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Saturday, September 10, 2011

Deliver us from Evil - Friendly Fire - The scientific and philosophical bankruptcy of BioLogos

“The moment you say ‘We have to abandon this theology in order to have the respect of the world,’ you end up with neither biblical orthodoxy nor the respect of the world.”

Al Mohler - President of the Southern Baptist Theological Seminary

One of the great tragedies afflicting modern culture in this country is the large number of so-called Christians (some are, some aren't and I am certainly not qualified to sort them out) who have determined that secular science has wisdom that trumps the wisdom found in the Bible.   It has been estimated that as many as 85% of Americans have identified themselves as Christians, Theists or Deists in one poll or another.  It is quite apparent that the definition of Christian is commonly misunderstood, so I made sure to include that in a recent post.  I will post the entire entry this time:

What is a Christian?

As far as I can tell, after thirty years of experiencing God and life as a "Christian" and after thinking about this experience from several perspectives, a Christian is...
a person who has a personal heart-to-heart relationship with the living God, characterized by warm and active acceptance on God's part; our honesty and dependence on the activities of Jesus Christ.
Let's look at this a little more closely.
"A personal heart-to-heart relationship":
The point of this is to exclude 'religious' relationships, in which an 'object' is revered 'from afar' but not approached in a personal way. God is indeed an 'awesome entity' but he is nonetheless a Person. A personal relationship is a reciprocal relationship, not a one-way deal. There is real interaction, real disclosure, real closeness that develops. The 'heart-to-heart' aspect intends to convey the honesty and openness of this relationship. There are no 'games' that can be played with an all-knowing God(!), no secrets withheld, no area of life concealed. (The interesting thing about this is that, even though God knows all about an area of our life, we might NEVER open it up to Him in discussion, in our efforts to 'hide' from His feedback!)
I cannot emphasize strongly enough the personal character of this relationship. I see so many aberrations and stunted-growth versions of it. It is not a formal relationship, a primarily legal one, or even simply a 'creature-Creator' relationship. (I find the human tendency to relegate God into a religious icon or image or object to depersonalize the relationship and short-change the possibilities of such a relationship--much as we do in other significant personal relationships in our lives.) 
"The living God":
 The subject of God is quite a vast one, but the main point here is that He is LIVING. There are feelings, and thoughts, and decisions, and actions, and initiatives, and responses, and values, and commitments... all the aspects of personal existence. He is not a force or an attitude or a "perspective on the universe". We walk around our lives 'face to face' with this One-- even if we ignore Him.
"Characterized by warm and active acceptance on God's part":
 From God's side, He accepts us. But this is not merely a 'political' acceptance--it has a warmth and joy to it. He 'smiles' upon us. He delights in us(!). This is more than simply the very important 'peace with God'; it is an active relationship. He gets involved in our lives for good--for our growth, our development, our character, our fulfillment, our stability, our significance in the lives and futures of others. He is always 'glad to see us'.
"Characterized by our honesty and dependence on":
 From our side, the relationship is one of honesty about who He is and who we are. We are not 'gods', and as such need our Maker for the realization of the purposes for which we appear in this universe. We are a people dependent on the universe He has produced, and we are people whose goodness has been severely compromised by our regular moral failures and pervasive spiritual apathy.
The main thing in the universe that God the Father God the Son. When we are honest with the Father about who his Son is, and what he did in history for us, God welcomes us into this warm relationship...We simply have to be honest with Him about his dearly-loved Son. The second part of this is dependence. We depend on Him for the 'repair' of our relationship WITH Him. He is the active one, coming in history to earth and taking upon Himself the consequences of our moral failure. We simply are honest about those actions/events to the extent that we rely upon those actions/events as an adequate basis for God's warm acceptance of us. In other words, we agree with God that his Son's life and work are sufficient grounds to accept us into this special relationship. It's that simple.
"The activities of Jesus Christ":
 The basic 'core' truth of Who he was/is and what he did are simple. He was God the Son, who took on human flesh, lived among us, suffered at the hands of His Father (on the cross) as our substitute, came back to life after his execution, and transported himself 'outside' space-time to 'heaven'. He will return to earth visibly in the future, but for now, He is involved invisibly in the macro-forces of history, and the micro-events of our lives. His death satisfied God the Father's just moral demands upon us, and 'freed' God to lavish his warm acceptance upon us.
This is the beautiful truth of what a Christian is...a beloved child of the living and loving God...and it starts with a simple conversation with God...telling Him that you accept "His version" of who his Son was, and what He did for you...

For just a tad more detail on the "WHAT and HOW", without going into too much intellectual musings, you might look here

The Christian ThinkTank...[] (Reference Abbreviations)


Christians tend to recognize born-again believers in Jesus Christ as Christians.  The word "Christian" doesn't appear in the Bible at all until the eleventh chapter of the Book of Acts,  11:25-26:  New King James Version (NKJV) -

Then Barnabas departed for Tarsus to seek Saul.  And when he had found him, he brought him to Antioch. So it was that for a whole year they assembled with the church and taught a great many people. And the disciples were first called Christians in Antioch.

So people were called "Christians" because they were doing the things Jesus told them to do.   Go out into the world and preach and teach the Gospel and bring people into belief, then baptize them and teach them to be disciples like yourselves so they will also go forth and preach and teach and rinse and repeat.  So if we go by the Biblical definition, to be saved and know you are going to Heaven makes you my brother or sister in Christ and part of the Kingdom of God.   But to truly be a Christian you are also doing something to advance the cause of Christ.   Note that belief comes before baptism.  Baptism is a symbolic act of obedience that a Christian chooses to do to associate himself with Christ.   I have known many Christians who have waited for years before being baptized for various reasons.   Being born-again is all about the relationship with God, while being baptized is an act of obedience.   If you do not believe and do it, you are simply getting wet.

Being an active Christian is not a cookie-cutter concept.  Some preach, some sing, some teach, some clean the church, some shake hands at the door, some are deacons dealing with church affairs or elders also dealing with church affairs and teaching in the main service.   Most church organizations have one head elder who is the pastor who does the bulk of the preaching from the pulpit and is the leader of the church organization.  Our pastor works himself silly and I sometimes ask him if he is doing too much?   

