What Does this Failure to Develop Resistance Say About Unaided Macro-Evolution?

So it turns out that this tuberculosis bacteria has been trying for seven decades to develop resistance to a particular anti-biotic that will still permit it to be viable- without success. This is equal to many millions of generations of bacteria in a population of many billions which were under stress due to the anti-biotic.

Does this say anything about the limits of purely natural evolution? I think so. Even if other bacteria species have made the jump and developed resistance to an anti-biotic (at the cost of reduced fitness otherwise) this one seems to have hit on a hard biological limit which unguided evolution cannot move it past. Surely this is not the only such hard limit in earth's living things. If this organism can't make this jump, how likely is it that the same mechanisms can cause a deer-like animal to develop into various types of whales in probably much fewer generations and far less tries?

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The Gene Changes Needed to Give Humans Big Brains Points to Design

There is a board I once frequented where I asked to quit getting notifications when I no longer wished to be associated with the board. In so doing, all my comments there got deleted, which I have no objection to and said so at the time. Still, I am glad a preserved some choice comments from a couple of threads. One thread concerned a study which reported on some amazing findings about the genetic differences between us and apes. On the thread I tried to point out that these differences aren't likely to be the product of mere chance with these comments about things said in the study. Quotes from the study in a white background and my comments on it shaded tan background below...

" they also didn’t see it in orangutans and found only truncated, inactive versions in our closest relatives, gorillas and chimpanzees." 

This is not a mere duplication. This is a crucial gene which does not exist except in chimps and gorillas, and then only in a truncated and inactive form. They said it somehow got “repaired” somewhere in the hominid line. You would think an inactive gene that was already truncated would collect more and more mutations until it was a real mess. But in this case when it gets turned back on it increases brain size? 

And check this quote out: 

"“What’s amazing is that there are many signaling pathways that control the development of the embryo and are completely conserved between species. The Notch signaling pathway is the oldest one. You can find it in every animal you look at. It has been used by developing embryos for as long as animals have existed. And yet, there is a very recent innovation in this pathway specifically in the human lineage, through NOTCH2NL,”

So the pathway is conserved in every animal species for hundreds of millions of years yet this quantum leap forward happened so far as we know just this once 3 million years ago? Is it not astounding that a path can be stable and essential for so long and then a game-changing improvement comes about via a repair to a long-deactivated and truncated gene? 

And that happening once is astounding enough, but did you catch this one?.. 

“The Vanderhaeghen team developed a tailored RNA sequencing analysis for specific and sensitive detection of human-specific genes in human fetal cerebral cortex. This allowed them to identify a repertoire of 35 genes unique to humans that are active during development of the cerebral cortex in humans, including NOTCH2NL genes.” 

THIRTY-FIVE functional genes unique to human linneage just on the development of our cerebral cortex. That they know of....

And it goes on like that. For those who will allow themselves the capacity to question whether humans are strictly the result of what we call "natural" evolutionary processes I think the results of the research point toward the answer being a resounding "no".

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The Great Ordovician Biodiversification Event Another Problem for Naturalists

The Cambrian Explosion refers to a geologically short period of time in which every type of basic body plan (phylum) of all animals alive today - and quite a few others which are now extinct- show up in the fossil record. Many scientists say that this happened within a 30 million year time period- a long time to us but shockingly fast if we are counting on naturalistic evolutionary forces to produce dozens of new body plans. But it gets worse because other research suggests that the real innovation occurred in only 20 million years.

Even that number probably over-estimates the time it took for all these new phyla to show up. This is because it is only a calculation based on the fossils we have found in the fossil record. What if the new phylum which shows twenty million years after the Cambrian begins is really of a creature who was around much earlier, we just haven't found an earlier fossil of it yet? So the short length of time is liable to get shorter as we learn more.

Of course naturalists don't like what this implies, so they have been hard at work producing speculation about how the life forms of the previous era were not so different after all and basically dreaming up everything they can to make the case that the Cambrian Explosion wasn't such a big deal after all.

