The fossil record fits best with progressive creation

Faith & Science Conversation
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Getting away from that tautology seems to me to be an impossible nut to crack with any scientific kind of nut-cracker. The materialist notes how convenient it is for the mystic that spiritual things are always neatly kept beyond science, and yet I don’t see how any definition of it could be otherwise. Science studies “nature”, so any aspect of anything we can study that way must be “natural”. And note that the definition of “natural” is every bit as difficult as supernatural, because to define one is to define the other (if we accept that every existent thing must be in one of those two categories - but not simultaneously in both if they are non-overlapping sets). The word “natural” or “physical” seem common enough in our discourse, but come to mean nothing useful at all when they are pushed by naturalist lips as meaning everything.

Anything that can be seen through microscope or telescope or be reduced to a formulaic predictive mechanism simply cannot be God in any Christian sense. Atheists can dismiss it as a convenience, but its convenience or inconvenience is not relevant the the question of the reality of it. Christians may indeed have some burden of scientific proof in the minds of skeptics that have demanded that. But many of us are happy to just leave that “burden” right where it is, since it won’t contain anything that will, in the end, be useful toward of life of faith under the Lordship of Christ. Burdens of proof (of the scientific variety) are for those who have restricted (whether for temporary usefulness and discourse, or in a more widely metaphysical way) their universe to that which they deem measurable. The Christian does find much of value in that world, but does not insist it is the sum of all existence. Indeed the very act of finding or awarding “value” (beyond personal preference) to anything at all already draws on something beyond the empirically measurable.

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This is why I prefer to define science by its methodology. Science tests falsifiable hypotheses using objectively and independently verifiable observations that can be repeated by others. No need to use the labels “natural” or “supernatural”. More over, science doesn’t exclude any idea. Instead, science has requirements for hypotheses and conclusions that need to be met before they can be considered scientific. If you want to call something scientific then you have to meet the requirements.

There are many atheists, myself included, who are just fine with religious claims being religious. The only time a rational objection can be made is when something is claimed to be scientific when it isn’t. We are told by theists that God isn’t allowed in science, but that misses the real issues at the heart of the whole discussion. As you state, there isn’t any way to incorporate God into science. The only conclusion we can draw from this situation is that religious beliefs aren’t scientific. Period.

On top of that, atheists are a motley bunch. There are atheists who believe in the paranormal and all sorts woo. Atheists also have non-scientific beliefs, such as the importance of family. I think there can be a lot of agreement about when science is useful and when it is not.

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I think this preference is fairly universal. Christians are asked to walk by faith rather than sight, but such an exhortation wouldn’t have been necessary apart from our obvious desire to make use of any sight that we do have. Much to agree on here.

[… realizing that I didn’t connect that thought very well, let me add here that I was thinking not just of formally recognized methodologies so much as commonly accepted practices of “trusting our eyes” when I quickly read that sentence. Perhaps the latter can be seen as the street-level application of the formally recognized philosophy].

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What did you think of my other suggestion?

Defining “the supernatural” is a toughie. …

When I think about the way I see the expression used it seems to mean “action caused by an intentionality not of this world”.

Does that square with what you think of as the supernatural?

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That sounds like a supernatural thing to me, though I shouldn’t imply that “supernatural” things or events are necessarily restricted to that.

[I’m not dogmatic about ‘supernatural’ actually having much real meaning in the end - if we were to know all. I do think it a mental category of convenience so we can have discussions like these. - and I am dogmatic about thinking that God is not a ‘thing’ within creation, realizing that this may contradict my opening-bracket comment.]

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From a biblical view, everything we see is really an outcome/evidence of the supernatural. John chapter 1 states that in the beginning was the ‘word’. Everything was created by God through the speaking of the ‘word’.
Just as a skilled author creates a story, God created life.

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Hi Marty -

Hope your Friday is going well.

To evaluate any inference, causal networks must be postulated, stochastic probabilities must be assigned, and evidence must be evaluated to arrive at a posteriori probabilities. I recommend Judea Pearl’s “The Book of Why: The New Science of Cause and Effect” if you want to explore this in more detail.