My wife writes letters to first-time visitors and we as a couple will visit people who ask for some personal discussion on spiritual matters, like how to know you are a born-again believer or perhaps something else.   I teach in the youth group and me, my son and my wife are youth staffers and small group leaders as well.  Once my knee is completely healed I will probably go back to being one of the church singers.   Monday the sutures come out and I am rehabbing and doing the recumbent bike with care.   It is a couple of months before I can probably play basketball half court again.   If I can do that, I can handle standing during the praise and worship service and I will volunteer to get back into harness.   My wife also makes art and gives it away to people.  She writes letters to the NIV translation team discussing some of the oddities (IMO more like heresies) of the latest translation because she knows one of them personally as they went to church together years before.   I do more than one blog but this is my worldview blog and I consider it ministry.  So what we do seems like normal Christianity to us.   God gifted us in certain ways and we use those gifts to advance the cause of Christ.  When I was younger I took on more responsibilities than I do now.   As we get older we will have to do less because we simply will not have the energy.  God understands.

There are many Christians who do more for the cause of Christ than we do. There are people at our church who do more than we do.  There are people who give more money than we give.   There are people who head up ministries while we just provide some of the staff.  As I said, I think our pastor works harder than anyone else and, guess what, pastors don't get paid all that well in an ordinary church.  He does it out of love.  He does it because he wants to advance the cause of Christ.  The point is that the ordinary Christian life involves people doing things to promote Christ and obey God and there are millions of Christians around the world involved in healing, teaching, missions, science, singing, building...myriad jobs for people to do done out of love for God and not for personal gain.   This is normal Christianity.

So I have difficulty understanding someone like Francis Collins, who I have written on previously, a geneticist who worked on and directed the NHGRI (the Human Genome Project) and was the founder of BioLogos, an organization devoted to making the Bible subservient to the latest pronouncements of Secular Science.   I have difficulty imagining that there are Christians involved in the talkorigins blog, which promotes Darwinism at all costs even when they are shown specifically that they have posted lies.  Collins left BioLogos to head the NIH, which he considered a conflict of interest, and I cannot fault him for that.   So far as I know, Collins is an earnest, honest man who truly believes what he is doing is a good thing.   Yet he is an enemy to the cause of Christ and the organization that he formed is a source of friendly fire, attacking the foundations of the very belief system that Collins claims to hold.   The sad thing is that Collins has had debates with Richard Dawkins, which is rather like having a liberal Democrat debating a moderate Independent voter and leaving the Conservative off of the platform.

It is not that Collins is not an honorable man.  I am not going to impugn his character because I believe he truly believes in what he says and does.   Nor can I claim that he is ignorant, for he is a brilliant scientist and an accomplished one at that.  But I can and do question his judgment and his internal list of priorities.   Somewhere within the mind and heart of Francis Collins he has ranked the current secular scientific story (which keeps changing, by the way) above the Word of God, the Bible.   Somewhere, somehow in the life of Collins he decided that what a Dawkins or a Hawking says has more importance than the Word given by God to Moses to enscribe and keep for all time for the benefit of all mankind.   The latest educated guess of secular science over Genesis?  The assertions of Stephen Hawking over the assertions of Jesus Christ?  Francis Collins may be accomplished and brilliant and earnest but he is quite foolish to elevate current secular scientific opinion above the unchanging Word of God.  It may not lead Collins to abandon his own personal faith, but the work of BioLogos is certainly leading others astray.  This has not escaped the notice of Christians who are scientists and Bible-believers.

The inanity of Darwinism is clear to those using common sense.  Mutations are supposedly the driver of evolution but you need to have something in existence to evolve in the first place.   In fact, not just something, but something alive!  Mutations are mistakes, they are the dropped glass that breaks, the hammer that slips and smashes your thumb.   If you took your car to the mechanic and he suggested whacking it with a sledgehammer to fix it you would put the car in reverse and get the heck out of there!  Yet this is the creative force Collins wants to credit above the Word of God and above God Himself!

Three articles follow.  The first is quite long but very readable until you get to "Analysis of the data at hand" at which point it gets more technical and for some of you it may be too much so to hold your interest.  But the second and third articles are much shorter and I highly recommend that, if you give up on article one partway through, that you navigate down to and read articles two and three.   They are succinct enough while still imparting scientific knowledge and are quite to the point.   I hope when you have read them through, you will agree with me that an organization like BioLogos is not only unnecessary, it is, like a mutation, likely to do more harm than good.

The Non-Mythical Adam and Eve!

Refuting errors by Francis Collins and BioLogos


[In view of the huge publicity that these claims undermining the biblical history of humanity are getting at present, we have chosen to replace our normal 2-day ‘weekend feedback’ with this important article in response by CMI scientist-speaker Dr. Robert Carter, who also researches in human genetics together with genetic engineering pioneer and former Cornell professor Dr. John Sanford.]
Published: 20 August 2011(GMT+10)
Adam and Eve
In recent weeks, we have received multiple inquiries about the historicity of Adam and Eve, including e-mail questions coming through,1 questions after church talks, seminary courses we have given, call-in questions during radio interviews, and questions after conference presentations. This has been precipitated by a significant amount of press coverage of Francis Collins and the other members of his organization, BioLogos.2Collins was the director of the Human Genome Project, and is currently serving as the director of the National Institutes of Health, so he is no lightweight in science. Also, Collins claims to be an evangelical Christian. When a person of his caliber speaks on the relationship between science and faith, people sit up and listen.
It cannot be overstated that … the two theistic evolutionists are basing their conclusions on evolutionary assumptions.
Yet, the things he has been saying are completely opposed to what CMI believes and what the Bible clearly teaches.3 The rash of questions we have received of late center around his claims that there is no evidence for Adam and Eve and that there is no physical way we could have come from two ancestors in the recent past. A high profile article appeared in Christianity Todaylast June, in which the following quotes appeared:
“Collins’s 2006 bestseller, The Language of God: A Scientist Presents Evidence for Belief [4] … reported scientific indications that anatomically modern humans emerged from primate ancestors perhaps 100,000 years ago—long before the Genesis time frame—and originated with a population that numbered something like 10,000, not two individuals.”
“In a recent pro-evolution book from InterVarsity Press, The Language of Science and Faith, Collins and co-author Karl W. Giberson escalate matters, announcing that ‘unfortunately’ the concepts of Adam and Eve as the literal first couple and the ancestors of all humans simply ‘do not fit the evidence’.”5
Collins has not restricted himself to the printed word, however, as he has been saying things like this all over the country, including a recent address he gave at Pepperdine University, when he said:
“There is no way you can develop this level of variation between us from one or two ancestors.”6

