https://en.wikipedia.org/wiki/Matryoshka_doll#/media/File:Russian-Matroshka.jpg
I know that the big one is the ancestral primate, and I’m the little one. But it looks like the big one is gorilla and the litttle one is a mouse lemur
Hi Joshua,
You misunderstood what I wrote. Here’s what I said:
they [“inoperable genes” and “nested hierarchy”] are not predicted by any parsimonious design hypothesis I have read. [emphasis added]
What I said, and what you said I said, are not the same thing.
Also, note that I included the word parsimonious. You evidently agree with me because you have said the model in question would be ad hoc. A model cannot be both parsimonious and ad hoc, would you not agree?
But let’s move on.
“Ad hoc” is a pretty good synonym for “is based on special pleading,” IMO.
IMO they are quite far apart.
A Christian who Accepts the Science of Evolution (CASE) would accept that speciation happens via mechanisms identified by biologists, such as fixation of different mutations in different populations, copy-and-modify mutations, constructive neutral evolution, horizontal gene transfer, natural selection, etc. Such a Christian would generally believe that God providentially and perhaps miraculously guides the whole process at every moment. (If it even makes sense to distinguish between providence and miracles, a discussion which is beyond my pay grade.)
The progressive creation adherent, on the other hand, tends to reject the mechanisms identified by biologists as an explanation for the diversity of life–at the level of class, phylum, and kingdom, at least.
Another reason the model you presented could be considered special pleading is that it would either: (1) be impossible to distinguish from standard evolution models, or (2) not be capable of yielding meaningful predictions. Here’s why: such a genomic copying model would necessarily involve one of two possibilities:
- A nucleotide-for-nucleotide copy of an existing genome, with the resulting new population being placed in a new environment for subsequent developments; OR
- A copy-with-modification in which the modifications set a new direction for the resulting new population.
The first alternative (nucleotide-for-nucleotide copy) would be indistinguishable from standard evolution models.
The second alternative (copy-with-modification) would make scientific predictions impossible because scientists would have no way to predict or even identify after the fact what modifications an infinitely wise and powerful Creator might have made.
So the 2 alternatives are copy-with-no-modifications or copy-with-modifications, and neither alternative yields a model which would be scientifically viable IMO.
Assuming this analysis is valid, I have nothing further to add. I’ve said quite a bit about why the model you have put forth in this thread leans heavily on special pleading and is not what a Christian who Accepts the Science of Evolution would favor. I leave the last word to you, should you care to say anything else.
Best,
Chris
1 Like
haha. I understand that. I just don’t “get” why nested hierarchies are such good evidence for evolution. Maybe it’s just me - maybe I’m terribly dense about it… It seems that when ever other arguments against evolution seem to have a lot of merit, and the argument for evolution over common design breaks down, the response is “but nested hierarchies!” It’s the trump card.
I was doing some searching; as far as I could tell this is the only paper everyone is citing. Interesting that everything that came up in google searches are forum posts and a few Evolution News blogs disputing this paper. Thanks for the explanation.
Because we know from the early history of studying them that retroviruses incorporate human genes. The first to be thoroughly studied were those that caused tumors in chickens and rodents because they carried activated versions of oncogenes found in the host genome: src, myc, ras, erbB.
There is no “huge mystery.”
Didn’t you recently write that you don’t understand nested hierarchies?
1 Like
limiting [it to] the “common ancestor” between Chimps and Humans was the most straightforward approach.It is worth noting that for a creationist who is concerned to show that there is no common ancestor of chimps and humans, this is highly relevant. For an evolutionary biologist who starts with all life being genealogically related, it is boring and uncontroversial that humans and chimps have a common ancestor. After all, so do all pairs of species.
4 Likes
Very simple, really. We naturally expect nested hierarchies to result from common descent with divergence. We have no other hypothesis that would naturally result in such a thing. Creation could do it, but we have no reason to suppose that it would unless there was an attempt to simulate common descent. And that involves a deceitful God.
4 Likes
Actually, no. The big one is all primates. In a nested hierarchy, everything inside the big doll counts as part of the big doll. Matryoshka dolls are actually a poor example of nested hierarchy. There would have to be a big doll with lots of little dolls inside it, some of them inside different medium-sized dolls within the big doll.
3 Likes
Ok, so it’s a requirement of evolution for evolution to make sense. But creationists can’t claim it would fit common design + evolution within kinds because it makes God deceptive. Therefore evolution is true, because a designer has to be good and any designer that makes something that men have decided is common descent isn’t good?
