God’s foreknowledge of our choices

Understanding our Creator is not an easy thing. Learning about His creations certainly help us understand about our Creator. If we look into any designed object, we certainly get some insight about the mind of the designer. Hence, I believe the information in this blog will help answer some of the most difficult questions in Christianity. The following question was asked by a Calvinist: Did God know specifically before the foundation of the world who would go to Hell and on to the Lake of Fire? Did He know? Yes or No? The question have specific implications. If God knew what choices we will make, then the future is already decided. If God doesn't know the future, then God is not sovereign.

We do have a choice

Scripture is filled with God giving us a choice.
Deut 30:19 “I call heaven and earth as witnesses today against you, that I have set before you life and death, blessing and cursing; therefore choose life, that both you and your descendants may live;
God is giving the children of Israel a choice. The first choice God gave Adam was not to eat from the tree of knowledge of good and evil as in Gen 2:16-17.  Nearly all the parables of Jesus are all about the choices that we must make to follow Him. Hence, without doubt, God is giving us a choice.

Future choices already known

Scripture also supports God knowing the future and the choices that we will make.
Luke 22:31-34 And the Lord said, “Simon, Simon! Indeed, Satan has asked for you, that he may sift you as wheat. But I have prayed for you, that your faith should not fail; and when you have returned to Me, strengthen your brethren. But he said to Him, “Lord, I am ready to go with You, both to prison and to death. Then He said, “I tell you, Peter, the rooster shall not crow this day before you will deny three times that you know Me.”
If you look into Peter's denial, Christ knew every detail of it and the choice Peter will make even before it happened.

Decisions and Choices

From the Scriptures, we understand the following points about God.
  • We were given a choice by God
  • Our future choices were already known to God
As you can see, the above two points are contrary to each other. If we do have a choice, then the future is not decided. If God already knew the future, then the future is already decided. This gave raise to Calvinism and Arminism. You can plot every single protestant denomination somewhere in between Calvinism and Arminism because Scripture does support both.

What does God know?

I must confess, I certainly does not know what God knows for He is beyond my ability to imagine. However, I want to show one of God's creation 'Quantum Mechanics' which is just the tip of an iceberg and it opens a whole new knowledge of God's handiwork and design which helps to understand the mind of the Designer. I am not going to explain about 'Quantum Mechanics' or any technical jargon here but want to show the conclusions and the implications it has on Christianity. If you look at Delayed Choice Quantum Eraser experiment based on the entangled particle, the future choices with the other entangled particle can be known even before the choice of measuring or not measuring was made. If man can do this, God can certainly know the choice of all men even before they do it. Yet, there is a "very important" catch. The choice that we make in the double slit experiment, will change the particle, as though the particle went back in time and even changes as though it has always been a particle from the very beginning. Hence, the choice that we make even changes the past. What God knew about my choice before the foundation of the world depends on my choice now. The questions we ask are always classic and not quantum, yet the entire universe was created and operates based on quantum mechanics at quantum level. A classic has only 'Yes' or 'No' but a quantum state has a superposition of Yes and No - both at the same time. It is important to acknowledge that such a state of superposition with two or more choices do exist in universe. Every decision that we will ever make is in superposition. Hence, God knows all the choices we have and all that we will ever do. Being in superposition is more like "all knowing" which is different from "not knowing". When a choice is made, the superposition collapses (i.e, wave function collapses) and when it collapses, if you go back and look from the beginning, it will be as though the choice was made from the very beginning was the same choice.

Conclusion

Hence, God giving us a choice and He knowing the future does not contradict each other but go together.

Designer 101 for every evolutionist!

I have my own thoughts and response esp., on evolution and the arguments put forward in favor of it using genetics. In this post, I will address every argument put in favor of evolution using standard procedures and methodologies used in most software companies for designing, developing, testing and roll-out of software.