During an interview on National Public Radio he reiterated these claims, as did another BioLogosfellow, Dennis Venema, who said:
“You would have to postulate that there’s been this absolutely astronomical mutation rate that has produced all these new variants in an incredibly short period of time. Those types of mutation rates are just not possible. It would mutate us out of existence.”7

BioLogos has thrown down the gauntlet, and, because of their status, theistic evolution seems to have suddenly come from a dismal place in the rear to perhaps the forefront of all the alternative views of Genesis. Yet, not everybody has been convinced by the strength of their arguments. In that same NPR piece, Al Mohler, President of the Southern Baptist Theological Seminary,8 said,
“The moment you say ‘We have to abandon this theology in order to have the respect of the world,’ you end up with neither biblical orthodoxy nor the respect of the world.”9

Mohler and others like him are willing to stand in the face of a significant challenge. Why is this? Perhaps it is because Dr. Mohler knows more than the average person about the relationship between science and faith. Could it be that he also knows more about science in general? Mohler is certainly right about the lack of respect one receives from the world when they mix evolution and Christianity. See the contempt coming from arch-atheist Richard Dawkins:
“Oh, but of course, the story of Adam and Eve was only ever symbolic, wasn’t it? Symbolic? So, in order to impress himself, Jesus had himself tortured and executed, in vicarious punishment for asymbolic sin committed by a non-existent individual? As I said, barking mad, as well as viciously unpleasant.”10

Dawkins pulls no punches when dealing with Christians who also hold to evolution:
I think the evangelical Christians have really sort of got it right in a way, in seeing evolution as the enemy. Whereas the more, what shall we say, sophisticated theologians are quite happy to live with evolution, I think they’re deluded. I think the evangelicals have got it right, in that there really is a deep incompatibility between evolution and Christianity … ”11

Getting to the root issue


It cannot be overstated that in each of the examples given above, the two theistic evolutionists are basing their conclusions on evolutionary assumptions. Specifically, they are appealing to deep time common ancestry mutation/drift/selection as the sole explanation of human genetics. They do indeed have a tremendous amount of data available to them, including the massive amounts generated by the Human Genome Project,12 the ENCODE project,13 the HapMap project,14 and the ongoing Thousand Genomes project. Yet, since these are public databases, creationists have access to the same data. Even while the world is soaking up their claims, why is it that the creationists are not running away?
What would occur at the Flood, over a millennium and a half later, when the world population was reduced to eight people, with only three reproducing couples, of whom the three men are brothers?
Needless to say, I take great exception to the dogmatism of the BioLogosspokespeople. I do not believe the data support their conclusions and I believe it is entirely unfair to exclude the creation model without ever considering what the implications of the model would be (in scientific terms, they failed to propose a null hypothesis that could be ruled out by the evidence). I have written about the predictions of a straightforward biblical model several times, including my articles on Adam, Eve, and Noah vs. Modern Genetics, The Neutral Model of Evolution and Recent African Origins, and Does Genetics Point to a Single Primal Couple?
There are two issues at hand. The first is their a priori exclusion of the biblical model from any and all consideration—following ardent atheists like Richard Lewontin. The second is their appeal to mutation as the sole source of genetic diversity. Of course there has not been enough time to accumulate all the diversity we see in people today if Adam was homozygous at all loci.15 But that is a straw-man argument. Why would anyone believe Adam had no genetic diversity built into his genome from the beginning?
As we will see, the amount of genetic diversity within people alive today, coupled with the distribution of alleles among world populations, is strong testimony to an original Adam. Add this to the genetic effects of the biblical Flood (with its severe but short population bottleneck) and the Tower of Babel (with its subsequent partitioning of the genes that were formerly on board the Ark) and we can go a long way to explain human genetic history, from a biblical perspective, while using the genetic data available to date.

Analysis of the data at hand


I believe Collins et al. have made a grievous mistake and that the data actually stand in contradiction to their claims. The remainder of my arguments will focus on an analysis of the HapMap16 data. This particular dataset includes over 1,300 people from 11 world populations. HapMap sequenced over one million individual DNA ‘letters’ (nucleotides) scattered through the genomes of each person in the study, with an average distance of 2,800 nucleotides between the sequenced letters.17 Thus, they covered a huge proportion of human genetic diversity and one can use the data to address many questions about human history. In fact, I have this data on hand and have spent a considerable amount of time analyzing it as I attempt to build a creationist model of human genetic history (I am not working on this alone!).
Relative proportions of the various types of variable positions in the HapMap dataset.
Figure 1. Relative proportions of the various types of variable positions in the HapMap dataset.
There are approximately 10 million common variants in the human genome. Most of these (several million) are quite common and can be found in most or all world populations. HapMap chose to focus on a selection of these.
When I began to analyze the data, I was at first struck by several things thatappeared to support the evolutionary model. For example, Figure 1 displays the relative proportions of the alleles analyzed by HapMap. One can easily see that the bulk of allelic variants are transitions18 (A/G or C/T). These are chemically (thus statistically) more likely than the transversions (A/C, A/T, C/G or G/T). Why are the two types of transitions evenly balanced? Because an A to G change on one strand creates a G to C change on the reverse strand of DNA, and vice versa. Given millions of years of random mutation, one might expect to find 1) more transitions than transversions and 2) equal levels of the reverse complements, because mutations should appear randomly on either strand. This second rule is followed in all the variant classes except between A/T and C/G, and could be interpreted as functional conservation of C and G position in the genome. This is not evidence against the creation model, however, as I do not believe the creation model makes any specific prediction about these ratios.19

A/G allele frequency variation within human chromosome 22 in the CEU population (people of European descent) of the HapMap data.
Figure 2. A/G allele frequency variation within human chromosome 22 in the CEU population (people of European descent) of the HapMap data. Over 7,000 alleles are plotted (tick marks on the X axis denote intervals of 100 alleles). Alleles are sorted according to frequency with the proportion of A increasing from left to right. A similar plot can be obtained for any of the other populations in the study and they more or less follow the same curve, with some population-specific deviations from this particular curve.

