Macro-Evolution's Rate Problem

The recent issue of Discover Magazine from July-August 2018 had some information in it that I have sought for a long time. It was an estimate of the number of genera, not just species, which had gone extinct in each of the earth's five great mass extinctions since the Cambrian explosion 543 million years ago. The ratio between lost species and lost Genera was roughly half in each of the five extinctions (some would argue we are in a sixth mass extinction now in part due to human activity).

I had used a higher ratio in the past when I went through this thought experiment. I used five or ten species per genera, but using these estimates the number should be closer to two. Though there are more than two species in the average Genera, it would make sense that a global extinction event that took out one species would also take out a closely related species more often than an unrelated one. Still, the ratio can serve as a rough proxy for the number of genera there were in the past when you consider that such a large proportion of the worlds species and genera were eliminated that the ratio-skewing would be minimized. Its like a poll taken that questions 3/4ths of all voters. It doesn't matter much if your sample is skewed because its such a large proportion of the whole.

Now all we need is a good estimate of the number of species around today. Though the vast majority of them have not been cataloged the current best estimate of that number is 8.7 million. Some of these are deep sea animals to which we have little access. In other cases the problem is that a group of animals looks so alike that we consider them the same species but they are actually two or more species and we just haven't looked close enough to notice that yet. So let's be very conservative and reduce the number of species to those which are so different from other populations and so accessible that we already know they are a species. That would be about 1 million. So as you can see I am really trimming the numbers here as far as what macro-evolution is required to do to be validated. I am allowing for how puny our powers of observation can be.

Earth has had five mass extinctions since 543 million years ago, each about 90 million years apart. The last one was 65 million years ago so it is reasonable to assume that the others produced at least as much diversity as the last one, since they have had on average significantly more time to do so. But let's be conservative and say they also only produced 1 million new species that are different and accessible enough so that were they around today we could recognize them as such.

So there was an initial burst of animal life in the Cambrian which produced, let us say, 1 million "spottable" species. Then five mass extinctions after that which did the same. That is a total of six million "spotable" species and therefore roughly three million genera over the past 543 million years. That's the "rate" at which evolution would have to produce new genera to explain what we see. You will note that these numbers are pretty conservative given the estimated number of actual living species, that the time to produce these species is much less than the average time between mass extinctions, and even though a species may be difficult to spot a genus should be much easier to detect.

But even using these conservative numbers 543 million years / 3 million genera from "spotable" species = and average of one new genus in less than 200 years. That's how fast evolution had to work in order to produce the diversity of life we see. Is that the rate of evolution which we observe? Has there been even one case of a new genus evolving in recorded human history?

It looks from here that something else was happening in the past, a force at work which is not at work today with the same power. This fits well with the cosmology put forth in Early Genesis, the Revealed Cosmology. In it, this realm is a copy of the Land Above, but one subjected to futility. Up there, when God speaks, it happens. Down here, its a bumpy process and though creation might try, it can't do God's will without God's help. Just like us.

Should RTB/OEC's Tweak Models in Light of New Data and if so How?

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 The current Reasons to Believe model for humanity has been challenged by the work of Dr. Joshua Swamidass. 

Even if his conclusions check out, this is not a death blow against OEC by any means, or even the overall RTB model, which they call the “testable creation model”. For example the astronomical aspects of their model still do quite well. The question of whether humanity evolved from a common ancestor with chimpanzees via known evolutionary processes is a separate question from whether there were humans outside the garden before Adam and Eve, how long ago all this happened, and also separate from the question of whether the flood of Noah eliminated the balance of humanity or just the balance of the line of Adam. 

This new data just means that they may need to adapt their model in a way which accommodates what we have learned, much like evolutionary theory itself changes to accommodate new data. They can continue to represent the OEC position (which I also think is the “most correct” overall view). 

If so, what should this model now look like with respect to humanity? I have a few suggestions and you may have some of your own. I realize the TE members of this board may not appreciate this exercise. I ask that they not switch forks on their putative evolutionary tree (go ape) over this, but I’d like to bring RTB closer to Peaceful Science by first getting us all to agree on what happened before we get to questions about how it happened. 

