Why are they unlikely through natural conditions? Optimization is exactly what evolutionary processes produce. Complexity is also an expectation of natural processes as discussed in Lynch’s famous paper on subfunctionalization.
Convergence at the molecular level is exceedingly rare, and I fail to see how selection of the same mutation in separate lineages would be a problem for natural processes.
no that is your defense in support of your own view that we cannot read ancient scripture. I read scripture an awful lot and what i do know is that rarely are your arguments even supported with scripture (so im not sure what study your are citing there)
Yours is an absurd argument given that:
note the images below when one follows the cross referencing. It is my habit to follow cross referencing to ensure its not my own words…thats the point. Its the internal consistency in the cross referencing below that clearly demonstrates me that you are completely wrong in your theology there!
I decided the whole thing was trash because of statements like this:
This suggests that the tree exhibits a higher level of optimization than would be expected in a purely random evolutionary process.
That and others showed that the idea is being tested against fiction, not against reality. Like this:
That’s not from the article, but it fits with the article’s repeated theme that evolution is random.
Which have yet to be found. It’s wishful thinking in search of confirmation.
Like the self-parking car software that can parallel-park cars in seemingly impossible spaces.
It is worth pointing out that genetic algorithms based on evolutionary processes often find more optimized solutions than top down designs by humans.
But YEC doesn’t even try to read ancient scripture, they just assume that their MSWV is correct and that of course the Holy Spirit was bound by that worldview that they grew up with. If you’re reading a translation without asking about the historical context you’re not reading ancient scripture, you’re reading a phantom created by forcing the text to speak in MSWV terms.
It’s no different than if you were to take a work of fiction written in tenth century Spain and read a translation without bothering to ask about tenth century Spanish culture – you’re going to miss a lot and get a lot wrong. Since the Hebrew scriptures are several times older than that, in an even more alien culture, the YEC approach is guaranteed to miss a lot and gt a lot wrong – like throwing most of the message of the first Creation account into the trash.
But He didn’t use modern words of men, He used ancient words. You have to read it as ancient words to know what was meant, and that means reading it as th ancient literature it is.
No, you only think they do because your logic sucks and you don’t understand what literature and even ordinary speech is. Your logic is like seeing a nail with a round cross-section and then looking at a barn wall with lots of round holes and concluding that someone took nails and pounded lots of holes into the barn wall.
We’re not even talking about theology except the theology of arrogance that demands that God had to speak in a way convenient to you so you don’t have to actually study to understand.
So have you admitted that Tom Clancy’s books are history?
But that’s precisely the part you’re not actually testing.
Again, that’s not what you’re testing for.
Let me summarize the situation. Phylogenies can show many kinds of patterns as a result of natural processes: everything from population bottlenecks to natural selection to APOBEC RNA editing can affect genetic diversity in a population, depending on the organism in question. Distinguishing these patterns from the simplest neutral evolution is indeed a reasonable thing to do – which is why an immense amount of scientific effort has gone into doing exactly that. When a colleague and I wrote a review paper on natural selection in the human lineage, we tabulated 40 different genetic tests for natural selection – and that was in 2006. There are many more today.
So no, there’s nothing wrong with coming up with tests of whether a phylogeny shows unusual patterns, although doing so without a broad knowledge of the tests that are already out there is not likely to be productive. What’s not valid, however, is treating any of the patterns that you’ve mentioned as somehow indicative of design. Every one of them is expected to occur as a result of processes that we know are occurring. “Design” is just being smuggled in without any scientific basis.
That’s what the Campus Crusade types couldn’t understand about our informal intelligent design club: we did not consider anyone’s scripture to be data; the conclusion of design had to come from our studies of science alone – no smuggling it in. The place of scripture was after the Design conclusion when the question became, “Is there anything that looks like the Designer trying to communicate with us?”
I’m replying to myself because folks can’t seem to get past the idea of Designarism to evaluate the hypothesis and preliminary analysis.