But it turns out they have another problem almost as big as the Cambrian Explosion and this one might be even harder to explain away. While all these new phyla show up in the Cambrian, they don't diversify for 40 million years. Each body plan has very few species with that plan. Then, all phyla start dramatically diversifying at once into new families. Its called "The Great Ordovician Biodiversification Event" and it happened in an even shorter period of time than the Cambrian Explosion.

Now it turns out that this event too happened in a much narrower window of time than one might expect with known naturalistic evolutionary mechanisms. Here is how the link described it....

The early evolution of animal life on Earth is a complex and fascinating subject. The Cambrian Explosion (between about 540 to 510 million years ago) produced a stunning array of body plans, but very few separate species of each, notes Stigall. But nearly 40 million years later, during the Ordovician Period, this situation changed, with a rapid radiation of species and genera during the Great Ordovician Biodiversification Event.

I think what they are trying not to say is that naturalists have two problems, not one, when it comes to explaining the diversification of life in the seas. The earth can bring forth living things after their kinds- there is a background sort of "evolution" going on, but the record also shows changes too big and too fast to reasonably explained by any known evolutionary method. It looks like at certain points, nature had help. Help to do things greater and faster than she can do on her own without it- we don't see that magnitude of rapid change now.

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I really did not know who "Joshua Harris" was but it appears that Christianity has had another celebrity professional Christian walk away from the faith. If this keeps up all God is going to have left are those who love Him for who He really is. Mere amateurs who don't get paid a nickel for their love nor one minute in the spotlight for their adoration will comprise the bulk of the church. The payment Christ made for their sins was enough for them. I think God can handle it.

It seems that Mr. Harris achieved fame young for a book he wrote about "giving up dating" (I Kissed Dating Goodbye) in favor of courtship. There is a lot wrong with modern dating, don't get me wrong. But whatever alternative Mr. Harris pursued wasn't foolproof either. Last year he separated from his wife. This year he loudly left the Christian faith, condemning the church for the usual laundry-list of misdeeds such as not accepting homosexual relationships as "marriages".

Since I don't know the fellow, apparently he didn't even know himself very well, I cannot say with any certainty what his motives are, except to say that even the best of them will be tainted with sin like mine and everyone else's. I do see a pattern though. He wanted praise from people. He wanted to one-up the works of others. When he was a Christian, his way of finding a spouse was more spiritual than yours. But when he couldn't live up to the expectations he set for himself he didn't find humility. The law isn't supposed to make us proud, it is supposed to make us humble and point to our need for grace through Christ. Those who hold up some law, even law based in scripture, and then make their boast in how well they follow that law are setting themselves up for failure. 

We were meant to fail in our own strength. That was the real point of the law. He had to fulfill it for us. What I think Joshua Harris has done is that in pride he has refused to take that last vital step. I wonder if he ever grasped the true essence of the Christian faith- that it is not about how good we are but about how good Christ is.

If you will think about it you will see that Joshua Harris has not changed a thing about himself. He simply changed value systems. He is still trying to be justified by works. He is still telling people that his set of good works are better than theirs. He is still seeking the approval of the masses, just different masses. Once he couldn't cut it under the Christian framework, he decided it was false. In truth, it was just no more use to him. Nor is it of use to anyone who approaches from an attitude of pride.

The Hermeneutic of Godlessness: Shoe-Horning Naturalism into the Interpretation of Scripture

Hermeneutics concerns itself with the frameworks or methods that one uses to interpret texts, in particular Divine texts. So for example a theologian might look at the Christ-centered model for Early Genesis and ask, "What Hermeneutic did you use to come to those conclusions?"  They are asking about the methods and premises and parameters that were used to draw a particular meaning from the text.  A similar term "Exegesis", is a subset of hermeneutics, and focuses on just the rules you used to interpret the text and not the overall narrative.

