will take it into consideration. U have been wrong before and even admitted it right in this forum.

 

[Tanj]

For a number of mutations, especially those in conserved genes, I can look at a wide range of species to determine what happened. For instance if I have a G in Humans but an A in Chimps, and I go look at Gorrillas, dogs and mice and they all have an A, then I can be confident the mutation happened in humans. Furthermore, for those mutations in less conserved regions there's no reason the consider that some alternative process applies.

Finally, within a controlled laboratory environment, I can sequence bacteria from a colony, subject said colony to some kind of stress, re-sequence, and see exactly where substitutions have occurred, and again there's no reason to think the process is different to what occurs everywhere else.

Note that last bit is not hypothetical, I have actually done it.

 

[Jimmy D]

Jim...can YOU show them to be true? Can you show something not there then being there or something being there and then not there in either genome or in a common ancestor? OR can YOU show that the mutation actually occurred causing one of these "substitutions" (you know first the un-mutated then the mutated)?

Yes or no? It is okay if you cannot...but I would like an honest answer. Show me and with an open mind I will take it into consideration. U have been wrong before and even admitted it right in this forum.

No, I can't Pshun, as I say I'm not really too au fait with the subject, I'm not above admitting I'm wrong though if that's shown to be the case.

The problem is that you are arguing against well a researched and rigorous modern understanding of the subject in question so you really need to demonstrate with some rock solid evidence and reasoning that your explanation is correct.

To suggest that they merely compare a sequence of letters and declare a "substitution" or "deletion" is spurious at best.

Please have a read through this paper, some of it is a bit heavy for us laymen (well me anyway) but there is some interesting stuff in there that might shed some light on your doubts....

Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

 

[Jimmy D]

Jim...can YOU show them to be true? Can you show something not there then being there or something being there and then not there in either genome or in a common ancestor? OR can YOU show that the mutation actually occurred causing one of these "substitutions" (you know first the un-mutated then the mutated)?

Yes or no? It is okay if you cannot...but I would like an honest answer. Show me and with an open mind I will take it into consideration. U have been wrong before and even admitted it right in this forum.

For a number of mutations, especially those in conserved genes, I can look at a wide range of species to determine what happened. For instance if I have a G in Humans but an A in Chimps, and I go look at Gorrillas, dogs and mice and they all have an A, then I can be confident the mutation happened in humans. Furthermore, for those mutations in less conserved regions there's no reason the consider that some alternative process applies.

Finally, within a controlled laboratory environment, I can sequence bacteria from a colony, subject said colony to some kind of stress, re-sequence, and see exactly where substitutions have occurred, and again there's no reason to think the process is different to what occurs everywhere else.

Note that last bit is not hypothetical, I have actually done it.

Sounds like you're better off talking to Tanj about this Pshun, unlike me he sounds like he knows the subject.

 

[Tanj]

...or you could read a paper like this:

Genome-wide patterns and properties of de novo mutations in humans

where they sequenced the mother, father and children from 250 families, and could directly identify the new mutations in the children not present in the parents.

 

[pshun2404]

For a number of mutations, especially those in conserved genes, I can look at a wide range of species to determine what happened. For instance if I have a G in Humans but an A in Chimps, and I go look at Gorrillas, dogs and mice and they all have an A, then I can be confident the mutation happened in humans. Furthermore, for those mutations in less conserved regions there's no reason the consider that some alternative process applies.

Finally, within a controlled laboratory environment, I can sequence bacteria from a colony, subject said colony to some kind of stress, re-sequence, and see exactly where substitutions have occurred, and again there's no reason to think the process is different to what occurs everywhere else.

Note that last bit is not hypothetical, I have actually done it.

Finally one intelligent response. A is not a good example in my opinion, but B was very good and shows how it can happen (not that it did in the millions of cases represented in the genomes). I do not doubt some reflect mutations in humans, and others in chimps, but to KNOW we have to see in humans or chimps that they were not and now are or were and now are not. Because humans have a G and all these other organisms have an A does not mean humans or their ancestor at one time had an A. Might have, could have, but had? Show me...

