The most impressive one I know is the two families of antifreeze proteins, one found in the Arctic, the other in the Antarctic. The functional part of both is nearly identical even though they appear to have very different evolutionary origins. In this case, however, that functional part consists of a single triplet of amino acids repeated many times – something so simple that convergence on it by chance is not unlikely.
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“Methodological naturalism” is a popular but bad name for “I am assuming that God’s ordinary patterns of running the universe are likely to apply in this situation, as an initial working assumption”. Science can only do certain things; it uses natural methods.
If someone claims that a supernatural cause has a regular physical effect, it is possible for science to examine that supposed effect. For example, you can get a bunch of people, check their birthdays, and see if the horoscope actually is better advice for people born at one time versus another. But the Bible shows miracles as distinctive events, exceptions to the normal course of events. If one could load a bunch of chemistry equipment into a time machine and have it analyzing the water at the wedding in Cana, it wouldn’t give us anything else useful for data. The Journal of Irreproducible Results made the point well with an article claiming to test whether angels could be used in place of lab rats. As they went through the walls of the mazes and weren’t interested in rat chow, it did not work well. Obviously silly, but one can’t stick an angel in a test tube and see what happens; indeed “You shall not put the Lord your God to the test”.
If you walk, drive, etc. to church, you are using a natural method. Would you not be more spiritual to assume that, if God really wants you to go to church, he’ll send an angel to carry you there like the apocryphal account of Habakkuk in the lion’s den? (Not real sure why there wouldn’t be an easier way to get a snack to Daniel than time-travel for Habakkuk.) But that is putting God to the test, albeit less dramatically than jumping off the temple.
Everyday experience tells us that assuming natural methods are in operation is a reasonable expectation. That’s also the pattern that we see in history, including the biblical accounts. When someone claims to see Jesus in their toast, it’s a pretty safe assumption that it is not actually miraculous. People claiming to actually work miracles are generally frauds, and people who admit that they achieve miraculous-looking effects by trickery are generally able to replicate those claimed acts.
That does not mean that it is inherently unreasonable to look for possible examples where natural law does not seem to work. But it does mean that those examples are likely to be uncommon. And the evidence needs to be good. For example, the Raelians were making headlines with their ID-type claims to have cloned humans, until it became obvious that they were not going to provide any evidence that their claims were true.
It is important to distinguish between multiple components of ID claims:
Is this particular example actually difficult to explain evolutionarily?
Is the reasoning good? For example, simplicity, not complexity, is more characteristic of intelligent human design. Randomness is complex, order is simple.
Should we expect to find lots of examples of God working by non-natural law means? Although I don’t know a specific theological principle, the pattern is minimizing the use of such intervention-style miracles. Turning water to wine instantaneously and without using a grapevine doesn’t occur normally, but it had to be served in the ordinary manner - the guests only thought it odd that the good stuff was saved for so long. Just the right wind angle and strength would create a seiche parting one of the Bitter Lakes. But it’s not as if this happened every afternoon and the Egyptians never noticed; the timing and the advance notice given to Moses are the exceptional components. Thus, there is no particular reason to think that we should find gaps in evolution. That doesn’t prove that there aren’t any, but it means that we should not demand to find them.
The burden of proof is on whoever is making a claim.
There is also a semantic question - if I draw a conclusion from the fact that science is not giving an answer, is that a scientific conclusion?
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That’s a critical point.
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This is not my argument.
I started this discussion by the question what makes that I see intelligent desing everywhere in biology and others don’t.
Then, it was asked if I could give examples of irreducible complexity. That’s the title of this topic.
I didn’t mention the nuclear pore complex. Instead, I have given extreme simple examples:
I seen irreducible complexity in the lens of the eye, in a hair and in an eye lid.
It would be nice if someone can give the mechanisms, that could have caused the origin of these so simple structures.
No answer until now.
Now you speak at the level of the whole genome. However, at the level of the gene, its effect is profound. In practice, regions without actual recombination are much longer. A hot spot doesn’t mean that recombination takes place every meiosis. For instance when the size of a hotspot is 1 kb and the activity is 0.4-300 cM/Mb, then the activity is 0.4- 300 *10^-3 cM/hotspot. This means a recombination frequency range of 0.4- 300 per 100.000 generations per hotspot. In the other regions, this frequency is ten times lower than the lower margin for a hotspot. In a cold spot (normal gene sequence), the chance of recombination between neighbouring nucleotices per generation is in the order of 10^-10, if my calculation is correct. Remember: it is thought that we are only 300 000 generations apart from apes.