After more than a century of hard work by paleontologists, biologists, geneticists, and computer scientists, the theory of evolution can provide both causal networks and stochastic probabilities that can be used for inference.

I submit that progressive creation cannot. The theory provides no basis for determining whether or not anyone interested in the question should expect normal scientific explanations to prevail with respect to the relationship between mammalian genera, between mammals and reptiles, between fish and reptiles, between conifers and flowering plants, etc. Without such a framework–another term for a causal network, Pearl’s preferred term–there is no way to evaluate the evidence and draw an inference.

The difference between progressive creation and CSI is that CSI has a very robust causal network to help evaluate evidence such as fingerprints, gunpowder, DNA, etc. We can assign probabilities for whether a fingerprint was laid by the suspect depending on where it showed up, how similar it is at 150 points to the suspect’s print, how old the print is, etc., which creates the causal network that allows us to draw the CSI inference. Progressive creation has nothing at all like that. Thus the comparison between PC and CSI is,I suggest, inapt.

Actually, evolutionary biologists can build a causal network based on our observations re: rates of genetic drift, selection pressure, pseudo-genes, changes in regulatory gene networks, and the like. This allows inference to be performed re: the mechanisms of evolution.

The only thing unscientific about the statement “macro took place by micro only” is that it is not a formulation a scientist would use. The statement makes some assumptions about biological mechanisms that are refuted by evidence, such as the evidence that Levin advanced.

I do not see these as offering proof beyond disputation of God’s involvement with us. I see them as suggestive–gentle nudges, if you will. Far stronger is the testimony of God’s work with Israel, culminating in the ministry of the Messiah in first-century Palestine, in my view.

With all due respect, Marty, I don’t think you read Levin carefully enough. He offered several specific pieces of evidence that directly refute the main arguments Behe had advanced, such as:

  • Step-wise mutations toward chloroquine resistance in mosquitoes, as seen in the appearance of individual mutations(“steps”) in different strains.
  • The ability for proteins to interact using an “interface” of fewer than five amino acids.
  • The evolutionary steps manifested in the “antifreeze” protein amongst certain cold-weather fish.

Would you agree with me that these citations to evidence should not be regarded as “invective,” Marty?

May the Lord bring you many blessings this Friday!

Chris

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How do you reconcile this belief with your other belief that the history of life can be explained by purely scientific means? I mean, if “all nature is affected by human sin”, wouldn’t this physically affect the material world - eg, biological observations - in some way? If so, doesn’t this render a scientific interpretation of the history of life rather clueless and impotent?

I am not a YEC, and I agree with you that the YEC model is inadequate. It’s had to imagine why the Lord equipped a vegetarian lion with gigantic fangs and claws, for example! And why would a vegetarian cheetah need to be able to run at 60 mph?

Well, I take this “cop out” even further: I believe a mélange of the natural and supernatural is responsible for the entire history of life. The effects of the Fall’s curse adds a further mysterious and unknowable dimension to this history. So, in my opinion, interpreting the history of life through the lens of science (ie, purely materialistically) is an exercise in ignorance and futility. That’s the sort of dead-end road of fantasy and superstition that atheists choose to go down.

Why would creationists need a “working model” (ie, a scientific model)? Creationism isn’t science.

Scientists can imagine a “working model” for the history of life that “sounds ‘plausible’ to them”, but such models are vain, delusional and worthless, in my opinion. It is tantamount to scientists imagining a working model for how Jesus turned water into wine that sounds plausible.

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I don’t think the effects of human sin are “magical.” They can be observed and explained. They are things like climate change, pollution, destruction of ecosystems because of greed, gluttony, war, etc.

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@T_aquaticus

And those “most people” would be quite correct.

Why would you quibble with @marty on this particular topic?

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I am trying to figure out if @marty thinks the supernatural can be measured scientifically.

