Answering Questions on Creation and Creationism

[Breckmin]

Someone suggested we take the discussion of retroviruses and reverse
transcription to this thread. Let me first say that this will be everyone's
thread, and certainly not mine because I do not have much time here.

I would like to answer the 10 questions that were posted in another
thread. I actually already answered them, but lost it all when I got
to question 9 or 10 so if I do it again, Lord willing, I will take them
one at a time.

I will attempt to move some of the other posts to this thread.
Is this against the rules?

~Michael

 

[Breckmin]

RE: ERV

Before I give my opinion on this, what exactly is the question?

I assume this is also related to apes and humans having a common ancestor
because of ERV and RNA that changed the DNA of the host that ends up in
germline cells, but what exactly is the question? I am quite interested.

~Michael
Creationists spend most of their time.....

studying evolution.

 

[plindboe]

Hi Michael. The following video is very good (with wonderful music as well) at explaining why ERVs are evidence for evolution:

http://www.youtube.com/watch?v=TUxLR9hdorI

I guess the question is: how does creationism/ID account for ERVs?

Peter

 

[Blayz]

I have a question Michael.

What is tRNA doing in there? It has nothing to do with RT or ERVs

 

[Tomk80]

I will attempt to move some of the other posts to this thread.
Is this against the rules?

~Michael

Moving other posts is okay. It might be good to notify the person who made the post that you copied it here.

 

[agentorange20]

RE: ERV

Before I give my opinion on this, what exactly is the question?

Breckmin, I propose we in discussing the genetic evidence for ERV's that we also include other recent genetic evidence, that of the evidence for Human Chromosome 2 fusion. If you want to discuss other evidence like cytocrome C, GULO and other evidence feel free to shoot away.

In regards to ERV's first a background... From what we know and understand about transposons and retro-elements we can see by comparing species genomes and the locations of specific locations and sequences of these transposons to meaning that species which carry them in idential locations must have gotten them by shared ancestry. Simple point mutations occur per generation, as do long sequences which are copied (or cut) and pasted elsewhere in the species genomes.

Once the transposons are copied or cut moved they can interfer with regulartor genes and other genes, however in many cases we find genes have been duplicated and thus even a transposon which finds itself interfering with a given gene, it ultimately wont affect the building of protiens as the species/population posses mulitple copies of this gene so mutations can affect these at free will without affecting the organism. Thse mutated duplicated genes can then be passed on to other generations and shared amongst cloesly related species. These mutated genes serve no current function, so from a 'desiger did it' view point they are entirely pointless.

We can deduce this relationship and shared ancestry based on how we know that these transposons can move freely within the genomes of species and thereofore find identical patterns emerging, should evolution and common ancestry not be true, this isn't something we find.

ERV's (Endogenus retro-virus) are retro-elements, and they consist of a process in which a virus reverse transcribes its RNA into the hosts DNA. Sometimes the virus' machinery doesn't fully work and it loses its fuction even though its inserted itself into the hosts genome. Some times the ERV inserts itself into the Germline (sex cells) of the host and this is how its propogated and passed on each generation. The important note is that with any particular ERV there exists between 50,000,000 and 500,000,000 possible insertion locations that it can at random choose to insert itself.

For ERV's these are long reverse transcribed sequences which bear the mark of archaic viruses, and like transposons they don't code for any active protiens so their fuctionality is non-existant. When we compare the sequences of these ERV's between us and Chimpanzees for instance, we find them to be 98% identical (keep in mind point mutations affect code) and most of the changes are simple deletions of insertions so we can still readily identify the ERV sequence. They, like Telomeric and Centromeric DNA stand out like sore thumbs.

Considering how their insertion is random, the question then is, if evolution is wrong, then why do we share such specific ERV's in idential genetic locations wih other species at all? Since they insert at random, how else but by common ancestry can such retro-elements be explained?

Google 'evidence for common ancestry ERV's', you'll find an excellent video by user bonobobill, fully cited and sourced.

 

[Naraoia]

May I chime in with a couple of posts from That Other Thread?

The infrastructure for creationism are still in their beginning stages just as a Darwinian interpretation of science was in the late 19th Century.

Creationism technically precedes the Darwin-Wallace theory of evolution. By about thousands of years, too. I hope you didn't mean this as an excuse.