Genetic similarity of humans with primates

One of the most common answers I always find is the genetic similarity of humans with primates. This statement must be analyzed what it means, to understand what is assumed. The assumption here is the consideration of only the genes and the rest of the Junk DNA is useless. Hence, the genes (which are the only biologically significant) are identical up to 90%. A gene is the basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. Every developer has a set of libraries. Most of the developers, don't develop these libraries with common functions from scratch. They put all common functions in one dll or library and link it either statically or dynamically with every other program they require. Hence, a gene is comparable to a function or set of functions, more like a library, a dll file, used in all the organisms that require it. Even though Microsoft Word and Excel loads the exact same set of common libraries and calls same functions, and has similar look and feel, they function differently and both are designed. Human and chimp using same genes for their function which is used as an evidence for evolution, is like saying Microsoft Word and Excel had a common ancestor and evolved because they share the same set of functions and load the same common libraries. Just because a dll is used in a program does not necessarily means the program will use all functions in that dll. A program will use only the functions it requires and the rest will never used. This is exactly why some genes are switched off or inactivated while others function. As we know operating systems came a long way, but does that have a common ancestor and evolved itself? Identical operating systems actually share code, libraries etc but they are always developed. Take Linux for example: They share code from Unix - Does that mean Linux evolved itself from Unix?


Hence, identical genes between species is actually an evidence for Designer at work rather than evolution.

C-value enigma or the Onion Test

Some organisms (like some amoebae, onions, some arthropods, and amphibians) have much more DNA per cell than humans, but cannot possibly be more developmentally or cognitively complex, implying that eukaryotic genomes can and do carry varying amounts of unnecessary baggage. If you look into the code of any developer, you might find unused functions, unused imports, unused libraries, debug and trace information. I personally have the habit of embedding the data within the code to make the code more portable. These things increase the size of the code but not it's functionality. For example, some software doing simple stuff like a dictionary are 100 MB in size, while Stuxnet which brought down Iranian nuclear reactors is just half a megabyte. The size of the code is not directly proportional to it's complexity, which every developer knows this. Any project manager would know that complexity does not depend on the number of code and does not estimate the costs based on lines of code required.
“Measuring programming progress by lines of code is like measuring aircraft building progress by weight.” --Bill Gates
Murphy's law on software engineering states, The chances of a program doing what it's supposed to do is inversely proportional to the number of lines of code used to write it. If this is the case for computer code designed and developed by humans, isn't it a perfect evidence for a grand Designer at work, creating complex organisms with less genomes perfectly satisfying Murphy's law? There is an another logic which is even used in DOS and Windows. If there is a fixed size and you are to write in them, the remaining left over space is huge when the actual information is very less, which makes the overall size huge. The DOS and Windows file systems use fixed-size clusters. Even if the actual data being stored requires less storage than the cluster size, an entire cluster is reserved for the file. This is why when very less information like 1 byte on a million files will not be 1 MB in size but rather, 4 GB for a 4K cluster. Does genome has such features? We do know introns within a gene are removed by RNA splicing indicating some kind of cluster like structures.

Hence, C-value enigma or Onion test is actually an evidence for Designer at work, satisfying Murphy's laws, cluster style design rather than evolution.

Reverse Engineering Genome

Most of the work biologists do today are just reverse engineering the genome, trying to understand it's design and documenting it. Most decompilers provide data region, code region, functions used, the data string used and the entry point. However, none of these luxury exists in genome reverse engineering. All we have is a sequence of code when executed has a specific functions and codons to identify them. Most of the remaining genome, we have no clue. If you look into the structure of any executable file, without having any clue of the structure, you can quickly come to conclusion that most of the info in there is junk. But if you know the actual structure, it isn't junk but actual data in them.


As you can see, the only readable info in the file is MZ. Apart from this, nothing is decode-able without actually having documentation on it.


The same logic is with genome. Just because a sequence of binary code is not a part of a function (or a gene), does not mean it is not used. If I want to be more accurate, a genome is not just a code, but much more to it. A genome is like a code that has instructions to build the computer itself and then install all the required operating systems and the application code and then finally make the computer boot execute the required code in the right order.

Conclusion

I would like to add more, but these are more than enough as it covers most of the arguments used in genetics. It's only a designer can understand and detect the architecture of an another Designer. People who can't detect design or understand the complex architecture do require some designing skills to actually understand them. If they can't, it is better to atleast see the computer word and understand in order to relate and detect design concepts. Evolutionary biologists are not designers or developers which is understandable, but that does not mean they should reject on design concepts and ways to detect design. In 16 trillion bits in my computer, there is not a single 0 or 1 was by chance.

True Age of mt-Eve based on Direct Pedigree Method

Since no one had took effort to calculate the true age of mtEve based on directly observed pedigree method (as I can't find any paper), I am taking that effort now to post it as a blog.