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Hi Chris. I doubt that my responses will satisfy, cuz I think we’d need too many hours. But I want to honor your post.

This is too aggressive for me. We make inferences all the time and the process is similar whether it’s formal or informal. I personally don’t feel the need to formalize this process at that level.

I’m honestly still waiting for someone to come out with a good mathematical demonstration that the math all works for evolution. If they are able to do that, I’ll change my tune. Little pieces of it, yeah.

Well, I’m not sure which is stronger. I see divine action in God’s first book and I agree that the Bible records more. I rejoice in all of God’s work, and hope sincerely that our different understandings of some of these details don’t cause you frustration.

But Chris, surely you can see the invective in the column. If Levin says something that is correct, that does not remove the bitter and hateful invective. Behe does not deserve that, and as far as I’m concerned, Levin’s need to do that undermines his credibility.

My response to your bullets: Behe never argued against the first point. Regarding the second, it is truly sloppy to say that examples of proteins with a two amino acid binding site refute Behe’s argument about those with a four or more amino acid binding site. Does Levin understand math?

The third bullet I could look into if I have time, but when the first two points are so poor, I didn’t bother. I did note that there could be something there, and that if Behe were writing the book today, he might need to adjust.

Let me summarize this book: malaria shows remarkable correlation in the calculated expected time for chloroquine resistance to show up, and the actual time it took. So run the the calculated expected time on protein complex binding sites, and the ones with four or more amino acids look to be beyond the edge of evolution.

If someone wants to run the probabilities and demonstrate otherwise, like I said, I’m open! I see no way for a process which is dependent on randomness (mutation) to provide enough information to the biosphere in the time available using only the processes which we know about.

Blessings, my friend!

Marty

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Lets use the human and chimp genomes as the basis for some back of the envelope calculations. Let’s also use some conservative numbers: 50 mutations per individual per generation (in line with direct observations), 25 year generation time, 5 million years since common ancestry, and a constant population of 100,000 individuals.

With those numbers we can determine how many mutations occurred in the human population over that time. We have 4 generations every century over 5 million years for a total of 200,000 generations. If there are 100,000 individuals per generation and 50 mutations per individual that gives us 5 million mutations per generation. 5 million mutations per generation for 200,000 generations gives us 1 trillion total mutations, or 1E12.

So how many mutations separate humans and chimps? About 40 million. If we assume that half of those mutations happen in each lineage that is 20 million mutations in the human lineage that were kept, or 20E6. There were 1E12 mutations that did happen. This means that out of all the mutations that did occur in the human lineage only 0.002% had to be kept.

The math seems to work out.

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@T_Aquaticist

When i read the discussion, @marty says “of course not”… and then you contradict him on what at most is a quibble.

So it doesnt seem like you were happy with Marty’s position.

And since you are supposed to be putting yourself into the mindset of a Christian Evolutionist… why would it be a problem if God is helping evokution along without any way to prove it with Science?

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He seems to contradict himself.

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@T_aquaticus,

It would seem the man you are quoting [that I quote above] is contradicting himself.

The one thing @Swamidass and i agree upon is that supernatural activities… by definition… cannot be distinguished between God or inadequate information regarding nature.

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That was my judgment as well. There also seems to be a conflation between detecting an intelligence and detecting the supernatural which is where I probably went a bit overboard in nit picking.

That is certainly a subject for an interesting debate someday, but for now I am more than happy to work from that axiom.

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@T_aquaticus

I was speaking about you. I was quoting YOU sounding contradictory.

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T – thanks for pointing that out, and as far as it goes, you are right. I am not explaining my issue clearly, so I need to do that. You’re right to focus on probabilities and instead of just saying “math,” I need to say “probability as applied to initial protein discovery” or “the arrival of fitness.” @Chris_Falter and @gbrooks9 - you guys may also find this helpful.

But please, just a note to all, read the full post before you react to the early parts.

