Viruses that prove common descent

[Barry Desborough]

It's a genetic fact.
You claim that "common descent is not an assumption. It's a genetic fact." Yet the truth is that the premise was totally accepted as true long before we could access the genome.

So why in order to make it appear as such, do we need to develop computer programs to pull apart the human and chimp genomes at certain places to allow for the bases to look as if they line up leaving apparent differences in sequences contained in one and not the other which are then explained as insertions and deletions?

You can CLAIM a deletion in these intelligently manipulated versions of the actual genomes but to actually demonstrate a deletion you must first show where they once were there and now are not....as for alleged insertions you must show when they once were not and now are, and you cannot, therefore the devised conclusion IS assumption based.

Some actual insertions and deletions do in fact occur but many (not all) are just an illusion created by this intended program.

One researcher (I forget his name at the time but I will look for the study) eliminated the matching "program" (devised by people already convinced) and strung the sequence of bases side by side and when this is done you end up with about a 24% difference in comparative base pairs (that's about 750,000,000 differences). Another taking into account other factors seemingly ignored was suggesting as much as a 70+% amount of differences.

So though in the second example in Barry's article (which had the CERV30 example) we see in the chimp genome a blank space about five letters long (which space is contrived via the program which pulled it apart here to create a match) in reality that space does not exist, it is one continuous unique stream of base pairs, which if undisturbed by those trying to create the Common Ancestor illusion (which may OR may not be true) throws off the order and alleged synchronicity of all that follow...

I am suggesting (and for such reasons as just mentioned) that there may be no deletion here at all (unless you can show something to previously having been there in that genome) and that this (without the false space) is just a normal sequence in their genome which is different in the human genome...

and that this same reasoning should be applied to insertions as well (as many are NOT anything more than normal, ever present, parts of the respective creature's genome). And to show them as actual "INSERTions" one has to show examples of when they were not there previously and now are.

If it is true then this should be no problem. So I am willing to concede I am incorrect (as I have sometimes done even on this forum which I believe Barry cannot do) if you can show me these "deletions" were actually there once, and/or that the "insertions" were previously not.

AND if this discrepancy or alternative yet totally logical reasoning alludes you so much as to fall back on "It must mean there was a Common Ancestor of both creatures" then fine I am willing to concede that point as soon as you produce your example of this so we can compare and see the same criteria met in that creature (not there then there, or once there and then not there)...

Simple right? If a truth, then there should be no problem on your part, so let's SEE? I will await either of you producing this PROOF of your claim.

Richard Feynman in his lectures on physics, said, "How do we know there are atoms? By one of the tricks mentioned earlier: we make the hypothesis that there are atoms, and one after the other the results come out the way we predict, as they ought to if things are made of atoms."

Similarly, we make the hypothesis of common ancestry, and acknowledge the observed fact that genomes have been subject to insertions and deletions, and hey presto! Virtually all ERVs in the genomes of chimps and humans align. In sequence. They also appear adjacent to the same or similar host genetic material and have the same content. That is sufficient to confirm the hypothesis is correct. Here is "Evolutionary Model" making the same point, and referencing the relevant literature. ERVs

Besides the above, you have a serious problem in explaining how and why these elements could have otherwise come to be where they are. Yes, some components serve useful and sometimes even vital functions. But what's all the rest of it for? And what is so important about its positioning?

And again, I make no apology for repeating the link explaining why everyone except those with a quasi-religious "objections" concludes that ERVs are the inherited remains of endogenized proviruses. You have addressed none of this. Veritas: ERV FAQ: Why do virologists and geneticists think that ERVs come from retroviruses? Isn't that just supposition on their part?

 

[Barry Desborough]

no. the problem here isnt about integration sites but about fixation event. if we need an erv to be fixed its need to be beneficial or at least neutral. so if the entire genome is already functional, there only about few places in the genome that we can actually add an erv to the genome.

Virtually all ERVs non-functional. (Some components of some ERVs are beneficial. Some are implicated in late onset diseases - invisible to selection). But the vast majority of this genetic material is adaptively neutral. This appears to be because it is mutated (reverse transcription is very error-prone) rather than because of its position.

But if you want to provide evidence that the entire genome is functional and that only a limited number of integration sites will fail to disrupt it, give it your best shot. Oh, and don't forget to explain why the ERVs themselves correspond, between species, in their content - gene variants, size, LTR-LTR discontinuity etc.