And misses the most relevant third category: organized complexity.
WEAVER1947-libre.pdf (d1wqtxts1xzle7.cloudfront.net)
It’s so basically intuitive that an infinite series cannot be made through successive addition, I find it easier to hold to the possibility that events don’t actually happen 
Remember this one, ChatGPT said it about as well as I have ever thought possible
That’s only the counting issue. As I said, depending on the nature of the universe it could be infinite and thus have an infinite set of galaxies, or stars, etc., or it can be ludicrously large – and the question is still an open one. If the universe is infinite, “successive addition” isn’t relevant because the universe is not assembled one item at a time, it was “assembled” all at once.
And in tune with the topic, an infinite universe is not irreducibly complex, it’s just mind-boggling.
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Link returns an error.
I think only the first one is a challenge. How about a biologist or two weighing in one this?
An infinite number of future recombinations is mind boggling because it is impossible for it to ever occur. How the past is considered, kind of depends on how you want to look at it. Talk about being given a choice.
Sad! For me it works.
May be when you google?:
SCIENCE AND COMPLEXITY
By WARREN WEAVER
Rockefeller Foundation, New York City
“Science and Complexity”, American Scientist, 36: 536 (1948)
Only if you insist that the starting set is finite.
If the universe started out infinite – in contents, not in time, since (as far as we know) time is accumulative and therefore additive – then it continues as infinite.
Cosmologists regard this as an important question, though sometimes I wonder why given that even though the observable universe is finite by definition (any three-dimensional, physical closed system must be) its contents are uncountable and thus functionally infinite. Though perhaps it makes a difference as to how the universe works on some fundamental level that I’m missing.
Found one that works:
That was a bit of a nostalgic trip; the format is like using an old microfilm reader, something I got boringly familiar with in grad school.
And for another reason: as a high school student I got to visit Rockefeller Center, and I think the Rockefeller Foundation was headquartered there at the time.
It was an interesting read. @paleomalacologist, since it was your post (#262) that prompted this, would you care to read the Weaver paper and comment?
It works just by looking at the occurrence of a single series of events, like cosmic recombinations, and seeing it proceed into the future.
But that is stepping back into a finite universe and countable events. An infinite universe from the beginning is not limited that way. And in an infinite universe if you select a finite set you’re no longer talking about the nature of that universe.
Put this way, the questions of seeing intelligent design everywhere, and giving a specific example of intelligent design are actually quite different questions.
I think all EC adherents see intelligent design everywhere as well, but in a bit different way, related to how all see God through creation as Paul stated in Romans 1:19-20, and to the way they read Psalm 139 and hold to God knitting us the womb, without abandoning the usual sperm-egg embryo development process. But, to say a specific biologic feature is a product of intelligent design and did not come about through natural processes or could not come about through natural processes is a high bar to jump. It would require showing that the required genetic changes were impossible by natural means, and in the Christian version of ID, that God could not have done it by the natural means he created but had to supernaturally intervene.
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Need to be grading finals, but from a quick skim:
There is a wide range of simplicity and complexity interconnected in nature. But the basic error of the ID argument is that complexity is not an indicator of intelligent design. Complexity is an indicator of complexity.
An eye lens is not irreducibly complex. It’s just an enclosed bit of clear stuff. The closer to the right shape it is, the clearer an image it can produce, but even a blurry image is useful - the complexity is completely reducible.
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Events and objects are countable. The choice is between looking at a universe that begins in the past or the present. But this is well beyond my initial comment to @Vanengelen about cosmic recombinations. We have also gone over this many times before. Feel free to write me privately if you want to continue the discussion.
A black swan event?
Seeing intelligent design everywhere, is like seeing God’s work in all things and yet it would seem like there is a parallel to that conversation Keener and Brown had with May about divine healing.
Just had to say that this is excellent, David. I’m gonna steal this entire post & hang onto it. 
Cheers.