A median human protein is about 275 Amino Acids (AA) long. Given that we have 20 AA’s to select from, the odds of DNA coming up with a sequence creating an exact protein that length by random mutations would be roughly 1 / (20 ^ 275) or 6e-357. Next we have to approximate the numerator, which would include 1) potential alternative structures that could do the same thing, 2) numbers of cells and generation times where said sequence could be incubating (this includes time, about 1.3e17 seconds since earth became somewhat habitable), etc. Other ideas might increase the numerator, but you hopefully get my drift.

The problem is that even with ridiculously generous assumptions for the numerator (like “only half the AA’s actually matter”), the denominator is just too large. Once we have a working protein, evolution can optimize it. But getting the first working one for a particular function, priceless. Given that there are only about 1e80 atoms in the universe, hopefully you can start to see how the possibility of even a single human protein forming by fundamentally random process is infinitesimally small. (Note that “random” means within the laws of physics, with various distributions for each type of possible genetic change.) So wherever any given protein or its analogues first arose in the history of life, that’s where the issue applies. The arrival of fitness.

But then the problem compounds further and this is also important: probabilities like this don’t just add. They multiply. Since many proteins have significant function only in complexes, we need to multiply those improbabilities. And since those complexes have meaningful function only in a metabolic pathway, there is additional multiplying of probabilities. Again, we might be able to add something to the numerator at each level, but in general, with each step as we look at proteins in cells, the probabilities spiral down out of control. We need to get within some few orders of magnitude of one but we’re so far away from there that it’s absurd.

I conclude “there’s clearly something going on that we don’t know about at this time from our science.” That “something” would need to greatly multiply the numerator and bring the ratio to reasonable values. There are a few options, which include 1) the possibility that the functional protein space for any given function is actually very large and we just haven’t figured that out yet, 2) there is another process or two going on that we have not discovered, or 3) there is someone, an intentional intelligence, monkeying around with the biology. I’m open to suggestions of other possibilities, and there may be some I have thought of that don’t come to mind now.

This is all clearly “back of the napkin” math, but the numbers are so overwhelming that a formal and exact calculation becomes moot. (Yet then when someone tries a more precise calculation like Behe did, he gets lambasted and bashed and hated on per Levin, and his arguments are not represented fairly or adequately countered. I tend to think that it’s partly because Behe’s arguments cannot be fairly countered, and for far too many people this is more about winning than figuring out the truth of the matter.)

On the other side, some, like Dennett, argue for this incredible “algorithm” called natural selection (NS), capable of amazing and awesome things, and how he cannot understand the darkness and ignorance of those who do not embrace it as a great creative force of life. But NS is not in any way “creative.” It can only select from what is presented to it by this fundamentally random process. And until a metabolic pathway is to some at least trivial extent “working,” doing something useful, however poorly, NS has nothing to select. So some level of “fitness” needs to “arrive” first.

In addition some use arguments like coin flipping and “selecting” the ones that come up heads. That analogy so grossly misrepresents what is going on in biology that those who press it should be ashamed.

There is a good video on the teleological problem here The Teleological Argument (What it really says) - YouTube and similar probability problems exist for the formation of a life-supporting planet, origins of life, and, as per this discussion, the development of life. I look at all this and conclude that there is more than luck going on. Only an intelligence vastly beyond our imaginations could have put all this together. If I did not believe that Jesus was who I think he claims to be, the vast power of this intelligence would sometimes frighten me – we are way too small, and from nature alone I would not know how to interpret this being’s intentions toward us.

So I find regarding evolution by natural processes that only the “probability against” finding meaningful metabolic pathways is too overwhelming. And that’s based on the science. Until someone can show a realistic means for accidentally getting the first biologically useful proteins (the numerator is massively expanded) for any given protein complex, I expect I will remain a skeptic.

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Hi Marty,

I described how science is done. If you don’t want to go through the process, that’s completely fine with me. I would only suggest that you not claim that your argument is based on science and math if you don’t want to do the work.

Of course, I also note that you made an effort at a somewhat more rigorous analysis after you made this statement. Tip o’ the hat to you, Marty. I respond to that below.