Hermeneutics are not a bad thing, but it's a subject for theologians, not teachers. Neither Moses, nor the Prophets, nor Christ, nor the Apostles, spent much if any time describing what their "hermeneutic" was. They just taught from the text as the Holy Spirit gave them utterance and left it for the theologians who came after to talk about how such meaning was derived and discover what rules the teachers used in expounding from scripture. I consider the teacher to be like Galileo or Copernicus. They describe the truth of the universe as they see it. The theologians are more like Newton. They come along afterward and say "Here are the rules concerning what they were talking about". It isn't that one is good and the other is bad, but it is not everyone's job to be both.

The truth is that often the apostles didn't follow what mainstream theologians would consider sound hermeneutics. In the second half of Galatians chapter four Paul writes about how the two sons of Abraham really represent two covenants. What rules did he use to get that connection? None that would be approved by most of today's theologians, but he is still right. After all, he was an apostle and his ministry was validated by extraordinary miracles. Those folks are getting their message directly from the Holy Spirit, so man-made rules (which are really what hermenutics are) are no obstacle.

I will say that even though I don't have a developed "hermenutic" and don't care to expend any effort forming one, I do realize that just because an apostle can make those types of leaps doesn't mean that you or I can. We can apply the connections they made because it is reasonable to suppose that their making a connection itself validates that connection. But we can't pull our own from the ether. We are not them. We have to make the case that a connection is valid by, for example, showing where it is pointed to in the rest of the body of scripture.

That's just a decent start on a principle of exegesis, it is a long way from a hermenutic. And while I don't say hermenutics are bad, they can be bad. Even when they are good, they can be a distraction which changes the subject from "what do you think the Holy Spirit showed you from God's word?" to the question of "what contexts, semiotics, presuppositions, and parameters did you use in coming up with that meaning?" Hey, I am just telling you what I think God told me. My focus in on the message, not devising a set of rules or contexts which determine how the message was derived. It's not my job.

Again, that doesn't mean they are bad, just not my thing and nothing I care to be distracted by. But they can be bad. Innately bad. You can have bad rules or methods for interpreting divine texts and one in that category would be a flawed or bad hermenutic. I've run into a perfect example of one recently. Here is the background for it....

The assumption of naturalism is that all causes and phenomena have natural causes. The use of methodological naturalism is a perfectly valid, and perhaps essential, tool to scientifically study the natural universe. This is the premise that for research purposes we will assume that all actions have natural causes- no supernatural causes can be considered. This is the standard operating procedure for "natural science", that is, the study of the natural universe. Because we are within nature we often used "science" and "natural science" interchangeably. But "science" is a method of study, not a subject matter. If one is not studying the natural universe, there is no reason in principle one must limit causes and meanings to natural ones. I speak about this in my call for theology to operate more like a science, as it once did.

While the natural sciences may use the methodology of naturalism to study nature, there is no reason this tool must be extended into a philosophy. It is one thing to say "we are only going to consider natural causes in this experiment because that is all we can test for" and quite another to say "there is no such thing as a supernatural cause." This is elevating a tool or method into a philosophy which makes claims about every area of existence.

What I have discovered is that there is a surprising number of theologians and "theologian-adjacent" people who insist on attempting to impose what is in effect philosophical naturalism as a requirement for any valid (in their view) interpretive method (hermenutic). They do this by saying that the meaning we derive from scripture must be limited to 1) the scope of understanding of the human author and 2) accessible to the audience of the day. Such arbitrary rules are in effect asserting that there is no detectable supernatural action involved in the scriptures. God can't have put a hidden meaning into the text to be revealed in later generations because such a message would be beyond the understanding of the human author and undetectable to an audience of his day. The text meaning is limited to human understanding at that time.

Some insist that these are the only valid ways to interpret religious texts even though the logic of their two requirements is almost self-refuting. The human author and the audience of the day considered much of the text to be prophetic utterances from God. They would have been completely comfortable with the idea that God would also be laying groundwork for some progressive revelation of His nature with these words. These rules would invalidate much of the exegesis of the apostles who often tied events in the Old Testament to events surrounding Christ. It was even expected that God could speak through someone who was not even aware that they were speaking by inspiration (John 11:50-51). So in effect these artificially imposed man-made rules claim that the text of scripture can only have a meaning that the audience of the day would understand, but that they were in fact dead wrong about what they understood!