Here’s a brief summary of the means, methods, and approach, keeping a skeptic’s perspective in mind:
Means:
The core of the analysis is focused on whether a phylogenetic tree—constructed from viral sequences—shows signs of optimization or order beyond what we’d expect from random processes. The analysis uses objective, measurable metrics like Shannon entropy and Complexity-Specified Information (CSI) to assess the tree’s structure.
Methods:
1. Observed Tree: A phylogenetic tree is constructed using standard methods like maximum likelihood (ML) or Bayesian approaches. This tree represents real evolutionary data.
2. Random Trees: A set of random trees is generated using a null model (e.g., Yule process), which assumes no evolutionary pressures or optimization, providing a baseline for comparison.
3. Comparison: The observed tree is compared to these random trees based on specific criteria (branch lengths, complexity, efficiency). The key question is: Is the observed tree more optimized or ordered than the random trees?
4. Statistical Analysis: The comparison includes statistical checks to determine if the differences are significant or just due to random chance.
Approach:
The approach is grounded in objectivity:
• Algorithms like entropy and CSI use established mathematical formulas to quantify order and complexity.
• By comparing the observed tree to randomly generated ones, we avoid assuming the tree is optimized based on how it was built.
• The analysis looks for patterns that couldn’t easily be explained by random chance.
The goal is not to prove design or preconceptions but to see if the observed tree stands out against random expectations. The entire process relies on data, objective metrics, and statistical comparisons, not personal assumptions.
How do you determine “signs of optimization or order beyond what we’d expect from random processes”? Also, shouldn’t that be natural processes instead of random processes? For example, natural selection is the opposite of random and it is an active part of shaping genomes, especially compact viral genomes.
This seems to me to be at the core of the original question. If something seems more optimized than a current generally accepted description of the (not really random, but more to the point, natural) processes, then we have to take a deeper look at the “natural processes” we assumede, and think about whether there is some other influencing factor we didn’t consider.
The bottom line theological point is this. I do believe that God exists, and that God created this universe in which we live. I also believe that God knew what She (note that God is not male or female, any Male Chauvinistic Pigs out there; that is my only reason for using the less common female word) was doing when He created this universe - from a physicist’s viewpoint, including the time and space dimensions that we feel as we live here. If God wanted us to know for certain that He does exist, He would have easily left such a clear signature that it would be obvious, even to us humans. So anyone who tries to prove that God exists by examining evidence is wasting his or her time, since that is not something that God wants us to know for sure - along with a lot of other things. God did not tell each of us exactly what is straight from Him, or what is some human’s interpretation of what that person thinks God said. Here again, God put us into an uncertain world, expects us to deal with the uncertainty that we face, and learn from our experiences in this world, where we do get to experience things that we will not experience in Heaven.
So, No, oddXian, you do not have a method for proving the existence of God. If there is something that seems more optimized than our current expectations, we can easily develop different natural explanations that give the observed results.
And, No, Adamjedgar, God did not give us an absolute source of truth, that we can explicitly understand exactly what God wants us to do, and consider everyone who doesn’t understand what we “know” to be the truth in exactly the same way we do, is wrong. There are many steps in your assumption that you have a perfect source of what God wanted to say to you in the bible. The first is really insurmountable: God has chosen to put us into a world where we cannot even prove that God exists. Thus, there is no way that anyone can prove that any written thing absolutely came from God. I do personally believe that the bible was inspired by God, but that is a belief, not a statement of fact, no matter how much I do not want to even think about the possibility that I might be believing something that is not 100% true. And then there are all the other aspects of interpreting the bible, many of which St. Roymond has pointed out. And the question of what is scripture, and what is not.
My conclusion is that God does not want me to prove anything, just to witness to what I believe and why, and maybe that will help someone else have a better relationship with Him.
Right off the bat, I would wonder how the work in the opening post models natural selection, or if it does at all. This is especially true of viruses where in many cases the genomes are under strong selection, large effective population size, high mutation rates in the case of RNA genomes, and quick generation times. As a contrast, perhaps @oddXian could do an analysis of shared introns from complex eukaryotes, or even compare shared exons and introns to see if they behave differently in the model.
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