Wait no more. Then check out this new tune.

I agree 100%.

These discussions require spiritual and emotional work, along with the scientific and logical work. That does not mean we should get frustrated. And I am sure that some of us on the forum occasionally tempt you to say, “I’m outta here!” So let’s just agree to march on as best we can, enabled by God’s grace and mercy toward us all.

Yes, he serves his entree of evidence and conclusions with a side of invective. I agree with you that, given the invective, we should be careful in evaluating the evidence and logical inference. I also think you agree with me that we should not ignore the evidence and logic, either.

I will accept in arguendo that the probability of a chloroquine resistance mutation is 10-20 per Falciparum cell, rather than 10-10 as Coyne and Levin seem to object. However, this does not begin to address the fundamental problem that Levin, Coyne, et al. point out: Behe’s model does not include survival analysis.

Because of this serious omission, Behe’s model ends up assuming that any event of chloroquine resistance (CR) is I.I.D with respect to its co-occurrence in the genome with other CR mutations. It is only by this unwarranted assumption that we can derive the probability of multiple mutations appearing in one genome by multiplication. In turn this unwarranted assumption leads to the further erroneous conclusion that the the accumulation of such mutations is beyond “the edge of evolution.”

However, when survival analysis is incorporated into the model, the probability that a second CR mutation will appear in the same genome as an earlier CR mutation approaches 1. Consequently, the only probability that needs to be considered is that of one CR mutation, which is 10-20. In a world where 1020 new Falciparum cells come into existence every year, this is easily within the “edge of evolution.”

While this argument is inherently complex, I have tried to simplify it as much as possible. I hope I have succeeded. Please offer any feedback about anything that needs to be clarified. Thanks!

I think you misread Levin here. His claim is that binding can begin with just two amino acids, then be refined into a stronger binding of say 5 amino acids by further mutations.

Speaking of invective…

This is the linchpin of your back-of-the-napkin analysis, Marty. I appreciate the effort that you went through to calculate probabilities and explain them. However, your analysis does not take into account two important considerations;

(1) Survival analysis - The genetic instructions for complex proteins can evolve over time from genetic instructions for simpler proteins. Each step/mutation along the way is well within the edge of evolution, and the probabilities of individual mutations should not be multiplied.

(2) Every day, something even less probable than the formation of that protein happens 360,000 times: A baby is born.

Consider that every cute, lovable baby has about 25,000 genes. Conservatively assume that every gene has just 2 different alleles. That means that the probability of a baby being born with the allele set of Marty is 2-25000, or 10-7526.(*) Couldn’t happen! There are only 10120 protons in the universe. But yet it did; Here is my friend Marty in the land of the living. And here, too, is Chris Falter, with the same inifinitesimal probability of existing (10-7526).

What are we to make of this? Simply that there is no need to explore the entire probability space. Once it is functioning, the stochastic process we call inheritance has a probability of basically 1.0 of producing really complex proteins. Our limit (our edge) is that we cannot predict in advance which exact protein chains will emerge, because any individual protein has such an infinitesimal probability. Just as the probability of 360,000 babies being born every day is basically 1.0, even though the probability of the birth of any of those 360,000 is on the order of 10-7526.

Here’s still another helpful analogy: suppose you have a bin of 357 fair dice. Each die is stamped with a tiny, unique ID. You stand on the top of an A-frame ladder in the middle of a basketball court with the bin. You shake it around as thoroughly as you can without compromising your safety, then you dump all 357 of the dice on the court. You carefully note the ID and face-up value of each die. What is the probability of your having observed the exact throw of the dice that you just observed?

The answer is 6-357, the same as the probability of the amino acid composition of that median human protein you cited.

So the conclusion of the matter is…you are special, Marty! And so am I! Let’s watch every episode of Mr. Rogers’ Neighborhood, while we’re at it. :smile:

Blessings,
Chris

(*) Assuming that the 2 alleles of a gene are uniformly distributed in the population.

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