A second type of analysis that seems to support the evolutionary model can be seen in Figure 2, where I plot the allele frequencies of all A/G variants on human chromosome 22 within the CEU population (people of European descent). There is a continuous distribution in this figure, with all possible frequencies of A and G found among the many alleles. At first glance, this appears to reflect millions of years of mutation, selection, and drift, for it would take a very long time for any new mutation (by definition starting at a very low frequency in the population) to approach anything like 10%, let alone 40 or 50%.
George Campbell, the politically and scientifically astute 8th Duke of Argyll wrote an essay in the late 1800s where he excoriates the “reign of terror” precipitated by the evolutionists against all opponents. While discussing how one of Darwin’s pet theories (on coral atoll formation) had been disproved after many years of strident support, he said, “And here we learn the important lesson that an hypothesis may adequately account for actual facts, and yet nevertheless may not be true.”20,21 We would do well to heed this warning, for the HapMap data, and the theistic and non-theistic evolutionists’ analyses of these data, are not what they seem at first glance.
Genetic drift in haploid systems (e.g., mitochondrial DNA, Y chromosomes, or last names) in a small population.
Figure 3. Genetic drift in haploid systems (e.g., mitochondrial DNA, Y chromosomes, or last names) in a small population. The individuals represented in each row were assigned 0, 1, or 2 children at random (the total number of children was always 10) each generation. Because the population is small and the size static, drift occurs rapidly, with fixation reached at generation 20 in this example.
In order to illustrate why Figure 2 is not predicted by evolutionary theory, refer to Figure 3. In this theoretical population of 10 reproducing couples, an allele starts off with ten variants (A–J). If this were mtDNA, only the females would be shown. To keep the population constant, each couple has 0, 1, or 2 female children, at random, each generation. It is easy to see that one or more variants are lost from this small population for the first several generations. Eventually, only two variants are left (F and I). At generation 12, they both represent half of the lineages and have an equal probability of persisting, but, due to chance alone, one of them eventually goes extinct. This is a simple illustration of genetic drift, but it illustrates one salient point—the likelihood of an allele reaching fixation is equal to its frequency at any specific point in time. Rare alleles are more likely to be lost. Common alleles are more likely to persist and are more likely to run to fixation.
Allele frequencies after many generations in a modeled human population.
Figure 4. Allele frequencies after many generations in a modeled human population. This figure shows how mutations accumulate in a population as it approaches mutation-drift equilibrium.22 Note the abundance of rare mutations and the general lack of polymorphisms above 20%.
In Figure 4, I show the results of mutation accumulation in a theoretical human population modeled with the program Mendel’s Accountant.23 This is a typical result that can be obtained using a range of parameter settings in both stationary and slowly-growing populations. Despite several thousand generations of selection and drift, there are few mutations in the central portion of the chart. This is due to drift. New mutations are, by definition, rare and are found on the left-hand edge. Thus, there will always be more rare alleles than common ones. These new alleles are constantly being pushed off the chart to the left by random drift. The infrequent mutation that reaches over 50% abundance suddenly experiences a ‘push’ to the right. Thus, the center is like a hill, with drift pushing alleles away from the middle in either direction. Because most of the mutations that enter from the left are lost, one would never expect an even distribution as in Figure 2.
Even though Figure 2 appears at first to support evolutionary theory, in fact it does not. The allele frequency distribution has too many alleles in the middle range. HapMap sequenced common alleles by design, ignoring rare alleles restricted to certain subgroups. In so doing, it did two things: 1) revealed the many unexpected alleles in the middle range, 2) inadvertently focused on ‘created diversity’ (more below), and 3) gave us a wonderful model of the effects of starting from a single ancestral pair only several thousand years ago.
Allele frequency curve for 1,000 theoretical A/G variations within Adam.
Figure 5. Allele frequency curve for 1,000 theoretical A/G variations within Adam. Since he has two copies of each autosome (excluding X and Y), all alleles must be in a 50:50 ratio.

What would we expect if the Bible were true?


Why is it that nobody at BioLogos has appeared to address the biblical model? Why have they swallowed the assumptions of evolutionary theory wholesale and used those assumptions to make strong conclusions in support of this theory? Their circular reasoning is obvious. However, it would not be wise to stop there. We need to introduce a model of what we would expect to be true if Adam really lived and if he lived only 6,000 years ago.
In Figure 5, I display a theoretical allele frequency curve for the human “population” at Creation. Here, I am assuming that Eve is a clone of Adam, because she was made from a hunk of Adam’s flesh (albeit the one bone that can re-grow). In this case, because she was female, Adam’s Y chromosome would have been removed and his X chromosome doubled, although this is not specifically necessary genetically or theologically.24

When Adam and Eve start having children, they are going to be given a random set of the alleles within the parents. In the case of two heterozygous individuals, we would expect 25% of the allele in each child to be AA, 50% to be AG, and 25% to be GG, according to the laws of genetics we all learned in school. Assuming no linkage, the allele frequency curve for each individual would appear as in Figure 6.
frequency curve for each of Adam and Eve’s children, assuming initial distribution as in Figure 5.
Figure 6. Allele frequency curve for each of Adam and Eve’s children, assuming initial distribution as in Figure 5.
Allele frequency curve for a 1st-generation population composed of two children from Figure 6.
Figure 7. Allele frequency curve for a 1st -generation population composed of two children from Figure 6.