And what of other creatures that have a G here (or nothing at all in some cases)? Maybe they are our ancestors.

 

[pshun2404]

No, I can't Pshun, as I say I'm not really too au fait with the subject, I'm not above admitting I'm wrong though if that's shown to be the case.

The problem is that you are arguing against well a researched and rigorous modern understanding of the subject in question so you really need to demonstrate with some rock solid evidence and reasoning that your explanation is correct.

To suggest that they merely compare a sequence of letters and declare a "substitution" or "deletion" is spurious at best.

Please have a read through this paper, some of it is a bit heavy for us laymen (well me anyway) but there is some interesting stuff in there that might shed some light on your doubts....

Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

I have read it Jim (more than once) and also I am not above being wrong (and admitting it).

My explanation was not the point it was the questions. My explanation was merely a viable possibility. If one divorces themselves from the presumption that there is a common ancestor and just looks at the two columns (full chimp genome next to the full human genome) there are literally millions of differences. They are NOT even 95% the same. The differences are far greater than claimed. It requires manipulation of the data sets by an outside intelligent force (a programmer) using a program DESIGNED to llok for what they expect, and then hypothesis based interpretation by another intelligence (the researcher) to emphasize the contrived 1.8% difference conclusion (thus confirmation bias is present just like in any study).

 

[pshun2404]

...or you could read a paper like this:

Genome-wide patterns and properties of de novo mutations in humans

where they sequenced the mother, father and children from 250 families, and could directly identify the new mutations in the children not present in the parents.

Without a doubt, and I am not saying mutations do not exist, they do and can be found in ALL heritable lines of organisms. But in this case (alleged substitutions) many may not be mutations at all (some undoubtedly are) but may actually be what is natural for that organism as opposed to any other, and for those that are, we cannot KNOW which are the mutation without seeing the original for comparison.

As for newly forming ones, this question I ask is answered because we can see they were not there, and now are, or have changed, and this is fine as far as I am concerned, and I would not doubt the conclusion in such cases. But the same logic applies to where one has a BP at a location and the other has nothing. One can say one is a deletion or insertion (and they may be) but one cannot insist dogmatically (and I am not saying you are) this is the case.

For insertion one must see they were NOT there and now are in the same creature or the alleged ancestor of that creature. For deletion to be declared with assurance one needs to show they were there (in the creature or in their common ancestor) and now are not, for they may simply be what is correct and natural for each respective creature and not related to a common ancestor at all.

Can any one show this common ancestor or their genome or that this was actually inserted or deleted? Now again for clarification I am not saying this never happens because we know it does and have seen it take place in modern times (for example when in some HIV patients part of the RV genome appears in the gametes though babies born with the insertion usually do not get the illness)...but that does not explain all the "resembles ERVs" sites or the alleged "partial", or even many of the sites labelled ERVs...some are said to possibly be the source segment for common retro viruses.

 

[pshun2404]

No, I can't Pshun, as I say I'm not really too au fait with the subject, I'm not above admitting I'm wrong though if that's shown to be the case.

The problem is that you are arguing against well a researched and rigorous modern understanding of the subject in question so you really need to demonstrate with some rock solid evidence and reasoning that your explanation is correct.

To suggest that they merely compare a sequence of letters and declare a "substitution" or "deletion" is spurious at best.

Please have a read through this paper, some of it is a bit heavy for us laymen (well me anyway) but there is some interesting stuff in there that might shed some light on your doubts....

Initial sequence of the chimpanzee genome and comparison with the human genome : Article : Nature

Jim consider just in the first paragraph. It reads

"we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements.

Are you not able to see that the rest is being looked at through this filter? The "Common Ancestor" concept is a definite possibility (which I do not deny) but the point is it is accepted as true first before the millions of differences are interpreted. It has been accepted as true long before any semblance of evidence was ever found that could be supportive in demonstrating it.

We were taught the Common Ancestor as truth since we were wee little ones and had it via drill and repetition planted in our heads year after year...we were even subjected to artistically contrived images (a standard propaganda technique) and reconstructions of fossil finds where stuff is pieced together just so and even added to and filed and stained and viola' there is the real creature (NOT!!!). Now most people (and myself included for decades) cannot step out of this box we were placed in and just look at the simple plain data.