What about exceptions to nested hierarchy?
My strategy is to start with a nonthreatening case…
I’m afraid that it just muddies up the explanation for no gain.
Not at all. A designer doesn’t have to be good, but I doubt that you would accept a lying designer. Was I wrong about that? Evolution is true as far as we can tell, because it’s the only hypothesis that explains the data. A lying designer explains nothing, because that designer could have shown us anything he felt like, so his existence is compatible with any data at all. It’s a useless hypothesis.
What about them? We expect certain categories of exceptions due to simple homoplasy, lineage sorting, horizontal transfer, hybrid speciation, and, very occasionally, real convergence. That doesn’t change the general pattern, and common descent explains that pattern.
3 Likes
I’m not the pro, but I think this is backwards. Nested hierarchy is observed. Common Descent is the hypothesis that makes sense of it.
6 Likes
I happen to agree, but I “liked” this post mostly because you used the word “omphalosy”.
1 Like
You’re missing the crucial point: As you say it is a requirement for evolution. That is to say, evolution predicts that this observation will be made.
And in the video that is the subject of the thread, they calculated the odds against the ERV insertions coinciding with what would be expected under common ancestry just by chance to be astronomical - for just two species. The odds of this being observed across every single species that we have looked at, which is the case, are even lower by many orders of magnitude.
Creation does not make such a prediction. If you are 100% committed to believing in creation, you can if you wish imagine that the Creator created this pattern for reasons only known to himself. But that would be the case for any other pattern we might observe, so that is scientifically useless.
If we are going by the rules of science, then there is no question that evolution is the only plausible explanation for the observation. Of course, creationists are not obliged to utilize science as a basis to their claims. But then they should just come clean about this, rather than trying to make scientific arguments and doing it wrong.
7 Likes
Perfectly good question. The reasons are at least twofold.
First of all because it’s statistically unavoidable that even totally random DNA will recruit transcription factors and enable regulation of downstream genes. With a large enough sample of random DNA, you will be guaranteed that some transcription initiation-protein from an organism can bind somewhere in that DNA and initiate transcription.
Transcription factors can require as little as 6-8 basepairs of DNA to bind to and elicit transcriptional activity. It varies from gene to gene how large and specific the promoter sequences their regulatory proteins prefer. But they never have zero activity for dissimilar sequences. Chances are that a transcription factor that has it’s highest degree of preference for sequence (say) AGGCTAC will have some degree of association with sequences that are chemically/structurally similar to it, such as GGGCTAC. Here I have replaced A (a purine nucleotide) with G (another purine nucleotide). The purines are chemically similar.
In a 10 000 basepair genome (which is typical for retroviruses and LTR retrotransposons) chances are good that there will be at least one location that is either identical to, or at least very similar to “canonical” binding spots for human regulatory proteins. When it comes to LTR retroviruses and retrotransposons, they even have canonical eukaryotic promoter regions, complete with enhancers, a TATA box, and initiators, in their LTRs.
Second is retrovirus (and retrotransposon) selection. When a retrovirus enters a host cell and gets it’s own genome inserted into the host, it also needs it’s own retrovirus genome expressed. That means it’s under some selection to be able to recruit host transcription factors and express it’s own genes. So the virus basically has a sort of survival interest in being able to mimic host transcription binding spots(to look like it is part of the host’s own genome), just as it is also well known that it has a direct survival interest in mirroring the host genetic code(otherwise it’s protein coding genes could not be translated).
The alternative would be that it needs to come packaged with it’s own already-synthesized transcription factor proteins and RNA, but that would incur a size, weight, and metabolic cost that can negatively affect both the host-cell’s ability to churn out more virus, and the virus’s ability to infect new hosts. So it simply works better (from the virus’s perspective) if it just “looks like” host DNA to the host. Viruses generally evolve much faster than host nuclear DNA, so it is extremely unlikely that any host will ever be able to “out-run” a retrovirus in a sort of transcription-initiation and regulation arms-race (so the host relies on the evolutionary capacity of the adaptive immune system instead).
In addition to the above links that explain normal eukaryote transcription-initiation and regulation, see also these articles that address the topic of getting reproducible gene-regulation activity from even random DNA:
https://www.pnas.org/content/early/2013/06/28/1307449110
How HIV (a retrovirus) gene regulation works:
6 Likes
Because common design + evolution within kinds wouldn’t produce independent but mutually concordant nested hierarchies unless God was being deceptive.