Allele frequency curve for a 1st-generation population composed of four children from Figure 6.
Figure 8. Allele frequency curve for a 1st-generation population composed of four children from Figure 6.
Allele frequency curve for a 1st-generation population composed of sixteen children from Figure 6.
Figure 9. Allele frequency curve for a 1st-generation population composed of sixteen children from Figure 6.
If we pool their children to create a population-level allele frequency curve, we get the results we see in Figures 7–9.
Can you see what is happening in Figures 7–9?25 As more children are added to the population, the population-level allele frequency curve starts to approach the initial, flat-line distribution of Adam (Figure 5). If Adam and Eve could have had a million children, the curve would be perfectly flat. However, they were limited in how many children they could have had and so the allele frequencies must drift in the first generation, with the amount of drift depending on the number of children. We are still far away from the HapMap distribution of Figure 2, but this is a step in the right direction. If we add new mutations to the population over time, however, low-frequency mutations will be added to the curve, as modeled in Figure 10. This is an additional step toward the distribution of Figure 2.
Same as in Figure 9, but with new mutations added to the ends of the distribution.
Figure 10. Same as in Figure 9, but with new mutations added to the ends of the distribution. The extra mutations are not meant to model anything specific. However, this final figure in the series does illustrate the general trend of genetic drift (change in allele frequency through random sampling from one generation to the next), how it is more prevalent in the small initial population, and how new mutations over time affect the allele frequency distribution.

Computer modeling of biblical genetics


At this point, we need something more powerful to model allele frequency changes in human history under the biblical parameters. To do this, I wrote a program in Perl that starts with a founder (Adam) and assigns him 1,000 heterozygous alleles. I assume Eve is a clone26 and give her the same set of variations. As they start having children, the children will be assigned a spouse after reaching a user-defined age of maturation. Spouses are chosen at random from all available unmarried people of the opposite sex. I assume mating for life. Also, unlike many other modeling programs that use discrete generations, I use overlapping generations. Thus, a person can marry anyone of the opposite sex, regardless of age (although an old, unmarried person is unlikely to exist) or relational status (with the exception of ancestors). Because I am tracking individuals, not averages, there is a greater demand on memory allocation, so the size of the population I am able to model is limited. However, this does allow me to model something that should more or less reflect biblical history.
There are three main parameters in this population model, the age of sexual maturity (Ym), the age of reproductive senescence (Ys), and the spacing between children (Yc). The combination of these three controls the total number of children per family and this, in turn, directly controls the amount of drift in subsequent generations (Figure 11).
Allele frequency changes in a population starting with two individuals.
Figure 11. Allele frequency changes in a population starting with two individuals. Samples were taken every 100 years in a population with the following parameters: Ym = 50; Ys = 350 (roughly based on Genesis 5 figures); Yc = 20. Adam and Eve are at t0, represented by the horizontal line at 0.5. Note that almost all of the allele frequency change occurs in the first 100 years. Once the exponentially-growing population reaches anything more than a few hundred individuals, drift effectively ceases. This is true irrespective of the initial settings of the main parameters. In this model run, there were more than 100,000 people after 800 years, the limit of computer memory.
The evolutionary models espoused by BioLogos and others depend on genetic drift and natural selection to influence allele frequencies. Because drift occurs so slowly in a large population, millions of years are needed to account for the allele frequency spectrum of modern man. The biblical model, however, starts with the smallest population possible (two individuals) and expects rapid drift in the antediluvian population. What would occur at the Flood, over a millennium and a half later, when the world population was reduced to eight people, with only three reproducing couples, of whom the three men are brothers? Using the same parameters as in Figure 11, I ran the model to simulate 1,500 years of marriage and birth, stopping every 500 years to reduce the population to three founding couples made up of three brothers (full siblings) and three women selected at random from the available unmarried women (Figure 12). From Figure 11, I knew that drift would effectively stop in any exponentially growing population prior to 500 years, so this seemed like a fair strategy.
What can we learn from Figure 12? First, as before, drift occurs from Adam and Eve (horizontal blue line) to the first sampling at 100 years (jagged brown line) and nearly no drift is noticeable 400 years later (smooth green line). A bottleneck occurred after year 500. One hundred years later, the population has drifted even farther (jagged dark blue line). In fact, each bottleneck drives the allele frequency distribution closer and closer to the modern average.
A model run with the same parameters as in Figure 11
Figure 12. A model run with the same parameters as in Figure 11, but with three repetitive 500-year population bottlenecks down to three couples, with the men all full sibling brothers.

Note also that some amount of diversity in Adam is lost after several bottlenecks. The final curves have a significant number of alleles that are 100% A or 100% G, meaning that the initial A/G variation in Adam was lost. Population geneticists call this ‘fixation’, and this was a surprising result for me as I had not previously considered that some of the diversity of Adam could have been lost this way.

Is it fair to model successive population bottlenecks when the Bible says there was only one? Actually, yes, for the only thing of importance is the history of Noah and his family. My model assumes random mating, but this is contrary to human history and human nature. If there was any degree of inbreeding (due to geographic separation of the antediluvian population, fighting among clans, racism or family snobbery, etc., etc.), drift would have been likely to occur. Also, this is a model. The point is to show what is possible and compare it to what is likely, not to make an absolute statement about history. In the end, the results are quite friendly to the biblical account.


Additional HapMap analyses


There are several other ways to analyze the HapMap data that might inform us about history. In Figure 13, I compare the allele frequencies of 10,000 randomly selected A/G variants within the CEU and YRI (individuals from the Yoruba tribe of Western Africa). Figure 14 shows the 95% confidence intervals of the same data. It is clear that these two populations came from the same source population, for the frequency of any allele in one population is a fair predictor of the frequency of that allele in the other. Also, the fact that each allele does not have the exact same frequency in both is testimony that genetic drift has occurred in the populations after they split, but also that not so much time has elapsed as to erase the commonality. Evolutionists accept this as well, many claiming the Out of Africa theory as an explanation. The multiple subpopulation bottlenecks that occurred when the clans were divided at the Tower of Babel event should be the creationist explanation.
Allele frequencies of 10,000 randomly selected A/G variants, YRI vs. CEU.
Figure 13. Allele frequencies of 10,000 randomly selected A/G variants, YRI vs. CEU.
One of the purposes of the HapMap project was to examine the history of chromosomal recombination in human history. The reason I started working on this data was to see how much of the original genomes of Adam and Eve could be seen in the modern genetic data. I have not yet gotten to this analysis, however. This will have to be the subject of further explorations. For now, we can be satisfied with several facts in our favor: 1) There are places in the human genome that have not recombined in all of human history. 2) There are not as many recombination blocks as predicted by evolutionary theory (this is one reason they have a bottleneck in Out of Africa scenarios). And 3) between two and four recombination blocks (e.g., the amount that could fit into Adam and Eve) can explain over 95% of the available block data. One thing in the evolutionists’ favor is their contention that the blocks found across the world are a mere subset of those found in sub-Saharan Africa, but this claim needs detailed examination.