Not related, but the same thing happens with people inundated with YEC opinion...no matter how hard you get them to consider alternatives they cannot free themselves from the program, and even MUST interpret all that challenges them through that filter.

 

[Jimmy D]

I have read it Jim (more than once) and also I am not above being wrong (and admitting it).

My explanation was not the point it was the questions. My explanation was merely a viable possibility. If one divorces themselves from the presumption that there is a common ancestor and just looks at the two columns (full chimp genome next to the full human genome) there are literally millions of differences. They are NOT even 95% the same. The differences are far greater than claimed. It requires manipulation of the data sets by an outside intelligent force (a programmer) and hypothesis based interpretation by another intelligence (the researcher) to emphasize the contrived 1.8% difference conclusion.

Right, I just took a look through the start of this thread, it seems your concerns have been addressed. If you won't accept correction off someone like SFS nothing I can say will make any difference.

However, if you want to convince anyone that the data obtained from the analysis of the genomes in question demonstrate special creation (or whatever you're suggesting) then put your money where your mouth is and show us.

The burden of proof is on you.

 

[pshun2404]

Right, I just took a look through the start of this thread, it seems your concerns have been addressed. If you won't accept correction off someone like SFS nothing I can say will make any difference.

However, if you want to convince anyone that the data obtained from the analysis of the genomes in question demonstrate special creation (or whatever you're suggesting) then put your money where your mouth is and show us.

The burden of proof is on you.

I am not saying that so no...and yes here on this forum I have gotten some great responses with lots of support for their view. Yes humans and chimps do share the most in common genomically (no doubt). That precludes similarity yes (but not lineage), and from all I have seen and read in 100s of papers and gotten from many forums, it remains MY OPINION that the actual differences far outweigh the projected % of similarities (for now at least, but I am ever learning).

 

[Jimmy D]

"we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements.

Are you not able to see that the rest is being looked at through this filter? The "Common Ancestor" concept is a definite possibility (which I do not deny) but the point is it is accepted as true first before the millions of differences are interpreted. It has been accepted as true long before any semblance of evidence was ever found that could be supportive in demonstrating it.

Of course it's looked at through that "filter", that "filter" is a fact - even if you don't like it. Funny how all these lines of evidence make complete sense when we assume common descent isn't it?

We were taught the Common Ancestor as truth since we were wee little ones and had it via drill and repetition planted in our heads year after year...we were even subjected to artistically contrived images (a standard propaganda technique) and reconstructions of fossil finds where stuff is pieced together just so and even added to and filed and stained and viola' there is the real creature (NOT!!!). Now most people (and myself included for decades) cannot step out of this box we were placed in and just look at the simple plain data.

Please. All you are doing is trying to find faults with the interpretation of the data and suggesting that everyone who's actually studied it - other than you of course - are blinded by bias and assumptions.

 

[pshun2404]

Of course it's looked at through that "filter", that "filter" is a fact - even if you don't like it. Funny how all these lines of evidence make complete sense when we assume common descent isn't it?

Please. All you are doing is trying to find faults with the interpretation of the data and suggesting that everyone who's actually studied it - other than you of course - are blinded by bias and assumptions.

No just tryng to separate the data from the interpretation and look at IT. Take your article for example. It starts with:

“Darwin and Huxley posited that humans share recent common ancestors with the African great apes. Modern molecular studies have spectacularly confirmed this prediction”

Sorry I do not agree, all that the evidence as demonstrated is that we share a lot in common genomicaly but that does not equal we shared a common ancestor. That is merely one way to interpret the data.

In YOUR article please note the following:

They used a specific method as opposed to others. Other methods may unveil slightly different results. That does not mean they are not great and effective methods, and after all, they are what we have...

Then they used two humanly designed computer programs designed by people who already accept the UCA concept as truth. The purpose of these programs is in fact to find similarities that can be used to support the opening premise.

