Ardi - Ardipithecus ramidus

[jlay]

In the simplest terms that I can understand this. If the ERVs do in fact play a role, then there could be a hard wired reason why they have inserted themselves at this position in chimps and humans. In other words, the ERV targets an area of the genome.

Consequently, it is entirely possible that the same virus infected both humans and apes, and targeted the same location. This seems especially plausible in light of the fact that humans and apes have tens of thousands of endogenous retroviruses in their respective genomes. In other words, given so many thousands of different types of ERVs all targeting fairly specific locations, it is actually likely that at least a few of these retroviruses will infect both humans and apes at the very same location within the respective genomes without any need to invoke the common descent hypothesis.

We know mammals share many physical and genetic traits, but this isn't proof that one descended from another. Do we see ERV insertions in species that we suspect there is NO common descent?
I must say, that I see a lot of presupposition.

We know that what was once considered junk is turning out to be treasure. And that junk was in fact waved as the banner of proof of common descent.



I don't want to get into a peeing contest. I could site several folks who were pro-evolution and have converted. that in and of itself is not proof for or against evolution.

[Gman]

A topic summary: humans and chimps share not one, but about 20 ERVs having the exact same corresponding position in their genomes. An ERV is a retrovirus that inserts its DNA at essentially random chromosome locations.

About 20 or more ERV's in common? Actually thanks for bringing that up. Because this is revealing a pattern of design. The more they have in common, the more patterns will be revealed between the two. In fact in time I believe the number will go up.

Besides the 20 or more ERV's we have in common, what else do we have in common with chimps besides that fact that chimps and humans both have teeth, both have two arms and legs, both have two eyes, etc...? Why aren't you mentioning those things? Again it's all matter how you view it..

What we are talking here is philosophy..

Whether those ERVs are/were functional or not is immaterial. Humans and chimps could not have independently been infected, especially given those many different ERVs. The only consistent sensible explanation is that each of those ERVs infected the human-chimp common ancestor once. Then when humans and chimps split apart over 6 million years ago, each species simply copied those ERVs down to the present through hundreds of thousands of generations.

This is pure speculation... Not even the U.S. Academy of Natural Sciences is claiming that ERV's are the empirical evidence for darwinian evolution. Get over it...

But how does ID creationism explain those matching ERV chromosome locations without using the obvious, simple, and fact-consistent idea of common descent?

One creationism defense against this common descent evidence is found in this very Ardi topic, viz., simply deny the voluminous field and lab findings and conclusions from every retrovirus scientist. And while doing this complete denial, feel free to misunderstand probability, ignore the main arguments, misrepresent scientific research, state irrelevant facts, and use logical fallacies.

Such a defense is surprisingly effective for some. But the following defense against common descent is even better.

Logical fallacies? Perhaps you would like to answer these questions..

"Presumably, the alleged prediction and fulfillment are:

1. If universal common ancestry is true, then the same endogenous retrovirus (ERV) will exist in the same chromosomal location in two or more species.
2. The same ERV exists in the same chromosomal location in two or more species.

Since this is the concept of “shared errors” applied to endogenous retroviruses (and since retroviruses are a type of transposon), much of the two preceding responses is applicable. It is not a prediction of the hypothesis of universal common ancestry or the more specific hypothesis of Neo-Darwinism that the same ERVs will exist in the same chromosomal location in two or more species. Evolution does not even predict the existence of ERVs, much less that they will be found at the same location in two or more species. After all, evolutionary theory was considered robust prior to the discovery of ERVs. This is but another example of taking an observation, claiming it as a prediction of evolution, and then using the fact the observation fits the prediction as evidence for the truth of evolution.

Moreover, ERVs are inadequate in principle to support the claim of universal common ancestry, because they are not shared by all groups of organisms. To quote Dr. Max once again, “Another limitation [of this argument] is that there are no examples of 'shared errors' that link mammals to other branches of the genealogic tree of life on earth. . . . Therefore, the evolutionary relationships between distant branches on the evolutionary genealogic tree must rest on other evidence besides 'shared errors.'”

In any event, not all ERVs are nonfunctional. Some are transcriptionally active, and studies have revealed ERV protein expression in humans.