Created diversity vs mutation


As detailed above, one of the arguments from BioLogos is that there has not been enough time to accumulate the mutations found among people today if we came from Adam and Eve. A corollary to that is, we could not survive that kind of mutation load. As I said above, however, this is assuming Adam had no heterozygosity, which is ridiculous. How much created diversity might we assume? One way of estimating this is to look at the number of alleles shared among all world populations. In the HapMap data, every single measured allele falls into this category. Each of these is also biallelic, that is, it has but two alternate letters (Aor G, C or T, etc.). Part of this was by design as the HapMap alleles were carefully selected, but this is a good statement about the state of human genetic diversity in general: most variation is biallelic and can be found in most populations. Thus, well over one million heterozygous, biallelic loci must have been present at Babel. These also should have been present at the Flood and at Creation a mere ten generations prior to that. Yet, HapMap did not measure every allele. Since most of the genetic diversity known today can be found among multiple world populations, most of the variation should have been here from the beginning.
95% confidence interval for the data in Figure 13.
Figure 14. 95% confidence interval for the data in Figure 13.
Is it possible for a single person to carry this much diversity? I ran an analysis of the HapMap data to measure the amount of heterozygosity within the HapMap individuals. Population-level differences were slight, with a global average of 4.33 ± 0.234 × 105(±SD) heterozygous alleles per person. Thus, approximately 30% of all HapMap alleles are heterozygous within each person. If there are 10 million common variants, a single individual would be expected to carry upwards of three or four million heterozygous alleles! Because most people are phenotypically normal, there is no reduction in fitness associated with these high levels of heterozygosity. Why should there be if most of this variation was created by God and engineered into the original genome? I expect Adam had about 10 million or more heterozygous loci and that each of his children had half that much.
Some alleles, however, have been added to the population through mutation. How much genetic diversity is due to mutation? Given the 10 million common variations in the human genome, there are many more ‘private’ and very rare variants that occur in one or a few individuals in specific populations. These should be mutations that have occurred since the Flood and Babel. With an average (modern) generation time of 30 years, there have only been about 150, perhaps as many 200, generations in all of human history. Assuming a conservative modern estimate of 100 new mutations per person per generation, that gives us between 15 and 20 thousand mutations per person. This is a huge number when added up across the world population, and most of these should be unique (perhaps even totaling more than the amount initially created). Yet, on the individual level, it might be expected that only a small fraction (less than 0.01%) of heterozygosity is due to mutation.



It is disingenuous for Biologos to claim no evidence for Adam and Eve for several reasons. First, their conclusions are based on evolutionary assumptions. One cannot legitimately claim something to be proven without testing the assumptions behind that claim. To do otherwise amounts to circular reasoning and question begging, and a rejection of any alternative theory following from this is thus reduced to nothing more than a straw man argument. Second, the majority of data fit nicely into the straightforward biblical model, including a single starting couple a mere 6,000 years ago. While there are several unresolved issues with the biblical model as it relates to the data at hand, the same can be said about every evolutionary model, so one cannot conclude that the Bible has been invalidated by the available evidence. Albert Einstein is rumored to have opined, “A thousand experiments cannot prove me right. A single experiment can prove me wrong.” This is sound logic. Francis Collins andBioLogos would do well to heed his advice.

Related articles

Evolutionary syncretism: a critique of Biologos
Harmony and discord
Is there enough time in the Bible to account for all the human genetic diversity?
Adam, Eve and Noah vs Modern Genetics
The Neutral Model of evolution and recent African origins
Does Genetics Point to a Single Primal Couple?

Further reading

Genetics Questions and Answers
Creation Compromises
Countering the Critics Questions and Answers