I almost feel embarrassed writing about it, so absurd is the assertion that what claims to be a Divine text only be evaluated for meaning under such man-made rules. The Holy Spirit is the real author, and He is not limited to the understanding of the human author through whom the texts were penned. Just the opposite. 1 Peter 1:20-21 says that no prophecy of scripture is a matter of private interpretation- it is not a question of what the author meant. Rather it says "holy men of God spake as they were moved by the Holy Spirit." The naturalist hermenutics deny what the scripture claims that it is. It presupposes rules which forbid consideration of any detectable Divine action - based on no evidence and in denial of the testimony and evidence which exists. You may have heard of "presuppositional apologetics"? This type of hermenutic is also presuppositional- just with premises which conform to naturalism rather than theism.

I view it as most often an attempt to rig the terms of debate in advance so that one side can't possibly win. Atheists do this when they, for example, demand "scientific" proof for the existence of God when by definition science cannot test for the supernatural. I can hear them protest, "but you are violating all the principles of sound hermenutics when you say it means this". No, I just feel no obligation to be bound by rules made up by people whose world-view I consider ridiculous. I don't care about the rules you made up, even if you put a fancy name to them and surround them with a bunch of $64 words. You don't get to make the rules for me, in particular if your rules assume the prophets and the apostles had it all wrong.

In conclusion, I see attempts to change the subject from what I am teaching to explaining, applying, or devising a methodology to describe how such a meaning was obtained into two categories: Attempts I am uninterested in and see as a distraction and attempts I am fundamentally opposed to.

The latter usually try to insist on premises which amount to philosophical naturalism, and this is an arbitrary restriction which I summarily reject. The former is more of a diversion from better things even if it is not bad in itself. Given the terrible theology and misunderstandings out there on early Genesis, it is enough of a challenge to get folks to see the material with new eyes and understand what I am saying. I have no time or inclination to hash out how such a meaning was derived. The message is too important to shift the conversation to its method of composition. Never mind that just now, I want people to know what it is saying. I am not opposed to such conversations, I just can't spare the time to be a part of them.

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Evidence for Early Dates for Gospels

Early dates for the gospels? What this link is claiming is that there is a document family, f35, which goes back to the 3rd century AD. None of the documents that old are complete so we can't tell if they had colophons at the end- we just have fragments and scraps from the documents that old. But  "descendants" of that document "family" from the 12th or 13th century do have colophons at the end. At least half of them do. And these complete documents with colophons at the end  claim that "this gospel was first released X years after the ascension of Christ". And those dates are quite early.  If indeed the complete documents we have from the 13th century were faithfully copying the colophons from earlier documents then it appears that the so-called "synoptic" gospels were released within 15 years after the Resurrection. Read about it here.

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Extreme Outlier Events - the Pattern in the Fossil Record

This article on Science Daily proclaimed, "A new normal: Study explains universal pattern in fossil record." Their summary was:

Instead of the typical bell-shaped curve, the fossil record shows a fat-tailed distribution, with extreme, outlier events occurring with higher-than-expected probability. Using the same mathematical tools that describe stock market crashes, scientists explain the evolutionary dynamics that give rise to universal patterns in the fossil record.

They were reporting on this Andrew J. Rominger study with the ungainly title "Nonequilibrium evolution of volatility in origination and extinction explains fat-tailed fluctuations in Phanerozoic biodiversity."

The Phanerozoic is the era of animal life as we know it, which is to say the last 543 million years according to most scientists. It seems they have realized for a while that new types of animals do not appear (and disappear) at a steady rate. There are bursts of the creation of new forms, and of extinctions of old ones. The distribution of events is "fat-tailed" and not what one would expect by chance.

