ERV evidence for pastor with a lawyer's mind

Someday I will find an application for phonetic science or the evolution of phonology in languages in an answer to some question posed on Biologos - then I’ll be the one trying to explain to the general public! But until then, I’m grateful for your efforts!

Hello and thank you for your post and links re ERVs.

I have a question about the charts; the chart in Nature you linked was from an article that did not allow me to read the article itself. But you did not reference the article but the chart. I found the chart ( 11) to be unintelligible without explanation. It certainly was not self explanatory.

The second chart was a bit more informative as it gave what appeared to be statistical comparisons. Also from Nature you linked “Table 2” titled “Tranposable element activity in human and Chimpanzee lineages” and then listed down the left side “Element” and began the left list with; Alu, LINE-1, SVA, ERV class 1, ERV class 2, (Micro) satellite.
Then, in column 2 and 3 was the comparison between Chimp and Human.
The footnote says "Number of lineage-specific insertions (with total size of sinserted sequences indicated…"
So “Alu” showed chimp with "2,340 (0.7 Mb) and the human comparison across from the chip was "7,082 (2.1Mb).

I won’t go through the six others on the left side list.
Would you please “translate” that Table 2 chart? Starting with Alu? And since this Table authenticates your description of the ERV comparison, please also help me understand why the list contains items other than ERV.

On the list, the fourth one down is “ERV class 1”…with Chimp at “234 (>1 Mb)” and Human at “5 (8 kb)”…
ERV class 2 is then listed with its comparisons.

Would you please explain the ERV comparisons and also explain the other non ERV items compared.

By the way, I understand how ERV works so I’m not needing a basic tutorial…I’m only needing help with the Table you linked which I outlined above.

Thank you so much for your help and patience.

Oh, and by the way…I’m a “lawyer with a pastor’s mind.”

That is unfortunate! The article should be open access IMO. I did find the full text available at Readcube, which is the source of the technology that Nature has been using for the last few years to allow non-subscribers to read papers online. The site is legit (i.e. it is allowed by the publisher). This link should get you the full text:
Initial sequencing and analysis of the human genome (2001 paper)

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I know your question is for @T_aquaticus but I thought I’d try to help here.

Overall: The table shows common transposable elements in human genomes. ERVs are a subset of these transposable elements. The title of the table is “Transposable element activity in…” The table authenticates the claims in the post by documenting the source of the numbers provided by @T_aquaticus regarding ERVs. His/her numbers come directly from the table: s/he wrote “When they sequenced the chimp genome they found that 82 of those human ERVs were not found at the same spot in the chimp genome” — 82 is the sum of the ERV numbers under “human” in the table.

Alu elements are extremely abundant transposable elements in primate genomes. They must be at the top of any list of transposable elements in humans.

Wonderful. I’m so interested in this subject so need lots of help. Thank you.

Thank you Stephen; I note the word “sum” was used which is an idea I can deal with! But where in the Table under human is the “sum” found? Are we at “ERV class 1”? Just go through the line with me and show me…sorry I’m so slow.

In the meantime, I’ll read the article if you don’t hear back from me for a while…thank you again.

The sum is 82, which is 77 and 5 added. That sum was computed by @T_aquaticus.

The table lists ERV class I, class II, and class III, which are the ERVs we are looking at. The heading on the first column is “Number of copies (x1000)” which translates to the number of insertions times one thousand. If you add up the number of insertions for class I-III you get 203,000 total ERV insertions. The other rows are other types of repetitive DNA. In the LTR group with ERVs are MaLRs which are transposons that have also picked up LTR sequence from ERVs.[quote=“senatorthomas, post:22, topic:36182”]
Would you please “translate” that Table 2 chart? Starting with Alu? And since this Table authenticates your description of the ERV comparison, please also help me understand why the list contains items other than ERV.
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The table lumps ERVs and transposons together because they are repetitive sequences of DNA that insert themselves all over in the genome (i.e. transposable element activity). Transposons will jump out of the genome and then insert themselves somewhere else. ERVs are viral DNA with repetitive DNA that insert themselves into the genome. Geneticists use algorithms that look for repetitive DNA, so these algorithms will detect transposons, ERVs, and micro-satellite DNA which is why you will often see them on the same charts. You can read more about repetitive DNA at Wikipedia:

