Another poor response to ERV evidence for common ancestry by a creationist.

Aeneas said:

So basically you don't understand what Loudmouth is saying and are attempting to dismiss it by calling it names. That's ad hominem.

Look, it isn't a requirement that everyone enjoy science, but if you don't, and you don't understand it, could you stop insulting those of us who do? kthxbai.

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The problem is that the religious community supports a very old and poor interpretation of genesis, and the science community is attacking the Bible thru them and their inability to accept Genesis as it is stated:


It is clear that the Universe DID have a beginning, 13.5 billion years ago.
(Gen 1:1)

There were seven long Cosmic "days" since that Big Bang, which we call the seven cosmic/geological Eras.

A Cosmic Dark Age did precede that advent of let there be light to flood the cosmos.
(Gen 1:3-5)

There was one ocean, once, where all the waters had been collected together.
(Gen 1:9)

Pangea/Rodinia did actually confirm that the dry land appeared surrounded totally by water.
(Gen 1:10)

The Plant kingdom did establish itself before the Animal kingdom.
(Gen 1:11)

Man WAS the last step in the evolution of Dominant Life on earth.
(Gen 1:27)

Aeness says
So basically you don't understand what Loudmouth is saying and are attempting to dismiss it by calling it names. That's ad hominem.

Look, it isn't a requirement that everyone enjoy science, but if you don't, and you don't understand it, could you stop insulting those of us who do? kthxbai.

No basically you lot have no come back and you think this reply is another hand wave of a refute.

I am not insulting anyone by saying your researchers do not know what they are talking about and describing the woffle you call data bla bla bla.

I enjoy science more than you and many of your researchers who have left the straightjacket of observation behind and now chase ghosts using biased numbers that are meant to reflect the complexity of the genome.

I am telling you, the algorithms used to produce your data on ERVs means nothing. They discount similarities such as sequence size and deletions to begin with and require bottlenecks to make sense of already biased data, Similar in the end may not be similar at all. You lot have assumed the case of ervs being remnant virus for lack of any other explanation that manintains the evolutionary myth. 200,000 Human Endgenous RetroVirus are mythical algorithmic constructs based on a handful of such active retrovirus around today.

You lot are chasing ghosts and HIV is just one example of it.

Loudmouth said:

Added in edit:

Found this electron micrograph of HIV viral particle:

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Pretty! I saw diagrams of HIV before I saw electron micrographs. Was quite surprised how similar the real thing looks to the drawings.

Astridhere said:

Well you hit the nail on the head..what would you know? What would any of your researchers know?

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Why don't you ask them? I'm sure there are plenty who devoted their lives to studying HIV.

I suppose you think this researcher is on her own do you?

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Not on her own, but in a tiny fringe group for sure.

There is plenty of irate researchers around that are peeved that the basics around retrovirus are so misunderstood in particular around AIDS as it is so well studied and drug companaies make a fortune from vaccines.

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I doubt anyone is making money off an HIV vaccine seeing as none have actually got past clinical trials yet. Usual disclaimer applies: if you know of one, do update me!

As for Loundmouth who says

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"Where does she think new HIV viral particles come from? How does she explain the correlation between HIV viral load and CD4+ counts? How doe they explain the infectious nature of HIV? Insane does not even start to touch HIV/AIDS denial, but oh well. Crazy is as crazy does."

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As for Loudmouth, I think you might want to answer these questions. You wouldn't want to just waffle and handwave, would you? That would be quite hypocritical of you...

I say you are more talk than anything else, Loudmouth. You do not fool me. You lot love to simplify it all with your gobble that really means nothing. This researcher is not on her own in her concerns that you dismiss with a hand wave and woffle.

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It's spelled "waffle", and that is exactly how the researcher in the interview dismissed observations of those pretty little objects Loudmouth was so kind to insert in his post.

This HIV stuff is about peoples lives and the gobble just doesn't cut it. These people want answers.

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The closest we have to an answer for them is, alas, called antiretroviral therapy.

Since 1996, real-time PCR has been used to claim quantification of a postulated HIV viremia, termed "viral load," in AIDS cases. These methods have been based on the study of patients' plasma samples: initially, samples originated from nuclei of peripheral blood mononuclear cells, and later from low-speed centrifugation pellets of plasma. (83) The various methods applied to the PCR measurement of the so-called "viral load" have one point in common: they all bypass direct isolation of retroviral particles demonstrable by EM. These methods are not expected to isolate, nor concentrate any retrovirus.