Obviously the OEC position in particular with respect to humanity is that both the race adam and the man Adam were specially created by God, though these can now be seen as separate events and therefore not necessarily done by the same means. The good thing about this for RTB is that they no longer have to stretch the genealogies to the breaking point with vast “gaps”. The genealogies are for the line of the man Adam, not the race adam which was already present (though not as agriculturalists) when Adam was formed. 

The new RTB model could reject the claim that humanity arose 310,000 years ago and propose a more recent though still ancient date. The molecular clock evidence suggesting a date for humanity of 260 K ago could be explained by the initial human population (in the new model God would have created a “host” of humans prior to Adam and Eve) containing some genetic diversity. That is, the initial human population was somewhat different from the start, thus not all of the differences were due to acquired mutations. This would show an older clock time than actual time. Some evidence suggests that molecular clocks run fast anyway. This would be easy to do because the evidence for a 300K plus date for humanity is very much over-blown IMHO. 

The issue of limited in-breeding between humans and other hominids should be addressed by the model. I propose that it be turned into a plus not a minus. It allows us to test for anomalies in the standard evolutionary model. While there is evidence that such in-breeding occurred, the same evidence indicates that there were barriers to hybrid fertility. Lions and tigers can sometimes produce offspring, but they are not known to breed in the wild and those offspring likewise have fertility problems. So we can see that in nature things can happen which nature itself does not “prefer” in terms of Darwinian outcomes. 

There is evidence to suggest that most of the genes which we may have acquired from hominids such as Neanderthals are slowly being weeded out of the human genome over time, as if nature was correcting a mistake. There are also signs that many other genes which were thought to be a result of such hybridization are now considered to be the ancestral state of our own species. That is, they represent a re-introduction of genes originally possessed but lost by chance in our own human ancestors and thus do not represent a genuine influx of new genetic material to our species. Perhaps it is best to consider Neanderthals and Denisovans to be like the satyrs of myth- like us, interested in us, but not really “of” us. 

That brings me to another point which could be a part of the new OEC model. Instead of humans originating in Africa, perhaps they originated in the mid-east or in many places at once but the vast majority of those who survived were from Africa. Thus the OOA movement 55-60K ago was humanity re-populating the rest of the old world, absorbing or wiping out small and scattered human groups- who may have been highly admixed with other hominids and the true source for much of the few non-human genes we still see in our own genomes. As our power to analyze genomes increases we see tantalizing hints of this previous larger human population in some isolated human groups, particularly those in SE Asia, and the islands near to Australia. I think they admixed with other human groups as well, but the work of Dr. Swamidass has shown how quickly genetic minorities can become genetic ghosts. This applies to more than just Adam. It could apply to this proposed non-African human population as well. 

In addition, much of what we think of as “human evolution” may simply be an artifact of the genetic impact of hybridization events with other hominids being weeded out over time. That is, the original group of human beings may have looked much like the San do now and not like “archaic” Homo Sapiens at all. The OEC position can postulate that the “archaic” appearance was a result of hybridization with these other hominids, and the loss of such “primitive” features would simply be “evolution” via reversion to the mean for humanity- a still ongoing process. 

Under this scenario I would expect to find in Africa an inconsistent pattern of human remains- features far too “modern” looking for their time in some finds and typically “archaic” in others. Perhaps even in the same digs. Thus Africa would represent a place where some populations of humanity resisted being “dragged down” by hybridization events which spelled doom both for the human populations whose participation in such events became the norm and the other hominid groups as well. Unfortunately I don’t think we have enough finds in Africa at present to establish much of a pattern either way. 

This brings me to Adam. While it may very well be that Adam and Eve have become “genetic ghosts”, if they left a detectable signature one of the traits of this signature would likely be an absence of other-hominid genes relative to surrounding  (Eurasian) populations. That is, they would not have had Neanderthal or Denisovan genes. Thus modern populations which contained more of Adam and Eve's genes would have fewer other-hominid genes than populations which had a lower proportion of genes from Adam and Eve. A sudden appearance in prehistory of a population with a reduced load of non-human genes in the same time and place as Adam would represent an anomaly explainable by a de-novo creation of Adam as a “re-do” of the original human condition. 