  1. For example, see Is there enough time in the Bible to account for all the human genetic diversity? Return to text.
  2.  Evolutionary syncretism: a critique of BioLogos. Return to text.
  3. CMI’s Statement of Faith. Return to text.
  4. See Lael Weinberger’s refutation, Harmony and discord, a review of The Language of God: A Scientist Presents Evidence for Belief by Francis S. Collins, J. Creation 21(1):33–37, 2007. Return to text.
  5. The Search for the Historical Adam, Christianity Today, pp. 23–24, June 2011. Return to text.
  6. Francis Collins speaking at the Christian Scholars’ Conference at Pepperdine University, 2011; see Noted scientist tackles question of religious faith, Malibu Times, 29 June 2011. Return to text.
  7. Haggerty, B.B., Evangelicals question the existence of Adam and Eve, NPR, 9 August 2011. Return to text.
  8. See interview with Lael Weinberger, Creation 33(1):16–18, 2011. Return to text.
  9. Haggerty, B.B., Evangelicals question the existence of Adam and Eve, NPR, 9 August 2011. Return to text.
  10. Dawkins, R., The God Delusion, p. 253, emphasis in original, 2006. See detailed critique. Return to text.
  11. Howard Condor interviewing Richard Dawkins on Revelation TV, Feb 2011; Return to text.
  12. Batten, D., Catchpoole, D., Wieland, C., Message Mania: Deciphering the human genome: what does it mean? Creation 23(3):16–19, 2001.Return to text.
  13.  Astonishing DNA complexity update. Return to text.
  14. Biswas, C., Founder mutations: evidence for evolution? Journal of Creation 20(2):16–17, 2006. Return to text.
  15. Our chromosomes come in pairs, with one copy of each coming from our father and the other coming from our mother. Adam and Eve had no parents, but Collins sets up a straw man by saying that Adam had identical chromosome pairs and, thus, no built-in variation. See Variation and natural selection versus evolution from Refuting Evolution. Return to text.
  16. Return to text.
  17. Note that there are 3 billion DNA letters in our genomes, with each of our hundred trillion cells (excluding red blood cells, which do not have nuclei) carrying two copies. Return to text.
  18. Purines are double-ringed nucleotides and pyrimidines are single-ringed nucleotides. A transition is a purine-purine or pyrimidine-pyrimidine swap. It is easier to get a transition than a transversion, which would involve a purine-pyrimidine swap. Return to text.
  19. One must carefully consider the ‘sphere of prediction’ inherent in any model or hypothesis. Different models incorporate different constraints and different specific predictions can be drawn from them. For example, the biblical model necessitates a genetic bottleneck associated with Noah’s Flood. Evidence for a genetic bottleneck has been found. The result is that evolutionists added this bottleneck to the Out of Africa hypothesis, even though there was no specific prediction that called for such a bottleneck. It is consistent with the theory even though not predicted from it. Likewise with the HapMap allele data from Figure 1, Creation makes no specific prediction in this case. Return to text.
  20. Duke of Argyll, A Great Lesson, The Nineteenth Century 22:308, September 1887. Return to text.
  21. See also Corals, genes and creation: Jonathan Sarfati chats with CMI’s marine biologist and geneticist Dr Robert Carter, Creation 33(1):53–55, 2010. Return to text.
  22. Mutation-drift equilibrium is that theoretical point at which mutations are entering the population at the same rate at which they are being removed by genetic drift. Return to text.
  23. Sanford, J., et al., Mendel’s Accountant: A biologically realistic forward-time population genetics program. SCPE 8(2):147–165, 2007; Return to text.
  24. Theological support for the clone theory is that the Bible attributes the Fall to Adam (Romans 5, 1 Corinthians 15), and our redemption to Jesus as “kinsman-redeemer” (Isaiah 59:20), who by definition is related by blood to those whom he redeems. I.e., all Adam’s descendants are affected by the Fall, but all are capable of redemption because Jesus, “the last Adam” (1 Corinthians 15:46) is also a descendant of Adam (Luke 3), thus our blood relative. But if Eve were genetically different, would she really be related to either the first or the last Adams? CMI is not dogmatic on this however. Return to text.
  25. The interested student might notice that these curves follow Pascal’s Triangle, level = n * 2 + 1. For a single individual, the ratio is 1:2:1 (level 3). For two individuals, the ratio is 1:4:6:4:1 (level 5). Etc. Return to text.
  26. With only the ‘X’ chromosome of Adam’s X-Y (male) pair duplicated to result in an X-X (female) pair in Eve. Return to text.

Frankly, Francis Collins should know better.  His blind acceptance of Darwinism before consideration of the Creation model makes him liable for error and that error is one that has consequences.   I have mentioned the term "error cascade", in which an assumption made at the start being wrong causes all following assumptions and actions to also be wrong, leading to possibly disastrous results.  Being a geneticist, Collins should know some basics about DNA that make Darwinism seem absurdly improbable.  For example:

Of Codes and RNA — August 26th, 2011 by Ann Gauger

Origin of life research has problems, and here’s why. DNA carries the information necessary to build proteins. It performs no chemistry and builds no cellular structures by itself. Rather, the information in DNA must be translated into proteins. But there is no direct way to convert a given DNA sequence into a protein sequence—no direct chemical association between DNA nucleotides and amino acids. Some sort of decoding mechanism is needed to translate the information encoded in DNA into protein.

That decoding mechanism involves a whole host of enzymes, RNAs and regulatory molecules, all functioning as an elegant, efficient, accurate and complicated system for copying and translating the information in DNA into a usable form. (For a comprehensive and engaging description of how information is processed in the cell, and how this process has been discovered, see Stephen C. Meyer’s Signature in the Cell [1].)

The problem is, this decoding system is self-referential and causally circular. Explaining its origin becomes a chicken and egg problem. Building the machinery that translates DNA into protein requires the prior existence of DNA, RNA and protein, all three. This should give us pause, because we have no naturalistic explanation for problems involving causal circularity.

So when it was discovered that some RNAs could carry out (very limited!) chemical reactions, scientists seeking a purely materialistic explanation for life’s origin were thrilled. Perhaps here was the solution to the conundrum. Perhaps RNAs could be both catalysts and information carriers. Perhaps the first living world was RNA-based.

Fast forward to now. Researchers continue to try to design RNAs that can copy themselves, and try to expand the range of chemistries they can carry out. The RNA world, if it ever existed, though, would be a very impoverished place, based on what human designers have been able to produce so far. And the problem of how an RNA world could become a DNA/RNA/protein world would remain.

Enter the Direct RNA Templating (DRT) model of Michael Yarus et al. [2]. The hypothesis was originally based on the discovery that the activity of one RNA catalyst could be blocked by the presence of the amino acid arginine. From this result Yarus hypothesized that perhaps other RNAs would show an affinity for particular amino acids. In a series of papers he and his coworkers identified other such RNAs and, based on statistical analysis, they argued that these RNAs contained a higher than expected frequency of triplets corresponding to the particular codons or anticodons now used to specify that amino acid in the modern genetic code [3].

But is their analysis correct? In a peer-reviewed paper published this week in BIO-Complexity, Stephen C. Meyer and Paul Nelson take on the DRT model [4]. They carefully examine the claims of Yarus et al. and find them wanting. Inadequate null hypotheses, arbitrary selection of data for analysis, and unrealistic assumptions about prebiotic chemistry are just a few of the problems. Rather than go through their arguments here, I encourage you to read their paper yourself.

Why does it matter? Critics of intelligent design have advanced the DRT model as the answer to the sequencing problem—how genetic information in RNA (in the hypothetical RNA world) eventually could have been translated into more stable and versatile proteins. Based on the analysis in this paper, however, the sequencing problem has not been solved, even partially. There is no natural affinity between RNAs, amino acids, and codes. And the origin of life remains inexplicable in materialistic terms.

[1] Signature in the Cell
[2] doi:10.1126/science.3381099
[3] doi:10.1007/s00239-009-9270-1
[4] doi:10.5048/BIO-C.2011.2


In fact, the origin of life by natural means seems to have been disproven by research.   Will the secular scientists begin to think about the results of their tests and realize it?

