Does the "clear meaning" of the scriptures trump science?

[davecarlson]

@r_speir

You know perfectly well what I mean when I say your so-called ‘trees’ are really in fact only pyramids.

I cannot speak for John, but I promise you with all sincerity that I have absolutely no idea what you mean by this.

[T_aquaticus]

@r_speir

No, we must not be communicating because you are back on historical insertions.

Those are insertions found in the human genome right now.

@r_speir

I wanted studies done today to see if the same susceptibility, at the same integration sites, was shared between the two species.

I already gave you that paper:

Human Endogenous Retroviruses are expected to be the remnants of ancestral infections of primates by active retroviruses that have thereafter been transmitted in a Mendelian fashion. Here, we derived in silico the sequence of the putative ancestral “progenitor” element of one of the most recently amplified family—the HERV-K family—and constructed it. This element, Phoenix, produces viral particles that disclose all of the structural and functional properties of a bona-fide retrovirus, can infect mammalian, including human, cells, and integrate with the exact signature of the presently found endogenous HERV-K progeny. We also show that this element amplifies via an extracellular pathway involving reinfection, at variance with the non-LTR-retrotransposons (LINEs, SINEs) or LTR-retrotransposons, thus recapitulating ex vivo the molecular events responsible for its dissemination in the host genomes. We also show that in vitro recombinations among present-day human HERV-K (also known as ERVK ) loci can similarly generate functional HERV-K elements, indicating that human cells still have the potential to produce infectious retroviruses.
Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements - PMC

@r_speir

Again, I am still unimpressed with historical retrovirus insertions. There are others ways to explain that.

You ask for empirical evidence, yet reject that empirical evidence in favor of claims that have zero empirical observations. Go figure.

[T_aquaticus]

@thoughtful

This quote was originally about sifting through science as a Christian. Just like anything else I sift it through my worldview.

I am asking if I understand your worldview. Would it be correct to say that you don’t care about the scientific evidence?

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@T_aquaticus

It’s in the chimp genome paper:

@T_aquaticus

Those are the lineage specific insertions, the insertions that aren’t shared by chimps and humans. There are 82 human ERV’s (endogenous retroviruses) not found in the chimp genome and 279 chimp ERV’s not found in the human genome. The rest of them are shared. So how many ERV’s are there in the human genome? That’s found in the human genome paper:

I knew in a general way about these discoveries but I had never seen the evidence displayed in such tables before. This is spectacular!

@thoughtful

If the explanation scientists give does not involve God actively acting in creation and the Bible does, then that particular science isn’t going to match up with my worldview.

I don’t think I’m following you here. Obviously the explanation scientists give does not make any mention of God (and his involvement or non-involvement) because that is theology, not science. So how could it possibly match or not match with your worldview or my worldview or anybody else’s?

When a mathematician states that the area of a circle is Pi x r^2, it makes no theological claims—so we can all recognize the value of the formula regardless of whether we are theist or non-theist and whether or not we personally hold to some sort of Biblical worldview. How is the evidence and implications of ERVs any different?

Are you saying that if someone rejects Common Descent based on their interpretation of the Bible, they must reject even ERV evidence out of hand?

A related question would be: If the overwhelming weight of the scientific evidence within the world God created conflicts with my preferred interpretation and translation of some passage(s) of the Bible, at what point am I willing to consider that my Biblical hermeneutics are flawed (and perhaps misled by popular Christian traditions?) There was a time when most Christians assumed that the Bible required belief in a geocentric universe. Once the scientific evidence became overwhelming for heliocentrism, most Christians abandoned that worldview—and most would say today that the Bible that the Bible never explicitly stated and demanded a geocentric worldview. Wasn’t that a good idea that people amended their worldview?

[John_Harshman]

@r_speir

You know perfectly well what I mean when I say your so-called ‘trees’ are really in fact only pyramids.

I really don’t know what you mean. What do you mean?

@r_speir

At the bottom of your study - the bottom of the pyramid - is only one substance, and that is DNA, the thing we all have in common.