Source: http://www.trueorigin.org/theobald1e.asp#pred21

Cool! Many years of worldwide science research, confirming ERV evidence supporting common descent, are all for nothing. Why? Because the Intelligent Designer temporarily suspended nature's known (and repeatedly tested) processes to manually and independently insert those 20 or so ERVs into the exact same chromosome locations in humans and chimps. And seemingly all of it was done in an ironic mischievous attempt to mislead scientists.

This "Designer did it" creationism defense is nothing short of exquisite.

The defense requires no thinking, much less years of tedious rigorous research. The defense can retroactively explain any new scientific discovery as supporting creationism. And because the Designer did it that way, answering "why" questions is a pointless waste of time. In fact, with such an impregnable defense, why creationism bothers to waste any time presuming to understand science is the real mystery.

In stark contrast, scientists have to shoulder a heavy albatross named the scientific method, which insists that ANY confirmed contradicting evidence invalidates the hypothesis. Why would any scientist in her right mind want to work in a hostile unforgiving environment like that?

The scientific method is raw science also called (methodological naturalism), however when you say Darwinian evolution (DE) did it or intelligent design (ID) did it, these statements are pretty much neutral to science. It's really not going to hurt or change how science is done if we talk about ID or DE in the classrooms. Maybe a different philosophical idea, but not how science is actually done. If you said that an intelligent designer did it, wouldn't you be curious to know how he did it like how naturalism may have done it? Basically you just go back to doing science again although the different philosophical premises or alternatives have changed. It really doesn't matter.

[Gman]

Section Non-random viral insertions: repeats Gman's argument, and like Gman, completely ignores the science which shows that the probability of independent ERV infections at the same chromosome location is still essentially zero.

Don't talk to me about ignoring science.. Again your Darwinian evolution is not science. You are simply ignoring our question that we posted earlier.

Please answer the following..

To expand a little on AoK's post, here's a list of questions (from this link) scientists need to answer before ERV's can be accepted as such:

How Did ERV Related Elements Insert Themselves into Germ Cells Thousands of Times Without Fatalistic Damage to the Host?

How is it that ERVS are Considered Copies of Disease Producing Exogenous Retroviruses but None Have Been Proven to Directly Cause Disease?

What Made ERV Elements Change From Viral Activities to Cellular Activities and Create New Essential Genes?

How Could ERVS Create a Specie-Specific Regulatory Network that Controls the Expression of Cells in a Collective Manner?

What Made Unrelated ERVS in Unrelated Species Create Almost the Same Gene (Convergent Evolution)?

What Made Two Unrelated ERV LTRS Evolve Independently in Creating the Same Regulatory Roles for the Same Gene (Convergent Evolution)?

What Made ERV LTRS Immediately Turn into Essential Gene Regulators Upon Insertion?

What Made LTRS Acquire Transcription Abilities for Essential Genes?

Where is the Proof that ERV LTRS can “Self-Replicate” and Why Don't We See them Doing it Now?

What made the same erv transcribe differently between supposedly closely related species?

What made the same erv transcribe differently among different cell types within the same organism?

There's a few more but you get the gist, too many questions, too many assumptions.

OK, so what am I ignoring?! Your creationism reference didn't have one relevant or valid criticism.

Then answer our questions... And while doing that, tell the Academy of Natural Science that you have the answer. That ERV's are the empirical evidence for evolution.

[derwood]

The creature is standing completely straight like we do. I find that hard to believe.

From an anatomical perspective?

Please expand on this. I have graduate training in anatomy and I would like to hear your explanation.

[derwood]

Anything else would be deceptive.

Like drawing a caucasian Jesus?

[zoegirl]

Derwood,

Please take some time to review the board guidelines

http://discussions.godandscience.org/vi ... f=6&t=2517

and understand the purpose here.

[derwood]

Derwood,

Please take some time to review the board guidelines

http://discussions.godandscience.org/vi ... f=6&t=2517

and understand the purpose here.

I believe I do.

I'm not sure why countering disinformation is an issue. Do Christians really not want to understand the things they discuss?

[zoegirl]

Derwood, we have several atheists and agnostics here but they also understand the main purpose here and when they post they post with that understanding and also with proper etiquette and tone.

