I am preserving this answer I made in a social media post because it sums up well the case I have sometimes made that a reasonable conclusion is the Cambrian explosion shows that naturalism isn't a good total explanation for the life we see on earth.......
When I say I am using science to challenge scientific conclusions, that's just how regular science is done. But what it can't do, and I am not claiming that it can, is say "so the scientific conclusion is that there was a supernatural act here". I am NOT claiming one can get to that point with science. Science, as it is conceived of today, is a search for NATURAL cause and effects only. It is utterly blind to God's direct action (that not done through Laws of nature which if He is, then He set up to operate) . This even if God were standing right in front of it.
Let's pretend that we were there at the account of Christ's first public miracle, turning water into wine. , if we were at the wedding in Galilee where Christ changed water into the best wine without ever touching vessels belonging to other people and even sending other people's servants to fetch water from a third-party source, science STILL cannot conclude that this was a divine act. ALL it can say is "we don't know what the natural cause of this event was but we can keep searching". It would be an anomaly.
I nevertheless claim that in that situation it would be reasonable to suppose that this Jewish religious figure had indeed performed a miracle. It doesn't mean that I think the search for natural causes should be banned. We could go right on looking for them. IOW, it would not stop science or scientific study of the question. But it is an acknowledgement that it is reasonable to think there may not be a "scientific" solution. To science, it would be an anomaly. That's as far as science can go, but it isn't as far as we as humans can go. Science may not be able to conclude it was a miracle, but we can.
Whether or not other claims of miracles were valid or invalid would be irrelevant to our evidence here. Whether or not other people had prayed for miracles and received none would likewise be irrelevant. The evidence that this religious figure provided a miracle just to save the host embarrassment might mean that He has access to God that the other folks praying for a miracle do not have. We need not consider their failures. Maybe they are mostly clowns that God doesn't entrust with His supernatural power. I don't claim to be fit for it either.
I've got an atheist friend named Wesley. We once worked together. He too kept saying "there is no evidence for God or His actions". I kept trying to get him to say what he would consider valid evidence for God. He kept refusing to be pinned down. Finally, in exasperation, I said "what if an angel appeared to you today and told you that the God of the bible is the Creator of the universe?". He said "I would assume that I was having a psychotic episode."
That's closed minded. He has made his mind up in advance that nature is all that there is, and nothing will change his mind about that, even his own mind and eyes are not to be trusted over his a priori conclusion that there is no God. Well, so far as I know, he is still an atheist. Because of the evidence? No. He won't let himself be anything else, regardless of evidence.
If that's you, there is no point in proceeding. There is no amount of logic, fact, or reason, that could shake Wesley of his conclusion. Evidence only works on people open to evidence, and he wasn't. If any natural explanation, no matter how desperate, is preferred over any supernatural explanation no matter how reasonable, then it isn't a problem of the evidence, it is a problem of the spirit. Last I talked to him he was going through a lot of trials, and I hope that he has changed, but I don't know.
So what am I trying to do with the Cambrian explosion? I NOT trying to prove with science that "God did it". I am trying to show with science that it is REASONABLE to conclude that the Cambrian explosion is an anomaly for which there is no good naturalistic explanation. That's as far as science can go. Logic, reason, and fact, will have to take it from there. But one cannot do that if one starts with the assumption that nature is all there is and so all thought of supernatural causes are wrong. That is very tight circular reasoning. It is assuming the answer to the question before it is asked.
Now when you appealed to all of the questions that men once attributed to direct divine action that we now know are the laws of nature at work, that was a long way of saying that I am making a "God of the Gaps Argument". And I am. But while such arguments can be invalid, I contend they are not invalid when certain parameters apply. If it is a question on which we have little natural knowledge (as was the case on almost everything a few hundred years ago) then yes, a God of the Gaps argument is a bad argument. If it is a problem we were not aware of until recently, so that science has not had much time to find a natural explanation, then yes, a God of the Gaps argument is a bad argument. But that isn't the case here. Listen to this quote from Charles Darwin...
//“[As to] why we do not find rich fossiliferous deposits belonging to these assumed earliest periods before the Cambrian system, I can give no satisfactory answer. The case at present must remain inexplicable; and may be truly urged as a valid argument against the views here entertained.”//
So science has been aware of this problem for a very long time, and has being trying to find a reasonable natural explanation for a very long time. One hypothesis was that ancestors for these creatures existed, we just hadn't found their fossils yet. Another was that they were there, but conditions were not right to make fossils until the Cambrian. Those were proposed natural explanations for the lack of evidence to support the origin of animal phyla.
Well they kept looking and after 150 years what they found was the worst possible outcome for naturalism. It could hardly be a bigger disaster. They DID find fossils in pre-Cambrian layers (so the hypothesis that things were there but they could not fossilize was out). But the fossils they found were of Vendian forms, which most of them are honest enough to admit are not good ancestors for what we see spring up in the Cambrian. I am prepared to show why the minority who think they do are reaching for straws. Further, the more they look, the more explosive the Cambrian Explosion got. It wasn't stretched over the whole Cambrian period, but just a fraction of it. Then they keep making finds like the Annelid find I have been trying to discuss- things they thought did not come along for 200 million years show up way early. I am prepared to show this happens again, and again, and again.
After 150 years of being aware of the problem, and all their looking only makes the problem worse, I say a reasonable person, one with an open mind and not utterly committed to the idea there is no supernatural no matter how big the anomalies get, should be open to the idea that the reason they are only in a deeper hole after 150 years of digging is that there is no natural explanation.
To see me at my grizzled worst and what I mean on the God of the Gaps in more detail... https://youtu.be/fsEeO5SPIGM?si=dl4M0GLIhVMYjf9n