I don't know when this will change, but there are all kinds of theories involving mtDNA halogroup lineages or geometric reversal or Lorentz
force and Maxwell equations which remain unpublished. I don't intend
to publish them here.

Which means we might as well consider them non-existent for the time being. "All kinds of theories" unfortunately doesn't offer us much to work with.

There is no contradiction between true science and the Torah,

And what would be "true" science? Just curious.

and conventional interpretations do not have a monopoly science itself.

Sure they don't. After all, evolution managed to break into science in its own time

In the fields of micro biology and genetics we see the clear need
for a Creator as a result of current positive data.

Let's see if I can see it (never saw any during my studies so far, but then I'm still a beginner)

You can start with the schematic complex information present in RNA and DNA which is a blue print for biological existence.

Ok, issues here. What does "schematic complex information" mean?

You can look at the "quote unquote" negative data involving abiogenesis

Sorry, what exactly is this "quote unquote" negative data?

and see clearly that we can not reconstruct a living cell or recreate life in any way.

Don't be hasty in declaring stuff like that. Are you familiar with Jack Szostak's work?

This video on a possible origin of life is based on his results. It is new stuff (for me at least ) and quite neat:

http://uk.youtube.com/watch?v=U6QYDdgP9eg

This is often a starting point for those who come out of the deception of common decent with modification as theory for an origin for all species.

This sentence doesn't entirely make sense. Is common descent the deception or is it its use as a theory [...]?

Anyway, universal common descent

(1) only applies to organisms alive today - i.e. there may have been different life forms of separate origin that we don't know anything about because they didn't make it into the family tree of modern life forms. Though if those things existed and deserved the name "life" then they would have their own common descent.

(2) explains the origin of species given that there is something capable of descent with modification. It has nothing to do with the origin of life itself (although, depending on how you define life, biological evolution may have predated life proper)

(semantics IOW)Evolution is just speciation and mutation...

Evolution at its most fundamental is mutation, selection and random drift. Speciation is made up of these, just like other evolutionary processes.

Common ancestry, speciation, and natural selection are all part of the creative processes that God used to make variety...

Against that I have no objection.

...which are falsely taken and induced to be an origin for all species.

One: again, what do you mean by "an origin for all species"? Universal common descent or the origin of life? Two: it'd be nice if you explained why it's used "falsely". That's a rather strong statement. It not only implies that we may not be right, it implies that we are wrong. And a statement like that requires some support (that is, support for "falsely" rather than "prematurely" or something like that).

My long 3 page endless litany on everything from HGP and PCR in the 90's and Darwinian interpretations being the only guiding force was just lost once again when I clicked on a different window.

Ctrl+c is your friend. (And PCR has been in use since the '80s )

To summarize I am not aware of any find where we have been able to observe the fusion of two chromosome feet to form one larger hromosome. Telomere to Telomere fusion of two ancestral apes
(chromosomes from them) may look like the right fit to a puzzle, but
"commonalities do not equal relatedness" UNLESS that relatedness
is observed within species, subspecies, breeds (and in some rare
cases of engineering with plants -genera)

What kind of arbitrary criterion is that? You don't technically observe relatedness at any level of classification unless the organisms in question breed right under your eyes. So I think you owe us another explanation there.

As for chromosome 2 specifically, are you just doubting for doubt's sake or do you have some more serious objections?

And don't forget that there's much more to the evidence for common descent than human chromosome 2.

The genetic code, for one. It's completely arbitrary, and I think no two organisms differ in more than half a dozen out of 64 codons (though it's been a while since I last looked up the various codes). Given 64 codons for 20 amino acids and a full stop, there are enough possible genetic codes that such a coincidence makes one wonder. (And if you only count those then you are missing codes that use more or fewer amino acids or codons of length other than 3, although I'm somewhat suspicious that we use 3-letter codons for good evolutionary - economic - reasons)

(now luckily I saved the small above, but I just lost a whole
section comparing this to pharyngeal gill slits)

I can't wait to see that section. Evo-devo is fun stuff.

Maybe I am trying to do too many things at once and I keep losing what I've typed here and I now feel like an idiot.