Several of your posts are derisive and antagonistic, not to mention posting multiple responses before hearing back from the people you are replying to.

Just making sure you understand our purpose and guidelines here.

[IgoFan]

About 20 or more ERV's[sic] in common? Actually thanks for bringing that up. Because this is revealing a pattern of design. The more they have in common, the more patterns will be revealed between the two.

Again you ignore the overwhelming implication of an ERV at the exact same chromosome location between humans and chimps, as making sense for common descent but no sense for design.

Besides the 20 or more ERV's we have in common, what else do we have in common with chimps besides that fact that chimps and humans both have teeth, both have two arms and legs, both have two eyes, etc...? Why aren't you mentioning those things?

Sharing similar arms, legs, and eyes is consistent with both common descent and common design. Sharing an ERV at the exact same location is beautifully consistent with common descent, but wildly incongruous with common design. I've already explained the reasons why multiple times.

Whether those ERVs are/were functional or not is immaterial. Humans and chimps could not have independently been infected, especially given those many different ERVs. The only consistent sensible explanation is that each of those ERVs infected the human-chimp common ancestor once. Then when humans and chimps split apart over 6 million years ago, each species simply copied those ERVs down to the present through hundreds of thousands of generations.

This is pure speculation...

You're confusing pure speculation with hypothosis backed up by strong evidence, because you consistently ignore or deny the ERV evidence referenced here that science has worked hard to produce.

Not even the U.S. Academy of Natural Sciences is claiming that ERV's are the empirical evidence for darwinian evolution. Get over it...

Let's see. You mention a 200 year old natural science organization, which collects biological specimens that support evolution studies. And then you use this highly pro-evolution organization's supposed lack of an explicit evolutionary claim about ERVs, as evidence against evolution. The mind boggles.

And what are you going to say if the Academy of Natural Sciences' relatively new molecular study department DOES make an explicit evolutionary claim about ERVs? Oh, wait, I've seen the answer to this question before in your 2009-Oct-22 post in this thread, in which you made near libelous accusations that evolutionary scientists are falsifying and hiding results for public money grants.

Logical fallacies? Perhaps you would like to answer these questions..

"Presumably, the alleged prediction and fulfillment are:

If universal common ancestry is true, then the same endogenous retrovirus (ERV) will exist in the same chromosomal location in two or more species. [...]

Priceless irony. I mentioned that you use logical fallacies, and in your very next response, you make the logical fallacy of switching the clauses of an if-then statement. "If A, then B" is quite different from "If B, then A".

Your statement should have been, and what I have been saying is: If ERVs exist at the same location, then common ancestry is strongly indicated. No wonder you're having trouble understanding.

But I probably shouldn't expect too much. If the world were truly a rational place, men would ride side-saddle.

[cslewislover]

The creature is standing completely straight like we do. I find that hard to believe.

From an anatomical perspective?

Please expand on this. I have graduate training in anatomy and I would like to hear your explanation.

Wow, I am so impressed!! Lol. I and others have already talked about it!

Anything else would be deceptive.

Like drawing a caucasian Jesus?

So . . . you have seen a caucasian drawing of Jesus that I did? How would you know how I would draw Jesus? This is a bizarre comment. I actually have never drawn Jesus - I don't know what He looks like. Hmmm. I have a graduate degree in history. Maybe I should know what color he was!! Exactly!

[derwood]

We know that what was once considered junk is turning out to be treasure. And that junk was in fact waved as the banner of proof of common descent.

Not quite.

Despite claims to the contrary, even by many evolutionists who rely on press releases and such, all noncoding DNA was NOT considered junkDNA, and junkDNA was NEVER all considered completely useless. And it was also never the case that 'junk was in fact waved as the banner of proof of common descent' - it is the fact that since noncoding DNA is not under the same selection pressures that coding DNA is that it is free to accumulate more mutations than is coding DNA, and as such is a potentially better source for what is called 'phylogenetic signal.'

Further, the claims that evolutionists 'ignored' junkDNA or even actively discouraged research on it and insisted that it is all 'worthless junk' are easily refuted by doing a simple literature search. Doing so, one finds prediction of function and the discovery of function in some junkDNA going back to the early 1970s, and even earlier if one considers that it was not called junkDNA until 1972.