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Urm, because that is completely unnecessary for their purposes. Others have taken quite neat pictures of the virus, as we have seen. Yet others sequenced complete HIV genomes. These people want to count viruses, not look at how pretty they are. And they know exactly what they're looking for.

This is like complaining about physicists who measure the mass of electrons but fail to test whether electrons exist

Moreover, as clearly stated during the South African 2000 conference, (26) not one single particle of retrovirus has ever been seen, by EM, in the blood plasma of any AIDS patient, even in those patients identified as presenting with a high so-called "viral load." That statement, widely publicized, has never been refuted nor challenged. (84)

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In light of the result of my and LM's searches, can we call this a plain old lie?

Moreover, HERVs put HIV researchers on the wrong track, creating the illusion of continuous HIV mutations--mutations that improperly served to explain the extreme difficulty in preparing anti-HIV vaccines. However, difficulties in developing anti-HIV vaccines might not be explained by a constantly mutating HIV, but rather by a lack of exogenous HIV.

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Flu certainly exists, and we can still barely keep up with it vaccine-wise. I'd say rapid mutation rate is a pretty good reason for vaccine difficulties. RNA viruses aren't known for the proofreading prowess of their polymerases.

As for HERVs, are there even HERVs similar enough to HIV to allow such a mix-up? This study, where the ERV classification on Wikipedia comes from, found no endogenous lentiviruses in humans. Remember how retroviruses from different genera don't align very well according to Posada and Crandall 2001 (which YOU posted)? How could someone mistake a HERV for a lentivirus, then?

Finally, the question as to whether HIV exists, or of whether researchers have been studying a harmless passenger virus, is a question that should be subject to open debate and careful consideration of scientific evidence or lack thereof. Alternative explanations for findings should be decided by the scientific evidence, not by consensus. The advancement of our understanding of AIDS demands nothing less

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Human endogenous retroviruses and AIDS research: confusion, consensus, or science? - Free Online Library

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Right. Who volunteers to have a sample of this harmless passenger virus injected into them and do a ten-year follow-up? Some people's mouths are in places I doubt they'd want their money to go.

You lot go bla bla bla and think that settles any matter in your own heads. The problem is what you say is just bla bla bla with more bla bla bla to refute it and more again to refute that...and on it goes in endless circles.

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I think you're hearing yourself. Pull your fingers out of your ears and be quiet for a moment, it might help.

Astridhere said:

I am not insulting anyone by saying your researchers do not know what they are talking about and describing the woffle you call data bla bla bla.

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Yes, you are.

Look, I'm not a virologist, not even much of an expert on the human genome. But at least I've seen protein and DNA sequences. I've used BLAST. I've made alignments and built phylogenies and tried hard to figure out whether certain sequences are orthologous. I'll bet most of the people you cited re: ERVs have done many times more than me on that front. (That Posada guy? He published one of the most widely used programs for model selection in phylogenetics, among others. Judging by his publications list, he seems to have spent half his life thinking about sequences and phylogenies. Oh, also, he studies HIV.)

Do you know what you are talking about?

I enjoy science more than you...

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No, we enjoy it more than you!

(And my argument has exactly as much merit as yours.)

Astridhere said:

No basically you lot have no come back and you think this reply is another hand wave of a refute.

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I don't typically feel much need to develop a refute to ad hominem, seeing as it is logical fallacy and all.

Astridhere said:

I am not insulting anyone by saying your researchers do not know what they are talking about and describing the woffle you call data bla bla bla.

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Saying someone who actually does scientific research is ignorant compared to you is rather insulting.

But your describing data as "bla bla bla" isn't, since that is merely you admitting you don't understand the topic. Scientific literacy is a beautiful thing, most people don't raise their own lack of it as a point in argument.

Astridhere said:

I enjoy science more than you and many of your researchers who have left the straightjacket of observation behind and now chase ghosts using biased numbers that are meant to reflect the complexity of the genome.

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Oh, so you don't understand that the scientific method involves experimentation as well as observation, and don't understand biostatistics. Fair enough.

Astridhere said:

I am telling you, the algorithms used to produce your data on ERVs means nothing. They discount similarities such as sequence size and deletions to begin with and require bottlenecks to make sense of already biased data, Similar in the end may not be similar at all. You lot have assumed the case of ervs being remnant virus for lack of any other explanation that manintains the evolutionary myth. 200,000 Human Endgenous RetroVirus are mythical algorithmic constructs based on a handful of such active retrovirus around today.

You lot are chasing ghosts and HIV is just one example of it.

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Because there are so many other explanations for what inactivated genes which code for viral proteins are doing in the genome other than retrovirus.