Next they aligned protein coding segments (which naturally do not align in many cases, and even are longer and shorter in more, and are not in the same place in many examples) by matching up the areas that are similar (few are exact).

Even some statistics were applied (which is highly influenced by sample selection, unknowable changes in rate of change, and more)

Finally, of course they interpret differences as being mutations, insertions, deletions, etc., instead of accepting them as simply evidence that we are different.

Surely any rational person can see the huge “human factor” influencing their findings.

Now I am not degrading these brilliant people or the scientific method. But remove the human factor and its effect and what do we see? Same or different? DO we see any indication or direct evidence for a common ancestor? The answer to both these question is in favor of there not necessarily being any common ancestor. It really is...

 

[Tanj]

Without a doubt, and I am not saying mutations do not exist, they do and can be found in ALL heritable lines of organisms. But in this case (alleged substitutions) many may not be mutations at all (some undoubtedly are) but may actually be what is natural for that organism as opposed to any other, and for those that are, we cannot KNOW which are the mutation without seeing the original for comparison.

They sequenced the parents. They did see the original. We can thus KNOW.

As for newly forming ones, this question I ask is answered because we can see they were not there, and now are, or have changed, and this is fine as far as I am concerned, and I would not doubt the conclusion in such cases. But the same logic applies to where one has a BP at a location and the other has nothing. One can say one is a deletion or insertion (and they may be) but one cannot insist dogmatically (and I am not saying you are) this is the case.

Except as I said in the case of this study, they sequenced the parents, so in fact they can decide if something is a deletion or an insertion. In the more general case, my previous point stands. If we see a particular piece of DNA present in mouse and chimps but not humans we can be pretty confident this is a deletion in humans.

Now again for clarification I am not saying this never happens because we know it does and have seen it take place in modern times (for example when in some HIV patients part of the RV genome appears in the gametes though babies born with the insertion usually do not get the illness)...but that does not explain all the "resembles ERVs" sites or the alleged "partial", or even many of the sites labelled ERVs...some are said to possibly be the source segment for common retro viruses.

Sorry, but I didn't really understand that. I think (and may be wrong) that what you are saying is that even if I can somehow prove insertion/deletion/substitution for a subset of mutations, it doesn't mean the same mechanism applied in the ones I cannot prove, that there exists some other possibly supernatural mechanism whose end result is the same but whose mechanism is entire different, a bit like Dad's deep state past.

If this is the case please confirm, if not please clarify. If it is the case I wont be responding, I don't how to discuss anything with someone that believes that. It's like saying people with bullet holes in then were only shot by people where you can absolutely prove someone used a gun, otherwise it might have been the hole fairies that made what looks exactly like a bullet hole with their magic dust.

 

[pshun2404]

I agree with this up to this statement (in fact you did make my point. Yes we can KNOW in the first scenario):

“If we see a particular piece of DNA present in mouse and chimps but not humans we can be pretty confident this is a deletion in humans.”

No, not really! Only if we assume a universal common ancestor. I mean why else would we ASSUME there is a standard genome we can all be compared to? An original one we each (each species) have added to or taken away from?

If you do not assume that, and just look at the raw data of the scenario you presented, all you would be confident in is that humans are not like them in this place in the genome (hence humans may not be a relative). Like your very astute and proper PROOF of insertion in the offspring example, to me logic dictates to be “confident” one has to show it was originally there in humans (or in a demonstrable common ancestor) and now is not.

Even though I am sure you disagree with my UCA position, can you at least see how this thinking makes sense? I am not even saying there is not one, but we do not have any actual example.

“Sorry, but I didn't really understand that. I think (and may be wrong) that what you are saying is that even if I can somehow prove insertion/deletion/substitution for a subset of mutations, it doesn't mean the same mechanism applied in the ones I cannot prove, that there exists some other possibly supernatural mechanism whose end result is the same but whose mechanism is entire different, a bit like Dad's deep state past.”