Think about it: A common designer is making protein randomin A for 10 independent kinds. This protein needs a 50AA stretch as a spacer, but absolutely any amino acids can be used in that region so long as there are 50 of them and you get identical function. A designer might decide to fill each stretch with a random sequence, or all of them with an identical sequence, or any of a number of other possibilities. The designer then needs to make randomin B (with a 42AA spacer) for those 10 independent kinds, and has the same options.
Now here is the question: What option could the designer pick such that the nested hierarchy of the 10 randomin A sequences is concordant with the nested hierarchy of the 10 randomin B sequences? Because it is absolutely true that both will form nested hierarchies no matter what, but that doesn’t matter since it is the mutual concordance of the hierarchies that actually matters.
Random fills are obviously out. You would get mutually concordant hierarchies within kinds, sure, but we need to explain the concordance between kinds. What about starting them identically? Well, no, that won’t work either. You would still get mutually concordant hierarchies within kinds (obviously), but you still can’t get concordance between them.
So what would work? The only thing is the designer starting with mutually concordant hierarchies for both proteins! But if the two spaces function identically regardless of sequence so long as they are the correct length, why introduce a completely unnecessary consistency between sequence identity, when the only result is to make two unrelated organisms look more related than they actually are?
So no, the creationist can’t claim our observations of nested hierarchies would fit common design + evolution within kinds because that actually wouldn’t fit!
2 Likes
That certainly isn’t true. If, for example, the designer makes all the sequences identical, there is no nested hierarchy. If he fills them all with randomly chosen AAs, there will be no nested hierarchy, though it’s probable that a likelihood analysis (but not parsimony) would come up with a single “best” tree. But having a single best tree is not, for that very reason, a sign of nested hierarchy. For that, we have various statistical tests. And the random data would not pass such a test.
Of course it would fit. The advantage, if you want to call it that, of common design is that anything at all would fit: identical sequences, random sequences, nested hierarchies, quinarian relationships, crossword puzzle clues. Anything.
A nested hierarchy is like a family tree in some sense, because both show common descent, so I would use the concept of a family tree to demonstrate why nested hierarchies are good evidence for evolutionary.
You have two parents, and each of your parents also have two parents as well. This necessarily means that a reconstruction of your family tree must place you somewhere on that tree. If a stranger came along and claimed you were not really a child to your present parents, it would mean that a reconstruction of your family tree would place you on a tree different from that of your current family. You decide to verify the stranger’s claim by having your genome, and those of your family members including your great grandparents (assuming they are alive) analyzed.
After analyzing the genomes of your family members, it was discovered you always appeared in the generation before the last generation: the last generation is that of your kids. This observed pattern is best explained by common descent, that is, a clear line of descent exists from your current great grandparents to your kids through you.
Of course, the stranger could claim you were designed by aliens or some rogue scientists in a way that makes your genome, when analyzed, place you in the pedigree of your current family. Alternatively, the stranger could allege that the genome analysts, your current family and yourself are in on a big conspiracy to hide the truth for some unknown gain. While these alternative explanations can explain the pedigree pattern, they are ad hoc and not supported by any data. The most parsimonious explanation for that pattern would be common descent.
Similarly, if a group of modern organisms share a common ancestor, then we should observe a generally consistent nested hierarchical pattern from genome and/or morphological analyses, and that’s what we see with regards to humans and other apes. Hope this helps. Corrections from experts will appreciated as well.
2 Likes
If all of the sequences are identical, then it will form a hierarchy based on the rest of the sequence, since the only necessarily constant region in my hypothetical was the spacer.
It will resolve to a nested hierarchy when you run the data through the algorithms, which was my point.
So yes, either case will resolve to nested hierarchies.
This is the core of your misunderstanding of what I am saying. The creationists are claiming that you can’t infer a ‘real’ hierarchy because the algorithms will resolve any data set into an ‘apparent’ nested hierarchy. And it is the appearance of the nested hierarchy that needs an explanation, not the reality of a nested hierarchy. And any data set for a single trait will produce a nested hierarchy.
Only if you allow intentional deception, which was the point.
1 Like
Given the genetic evidence as demonstrated in the video, why would you not conclude that humans and chimps belong to the same baramin? YEC presents the baramin as a scientific construct. What definition of a baramin allows creatures which are more genetically dissimilar to fit evolution within kinds, while not recognizing the same for humans and chimps?
3 Likes