DNA the New Fronter

[_spotlight]

Let's look at some of the objections to endogenization and see if they are reasonable ones.

1) An ERV does not derive from a retrovirus. There are so many uniquely retroviral features of ERVs that make this idea unworkable. Even when a fragment of an ERV does something (you would never want an ERV to function in its entirety) the rest of the ERV makes no sense. Why the reverse transcriptase? Why the integrase? Why the repetition of DNA, like bookends, either side of the up and downstream LTRs, exactly where we would expect to see the if the ERV had been integrated by integrase?

2) Different species can be directly infected by the same retrovirus. Yes they can, but retroviruses do not target specific locations in DNA. Gene therapists and genetic engineers would sell their souls in an instant if they could find a way of doing that. That's one of the main reasons they research the action of integrases and integration target preference so diligently. Common ERVs exist in corresponding locations in the DNA of all your cells, all of my cells, and all of Charlie the chimp's cells because we have all inherited them from ancestors we all share. There is no other explanation that makes any sense.

3) Only a handful of ERVs are shared between chimps and humans. This is untrue. It seems to stem from a misreading (probably due to confirmation bias) of Theobald's piece in Talk Origins which mentions the handful of commonly located ERVs unique to humans and chimps that were known at the time. This is no help anyway. I'm going to be ridiculously generous and use a probability of common location by coincidence of 1/100. Using this figure, the probability of seven such common ERVs by coincidence is 1/1007 = 1/100,000,000,000,000. One in a hundred billion. In other words, you would have to search a hundred billion earths, each with their own unrelated chips and humans, in order to find the one earth where it misleadingly appears that the two species are related.

The real figure for shared ERVs and ERV fragments is not seven. It's more like 200,000. With a probability as much as 1/100 for a single coincidence, that's a likelihood of one in ten followed by 399,999 zeros!

4) ERVs are not junk. Not entirely. They are the remnants of fully working sets of genes - for making retroviruses.

5) ERVs could have been designed - particularly to aid evolution by increasing variation and gene sharing. Doesn't make much sense in the light of the facts that retroviruses are "designed" to make retroviruses, that only components of some ERVs have an exaptated function, while other components do nothing, or even cause diseases. And even if a Mischievous Designer did make retroviruses and let them loose, endogenization in common ancestors is still the only explanation for multiple commonly located ERVs.

6) There are common ERVs that do not conform to the generally accepted phylogeny. That is true, but rare. I only know of one confirmed case, and one suspected, possible case. This is trotted out as if it is a show stopper, but the only viable explanation is incomplete lineage sorting, and it doesn't falsify common descent. You are still left with the task of explaining the ERVs that are commonly located in different species.There will be other differences that will have happened after speciation, of course. These are independent endogenizations. In closely related, recently separated species, we would expect them to share the majority of their ERVs, and then have some different new ones acquired after speciation, which we would expect to appear more recent (less mutated and recombined). This is exactly what we see with chimps and humans.

7) 200,000 ERVs in 25 million years would drive a species to extinction. Well, make up your mind whether there are just a handful or 200,000 ERVs! Reverse transcription is error prone. It doesn't need to be accurate if enough cells get to reproduce the virus. Most ERVs are inactive - either because of mutation and cutting up by recombination, but also because, probably, many of them were never viable viruses in the first place. Let's take 25 million years & 200,000 ERVs. That's 1 successful endogenization every 125 years. (Successful, meaning it doesn't kill the host and then proceeds to become fixed in the population. Doesn't seem unreasonable to me.

8) A few components of a few ERVs are known to do something useful and even vital. In the case of syncytins - they look like mutated retroviral env genes, and are found in ERVs where you expect to find env genes - we have genes that allow placental attachment. Env genes help the virion to attach to the host cell. Syncytins are vital to some species (not to all species, but to the species they are vital to). But there are different syncytins, in different ERVs, in different places in the DNA of several different mammalian lineages. What for? Common designer? Hardly. And several ERV components are implicated in late onset diseases, particularly cancers. And what are all those other non-beneficial, non-deadly retroviral components for? It's clear that they were for getting retroviruses reproduced. Why the heck would an intelligent designer put useful, deadly and unnecessary retroviral genes in a structure that falsely mimics an ERV, mimics an evolutionary phylogeny, and puts fake watermarks of the non-existent action of a non-existent integrase enzyme in there too? And by the way, the position of an item of genetic material is largely irrelevant. Not always, but as a general rule. Otherwise, GM would not work.