[ageofknowledge]

Please stop with the baloney sandwhiches already!

Before 1972 scientists called junk DNA: pseudogenes (commonly thought of as defunct relatives of known genes that do not code for proteins). Today they call it non coding DNA.

Evolutionary biologists certainly DID assume that non-coding DNA was merely a “genetic fossil” that may have been useful somewhere in our evolutionary past but had been discarded as we evolved into more complex, higher organisms. Since this “junk” DNA was no longer needed, it would not be under selective pressure, and mutations could accumulate without any harm to the organism.

Unfortunately, for many years this notion that non-coding DNA was not functional (“junk”) actually inhibited science. Older journal articles are clearly biased by this notion. As a result, many scientists didn't spend their time studying it because of their evolutionary presuppositions that it was worthless DNA.

They wrote long and hard that the existence of junk DNA as one of the most potent pieces of evidence for biological evolution in this vein which makes your assertion they did not a false one derwood. This is a case where evolutionary theory inhibited science.

Today, they've turned the corner that non coding DNA is not junk DNA which they claim results when undirected biochemical processes and random chemical and physical events transform a functional DNA segment into a useless molecular artifact. Junk pieces of DNA remain part of an organism's genome solely because of its attachment to functional DNA persisting from generation to generation.

So today evolutionists highlight the fact that in many instances identical (or nearly identical) segments of junk DNA appear in a wide range of related organisms. Frequently the identical noncoding DNA segments reside in corresponding locations in these genomes. For evolutionists, this clearly indicates that these organisms shared a common ancestor. Accordingly, the junk DNA segment arose prior to the time that the organisms diverged from their shared evolutionary ancestor.

Evolutionists have published the question over and over in asking, “Why would a Creator purposely introduce nonfunctional, junk DNA at the exact location in the genomes of different, but seemingly related, organisms?”

Proponents of intelligent design and creationism respond to this objection by highlighting recent discoveries that attribute function to junk DNA. The recognition that junk DNA has function weakens the best argument for biological evolution and common descent. It also explains why identical junk DNA sequences appear in corresponding regions of the genomes of related organisms.

Two recent studies raise much more fundamental questions about junk DNA and, as a consequence, the evolutionary paradigm. One study appeared in a recent issue of PLoS Biology. This work examined the functional significance of a class of junk DNA referred to as ultraconserved elements (UCEs). UCEs don't code for proteins. Because they are noncoding, evolutionary biologists in the past would have considered these DNA elements to be junk. In the genomes of humans, rats, and mice, however, these DNA elements display virtually identical sequences. (There are approximately 480 UCEs in the human genome.)

Biologists immediately regarded this level of sequence identity as evidence that the UCEs must be functional, though they had no idea about the specific utility of these sequence elements. From an evolutionary standpoint, conservation of DNA sequences serves as a powerful indicator for function, since any change in these sequences via mutations would be weeded out by natural selection. From an evolutionary perspective, rats, mice, and humans share a common ancestor. As these lineages diverged from one another, the UCEs presumably remained unchanged because of their functional importance.

The idea that functional DNA sequences resist change and nonfunctional DNA sequences vary freely is one of the central tenets of molecular evolution. If the UCEs were nonfunctional, then mutational changes should be inconsequential. Over time, changes in the DNA sequences should accrue as rats, mice, and humans evolved along different evolutionary trajectories. As a consequence the sequences of the UCEs in these species should differ.

Biologists have speculated that UCEs regulate gene activity. For example, these sequence elements cluster near developmental genes. Researchers confirmed the functional importance of UCEs by deleting four carefully selected UCEs in the mouse genome. The deleted UCEs otherwise reside near key developmental genes. Presumably, their close proximity to these genes reflects the regulatory influence that these UCEs exert on the developmental genes.

To everyone's surprise, the mice with deleted UCEs were perfectly healthy. This result suggests that UCEs are not functional.

It is still possible that UCEs are functional. For example, if the UCEs are redundant within the genome, disabling a limited number of them would not harm the mice, since back-up copies of the UCEs would take over the function of the deleted sequences. The experimental design did not take into account this possibility.