Astridhere said:

Does this mean Darwin was...(dare we creationists say it)...WRONG?

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Darwin was wrong on quite a few things. Why do creationists always expect that to shock us?

I note the one thing neither of you two go near is the fact that your researchers in their useless algorithms ignore differences like size or length of sequence & deletions etc, then use this simplistic data to arrive at what may or may not look sort of similar in a kind of sort of a way with more deletions and nonsense mutations, then throw in a bottleneck to apply a bandaid to the data that just wont add up.

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Indels are part and parcel of molecular evolution. If you had ever, ever done any sequence comparison, you would know that. So long as a deletion doesn't remove all diagnostic motifs from a sequence, identification remains possible.

The really simplistic thing to do is to go "but half of it is missing" and automatically discount homology. (Just compare most fruit fly Hox genes to their vertebrate orthologues. The coding portions of the fly genes are often like twice the size of the corresponding vertebrate cds. Yet they are not only recognisable across species, some of the vertebrate genes can substitute almost perfectly for the missing fly orthologue. And yes, labial protein is almost exactly twice as long as chicken HoxB1.)

Throw in a few likely's and maybe's and presto this is what you like to pass off as support, or worse you call it evidence, for comon ancestry.

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If ERVs are too "maybe" for you, do ponder that TalkOrigin FAQ on ordinary phylogenies.

The thing about HIV is that while it has been shoved under the radar in order to protect the Hay Life, we bow have drugs keeping infected people alive for 20 years, sexually active, and dangerously doubling the cases even seven years perhaps, from some Stats on the issue.

At some point some system to ID infected potential sex partners needs be used to quarantine them.
Perhaps Tattoos on the belly in a specific place small but easy to check would be the solution.











Doubling down is a killer, whether at the Casino or with AIDS in America:

1) 2001 = 1 million HIV/AIDS Carriers

2) 2008 = 2 million HIV/AIDS Carriers

3) 2015 = 4 million HIV/AIDS Carriers

4) 2022 = 8 million HIV/AIDS Carriers

5) 2029 = 16 million HIV/AIDS Carriers

6) 2036 = 32 million HIV/AIDS Carriers

7) 2042 = 64 million HIV/AIDS Carriers

8) 2049 = 128 million HIV/AIDS Carriers

9) 2056 = 256 million HIV/AIDS Carriers

(Tattoo all infected Carriers, now, while their numbers are small and it is still possible, or else.)

~~~~~~~~~~~~MOD HAT ON!!~~~~~~~~~~~~~~

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Flaming
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Nevermind, I see the moderator just made a post about this sort of behavior and how to deal with it.

Astridhere said:

I believe any mucking around and intergration into the germ line of an RVs genomic material is going to cause havoc and reduce fitness, and unlikely to fix in any population.

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This is just the opposite of what you have claimed through this entire thread. You have been arguing that these ERV's have beneficial functions, have you not? Why the about face?

This article supports my claim that the endogenization of an RV is likely or at least may, cause havoc as one of the events following endogenization of a retrovirus..

Evolutionary Aspects of Human Endogenous Retroviral Sequences (HERVs) and Disease - Madame Curie Bioscience Database - NCBI Bookshelf

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For someone who complains about "maybes" and "waffling" why would you pick a paper that concludes:

"In most cases, much work remains before a pathogenic mechanism is established. The biology of HERVs must be better understood in order to understand their role in human disease."

I note the one thing neither of you two go near is the fact that your researchers in their useless algorithms ignore differences like size or length of sequence & deletions etc,

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Please show that the algorithms used for determining orthology of ERV's in both humans and chimps actually does what you claim. Otherwise, you are just blowing smoke. It is time that you stop making baseless allegations and actually present the evidence that backs your assertions.

Rather the discovery of so called ervs demonstrates that vaguely similar sequences to virus are present and created in the genome to provide a multitude of genome functions one of which is maintainence of mammalian pregnancy and non rejection of the embryo. This sequence, or rather remnant ghost, has nothing to do with any imaginary possibly, likely or maybe virus that you imagine existed long ago.

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So what should ERV's look like if they were from ancient retrorviral insertions? What do ERV's lack?

Astridhere said:

There is plenty of irate researchers around that are peeved that the basics around retrovirus are so misunderstood in particular around AIDS as it is so well studied and drug companaies make a fortune from vaccines.

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This, coming from someone who denies the link between HIV and AIDS. Sorry, but you really need to examine what you have been saying.

Let me ask you this. Would you accept a blood transfusion from someone who was HIV positive? If not, why not? You claim that there is no risk.

Here is a snip from an article by Etienne de Harven, M.D., Brussels University (ULB), 1953, became a full member of Sloan Kettering Institute, New York, N.Y, in 1968, and is emeritus professor of pathology, University of Toronto.

Since 1996, real-time PCR has been used to claim quantification of a postulated HIV viremia, termed "viral load," in AIDS cases. These methods have been based on the study of patients' plasma samples: initially, samples originated from nuclei of peripheral blood mononuclear cells, and later from low-speed centrifugation pellets of plasma. (83) The various methods applied to the PCR measurement of the so-called "viral load" have one point in common: they all bypass direct isolation of retroviral particles demonstrable by EM. These methods are not expected to isolate, nor concentrate any retrovirus. Moreover, as clearly stated during the South African 2000 conference, (26) not one single particle of retrovirus has ever been seen, by EM, in the blood plasma of any AIDS patient, even in those patients identified as presenting with a high so-called "viral load." That statement, widely publicized, has never been refuted nor challenged. (84)

The existence of endogenous human retroviruses has been known for some time, but their interference in HIV/AIDS research has yet to be widely appreciated. Of course, HIV should not be considered an HERV, since the hypothetical HIV is supposed to be an exogenous, infectious microorganism, while HERVs are fundamentally endogenous, non-infectious, vertically transmitted, defective viruses. Still, HERVs have been a "confounding" factor in HIV/AIDS research, (92) and have caused confusion in interpreting the concept of "viral load." Moreover, HERVs put HIV researchers on the wrong track, creating the illusion of continuous HIV mutations--mutations that improperly served to explain the extreme difficulty in preparing anti-HIV vaccines. However, difficulties in developing anti-HIV vaccines might not be explained by a constantly mutating HIV, but rather by a lack of exogenous HIV.

Finally, the question as to whether HIV exists, or of whether researchers have been studying a harmless passenger virus, is a question that should be subject to open debate and careful consideration of scientific evidence or lack thereof. Alternative explanations for findings should be decided by the scientific evidence, not by consensus. The advancement of our understanding of AIDS demands nothing less
Human endogenous retroviruses and AIDS research: confusion, consensus, or science? - Free Online Library

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So where does it explain the correlation between T-helper cell counts and the results from PCR assays? It doesn't. It ignores the correlation. Whether the amplification is of viral particles or endogenized virus the implications are the same. Also, it didn't explain why HIV is being spread. Do you think the rapid increase in child AIDS mortality in African countries is just a coincidence? Are you really saying that no one should protect themselves from contracting HIV? How do you explain known antibody production to known HIV protein markers? You don't get antibodies to a protein if it never produced. Therefore, there are viral particles with functional proteins associated with them.

You want to claim that my claims are dangerous somehow, but I am not the one trying to make HIV into a virus worth ignoring. You may want to think about that.

You lot go bla bla bla . . .

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More evidence that your mind is already madeup and no evidence will ever convince you otherwise.

Your algorithms . . .

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Which algorithms are being used to determine that an ERV is at the same location in two genomes? Time to back your assertions, or admit that you don't know what you are talking about.

dad said:

Yes. The only pre flood and early post flood records man has.

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Sorry, that is not evidence.

You lose.

dad said:

False! The records state that they were not.

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What 'record' is that?

If anyone claims science for a claim that they were a certain way, now is the time to show and tell! But I know that science doesn't know. That leaves you in a real pickle.

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Not as much of a pickle as relying on the flawed and fallacious contradictory testimony of unknown authors of ancient uncorroborated fairy tales.

SLP said:

Sorry, that is not evidence.

You lose.

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Science doesn't know. If you want to reject the observational records man does have, where does that leave you?


Jer 13:16 -Give glory to the LORD your God, before he cause darkness, and before your feet stumble upon the dark mountains, and, while ye look for light, he turn it into the shadow of death, and make it gross darkness.

SLP said:

What 'record' is that?

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Bible, as well as Sumer and Egypt to some extent.

Not as much of a pickle as relying on the flawed and fallacious contradictory testimony of unknown authors of ancient uncorroborated fairy tales.

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Either you know or not. The degree of seriousness of the repercussions of not knowing is not something we need be concerned with here.

Now, if the different state past did see ERVs get transferred in different ways, then all meaning is lost for those seeking to limit all reality and interpretation to this present time.

SLP said:

Not as much of a pickle as relying on the flawed and fallacious contradictory testimony of unknown authors of ancient uncorroborated fairy tales.

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Science IS "corroborating" the story as a clear and specific poetic way of saying that 40,000 years ago Neanderthals and all other kinds of Humanoids disappeared, as modern man (who had evolved 100,000 years prior to that event) came Out of Africa and "flooded" even to the mountain tops.




www. anthro.palomar.edu/homo2/mod_homo_4.htm

The replacement model of Christopher Stringer and Peter Andrews:
This hypothesis is also referred to as the "out of Africa", "Noah's ark" and "African replacement" model.

cupid dave said:

...all other kinds of Humanoids disappeared...

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Humanoids?

Genetic algorithms lack sense of context.

The foundation assumed by these programs presuppose of common decent rather than concealed function. The DNA code is the most complex and ingenious programming man has ever embarked upon technically. Scientists like John von Neumann attempted to abstract the function of life in a quantitative way. In the end his construct falls short because of the enormity of the problems involved yet the tiny cell accomplishes the task in a deceivingly trite way every day.

Paleovirology is nothing more than a modern alchemy….

cupid dave said:

Science IS "corroborating" the story as a clear and specific poetic way of saying that 40,000 years ago Neanderthals and all other kinds of Humanoids disappeared, as modern man (who had evolved 100,000 years prior to that event) came Out of Africa and "flooded" even to the mountain tops.

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Neanderthals were around 30,000 years ago.

H. sapiens are the forerunner to modern humans. The very earliest we can determine Homo sapiens sapiens existed is 50-75,000 years ago.

The "Out of Africa" event occured 150,000 years ago.

"even to the mountain tops" is a poetic allusion to the Noah story created by you meant to reconcile the flood story as covering the whole earth, but we know the insinuation is wrong. Regarding both locaility or population, the earth was not "flooded" by humans by any stretch of the imagination.

Furthermore, your claim fully discards the biblical flood story almost to it's entirety to try to force it upon your version of the "out of Africa" events.

Where does the dove and raven come to play? The collecting of animals two by two and seven by seven? The fact that all humans were killed except for the 8 before the ark even began to rise off the ground? The rainbow as God's promise never to flood the earth again? You know we just hit over 7 BILLION humans on the planet, right? How can your version be true when we have more humans now than ever?

Your belief completely discards the bulk of this story. You're throwing the baby out with the floodwater.

Zaius137 said:

Genetic algorithms lack sense of context.

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Your comment lacks a sense of context. Whether or not an ERV is found at the same location in two genomes is the question.

"Given the size of vertebrate genomes (>1 × 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."
Constructing primate phylogenies from ancient retrovirus sequences

So how did these authors determine if the same ERV was at the same location in the genome of humans and chimps? They didn't use genetic algorithms. They used PCR.

"PCR products were gel purified and sequenced directly on both strands by using the ABI Prism Dye-Terminator Cycle Sequencing Ready Reaction Kit and analyzed with an ABI 373 Stretch automated sequencer (Perkin–Elmer).
Each of the proviruses used in this study maps to a different human chromosome, according to information available in the sequence databases, or by PCR screening of monochromosomal human × rodent somatic cell hybrids (data not shown)."
Source = same paper

Then you just do a BLAST or CLUSTAL alignment. No assumption of common ancestry. No genetic algorithms. Just amplify the ERV and the flanking DNA, and then align the flanking DNA. That's it. They found that the same ERV is found at orthologous positions between humans and other apes. This is smoking gun evidence of common ancestry.

The only place that genetic algorithms are used is to map the differences between the ERV's and within the ERV, especially when it comes to LTR's.

The foundation assumed by these programs presuppose of common decent rather than concealed function.

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False. Parsimony is the only assumption. The genetic algorithms then produce a phylogeny based on the assumption of parsimony. The test is whether or not the phylogeny produced by the genetic algorithm matches the phylogeny that is based on morphology. Only then can you conclude if they shared a common ancestor or not. Common ancestry is not being assumed by these algorithms. It is being tested.

The DNA code is the most complex and ingenious programming man has ever embarked upon technically. Scientists like John von Neumann attempted to abstract the function of life in a quantitative way. In the end his construct falls short because of the enormity of the problems involved yet the tiny cell accomplishes the task in a deceivingly trite way every day.

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What does this have to do with anything?

Paleovirology is nothing more than a modern alchemy….

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Empty claims are empty claims. Do you really think that you can make the evidence go away by mocking it?

SLP said:

Sorry, that is not evidence.

You lose.

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That is evidence I accept. There is no other. If you could present any, you might have a point.