9) ERVs promote transcription of native DNA. Yes, many of them do. Retroviruses come with their own promoters. They are needed to get their own genes transcribed. But mutate the provirus and chop it up, littering the genome with odd promoters in odd places there is a good chance they will promote something. This is not design.

[_spotlight]

Indeed, similar design could be evidence of a common designer… or common ancestry. But how can we tell the difference? And are their any clues either way? I think there are, and I address a number of them in Question #34.

But to use your car analogy, imagine if GM realized they’d made a mistake in one of their cars, they probably wouldn’t continue to design new cars with the same flaw, they would correct their mistake. Humans, chimps, and most monkeys are unable to produce Vitamin C the way most all other mammals do, because our genes are broken in the same way. This flaw is more consistent with the idea of common ancestry (passing down a defect) than the idea of God designing us independently, but all with the same defect.

To give another car analogy, imagine if GM were secretly designing a device that would allow cars to fly at the same time as a competitor. If they both unveiled the EXACT same flying device, we would suspect that both came from a common designer. However, if they were completely different designs, then we would assume they were designed independently. We see this kind of independent design in “convergent evolution,” when different classes of animals benefit from similar adaptations (such as being able to fly) but they arrive at them though unique designs. If all animals were designed, the designer could simply reuse his existing designs across dissimilar classes. Instead, these similar features (that evolved after two classes of animals have split) all have unique designs, suggesting they evolved without common oversight.

Sorry, these are snippets I've collected over the months from discussion forum etc and so I have not the specific references for all of them. But the arguments stand on their own merits.

[_Quasimodo]

DrW,

Thanks for that reminder. You are obviously right about that. It probably is a waste of time to engage him. I hope, though, that at least some, if not most, can see how he further damages the credibility of his views with every post he makes.

Thanks also for all I have learned from your posts! You have long been one of my very favorite contributors to this forum!

Nipper does have some value. Refuting his illogical contortions (cleaning his clock) does give those lurkers out there (that may be on the fence) some reliable data to help them understand the issues.

Nipper gets to play Dr. Watson on this board. A literary device that allows others to explain where he went wrong.

[_spotlight]

The ERVs also share mutations with each other as well as their homologous position in the genome... ERVs have been involved in other types of mutational rearrangements after their initial insertion into the primate gene pool. These have generated weird and wonderful derivatives. Such mutational events would be expected to arise as essentially unique happenings, and therefore the presence of such ERV derivatives in multiple species would be a further stratum of evidence that those species are descended from the individual in which the novelty arose. For example, an ERV- H and an ERV- E have been joined together (as the result of a large deletion of genetic material) to form a chimaeric ERV. The deletion extends from the pol gene of the ERV-H to just downstream of the left- hand LTR of the ERV- E. This chimaeric ERV is found in humans, chimpanzees and gorillas, and the ERV- H/ERV- E junction point is the same in each species. We can therefore conclude that humans, chimps and gorillas have inherited that singular ERV from the common ancestor in which the gene deletion event occurred. Multiple copies of this chimaera are also present in each species, indicating that the unique ERV- H/E has been ‘copied and pasted’ during subsequent history.

[_Maksutov]

DrW,

Thanks for that reminder. You are obviously right about that. It probably is a waste of time to engage him. I hope, though, that at least some, if not most, can see how he further damages the credibility of his views with every post he makes.

Thanks also for all I have learned from your posts! You have long been one of my very favorite contributors to this forum!

Nipper does have some value. Refuting his illogical contortions (cleaning his clock) does give those lurkers out there (that may be on the fence) some reliable data to help them understand the issues.

Nipper gets to play Dr. Watson on this board. A literary device that allows others to explain where he went wrong.

Interesting comparison, Quasi. How about Simplicio, as created by Galileo in his Dialogue Concerning the Two Chief World Systems?

"Simplicio, a dedicated follower of Ptolemy and Aristotle, presents the traditional views and the arguments against the Copernican position. He is supposedly named after Simplicius of Cilicia, a sixth-century commentator on Aristotle, but it was suspected the name was a double entendre, as the Italian for "simple" (as in "simple minded") is "semplice"."

https://en.wikipedia.org/wiki/Dialogue_ ... ld_Systems

[_spotlight]

Why is it that we have pseudogenes in our DNA??