HVR1 Estimation

Based on a recently published paper High Mitochondrial Mutation Rates Estimated From Deep-Rooting Costa Rican Pedigrees, I thought of estimating the age of mt-Eve. The paper is the result of the analysis of HVR1 on 19 deep-rooted pedigree in a population of mixed origin in Costa Rica.

Fig. 1 (High Mitochondrial Mutation Rates Estimated
From Deep-Rooting Costa Rican Pedigrees)

As you can see, there are at-least 7 mutations in 289 transmissions. Which means, there is a probability of (7/289) 0.024221 for every transmission to have a mutation. In other worlds, 1 new mutation can occur every 41 generations.

Now, let us consider how much mutations we have from mtEve. To look into it, let me consider the number of mutations from several FTDNA projects to find the maximum and minimum genetic distance. Kit #50252 from Cumberlandgap-mtdna project as 14 mutations while Kit #258240 has only 3 mutations, from X mtDNA project. As you can see, the HVR1 mutations vary from 3 to 14 as distance from RSRS (or mtEve). There could be even more extremes but, let's consider an average 8.5 mutations from mtEve for HVR1. This is reasonable because, if you take any mtDNA project from FTDNA, you will notice atleast on average 8 mutations in HVR1 for RSRS.

One mutation can occur every 41 generations and humans have 8.5 mutations on average as genetic distance from mtEve. So, there should be 41*8.5 generations from mtEve. If we consider 20 years for 1 generation, we have 41*8.5*20 = 6970 years as the age for mtEve.

The age of mtEve using HVR1 alone gives 6970 years.

HVR1 & HVR2 Estimation - Parsons Paper

In the paper, A high observed substitution rate in the human mitocondrial DNA control region, which includes HVR1 and HVR2, they took samples from Armed Forced DNA Identification Laboratory, Oxford British families, CEPH pedigree cell lines and Old Order Amish pedigree cell lines.

Fig 2. (A high observed substitution rate in
the human mitocondrial DNA control region)
They found 10 mutations in 327 generational events. Which means, there is a probability of (10/327) 0.03058 for every transmission to have a mutation. In other worlds, 1 new mutation can occur every 33 generations.

Now, let us consider how much mutations we have from mtEve. To look into it, let me consider the number of mutations from several FTDNA projects to find the maximum and minimum genetic distance. Based on kits #282059 and #50252 from Cumberlandgap-mtdna project, the maximum mutations for HVR1 and HVR2 from RSRS is 22. Based on kits #N48849 and #N23635 from X mtDNA project, the minimum mutations from RSRS is 10. As you can see, the HVR1 and HVR2 mutations vary from 10 to 22 as distance from RSRS (or mtEve). So, let's consider an average 16 mutations from mtEve for HVR1 and HVR2. This is reasonable because, if you take any mtDNA project from FTDNA, you will notice atleast on average 16 mutations in HVR1 and HVR2 for RSRS.

One mutation can occur every 33 generations and humans have 16 mutations on average as genetic distance from mtEve. So, there should be 33*16 generations from mtEve. If we consider 20 years for 1 generation, we have 33*16*20 = 10560 years as the age for mtEve.

The age of mtEve using HVR1 and HVR2 gives 10560 years.

HVR1 and HVR2 Estimation - Santos Paper

In the paper, Understanding Differences Between Phylogenetic and Pedigree-Derived mtDNA Mutation Rate: A Model Using Families from the Azores Islands (Portugal), based on 321 mtDNA transmissions they detected 11 substitutions in the D-loop (more precisely, in 973 bp located between positions 16024–16596 of HVR1 and 1–400 of HVR2), which implies that 0.0343 mutations occur (at a detectable level) in the D-loop in each generation (95% CI: 0.014–0.054). The paper then adds, if we employ the same definition of mutation used by other authors (for example Howell et al. 2003), only mutations for which there is evidence that they are germinal should be considered (see table 2). This implies that the mutation rate would be reduced almost by half: six mutations in 321 mtDNA transmissions, that is, 0.0187 mutations/generation for the entire D-loop.

In other words, 1 mutation can occur every 53.5 generations. With humans having 16 mutations from RSRS for HVR1 and HVR2, mtEve should be 53.5*16 generations. If we consider 20 years for 1 generation, we have 53.5*16*20 = 17120 years as the age for mtEve.