 

[TagliatelliMonster]

but we also understand that the opposite can be true- a retrovirus can add host genes to its genome.

Which would not and could not explain the thousands of shared ERV's between humans and chimps.

The actual ERV's in our collective genomes, are the result of ancient insertions in common ancestors.

You keep coming back to this as if it means something, but it does not.

What you are refering to DOES NOT EXPLAIN, in ANY way, that humans and chimps share thousands of ERV's in the exact same locations in the DNA.

The ONLY thing that explains these shared ERV's is the fact of ancient insertion inherited by off spring.

not realy. this is the argument from similarity. but common similarity can also be explain by a common designer (two objects like cars are similar because they shared a common designer- human). so again: not a fact, just a belief.

No. I'm sure dozens of people have already explained to you that it's not about mere "similarity". I'm actually positive, because I was one of them.

 

[pshun2404]

Perhaps neither of you are aware of what is known as the expectancy effect or expectancy bias in interpreting quantitative data. This is a form of unconscious or subconscious reactivity that occurs because the presupposed belief or cognitive position of the researcher subconsciously influences the meaning of the data.

What this causes (though non-intentionally in most cases) is what is known as a confirmation bias which leads the researcher to look for information that conforms to their hypothesis, and overlook information that argues against it.

(You can read more about this if you would like in Bruce Goldstein’s, Cognitive Psychology. Wadsworth, Cengage Learning, 2011)

This is what I have noted here regarding this subject matter. It is NOT just some stammering from some creatard. This totally human factor influences and can pose threats to a conclusion’s validity. In research, experimenter bias can and often does affect the conclusion reached (see Sackett, D. L. (1979). "Bias in analytic research".Journal of Chronic Diseases. 32 (1–2): 51–63.).

Computer programs used are such an example because the bias is unknowingly often infused into the construction of the algorithms (the gigo effect). Then the next step involves adjusting the results to reflect patterns (often made to conform to those desired or expected). Local alignments are most often used because they can be lined up (even if loci are not exact and sometimes clearly separate) to reflect similarity, where very long or complete comparisons reveal non-similarities which the experimenter (trying to make his/her point) wants to avoid.

 

[Gene Parmesan]

Perhaps neither of you are aware of what is known as the expectancy effect or expectancy bias in interpreting quantitative data. This is a form of unconscious or subconscious reactivity that occurs because the presupposed belief or cognitive position of the researcher subconsciously influences the meaning of the data.

What this causes (though non-intentionally in most cases) is what is known as a confirmation bias which leads the researcher to look for information that conforms to their hypothesis, and overlook information that argues against it.

(You can read more about this if you would like in Bruce Goldstein’s, Cognitive Psychology. Wadsworth, Cengage Learning, 2011)

This is what I have noted here regarding this subject matter. It is NOT just some stammering from some creatard. This totally human factor influences and can pose threats to a conclusion’s validity. In research, experimenter bias can and often does affect the conclusion reached (see Sackett, D. L. (1979). "Bias in analytic research".Journal of Chronic Diseases. 32 (1–2): 51–63.).

Computer programs used are such an example because the bias is unknowingly often infused into the construction of the algorithms (the gigo effect). Then the next step involves adjusting the results to reflect patterns (often made to conform to those desired or expected). Local alignments are most often used because they can be lined up (even if loci are not exact and sometimes clearly separate) to reflect similarity, where very long or complete comparisons reveal non-similarities which the experimenter (trying to make his/her point) wants to avoid.

Claiming that these biases exist (I agree) is one thing. Can you demonstrate that that is what has happened here?

 

[pshun2404]

So once again (third or fourth time you avoid the issue entirely)

As I suggested, there may be no deletion here at all (unless you can show something to previously having been there in that genome) and that this (without the false space) COULD BE just the normal sequence in their genome, which is different in the human genome...(show it was there and now is not there in the same creature please or admit it cannot be shown to be true)

AGAIN, this same reasoning should be applied to insertions as well (as many MAY NOT BE anything more than normal, ever present, parts of the respective creature's genome). TO show them as actual "INSERTions", one has to show examples of when they were not there previously and now are.

If it is true then this should be no problem. So I am willing to concede I am incorrect (as I have sometimes done even on this forum which I believe Barry cannot do) if you can show me these "deletions" were actually there once, and/or that the "insertions" were previously not.