Apart from this caveat, taken at face value the deletion experiments indicate that UCEs are not functional. This, of course, is troubling for intelligent design and creationism models, which maintain that all of the classes of junk DNA will ultimately turn out to be functional. Ironically, however, this discovery is much more troubling for the evolutionary paradigm.

One of the cornerstone ideas supporting molecular evolution is the notion that conserved DNA sequences are functional. But this recent study raises the very real possibility that this is not the case at all. If so, then the deletion result makes absolutely no sense. Why would evolutionary processes preserve UCEs if their loss has no significant impact on the mice? Could it be that fundamental deficiencies exist in the evolutionary paradigm?

Equally problematic are the results from the pilot phase of the ENCODE project, published in the summer of 2007. The ENCODE project is a multi-million dollar international effort to catalog all of the functional sequences in the human genome. The initial stage of the project involved a detailed search for every functional element contained in a 1% sample of the human genome.

Based on this survey, researchers discovered that parts of the human genome previously viewed as nonfunctional junk are transcriptionally active, signifying function. Surprisingly, these sequences show little conservation in the genomes of other mammals. In other words, functional sequences freely vary without any evidence for evolutionary constraint.

This recognition runs contrary to the central ideas of molecular evolution and, too, raises fundamental questions about the validity of the evolutionary paradigm.

Consequently, junk DNA is not just a problem for intelligent design proponents and creationists. It is a problem for evolutionary biologists as well.

If evolutionary biologists bring up junk DNA as a challenge to the work of a Creator, they must be willing to explain the new understanding of junk DNA behavior within an evolutionary framework. Based on these new discoveries, the fundamental ideas about molecular evolution and the behavior of functional and nonfunctional DNA sequences no longer hold.

But initially evolutionary theory certainly did inhibit science. You made a false assertion derwood.

[Gman]

Again you ignore the overwhelming implication of an ERV at the exact same chromosome location between humans and chimps, as making sense for common descent but no sense for design.

Again you are ignoring our questions. The claim falls beautifully and scientifically into a common design theory.

Sharing similar arms, legs, and eyes is consistent with both common descent and common design. Sharing an ERV at the exact same location is beautifully consistent with common descent, but wildly incongruous with common design. I've already explained the reasons why multiple times.

And I have already explained the exact same location is beautifully consistent with common design, but wildly incongruous with a common ancestor.

You're confusing pure speculation with hypothosis backed up by strong evidence, because you consistently ignore or deny the ERV evidence referenced here that science has worked hard to produce.

And you're confusing pure speculation with hypothosis backed up by strong evidence. You have no empirical evidence for your idea, just an assumption.

Let's see. You mention a 200 year old natural science organization, which collects biological specimens that support evolution studies. And then you use this highly pro-evolution organization's supposed lack of an explicit evolutionary claim about ERVs, as evidence against evolution. The mind boggles.

Yes, given the fact that the Academy of Natural Science is a 200 year old natural science organization gives more clout to the argument. Because NO WHERE will they ever use ERV's as empirical evidence for evolution. They will use other arguments in defense of micro-evolution but NEVER ERV's. The mind boggles...

And what are you going to say if the Academy of Natural Sciences' relatively new molecular study department DOES make an explicit evolutionary claim about ERVs?

They never have... And they never would.. Because it's speculation after the fact.

Oh, wait, I've seen the answer to this question before in your 2009-Oct-22 post in this thread, in which you made near libelous accusations that evolutionary scientists are falsifying and hiding results for public money grants.

I don't know about the Academy, but yes there are some scientists that will jump on the evolutionary ban wagon to become famous and get grants. We even have some scientists that have already confessed this.

Priceless irony. I mentioned that you use logical fallacies, and in your very next response, you make the logical fallacy of switching the clauses of an if-then statement. "If A, then B" is quite different from "If B, then A".

Your statement should have been, and what I have been saying is: If ERVs exist at the same location, then common ancestry is strongly indicated. No wonder you're having trouble understanding.

Your statement should have been, and what I have been saying is? Wow. Sounds logical to me.

But I probably shouldn't expect too much. If the world were truly a rational place, men would ride side-saddle.

Well your horse just ran off into the sunset.. Riderless.

[N4SC]

Well done. Science has now discovered bones. I think congratulations are in order.