So while the new findings may be considered a setback for some aspects of that specific model, the new data presents new opportunities to explore and improve OEC models.

Of course the OEC model I advocate can be found in my book, which resolves these and many other paradoxical issues...

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Study Supports Christ-Centered Model Theory for Origin of Canaanites

A new genetic study has confirmed the scenario laid out in "Early Genesis the Revealed Cosmology" in terms of dates and population structure for the origin of the Canaanites. This is important because it supports the Christ-centered model's date for the flood of Noah (6,500 YBP), its extent (the line of Adam and not all of humanity), and the location of Adam and Eve's clan post-garden (from the Taurus Mountains to the Zagros Mountains).

I postulated an origin for Adam and Eve and the families of Noah in Anatolia and the Taurus and Zagros mountains. Further, that the clans of Noah entered Mesopotamia and started the Uruk expansion, which ended around 3100 BC. This corresponds to the scattering after Babel where it is written “afterward were the families of the Canaanites scattered abroad.” Further, I postulated that the references to the families of Noah in Gen. 9 and 10 (“by these were the earth divided”) does NOT refer to a situation where these families constituted the whole human population but rather that they added the natives into their households wherever they went and these became the core of new nations.

So about 5100 years ago people with the J1 Y-haplogroup (the Cohen Y-hap) who originated in NE Anatolia and NW Iran, after a stop in Mesopotamia, left for Canaan and mixed with the locals creating a new population. The study is saying just what I said in the book. They said it based on a DNA study, I said it based on a study of the scriptures.
Here is a partial run-down of some highlights of the study put together by a colleague (with his own ideas on these matters) on the Peaceful Science blog:

POINT ONE: Y haplogroups J-58 ARE COMMON IN PRESENT NEAR EAST - -
“… the two Sidon_BA [Phoenician Bronze Age] males carried the Y-chromosome haplogroups45 J-P58 (J1a2b) and J-M12 (J2b) (Tables 1 and S4; Figure S11), both common male lineages in the Near East today.”

**POINT TWO: ORIGIN OF J-P58 MAY BE ZAGROS/TAURUS REGION - - **
“Haplogroup J-P58 is frequent in the Arabian peninsula with proposed origins in the Zagros/Taurus mountain region.46 It forms the vast majority of the Y chromosomes in southwestern Mesopotamia and reaches particularly high frequencies (74.1%) in Marsh Arabs in Iraq.47” [Speculation: Marsh Arabs have high Scythian-like genetic component!]

POINT THREE: J-M12 MOST CONCENTRATED IN BALKANS (extending to India) - -
On the other hand, haplogroup J-M12 is widespread at low frequency from the Balkans to India and the Himalayas, with Albanians having the highest proportions (14.3%).48

POINT FOUR: IRANIAN CHALCOLITHIC ARRIVED IN LEVANT WITH METAL WORK - -
We compiled frequencies of Y-chromosome haplogroups in this geographical area and their changes over time in a dataset of ancient and modern Levantine populations (Figure S12), and note, similarly to Lazaridis et al.,13 that haplogroup J was absent in all Natufian and Neolithic Levant male individuals examined thus far, but emerged during the Bronze Age in Lebanon and Jordan along with ancestry related to Iran_ChL (Iran Chalcolithic).

POINT FIVE: ARRIVAL EST. 3000 BCE [LUWIAN/MITANNI METAL WORKERS?] - -
We next sought to estimate the time when the Iran_ChL-related ancestry penetrated the Levant…. Using ALDER50 (with mindis: 0.005), we set the Lebanese as the admixed test population and Natufians, Levant_N, Sidon_BA, Iran_N, and Iran_ChL as reference populations. ….The most significant result was for mixture of Levant_N and Iran_ChL (p = 0.013) around 181 ± 54 generations ago, or ∼5,000 ± 1,500 ya …. This admixture time, based entirely on genetic data, fits the known ages of the samples based on archaeological data since it falls between the dates of Sidon_BA (3,650–3,750 ya) and Iran_ChL (6,500–5,500 ya).