Don't, it happens regularly to me when I forget my friend ctrl+c... (and then I say things that wouldn't make it past the prudery filter here )

I would love to spend (more) time on this, because believe me, I have a lot more to say. But it doesn't really matter whether you compare
rats to mice. bears to dogs. or chimpanzees to humans to try and
make your induction (and BTW, rats and mice are a possibility with
many creationists)just think of the difference that 1% or more makes.

... and what, according to you, should we think of that difference?

IOW, you can compare orthologous proteins and nucleotide alignments all you want, but just ask yourself "how many millions and millions of nucleotides are there?

Which is precisely why it's amazing that so many of them line up so neatly. AND often so consistently with our morphology-based ideas of relatedness.

I understand about finding the uniqueness of finding chromosomes that appear as though they could fuse together as 2A and 2B. But what evidence do we have to support that this actually occurs?

Let me turn this question around. What other explanation could you suggest for the similarity between the two chimp chromosomes and the one human chromosome? Including the telomeres - which are more than useful at the end of a chromosome but what on earth are they doing in the middle?

 

[Naraoia]

Breckmin, I propose we in discussing the genetic evidence for ERV's that we also include other recent genetic evidence, that of the evidence for Human Chromosome 2 fusion. If you want to discuss other evidence like cytocrome C, GULO and other evidence feel free to shoot away.

GULO? Is that the thingie more commonly known as the vitamin C gene?

Once the transposons are copied or cut moved they can interfer with regulartor genes and other genes, however in many cases we find genes have been duplicated and thus even a transposon which finds itself interfering with a given gene, it ultimately wont affect the building of protiens as the species/population posses mulitple copies of this gene so mutations can affect these at free will without affecting the organism. Thse mutated duplicated genes can then be passed on to other generations and shared amongst cloesly related species. These mutated genes serve no current function, so from a 'desiger did it' view point they are entirely pointless.

Umm, wait, are you sure you said what you wanted to say (just 'cause I don't quite get your point and I kind of study this stuff at uni...)?

Gene duplications can and do result in new useful functions. The trichromatic vision of Old World monkeys is a prime example (one more opsin), but there are less obvious and more complicated ones; just look at the vertebrate blood clotting cascade as explained here.

ERV's (Endogenus retro-virus) are retro-elements, and they consist of a process in which a virus reverse transcribes its RNA into the hosts DNA. Sometimes the virus' machinery doesn't fully work and it loses its fuction even though its inserted itself into the hosts genome. Some times the ERV inserts itself into the Germline (sex cells) of the host and this is how its propogated and passed on each generation. The important note is that with any particular ERV there exists between 50,000,000 and 500,000,000 possible insertion locations that it can at random choose to insert itself.

That's the point of the ERV business

For ERV's these are long reverse transcribed sequences which bear the mark of archaic viruses, and like transposons they don't code for any active protiens so their fuctionality is non-existant.

Actually, I used to think that with no real basis other than "used to be a parasite? Sure it's not useful!", but that's not quite the case. Case in point: syncytin. A retroviral gene and involved in placenta formation. (wow, it seems I found the original paper about it?)

 

[agentorange20]

GULO? Is that the thingie more commonly known as the vitamin C gene?

Ssssssshhhhhh, quite....you wouldn't want to let them know they carry the same defunct vitamin C synthesis pseudo-gene as other extant apes and in the exact same genetic location.

Plenty others though, GBA, for instance. Go to a genome.gov or other genetic data bases and you can compare them.

Umm, wait, are you sure you said what you wanted to say (just 'cause I don't quite get your point and I kind of study this stuff at uni...)?

My point wasn't that transposons result only in defunt duplicated genes. Sometimes they 'cut and paste', other times its a 'copy and paste' and in the later case we have clear indicators. Transposons (the pseudo gene variety) are useful in showing relatedness via descent, there is no real *other* explanation for many long sequences which are non-coding and found in identical genomic locations and are virtually identical save for few point mutations. Obviously, the entire copying and translocation of certain functional genes also support it, but the psedo genes are more compelling as from a 'designer did it' angle it can't work in explaining why for instance we and extant apes all share this GULO gene.

Gene duplications can and do result in new useful functions.

I know, but I wasn't implying they couldn't. Some gene duplications, as you may know, result in multiple copies of a single gene which can then be later inherited and when compared genomically across species the indications are obvious. Descent. It's the only way you get 500+ long base pair sequenes and to have them all shared in the same genomic location. They don't function as virtually always as they are duplicated they are moved without or away from their regulation genes, so they can be freely mutated, and this we do find.