Alu and LINE-1 insertions are transposons. The stuff we are interested in is the retroviral insertions, which are listed in the ERV rows. The numbers in the chimp column are the insertions found in the chimp genome, but not in the same position in the human genome. The numbers in the human column are the insertions found in the human genome, but not in the same position in the chimp genome. This is why they are called “lineage specific”, because those insertions were produced after the chimp and human lineage split from their common ancestor. The XX Mb represents the number of DNA bases in these insertions (M = 1 million, 1 Mb is one million base pairs). When we compare both tables, what we see is that there are about 203,000 total ERVs in the human genome, and only 82 (77+5) of those human ERVs are found only in the human genome. The rest of the 203,000 human ERVs are found in the chimp genome at the same spot (i.e. orthologous).

Transposons can also be used as evidence in the same way that ERVs are used, but they are a bit harder to track due to much higher activity and other funky stuff that they like to do (e.g. higher recombination rates, excision). ERVs are a bit more straightforward.

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Welcome! Nice to see that you made it over here to our crazy little corner of the interwebs.

Hi Mary,

The laws governing the universe are composed of stochastic processes (see def. below). So, consider chemotherapy.

The success of chemotherapy is dependent on the random outcome of millions of individual drug interactions. If the great majority of those outcomes are positive, the chemotherapy is likely to succeed. On the other hand, the failure of even one of those interactions may result in a reoccurrence. So, even though a particular chemotherapy protocol is based on random interactions, the chemotherapy is not without purpose.

But wait, there’s more. There’s actually a great biblical example. In Genesis 1:11-12, God delegates the creation of fruit trees to nature. But, in the delegation God describes the kind of fruit tree He wants nature to produce: God wants nature to produce “trees bearing fruit making fruit”. But in the next verse, nature - composed of stochastic processes - is only able to produce “trees making fruit”. So, God wanted fruit trees making fruit, and nature was only able to give Him trees making fruit. But, evidently God was satisfied with His fruit trees and pronounced it all good.

More simply put, the creationists you read or listened to, do not understand the workings of randomness in evolution.

Blessings,

Michael

sto·chas·tic
stəˈkastik/Submit
adjective
randomly determined; having a random probability distribution or pattern that may be analyzed statistically but may not be predicted precisely.

Don’t worry, I am not convinced by their view of randomness, it is just that some people who don’t understand “random” do use this argument against evolution, because they think God cannot do something so lacking in purpose in their eyes. Thanks for your examples. I think the one that will appeal the most is imagining someone tipping water over me - they do not know exactly where the water will fall, but they have a purpose to get me wet!

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The other part is that having a random component does not make the entire process random. If you find a creationist who makes this claim, you should challenge him to play poker with a champion, because the shuffle is random, then bet heavily against him.

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I like Michael’s point; and as I’ve been reading articles on quantum mechanics in the past few years I have seen the same point (I think) he is making. Notice the Hebrew word for create in Genesis 1:1… to create as in out of nothing is BARA. In later verses the word “make” is used (not BARA)…speaking of the sun and moon. (The idea he “makes them to appear on earth” That is not the word used later (note there is the exception with “humans”}…but the idea seems to be nature indeed can create. (“Let the earth bring forth…” ) The Creationists don’t have a problem with variety within species; you can start with wolf and without Divine Intervention get chihuahua or great- Dane over time. But they will defy you on going from Chihuahua to cat…or what ever.
Back to Michael’s point. Using quantum mechanics theory you can’t know with absolute certainty an outcome. But Einstein protested (it is believed he said) “God doesn’t play dice with the universe” in speaking of the quantum mechanics problem (uncertainty). Well…if that is so; then Michael’s point again…humans may be subject to the Heisenberg Uncertainty principle…but not God. Thus, whatever God allows in nature, for nature to bring about, God is not surprised and is approving of it (speaking of nature’s offspring) as a father would be in watching his children accomplish good things in life. God is creative and may just enjoy his created offspring create at His pleasure…knowing the exact outcome. Or maybe I’m enough of an Armenian to think a heretical thought; maybe surprised on occasion at a good outcome … who would have thought a papaya would taste so good. Don’t tell any of my Calvinists friends I uttered such a thought.