AND if this discrepancy or alternative yet totally logical reasoning alludes you so much as to fall back on "It must mean there was a Common Ancestor of both creatures" then fine I am willing to concede that point as well, as soon as you produce your example of this so we can compare and see the same criteria met in that creature (not there then there, or once there and then not there)...

 

[pshun2404]

Claiming that these biases exist (I agree) is one thing. Can you demonstrate that that is what has happened here?

Please note that in 99% of the cases these biases are inherent on the mental construct of the researcher and ARE NOT a devious plan (it happens quite subconsciously among those already convinced). So...in answer to your question,

Yes! The theoretical notion of coming from a common ancestor has been around and "believed to be true" from long before we had access to the genome. The researcher believes this going in. Has programs devised that split the genomes creating gaps that are not actually there in those genomes and then they interpret the items present in one and not the other as additions but fail continuously to show they were added in that genome, and likewise because the conclusion is already accepted interpret the many of the now blank spaces (which also do not actually exist) as deletions but fail continuously to show when or in what they previously were and now are not.

The point is even the true insertions and deletions do not CONFIRM the already presupposed notion as these can be explained in another way. If this IS the true and correct interpretation then SHOW where in such an ancestor, or in what grandaddy creature this occurred so we can DEMONSTRATE or OBSERVE it actually was not there once and now is (hence to be inserted), and/or SHOW where or in what a deletion actually occurred by demonstrating or letting us observe it was once there and now is not (hence to be deleted).

This is a very reasonable and logical expectation if this alleged Common Ancestor is to be CONFIRMED since science is about observation and demonstration as much as it is about inferences drawn which by themselves are merely plausibilities not established facts.

 

[Barry Desborough]

Please note that in 99% of the cases these biases are inherent on the mental construct of the researcher and ARE NOT a devious plan (it happens quite subconsciously among those already convinced). So...in answer to your question,

Yes! The theoretical notion of coming from a common ancestor has been around and "believed to be true" from long before we had access to the genome. The researcher believes this going in. Has programs devised that split the genomes creating gaps that are not actually there in those genomes and then they interpret the items present in one and not the other as additions but fail continuously to show they were added in that genome, and likewise because the conclusion is already accepted interpret the many of the now blank spaces (which also do not actually exist) as deletions but fail continuously to show when or in what they previously were and now are not.

The point is even the true insertions and deletions do not CONFIRM the already presupposed notion as these can be explained in another way. If this IS the true and correct interpretation then SHOW where in such an ancestor, or in what grandaddy creature this occurred so we can DEMONSTRATE or OBSERVE it actually was not there once and now is (hence to be inserted), and/or SHOW where or in what a deletion actually occurred by demonstrating or letting us observe it was once there and now is not (hence to be deleted).

This is a very reasonable and logical expectation if this alleged Common Ancestor is to be CONFIRMED since science is about observation and demonstration as much as it is about inferences drawn which by themselves are merely plausibilities not factual.

Richard Feynman in his lectures on physics, said, "How do we know there are atoms? By one of the tricks mentioned earlier: we make the hypothesis that there are atoms, and one after the other the results come out the way we predict, as they ought to if things are made of atoms."

Similarly, we make the hypothesis of common ancestry, and acknowledge the observed fact that genomes have been subject to insertions and deletions, and hey presto! Virtually all ERVs in the genomes of chimps and humans align. In sequence. They also appear adjacent to the same or similar host genetic material and have the same content. That is sufficient to confirm the hypothesis is correct. Here is "Evolutionary Model" making the same point, and referencing the relevant literature. ERVs

Besides the above, you have a serious problem in explaining how and why these elements could have otherwise come to be where they are. Yes, some components serve useful and sometimes even vital functions. But what's all the rest of it for? And what is so important about its positioning?

And again, I make no apology for repeating the link explaining why everyone except those with a quasi-religious "objections" concludes that ERVs are the inherited remains of endogenized proviruses. You have addressed none of this. Veritas: ERV FAQ: Why do virologists and geneticists think that ERVs come from retroviruses? Isn't that just supposition on their part?

 

[Barry Desborough]

Dear readers, please note that I have found email notifications to be very unreliable on this site. If I haven't responded to you as you might expect, send me a link to my email address, which is my name with a dot between first and second names, at gmail dot com.

 

[TagliatelliMonster]

Perhaps neither of you are aware of what is known as the expectancy effect or expectancy bias in interpreting quantitative data. This is a form of unconscious or subconscious reactivity that occurs because the presupposed belief or cognitive position of the researcher subconsciously influences the meaning of the data.