Again, I have no idea what you mean. To be fair, neither do you.

@r_speir

You have only shown we share DNA like all other living things.

I’m sorry. There’s nothing I can do for you until you admit you have a problem. Did you even look at the paper?

[r_speir]

@John_Harshman

I really don’t know what you mean.

The further back in time you go (to the LEFT WITH THE ARROW), the broader the baseline. And that baseline is simply the DNA that God made all living things to share. The big red box with the red X in it signifies the BOTTOM of the pyramid. There is nothing remarkable about this study. You have not tied us to a great ape ancestor because this NOT a true ancestry tree. It does not narrow to the left, but rather gets more broad. It is a sideways pyramid…not a tree.

[Mark10.45 (Mark McGowan)]

@AllenWitmerMiller

If the overwhelming weight of the scientific evidence within the world God created conflicts with my preferred interpretation and translation of some passage(s) of the Bible, at what point am I willing to consider that my Biblical hermeneutics are flawed (and perhaps misled by popular Christian traditions?)

Amen…it’s odd for me as a new Christian that I am now associated with a group of people that cannot see truth in science (if it conflicts with their prior beliefs). It seems to me that all of creation (nature/life/evolution/science) is just as much a fingerprint of God as the bible and neither is more important than the other.

@GutsickGibbon had some good informational videos (youtube) on the chimp/human genome comparisons that laid it out for me in easy to understand layman format. (with cool animation too!). It seems obvious that we are related (with other large apes also, can’t remember the names now), and I don’t understand why some Christians would insist that a misunderstood or vague scripture is more important to hang on to than that obvious scientific truth.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@r_speir

It does not narrow to the left, but rather gets more broad. It is a sideways pyramid…not a tree.

Wow. I used to teach graph theory / network theory. Believe me, this is a tree. It displays a summary of the underlying data in a very convenient way.

[colewd (Bill Cole)]

@Mark10.45

. It seems obvious that we are related (with other large apes also, can’t remember the names now), and I don’t understand why some Christians would insist that a misunderstood or vague scripture is more important to hang on to than that obvious scientific truth.

This is a scientific hypothesis but the claim that both share a common ancestor is not tested. The DNA sequences are similar but this is a piece of the story. There are large gene expression and alternative splicing differences.

This is not an obvious “scientific truth” such as bacteria adapting to antibiotics which is a tested hypothesis.

[r_speir]

@AllenWitmerMiller

Believe me, this is a tree

Think of nested hierarchies. They give the illusion of a tree when in fact, in the below diagram, all 7 organisms share Vertebrae, 6 share Bony Skeletons, 5 share Four Limbs, 4 share Amniotic Eggs, and two groups of 2 share Hair and Post-orbital Fenestrae. You are fooled into thinking that they all have a common ancestor when in reality a pyramid best describes their relatedness.

[T_aquaticus]

@colewd

This is a scientific hypothesis but the claim that both share a common ancestor is not tested. The DNA sequences are similar but this is a piece of the story. There are large gene expression and alternative splicing differences.

Gene expression and alternative splicing are both the result of DNA sequence. Human adult lactose tolerance is a perfect example where a mutation in the promoter of the lactase gene allows for continued expression in adulthood.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@T_aquaticus

Human adult lactose tolerance is a perfect example where a mutation in the promoter of the lactase gene allows for continued expression in adulthood.

This also brings to mind the various creatures (humans and guinea pigs included) which can’t biosynthesize Vitamin C—and that a study of their genetics yields another beautiful set of tree diagrams:

The Genetics of Vitamin C Loss in Vertebrates

And regarding a prior post, it’s as if @r_speir’s “pyramid” is a stand-in for a Venn diagram. (??)

[r_speir]

@Mark10.45

Amen…it’s odd for me as a new Christian that I am now associated with a group of people that cannot see truth in science (if it conflicts with their prior beliefs)

Can I say something with full respect for you as an individual but something that also includes a warning?

You are far too green in this thing of Christianity and science to be making such declarations as above. I am going to speak to your spirit because I know that is the language you understand most. Please prayerfully consider that nothing in science should be taken at face value, but everything, (remember the Scripture to try the spirits whether they be of God) needs to be weighed and tested against Truth.