Playing biology Nazi for the moment . . .

What you describe is a common misconception. Modern species do not evolve from other modern species. Rather, modern species evolved from a common ancestor that unlike either modern species. It goes back to the tree of life analogy, where the tips of the branches represent modern species that branch from a common node. The most primitive fossil species members of the Carnivora clade include Tapocyon and Oödectes, if you feel like looking them up, and they were neither a modern dog nor a modern cat.[quote=“senatorthomas, post:35, topic:36182”]
Well…if that is so; then Michael’s point again…humans may be subject to the Heisenberg Uncertainty principle…but not God. Thus, whatever God allows in nature, for nature to bring about, God is not surprised and is approving of it (speaking of nature’s offspring) as a father would be in watching his children accomplish good things in life. God is creative and may just enjoy his created offspring create at His pleasure…knowing the exact outcome.
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I thought you might enjoy this quote from Charles Darwin:

"It can hardly be supposed that a false theory would explain, in so satisfactory a manner as does the theory of natural selection, the several large classes of facts above specified. It has recently been objected that this is an unsafe method of arguing; but it is a method used in judging of the common events of life, and has often been used by the greatest natural philosophers … I see no good reason why the views given in this volume should shock the religious feelings of any one. It is satisfactory, as showing how transient such impressions are, to remember that the greatest discovery ever made by man, namely, the law of the attraction of gravity, was also attacked by Leibnitz, “as subversive of natural, and inferentially of revealed, religion.” A celebrated author and divine has written to me that “he has gradually learnt to see that it is just as noble a conception of the Deity to believe that He created a few original forms capable of self-development into other and needful forms, as to believe that He required a fresh act of creation to supply the voids caused by the action of His laws.”

— Charles Darwin, The Origin of Species (1859)

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In response to “common misconception”…you discuss the evolution from “common ancestor” that looked like neither dog nor cat. Well, of course, the ancestor was a species itself. The creationist denies that you can show gradual development from a species precedent to another species…to get to dog or cat. Nor does variation within the species demonstrate evolution indicative of development from a species to another species. I’m sure you get what I’m saying. Oh, by the way; are you saying that modern species are NOT evolving? Are you contending that they have reached a sort of apex of development? Have we (all species) basically, except for variation within species, now ceased developing into new species? Or can one only tell that with hindsight…if one could see over time such development by looking backwards. Or let me ask it another way…do you think you can clearly identify development in secies x, y and z that is clearly taking that species beyond what the species is and making it a new and different species so that on close examination one could say; yes I can see the clear living linage from horse to hippo…just look at the living intervening animals that transition to hippo…so we have horse a, horse ab, horse abc, horse abcd, horse abcde, horse abcdef, horse abcdefg, horse abcdefgh, Hippo abcdef, Hippo abcde, Hippo abcd, Hippo abc,Hippo, ab, Hippo a, Hippo…all living (so we don’t have to figure out the maze of fossils)… and everyone could see a living illustration of species to species development. Do we have five or six examples of living transition? And please do not cite the Long Term E Coli Experiment as some proof. That is the opposite of what I’m talking about. The E Coli after 60,000 generations is still…E Coli. Thanks for your insights.

It appears they are. See here for many documented examples.

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This turned out to be a rather long post, so I apologize if it is more information than you wanted. I can only blame you for this post because you asked such wonderful and insightful questions. :wink:

I would agree that creationism is primarily a form of denialism.

What I do find interesting within creationist arguments is the appearance that they think fossils are the only evidence we have. Drawing an analogy to criminal law, it is a bit like saying that eyewitness accounts are the only type of evidence we can ever collect. Do we have to have an eyewitness to a murder in order to convict? Do we have to have security camera footage? Or, can we also have forensic evidence such as fingerprints, DNA, fibers, and shoe prints? The same applies to evolution. The most impressive evidence is DNA evidence. We know that species shared a common ancestor because that is what the DNA evidence tells us. We don’t need a single fossil in order to determine that evolution is true. Fossils are just icing on the cake.[quote=“senatorthomas, post:37, topic:36182”]
Oh, by the way; are you saying that modern species are NOT evolving?
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All species are evolving. As long as you have organisms that produce imperfect copies of themselves (i.e. biological reproduction) and compete for limited resources you will have evolution. Evolution has to happen when these conditions are met because there will have to be winners and losers that are ultimately determined by the DNA sequences they carry in their genomes.