No! I am not saying anything of the sort. I am saying we know for sure (as you demonstrated) that insertions and possibly deletions are real and do in fact happen, but I am also saying many substitutions, areas that “RESEMBLE” ERVs (in other words look like they may be) and areas with small numbers of BPs considered residue portions of ERVs (also considered to be inserted without evidence they were), may not have been ERVs at all, but normal parts of the human or chimp or mouse genome and were never insertions in the first place.

The main reason for seeing these as insertions and deletions is to preserve or support the premise of a common ancestor. So great, if there is one then show me...

 

[Tanj]

No, not really! Only if we assume a universal common ancestor. I mean why else would we ASSUME there is a standard genome we can all be compared to? An original one we each (each species) have added to or taken away from?

What I said earlier still applies. I can (and people have) sequence children and their parents. They have directly observed substitutions, deletions, insertion etc. All of which can be explained in the context of the child having common ancestors.

When we look more broadly, we see exactly the same things in other animals. Despite your denial, you are indeed saying

"substitutions, indels, other mutations we see in children are real and can be explained by common ancestor to parents. the same thing in other organisms look the same but have a completely different mechanism"

If you do not assume that, and just look at the raw data of the scenario you presented, all you would be confident in is that humans are not like them in this place in the genome (hence humans may not be a relative).

Except I would never just use 1 single line of evidence. I'd use it all. I'd ask what theory BEST explains ALL of the existing data.

Even though I am sure you disagree with my UCA position, can you at least see how this thinking makes sense?

As I explained above, no I cannot.

No! I am not saying anything of the sort. I am saying we know for sure (as you demonstrated) that insertions and possibly deletions are real and do in fact happen, but I am also saying many substitutions, areas that “RESEMBLE” ERVs (in other words look like they may be) and areas with small numbers of BPs considered residue portions of ERVs (also considered to be inserted without evidence they were)

What are you talking about? There's plenty of evidence. There's whole threads in this board and elsewhere explaining said evidence.

The main reason for seeing these as insertions and deletions is to preserve or support the premise of a common ancestor.

That is the exact opposite of what we actually do. It's also professionally insulting. Please stop calling me a fraud. I have no vested interest in preserving or supporting the premise of a common ancestor, and I am currently involved in a project that supports a lamarckian style of evolution. If I could disprove a common ancestor, I'd do it in a heartbeat then sit back and wait for my Nobel prize.

 

[Jimmy D]

Sorry I do not agree, all that the evidence as demonstrated is that we share a lot in common genomicaly but that does not equal we shared a common ancestor. That is merely one way to interpret the data.

So how do you interpret the data?

They used a specific method as opposed to others. Other methods may unveil slightly different results. That does not mean they are not great and effective methods, and after all, they are what we have...

Then they used two humanly designed computer programs designed by people who already accept the UCA concept as truth. The purpose of these programs is in fact to find similarities that can be used to support the opening premise.

The "opening premise" is confirmed by multiple lines of evidence though, not some wild guess or hypothesis. They aren't trying to support the concept of common descent, it needs no further support to be accepted as fact, they are trying to investigate the specifics of the mechanisms.

Next they aligned protein coding segments (which naturally do not align in many cases, and even are longer and shorter in more, and are not in the same place in many examples) by matching up the areas that are similar (few are exact).

Come on Pshun, even I know why this is done I've seen it explained so many times on this forum.

ven some statistics were applied (which is highly influenced by sample selection, unknowable changes in rate of change, and more)

Finally, of course they interpret differences as being mutations, insertions, deletions, etc., instead of accepting them as simply evidence that we are different.

Who doesn't accept them as evidence of difference? They explain the difference.

Surely any rational person can see the huge “human factor” influencing their findings.

Come on.

Now I am not degrading these brilliant people or the scientific method. But remove the human factor and its effect and what do we see? Same or different? DO we see any indication or direct evidence for a common ancestor? The answer to both these question is in favor of there not necessarily being any common ancestor. It really is...

I'm afraid I can't make sense of this Pshun.

I appreciate that you are raising questions over the interpretation of this data rather than necessarily claiming it's wrong or that you know the real answers, in my view I suppose a degree of skepticism is healthy. I really don't mean this as an insult, but I suspect that many of your objections stem from lacking a detailed understanding of the subject.