Common ancestry also predicts that, beyond human-chimpanzee common ancestry, the common primate ancestor also shares ancestry with other vertebrates in the more distant past. For example, evolutionary theory predicts that humans, like all vertebrates, are descended from egg-laying ancestors. As with all placental mammals, humans do not use egg yolk as a source of nutrition for their embryos. Other vertebrates such as fish and birds do employ egg yolk, as do a small number of extant mammals such as the platypus.

But it turns out, humans still retain the remnants of these yolk-producing genes. A particular protein used as a component in egg-development in egg-laying vertebrates is produced by a gene called vitellogenin. And recently some researchers decided to find out if humans carry the pseudogene for vitellogenin.

They did this by first locating the functional vitellogenin gene in the chicken genome. They examined all the genes flanking the vitellogenin sequence–and then tracked these same genes in the human genome.

They found that these genes were present side-by-side and functional in the human genome; then they performed an examination of human sequence between them. As expected, the heavily mutated, pseudogenized sequence of the vitellogenin gene was present in the human genome at this precise location. The human genome thus contains the mutated remains of a gene devoted to egg yolk formation in egg-laying vertebrates at the precise location predicted by shared synteny derived from common ancestry.

This is certainly one of the more extraordinary pieces of evidence for common ancestry as Darwin first proposed it.

It’s one thing to tell your kids or students that we share some obvious gene sequences with animals (like primates) that look a lot like us. They think that’s cool.

It’s another to watch their expressions when you tell them we still carry the remains of genes... for making egg yolk.

http://www.forbes.com/sites/johnfarrell ... our-genes/

[_Quasimodo]

We have experimental evidence for junk DNA.

Edward Rubin's team at the Lawrence Berkeley National Laboratory in California has shown that deleting large sections of non-coding DNA from mice appears not to affect their development, longevity or reproduction.

http://www.nature.com/news/2004/041018/ ... 018-7.html

Experimental confirmation that further falsifies your assertion that there is no junk DNA.

Junk DNA (non-coding DNA) has some fun possibilities. Like reverse engineering dinosaurs from chickens. I hear they are having some interesting success at doing that.

https://www.washingtonpost.com/national/health-science/paleontologist-jack-horner-is-hard-at-work-trying-to-turn-a-chicken-into-a-dinosaur/2014/11/10/cb35e46e-4e59-11e4-babe-e91da079cb8a_story.html

[_The CCC]

DrW,

Thanks for that reminder. You are obviously right about that. It probably is a waste of time to engage him. I hope, though, that at least some, if not most, can see how he further damages the credibility of his views with every post he makes.

Thanks also for all I have learned from your posts! You have long been one of my very favorite contributors to this forum!

LittleNipper is the embodiment of the nonsense fabricated and churned out by the Morris dynasty of religious frauds. Creationism is the signature enterprise of the Seventh Day Adventists who, like the Mormons, have improbable religious, scientific and historical claims that are self-refuting. And yet these kind of folks manage to get a state government to underwrite their projects (the Ark Park) even though doing so is obviously unConstitutional. This is one of those instances where Europeans and the UK look at the US and shake their heads.

SEE https://www.LDS.org/topics/book-of-morm ... s?lang=eng

[_Quasimodo]

Nipper does have some value. Refuting his illogical contortions (cleaning his clock) does give those lurkers out there (that may be on the fence) some reliable data to help them understand the issues.

Nipper gets to play Dr. Watson on this board. A literary device that allows others to explain where he went wrong.

Interesting comparison, Quasi. How about Simplicio, as created by Galileo in his Dialogue Concerning the Two Chief World Systems?

"Simplicio, a dedicated follower of Ptolemy and Aristotle, presents the traditional views and the arguments against the Copernican position. He is supposedly named after Simplicius of Cilicia, a sixth-century commentator on Aristotle, but it was suspected the name was a double entendre, as the Italian for "simple" (as in "simple minded") is "semplice"."

https://en.wikipedia.org/wiki/Dialogue_ ... ld_Systems

I hadn't heard of that. I followed your link to learn about it (you clever man). It does seem to be a great analogy!

[_Maksutov]

LittleNipper is the embodiment of the nonsense fabricated and churned out by the Morris dynasty of religious frauds. Creationism is the signature enterprise of the Seventh Day Adventists who, like the Mormons, have improbable religious, scientific and historical claims that are self-refuting. And yet these kind of folks manage to get a state government to underwrite their projects (the Ark Park) even though doing so is obviously unConstitutional. This is one of those instances where Europeans and the UK look at the US and shake their heads.

SEE https://www.LDS.org/topics/book-of-morm ... s?lang=eng

I'm not seeing the relevance, CCC. Please explain.