You mean like how creationists who have already decided how humans originated, are unable to accept any kind of evidence that contradicts those faith-based presuppositions?

The irony is delicious.

 

[TagliatelliMonster]

Yes! The theoretical notion of coming from a common ancestor

It's not theoretical. It's genetic fact.

has been around and "believed to be true" from long before we had access to the genome.

And access to the genome only further confirmed that idea. With solid facts.
It's kind of funny actually, because it could have been said to be a hypothetical before we knew about DNA. Not so much after that....

DNA only confirmed the common ancestry hypothesis to a degree that Darwin couldn't even imagine.

The researcher believes this going in. Has programs devised that split the genomes creating gaps that are not actually there in those genomes and then they interpret the items present in one and not the other as additions but fail continuously to show they were added in that genome, and likewise because the conclusion is already accepted interpret the many of the now blank spaces (which also do not actually exist) as deletions but fail continuously to show when or in what they previously were and now are not.

The point is even the true insertions and deletions do not CONFIRM the already presupposed notion as these can be explained in another way. If this IS the true and correct interpretation then SHOW where in such an ancestor, or in what grandaddy creature this occurred so we can DEMONSTRATE or OBSERVE it actually was not there once and now is (hence to be inserted), and/or SHOW where or in what a deletion actually occurred by demonstrating or letting us observe it was once there and now is not (hence to be deleted).

This is a very reasonable and logical expectation if this alleged Common Ancestor is to be CONFIRMED since science is about observation and demonstration as much as it is about inferences drawn which by themselves are merely plausibilities not established facts.

Are you aware that we can take your DNA and that of your sibling, along with any number of random DNA samples, and actually determine your sibling's DNA?

How is it that we can do that, if what you say is true?

 

[pshun2404]

Apology accepted. Now show us when it was and now is not or when it was not and now is...I am genuinely eager to see this. You claim this ancestor exists...okay show me...

Why is this so hard to grasp by such a smart man....re-read post 284 then respond to 286...simple! Really! All diversions, avoidance, twists, and false implications of my words are not necessary. Address the logic and content of Post 286 (which is a 2nd or 3rd re-phrasing because you continuously claim to not get it)...if it is a true deletion in must have previously been there (show me) if an insertion it must previously not have been there (show me)....if it was some ancestor (show me)...

Are you able to, yes or no? If so then do it next (I will be ignoring all further references to YOUR blog)

 

[pshun2404]

You mean like how creationists who have already decided how humans originated, are unable to accept any kind of evidence that contradicts those faith-based presuppositions?

YES!!! Exactly! Hoorah!!!! You finally get it...now show me...

 

[pshun2404]

Have to return some Library books be back soon...

 

[Barry Desborough]

You mean like how creationists who have already decided how humans originated, are unable to accept any kind of evidence that contradicts those faith-based presuppositions?

The irony is delicious.

You couldn't make this stuff up. Neither could I. But obviously, some can, without even blushing.

 

[dad]

so we need to ignore all the evidences we have and accept a belief about the past without any evidence? its not sound like a scientific method to me.

That is the essence of science actually. They ignore evidences and accept a belief in a same nature in the future and far past. No reason. They then model all origins theories on that. Welcome to the new reality.

 

[dad]

Except that we can..

You may be able to show it happens that way now. You cannot and never will be able to show it happened that way in the early history of earth. In other words, who really cares how viri are now transferred in the origins debate?

 

[pshun2404]

So Parm what did you think about the answer in post 287?

 

[Gene Parmesan]

So Parm what did you think about the answer in post 287?

I was content to just let the conversation continue as it was. Can't say this field is my forte, which is why I was asking the question.

You mentioned a the frame of mind and the presuppositions of some unnamed scientist, which I suppose could be true of someone out there but it does little to undermine my understanding of the research into ERVs. But I will almost always read and look into any reputable sources provided by a kind interlocutor such as yourself.

 

[pshun2404]

Thanks...I thought you had more of a purpose in asking. The presupposition I was mostly concerned with was one which many scientists (and others) make regarding the Common Ancestor, allegedly confirmed by these genetic curiosities (like the title implies but no one can show).

Whether or not you agree with what I assess for how it needs to be confirmed, do you at least see the need for this before it is declared emphatically to be so? Don't we at least need to see that they were inserted or deleted to be able to SAY they were inserted or deleted? Otherwise why should we assume they were?