Actually, I used to think that with no real basis other than "used to be a parasite? Sure it's not useful!", but that's not quite the case. Case in point: syncytin. A retroviral gene and involved in placenta formation.

Syncytin, this is a much, much older ERV that those other more recent ones only found in the primates and this is important to note.

 

[agentorange20]

To summarize I am not aware of any find where we have been able to observe the fusion of two chromosome feet to form one larger hromosome.

It's been observed in horses.

Telomere to Telomere fusion of two ancestral apes(chromosomes from them) may look like the right fit to a puzzle,

'Look' like the right fit? It's a matter of observation and evidence and they both imply descent. And it's not just Human Chromosome 2 and its evidence, it's all of the genetic evidence being explained in a consistant manner and descent explains it in spades.

The extant apes correlating chromosomes (in Chimps 2a and 2b) just happen to *look* like they line up by karyotype analysis (say nothing of the whole simmilarity in their entire genomes!). Homo Sapiens differ by chimps by some 40,000,000 single base pairs (some 1.3 % genomically.), much of it single deletions or insertions and not entire new sequences. I touched on some of the *other* genetic evidence, like GULO and others which all in unison scream descent.

but "commonalities do not equal relatedness" UNLESS that relatednessis observed within species, subspecies, breeds (and in some rare cases of engineering with plants -genera)

The commonalities in morphology is a direct reflection of their genetics, the genetic view is just a more in your face vision of the same view when done by comparitive ananotmy or embryology.

 

[Breckmin]

Hi Michael. The following video is very good (with wonderful music as well) at explaining why ERVs are evidence for evolution:

I guess the question is: how does creationism/ID account for ERVs?

Peter

I look at this little video and see God's Trademark in Creation and
the beauty of His Order and Sustaining Power, even though the
creation has been cursed with certain defects.

This doesn't prove anything because it is EXACTLY what we would
expect to find. Champanzees are the closest creation to our human
morphology to remind us how different we are from animals in
intelligence. We are created in God's Image and these animals
share almost 99% of our DNA and yet they are clearly NOT
created in His Image.
They have no human consciousness from which to be creative
understand complicated mathematics or abstract concepts or
infinity. This is what <<screams>> from this observation and
yet DET biologists are oblivious to it.

The arguments made from the creationist POV are something
I will look into but I have agreed in the past with one of them.

What you need to understand is the difference in interpreting
evidence. For instance, if you believe in endosymbiotic theory
your interpretation of micro biology and mitochondria is going
to be different than if you knew there was really no such
thing as prokaryotes. For the record I may use this term
in the future out of habit, but that does not mean I believe
in endosymbiotic theory.

The bottom line is that the ERV's are EXACTLY where we
would expect to find them, just as we would expect to see
identical proteins and the arrangement of nucleotides to also
be almost exactly the same.
~Michael

 

[Breckmin]

I have a question Michael.

What is tRNA doing in there? It has nothing to do with RT or ERVs

<<nothing to do with??>> To my recollection it would depend on what
viruses are being reverse transcribed. There are single-stranded RNA
viruses that need a DNA intermediate to replicate. Perhaps I was
wrong to draw attention to the wrong RNA in its context.
But I always look for a window to take about the beauty of transfer
RNA because when they primer, they act sort of like a key that
unlocks code.
The beauty of this complexity shows the need for a Creator to
have set this "complex" process into motion.
~Michael

 

[Breckmin]

Moving other posts is okay. It might be good to notify the person who made the post that you copied it here.

Thank you, Tom, for the most part I have no clue what I am doing here.
~Michael

 

[Breckmin]

Breckmin, I propose we in discussing the genetic evidence for ERV's that we also include other recent genetic evidence, that of the evidence for Human Chromosome 2 fusion. If you want to discuss other evidence like cytocrome C, GULO and other evidence feel free to shoot away..

I don't see how this is evidence of when we don't ever see those kinds
of mutations resulting in speciation beyond the genus level. Without
transitional species to observe such mutations to conclude common
ancestry between apes and humans, you have to assume it and then
prove it by showing all the different commonalities.