The age of mtEve using HVR1 and HVR2 gives 17120 years.

HVR1 and HVR2 Estimation - Other Papers

Some of the other papers that agree with the above two results include the following:

Data Set Region Analyzed No. of Mutations /  Generations Mutations from Eve Years Before Present
Howell et al. 1996 Control 2/88 16 14080
Bendall et al. 1996 HVR1 4/360 8.5 15300
Mumm et al. 1997 HVR1 1/59 8.5 10030
Parsons et al. 1997c HVR1, HVR2 1/32 16 10240
Parsons and Holland 1998 HVR1, HVR2 10/306 16 9792

Hence, based on HVR1 and HVR2, the age of mtEve should be approximately within a range of 9000 to 17000 ybp.

HVR1, HVR2 and Coding Region Estimation

Based on the paper, The pedigree rate of sequence divergence in the human mitochondrial genome: There is a difference between phylogenetic and pedigree rates,
The cumulative coding region data presented here can be combined with those published elsewhere (Howell et al. 1996), to derive a preliminary estimate of the pedigree divergence rate. Excluding the LHON mutations, the rate of newly arising germline mutations in the coding region is as follows: TAS1, 0 mutations/107 transmission events; ENG1, 1 mutation/26 transmission events; USA1, 1 mutation/11 transmission events; NWC1, 1 mutation/9 transmission events; and QLD1, 1 mutation/17 transmission events. Thus, there are 4 coding region mutations/170 transmission events, or ∼0.15 mutations/bp/Myr (99.5% CI 0.02–0.49).
Thus 4 coding region mutations for 170 transmissions. In other words, 4/170 = 0.02353 mutations per generation. For HVR1 and HVR2, we have 10/327 = 0.03058 mutations per generation (based on Parsons Paper). Since these two events are not mutually exclusive and the formula is P(A or B) = P(A) + P(B) - P(A and B).

P(Any mutation HVR1,HVR2 or CR) = 4/170 + 10/327 - (4/170 * 10/327) = 0.05339 (or 1 mutation every ~18 generations). With 57 mutations from mtEve, and 1 mutation takes 18 generations, mtEve must be 1026 generations back. Considering 20 years for 1 generation, mtEve must be 1026*20 = 20520 ybp.

Considering Santos Paper, having a mutation rate of 6/321 per generation, and combining with coding region mutation rate, we get,
P(Any mutation HVR1,HVR2 or CR) = 4/170 + 6/321 - (4/170 * 6/321) = 0.04178 (or 1 mutation every ~24 generations). With 57 mutations from mtEve, and considering 20 years for 1 generation, mtEve must be 24*57*20 = 27360 ybp.

Hence, mtEve based overall mtDNA mutations including HVR1, HVR2 and Coding Region, gives a range of 20520 to 27360 years before present.

Conclusion

  • HVR1 alone provides an age estimation of 6970 ybp.
  • HVR1 and HVR2 provides an age estimation of 9000 to 17000 ybp.
  • HVR1, HVR2 and Coding Region provides an age estimation of 20520 to 27360 ybp.
Since some mutations on coding region can be lethal, estimation based on coding region can be inaccurate and too exaggerated because, the harmful mutations might be missing as they would have made the mutated person dead and thus the lineage is lost and the number of observed mutations become less. Hence, the overall estimation should be taken with a grain of salt must be taken well below the lower end for calculation that includes coding region. 

Many scientists do acknowledge that the direct verifiable pedigrees mtDNA mutation rates are observed to be much higher in the order of 10x times compared to the phylogenetic mutation rates which are non-observable and has several assumptions.
The real value of mutation rate in humans has recently been the subject of an intense debate between those advocating the use of a phylogenetic mutation rate (~3 x 10^-6 substitutions per site per generation of 20 yr) calibrated by the divergence between humans and chimpanzees (Jazin et al. 1998) and those studying the mutation process directly on pedigrees giving numbers ~10 times larger (~2.7-3 10^-5 substitutions per site per generation; Howell et al. 1996; Parsons et al. 1997; Parsons and Holland 1998). 

Hence, the true mtEve age should be between 6000 - 25000 ybp based on directly observed pedigree method.