An Old Earther on Peaceful Science

I write an article for the Peaceful Science blog.

Intervention Started Early on Road to Humanity

There is a lot which early Genesis chapter one does not say about creation. The language on days five and six in particular lend one to believe God intervened personally and repeatedly in fashioning the creatures of the land and seas. Most particularly, they point towards His intervention in the formation of the human race.

Well genetic biology is not my field, but I have an acquaintance who is an expert in that and he is both a Christian and an evolutionist. He believes that God guided the process in some way undetectable by science but that evolution was the process that He used. I myself have pointed to some gray areas between theistic evolution, intelligent design and special creation but I see the text as much further on the creationist side of things with humanity in particular.

At any rate we were having a dialogue about the Cambrian Explosion. He was insisting that it was not a problem for evolution. I said the molecular clocks showed more time was needed than the fossils showed they had in order to develop 70 new phyla of life. He chalked it up to inadequacies in the fossil record from the period when soft-bodies were the thing, along with a clock that only worked on closely relate groups. I countered that perhaps it only works for closely related groups because that was as far as nature could go with evolution. The distinct groups themselves then would have come about by some sort of special creation and diversified from there.

He countered that the link between chimps and humans was very strong, which should not be so if they were not related. Previously we had had a discussion where I had thought that there was more difference than time allowed between the two genomes but I was going off of old research. The latest research "looks like" it should look if they had a common ancestor six million years ago. Did they just re-measure until they got a value that fit their biases? I am not versed enough to say so, but he is and he doesn't think so. Of course that is a measure of mostly "noise" in the genome rather than functional change, but it shows what it shows.

So I was looking for "the fingerprints of God" in the genome. Places where change happened at a rate too fast for normal evolutionary mechanisms, indicating that something else was happening. I wasn't finding it anywhere between Chimps and humans. Of course He could, and I am sure does, operate in ways both subtle and sublime. We may not be able to detect His action, even if it permeated reality under certain models. Particularly with our current level of science (or as my associate points out maybe never and if we could science still could not demonstrate it was God's doing, just an anomaly).

At any rate, I think I found it. The anomaly, the fingerprints, whatever you want to call them. Again this can't be shown scientifically to be God's action, but it can be shown to be something out of the norm. It is up to humans to ascribe meaning. In this case the big fast change did not occur between chimps and humans, but according to this study it happened between chimps and humans together vs. everything else.

Here is a sample of what they found..

Eichler's research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period. "There's a big burst of activity that happens where genomes are suddenly rearranged and changed," he says. Surprisingly, the rate of duplications slowed down again after the lineages leading to humans and to chimpanzees diverged.

Well, that sounds a lot like what special creation would look like. Maybe the special creation was not a human but it was more like a "test model". One branch of the test went one way and another branch went another via the significant but not unlimited amount of evolution which can and does occur. In other words chimpanzees are not the original form but a derived form of something which was originally less adapted for living in trees. The other branch led to the hominids. Perhaps there were no more "major reorganizations" between human genomes and that of chimps because the rest of the job could be done with relatively minor tweaks in the genetic code that did not stick out from genetic background noise. Not many changes to that hominid template need be made when forming humanity, because they were already made on the changes which got us to that template.

In other words, using the chimp-human genomes to say there are nothing like Divine fingerprints to be found is just cherry-picking the data. The fingerprints are found just before that point. Does that mean this was the only place God intervened and humans just evolved from a common chimp ancestor from that point? Not at all. It could just mean that the other interventions were too "light touch" to be detected as anomalies by our present level of understanding. But we don't need to locate every fingerprint to make the case for some form of special creation. Finding a few of the big ones makes the point.

I would also say that the Christ-centered framework for early Genesis make more sense out of this possibility than traditional models, though the following paragraph probably won't make much sense unless the reader already understands the framework. That said, the puzzle is why get some creatures all the way up to "near human" before finally creating Man?