Scientists are so busy trying to find ways to prove relatedness, that
they never stop to actually think whether there "is" relatedness.
~Michael

 

[Breckmin]

In regards to ERV's first a background... From what we know and understand about transposons and retro-elements we can see by comparing species genomes and the locations of specific locations and sequences of these transposons to meaning that species which carry them in idential locations must have gotten them by shared ancestry.

Or this is the most logical place for them to be.

Simple point mutations occur per generation, as do long sequences which are copied (or cut) and pasted elsewhere in the species genomes.

Once the transposons are copied or cut moved they can interfer with regulartor genes and other genes, however in many cases we find genes have been duplicated and thus even a transposon which finds itself interfering with a given gene, it ultimately wont affect the building of protiens as the species/population posses mulitple copies of this gene so mutations can affect these at free will without affecting the organism. Thse mutated duplicated genes can then be passed on to other generations and shared amongst cloesly related species. These mutated genes serve no current function, so from a 'desiger did it' view point they are entirely pointless.

Serving no current function does NOT mean the Designer or the Creator
didn't first set a course of action. I have still have my appendix but its
function is currently pointless, unless it gets infected then it is worse.
From a creationist theory standpoint, Adam had a working one with his
cecum and had a better digestive tract and lived longer because of it
(and many other reasons).

Any mutated genes that appear pointless may be at that point in
time, or they may be hazardous. This doesn't take away from the
complexity of the universe, its order, nor its NEED for special creation.

 

[Blayz]

I will never really understand the hubris and arrogance that allows an armchair layman to think that that 20 years of professional science I have performed, including the several degrees, can be matched by a 5 minute skim of a bunch of crapulent web sites.

Seriously, where do you get off? Can I willy nilly interpret biblical passages because I spent 2 minutes looking at the skeptics bible?

Creationism models nothing and predicts nothing. It is worse than useless for any practical biological application.

My time is limited, so I will just respond to one of your posts.

<<nothing to do with??>> To my recollection it would depend on what
viruses are being reverse transcribed. There are single-stranded RNA
viruses that need a DNA intermediate to replicate. Perhaps I was
wrong to draw attention to the wrong RNA in its context.

Well considering tRNA is used in the translation of mRNA into protein, and the steps involved in retroviral insertion involve reverse transcription and integration and have nothing to do with translation, I think it clear that you were indeed WRONG.

But I always look for a window to take about the beauty of transfer
RNA because when they primer, they act sort of like a key that
unlocks code.
The beauty of this complexity shows the need for a Creator to
have set this "complex" process into motion.
~Michael

This, and much of your other posts, are sad arguments from incredulity, luckily for me, your severe lack of cognitive ability and slavish need to say at the earliest opportunity "oooh...so complex....goddidt..case closed" in no way limts my reality.

Come back to me when you have got your PhD. Until then, sit back in your armchair and leave the science to the scientists.

 

[Breckmin]

We can deduce this relationship and shared ancestry based on how we know that these transposons can move freely within the genomes of species and thereofore find identical patterns emerging, should evolution and common ancestry not be true, this isn't something we find.

I did laugh we I read this, only because you "did" find identical patterns
where common ancestry wasn't taking place...

~Michael

 

[Breckmin]

Ssssssshhhhhh, quite....you wouldn't want to let them know they carry the same defunct vitamin C synthesis pseudo-gene as other extant apes and in the exact same genetic location.

Which we would expect, BTW.
~Michael

 

[Breckmin]

Well considering tRNA is used in the translation of mRNA into protein, and the steps involved in retroviral insertion involve reverse transcription and integration and have nothing to do with translation,

I don't know..what about those with DNA?

~Michael

 

[sbvera13]

The irony of using a "complexity->god did it" argument is that the very CPU chip you are computing on was very likely designed with the help of an evolutionary algorithm. Said algorithm was, in turn, programmed in such a way that it mimics nature. It's rather unfortunate that the process you claim can't happen has actual industrial applications. Oops.

Evolution is a natural process that results in complexity, and even when that process is copied into another medium (computer programing), it still produces complexity. If you want to argue that evolution itself was created by god, that's fine, since it contradicts nothing. Just don't make the mistake of attacking evolution itself, since there are multiple billion-dollar a year industries that rely on evolutionary models for their operations. Even overcoming the economic hurdles to refuting evolution is insurmountable, to say nothing of the actual evidence for it.