Imagine you flipped 100,000 coins every year for 543 million years. You would expect the number of heads (which we could equate to a new organism showing up in the fossil record) and tails (which we could equate to an organism vanishing from the fossil record at a given point in time) to be about the same. But that's not what they see. They see periods where heads vastly outnumber tails and vice-versa. Not just at key periods like surrounding mass extinctions, but for the whole era! Why doesn't nature produce new types at a steady rate, forming a nice bell-shaped curve?

The study is extraordinary for many reasons. One is that it uses the term "macroevolution". This is a term that many are loathe to use because they dogmatically insist that there is only one type of evolution- the processes we see going on today producing small changes are responsible for the big changes we see in the fossil record.  The second section, paragraph three says:

The different regions of adaptive space occupied by different clades can be conceptualized as islands with unique dynamic equilibria, albeit with macroevolutionary processes determining the “colonization” of adaptive peaks, as opposed to short time scale biogeographic processes.

Granted they may not be using the term exactly like I would, but they are coming very close to what many creationists and theistic evolutionists have been saying for a while: that there is a type of background evolution that the earth does by itself in shaping species and a larger-scale force for change which is something different than that.

I also found it interesting that they used taxonomic categories to define their clades, and the reason for this"

We define potentially equilibrial subsystems based on taxonomic hierarchies, as a full phylogenetic hypothesis for all marine invertebrates is lacking.

There results were also very interesting. It turns out that what is driving the "fat-tailed" non-Gaussian distribution of new types is not at the family level or below. Those are stable and well represented by bell-curves. Instead it is events above the Family level.....somewhat in the case of Orders but really the Class and Phylum level that are skewing the whole fossil record. From the "Results":

We first evaluate the local equilibria of clades from family level to phylum. We find that family-level fluctuation distributions are well approximated by Gaussians (Fig. 1 and fig. S3). Three exemplar family-level dynamics are highlighted in Fig. 1 to illustrate how different volatility equilibria express themselves as actual richness time series. This Gaussian approximation also largely holds for orders, but classes and phyla increasingly show deviations from Gaussian with greater kurtosis, corresponding to more frequent outliers at these taxonomic levels (fig. S3).

Now they attribute this to the idea that a new Order or Phylum has a lot of new possibilities in form and function and as it diversifies can impact many environmental niches while Families generally occupy a more narrow range of niches so that changes within them are more in equilibrium. OK, I can buy, that, but that only explains that the "fat-tailed" improbable events are happening when a new Class or Phylum (and sometimes Order) appears. It doesn't explain how they got there or why it occurs in bursts and not on a regular basis. In fact the start of the study dismisses most explanations for this. It is one thing to say that a new Class of organism showing up, which then rapidly differentiates into various Families, shakes things up. It is another to say how that new Class got there and how it diversified so quickly after a long period of stasis. Indeed the study implies that the new Class generated Orders and Families which shook things up for existing ones which were in equalibria.

Does it make sense to you under evolutionary assumptions? I mean that a new class can spin off numerous new families that can go in and out-compete existing families that have long been honed and adapted to fill a given eco-space? It doesn't to me. The only thing that makes sense, and what I have heard a lot, is that right after mass-extinctions there is a "reset" of sorts where all surviving Classes get a new chance to adapt into an empty niche. And while I have heard that a lot the researchers don't seem to buy that or any other explanation for the patterns in the data that they see. The introduction concludes with " Thus, we still lack a theory to describe the striking fat-tailed nature of fluctuations throughout the Phanerozoic." Not just after the few mass-extinction events, but the whole era.

This is not what one would expect to find under a naturalistic evolutionary scenario. Not in the sense that the exceptional events do not follow a bell-curve distribution pattern but follow patterns in systems with intelligent input such as stock-markets. Nor in the sense that if random unguided processes could produce a new Class or Phylum that it could quickly differentiate into new families adept enough at exploiting new niches that they could not only survive but shake up things in the organisms which had been adapting to those niches for some time. Intelligent Design has no problem explaining either of those observations. It is what we would expect to see!

I don't see much stomach or intellectual curiosity among naturalists to face up to and examine these red flags to their paradigm. But that's not going to stop such flags from popping up as they learn to more deeply examine what is after all, God's Creation.

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