In the Christ-centered model the second Person of the Trinity fused with humanity in Genesis 1:27. Whatever traits are temporarily set aside when a member of the Godhead takes bodily form would be in play. Whatever limitations which may come from that would be in play. So then, perhaps the Logos got things prepared so that when He assumed the more anthropogenic form of God (often referred to as "Yahweh") there was only so much left to do - just create and form man. And this was arranged to be a smaller step than it otherwise would be due to the hominids. He did not have to do the  the DNA part from "scratch". He just took the DNA code from the hominid line and made some tweaks. The changes in the soul and spirit part were greater, though hard to measure through science..

Understand that there is no necessity to detect God's fingerprints on creation. He could have done it all "light touch" if He wanted to. And even if we find them, we can't scientifically prove that this is what they are. Evidence is a mirror which says as much about the person viewing it as it does the natural universe. But I am in favor of looking none the less.

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Why Didn't the Ark Riders See any Mountains?

My model of early Genesis has a regional flood in the highlands North and East of Mesopotamia as the epicenter of the flood. Mesopotamia got a "glancing blow". The target was not all of humanity, nor all animals, but rather the Adamic line which was given to produce Messiah and had gone badly astray. This was around 6,500 years ago.

One of the challenges in this model is the charge that it should not have taken so long for the tops of mountains to be seen if indeed it was a regional flood in the highlands. A closer look at the text shows that this is not the problem that it is made out to be.

First let's look at a couple of basic facts about spotting things on the horizon.....

The ark was 30 cubits tall, which we think is about 45 feet. The text hints that the draft of the vessel was 15 cubits because it says that the mountains were covered to at least that depth (Gen.7:20). So the top deck was about 22.5 feet off of the water. If their view was otherwise unobstructed this would be consistent with a visual horizon over the water of 5.8 miles.

Even if they were in some depression, say near Lake Urmia, until the east wind blew them unto the "mountains of Ararat" there were still some mountains which loom many thousands of feet higher than the surrounding terrain. It strains credulity to claim that those highest peaks were underwater for any length of time, especially for months. For example, a peak 5,000 feet higher than the surrounding terrain- be it earth or water, should be visible from sea level 86 miles away. A peak which soared 10,000 feet high, and there are several like that in this area even if the water was still 1,000 feet deep, should be visible a whopping 122 miles away with clear viewing. There is really not sufficient room for a vessel to drift for months without coming near to at least some of them.

Never the less, they (Shem, Ham, and Japheth) reported early on that "all of the mountains were covered". This report could be based on the fact that they drifted for months without ever running aground. It was not until the seventh month, the sixth month of their ordeal, that the ship ran aground. And it was not until two and a half months later, in the tenth month, that they reported "the tops of the mountains appeared".

I think some of the confusion can be cleared up if we put out of our mind the picture we have of the ark and instead go back to the text and see what it says things were like. I mean, if they drifted around for months with a crow's nest like modern vessels without seeing any land of course that strongly mitigates against a regional highland flood. But the ark was not built like that. The pictures and recreations we see of the ark with a row of windows on the upper deck are not what the text says that it looked like.

Instead, ark was built with the top cubit unfinished except for the spines to support a covering. This is the "window" mentioned when God is giving instructions for the ark. It's not really a window, and another word is used for the window which Noah opened to release the birds later in the account. Instead, that last 1.5 feet was left unfinished except for the framing for lighting and ventilation. A "cover" or "roof" was stretched out over the top of this, and based on the word used it was likely made of animal skins. Lamb skin perhaps? This was very much like what we would think of as an "awning" to keep the rain out.

So far as we can tell, that is all they had for visibility. The "door" of the ark was shut with pitch and could not be open and shut easily. There is no indication that Noah ever opened the "window" which he used to let the birds out until he in fact used it for that purpose after the ship ran aground. It is likely that opening the window broke the pitch seal, which would have been problematic if it rained again.

In the same way 8:13 is written like Noah and his family don't get a really good look at the surrounding landscape until they cast aside the cover of the ark. Again, he seemed very reluctant to take that cover off. I would imagine if they took it off too early and found the ground a swamp, replacing the cover from inside the ark would have been a difficult to impossible task. If they had taken off the cover and found a swamp they were in trouble if it rained again.