Explaining Life by Explaining it Away — February 6th, 2010 by Douglas Axe

Reading Stuart Kauffman’s book At Home in the Universe some fourteen years ago, I encountered the following:
I hope to persuade you that life is a natural property of complex chemical systems, that when the number of different kinds of molecules in a chemical soup passes a certain threshold, a self-sustaining network of reactions—an autocatalytic metabolism—will suddenly appear. Life emerged, I suggest, not simple, but complex and whole, and has remained complex and whole ever since… The secret of life, the wellspring of reproduction, is not to be found in the beauty of Watson-Crick pairing, but in the achievement of catalytic closure. [1]
When chemicals react, they produce different chemicals. So the idea here—call it Kauffman’s conjecture—was that mixtures with a sufficient number of different chemicals are bound to give rise to local compositions that continually replenish themselves through a self-catalyzed network of chemical reactions.  Those special compositions would typically differ from the original mixture, but since they make more of themselves, they should be able to ‘grow’ by establishing themselves repeatedly in local pockets.  The ability to propagate in this way, if proven, would be something like reproduction, only at the low level of chemical composition rather than at the high level of organismal form.

It was clear enough to me why Kauffman and others liked this idea.  If some kind of reproduction and inheritance could conceivably be achieved in systems that are much, much simpler than anything we think of as living, then maybe scientists were making the problem of explaining life much, much harder than it really needed to be.

I saw that, but ultimately I still found the proposal unpersuasive.  It’s not that I had any problem with autocatalysis or reaction networks, but rather that equating such things with life seemed like gross oversimplification—like equating Kauffman’s book with ink and paper.  Even if there was a grain of truth in his proposal, it left too much unexplained.

At the time, my work was focusing on the profound differences between the simple catalysis caused by small molecules and the elaborately orchestrated and stunningly efficient catalysis achieved by enzymes—the catalysts of life.  Kauffman was equating complexity with the sheer numbers of chemical species and reactions, whereas my concern was with the mode of reaction.  Since Kauffman’s model employed reactions that were fundamentally simple, with no discernable prospect of rising above this, I saw no satisfactory connection between his model and life.

But the difficulty of explaining life’s origin makes even hints of progress a big deal, and many saw in Kauffman’s simple model the potential for something bigger.  The reason for their optimism, I think, was expressed by Daniel Dennett around the time of Kauffman’s writing: “Evolution will occur whenever and wherever three conditions are met: replication, variation (mutation), and differential fitness (competition).” [2] The hope was that if autocatalytic networks can deliver those three things, then whatever they lack in comparison to modern life they can acquire through progressive evolution.

I think it’s fair to say that the optimism has faded as the years have passed without anything like a convincing demonstration—at least nothing that could be called “autocatalytic metabolism.” Now it seems things may be drawing to a close with a new paper by Vasas, Szathmáry, and Santos. [3] Their work calls this whole notion of life starting with raw metabolism into question by seriously undermining the biological relevance both of Kauffman’s conjecture and of Dennett’s dictum.

The paper’s title is a diplomatic statement of its main conclusion: Lack of evolvability in self-sustaining autocatalytic networks constrains metabolism-first scenarios for the origin of life. [4] It becomes clear on reading the paper that the word constrains is here being used euphemistically. After testing the effect of fitness on the evolution of their model compositional assemblies, they report that “some slight relative increases and decreases in their replication-mutation equilibrium frequencies are detected, but the effects are so minor that it is hard to think of any evolutionary relevance.”  The problem is that the behavior of the whole system is almost completely determined by the inherent chemistry, leaving no room for selection to do anything interesting.

The paper’s conclusions speak to the whole field of pre-biotic evolution:
There is always a danger in using terms that acquire implicit theoretical content as, for example, the term evolution that in biology is normally used to mean Darwin’s theory of evolution by natural selection… Restricting ourselves to this usage of the word “evolution,” the computed population dynamics of growing noncovalent molecular assemblies that undergo splitting when a critical size is reached clearly illustrates that compositional assemblies do not evolve.
And as a finale:
We now feel compelled to abandon compositional inheritance as a jumping board toward real units of evolution.
Now, I’m not suggesting that they favor intelligent design.  I’m simply pointing out that yet another once-favored alternative to ID seems to have been reduced to an epitaph.  Moreover, while the excellent work of Vasas, Szathmáry, and Santos brings clarity to the situation, we should have known this day would come all along.  How?  Because whether or not there was a jumping board to real evolution, it’s virtually certain that there isn’t a jumping board to real life.

Think of it this way.  If no conceivable mixture of small molecules provides even a faint hope for the emergence of metabolism catalyzed by genetically encoded enzymes, then whatever these mixtures may or may not do, they can’t explain life as we see it.  And as the evidence now stands, one would be hard pressed to argue that there is even a faint hope. Vasas, Szathmáry, and Santos have urged the origin-of-life community to keep the true essence of Darwinian evolution in mind, which is clearly important.  Even more important, though, is the need to keep the true essence of life in mind.

[1] ISBN: 0-670-84735-6
[2] ISBN: 0-713-99090-2
[3] doi:10.1073/pnas.0912628107
[4] The actual title of the PNAS early edition has the word ‘constraints’ in place of ‘constrains’, which appears to be a typographical error. PubMed lists the title as: Lack of evolvability in self-sustaining autocatalytic networks: A constraint on the metabolism-first path to the origin of life.


Again, the contempt coming from arch-atheist Richard Dawkins:
“Oh, but of course, the story of Adam and Eve was only ever symbolic, wasn’t it? Symbolic? So, in order to impress himself, Jesus had himself tortured and executed, in vicarious punishment for asymbolic sin committed by a non-existent individual? As I said, barking mad, as well as viciously unpleasant.”

It would suggest that it is Richard Dawkins and not Jesus Christ who is "barking mad."   Darwinism has actually been disproven by the findings of modern science, it only falls to the sensible among them to realize this and then the entire Darwinist paradigm will crash to the ground.   It will enter the Hall of Laughability and things like Nebraska Man and Pakicetus will be punchlines to scientific jokes.   Meanwhile Jesus Christ will still be the Living God and welcoming all who will come to Him until the time God has decided to put an end to this world.  Haste the day that Darwinism is recognized for the joke that it is!