Please be more cautious in your approach to high-sounding scientific jargon that is above your understanding.

[AllenWitmerMiller (Semi-Expired Professor & Minister.)]

@r_speir

Please prayerfully consider that nothing in science should be taken at face value, but everything, (remember the Scripture to try the spirits whether they be of God) needs to be weighed and tested against Truth.

I agree. The same rule should be applied to hermeneutics. Even your hermeneutics.

God has revealed his truths in his scriptures and in his creation. The pattern I see emerging is that you refuse to consider the truths revealed in his creation—and confuse your personal hermeneutics with a standard of absolute truth.

@Mark10.45 has also recognized the truth of Proverbs 15:22: “There is safety in many counselors.”

When we assume that we have a “corner” on all truth which everybody who disagrees with us lacks, we are especially prone to overlook the truths which God has revealed.

God said that his creation is “very good”. So don’t reject it out of hand whenever you are confronted by its truths.

[colewd (Bill Cole)]

@T_aquaticus

Gene expression and alternative splicing are both the result of DNA sequence. Human adult lactose tolerance is a perfect example where a mutation in the promoter of the lactase gene allows for continued expression in adulthood.

To some extent you are right.

The bigger issue is these differences change protein frequency and protein types in the case of alternative splicing. These are factors that can have profound differences in embryo development.

[T_aquaticus]

@colewd

The bigger issue is these differences change protein frequency and protein types in the case of alternative splicing.

Alternate splicing is also the result of DNA sequence. If you have two genetically identical cells in identical environments you get identical splicing.

If you think I am wrong, the please explain why alternate splicing can be different.

[John_Harshman]

Incidentally, your pyramid only exists because the characters chosen for display fit into a ladder, except for the last two. Notice you had to split the pyramid step in half at that point. There, you have the beginnings of a tree. If the original tree had displayed characters on the currently empty branches, which it easily could have done, and put in more branches, subdividing the tips, your pyramid would be forced to look more and more like a tree. In other words, this pyramid is an artifact of your limited perception and the particular tree you chose to model, poorly.

[John_Harshman]

@r_speir

The further back in time you go (to the LEFT WITH THE ARROW), the broader the baseline.

No, still don’t know what that means. Do you mean that the further you go back, the more sequence similarity there should be between created kinds? But there’s no reason to expect that similarity to show a nested hierarchy. The only reasonable expectation from your model would be what’s called a star tree, just a bundle of branched coming together only at the beginning.

I have to say that you’re very bad at explaining your points. You just repeat the same words over and over.

@r_speir

They give the illusion of a tree when in fact, in the below diagram, all 7 organisms share Vertebrae, 6 share Bony Skeletons, 5 share Four Limbs, 4 share Amniotic Eggs, and two groups of 2 share Hair and Post-orbital Fenestrae. You are fooled into thinking that they all have a common ancestor when in reality a pyramid best describes their relatedness.

Nope, still not getting what you think your point is. The pattern you show is exactly what we would expect from a tree of relationships: the characters shared by all are the ones that evolved first, at the base of the tree.

@colewd

This is a scientific hypothesis but the claim that both share a common ancestor is not tested.

How would you test it? What other explanation can you come up with for the data? In this case I ask specifically about the paper I cited for @r_speir, this one.

For those following along at home, that’s Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, et al. (2011) A Molecular Phylogeny of Living Primates. PLoS Genet 7(3): e1001342.

[thoughtful (Valerie (non-scientist))]

@T_aquaticus

I am asking if I understand your worldview. Would it be correct to say that you don’t care about the scientific evidence?

I definitely do care.

[colewd (Bill Cole)]

@T_aquaticus

If you think I am wrong, the please explain why alternate splicing can be different.

I agree with you most issues in the cell we can point to DNA having an effect. Some of those effects are indirect. The point is from the outside that looks similar (by sequence comparison) can operate very differently. Different AS patterns produce different proteins as you know.