This is a strong hint that the eaves of the awning extended far over the sides and limited their view from these openings until it was removed. That would also explain Noah sending out the birds in hopes they would find dry ground. They couldn't see very far until they removed the cover or roof. They didn't have a row of unobstructed windows in the top of their vessel from which they could view the horizon and beyond. They could have drifted within a few miles of mountain tops and never seen them.

In verse 8:5 it says that "the tops of the mountains were seen". I had always assumed that meant distant mountains, but now I realize that the text does not support the idea that they had such visibility. Instead it was referring to the mountains on which they had run aground a month or two before. Earlier in the text there is a mention of "high" or "exalted" mountains. These are just mountains. They can start to see the tops of the mountains rising up out of the water in their immediate area. This leads them to wonder if there is not higher and drier ground just a couple of miles away. So they release the dove to go check. Because they can't see that far due to the awnings.

So once again, the solution to the paradox is to be found in the text. The text describes a situation where the ark-riders had limited visibility until the cover was removed from the ark. Thus, the regional highland flood model remains plausible.

Gray Areas in Evolution, Intelligent Design, and Special Creation

Getting our definitions straight is essential to sorting this out and preventing us from talking past one another. We can’t tell to what extent we agree or disagree without it.

For example “Descent with modification” is one definition of evolution, I guess a preferred one. To me it could also be a form of creationism or at least intelligent design, depending on how the "modifications" occur. For example, farmers breed animals for certain traits and get them through descent with modification. They select far more powerfully for desired traits than nature does. So that fits this definition of evolution, but surely it is intelligent design as well.

Let’s have a thought experiment: Now suppose instead of farmers who went around selecting for traits, God Himself did so. If a certain group got a rare mutation that would produce a benefit if paired with another rare mutation which existed only in a second isolated group He would know it and be able to put those two populations together so that they would have the suite of mutations that, when combined with yet another rare mutation four generations from now, would result in a new function. So He is using Divine knowledge to leverage natural processes to produce something new. I would say that is evolution (descent through modification), intelligent design (intent drives the changes not natural selection) and “soft-touch” creationism (He intervened in the natural world to produce outcomes even if He never touched the genomes directly, He merely guided natural events in a way that nature would not in herself at anything like the same rate).

Now suppose that instead of taking the role of a selective breeder (with perfect knowledge) only, He also assumed the role of Genetic Engineer. That is, instead of strictly waiting for Nature to come up with mutations which could be combined to create new function, He did just what our engineers do. He made cuts and inserts in genetic code. Maybe nature would never get a particular protein to fold just right waiting for chance or mutation so He inserted a gene which would. So when our scientists make mice which glow because jellyfish genes have been inserted in them, and this population breeds, is this “descent with modification”? Well maybe, but the modification did not come wholly by "natural" descent. It is doubtless intelligent design and special creation, and questionably evolution as well.

That said, such a situation could still involve natural descent, but that would not be where the key modification would come from. Take the gap between a fish and an amphibian. What if over the course of thirty or forty generations God acted to put just enough changes in each generation that they would still be able to be birthed and bred by natural means but each generation would also be further toward the amphibian end of things? This so that even though no amphibian was created out of thin air, or clay, one still had a very different creature though only forty generations removed from the fish. That result would be due to genetic engineering moving things a bit further along each generation. That is “descent with modification” but the modification that matters is via genetic engineering. So is that evolution, special creation and intelligent design all rolled up into one?

Is there really any scientific evidence that known evolutionary processes can operate at the rate and scale necessary to explain all of the "modification" of life on earth through its history? Another way to ask it would be like this, suppose there were a billion earth-like planets and a single celled organism was placed on each. How many of them, using only known biological processes without any intelligent intervention, would have a biotic phase which looks anything like the history of life on earth?  I think the number would be "zero". Someone else might think the answer would be in the thousands or even millions, but none of us have done the experiment or anything like it to say for sure. Therefore neither side has a scientific basis for saying either way, though one might have naturalistic assumptions on the question. It is a pity so few can even recognize that there is a difference between the two.

Like Jon Garvey, I don’t think “natural selection” or any of the natural means we have discovered could have, on its own, produced the vast diversity we see today or in the fossil record. I think nature had help. And I think some of this arguing we are doing over it is because we are talking past one another on terms.