However, not all lineages will see the same amount of morphological (i.e. shape of the organism) change. If selection pressures favor current morphologies then those morphologies will be selected for. Does this mean that there are species that are experiencing no change at all? I highly, highly doubt it because no species is perfect and no environment is perfectly stable. At the DNA level, DNA sequences not under selection will continue to accumulate mutations at a rate consistent with chance, what geneticists call genetic drift.

On top of all of that, we must also remember that there is no objective and non-arbitrary line between one species and the next as we move through time. To use an analogy, it is a bit like trying to pick the nanosecond when you went from being short to being tall. Any point you pick is going to be arbitrary. The way in which we group modern species and fossil species is also arbitrary. We could put all primates in one genus, if we wanted to.[quote=“senatorthomas, post:37, topic:36182”]
Or let me ask it another way…do you think you can clearly identify development in secies x, y and z that is clearly taking that species beyond what the species is and making it a new and different species so that on close examination one could say; yes I can see the clear living linage from horse to hippo…just look at the living intervening animals that transition to hippo…so we have horse a, horse ab, horse abc, horse abcd, horse abcde, horse abcdef, horse abcdefg, horse abcdefgh, Hippo abcdef, Hippo abcde, Hippo abcd, Hippo abc,Hippo, ab, Hippo a, Hippo…all living (so we don’t have to figure out the maze of fossils)… and everyone could see a living illustration of species to species development. Do we have five or six examples of living transition?
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You can’t use fossils in that way. Fossils can’t tell us who their ancestors were or who their descendants are. It is a misconception that fossils can tell us this. We can use fossils to model what we think a common ancestor probably looked like, but we can never say that any fossil has any descendants.

Fossils are used in a different manner than what you describe. The ultimate test for the theory of evolution is the nested hierarchy, which is analogous to a branching tree. The theory predicts which combinations of features past species should have had, and which combinations species should not have had. For example, the theory predicts that there should have been species that had a mixture of mammal and reptile features, and it also predicts that we should NOT have seen species with a mixture of mammal and bird features. Each and every fossil is a test of these predictions. As of now, every single fossil we have found fits the predictions made by the theory. We only see the mixtures of features that the theory predicts we should see, and we don’t see any of the mixtures of features that the theory predicts we shouldn’t see.

So to get to your question, the fact that every single fossil we have fits the predictions of the theory of evolution is what tells us that the theory is (tentatively) true. Creationism, on the other hand, makes no predictions about what types of fossils we should find. That is why the theory of evolution is preferred over creationism in scientific circles.[quote=“senatorthomas, post:37, topic:36182”]
And please do not cite the Long Term E Coli Experiment as some proof. That is the opposite of what I’m talking about. The E Coli after 60,000 generations is still…E Coli. Thanks for your insights.
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Our common ancestor shared with chimps was a primate. Humans are still primates. Does that not count?

Our common ancestor shared with polar bears was a mammal. Both humans and polar bears are still mammals.

Our common ancestor shared with trout was a vertebrate. Both humans and trout are still vertebrates.

IT would seem that calling two things by the same name is a poor way of determining if evolution has occurred.

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[quote=“senatorthomas, post:37, topic:36182”]
The creationist denies that you can show gradual development from a species precedent to another species…to get to dog or cat.[/quote]
The creationist is conflating development (fertilized egg to adult) of a single organism with evolution. Why is the creationist conflating such well-understood terms?

No, variation within the species exists. It is the substrate for evolution. Evolution is the change in allele frequencies over time. If you think that this is trivial, please enumerate the number of genetic differences between you and a chimp that are allelic and non-allelic.

You also don’t seem to understand that one species rarely goes to another single species. It’s about splitting.

[content deleted by moderaror]

So if evolution threatens you theologically, don’t you have an enormous obligation to understand it first instead of going after silly straw men? [content deleted by moderator]

No and no. [content deleted by moderator]

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